Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation Bernhard Tschitschko, Timothy J. Williams, Michelle A. Allen, David Páez-Espino , Nikos Kyrpides, Ling Zhong, Mark J. Raftery and Ricardo Cavicchioli

Supplementary Information

Materials and methods Sample collection from Deep Lake Biomass was collected from Deep Lake (68°33’36.8S, 78°11’48.7E), Vestfold Hills, Antarctica between November 30 and December 5, 2008, by filtering water taken from 5, 13, 24 and 36 m depths, through a 20 µm prefilter sequentially onto 293 mm polyethersulfone membrane filters with 3.0, 0.8 and 0.1 µm pore sizes, as described previously (DeMaere et al., 2013). In addition, a surface sample was taken from close to the lake shore. All filters were placed in storage buffer, frozen in liquid nitrogen and cryogenically maintained at -80°C until being processed (DeMaere et al., 2013). Metaproteomics Protein extractions, mass spectrometry and data analysis were performed based on methods described previously (Ng et al., 2010; Williams et al., 2012; Williams et al., 2013), with minor modifications. Briefly, proteins were extracted without filtering protein suspensions through a 0.22 µm filter, protein concentrations were determined with the Pierce BCA Protein Assay Kit (Thermo Fisher Scientific, Rockford, IL, USA), and 25 µg protein of each sample was processed for mass spectrometry (MS) in a buffer containing a final concentration of 25 mM NH4HCO3, pH 8 – 8.5 (assessed using pH indicator strips). Samples were reduced with 2.5 mM dithiothreitol for 30 min at 37°C in the dark, alkylated with 5 mM iodoacetamide for 30 min at room temperature in the dark, trypsin digestion performed with 0.3 µg trypsin (Sequencing Grade Modified Trypsin, Promega, Madison, WI, USA) overnight at 37°C, and peptides stored at -80°C until MS analysis. Peptide solutions were diluted 1:2 in 1% formic acid, 0.05% heptafluorobutyric acid and subjected to LC-MS/MS. LC-MS/MS was performed as described in Williams et al (2012), with the only modification being the use of 3 µ, 200 Å instead of 5 µ, 200 Å C18 media in the nano column (Magic, Michrom Bioresources, Auburn CA, USA). At least two technical replicates were performed for each sample.

Peak lists from Orbitrap Velos mass spectra were generated using extract_msn and peptides identified through automated database searches using Mascot Daemon and the Mascot server (version 2.3; Matrix Science, Thermo, London, UK) with ThermoFinnigan LCQ/DECA RAW file as the import filter and the following settings: one accepted missed cleavage for the tryptic digest, peptide mass tolerance of +/- 4 p.p.m., fragment mass tolerance of +/- 0.4 Da and variable modifications of oxidation and carbamidomethylation. Ions were matched against peptides using a composite databases consisting of: 1) Deep Lake metagenome data, which comprised 5,837 contigs > 2 kb in length from the assembled contigs previously generated and annotated using SHAP representing 38,071 predicted protein sequences (DeMaere et al., 2011; DeMaere et al., 2013) available at http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=AntLakMetagenome (Antarctic Lakes Metagenome: whole_lake.gbk); and 2) all 14,181 predicted protein sequences from tADL, DL31, Hrr. lacusprofundi and DL1 sourced from the IMG portal (http://img.jgi.doe.gov/) (Markowitz et al., 2010). To facilitate calculations of false discovery rates (FDRs), the database contained randomized decoy proteins equal in number to those

present in the reference database. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaíno et al., 2014) with the dataset identifier PXD001436 and DOI 10.6019/PXD001436.

All technical replicates of a sample were combined and merged into a single sample file during Mascot analysis, resulting in 15 sample files (5 depths x 3 filters). Peptide and protein validation and further analysis was performed using Scaffold (version Scaffold_4.2.1, Proteome Software Inc., Portland, OR, USA) with strict settings of 95% minimum peptide identification probability and 99% minimum protein identification probability. The majority of proteins were identified with at least two peptide matches. The number of confidently identified proteins was maximized while minimizing false positives by including single peptide matches but maintaining low FDRs, as has been recommended (Gupta and Pevzner 2009; Claassen 2012) and successfully applied in recent metaproteomic studies (Morris et al., 2010; Schneider et al., 2012; Herbst et al., 2013); the spectra for the single peptide matches are included in Figure S10. The peptide and protein FDRs were 0.06% and 0.4%. For quantitative analyses the Normalized Total Spectrum Count (Scaffold_4.2.1, Proteome Software Inc., Portland, OR, USA) for each identified protein was combined across all 15 samples and used to quantify abundance.

All identified proteins were manually annotated using BLASTP searches against the genome encoded proteins of tADL, DL31, Hrr. lacusprofundi an DL1 on IMG, and against all entries in the ExPASy database (Artimo et al., 2012), recording the best overall match including percentage identity, and organism. Annotated proteins were categorized into taxonomic and functional groups. Taxonomic categories were tADL, DL31, Hrr. lacusprofundi, DL1, other Halobacteriaceae (best match to a member of the Halobacteriaceae other than the four Deep Lake isolates), other Archaea (best match to a member of the Archaea other than Halobacteriaceae), Bacteria, viruses and Dunaliella sp..

Gene and protein sequence analyses Fragment recruitment of metagenomic reads to the genomes of the four isolate genomes was analysed using Artemis (Carver et al., 2012). Aligned metagenomic reads were loaded into Artemis using BAM files, generated by GS Reference Mapper v2.6 as described previously (DeMaere et al., 2013). The quantitative value used for comparing recruited reads between different genes was reads per kilobase per recruited reads (rpkm).

All CRISPR repeat sequences identified by CRISPR Recognition Tool (CRT; Bland et al., 2007) were re-examined using CRISPRFinder (default settings; Grissa et al., 2007) and inspected for motifs associated with functional repeats (Maier et al., 2013). CRISPR repeat sequences were analyzed by BLAST against the four genomes db or the metagenome db (see Metaproteomics above) using default settings, with matches required to have 100% identity over their full length.

An initial bootstrap consensus tree of CRISPR array repeat sequences identified in Deep Lake and from reference haloarchaeal taxa was constructed by performing alignments in MEGA5 (Tamura et al., 2011) using the Clustal algorithm (Thompson et al., 1994) with additional manual curation, and using the Neighbor-Joining (NJ) method (Saitou and Nei, 1987). Positions with less than 90% site coverage were eliminated, resulting in 25 positions in the final dataset. 1000 bootstrap replicates (Felsenstein, 1985) were performed and branches corresponding to partitions reproduced in less than 50% bootstrap replicates were collapsed. Poorly aligning repeats from unknown organism’s, and repeats ≤ 29bp were then excluded to create an improved alignment and NJ tree. Positions with less than 95% site coverage were eliminated, resulting in 30 positions remaining in the final dataset. Sequence

frequency plots were created from the improved alignment using WebLogo 2.8.2 (Crooks et al., 2004), with hairpin secondary structures identified (Maier et al., 2013).

CRISPR spacer sequences identified using CRT were compared against the four genome db or the metagenome db using BLAST with default settings except that matches were required to have at least 97% identity over the full spacer length (no more than 1 bp mismatch over a 30 bp sequence), with all except 10 of the 194 resulting hits having 100% identity over their full length. The taxonomic affinities of the sources of CRISPR spacer sequences were determined using the identities of the adjacent CRISPR repeat sequences. Contigs in the metagenome assembly that represented the invading DNA that prompted the generation of the spacers were manually annotated using BLASTP searches. Identification of leader sequences of CRISPR loci were identified following Li et al (2013).

Cas protein sequences (including Csh and Csc) were identified from the Deep Lake metagenome using BLAST with the Hrr. lacusprofundi type I-B and type I-D Cas proteins as queries, and the requirement that matches cover at least 90% of the length of the query protein. Cas proteins from all complete haloarchaeal genomes in IMG that contained CRISPR systems (an additional 12 taxa, as at 25th Aug 2014) were included for reference, along with orthologous Cas proteins present in Escherichia coli K-12 substr. MG1655, Methanobacterium thermoautotrophicum str. Delta H, Methanosarcina acetivorans str. C2A and Pyrococcus furiosus DSM 3638. Protein alignments were performed using Muscle (Edgar, 2004), and for each protein, phylogenetic trees were constructed using both the NJ method (Saitou and Nei, 1987) with 1000 bootstraps (Felsenstein, 1985), and the Maximum-Likelihood (ML) algorithm (Jones et al., 1992) in MEGA5 (Tamura et al., 2011). The evolutionary distances were computed using the p-distance method (Nei and Kumar, 2000) and are in the units of the number of amino acid differences per site. For ML reconstructions the tree with the highest log likelihood was calculated from an initial tree obtained automatically either by maximum parsimony when the number of common sites was < 100 or less than one fourth of the total number of sites, or otherwise by the BIONJ method with maximum composite likelihood distance matrix.

Multiple sequence alignments were created using Clustal Omega (McWilliam et al., 2013) with output files loaded onto the ENDscript server (Robert and Gouet, 2014) and alignments generated using default settings. Additional results Genomes of the four Deep Lake isolates The genomes of the four Deep Lake isolates consist of: tADL, 1 replicon 3.33 Mb; DL31, 3 replicons totalling 3.64 Mb; Hrr. lacusprofundi, 3 replicons totalling 3.69 Mb; DL1, 2 replicons totalling 3.16 Mb (DeMaere et al., 2013). Details of the names of the organisms and replicons that have changed in IMG since the original publication (DeMaere et al., 2013) are as follows: tADL: Halohasta litchfieldae tADL: Hlit_replicon (old name: halophilic archaeon sp. True-ADL: Contig32); DL31: DL31_replicon 1 (old name: Contig115), DL31_replicon 2 (old name: Contig114), DL31_replicon 3 (old name: Contig113); Hrr. lacusprofundi: Hlac_replicon 1 (old name: chromosome 1: NC_012029), Hlac_replicon 2 (old name: chromosome 2: NC_012028), Hlac_replicon 3 (old name: plasmid pHLAC01: NC_012030); DL1 (names currently unchanged): HalDL1_Contig38: primary replicon (>3000 genes); HalDL1_Contig37: secondary replicon. Proteins identified in the metaproteome All protein identifications required peptides matches of 100% (see Materials and methods). Taxonomic origin and gene function was subsequently inferred by using the Integrated Microbial Genomes and Metagenomes (IMG) portal (Markowitz et al., 2010) to determine

the best match to translated sequences of the genomes of the four isolates, and all entries in the ExPASy database (Table S1, S2).

As environmental viruses are numerous and diverse, tend to have high rates of sequence divergence, and are poorly represented in public sequence databases leading to missed proteins from mass spectra data, it is likely that some viral proteins present in the metaproteome went undetected. A high proportion of proteins assigned to other members of the Halobacteriaceae (29 of the total 93; 60% of spectra) were cell surface proteins, with 24 of those having < 60% sequence identity to the best corresponding BLAST match. Similarly, of the four proteins assigned to Archaea, two are cell surface proteins with < 50% identity to their best BLAST match, which accounted for ~95% of the assigned spectra. In view of a high level of variation occurring for cell surface proteins from the four Antarctic isolates, it is possible that some of these proteins assigned to other members of the Halobacteriaceae or Archaea are from one of the isolates.

A total of 86 protein identifications (protein families) each comprising two or more sequences and sharing the same set of detected peptides were identified. Seventy two of these protein families consist of sequences matching the same gene product from one of the four isolate genomes but with different degrees of sequence similarity. They all contain a 100% matching sequence plus one or more <100% matching sequences. While it is not possible to determine which of the proteins in a protein family were expressed in Deep Lake, the presence of the <100% matching sequences provides further evidence for the presence of variants and hence phylotypes. Cell surface proteins Annotation as a ‘cell surface protein’ (i.e. predicted to be exposed to the external environment) required the presence of an N-terminal secretion signal peptide and/or a single C-terminal transmembrane helix and/or homology to experimentally characterized cell surface proteins, including S-layer and archaella (archaeal flagella) proteins. Further supporting features were the presence of putative cell surface domains (e.g. PKD). The taxonomic composition and abundance of all proteins, as well as just the cell surface proteins, including variant and non-variant forms in the Deep Lake metaproteome is shown in Table S2.

The S-layer genes are located on the primary replicon in DL31 (DL31_replicon 1) and tADL (Hlit_replicon), and Hlac_0412 is on the primary (Hlac_replicon 1) and Hlac_2976 on a secondary (Hlac_replicon 2) replicon in Hrr. lacusprofundi. Because the secondary replicon of Hrr. lacusprofundi contains numerous ISs that have orthologs throughout the isolate genomes (DeMaere et al., 2013), the rpkm value for the replicon is probably overestimated; nevertheless, the trend for FR coverage of these S-layer genes is clear (see main text).

For tADL the G+C mol% mimics FR coverage, being 60% for the genome and 59% in the region encoding the end of halTADL_1043, but 54% in the region of low FR (Table S3). However, this pattern was not apparent for DL31 or Hrr. lacusprofundi which have replicon/S-layer gene G+C mol% of 65/63 and 58/59, respectively. Although the second S-layer gene of Hrr. lacusprofundi, Hlac, 0412, has a G+C mol% of 60% compared to 68% for the replicon.

Given the overall low abundance and few protein matches to DL1, the relatively high spectral count for the non-variant DL1 S-layer protein, may indicate that unlike the lake populations of tADL, DL31 and Hrr. lacusprofundi, the DL1 population does not accumulate variation in S-layer genes.

For the Hrr. lacusprofundi archaellin gene Hlac_2557, the FR coverage is very high (4155 rpkm) in the area corresponding to the N-terminal region (1 – 120) compared to the remainder of the gene (202 rpkm). This N-terminal region also corresponds to the only

segment of the variant which matches well (83%) to the genome sequence, indicating that the FR has captured sequences from numerous lake phylotypes. For tADL archaeallin genes with detected protein variants (halTADL_0078/1544/1812/ 1813) the G+C mol% for these tADL genes was lower (51 – 55%) than the genome average (60%), although FR coverage was only lower (368 rpkm) for 1812 (Table S3). These data for variation and abundance indicate that variation in assembled archaella could occur through differential expression of orthologs within strains, and through phylotype variation within members of the lake population.

The abundance of the variant forms of the six tADL cell surface proteins, halTADL_0751/0878/ 1047/1403/1761/1765 (see main text) was lower or equivalent to their non-variant forms, except halTADL_0751/1047/1403 for which only the variants were identified. The halTADL_0751/1047/ 1403 genes had low FR coverage (182/139/118 rpkm).

For Hrr. lacusprofundi, a protein with 49% identity to Hlac_0476 (TAT signal sequence plus extra-cytoplasmic domain) was identified with higher abundance than the non-variant form (Table S5). The gene has low FR coverage (153 versus 452 rpkm for the replicon) and low G+C mol% (59 versus 68%). A variant of Halar_2364 (one adhesion domain) with 39% identity was detected. The gene has low FR coverage (273 rpkm), low G+C mol% (54%), is annotated in IMG as a pseudogene, and is located near a transposase (Halar_2366). The PKD-containing protein Hlac_2824, discussed in the main text, is encoded by a gene that is part of a low FR coverage region that contains six genes flanked by ISs; Hlac_2825 has similarity to uncharacterized HCTV-2 and HHTV-1 viral proteins (Figure S3c, Table S3). Viruses, CRISPR and BREX Because metaproteome matches were made to metagenome contigs and not assembled virus genomes, it is not possible to unambiguously determine whether the proteins were derived from extracellular virions, viruses undergoing a lytic cycle, integrated active viruses (proviruses), or integrated inactivated viruses (viral remnants). However, as described in the main text, the use of metaproteome data and logistical aspects of sampling helped to strongly discriminate between these possibilities.

CRISPR nomenclature is based on Makarova et al (2011). In general, the gene order of cas gene clusters in the four isolate genomes was similar for the I-D and I-B systems (Figure 3), which is contrary to the previously reported order of cas3 at the 5’ end and cas6 adjacent to cas4 in I-D systems (Makarova et al., 2011). Our analyses also determined that for the complete haloarchaeal genomes in IMG which possess a full cas gene cluster, all possess I-B systems, except for DL31 and Natronomonas pharaonis Gabara DSM 2160 which have I-D systems. In addition, Hrr. lacusprofundi and Haloquadratum walsbyi C23 both possess I-B and I-D systems. For tADL, repeats for loci 1 and 4 are identical, differing to those from each of loci 2 and 3; overall the four loci are similar (Table S7) with 77 – 99% pair-wise identity. Spacers matched to sequences in metagenomic contigs derived from all four tADL CRISPR loci, although for metagenome contigs containing spacers and repeats, it was not possible to assign spacers specifically to loci 1 or 4 (Table S10). The repeats of DL31 CRISPR locus 1 (immediately adjacent to the cas gene cluster) clustered with CRISPR type I-D system repeats (Figure S5). However, DL31 locus 2 clustered with type I-B system repeats; thus, it is not clear if this locus functions with the DL31 CRISPR system. The DL31 locus 2 repeat has high sequence identity to the DL1 type I-B repeat, differing by 2 nt over the total 30 nt length. The two repeat sequences of Hrr. lacusprofundi loci are distinct, corresponding to the two CRISPR systems (type I-B and I-D). For both DL31 and Hrr. lacusprofundi, spacers from both of their CRISPR loci matched sequences in metagenome contigs (see main text).

One contig (ctg7180000459076) contained a CRISPR repeat sequence that matched to tADL locus 2, with cas genes which had ~70 – 95% sequence identity to those from tADL. The contig could represent a tADL phylotype with cas genes divergent to the isolate and with

rearranged loci. Other contigs from the metagenome encoded Cas proteins and/or CRISPR repeats with high sequence identities to other haloarchaea (Table S8, S10, Figure S4, S5). One contig also contained a cas cluster with the encoded proteins exhibiting the highest identities to the halophilic gammaproteobacterium Halomonas (Table S8); repeats from a CRISPR locus in the metagenome also had highest identity to CRISPR repeats of Halomonas (Table S10).

For a given genome or metagenome, the presence of a spacer matching to a sequence in a mobile element, such as a virus or plasmid, indicates that the organism that generated the CRISPR spacer did so in response to the presence of the mobile element. Compared to tADL, DL31 and DL1, Hrr. lacusprofundi is unique in encoding two CRISPR systems (type I-B and type I-D), both of which incorporated spacers from Deep Lake mobile elements.

A CGΦ46-like virus was also targeted by tADL and DL31 CRISPR systems, although it is not clear if the contigs (deg7180000401097, deg7180000401099) come from the same CGΦ46-like virus (Table S10). The data also showed that the Deep Lake CRISPR systems target viruses that can integrate into the host chromosome, as a tADL metagenome contig (ctg7180000397348) has a CGΦ46-like provirus inserted at the position where tRNA-Lys is located in the genome sequence of the tADL isolate (Figure S3b).

Only one definite pleolipovirus-derived (HRPV-1-like) contig (ctg7180000266221) was found and it was targeted solely by Hrr. lacusprofundi (Figure 3, Table S10), although another contig (ctg7180000459513) with a pleolipovirus ORF targeted by tADL and Hrr. lacusprofundi was identified. This latter contig also encodes an integrase and homologs of tADL and Halorubrum spp. genes, including a pilin (halTADL_1885) which was detected in the metaproteome (Figure S3a, Table S5). As pleolipoviruses appear to be host specific (Atanasova et al., 2012; Pietila et al., 2012), this latter contig may represent a mosaic virus that acquired a pleolipovirus ORF, and expresses the host derived pilin gene during its life-cycle.

Other evidence for CRISPR systems targeting mosaic viruses, including those with characteristics of bacteriophages, comes from contigs with haloarchaeal cellular genes and bacteriophage genes (ctg7180000439875), and contigs with bacteriophage-related gene clusters matching Firmicutes bacteria (deg7180000395624) (Figure 3, Table S10). Some genes may also have originated from either plasmids or viruses (e.g. ViPREs), including a repH gene (ctg7180000271318) targeted by DL1, and the DNA primase gene from DL31 replicon 3 (formerly “Contig113”) was targeted by an unknown haloarchaeal CRISPR system (identified on a metagenome contig; Table S10). This 23659 bp replicon from DL31, which contains mostly ORFs for hypothetical proteins (including viral genes) and transposases, likely represents a mobile element. One protein from this replicon was detected in the Deep Lake metaproteome, a putative surface lipoprotein (Halar_0006).

As discussed in the main text, BREX gene clusters (Type 5) were identified in the genomes of Hrr. lacusprofundi (Hlac_3187-3197) and DL31 (Halar_0254-0263) (Goldfarb et al. 2015; Figure S7, Table S9). Individual BREX system proteins share high sequence identities (85-100%), with Hlac_3197 and Halar_0254 sharing 100% identity, and Hlac_3196 and Halar_0255 sharing 100% identity across the N-terminal segment (613 amino acids), and 95% overall. BREX genes Hlac_3197/_3196 (N-terminal segment: amino acids 1-608) and Halar_0254/_0255 (N-terminal segment: amino acids 1-608) are part of a HIR (14502 bp long; only a single nucleotide mismatch) that spans Hlac_3196 to Hlac_3210 in Hrr. lacusprofundi, and from Halar_0243 to Halar_0255 in DL31. This HIR contains genes for hypothetical proteins, transposases, and a helicase/endonuclease.

For DL31, the region containing Halar_0260 (the pglX gene; methylase), the adjacent Halar_0261 (hypothetical), and the N-terminal portion of Halar_0262 (pglZ) has low FR coverage (Figure S8, Table S9). Halar_0261 is not a recognized BREX gene, although it is

conserved within BREX gene clusters of certain haloarchaea (e.g., Haloarcula californiae ATCC 33799; Halobacterium salinarum R1). Halar_0261 encodes a small protein (178 amino acids) with no known function and no identifiable domains. The average coverage of the Hrr, lacusprofundi BREX cluster is 2367 rpkm, with Hlac_3189 (pglX) being the only gene with coverage (1458 rpkm) below the average (Table S9). Overall, the metagenome FR data indicates that the region containing the pglX gene is subject to sequence variation within the Hrr. lacusprofundi and DL31 populations in Deep Lake, which is consistent with the suggestion from genomic analyses that the pglX gene is prone to variation (Goldfarb et al. 2015).

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Antarctica revealed using metagenomics and metaproteomics. Environ Microbiol 15: 1302–1317

List of SI Figures and Tables

Figure S1. Multiple sequence alignments of S-layer proteins. S-layer protein sequences from genome sequences of tADL (A), DL31 (B) and Hrr. lacusprofundi (C) aligned with sequences of variants present on Deep Lake metagenome contigs. All proteins were detected in the metaproteome. Figures were created using Clustal Omega and the ENDscript server. Identical residues (white characters on red background) and similar residues (red characters on white background, similarity score > 0.6) are framed in blue. Figure S2. Multiple sequence alignment of tADL archaella proteins. Archaella protein sequences from the genome sequence of tADL were aligned with sequences of variants present on Deep Lake metagenome contigs. All proteins were detected in the metaproteome. The figure was created using Clustal Omega and the ENDscript server. Identical residues (white characters on red background) and similar residues (red characters on white background, similarity score > 0.6) are framed in blue. Figure S3. Arrangement of genes in select metagenomic contigs and genomic regions. (A) metagenomic contig (ctg7180000459513) that includes ORFs homologous to the tADL pilus protein halTADL_1885 and putative viral ORFs. (B) comparison of a region of the tADL genome and a matching metagenome contig (ctg7180000397348), with the latter showing a putative provirus inserted at the tRNA-Lys position in the tADL genome. (C) region of the Hrr. lacusprofundi genome marked by six ORFs (including one of putative viral origin) flanked by IS elements. HP, hypothetical protein; PKD, PKD adhesion domain; SiR/NiR (4Fe-4S), sulfite reductase/nitrite reductase, 4Fe-4S component; ORFs encoding haloarchaeal proteins (blue); ORFs encoding viral proteins (red); transposase IS elements (green); ORFs encoding proteins with no known homologs (gray); tRNA gene (yellow); gene annotations (above each ORF0; known haloarchaeoviruses (underlined). (A) and (B), the tADL locus tag (all prefaced with halTADL) are shown underneath each ORF that encodes a tADL protein, and for (C), the Hrr. lacusprofundi locus tag (all prefaced with Hlac) is shown underneath each ORF. Full details of each contig are in Table S11. Figure S4. Phylogenetic trees of Cas proteins. Optimal tree constructed by the NJ method (trees constructed by Maximum Likelihood showed negligible differences). Sequences for Cas proteins in the genomes of tADL, DL31, Hrr. lacusprofundi or DL1 (red) and Deep Lake metagenome contigs (blue). The trees for Cas1 (A), Cas2 (B) and Cas3 (C) were rooted using the respective Escherichia coli sequence as the outgroup, and all other trees shown are unrooted. Bootstrap values < 50% are not shown. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. The number of positions retained were: (A) Cas1, 315 positions; (B) Cas2, 86 positions; (C) Cas3, 459 positions; (D) Cas4, 161 positions; (E) Cas6, 209 positions; (F) Cas8b (=Csh1), 618 positions; (G) Cas7 (=Csh2), 320 positions; (H) Cas5, 220 positions; (I) Csc1, 205 positions; (J) Csc2, 298 positions; (K) Cas10d (=Csc3), 754 positions. Trees were drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree.

Figure S5. Phylogenetic tree and consensus sequences for CRISPR repeats. (A) Optimal tree constructed by the NJ method. Bootstrap consensus tree of CRISPR locus repeat sequences identified in the genomes of tADL, DL31, Hrr. lacusprofundi, DL1 (highlighted in red font), Deep Lake contigs and reference haloarchaeal taxa (boostrap values < 50% are not shown). (B) Consensus for all Type I-B repeats except Hrr. lacusprofundi locus 1, Hfx. mediterranei ATCC 33500 I and II and Hqr. walsbyi C23 CRISPR 2 and 3, for which the consensus is shown in (C). An asterisk (C) indicates that only Hrr. lacusprofundi locus 1 contains a T at position 26 of this sequence logo, whereas the other four repeats contain a gap at this position. (D) Consensus of the four 37 bp Type I-D repeats. Figure S6. CRISPR leader sequences for Deep Lake CRISPR systems. Figure S7. BREX system gene clusters in the genomes of Hrr. lacusprofundi and DL31. Genes are color coded as follows: BREX genes (orange), toxin-antitoxin system (pink), transposase IS elements (green) and function unknown (gray). Nomenclature of BREX system genes follows Goldfarb et al. (2015). Figure S8. Metagenome FR coverage of DL31 BREX cluster showing low coverage for the pglX gene (Halar_0260). FR coverage was obtained from Deep Lake metagenome reads using the DL31 genome (DeMaere et al., 2013) viewed using Artemis (Carver et al., 2012). HP, hypothetical. Figure S9. Phylogenetic analysis of pilin protein (PilA) homologs from Euryarchaeota. There is a close relationship between a pilin protein encoded in the tADL genome and a pilin protein (224467999) encoded on Deep Lake metagenome contig that is inferred to be of viral origin (both proteins shown in bold). Haloarchaea are shown in red, methanogens in green. A putative pilin protein from Archaeoglobus fulgidus DSM 4304 is the outgroup. Deep Lake haloarchaeon PilA sequences and full length reference proteins containing Pfam domain PF07790 were aligned using Muscle and the phylogenetic tree was constructed using the Neighbour-Joining method in MEGA5. All positions with less than 80% site coverage were eliminated (i.e., fewer than 20% alignment gaps were allowed at any position). Only bootstrap values of at least 50% are shown. There were a total of 39 amino acid sequences and 142 positions in the final dataset. Figure S10. MS spectra details for proteins with a single peptide identification. Data including the annotated spectra and fragmentation tables were exported from Mascot. Protein identification number and number of samples in which the peptide was detected is shown (blue font, top of page). For peptides detected in more than one sample, the spectrum with the highest mascot ion score is shown. Table S1. Complete list of proteins identified in the Deep Lake metaproteome. Column A: identification number; Column B: Result of manual annotation; Column C – E: Result of BLAST searches including sequence identity (C), locus tag (D) and organism (E); Proteins are ranked according to their Normalized Total Spectrum Count (Column F). Table S2. Taxonomic composition and abundance of all proteins and just cell surface proteins in the Deep Lake metaproteome. Table S3. Characteristics of cell surface proteins with variation. Properties of cell surface proteins discussed in the main text, including S-layer, archaella, adhesion and others are

described in separate sheets for tADL, DL31, Hrr. lacusprofundi (Hlac) and DL1. Column A: matching locus tag; Column B: sequence identity of detected protein and best matching locus tag; Column C: identification number; Column D: full protein sequence; Column E: protein length; Column F: detected peptides corresponding to the protein; Column G: amino acid coordinates corresponding to protein domains; Column H: protein domains; Column I: fragment recruitment of the respective gene (rpkm values); Column J: G+C mol% of the respective gene; Column K: Normalized Total Spectrum Count for each protein. Table S4. Characteristics of proteins in the metaproteome encoded in High Identity Regions (HIR). Column A: identification number; Column B: annotated function; Column C: matching locus tag; Column D: organism; Column E: protein sequence; Column F: detected peptides; Column G: description of genes of putative viral origin within or adjacent to the HIR; Column H: Normalized Total Spectrum Count for each detected protein Table S5. Proteins identified in the Deep Lake metaproteome inferred to be of viral origin. Contigs targeted by CRISPR spacers in either the four genomes db or the metagenome db (see Table S10) are underlined. Full contig details are given in Table S11. * Designates an ambiguous match (protein family). Table S6. CRISPR-associated (Cas) proteins identified in the Deep Lake metaproteome. * Designates an ambiguous match (protein family). Table S7. CRISPR loci for tADL, DL31, Hrr. lacusprofundi and DL1. Table S8. Cas genes identified in Deep Lake metagenome contigs that could not be assigned to tADL, DL31, Hrr. lacusprofundi or DL1. Encoded proteins detected in the Deep Lake metaproteome are shown (Identification; bold font). Table S9. BREX clusters in Hrr. lacusprofundi and DL31. Protein sequence identity between the Hrr. lacusprofundi and DL31 homologues is given in percent. Metagenome fragment recruitment (FR) coverage of genes is given as rpkm (reads per kilobase per 1000000 recruited reads) values. Table S10. The species identified as the source of the spacers present in CRISPR loci identified in the genomes of tADL, DL31, Hrr. lacusprofundi, DL1 and metagenome contigs. For Hrr. lacusprofundi, which has two separate CRISPR systems, the two possible types (I-B and I-D) are given. Contig descriptions outline the evidence for the inferred sources of the spacers. Some contigs match to spacers from more than one source (CRISPR spacer source; shaded in gray), and some contigs encoded proteins detected in the Deep Lake metaproteome (Contig or genome name; bold text). Detailed descriptions of each contig are provided in Table S11. Cdc6, cell division control protein 6; PLD, Phospholipase D Active site domain; PQQ/WD-40, pyrrolo-quinoline quinone repeat; UspA, universal stress protein A; VP, virion protein; VWA, von Willebrand factor type A domain. Table S11. Complete annotations for known ORFs on Deep Lake metagenome contigs utilized in this study. The best matches are given for all proteins encoded on the contigs. For certain proteins, no homologs were identified (= no matches). Proteins detected in the Deep Lake metaproteome are shown in bold font with the protein number in parentheses.

Figure S1. Multiple sequence alignments of S-layer proteins. S-layer protein sequences from genome sequences of tADL (A), DL31 (B) and Hrr. lacusprofundi (C) aligned with sequences of variants present on Deep Lake metagenome contigs. All proteins were detected in the metaproteome. Figures were created using Clustal Omega and the ENDscript server. Identical residues (white characters on red background) and similar residues (red characters on white background, similarity score > 0.6) are framed in blue.

1 10 20 30 40 50 60 X X X X X X X halTADL_1043_variant1 DEF DEEEF DEEEEF DF DEEEF DEF D TKI AVFL LMVLSM A AAF AAA D...............MTYSR N SA VA G AAP QTDAVQEDEVSIGGSTVTVNTGGANSISVS halTADL_1043 KdG KdddG KddddG KG KdddG KdG K NKL AIFLA IMV SV G MAFSG AAA D.............MTNENYS R F T F GA G VPADPAPS..................AEDV halTADL_1043_variant3 KdG KdddG KddddG KG KdddG KdG K NKL AVFLA IMV SV G VAFTG AAA .............MTQTNYR R F T F GA T ANVGQDVA.......................halTADL_1043_variant4 KdG KdddG KddddG KG KdddG KdG K A IVMMSV GM VAFTG AAA EVF............L............. A V S S TEPESVN....................... halTADL_1043_variant2 KdG KdddG KddddG KG KdddG KdG K N V V VTV L A F DMFDVDTDDLEAGDYIVVDSS D GR .RSNTFE QD S E DDD................................. halTADL_1043_variant5 JIH JIIIH JIIIIH JH JIIIH JIH J................................................................................

70 80 90 100 110 120 X X X X X XhalTADL_1043_variant1 c EF DF DF DEF DEF DF DEEF DEEF A V LP GS GSI S FT AGVEVTDV.......SDG YNED...E LY NFGDGLPSTVT LTPTGFDAGDT DFT...............VhalTADL_1043 c dG KG KG KdG KdG KG KddG KddG B V V N G TSA GTI IS D TF TAE D TDGVQTQEISFTAE EPGD DYNNG N T .......PVA L DNVSVDSVDG V NGDIVVTVDAVNTVhalTADL_1043_variant3 c dG KG KG KdG KdG KG KddG KddG B V NN GQ TA I DYT D D ..........EYT.P PYQ D...V NA.SE V.......ESN LR......... VD T NGNVT.........halTADL_1043_variant4 c dG KG KG KdG KdG KG KddG KddG B V IP NT GQ S A GS V D Y V D ............. VYP EFNT V H QF P........RG DA L......... E QR A.............halTADL_1043_variant2 c dG KG KG KdG KdG KG KddG KddG B V LP Q STA V S YSY SA .............A V...DNFED ELD SS ........RGT N......... G................halTADL_1043_variant5 c IH JH JH JIH JIH JH JIIH JIIH C V SAD ............................................................ ................

130 140 150 160 170 180 X X X X X X halTADL_1043_variant1 GGSDVSLTVVGDSDE............PEDEPEDEPEDSPEDSDSSADVGDLDGNLYWAGQTISVSG...LDANTDVQLRhalTADL_1043 TASEVDITVNAEVDPSGTTAASGTYDLESDSGSDQTAEFDITSSGSGDANLGSGATFWEGQNLDLFIRSNVDDTTDYQVRhalTADL_1043_variant3 ................................................................................halTADL_1043_variant4 ................................................................................halTADL_1043_variant2 ................................................................................halTADL_1043_variant5 ................................................................................

190 200 210 220 230 X X X X X halTADL_1043_variant1 DEF DEEF DF DEEEEEEEEEF DF DF DEEF A A DEEEEEE G TSL LT DS EV IDT LE DY LSNA S TFQDEG..DD .... EGQ ...T NG .L AD S.G Y G................SQMDAD DDIE halTADL_1043 KdG KddG KG KdddddddddG KG KG KddG B B Kdddddd GE LV VS DSDD S DS L DY IT A S G TNNA FELDTTAND GSIEG EE ...I RTL Y EG N..G V P DDS TAIVFENGIANSTVTDS TD G halTADL_1043_variant3 KdG KddG KG KdddddddddG KG KG KddG B B Kdddddd ST V IT SDDEV IET ID EY LT G QN F............D F KE ...AN .I EG AGE F ................GENLLGD GVP EV halTADL_1043_variant4 KdG KddG KG KdddddddddG KG KG KddG B B Kdddddd G I TSLV LN D D Y VDT LE EY ISN Q TS TF........ S DG GT PTAD AT NY E SN PST G TSSY ................GAS VVQ halTADL_1043_variant2 KdG KddG KG KdddddddddG KG KG KddG B B Kdddddd GDL DEDLFNI T VT A S G TNN ATW........ S............... F LNYVDDYSTT P ADF ................V A G halTADL_1043_variant5 JIH JIIH JH JIIIIIIIIIH JH JH JIIH C C JIIIIII GDL D LFNL T Y NN N G N TATW........ E...............R Q F SAQLDGAA RG SDFD ................P DI G

240 250 260 270 280 290 X X X X X X halTADL_1043_variant1 c EF DF DEEEEEEEEEEEF DEF DEEEEEEF DEEEEEEEEEEEEEF DEEEEEEEF A A F EV EQSLDIAFDDESV GD TELDVETN RGSSDVVVHA GDLD EEL QI T ........S DK T.. .... D D T E EGDL........halTADL_1043 c dG KG KdddddddddddG KdG KddddddG KdddddddddddddG KdddddddG B B F EV EQSL VAFDDENV E T LDLDTN RGTTDVVVHA GDLD ED ETI N T ........T S DDS T.. Y .... N D F DTDADY ......halTADL_1043_variant3 c dG KG KdddddddddddG KdG KddddddG KdddddddddddddG KdddddddG B B F EV EQTLDVAFDDD V GDE SELDLETN RGSSDLIVHA GDLD DLENI TS Q ........R E ST .. .... N QS ...DF ......halTADL_1043_variant4 c dG KG KdddddddddddG KdG KddddddG KdddddddddddddG KdddddddG B B F V EG FDDDSV D S IELDS R N V V P D D D LD L N T S IN FSAQ........ .DET SD I DRQST Y LT S DG D F A M D VTNNPGYEV NSDhalTADL_1043_variant2 c dG KG KdddddddddddG KdG KddddddG KdddddddddddddG KdddddddG B B F EA EG S DV FDD S G E VE S S AG D N S TD GLKLVNG S T A DYP F DGDV FS PYDAAEYA N..SG N FNIT....P AAVNSSE LQ SGShalTADL_1043_variant5 c IH JH JIIIIIIIIIIIH JIH JIIIIIIH JIIIIIIIIIIIIIH JIIIIIIIH C C F V EG DS V S TEL DS D I G L S S V DN GLSVV DDGR LQAG ........ SY PWNALENAG .. PS .......... G Y....... GVS

300 310 320 330 340 350 X X X X X X halTADL_1043_variant1 c c c c DF DEF DF DF DEEEEEEEEEEEEF DF DEEEEF DEEEF DF DEEEEEEEEEEEEEEEEEE D Y F F SV LN NEA DLDDDY LD DEAVVI LSDLD DD G LNFTDI GE E Q D....................... RA D S S S ES P EQ T T halTADL_1043 c c c c KG KdG KG KG KddddddddddddG KG KddddG KdddG KG Kdddddddddddddddddd D Y F F L TL S EV DLDDDY LD EDAVVL VSDLD DD G A FSDI GE D Q D....................... DL D G D D Q RD T EN P D M halTADL_1043_variant3 c c c c KG KdG KG KG KddddddddddddG KG KddddG KdddG KG Kdddddddddddddddddd D Y F F TA TQTEE DLDDDY L DDAIIL VSDLD DD DG VNFTDI EGE E Q D....................... TDF D D NP ED P N T halTADL_1043_variant4 c c c c KG KdG KG KG KddddddddddddG KG KddddG KdddG KG Kdddddddddddddddddd D Y F F NH DGD VT V NLSN DA DD D LL E D GE E E DLPL LGYD G ELRDDGY TL MS GF .....L GDD AHFD....... L DGEGLP G IhalTADL_1043_variant2 c c c c KG KdG KG KG KddddddddddddG KG KddddG KdddG KG Kdddddddddddddddddd D Y F F SH DGD VT SA TL NN IV L DE DE VVL A D E DVSF I E D DSNAF .... V ...NNSG F G W G Y DAENY K YQ G .....V T AG DS S halTADL_1043_variant5 c c c c JH JIH JH JH JIIIIIIIIIIIIH JH JIIIIH JIIIH JH JIIIIIIIIIIIIIIIIII D Y F F TH DGD LN V T DV I E D E IVV D E DVSF A E D E DDLEV .... V ...KSG. TTFD GAW A YG NAD Y NK T.SA .....T A IG N T

360 370 380 390 400 410 420 430 X X X X X X X X halTADL_1043_variant1 c c c c c ccc cc c c c c ccEEEEEEEEEEEEEEEEEEEEEEF DEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEF DEEV D E D F AGD ED Q G D D NT S SDA DT TI VT T V AS EGV T V FSVEM YV DE VGYA ILYLEDD DDDEVSV V A S E D A V GT Y Q ASSA F T W halTADL_1043 c c c c c ccc cc c c c c ccddddddddddddddddddddddG KddddddddddddddddddddddddddddddddddddddddddddddddddG KddV D E D F AGD ED Q G D D NT S T ASDSASISVT V A E VTTSA LVEFTVEM ETFI I DEDVGFV L VEDD DD EVT V A E D E T D AS F H G FT halTADL_1043_variant3 c c c c c ccc cc c c c c ccddddddddddddddddddddddG KddddddddddddddddddddddddddddddddddddddddddddddddddG KddV D E D F AGD ED Q G D D NT S TD SDSASISVT IS EGV T I E TLEL TDD FI I EEAGYV II V DE DDDEVT T E GD S Y KT Q I G S E S FEF halTADL_1043_variant4 c c c c c ccc cc c c c c ccddddddddddddddddddddddG KddddddddddddddddddddddddddddddddddddddddddddddddddG KddV D E D F AGD ED Q G D D NT T T ATAT TISIS S AS G Q A IAEF EL TDETWI I D DSDFV VLYV AD E E VTV V G D EG AS TY A EF A Q S P K halTADL_1043_variant2 c c c c c ccc cc c c c c ccddddddddddddddddddddddG KddddddddddddddddddddddddddddddddddddddddddddddddddG KddV D E D F AGD ED Q G D D NT T TEASASA A L Q VSAS EGVSQTA I EFTV L TDETWV I EDSDFV VLYL AD EDE MTV V D E V D T S G K S Q halTADL_1043_variant5 c c c c c ccc cc c c c c ccIIIIIIIIIIIIIIIIIIIIIIH JIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIH JIIV D E D F AGD ED Q G D D NT T TEASATA AS Q LSAS EGVSQTA IAEFTLEL TDETWV I EDSDFV VLYLEAD DE MTV I D TV D G T P E

440 450 460 470 480 490 X X X X X X halTADL_1043_variant1 c cc c EEEEF DEF DEEEEEEEEEEEEEEEF A DEF DF DEEEEEEEF DEEEEEEEEEEEEF DFR GT D AV A S DIY SE D V E A N V F DED E A L D ED D D LD Y . DI DSY YSVGPDN PAD FED E LN PLNGN.............. D T N YR halTADL_1043 c cc c ddddG KdG KdddddddddddddddG B KdG KG KdddddddG KddddddddddddG KGR GT D TL V T VYDSE D II SEVH GA FYD DEDN FE YLDQL LID DE A D E.R . D. N GDD........T E LLNASNNPDTNSD V D VA halTADL_1043_variant3 c cc c ddddG KdG KdddddddddddddddG B KdG KG KdddddddG KddddddddddddG KGR GT D LA ANT EVYESE E EVLES VH A F D EN NF EYLE LV N DD D N. . N A DGS........TS T E N ...........SL T AQD N V halTADL_1043_variant4 c cc c ddddG KdG KdddddddddddddddG B KdG KG KdddddddG KddddddddddddG KGR GT D LL SI E D ENADTIES H A TNT GV IFE DGDTT Q DEYV LGIADS ST DG NVY V AY DADGG M PD T N........GN L ND ...halTADL_1043_variant2 c cc c ddddG KdG KdddddddddddddddG B KdG KG KdddddddG KddddddddddddG KGR GT D TL ASL VYDE DNVDTIES IH L NT I LYE DGN Q NF EYLDSLGIIDN E G GQ. G K S..DG T PSGS G D ........... N DN halTADL_1043_variant5 c cc c IIIIH JIH JIIIIIIIIIIIIIIIH C JIH JH JIIIIIIIH JIIIIIIIIIIIIH JHR GT D TL A L VY E DNV TIESEVH I STT GA LYE DGNTQ NFD YLDNLGII S D G G GE. S G A G..G. . PG A ........... A N DN

500 510 520 530 540 550 560 570 X X X X X X X X halTADL_1043_variant1 c cc c c DEEEEEEEEEEEEEEEEEEEF DEEEEEEEEEEEEEEEEEF A DEEEEEEEEEEEEEEEEF DEEEF DF DEEE L RP Q Y E I PAD ELSI D F INDDDE E QEEL S VIELQAPEIGDITTHVAP NADED NL DL DLDI D D N.....G DG I S S D G SD D E G halTADL_1043 c cc c c KdddddddddddddddddddG KdddddddddddddddddG B KddddddddddddddddG KdddG KG Kddd L RP Q Y QEQ T L PAE DI A E F VN DDE EANEEL LLEL AP IGDLTTHVA ADED NV DLL TA IT DFADEG GE G S A SAA E T SAAD D E GhalTADL_1043_variant3 c cc c c KdddddddddddddddddddG KdddddddddddddddddG B KddddddddddddddddG KdddG KG Kddd L RP Q Y TDQ T M PAD DL A ADSLF LN DDE EA DEI S LLELTAPELGDITTHVAP KG I S..... V S S D A G RR.............halTADL_1043_variant4 c cc c c KdddddddddddddddddddG KdddddddddddddddddG B KddddddddddddddddG KdddG KG Kddd L RP Q Y SEQ T L T EIQLAGTD VDNALFD D GEAN L S VLEL PEIGDIT H AP SA DE I ELVD.A A S .. A SGA NQ G A EN V T GE N TE S halTADL_1043_variant2 c cc c c KdddddddddddddddddddG KdddddddddddddddddG B KddddddddddddddddG KdddG KG Kddd L RP Q Y EQ T L PTD EITVAGTD VDNALFDSD GDANDEL S VLELQ PEIGDI TH AP NADD NV ELVENYD .. AS. A K Q V T SA TS S halTADL_1043_variant5 c cc c c JIIIIIIIIIIIIIIIIIIIH JIIIIIIIIIIIIIIIIIH C JIIIIIIIIIIIIIIIIH JIIIH JH JIII L RP Q Y DQ T L TD EITV GTD VDTALFDSD GDANDE DEG A G .. AG. .....................................

580 590 600 610 620 630 640 X X X X X X X halTADL_1043_variant1 EEF DEEEEEEEEEEEEEEEEEEEEEEEF DF DEEEEF DF DF DEEEF DEF DAVT REEIALDDRLVI AEATGIYGAL I E D GLS LV NE VS EV AEE Q K G ISD.....QTPD LT N GDEFAD .EGSDSEWD D L E AIhalTADL_1043 ddG KdddddddddddddddddddddddG KG KddddG KG KG KdddG KdG K VT REEIA DDRLVIQVEATG GALV FD LEDGMT II SE INF V ADD TS P E FE DSTG.....D.. S LAEFNG NDSEDADWA G N E A halTADL_1043_variant3 ddG KdddddddddddddddddddddddG KG KddddG KG KG KdddG KdG K................................................................................halTADL_1043_variant4 ddG KdddddddddddddddddddddddG KG KddddG KG KG KdddG KdG KAAT RDEIAIEDRLIVQVEATGLYG LVA WD LEEGVS LI NE INFEI AEE T A G GADGDAAADPN R TDVLYD EN.....T. S V T halTADL_1043_variant2 ddG KdddddddddddddddddddddddG KG KddddG KG KG KdddG KdG KAAT REEIAVED LIVQVEATGIYGALVA FD LEDGMS LV SE INFEV AEE T E Q GPNNG.NLNSD R ASVLHN EN.....TD S I T halTADL_1043_variant5 IIH JIIIIIIIIIIIIIIIIIIIIIIIH JH JIIIIH JH JH JIIIH JIH J................................................................................

650 660 670 680 690 700 710 720 X X X X X X X X halTADL_1043_variant1 EEEEF DEEEF DF DEEEEF A DEEEEEEEEF A DF DF DEEEEEEEF DEEF DEEF A GNQDP L LN A VVVD E G FYVIVDTS S S D FSA LEY DSD D A P NQ Q DLDSDQ H Q A E D. ETF RS.LS GDE T ST FE.R L SP.. YEN.halTADL_1043 ddddG KdddG KG KddddG B KddddddddG B KG KG KdddddddG KddG KddG B GNQD ELDL ES AFVV D D GQFFVVVDTS SG DD TFTAEMEYE D DD Y FA P AT ENDD Q F E N AGDDVF S.I GD T E R. A DG.. VEPYhalTADL_1043_variant3 ddddG KdddG KG KddddG B KddddddddG B KG KG KdddddddG KddG KddG B ................................................................................halTADL_1043_variant4 ddddG KdddG KG KddddG B KddddddddG B KG KG KdddddddG KddG KddG B GNQDP EVDLQ DS YVLID D GQFFVIVDTS S NG ED SFTAELEYD DNDD YEF P L NGG DS N G SD AFA DAP DV A NR DGSND DPFShalTADL_1043_variant2 ddddG KdddG KG KddddG B KddddddddG B KG KG KdddddddG KddG KddG B GNQEP EVDLQ DS VFVVLD E GQFFVVADTS N NG DE TFTAELEYD DN D YEFA P I DSS D E N SD AFA DAP DT A G NR DTAD APFDhalTADL_1043_variant5 IIIIH JIIIH JH JIIIIH C JIIIIIIIIH C JH JH JIIIIIIIH JIIH JIIH C ................................................................................

730 740 750 760 770 780 790 800 X X X X X X X XhalTADL_1043_variant1 A DEF DEEEEEEEEEF A DEEEEEEEF DEEEEEEEF DEEEEEEEEEEEEEEEEEEEEEEEEE D YPY TL SSAEF A R VSFDNV VD LL AENTEE ISGTTNVAPGTD EIRVSSTDAS S.APTSTG NGPG FAEDT D TF E S D D Q LV S I halTADL_1043 B KdG KdddddddddG B KdddddddG KdddddddG Kddddddddddddddddddddddddd E YPY TVTS A FDIV VNFDNVNVD LEAEN ED EISGTTNVAPGTDGEI VSSTDASTSNGEADND GGPA FQADS E T APE GN I A Q halTADL_1043_variant3 B KdG KdddddddddG B KdddddddG KdddddddG Kddddddddddddddddddddddddd................................................................................halTADL_1043_variant4 B KdG KdddddddddG B KdddddddG KdddddddG Kddddddddddddddddddddddddd D YPY SLSSSAEFDL R VTF NLNVD VLEAENTEE EITGTTNVAPGT GEIRV STDA TSAA..... GAEN LPQGD TP M G S S G A G halTADL_1043_variant2 B KdG KdddddddddG B KdddddddG KdddddddG Kddddddddddddddddddddddddd YPY TLSSS E DLA R I FDNVNVD VLEAENTED EISGTTNVAPGTEGELRVSSTDASSTNTKNPAAQEYHN LLQGE S L P N D D S halTADL_1043_variant5 C JIH JIIIIIIIIIH C JIIIIIIIH JIIIIIIIH JIIIIIIIIIIIIIIIIIIIIIIIII................................................................................

810 820 830 840 850 860 870 880 X X X X X X X XhalTADL_1043_variant1 EEEF DEEEEEEEEEEEEEEEF DEEEEEEEEEEEEEEF DEEEEEEEEEEEEF DEEEEEEF DEF DF FRSG VNITEDGEISAEFDF QEVDDEFDTSFRVGGS VD VESIIVEEGTL EEAPEEDD DD DD ED GD S D S GES GES GMTDDGEhalTADL_1043 dddG KdddddddddddddddG KddddddddddddddG KddddddddddddG KddddddG KdG KG FRNG SVNISEDGEISAEFDFS QEVDDEFDTSFRVGGS IDSV SILVEEGTL DDAPEEDD EDD DD Q D D S E ES. MS GESDDSAhalTADL_1043_variant3 dddG KdddddddddddddddG KddddddddddddddG KddddddddddddG KddddddG KdG KG ................................................................................halTADL_1043_variant4 dddG KdddddddddddddddG KddddddddddddddG KddddddddddddG KddddddG KdG KG FR G SV ISDDG ISAEFDFS QDV DEF TTYRVGGS VDTVDSILVE GSL EDAPEEEE E E E I E E S S G T S A S PEE P EEP EEP....halTADL_1043_variant2 dddG KdddddddddddddddG KddddddddddddddG KddddddddddddG KddddddG KdG KG FRNG S TV DDGEVS EFDFS QE ED FETSFRIGGS VDTVDSMLVEEGTL DDAPEEDD EDE DD Q F G G G F Q A E ESE SE ESE....halTADL_1043_variant5 IIIH JIIIIIIIIIIIIIIIH JIIIIIIIIIIIIIIH JIIIIIIIIIIIIH JIIIIIIH JIH JH ................................................................................

890 900 910 920 930 X X X X X halTADL_1043_variant1 DF DEF DEF DEEEEEEEEEEEEEEEEEEF A DEEEF DEF DD SDD SDD SDDSSSEETPGFGAIVALVA L AALLA RRQ SDDGES GE SA GE V G T N halTADL_1043 KG KdG KdG KddddddddddddddddddG B KdddG KdG DD SDD SDD SDDSSSEETPGFGAIVALVA L AALLA RRQ SDDGES SA SA GE V G T N halTADL_1043_variant3 KG KdG KdG KddddddddddddddddddG B KdddG KdG ..................................................... halTADL_1043_variant4 KG KdG KdG KddddddddddddddddddG B KdddG KdG ED ED SDD TDDST DETPGFGALVALVA V AALLA RRQ ...... DTP DT DS D F A V D halTADL_1043_variant2 KG KdG KdG KddddddddddddddddddG B KdddG KdG DD S TDDS S ...... SE ......... E N.......................... halTADL_1043_variant5 JH JIH JIH JIIIIIIIIIIIIIIIIIIH C JIIIH JIH .....................................................

1 10 20 30 40 50 60 70 X X X X X X X X Halar_0829_variant2 DEEEEEEEF A A DEEEEEEEEEEEEEEF DEF A DF A A A DEEEEF A A DF A MTDTNTKIR L L ALMVFSVFAGTVALSG AAA A TN I Q S NVTFNV N D GD T S V A A DATAFT. GSA VE G. D VTQ TAS D M NV IDISHalar_0829 KdddddddG B B KddddddddddddddG KdG B KG B B B KddddG B B KG B MTDNNNKIR L L ALMVFSVFAGTIALTG AAA V TN V S T TVNFTV S D GE T A F T T VNDTDIA DEF KT YE S TLH KNL S P DT T...Halar_0829_variant1 JIIIIIIIH C C JIIIIIIIIIIIIIIH JIH C JH C C C JIIIIH C C JH C ................................................................................

80 90 100 110 120 130 140 150 X X X X X X X X Halar_0829_variant2 c A DEEEEEEF DF DEF A DF A DEEF A A DEF DEEEEEF A DEF DEF DF DEEE G A GVTVNSVS SS NGN A NG T IVVN S T NAS TVTVTLD N VSS GVS I D ASDA A S WTAT VQ .. D V D ANDGT S H TTG TAS FP TVR GHalar_0829 c B KddddddG KG KdG B KG B KddG B B KdG KdddddG B KdG KdG KG Kddd G I GATVNNVS NS NGT V TG N IVVT N T NAS TLSATVE T VSS GVS VD SD S TLPS Q F NASF SA SS K T N ....D F V WPS DTD IT D Halar_0829_variant1 c C JIIIIIIH JH JIH C JH C JIIH C C JIH JIIIIIH C JIH JIH JH JIII G D T S.........................................................................Q K T

160 170 180 190 200 210 220 230 X X X X X X X X Halar_0829_variant2 cc cccc c ccc c c c EF A DF DF A DEEEEEEEEEEEEEEF DEF A DEEEEF DEEEEEEEEEEEEEEF A DEF DEEF LV GQTV F LRR V G V Q S LV SA D TTNNGS FQ SG D LT T TSF RQISAD VA TSGL SGSV FD DTA D ADVDL YG GA KT V DSG AD. E S SHalar_0829 cc cccc c ccc c c c dG B KG KG B KddddddddddddddG KdG B KddddG KddddddddddddddG B KdG KddG LV GQTV F LRR V G V SV N LL TI D AS SSPT FQ NG DVQ SESSTF R LTADST VV SS L TVT SG ... T TKT AE LA HS.G GG G . Q D N DHalar_0829_variant1 cc cccc c ccc c c c IH C JH JH C JIIIIIIIIIIIIIIH JIH C JIIIIH JIIIIIIIIIIIIIIH C JIH JIIH LV GQTV F LRR V G V NV LTSSS W D DVQ TSDSSS Q ST T G V................. AKP A GTAA ND V N L V QKNT D Y EFK A RP

240 250 260 270 280 290 300 310 X X X X X X X X Halar_0829_variant2 c cc c c c ccc ccc c c A DEEEEEEF A DEEEEEEEEEEEEEF DEEEEF DEEEF DEEEEEF DEF A DF DEEEEEEEEEEEEEF A Y FE A Q V GGS SNR L I G D L NG N V I S SVSADDG N E F V GG FD V AT DGEAASNT QN F A A . R V .D RLD F A ND N M T A S T VE S L T ED THalar_0829 c cc c c c ccc ccc c c B KddddddG B KdddddddddddddG KddddG KdddG KdddddG KdG B KG KdddddddddddddG B Y FE A Q V GGS SNR L I G FVT S S V V SLTVSADDG DN TTEE IE GG F H I D ASQ E Q FG G ET GS T AQY E D LT E N T ....SS D D L SSAHalar_0829_variant1 c cc c c c ccc ccc c c C JIIIIIIH C JIIIIIIIIIIIIIH JIIIIH JIIIH JIIIIIH JIH C JH JIIIIIIIIIIIIIH C Y FE A Q V GGS SNR L I D FLTTGT S L ISA DN TT DF AE YEH L AT EGDAV SD Q G A .TG G TYK T E DFAADT A V E AS. V E Y AA D L G G

320 330 340 350 360 370 380 X X X X X X X Halar_0829_variant2 cc cc c cc c c c c c cc c c DF DEEEEEEEEEEEEEEEEEEEEEEEEEEEEEF DEEEEEEEEF DEEEEEEEEF DEEEEEEEEEF DEEEEEE NF AG V DT S V V G F VS G A SV DSE V V SDGSSFD TGA T NFT TA S T TEIGV VT A N S G IT ...... T E TV G P H FD A VEE G D AY K N E Halar_0829 cc cc c cc c c c c c cc c c KG KdddddddddddddddddddddddddddddG KddddddddG KddddddddG KdddddddddG Kdddddd NF AG V DT S V V G F VS G A D DDVALVGSDGTT DL S LD SYSF S Q TA DS T N TDVGA AT ANSSV I SVTV.....A GE A E DV F S E Q D Halar_0829_variant1 cc cc c cc c c c c c cc c c JH JIIIIIIIIIIIIIIIIIIIIIIIIIIIIIH JIIIIIIIIH JIIIIIIIIH JIIIIIIIIIH JIIIIII NF AG V DT S V V G F VS G A TV DDTDELVVAGT TF A SGAD NYT T T N V DS T DV A TSTIQ GI SI KDADD SDD S V T G A E I SS E D N E D

390 400 410 420 430 440 450 460 X X X X X X X X Halar_0829_variant2 c cc cc c ccccc ccc ccccc cccc cc c cc cc c c EEEEEEEF DEEEEEEEEF DEEEEEEEEEEEEEEEEEF DEEEEEEEEF DEF DEEEEEEEF DEEEF DF DEEE L AT GT G GYQAN FTD DGEVT FNTY AG V AA DD T L L TG LVV QEEN IT ND I A N G D S D L NL D N G D S S R PEASI .E E ASVQ G .. GD Halar_0829 c cc cc c ccccc ccc ccccc cccc cc c cc cc c c dddddddG KddddddddG KdddddddddddddddddG KddddddddG KdG KdddddddG KdddG KG Kddd L AT GT G GYQAN FTD DGEVT FNTY AG V AA DD T L ID S A II SD IS GND V NVS T V N TVT DSQ L NL D E G F .DA Q T GA T D L ...D A Halar_0829_variant1 c cc cc c ccccc ccc ccccc cccc cc c cc cc c c IIIIIIIH JIIIIIIIIH JIIIIIIIIIIIIIIIIIH JIIIIIIIIH JIH JIIIIIIIH JIIIH JH JIII L AT GT G GYQAN FTD DGEVT FNTY AG V AA DD T L VE SGA LVI EES VS G V A SMN T V GS SVS NS D MI M K D D DS M NG W FN QT SA A

470 480 490 500 510 520 X X X X X X Halar_0829_variant2 c c ccc c ccccc cccc c EEEEEEEEEEF A DF DF DEEEEEF DEEEEEEEF DEEEEEEEF DEF A DEEEEF DEEEEEEF DE G Y LAV D RSTDS WTAP T E D SAT AV N S AL IG M L GAAS D L DT G ADQDGD F SGE FS S P Q ASDVF................ ST .Q Halar_0829 c c ccc c ccccc cccc c ddddddddddG B KG KG KdddddG KdddddddG KdddddddG KdG B KddddG KddddddG Kd G Y LAV D RSTDS WTAP T D E E N V TD P VG V L E I GAA DLD D VSESEV AVD GLI DN GTGD .... SV S D T F T QL EG ADD GT MA A Q. Halar_0829_variant1 c c ccc c ccccc cccc c IIIIIIIIIIH C JH JH JIIIIIH JIIIIIIIH JIIIIIIIH JIH C JIIIIH JIIIIIIH JI G Y LAV D RSTDS WTAP T D SAS T AA D PQ LGAL IGE I L T DAD E VTESDI LVEDGMV Q T S A... TK E V K SGT F ..G DG GS EASG

530 540 550 560 570 580 590 600 X X X X X X X X Halar_0829_variant2 cc c ccc cccc c c c c cc c cc c c c EEF DEEEEEEEEEEEEEEEEEF DEEF DEEEEEEEEEEEEEF A DF DEF DEEEEF A DEF DEF DEEEEEETI D HQV ATGL G A G A QT N PK N S I N WVI S LVD S LGNGL NVSVM S Q L LTA S V A TYY A AK G K DF A . EASTR R K P DA QLW DSDND Halar_0829 cc c ccc cccc c c c c cc c cc c c c ddG KdddddddddddddddddG KddG KdddddddddddddG B KG KdG KddddG B KdG KdG KddddddTI D HQV ATGL G A G A QT N PK N S I T T LI N E VID GL I SG INVTV N P N L LS T ALT VVE EG FF I T L N MG E S E .. GR A V D D QN . A G Halar_0829_variant1 cc c ccc cccc c c c c cc c cc c c c IIH JIIIIIIIIIIIIIIIIIH JIIH JIIIIIIIIIIIIIH C JH JIH JIIIIH C JIH JIH JIIIIIITI D HQV ATGL G A G A QT N PK N S I T YMV S D VIE GLS LGS AV LSIV N P Q V VSA LT LVE DGSYY V AG E D D M .. V SD E ....T . G

610 620 630 640 650 660 670 X X X X X X X Halar_0829_variant2 c cc c c cc cc c cc c c EEF DEEEEF DEEEEEEEEEEEEEEEEEEEEEEEF A DEEEEEEEEF A DEEEEEEEEEEEEEEEE E AT V L SV FE L PV A S IDT EAMFDR QRTVAA E YT FT D K VGED NAT IV S S TAQ A GQQ E GSM....... D D S ....TE ERTA N T Halar_0829 c cc c c cc cc c cc c c ddG KddddG KdddddddddddddddddddddddG B KddddddddG B Kdddddddddddddddd E AT V L SV FE L PV A S ID DA FDR N TAA GD FN S ADDK LGDE A Q SAN V P T DSD NVT T AA D VADDGTITSG L D I D ..E ES M E . NA Halar_0829_variant1 c cc c c cc cc c cc c c IIH JIIIIH JIIIIIIIIIIIIIIIIIIIIIIIH C JIIIIIIIIH C JIIIIIIIIIIIIIIII E AT V L SV FE L PV A S A T LV E K I AG F FT A DR L D A Q N T VV P TT DND QVQ A GQT K SG L DT.........P E K N K N RS G EDH T A E

680 690 700 710 720 730 740 750 X X X X X X X X Halar_0829_variant2 c c cccc cc c c c c c cc ccc c ccc c cccc c ccc EEEEEEEEEEEEEEEEEEF DEEEEEEEEF DEEEEEEEEEEEEEEEEEEEEEEEF DEEF DEF DEEEEEEEEEEEEEI G APGT TV S D P F T VQ DGT N DFS Q GDTF V ADG S SF VK G TS R Y N AT A W VT E S A G MIS EI EN TA M A TF T A K P V V S R LN ... G A Halar_0829 c c cccc cc c c c c c cc ccc c ccc c cccc c ccc ddddddddddddddddddG KddddddddG KdddddddddddddddddddddddG KddG KdG KdddddddddddddI G APGT TV S D P F T VQ DGT N DFS Q GDTF V ADG S TTNY EL RAR G TQ R FNT VT F ASF SS TVR GS VAT IMESTS T K P A G FS P N THalar_0829_variant1 c c cccc cc c c c c c cc ccc c ccc c cccc c ccc IIIIIIIIIIIIIIIIIIH JIIIIIIIIH JIIIIIIIIIIIIIIIIIIIIIIIH JIIH JIH JIIIIIIIIIIIIII G APGT TV S D P F T VQ DGT N DFS Q GDTF V ADG T SNY EL RVR T FNT V A F ASF E T TVR GGT LAS EVVD QTA A GS V G Q M A A K T A

760 770 780 790 800 810 820 X X X X X X X Halar_0829_variant2 cc cc c ccccc ccc cccc c c cccccccccccccccccccccccc F DEEEF DEEEF DEEEEEEF DEEEF DEEEF A DEF A DEEEEEEEEEEEEEEEEEEEEEEEEEEF AT TA T TATAT TDM TDTA T E TPGFGVAVALIALLAAALLAGRRE T AT A TPE A A PE T E DD T T E P TA STTD T T D P... G E Halar_0829 cc cc c ccccc ccc cccc c c cccccccccccccccccccccccc G KdddG KdddG KddddddG KdddG KdddG B KdG B KddddddddddddddddddddddddddG AT TA T TATAT TDM TDTA T E TPGFGVAVALIALLAAALLAGRRE AT A PD A PD T E DD T S D PT .. E ...G E A A N S.D TE G Halar_0829_variant1 cc cc c ccccc ccc cccc c c cccccccccccccccccccccccc H JIIIH JIIIH JIIIIIIH JIIIH JIIIH C JIH C JIIIIIIIIIIIIIIIIIIIIIIIIIIH AT TA T TATAT TDM TDTA T E TPGFGVAVALIALLAAALLAGRRE T T A D D S E AT. T.. .....A .EAA P AATDEP T TET

1 10 20 30 40 50 60 X X X X X X X Hlac_2976 ccc cccccccccccccccccccccc ccccccccc c c cc DEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEF A A A A A A DF MTN TNYRTKANAVFFAAIMVVSMVA GFAAAPAAA Q G DG D L V I V A I GGGED TFSD E...........LGDD N T T TH TTGV.Hlac_2976_variant ccc cccccccccccccccccccccc ccccccccc c c cc JIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIH C C C C C C JH MTN TNYRTKANAVFFAAIMVVSMVA GFAAAPAAA Q G DG E V A V I I L TTDLT DGPV SGNDASGTVENDTDST D Y V DE DGTYD

70 80 90 100 110 120 130 X X X X X X X Hlac_2976 cc c cc c c c c c c c c c c c DF A DF DEF A DF A A A DEF A A DF A A A A DF DG I SG T G G V G P T S V N S V T N V N EVE A V N S I YNDS T VA E VDS.A SID ............ DDG F GAH HLTND ASTQT GNS V A IHlac_2976_variant cc c cc c c c c c c c c c c c JH C JH JIH C JH C C C JIH C C JH C C C C JH DG I SG T G G V G P T S V N S A S S L T DLD I A S E N QAAA L WS S DGLDE DYT YAYQNASLNDGA MNA Q TTL D..DT SELRK THY S N .

140 150 160 170 180 190 X X X X X X Hlac_2976 c c c ccc cc c c c cA A DEEEF A A DF DEF DF DEF A DF DEEEF D T T FAD LR A I G EV S VVYS L V SD E T T G L NS SA A VTG TQFQGQELTQN GQ T L SID SE .......................SE Hlac_2976_variant c c c ccc cc c c c cC C JIIIH C C JH JIH JH JIH C JH JIIIH D T T FAD LR A I G EI T LAFN V I TE D S S P I GA IE T DAS I..D....AAD VG G S GSA AG SAGSADGQIFVNTSSTVYNNVENVS

200 210 220 230 240 250 260 X X X X X X XHlac_2976 c c c c c c cc c c c c c c c A DEF A A A A DF A A DEF DEF A A A D Y V D E G RG V A F V G S E L S E L N V QA ...TTQ G ETVSFDT DL P VYAVTNQT ND S.... ETT VTQ TEFDEDSVG ... DG D..EVHlac_2976_variant c c c c c c cc c c c c c c c C JIH C C C C JH C C JIH JIH C C C D Y V D E G RG V A F V G S E A T D V Q L DS GNAVVE D TFGPTTV TR D SS..YEAF EN VLEGN GDA EGE RTRGTGAGS VYV NT NFVGD

270 280 290 300 310 320 X X X X X X Hlac_2976 c c cc ccc c c c c c c cccc c DF DEEEF A DEEF DEEEF A A A A A DF A A DEEEF A A I N VS GLD E F D D D D DAEG F DF SSSQ VE A N E D L D L D R .TYD AD ELANI T S.........GAF E ...... VTE E D IVLS HT N THlac_2976_variant c c cc ccc c c c c c c cccc c JH JIIIH C JIIH JIIIH C C C C C JH C C JIIIH C C I N VS GLD E F D D D D DAEG F EY TNNN LD V T D E V E V N N AETT EL VDEEE E DEDVTATVTSDTI R ITAELI SDG Y T EGTI LE D G

330 340 350 360 370 380 390 400 X X X X X X X X Hlac_2976 c c c c cc ccc c c c c c cc c c cccc A A A A A DF A DF DEEEF A A DEEEEEF DF DF DEEF DEEF DF DEEEE V Y E V DG QGD E V D T G VV G D YQAN S T DT DV EVN Q S Q IV N A NS V D VD DA.GE EF T VTD .TAE SSVT E A IE S LTQ F T GA T GQ FG Hlac_2976_variant c c c c cc ccc c c c c c cc c c cccc C C C C C JH C JH JIIIH C C JIIIIIH JH JH JIIH JIIH JH JIIII V Y E V DG QGD E V D T G VV G D YQAN T S ES EA DAS N T T VA T L QN I E IT SDADT TI V DDN GITA GDFE V R FA G TEV I E .N Y NA DN

410 420 430 440 450 460 470 X X X X X X X Hlac_2976 cccc c c c ccccccc c c cc c c cc c EEEF A A DEEEEEEEEEF DEEEF DF A A DF DEEEEF A SITD D D T FNTYAAG V A DD V L TG Y I LA I D D L I D DI S FG ..... DQ DGVAATDAVT D NIN ......EEAEQ SG A SSSSA NDPHlac_2976_variant cccc c c c ccccccc c c cc c c cc c IIIH C C JIIIIIIIIIH JIIIH JH C C JH JIIIIH C SITD D D T FNTYAAG V A DD V L TG Y V IL V E E V L E EM Q GV DADDA GE NNTYT..... S DEA LENEKHTIQTD DN D IAAAN DSA

480 490 500 510 520 530 540 X X X X X X XHlac_2976 cc c cc c c ccc c c cc c c ccc c c c A DF A DF A A DEF A DF A DEEEF DF DF DF DEF DEF A A DEF DN D VA L I ERS W D DA D E AVE T T D E I I S VL E L LT LI T N V A TL S D T F E TDG Q TA DSNAN DE Q... T G SD Q ........G VAH SHlac_2976_variant cc c cc c c ccc c c cc c c ccc c c c C JH C JH C C JIH C JH C JIIIH JH JH JH JIH JIH C C JIH DN D VA L I ERS W D DA D E AVE T T D D M L T LA D V VN AV S S I S AF E A G L Q APE A RT GDAQE LG DVDA A A DG E DTIAIDTSS PSD L

550 560 570 580 590 600 610 X X X X X X X Hlac_2976 cc c cc ccc c c c cc cc c c cc c c c cDEEEEF DF DEF DEF A A A DF A A DEF A A A DF A A DF A HQ A GL GAL G D Q NL DL E G NA D D S FI IS AA S N N L S D S S A DLTGSD E V FA TTLD E LGGQA RIR TRA A P QR T........V ID N Hlac_2976_variant cc c cc ccc c c c cc cc c c cc c c c cJIIIIH JH JIH JIH C C C JH C C JIH C C C JH C C JH C HQ A GL GAL G D Q NL DL E G NA D D S FV VT VV T Q Q A N E P E S GD.... A E LE LDNQ G NSAYS VFE ..Q P R EP IVNATDLTGT DF V

620 630 640 650 660 670 680 690 X X X X X X X XHlac_2976 ccc cc c cc ccc c cc c c c cc cc cc c c DF DEEF DEEEEEF DF A DF DEEEEF A DF A DF A A DEF DF DEEEF DEE DEE YY D EF EFT E LL D D E ED FS EE A F IL N LVL T IT E V VT P T L VT I E D V DE SD VDGDSLDNS DY D S R N ED .. KS F HQE TP RT Hlac_2976_variant ccc cc c cc ccc c cc c c c cc cc cc c c JH JIIH JIIIIIH JH C JH JIIIIH C JH C JH C C JIH JH JIIIH JII DEE YY D EF EFT E LL D D E ED FS EE A F VV T ILV Q LN D A IQ G S A AN V D T Y SN DA SAAP.DSFE GD S D Q R SG FD GE L YET AT AE

700 710 720 730 740 750 760 X X X X X X X Hlac_2976 c c ccccccc c c cc cc c c c c c c ccc cc ccc c c cF A DF DEEEEEEEF DEEEEF DF DEF A A DEEEEEEEEF DF DEF A A A DD V GTTNVAP T F VR RS T P F T V V ADG FD SGQ V D Q S DS T D T Q D N S SW Y EDPY...NV NT EE G S ASG S VK NS STE F S G E TFRVQ Hlac_2976_variant c c ccccccc c c cc cc c c c c c c ccc cc ccc c c cH C JH JIIIIIIIH JIIIIH JH JIH C C JIIIIIIIIH JH JIH C C C JD V GTTNVAP T F VR RS T P F T V V ADG FD SGQ V D Q T EN S E S S E T N TF F VNADDEIET AE AT S L TDD R TL DD EAS L A N T EATFH

770 780 790 800 810 820 830 840 X X X X X X X X Hlac_2976 ccc ccccc ccccc cccc cc c cc cc cccccccccc c c cc cccF DEF DEEEEEEF DEEEEEEEEF DF A A DEEEF DEEEEEEEEEF A A DF DEE VDG VEAVD DDDST DDST DD D ST DD TDDDSTDDDS D S DD SSGL V DG E S E T GLNDAVE T T T D ATDD S S SSEDDSSSED SS E S Hlac_2976_variant ccc ccccc ccccc cccc cc c cc cc cccccccccc c c cc cccH JIH JIIIIIIH JIIIIIIIIH JH C C JIIIH JIIIIIIIIIH C C JH JII VDG VEAVD DDDST DDST DD D ST DD TDDDSTDDDS D S DD SSGA I EP D T D S AFDGQDA V V D S DD.. . . .........T DD T D

850 860 870 880 X X X X Hlac_2976 ccccccc ccccccccccccccccccccccccc EEEEEEF DEEEEEEEEEEEEEEEEEEEEEEEF DDSTTED TPGFGAIVALVALIAAALLATRRNE D Hlac_2976_variant ccccccc ccccccccccccccccccccccccc IIIIIIH JIIIIIIIIIIIIIIIIIIIIIIIH DDSTTED TPGFGAIVALVALIAAALLATRRNE G

Figure S2. Multiple sequence alignment of tADL archaella proteins. Archaella protein sequences from the genome sequence of tADL were aligned with sequences of variants present on Deep Lake metagenome contigs. All proteins were detected in the metaproteome. The figure was created using Clustal Omega and the ENDscript server. Identical residues (white characters on red background) and similar residues (red characters on white background, similarity score > 0.6) are framed in blue.

1 10 20 30 40 50 60 X X X X X X X halTADL_0078_variant ccccccccccccccccccccccccccccccccccccccccc c ccccc cccc DEF DEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEF A RGQVGIGTLIVFIAMVLVAAIAAGVLINTAGLLQTQAEATG E QVSDR SATG STQ INI NVT N .....MFTEN Q L D ......halTADL_1813_variant ccccccccccccccccccccccccccccccccccccccccc c ccccc cccc KdG KdddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddG B RGQVGIGTLIVFIAMVLVAAIAAGVLINTAGLLQTQAEATG E QVSDR SATG M T E STQ LQIQ TV S .... L DNN DN G...SThalTADL_1812_variant ccccccccccccccccccccccccccccccccccccccccc c ccccc cccc KdG KdddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddG B RGQVGIGTLIVFIAMVLVAAIAAGVLINTAGLLQTQAEATG E QVSDR SATG MFN D E S Q IQIQ V .... DT A V GD.......halTADL_0078 ccccccccccccccccccccccccccccccccccccccccc c ccccc cccc KdG KdddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddG B RGQVGIGTLIVFIAMVLVAAIAAGVLINTAGLLQTQAEATG E QVSDR SATG MF D E SSQ IQIQ V N .... EHS A VY ADGKENhalTADL_1812 ccccccccccccccccccccccccccccccccccccccccc c ccccc cccc KdG KdddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddG B RGQVGIGTLIVFIAMVLVAAIAAGVLINTAGLLQTQAEATG E QVSDR SATG VFN E E SSQ LQIQ IN T MFET AD E S R.....halTADL_1813 ccccccccccccccccccccccccccccccccccccccccc c ccccc cccc KdG KdddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddG B RGQVGIGTLIVFIAMVLVAAIAAGVLINTAGLLQTQAEATG E QVSDR SATG MFN D E SSQ LQIQ NVT .... DT ..G.....halTADL_1544 ccccccccccccccccccccccccccccccccccccccccc c ccccc cccc KdG KdddddddddddddddddddddddddddddddddddddddddddddddddddddddddddddG B RGQVGIGTLIVFIAMVLVAAIAAGVLINTAGLLQTQAEATG E QVSDR SATG LFN D E ST INIQ NVT S MFSK NE E D G.....halTADL_1544_variant ccccccccccccccccccccccccccccccccccccccccc c ccccc cccc JIH JIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIH C RGQVGIGTLIVFIAMVLVAAIAAGVLINTAGLLQTQAEATG E QVSDR SATG LFN E QQ IQVQ NVT T MFAT NDK A G GT...S

70 80 90 100 110 120 130 140 X X X X X X X X halTADL_0078_variant c c cc cc cccc c cc c c c c ccccc c ccc c A DEEEEEEEEEEEEEEEEEEEEEEEF A A DEEF DEEEEEF A DEEEEEEEEEF DEEEEF N T TK GA DIQL Y VT V T I T DNVIT R DRY F I V V L A E ENVT EF D GVV SISN T D S I NAT DD DK A S S S GTS....DA SA N K E N...halTADL_1813_variant c c cc cc cccc c cc c c c c ccccc c ccc c B KdddddddddddddddddddddddG B B KddG KdddddG B KdddddddddG KddddG N T TK GA DIQL Y VT V T I T DNVIT R DRY F I V I V AP ENVT EF GVV SI T S LQ Q AN TE G DND T NEG....GS KY NE A S I TDT...halTADL_1812_variant c c cc cc cccc c cc c c c c ccccc c ccc c B KdddddddddddddddddddddddG B B KddG KdddddG B KdddddddddG KddddG N T TK GA DIQL Y VT V T I T DNVIT R DRY F V V L V AP D NVT EF D VM SISQ TA N LS A EN TR A D Q T N EPDDLGNGS E D S V V ED...halTADL_0078 c c cc cc cccc c cc c c c c ccccc c ccc c B KdddddddddddddddddddddddG B B KddG KdddddG B KdddddddddG KddddG N T TK GA DIQL Y VT V T I T DNVIT R DRY F L I L V AP D ENVT EF D GVL ISN TA D S LT AS YN TE S S I EEG......K Q N K D S...halTADL_1812 c c cc cc cccc c cc c c c c ccccc c ccc c B KdddddddddddddddddddddddG B B KddG KdddddG B KdddddddddG KddddG N T TK GA DIQL Y VT V T I T DNVIT R DRY F V V I V AP D ENVT EF D VL QITN SA D S LN AS EV TA S K I N SES...... E N Q D E...halTADL_1813 c c cc cc cccc c cc c c c c ccccc c ccc c B KdddddddddddddddddddddddG B B KddG KdddddG B KdddddddddG KddddG N T TK GA DIQL Y VT V T I T DNVIT R DRY F I V I V AP D ENVT EF D VV QVS TA D S L N T EE DS S Q I D AAG...... E A S Q E T ....halTADL_1544 c c cc cc cccc c cc c c c c ccccc c ccc c B KdddddddddddddddddddddddG B B KddG KdddddG B KdddddddddG KddddG N T TK GA DIQL Y VT V T I T DNVIT R DRY F I L L S GVL I T D S VQ NIS .D DQF SA G NET QI DGA K SGN....ATV GA SE P E TVGGhalTADL_1544_variant c c cc cc cccc c cc c c c c ccccc c ccc c C JIIIIIIIIIIIIIIIIIIIIIIIH C C JIIH JIIIIIH C JIIIIIIIIIH JIIIIH N T TK GA DIQL Y VT V T I T DNVIT R DRY F V L L P D D VS G L I Q TA D VQ NLS ST DTF S D QI DQA E T SGN....ATI G A D A E VSS.

150 160 170 180 X X X X halTADL_0078_variant cc ccccc ccccc cccccccc cc c A DEEEEEEEEEEEEEEEEEEEEEEEEEEEEF DEEF A GG TLTTA GASTV ELRVPDSL AV L I LN DRVTL P T V KS ........A GGK S S halTADL_1813_variant cc ccccc ccccc cccccccc cc c B KddddddddddddddddddddddddddddG KddG B GG TLTTA GASTV ELRVPDSL AV L M LQ DRVSV T V RS ........A GAY A D A halTADL_1812_variant cc ccccc ccccc cccccccc cc c B KddddddddddddddddddddddddddddG KddG B GG TLTTA GASTV ELRVPDSL AV L L L DKVSV T V RS ........T GGD D A S S halTADL_0078 cc ccccc ccccc cccccccc cc c B KddddddddddddddddddddddddddddG KddG B GG TLTTA GASTV ELRVPDSL AV L L LQ E VTV P T I KS ........D NGN Q G K halTADL_1812 cc ccccc ccccc cccccccc cc c B KddddddddddddddddddddddddddddG KddG B GG TLTTA GASTV ELRVPDSL AV L L LQ EKISV P T V RS ........D DGD D K halTADL_1813 cc ccccc ccccc cccccccc cc c B KddddddddddddddddddddddddddddG KddG B GG TLTTA GASTV ELRVPDSL AV L Q DKI V P T V RS ........HFDTNF A D K halTADL_1544 cc ccccc ccccc cccccccc cc c B KddddddddddddddddddddddddddddG KddG B GG TLTTA GASTV ELRVPDSL AV L I LQ E V V V KS APTYPDQEI GTA S R A A D S halTADL_1544_variant cc ccccc ccccc cccccccc cc c C JIIIIIIIIIIIIIIIIIIIIIIIIIIIIH JIIH C GG TLTTA GASTV ELRVPDSL AV L L LT D VQV P T V RQ ..VSGDKNI DSG S S S

Figure S3. Arrangement of genes in select metagenomic contigs and genomic regions. (A) metagenomic contig (ctg7180000459513) that includes ORFs homologous to the tADL pilus protein halTADL_1885 and putative viral ORFs. (B) comparison of a region of the tADL genome and a matching metagenome contig (ctg7180000397348), with the latter showing a putative provirus inserted at the tRNA-Lys position in the tADL genome. (C) region of the Hrr. lacusprofundi genome marked by six ORFs (including one of putative viral origin) flanked by IS elements. HP, hypothetical protein; PKD, PKD adhesion domain; SiR/NiR (4Fe-4S), sulfite reductase/nitrite reductase, 4Fe-4S component; ORFs encoding haloarchaeal proteins (blue); ORFs encoding viral proteins (red); transposase IS elements (green); ORFs encoding proteins with no known homologs (gray); tRNA gene (yellow); gene annotations (above each ORF0; known haloarchaeoviruses (underlined). (A) and (B), the tADL locus tag (all prefaced with halTADL) are shown underneath each ORF that encodes a tADL protein, and for (C), the Hrr. lacusprofundi locus tag (all prefaced with Hlac) is shown underneath each ORF. Full details of each contig are in Table S11.

z9400369

Typewritten Text

Figure S3

Figure S4. Phylogenetic trees of Cas proteins. Optimal tree constructed by the NJ method (trees constructed by Maximum Likelihood showed negligible differences). Sequences for Cas proteins in the genomes of tADL, DL31, Hrr. lacusprofundi or DL1 (red) and Deep Lake metagenome contigs (blue). The trees for Cas1 (A), Cas2 (B) and Cas3 (C) were rooted using the respective Escherichia coli sequence as the outgroup, and all other trees shown are unrooted. Bootstrap values < 50% are not shown. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. The number of positions retained were: (A) Cas1, 315 positions; (B) Cas2, 86 positions; (C) Cas3, 459 positions; (D) Cas4, 161 positions; (E) Cas6, 209 positions; (F) Cas8b (=Csh1), 618 positions; (G) Cas7 (=Csh2), 320 positions; (H) Cas5, 220 positions; (I) Csc1, 205 positions; (J) Csc2, 298 positions; (K) Cas10d (=Csc3), 754 positions. Trees were drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree.

Figure S4A Cas1

Type I-B

Type I-D

halTADL 1356 halophilic archaeon sp. True-ADL

DL metagenome 224443710 ctg7180000397074

DL metagenome 224467803 ctg7180000459076

Hqrw 2364 Haloquadratum walsbyi C23

HAH 4162 Haloarcula hispanica CGMCC 1.2049

HISP 17975 Haloarcula hispanica N601

Natgr 3461 Natronobacterium gregoryi SP2 DSM 3393

DL metagenome 224471523 ctg7180000278686

HalDL1 3066 Halobacterium sp. DL1

DL metagenome 224424489 ctg7180000412256

Huta 1449 Halorhabdus utahensis DSM 12940

Hmuk 2838 Halomicrobium mukohataei DSM 12286

NJ7G 0929 Natrinema sp. J7-2

pNG4053 Haloarcula marismortui ATCC 43049

HFX 6320 Haloferax mediterranei R-4 ATCC 33500

BM92 16400 Haloferax mediterranei ATCC 33500

Hlac 3327 Halorubrum lacusprofundi ATCC 49239

HVO A0211 Haloferax volcanii DS2

DL metagenome 224458174 ctg7180000441522

MA3670 Methanosarcina acetivorans str. C2A

MTH1084 Methanobacterium thermoautotrophicum str. Delta H

PF1118 Pyrococcus furiosus DSM 3638

NP3274A Natronomonas pharaonis DSM 2160

Halar 0916 halophilic archaeon sp. DL31

DL metagenome 224464431 ctg7180000435228

Hqrw 1377 Haloquadratum walsbyi C23

Hlac 3578 Halorubrum lacusprofundi ATCC 49239

DL metagenome 224486061 ctg7180000293457

b2755 Escherichia coli str. K-12 substr. MG1655

100

96 74

99

100

75 100

98 100

100

100

100

100

100

100

100 97

71

100

100

69

67

86

100

82

0.1

Figure S4B Cas2

Type I-B

Type I-D

DL metagenome 224443706 ctg7180000397074

halTADL 1355 halophilic archaeon sp. True-ADL

DL metagenome 224467805 ctg7180000459076

Hqrw 2365 Haloquadratum walsbyi C23

HAH 4161 Haloarcula hispanica CGMCC 1.2049

HISP 17980 Haloarcula hispanica N601

Natgr 3462 Natronobacterium gregoryi SP2 DSM 3393

DL metagenome 224471529 ctg7180000278686

DL metagenome 224424503 ctg7180000412256

HalDL1 3067 Halobacterium sp. DL1

HFX 6321 Haloferax mediterranei R-4 ATCC 33500

BM92 16395 Haloferax mediterranei ATCC 33500

Hmuk 2839 Halomicrobium mukohataei DSM 12286

NJ7G 0930 Natrinema sp. J7-2

pNG4054 Haloarcula marismortui ATCC 43049 plasmid pNG400

Huta 1448 Halorhabdus utahensis DSM 12940

Hlac 3326 Halorubrum lacusprofundi ATCC 49239

DL metagenome 224458170 ctg7180000441522

HVO A0212 Haloferax volcanii DS2

MA3669 Methanosarcina acetivorans str. C2A

PF1117 Pyrococcus furiosus DSM 3638

MTH1083 Methanobacterium thermoautotrophicum str. Delta H

Hqrw 1378 Haloquadratum walsbyi C23

NP3276A Natronomonas pharaonis DSM 2160

DL metagenome 224464422 ctg7180000435228

Halar 0915 halophilic archaeon sp. DL31

DL metagenome 224486065 ctg7180000293457

Hlac 3579 Halorubrum lacusprofundi ATCC 49239

b2754 Escherichia coli str. K-12 substr. MG1655

100

79

91

54

100

99

100

63

99

99

99

63

53

100

81

68 100

71

99 99

91 85

97

91

62

0.1

c) Cas3 HAH 4164 Haloarcula hispanica CGMCC 1.2049

HISP 17965 Haloarcula hispanica N601

halTADL 1358 halophilic archaeon sp. True-ADL

DL metagenome 224467799 ctg7180000459076

Natgr 3459 Natronobacterium gregoryi SP2 DSM 3393

pNG4051 Haloarcula marismortui ATCC 43049

Huta 1451 Halorhabdus utahensis DSM 12940

HFX 6318 Haloferax mediterranei R-4 ATCC 33500

BM92 16410 Haloferax mediterranei ATCC 33500

Hmuk 2836 Halomicrobium mukohataei DSM 12286

NJ7G 0927 Natrinema sp. J7-2

DL metagenome 224424467 ctg7180000412256

HalDL1 3064 Halobacterium sp. DL1

DL metagenome 224467787 ctg7180000459074

DL metagenome 224471510 ctg7180000278686

Hqrw 2362 Haloquadratum walsbyi C23

DL metagenome 224496691 ctg7180000287417

Hlac 3329 Halorubrum lacusprofundi ATCC 49239

DL metagenome 224458182 ctg7180000441522

HVO A0209 Haloferax volcanii DS2 plasmid pHV4

DL metagenome 224464445 ctg7180000435228

Halar 0918 halophilic archaeon sp. DL31

DL metagenome 224486053 ctg7180000293457

DL metagenome 224468149 ctg7180000460297

Hlac 3576 Halorubrum lacusprofundi ATCC 49239

NP3270A Natronomonas pharaonis DSM 2160

Hqrw 1375 Haloquadratum walsbyi C23

MTH1086 Methanobacterium thermoautotrophicum str. Delta H

MA3665 Methanosarcina acetivorans str. C2A

PF1120 Pyrococcus furiosus DSM 3638

b2761 Escherichia coli str. K-12 substr. MG1655

100 100

100 100

100

100

100

100

98

80 100

100

100

100

87

100

99

95 58

68

91

95

87 100

59

59

0.1

Figure S4C Cas3

Figure S4D Cas4

DL metagenome 224443714 ctg7180000397074

halTADL 1357 halophilic archaeon sp. True-ADL

DL metagenome 224467801 ctg7180000459076

Hqrw 2363 Haloquadratum walsbyi C23

HAH 4163 Haloarcula hispanica CGMCC 1.2049

HISP 17970 Haloarcula hispanica N601

Natgr 3460 Natronobacterium gregoryi SP2 DSM 3393

DL metagenome 224471516 ctg7180000278686

DL metagenome 224424478 ctg7180000412256

HalDL1 3065 Halobacterium sp. DL1

Hmuk 2837 Halomicrobium mukohataei DSM 12286

NJ7G 0928 Natrinema sp. J7-2

HFX 6319 Haloferax mediterranei R-4 ATCC 33500

BM92 16405 Haloferax mediterranei ATCC 33500

pNG4052 Haloarcula marismortui ATCC 43049

Huta 1450 Halorhabdus utahensis DSM 12940

DL metagenome 224458178 ctg7180000441522

HVO A0210 Haloferax volcanii DS2

DL metagenome 224488541 ctg7180000445955

Hlac 3328 Halorubrum lacusprofundi ATCC 49239

MA3671 Methanosarcina acetivorans str. C2A

MTH1085 Methanobacterium thermoautotrophicum str. Delta H

PF1119 Pyrococcus furiosus DSM 3638

DL metagenome 224464438 ctg7180000435228

Halar 0917 halophilic archaeon sp. DL31

DL metagenome 224486057 ctg7180000293457

Hlac 3577 Halorubrum lacusprofundi ATCC 49239

NP3272A Natronomonas pharaonis DSM 2160

Hqrw 1376 Haloquadratum walsbyi C23

100 100

100 99

100

100

91

100

99

100

100

100

100

100

100

100 82

88

99

97

93

95

62

61

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0.1

Figure S4E Cas6

*

HAH 4168 Haloarcula hispanica CGMCC 1.2049

HISP 17945 Haloarcula hispanica N601

Hqrw 2358 Haloquadratum walsbyi C23

DL metagenome 224443738 ctg7180000397074

halTADL 1362 halophilic archaeon sp. True-ADL

Natgr 3455 Natronobacterium gregoryi SP2 DSM 3393

DL metagenome 224488518 ctg7180000445955

Hlac 3333 Halorubrum lacusprofundi ATCC 49239

DL metagenome 224467779 ctg7180000459074

HalDL1 3060 Halobacterium sp. DL1

pNG4046 Haloarcula marismortui ATCC 43049

Huta 1455 Halorhabdus utahensis DSM 12940

Hmuk 2832 Halomicrobium mukohataei DSM 12286

NJ7G 0923 Natrinema sp. J7-2

HFX 6314 Haloferax mediterranei R-4 ATCC 33500

DL metagenome 224496710 ctg7180000287417

DL metagenome 224458211 ctg7180000441522

HVO 0205 Haloferax volcanii DS2

MA3672 Methanosarcina acetivorans str. C2A

MTH1091 Methanobacterium thermoautotrophicum str. Delta H

PF1131 Pyrococcus furiosus DSM 3638

PF0393 Pyrococcus furiosus DSM 3638

DL metagenome 224432855 ctg7180000469294

Halar 0922 halophilic archaeon sp. DL31

NP3262A Natronomonas pharaonis DSM 2160

Hqrw 1371 Haloquadratum walsbyi C23

DL metagenome 224432036 ctg7180000296155

Hlac 3572 Halorubrum lacusprofundi ATCC 49239 100 98

89

100

100

100

82

51

100

100

100

100

100

100

98

69

93

51

94

99

77

64

76

100

0.1

Figure S4F Cas8b (= Csh1) (found in Type I-B)

* DL metagenome 224443734 ctg7180000397074

halTADL 1361 halophilic archaeon sp. True-ADL

DL metagenome 224469892 ctg7180000277681

DL metagenome 224467793 ctg7180000459076

HAH 4167 Haloarcula hispanica CGMCC 1.2049

HISP 17950 Haloarcula hispanica N601

Natgr 3456 Natronobacterium gregoryi SP2 DSM 3393

pNG4047 Haloarcula marismortui ATCC 43049

Huta 1454 Halorhabdus utahensis DSM 12940

HFX 6315 Haloferax mediterranei R-4 ATCC 33500

BM92 16425 Haloferax mediterranei ATCC 33500

Hmuk 2833 Halomicrobium mukohataei DSM 12286

NJ7G 0924 Natrinema sp. J7-2

DL metagenome 224424428 ctg7180000412256

HalDL1 3061 Halobacterium sp. DL1

DL metagenome 224496704 ctg7180000287417

DL metagenome 224471486 ctg7180000278686

Hqrw 2359 Haloquadratum walsbyi C23

DL metagenome 224467781 ctg7180000459074

DL metagenome 224458207 ctg7180000441522

HVO A0206 Haloferax volcanii DS2

DL metagenome 224488522 ctg7180000445955

Hlac 3332 Halorubrum lacusprofundi ATCC 49239 100 77

100

100

100

100

100

51

100

99

100

100

100

100

60

100

99

100

0.05

Figure S4G Cas7 (= Csh2) (found in Type I-B)

*

*

*

*

DL metagenome 224443730 ctg7180000397074

halTADL 1360 halophilic archaeon sp. True-ADL

DL metagenome 224467795 ctg7180000459076

Natgr 3457 Natronobacterium gregoryi SP2 DSM 3393

pNG4049 Haloarcula marismortui ATCC 43049

Huta 1453 Halorhabdus utahensis DSM 12940

HAH 4166 Haloarcula hispanica CGMCC 1.2049

HISP 17955 Haloarcula hispanica N601

HFX 6316 Haloferax mediterranei R-4 ATCC 33500

BM92 16420 Haloferax mediterranei ATCC 33500

DL metagenome 224424442 ctg7180000412256

HalDL1 3062 Halobacterium sp. DL1

Hmuk 2834 Halomicrobium mukohataei DSM 12286

NJ7G 0925 Natrinema sp. J7-2

DL metagenome 224471491 ctg7180000278686

Hqrw 2360 Haloquadratum walsbyi C23

DL metagenome 224458190 ctg7180000441522

HVO 0207 Haloferax volcanii DS2

DL metagenome 224488526 ctg7180000445955

Hlac 3331 Halorubrum lacusprofundi ATCC 49239

DL metagenome 224467783 ctg7180000459074

DL metagenome 224496699 ctg7180000287417

100

74

100

100

100

100

100 67

99

100

100 100

99

89

99

67 90

0.05

Figure S4H Cas5 (found in Type I-B) DL metagenome 224443726 ctg7180000397074

halTADL 1359 halophilic archaeon sp. True-ADL

DL metagenome 224467797 ctg7180000459076

HAH 4165 Haloarcula hispanica CGMCC 1.2049

HISP 17960 Haloarcula hispanica N601

Natgr 3458 Natronobacterium gregoryi SP2 DSM 3393

pNG4050 Haloarcula marismortui ATCC 43049

Huta 1452 Halorhabdus utahensis DSM 12940

HFX 6317 Haloferax mediterranei R-4 ATCC 33500

BM92 16415 Haloferax mediterranei ATCC 33500

Hmuk 2835 Halomicrobium mukohataei DSM 12286

NJ7G 0926 Natrinema sp. J7-2

DL metagenome 224424453 ctg7180000412256

HalDL1 3063 Halobacterium sp. DL1

DL metagenome 224471497 ctg7180000278686

Hqrw 2361 Haloquadratum walsbyi C23

DL metagenome 224467785 ctg7180000459074

DL metagenome 224496695 ctg7180000287417

DL metagenome 224458186 ctg7180000441522

HVO 0208 Haloferax volcanii DS2 plasmid pHV4:

DL metagenome 224488529 ctg7180000445955

Hlac 3330 Halorubrum lacusprofundi ATCC 49239 100

100

72

100

100

100

100

100

68

60

83

91

85

81

96

63

56

50

98

0.05

Figure S4I Csc1 (found in Type I-D)

NP3268A Natronomonas pharaonis DSM 2160

Hqrw 1374 Haloquadratum walsbyi C23

Hlac 3575 Halorubrum lacusprofundi ATCC 49239

DL metagenome 224492763 ctg7180000295653

Halar 0919 halophilic archaeon sp. DL31

100 78

0.1

Figure S4J Csc2 (found in Type I-D)

*

NP3266A Natronomonas pharaonis DSM 2160

Hqrw 1373 Haloquadratum walsbyi C23

Hlac 3574 Halorubrum lacusprofundi ATCC 49239

DL metagenome 224492771 ctg7180000295653

DL metagenome 224464458 ctg7180000435228

Halar 0920 halophilic archaeon sp. DL31 100

100

0.1

Figure S4K Cas10d (= Csc3) (found in Type I-D)

*

NP3264A Natronomonas pharaonis DSM 2160

Hqrw 1372 Haloquadratum walsbyi C23

Hlac 3573 Halorubrum lacusprofundi ATCC 49239

Halar 0921 halophilic archaeon sp. DL31

DL metagenome 224468147 ctg7180000460297

100 100

0.1

Figure S5. Phylogenetic tree and consensus sequences for CRISPR repeats. (A) Optimal tree constructed by the NJ method. Bootstrap consensus tree of CRISPR locus repeat sequences identified in the genomes of tADL, DL31, Hrr. lacusprofundi, DL1 (highlighted in red font), Deep Lake contigs and reference haloarchaeal taxa (boostrap values < 50% are not shown). (B) Consensus for all Type I-B repeats except Hrr. lacusprofundi locus 1, Hfx. mediterranei ATCC 33500 I and II and Hqr. walsbyi C23 CRISPR 2 and 3, for which the consensus is shown in (C). An asterisk (C) indicates that only Hrr. lacusprofundi locus 1 contains a T at position 26 of this sequence logo, whereas the other four repeats contain a gap at this position. (D) Consensus of the four 37 bp Type I-D repeats.

Repeats from Type I-D CRISPR systems

(37bp long)

Repeats from Type I-B CRISPR systems

(30-31bp) Figure S5A ctg7180000278686

unknown haloarchaeon 1

Haloarcula marismortui ATCC 43049 II

ctg7180000412256

DL1 locus 1

DL31 locus 2

Haloferax volcanii DS2 I

Haloferax volcanii DS2 II

unknown haloarchaeon 2

Haloferax mediterranei ATCC 33500 I

Haloferax mediterranei ATCC 33500 II

Halorubrum lacusprofundi locus 1

Haloquadratum walsbyi C23 CRISPR 2

Haloquadratum walsbyi C23 CRISPR 3

tADL locus 2

ctg7180000397074

tADL locus 1

tADL locus 4

Haloarcula hispanica CGMCC 1.2049

Haloarcula hispanica N601

Natronobacterium gregoryi SP2 DSM 3393

tADL locus 3

Haloarcula marismortui ATCC 43049 I

Natrinema sp. J7-2

Halomicrobium mukohataei DSM 12286

Halorhabdus utahensis DSM 12940

Haloquadratum walsbyi C23 CRISPR 1

DL31 locus 1

Halorubrum lacusprofundi locus 2

Natronomonas pharaonis DSM 2160 59 68

99

82

68

76

74

70

0.2

*

Figure S5B

Figure S5C

Figure S5D

Figure S6. CRISPR leader sequences for Deep Lake CRISPR systems.

Figure S6. CRISPR leader sequences for Deep Lake CRISPR systems.

Motifs BRE TATA -10 element TSS leader motif tADL locus 1 GTTTCCGTCAACCCCCCGGGGGTTTGGGGGTGATTGGGGGTCGACCGAAGTGCTTTAGTATAGCCGTCCGGTAGAGAGCTTGTGACCCGTATTTCGGGCATG tADL locus 2 CTACTTTCACTGCGCTTTACATTCTTTTATATACTGTCTGTGAGTATTAAGTATTGGATGACATCCCCCAATCACAGAGGTGAGTCCAGTAAGTGCGCGTAA tADL locus 3 CTCTGTAGTCGACCCCCACACCTTTGAGGTGTATTGATGGTCGACTGAGTTGTCAACCTATTACTCCCTGGTAGAGAGGTTGAAACCGCCACTTTAGGCATG tADL locus 4 GTTTCGGTCGACCTCCCCGGGGTGAGAGGGGTATTGGAGGTCGACAGAACATCTTTGTGCAAACCCCGCATTATAGCATCTGTAGCCGGTATATCCGGCATG H.lac locus 1 TTTTCCGTCGACCCCCTAGGGTTTGGCCAGAATTGGAGGTCGACGAAAGTTCTAAATCATAGACCACGTATATGAGCCTTGTGTGGCCTATATTGGCACAT H.lac locus 2 GACCCTTATTAAGTCTCTGTACAGCCCCAGTCGACGTAGCGGGGGTTAGATTTTGAGCACTGAGAAAGGCTTTTGACCCCTATAACCGTATATTCACCCCCT DL31 locus 1 CCTTTATTAGTTCGGTGTACAGTCCCAGTCGACGTAACGAGGGGGAGATTTCCGGTACTGAGAAAGCTTTTTGACCCTTATCGCCGTATTTACACCCCCT DL31 locus 2 CTGATGTCGACCCCCGGGGGTACTGGGGTGATTGCGGGTCGACGGAAACTACTTGTGCAAGACGGCCATTTTACTGTCTGTGTGCCCAAAATCGGGCAC DL1 locus 1 CTGATGTCGACCCCCAGGGGGTTTGGGGGGGATTGCGGGTCGACGGAAATGATGAAGTGTATTCCACTGGTAGAGGTGATATGGTGGACAAAATCACCATG ctg7180000459076 TCTTGGTCGACCCCCTGGGGGTAGCGGGGGTATTGAGGGTCGACGGAACATCTTTGTGATAGCTCCCCGTTAGAGCGCCTATGCTCCGTATATCGGGCATGG ctg7180000278686 GCTGATGTCGACCCCCGGGGGTACTGGGGTGATTGCGGGTCGACGGAAACTATTTGTGCAAGACGGCTATATTAGTGGCTGTGTGCCCACAATCGGGCACG

Figure S7. BREX system gene clusters in the genomes of Hrr. lacusprofundi and DL31. Genes are color coded as follows: BREX genes (orange), toxin-antitoxin system (pink), transposase IS elements (green) and function unknown (gray). Nomenclature of BREX system genes follows Goldfarb et al. (2015).

z9400369

Typewritten Text

Figure S7

Figure S8. Metagenome FR coverage of DL31 BREX cluster showing low coverage for the pglX gene (Halar_0260). FR coverage was obtained from Deep Lake metagenome reads using the DL31 genome (DeMaere et al., 2013) viewed using Artemis (Carver et al., 2012). HP, hypothetical.

brxA brxC/pglY brxB brxC/pglY pglX HP pglZ brxHII

vapC vapB

Figure S9. Phylogenetic analysis of pilin protein (PilA) homologs from Euryarchaeota. There is a close relationship between a pilin protein encoded in the tADL genome and a pilin protein (224467999) encoded on Deep Lake metagenome contig that is inferred to be of viral origin (both proteins shown in bold). Haloarchaea are shown in red, methanogens in green. A putative pilin protein from Archaeoglobus fulgidus DSM 4304 is the outgroup. Deep Lake haloarchaeon PilA sequences and full length reference proteins containing Pfam domain PF07790 were aligned using Muscle and the phylogenetic tree was constructed using the Neighbour-Joining method in MEGA5. All positions with less than 80% site coverage were eliminated (i.e., fewer than 20% alignment gaps were allowed at any position). Only bootstrap values of at least 50% are shown. There were a total of 39 amino acid sequences and 142 positions in the final dataset.

z9400369

Typewritten Text

Figure S9

Figure S10. MS spectra details for proteins with a single peptide identification. Data including the annotated spectra and fragmentation tables were exported from Mascot. Protein identification number and number of samples in which the peptide was detected is shown (blue font, top of page). For peptides detected in more than one sample, the spectrum with the highest mascot ion score is shown.

Mascot Search Results

Peptide View

MS/MS Fragmentation of TLSIDTAGDADAFLSITK

Found in lcl|featureId|224483443 in meta-bt-d, hypothetical

Match to Query 2566: 1837.933848 from(919.974200,2+) index(5297)

Title: Bernhard-20130703-631-1.6944.6944.2.dta

Data file F:\MatrixScience\MGF\399 Bernhard-24m-01um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1837.9309

Ions Score: 105 Expect: 2.7e-009

Matches : 27/168 fragment ions using 45 most intense peaks (help)

# b b++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 102.0550 51.5311 84.0444 42.5258 T 18

2 215.1390 108.0731 197.1285 99.0679 L 1737.8905 869.4489 1720.8640 860.9356 1719.8800 860.4436 17

3 302.1710 151.5892 284.1605 142.5839 S 1624.8065 812.9069 1607.7799 804.3936 1606.7959 803.9016 16

4 415.2551 208.1312 397.2445 199.1259 I 1537.7744 769.3909 1520.7479 760.8776 1519.7639 760.3856 15

5 530.2821 265.6447 512.2715 256.6394 D 1424.6904 712.8488 1407.6638 704.3355 1406.6798 703.8435 14

6 631.3297 316.1685 613.3192 307.1632 T 1309.6634 655.3354 1292.6369 646.8221 1291.6529 646.3301 13

7 702.3668 351.6871 684.3563 342.6818 A 1208.6157 604.8115 1191.5892 596.2982 1190.6052 595.8062 12

8 759.3883 380.1978 741.3777 371.1925 G 1137.5786 569.2930 1120.5521 560.7797 1119.5681 560.2877 11

9 874.4153 437.7113 856.4047 428.7060 D 1080.5572 540.7822 1063.5306 532.2689 1062.5466 531.7769 10

10 945.4524 473.2298 927.4418 464.2245 A 965.5302 483.2688 948.5037 474.7555 947.5197 474.2635 9

11 1060.4793 530.7433 1042.4687 521.7380 D 894.4931 447.7502 877.4666 439.2369 876.4825 438.7449 8

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:31 AM

12 1131.5164 566.2619 1113.5059 557.2566 A 779.4662 390.2367 762.4396 381.7234 761.4556 381.2314 7

13 1278.5848 639.7961 1260.5743 630.7908 F 708.4291 354.7182 691.4025 346.2049 690.4185 345.7129 6

14 1391.6689 696.3381 1373.6583 687.3328 L 561.3606 281.1840 544.3341 272.6707 543.3501 272.1787 5

15 1478.7009 739.8541 1460.6904 730.8488 S 448.2766 224.6419 431.2500 216.1287 430.2660 215.6366 4

16 1591.7850 796.3961 1573.7744 787.3909 I 361.2445 181.1259 344.2180 172.6126 343.2340 172.1206 3

17 1692.8327 846.9200 1674.8221 837.9147 T 248.1605 124.5839 231.1339 116.0706 230.1499 115.5786 2

18 K 147.1128 74.0600 130.0863 65.5468 1

NCBI BLAST search of TLSIDTAGDADAFLSITK

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

104.6 1837.9309 0.0029 TLSIDTAGDADAFLSITK

2.4 1837.8040 0.1299 DEGLKDFEGNEPMTEK

0.8 1837.7896 0.1442 TVTLDVPGMDCPSCAEK

0.8 1837.7896 0.1442 TVTLDVPGMDCPSCAEK

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:31 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of TGTDVTDTANDISR

Found in 2507054537 in 4G-BT-D, HalDL1_0395 hypothetical protein [Halobacterium sp. DL1]

Match to Query 2892: 1464.669848 from(733.342200,2+) index(5347)

Title: Bernhad_31_5_13_682_2.3945.3945.2.dta

Data file F:\MatrixScience\MGF\390 Bernhard-surface-01um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1464.6692

Ions Score: 94 Expect: 3.4e-008

Matches : 29/136 fragment ions using 36 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 102.0550 51.5311 84.0444 42.5258 T 14

2 159.0764 80.0418 141.0659 71.0366 G 1364.6288 682.8181 1347.6023 674.3048 1346.6183 673.8128 13

3 260.1241 130.5657 242.1135 121.5604 T 1307.6074 654.3073 1290.5808 645.7940 1289.5968 645.3020 12

4 375.1510 188.0792 357.1405 179.0739 D 1206.5597 603.7835 1189.5331 595.2702 1188.5491 594.7782 11

5 474.2195 237.6134 456.2089 228.6081 V 1091.5327 546.2700 1074.5062 537.7567 1073.5222 537.2647 10

6 575.2671 288.1372 557.2566 279.1319 T 992.4643 496.7358 975.4378 488.2225 974.4538 487.7305 9

7 690.2941 345.6507 672.2835 336.6454 D 891.4167 446.2120 874.3901 437.6987 873.4061 437.2067 8

8 791.3418 396.1745 773.3312 387.1692 T 776.3897 388.6985 759.3632 380.1852 758.3791 379.6932 7

9 862.3789 431.6931 844.3683 422.6878 A 675.3420 338.1747 658.3155 329.6614 657.3315 329.1694 6

10 976.4218 488.7145 959.3952 480.2013 958.4112 479.7093 N 604.3049 302.6561 587.2784 294.1428 586.2943 293.6508 5

11 1091.4487 546.2280 1074.4222 537.7147 1073.4382 537.2227 D 490.2620 245.6346 473.2354 237.1214 472.2514 236.6293 4

12 1204.5328 602.7700 1187.5063 594.2568 1186.5222 593.7648 I 375.2350 188.1212 358.2085 179.6079 357.2245 179.1159 3

13 1291.5648 646.2861 1274.5383 637.7728 1273.5543 637.2808 S 262.1510 131.5791 245.1244 123.0659 244.1404 122.5738 2

14 R 175.1190 88.0631 158.0924 79.5498 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:34 AM

NCBI BLAST search of TGTDVTDTANDISR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

94.1 1464.6692 0.0006 TGTDVTDTANDISR

27.1 1464.7143 -0.0445 RGFLCDDNAVLSR

18.2 1464.6662 0.0036 ESLMDVICCPLDK

16.8 1464.7209 -0.0510 FNITGAEDSRDIK

15.6 1464.6984 -0.0285 SAPTVDIEYDDIK

12.4 1464.7613 -0.0914 FVFGTIPETVAER

10.5 1464.6991 -0.0292 RAVETDCAITGSSR

10.4 1464.7208 -0.0510 NDYEVNRSLIDK

9.9 1464.6991 -0.0292 KACNASASAADTLSR

8.2 1464.5926 0.0772 VDDVDMDGDEIDK

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:34 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of LVDEEIPNIQVVK

Found in lcl|featureId|224482784 in meta-bt-d, hypothetical

Match to Query 1632: 1494.830848 from(748.422700,2+) index(1290)

Title: Bernhard_20130712_676-test3.5380.5380.2.dta

Data file F:\MatrixScience\MGF\396 Bernhard-13m-01um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1494.8293

Ions Score: 67 Expect: 1.7e-005

Matches : 17/110 fragment ions using 25 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 114.0913 57.5493 L 13

2 213.1598 107.0835 V 1382.7526 691.8799 1365.7260 683.3666 1364.7420 682.8746 12

3 328.1867 164.5970 310.1761 155.5917 D 1283.6842 642.3457 1266.6576 633.8324 1265.6736 633.3404 11

4 457.2293 229.1183 439.2187 220.1130 E 1168.6572 584.8322 1151.6307 576.3190 1150.6467 575.8270 10

5 586.2719 293.6396 568.2613 284.6343 E 1039.6146 520.3109 1022.5881 511.7977 1021.6041 511.3057 9

6 699.3559 350.1816 681.3454 341.1763 I 910.5720 455.7897 893.5455 447.2764 8

7 796.4087 398.7080 778.3981 389.7027 P 797.4880 399.2476 780.4614 390.7343 7

8 910.4516 455.7295 893.4251 447.2162 892.4411 446.7242 N 700.4352 350.7212 683.4087 342.2080 6

9 1023.5357 512.2715 1006.5092 503.7582 1005.5251 503.2662 I 586.3923 293.6998 569.3657 285.1865 5

10 1151.5943 576.3008 1134.5677 567.7875 1133.5837 567.2955 Q 473.3082 237.1577 456.2817 228.6445 4

11 1250.6627 625.8350 1233.6361 617.3217 1232.6521 616.8297 V 345.2496 173.1285 328.2231 164.6152 3

12 1349.7311 675.3692 1332.7046 666.8559 1331.7205 666.3639 V 246.1812 123.5942 229.1547 115.0810 2

13 K 147.1128 74.0600 130.0863 65.5468 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:52 AM

NCBI BLAST search of LVDEEIPNIQVVK

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

67.0 1494.8293 0.0015 LVDEEIPNIQVVK

19.9 1494.9133 -0.0825 LVVDSALVLLALNR

15.5 1494.7170 0.1138 DVSNMSMILAQVR

12.4 1494.8770 -0.0461 AESLVVTPLLANLR

10.4 1494.7283 0.1026 RAAGTELTCSSMLR

10.3 1494.7202 0.1107 LDELDLDYESRK

10.3 1494.8882 -0.0574 VGASVRNLIPQTLK

5.8 1494.8994 -0.0686 LVVQGISGRLALNR

4.2 1494.9246 -0.0937 VLGDAVSLRLLIAR

4.1 1494.7977 0.0332 HRGEAVEMLINVK

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:52 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of VVWTNPSGGSSNTLAER

Found in 2507075793 in 4G-BT-D, halTADL_1387 flagellin domain protein [halophilic archaeon sp. True-ADL]

Match to Query 4568: 1773.865248 from(887.939900,2+) index(2068)

Title: Bernhad_31_5_13_682.5400.5400.2.dta

Data file F:\MatrixScience\MGF\390 Bernhard-surface-01um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1773.8646

Ions Score: 104 Expect: 3.3e-009

Matches : 40/176 fragment ions using 57 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 100.0757 50.5415 V 17

2 199.1441 100.0757 V 1675.8034 838.4054 1658.7769 829.8921 1657.7929 829.4001 16

3 385.2234 193.1153 W 1576.7350 788.8712 1559.7085 780.3579 1558.7245 779.8659 15

4 486.2711 243.6392 468.2605 234.6339 T 1390.6557 695.8315 1373.6292 687.3182 1372.6451 686.8262 14

5 600.3140 300.6606 583.2875 292.1474 582.3035 291.6554 N 1289.6080 645.3077 1272.5815 636.7944 1271.5975 636.3024 13

6 697.3668 349.1870 680.3402 340.6738 679.3562 340.1817 P 1175.5651 588.2862 1158.5386 579.7729 1157.5545 579.2809 12

7 784.3988 392.7030 767.3723 384.1898 766.3882 383.6978 S 1078.5123 539.7598 1061.4858 531.2465 1060.5018 530.7545 11

8 841.4203 421.2138 824.3937 412.7005 823.4097 412.2085 G 991.4803 496.2438 974.4538 487.7305 973.4697 487.2385 10

9 898.4417 449.7245 881.4152 441.2112 880.4312 440.7192 G 934.4588 467.7331 917.4323 459.2198 916.4483 458.7278 9

10 985.4738 493.2405 968.4472 484.7272 967.4632 484.2352 S 877.4374 439.2223 860.4108 430.7091 859.4268 430.2170 8

11 1072.5058 536.7565 1055.4793 528.2433 1054.4952 527.7513 S 790.4054 395.7063 773.3788 387.1930 772.3948 386.7010 7

12 1186.5487 593.7780 1169.5222 585.2647 1168.5382 584.7727 N 703.3733 352.1903 686.3468 343.6770 685.3628 343.1850 6

13 1287.5964 644.3018 1270.5699 635.7886 1269.5858 635.2966 T 589.3304 295.1688 572.3039 286.6556 571.3198 286.1636 5

14 1400.6805 700.8439 1383.6539 692.3306 1382.6699 691.8386 L 488.2827 244.6450 471.2562 236.1317 470.2722 235.6397 4

15 1471.7176 736.3624 1454.6910 727.8492 1453.7070 727.3571 A 375.1987 188.1030 358.1721 179.5897 357.1881 179.0977 3

16 1600.7602 800.8837 1583.7336 792.3705 1582.7496 791.8784 E 304.1615 152.5844 287.1350 144.0711 286.1510 143.5791 2

17 R 175.1190 88.0631 158.0924 79.5498 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:20 AM

NCBI BLAST search of VVWTNPSGGSSNTLAER

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

103.9 1773.8646 0.0007 VVWTNPSGGSSNTLAER

14.0 1773.8679 -0.0027 TPLRGSAPAASSIDMER

8.4 1773.9373 -0.0721 DTHPQDLAAEPLKALR

6.7 1773.9018 -0.0365 ATMMFAANRPPILGER

6.2 1773.9122 -0.0469 RFNLGDENAGVNLTVR

5.9 1773.9057 -0.0404 VVEGVAREHHACLAAGR

5.9 1774.0141 -0.1489 IIANFDIKYPILAQR

4.8 1773.7805 0.0847 LDEEHSFEGNEIAER

1.9 1773.9447 -0.0795 GAYPAAMLTIIGTNPLR

1.7 1774.0352 -0.1700 LLIFLESVEVSTRLR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:20 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of VLASVADEFEPASEV

Found in 2507057241 in 4G-BT-D, HalDL1_3100 Uncharacterized conserved protein [Halobacterium sp.

DL1]

Match to Query 5840: 1561.752848 from(781.883700,2+) index(4134)

Title: Benni-20130617-633-1.6837.6837.2.dta

Data file F:\MatrixScience\MGF\392 Bernhard-5m-08um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1561.7512

Ions Score: 72 Expect: 5.1e-006

Matches : 32/104 fragment ions using 53 most intense peaks (help)

# b b++ b0 b0++ Seq. y y++ y*++ y0 y0++ #

1 100.0757 50.5415 V 15

2 213.1598 107.0835 L 1463.6900 732.3487 1445.6795 723.3434 14

3 284.1969 142.6021 A 1350.6060 675.8066 1332.5954 666.8013 13

4 371.2289 186.1181 353.2183 177.1128 S 1279.5689 640.2881 1261.5583 631.2828 12

5 470.2973 235.6523 452.2867 226.6470 V 1192.5368 596.7721 1174.5263 587.7668 11

6 541.3344 271.1709 523.3239 262.1656 A 1093.4684 547.2378 1075.4578 538.2326 10

7 656.3614 328.6843 638.3508 319.6790 D 1022.4313 511.7193 1004.4207 502.7140 9

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 3 3/17/2015 6:42 AM

8 785.4040 393.2056 767.3934 384.2003 E 907.4044 454.2058 889.3938 445.2005 8

9 932.4724 466.7398 914.4618 457.7345 F 778.3618 389.6845 760.3512 380.6792 7

10 1061.5150 531.2611 1043.5044 522.2558 E 631.2933 316.1503 613.2828 307.1450 6

11 1158.5677 579.7875 1140.5572 570.7822 P 502.2508 251.6290 484.2402 242.6237 5

12 1229.6048 615.3061 1211.5943 606.3008 A 405.1980 203.1026 387.1874 194.0974 4

13 1316.6369 658.8221 1298.6263 649.8168 S 334.1609 167.5841 316.1503 158.5788 3

14 1445.6795 723.3434 1427.6689 714.3381 E 247.1288 124.0681 229.1183 115.0628 2

15 V 118.0863 59.5468 1

NCBI BLAST search of VLASVADEFEPASEV

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

72.4 1561.7512 0.0017 VLASVADEFEPASEV

15.6 1561.7446 0.0082 EDTVGAVELFMSHK

9.0 1561.8675 -0.1147 SSIELTSSQKTILR

8.1 1561.7835 -0.0307 TSDDIGETLETLLR

8.1 1561.7658 -0.0129 GIITVGDGLEMNTDK

7.5 1561.7657 -0.0129 ADLLAMLTSEETPR

6.8 1561.6856 0.0673 LDESGEIREDEDR

4.0 1561.8109 -0.0580 AMMPAIERDFLLR

3.2 1561.6631 0.0897 EDEAGLEPESETVAS

2.9 1561.7373 0.0156 SDGNQPSLFDVIDR

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 3 3/17/2015 6:42 AM

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

3 of 3 3/17/2015 6:42 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of GTDTSVLQGQDER

Found in lcl|featureId|224432828 in meta-bt-d, P61118|FLAA1_HALSA Flagellin A1 precursor - Halobacterium salinarium

(Halobacterium halobium)

Match to Query 2481: 1404.648048 from(703.331300,2+) index(5279)

Title: Bernhad_31_5_13_682_2.3843.3843.2.dta

Data file F:\MatrixScience\MGF\390 Bernhard-surface-01um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1404.6481

Ions Score: 62 Expect: 6.1e-005

Matches : 19/126 fragment ions using 24 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 58.0287 29.5180 G 13

2 159.0764 80.0418 141.0659 71.0366 T 1348.6339 674.8206 1331.6074 666.3073 1330.6234 665.8153 12

3 274.1034 137.5553 256.0928 128.5500 D 1247.5862 624.2968 1230.5597 615.7835 1229.5757 615.2915 11

4 375.1510 188.0792 357.1405 179.0739 T 1132.5593 566.7833 1115.5327 558.2700 1114.5487 557.7780 10

5 462.1831 231.5952 444.1725 222.5899 S 1031.5116 516.2594 1014.4851 507.7462 1013.5010 507.2542 9

6 561.2515 281.1294 543.2409 272.1241 V 944.4796 472.7434 927.4530 464.2302 926.4690 463.7381 8

7 674.3355 337.6714 656.3250 328.6661 L 845.4112 423.2092 828.3846 414.6959 827.4006 414.2039 7

8 802.3941 401.7007 785.3676 393.1874 784.3836 392.6954 Q 732.3271 366.6672 715.3006 358.1539 714.3165 357.6619 6

9 859.4156 430.2114 842.3890 421.6982 841.4050 421.2062 G 604.2685 302.6379 587.2420 294.1246 586.2580 293.6326 5

10 987.4742 494.2407 970.4476 485.7274 969.4636 485.2354 Q 547.2471 274.1272 530.2205 265.6139 529.2365 265.1219 4

11 1102.5011 551.7542 1085.4746 543.2409 1084.4905 542.7489 D 419.1885 210.0979 402.1619 201.5846 401.1779 201.0926 3

12 1231.5437 616.2755 1214.5172 607.7622 1213.5331 607.2702 E 304.1615 152.5844 287.1350 144.0711 286.1510 143.5791 2

13 R 175.1190 88.0631 158.0924 79.5498 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:36 AM

NCBI BLAST search of GTDTSVLQGQDER

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

61.9 1404.6481 -0.0001 GTDTSVLQGQDER

20.4 1404.6303 0.0178 EQREMELDAER

17.1 1404.6667 -0.0187 LCTEEVIGGSANR

15.1 1404.7282 -0.0802 STDILAMKEIER

14.9 1404.5753 0.0728 REEEEENDAER

13.2 1404.7474 -0.0993 LGGRAFEGGVSSIR

13.1 1404.6667 -0.0187 MTPAQSADAASSIR

12.5 1404.6820 -0.0339 MAGSLKQWSPER

12.4 1404.6885 -0.0405 FGTIGDPETLAER

12.3 1404.7150 -0.0669 FAEARVPAPYER

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:36 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of LLDSIEVGVDFDPNA

Found in 2507075278 in 4G-BT-D, halTADL_0878 hypothetical protein [halophilic archaeon sp. True-ADL]

Match to Query 2325: 1602.779848 from(802.397200,2+) index(6315)

Title: Bernhard-20130627-634neattest.7632.7632.2.dta

Data file F:\MatrixScience\MGF\393 Bernhard-5m-01um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1602.7777

Ions Score: 39 Expect: 0.0098

Matches : 10/130 fragment ions using 14 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 114.0913 57.5493 L 15

2 227.1754 114.0913 L 1490.7009 745.8541 1473.6744 737.3408 1472.6904 736.8488 14

3 342.2023 171.6048 324.1918 162.5995 D 1377.6169 689.3121 1360.5903 680.7988 1359.6063 680.3068 13

4 429.2344 215.1208 411.2238 206.1155 S 1262.5899 631.7986 1245.5634 623.2853 1244.5794 622.7933 12

5 542.3184 271.6629 524.3079 262.6576 I 1175.5579 588.2826 1158.5313 579.7693 1157.5473 579.2773 11

6 671.3610 336.1842 653.3505 327.1789 E 1062.4738 531.7406 1045.4473 523.2273 1044.4633 522.7353 10

7 770.4294 385.7184 752.4189 376.7131 V 933.4312 467.2193 916.4047 458.7060 915.4207 458.2140 9

8 827.4509 414.2291 809.4403 405.2238 G 834.3628 417.6851 817.3363 409.1718 816.3523 408.6798 8

9 926.5193 463.7633 908.5088 454.7580 V 777.3414 389.1743 760.3148 380.6610 759.3308 380.1690 7

10 1041.5463 521.2768 1023.5357 512.2715 D 678.2729 339.6401 661.2464 331.1268 660.2624 330.6348 6

11 1188.6147 594.8110 1170.6041 585.8057 F 563.2460 282.1266 546.2195 273.6134 545.2354 273.1214 5

12 1303.6416 652.3245 1285.6311 643.3192 D 416.1776 208.5924 399.1510 200.0792 398.1670 199.5872 4

13 1400.6944 700.8508 1382.6838 691.8455 P 301.1506 151.0790 284.1241 142.5657 3

14 1514.7373 757.8723 1497.7108 749.3590 1496.7268 748.8670 N 204.0979 102.5526 187.0713 94.0393 2

15 A 90.0550 45.5311 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:11 AM

NCBI BLAST search of LLDSIEVGVDFDPNA

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

39.4 1602.7777 0.0021 LLDSIEVGVDFDPNA

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:11 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of EQTLDVAFDDDEVSTGDESELDLETNR

Found in lcl|featureId|224445091 in meta-bt-d, nph:NP4734A probable cell surface glycoprotein

Match to Query 24691: 3041.329448 from(1521.672000,2+) index(26170)

Title: Bernhard-20130722-629repeat2.6955.6955.2.dta

Data file F:\MatrixScience\MGF\397 Bernhard-24m-3um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 3041.3109

Ions Score: 76 Expect: 1.2e-006

Matches : 13/306 fragment ions using 16 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 130.0499 65.5286 112.0393 56.5233 E 27

2 258.1084 129.5579 241.0819 121.0446 240.0979 120.5526 Q 2913.2756 1457.1414 2896.2490 1448.6282 2895.2650 1448.1362 26

3 359.1561 180.0817 342.1296 171.5684 341.1456 171.0764 T 2785.2170 1393.1121 2768.1905 1384.5989 2767.2064 1384.1069 25

4 472.2402 236.6237 455.2136 228.1105 454.2296 227.6185 L 2684.1693 1342.5883 2667.1428 1334.0750 2666.1588 1333.5830 24

5 587.2671 294.1372 570.2406 285.6239 569.2566 285.1319 D 2571.0853 1286.0463 2554.0587 1277.5330 2553.0747 1277.0410 23

6 686.3355 343.6714 669.3090 335.1581 668.3250 334.6661 V 2456.0583 1228.5328 2439.0318 1220.0195 2438.0478 1219.5275 22

7 757.3727 379.1900 740.3461 370.6767 739.3621 370.1847 A 2356.9899 1178.9986 2339.9634 1170.4853 2338.9793 1169.9933 21

8 904.4411 452.7242 887.4145 444.2109 886.4305 443.7189 F 2285.9528 1143.4800 2268.9263 1134.9668 2267.9422 1134.4748 20

9 1019.4680 510.2376 1002.4415 501.7244 1001.4575 501.2324 D 2138.8844 1069.9458 2121.8578 1061.4326 2120.8738 1060.9405 19

10 1134.4950 567.7511 1117.4684 559.2378 1116.4844 558.7458 D 2023.8574 1012.4324 2006.8309 1003.9191 2005.8469 1003.4271 18

11 1249.5219 625.2646 1232.4954 616.7513 1231.5113 616.2593 D 1908.8305 954.9189 1891.8040 946.4056 1890.8199 945.9136 17

12 1378.5645 689.7859 1361.5379 681.2726 1360.5539 680.7806 E 1793.8036 897.4054 1776.7770 888.8921 1775.7930 888.4001 16

13 1477.6329 739.3201 1460.6064 730.8068 1459.6223 730.3148 V 1664.7610 832.8841 1647.7344 824.3708 1646.7504 823.8788 15

14 1564.6649 782.8361 1547.6384 774.3228 1546.6544 773.8308 S 1565.6926 783.3499 1548.6660 774.8366 1547.6820 774.3446 14

15 1665.7126 833.3599 1648.6861 824.8467 1647.7021 824.3547 T 1478.6605 739.8339 1461.6340 731.3206 1460.6500 730.8286 13

16 1722.7341 861.8707 1705.7075 853.3574 1704.7235 852.8654 G 1377.6128 689.3101 1360.5863 680.7968 1359.6023 680.3048 12

17 1837.7610 919.3842 1820.7345 910.8709 1819.7505 910.3789 D 1320.5914 660.7993 1303.5648 652.2861 1302.5808 651.7940 11

18 1966.8036 983.9054 1949.7771 975.3922 1948.7931 974.9002 E 1205.5644 603.2859 1188.5379 594.7726 1187.5539 594.2806 10

19 2053.8356 1027.4215 2036.8091 1018.9082 2035.8251 1018.4162 S 1076.5218 538.7646 1059.4953 530.2513 1058.5113 529.7593 9

20 2182.8782 1091.9428 2165.8517 1083.4295 2164.8677 1082.9375 E 989.4898 495.2485 972.4633 486.7353 971.4793 486.2433 8

21 2295.9623 1148.4848 2278.9358 1139.9715 2277.9517 1139.4795 L 860.4472 430.7272 843.4207 422.2140 842.4367 421.7220 7

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 5:53 AM

22 2410.9892 1205.9983 2393.9627 1197.4850 2392.9787 1196.9930 D 747.3632 374.1852 730.3366 365.6719 729.3526 365.1799 6

23 2524.0733 1262.5403 2507.0468 1254.0270 2506.0627 1253.5350 L 632.3362 316.6717 615.3097 308.1585 614.3257 307.6665 5

24 2653.1159 1327.0616 2636.0894 1318.5483 2635.1053 1318.0563 E 519.2522 260.1297 502.2256 251.6164 501.2416 251.1244 4

25 2754.1636 1377.5854 2737.1370 1369.0722 2736.1530 1368.5801 T 390.2096 195.6084 373.1830 187.0951 372.1990 186.6031 3

26 2868.2065 1434.6069 2851.1800 1426.0936 2850.1959 1425.6016 N 289.1619 145.0846 272.1353 136.5713 2

27 R 175.1190 88.0631 158.0924 79.5498 1

NCBI BLAST search of EQTLDVAFDDDEVSTGDESELDLETNR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

76.0 3041.3109 0.0185 EQTLDVAFDDDEVSTGDESELDLETNR

0.1 3041.4189 -0.0895 DIDFSGTPRSLSSDWGGYTHGMTANIIK

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 5:53 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of QVTVSIQPDQETLQAR

Found in lcl|featureId|224441110 in meta-bt-d, hypothetical

Match to Query 7455: 1811.938048 from(906.976300,2+) index(2723)

Title: Benni-20130617-633-1.5269.5269.2.dta

Data file F:\MatrixScience\MGF\392 Bernhard-5m-08um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1811.9377

Ions Score: 75 Expect: 2.8e-006

Matches : 45/168 fragment ions using 92 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 129.0659 65.0366 112.0393 56.5233 Q 16

2 228.1343 114.5708 211.1077 106.0575 V 1684.8864 842.9469 1667.8599 834.4336 1666.8759 833.9416 15

3 329.1819 165.0946 312.1554 156.5813 311.1714 156.0893 T 1585.8180 793.4127 1568.7915 784.8994 1567.8075 784.4074 14

4 428.2504 214.6288 411.2238 206.1155 410.2398 205.6235 V 1484.7703 742.8888 1467.7438 734.3755 1466.7598 733.8835 13

5 515.2824 258.1448 498.2558 249.6316 497.2718 249.1396 S 1385.7019 693.3546 1368.6754 684.8413 1367.6914 684.3493 12

6 628.3665 314.6869 611.3399 306.1736 610.3559 305.6816 I 1298.6699 649.8386 1281.6434 641.3253 1280.6593 640.8333 11

7 756.4250 378.7162 739.3985 370.2029 738.4145 369.7109 Q 1185.5858 593.2966 1168.5593 584.7833 1167.5753 584.2913 10

8 853.4778 427.2425 836.4512 418.7293 835.4672 418.2373 P 1057.5273 529.2673 1040.5007 520.7540 1039.5167 520.2620 9

9 968.5047 484.7560 951.4782 476.2427 950.4942 475.7507 D 960.4745 480.7409 943.4480 472.2276 942.4639 471.7356 8

10 1096.5633 548.7853 1079.5368 540.2720 1078.5528 539.7800 Q 845.4476 423.2274 828.4210 414.7141 827.4370 414.2221 7

11 1225.6059 613.3066 1208.5794 604.7933 1207.5953 604.3013 E 717.3890 359.1981 700.3624 350.6849 699.3784 350.1928 6

12 1326.6536 663.8304 1309.6270 655.3172 1308.6430 654.8251 T 588.3464 294.6768 571.3198 286.1636 570.3358 285.6715 5

13 1439.7377 720.3725 1422.7111 711.8592 1421.7271 711.3672 L 487.2987 244.1530 470.2722 235.6397 4

14 1567.7962 784.4018 1550.7697 775.8885 1549.7857 775.3965 Q 374.2146 187.6110 357.1881 179.0977 3

15 1638.8333 819.9203 1621.8068 811.4070 1620.8228 810.9150 A 246.1561 123.5817 229.1295 115.0684 2

16 R 175.1190 88.0631 158.0924 79.5498 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:16 AM

NCBI BLAST search of QVTVSIQPDQETLQAR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

74.7 1811.9377 0.0003 QVTVSIQPDQETLQAR

5.4 1812.0410 -0.1029 LRLPEFLSSWALKPR

5.0 1811.8537 0.0843 ESLLEDIQEELDHSR

4.4 1811.9013 0.0367 AGEATAEAIEQNLGPVSR

3.5 1811.9125 0.0255 AIDQEAAELREAVANGR

0.4 1811.9788 -0.0408 SGRPVVTAECKPTRVR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:16 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of AALEDAYANIER

Found in 2507075499 in 4G-BT-D, halTADL_1095 extracellular solute-binding protein family 1 [halophilic archaeon sp. True-ADL]

Match to Query 2639: 1334.646848 from(668.330700,2+) index(2540)

Title: Bernhad_31_5_13_681.5675.5675.2.dta

Data file F:\MatrixScience\MGF\389 Bernhard-surface-08um\mascot_daemon_merge.mgf

Click mouse within plot area to zoom in by factor of two about that point

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Monoisotopic mass of neutral peptide Mr(calc): 1334.6466

Ions Score: 77 Expect: 1.7e-006

Matches : 12/108 fragment ions using 12 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 72.0444 36.5258 A 12

2 143.0815 72.0444 A 1264.6168 632.8120 1247.5903 624.2988 1246.6062 623.8068 11

3 256.1656 128.5864 L 1193.5797 597.2935 1176.5531 588.7802 1175.5691 588.2882 10

4 385.2082 193.1077 367.1976 184.1024 E 1080.4956 540.7515 1063.4691 532.2382 1062.4851 531.7462 9

5 500.2351 250.6212 482.2245 241.6159 D 951.4530 476.2302 934.4265 467.7169 933.4425 467.2249 8

6 571.2722 286.1397 553.2617 277.1345 A 836.4261 418.7167 819.3995 410.2034 818.4155 409.7114 7

7 734.3355 367.6714 716.3250 358.6661 Y 765.3890 383.1981 748.3624 374.6849 747.3784 374.1928 6

8 805.3727 403.1900 787.3621 394.1847 A 602.3256 301.6665 585.2991 293.1532 584.3151 292.6612 5

9 919.4156 460.2114 902.3890 451.6982 901.4050 451.2061 N 531.2885 266.1479 514.2620 257.6346 513.2780 257.1426 4

10 1032.4997 516.7535 1015.4731 508.2402 1014.4891 507.7482 I 417.2456 209.1264 400.2191 200.6132 399.2350 200.1212 3

11 1161.5422 581.2748 1144.5157 572.7615 1143.5317 572.2695 E 304.1615 152.5844 287.1350 144.0711 286.1510 143.5791 2

12 R 175.1190 88.0631 158.0924 79.5498 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:39 AM

NCBI BLAST search of AALEDAYANIER

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

77.5 1334.6466 0.0003 AALEDAYANIER

17.0 1334.7558 -0.1089 ALALVEAPPGIER

10.2 1334.7419 -0.0950 NLGVHREILER

10.1 1334.6401 0.0067 GNSGLAMSAWLGR

9.7 1334.5772 0.0696 LGVDADCETAER

9.3 1334.7194 -0.0725 DAYGLITAKVER

8.0 1334.6215 0.0254 DYGPRTDNLER

6.6 1334.6248 0.0220 DAMVSDDARSLR

6.4 1334.7419 -0.0950 DLRLQVGHIER

6.4 1334.7710 -0.1242 AFGLNVYAVLIR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:39 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of VYMLDMTTQQDPVTGQNIPK

Found in lcl|featureId|224480742 in meta-bt-d, hypothetical

Match to Query 6410: 2294.099448 from(1148.057000,2+) index(2587)

Title: Bernhad_31_5_13_682.5963.5963.2.dta

Data file F:\MatrixScience\MGF\390 Bernhard-surface-01um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 2294.0923

Variable modifications:

M6 : Oxidation (M), with neutral losses 0.0000(shown in table), 63.9983

Ions Score: 70 Expect: 6.3e-006

Matches : 42/300 fragment ions using 68 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 100.0757 50.5415 V 20

2 263.1390 132.0731 Y 2196.0311 1098.5192 2179.0046 1090.0059 2178.0206 1089.5139 19

3 394.1795 197.5934 M 2032.9678 1016.9875 2015.9413 1008.4743 2014.9572 1007.9823 18

4 507.2636 254.1354 L 1901.9273 951.4673 1884.9008 942.9540 1883.9168 942.4620 17

5 622.2905 311.6489 604.2799 302.6436 D 1788.8433 894.9253 1771.8167 886.4120 1770.8327 885.9200 16

6 769.3259 385.1666 751.3153 376.1613 M 1673.8163 837.4118 1656.7898 828.8985 1655.8058 828.4065 15

7 870.3736 435.6904 852.3630 426.6852 T 1526.7809 763.8941 1509.7544 755.3808 1508.7704 754.8888 14

8 971.4213 486.2143 953.4107 477.2090 T 1425.7332 713.3703 1408.7067 704.8570 1407.7227 704.3650 13

9 1099.4798 550.2436 1082.4533 541.7303 1081.4693 541.2383 Q 1324.6856 662.8464 1307.6590 654.3331 1306.6750 653.8411 12

10 1227.5384 614.2729 1210.5119 605.7596 1209.5279 605.2676 Q 1196.6270 598.8171 1179.6004 590.3039 1178.6164 589.8118 11

11 1342.5654 671.7863 1325.5388 663.2730 1324.5548 662.7810 D 1068.5684 534.7878 1051.5419 526.2746 1050.5578 525.7826 10

12 1439.6181 720.3127 1422.5916 711.7994 1421.6076 711.3074 P 953.5415 477.2744 936.5149 468.7611 935.5309 468.2691 9

13 1538.6865 769.8469 1521.6600 761.3336 1520.6760 760.8416 V 856.4887 428.7480 839.4621 420.2347 838.4781 419.7427 8

14 1639.7342 820.3708 1622.7077 811.8575 1621.7237 811.3655 T 757.4203 379.2138 740.3937 370.7005 739.4097 370.2085 7

15 1696.7557 848.8815 1679.7291 840.3682 1678.7451 839.8762 G 656.3726 328.6899 639.3461 320.1767 6

16 1824.8143 912.9108 1807.7877 904.3975 1806.8037 903.9055 Q 599.3511 300.1792 582.3246 291.6659 5

17 1938.8572 969.9322 1921.8306 961.4190 1920.8466 960.9270 N 471.2926 236.1499 454.2660 227.6366 4

18 2051.9413 1026.4743 2034.9147 1017.9610 2033.9307 1017.4690 I 357.2496 179.1285 340.2231 170.6152 3

19 2148.9940 1075.0006 2131.9675 1066.4874 2130.9835 1065.9954 P 244.1656 122.5864 227.1390 114.0731 2

20 K 147.1128 74.0600 130.0863 65.5468 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:55 AM

NCBI BLAST search of VYMLDMTTQQDPVTGQNIPK

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence Site Analysis

70.3 2294.0923 0.0072 VYMLDMTTQQDPVTGQNIPK Oxidation M6 94.43%

58.0 2294.0923 0.0072 VYMLDMTTQQDPVTGQNIPK Oxidation M3 5.57%

8.7 2294.3283 -0.2288 SIRMSVAELIEITIATPLPIK

6.6 2294.1278 -0.0284 ETAPDQPSGDTQLVVLDGIPDK

0.9 2294.1978 -0.0984 QIAGILVSATNQKGQESNATHK

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:55 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of STTEEAMMR

Found in lcl|featureId|224479435 in meta-bt-d, hypothetical

Match to Query 618: 1054.441248 from(528.227900,2+) index(2051)

Title: Bernhard-20130626-650-1.3633.3633.2.dta

Data file F:\MatrixScience\MGF\402 Bernhard-35m-01um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1054.4423

Ions Score: 50 Expect: 0.00089

Matches : 13/72 fragment ions using 17 most intense peaks (help)

# b b++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 88.0393 44.5233 70.0287 35.5180 S 9

2 189.0870 95.0471 171.0764 86.0418 T 968.4176 484.7124 951.3910 476.1992 950.4070 475.7071 8

3 290.1347 145.5710 272.1241 136.5657 T 867.3699 434.1886 850.3434 425.6753 849.3593 425.1833 7

4 419.1773 210.0923 401.1667 201.0870 E 766.3222 383.6647 749.2957 375.1515 748.3117 374.6595 6

5 548.2198 274.6136 530.2093 265.6083 E 637.2796 319.1435 620.2531 310.6302 619.2691 310.1382 5

6 619.2570 310.1321 601.2464 301.1268 A 508.2370 254.6222 491.2105 246.1089 4

7 750.2974 375.6524 732.2869 366.6471 M 437.1999 219.1036 420.1734 210.5903 3

8 881.3379 441.1726 863.3274 432.1673 M 306.1594 153.5834 289.1329 145.0701 2

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:56 AM

9 R 175.1190 88.0631 158.0924 79.5498 1

NCBI BLAST search of STTEEAMMR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

49.9 1054.4423 -0.0011 STTEEAMMR

24.0 1054.4567 -0.0155 TSDDSLFDR

14.9 1054.5196 -0.0783 AFSQGGAVYR

14.4 1054.5448 -0.1035 TGLFFSDLR

11.4 1054.5923 -0.1511 STFRIYLR

10.0 1054.5771 -0.1359 STLQSGPLPR

9.2 1054.4536 -0.0123 MASLSGCSQR

9.0 1054.4423 -0.0011 MGVDMSLDR

9.0 1054.4246 0.0167 ECECMIVR

8.6 1054.5117 -0.0705 GYSSIELMR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:56 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of IGLAINLDQDIK

Found in lcl|featureId|224441760 in meta-bt-d, hypothetical

Match to Query 1252: 1311.740248 from(656.877400,2+) index(5857)

Title: Bernhard-20130627-634neattest.6984.6984.2.dta

Data file F:\MatrixScience\MGF\393 Bernhard-5m-01um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1311.7398

Ions Score: 68 Expect: 1.3e-005

Matches : 20/104 fragment ions using 33 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 114.0913 57.5493 I 12

2 171.1128 86.0600 G 1199.6630 600.3352 1182.6365 591.8219 1181.6525 591.3299 11

3 284.1969 142.6021 L 1142.6416 571.8244 1125.6150 563.3111 1124.6310 562.8191 10

4 355.2340 178.1206 A 1029.5575 515.2824 1012.5310 506.7691 1011.5469 506.2771 9

5 468.3180 234.6627 I 958.5204 479.7638 941.4938 471.2506 940.5098 470.7585 8

6 582.3610 291.6841 565.3344 283.1709 N 845.4363 423.2218 828.4098 414.7085 827.4258 414.2165 7

7 695.4450 348.2262 678.4185 339.7129 L 731.3934 366.2003 714.3668 357.6871 713.3828 357.1951 6

8 810.4720 405.7396 793.4454 397.2264 792.4614 396.7343 D 618.3093 309.6583 601.2828 301.1450 600.2988 300.6530 5

9 938.5306 469.7689 921.5040 461.2556 920.5200 460.7636 Q 503.2824 252.1448 486.2558 243.6316 485.2718 243.1395 4

10 1053.5575 527.2824 1036.5310 518.7691 1035.5469 518.2771 D 375.2238 188.1155 358.1973 179.6023 357.2132 179.1103 3

11 1166.6416 583.8244 1149.6150 575.3111 1148.6310 574.8191 I 260.1969 130.6021 243.1703 122.0888 2

12 K 147.1128 74.0600 130.0863 65.5468 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:14 AM

NCBI BLAST search of IGLAINLDQDIK

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

68.3 1311.7398 0.0005 IGLAINLDQDIK

15.0 1311.6531 0.0871 THDNDISRINK

9.5 1311.5613 0.1790 SDGVGSDCSSITK

7.2 1311.7146 0.0256 KPEREVAAGEVK

4.4 1311.7510 -0.0108 VPSAKVSQVIER

4.2 1311.6856 0.0546 YMASLESRVLK

4.0 1311.5691 0.1711 HQATGNAEEDIQ

3.7 1311.7034 0.0368 VDPRLLDEEVK

3.3 1311.6380 0.1022 MEIESQYATIK

3.0 1311.6459 0.0943 EVPFADDAHALK

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:14 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of LDSDSAILLLNDSR

Found in lcl|featureId|224463862 in meta-bt-d, Linocin_M18 bacteriocin protein

Match to Query 1991: 1530.793048 from(766.403800,2+) index(1317)

Title: Bernhard-20130627-650-1r_130627212301.6369.6369.2.dta

Data file F:\MatrixScience\MGF\402 Bernhard-35m-01um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1530.7889

Ions Score: 43 Expect: 0.0044

Matches : 9/132 fragment ions using 13 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 114.0913 57.5493 L 14

2 229.1183 115.0628 211.1077 106.0575 D 1418.7122 709.8597 1401.6856 701.3464 1400.7016 700.8544 13

3 316.1503 158.5788 298.1397 149.5735 S 1303.6852 652.3462 1286.6587 643.8330 1285.6747 643.3410 12

4 431.1773 216.0923 413.1667 207.0870 D 1216.6532 608.8302 1199.6266 600.3170 1198.6426 599.8250 11

5 518.2093 259.6083 500.1987 250.6030 S 1101.6262 551.3168 1084.5997 542.8035 1083.6157 542.3115 10

6 589.2464 295.1268 571.2358 286.1216 A 1014.5942 507.8007 997.5677 499.2875 996.5837 498.7955 9

7 702.3305 351.6689 684.3199 342.6636 I 943.5571 472.2822 926.5306 463.7689 925.5465 463.2769 8

8 815.4145 408.2109 797.4040 399.2056 L 830.4730 415.7402 813.4465 407.2269 812.4625 406.7349 7

9 928.4986 464.7529 910.4880 455.7476 L 717.3890 359.1981 700.3624 350.6849 699.3784 350.1928 6

10 1041.5827 521.2950 1023.5721 512.2897 L 604.3049 302.6561 587.2784 294.1428 586.2943 293.6508 5

11 1155.6256 578.3164 1138.5990 569.8032 1137.6150 569.3111 N 491.2209 246.1141 474.1943 237.6008 473.2103 237.1088 4

12 1270.6525 635.8299 1253.6260 627.3166 1252.6420 626.8246 D 377.1779 189.0926 360.1514 180.5793 359.1674 180.0873 3

13 1357.6846 679.3459 1340.6580 670.8326 1339.6740 670.3406 S 262.1510 131.5791 245.1244 123.0659 244.1404 122.5738 2

14 R 175.1190 88.0631 158.0924 79.5498 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 7:01 AM

NCBI BLAST search of LDSDSAILLLNDSR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

42.9 1530.7889 0.0041 LDSDSAILLLNDSR

16.4 1530.7103 0.0828 FEITNPEPGEGWR

9.8 1530.7137 0.0794 AHGEFTATLMPNDK

7.6 1530.6872 0.1059 MDDELIDEADIPR

6.9 1530.8076 -0.0145 MDDLINQILTLAR

6.9 1530.8327 -0.0397 METIIEEVLVLAR

6.8 1530.6797 0.1133 AAADVEEELNNNDK

6.8 1530.7175 0.0755 AFHNTDELDARSR

6.0 1530.7804 0.0127 YRPHVQFRADSR

5.6 1530.7750 0.0180 SVTLRPNSVSNDSR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 7:01 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of TVEVGGEDPSAEFSISPSDPLPDEK

Found in lcl|featureId|224475170 in meta-bt-d, sil:SPO0571 PKD domain protein

Match to Query 22781: 2601.213448 from(1301.614000,2+) index(3184)

Title: Bernhard-20130722-629test2-2.6696.6696.2.dta

Data file F:\MatrixScience\MGF\397 Bernhard-24m-3um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 2601.1970

Ions Score: 66 Expect: 1.6e-005

Matches : 15/238 fragment ions using 17 most intense peaks (help)

# b b++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 102.0550 51.5311 84.0444 42.5258 T 25

2 201.1234 101.0653 183.1128 92.0600 V 2501.1566 1251.0819 2484.1300 1242.5687 2483.1460 1242.0766 24

3 330.1660 165.5866 312.1554 156.5813 E 2402.0882 1201.5477 2385.0616 1193.0344 2384.0776 1192.5424 23

4 429.2344 215.1208 411.2238 206.1155 V 2273.0456 1137.0264 2256.0190 1128.5132 2255.0350 1128.0211 22

5 486.2558 243.6316 468.2453 234.6263 G 2173.9772 1087.4922 2156.9506 1078.9789 2155.9666 1078.4869 21

6 543.2773 272.1423 525.2667 263.1370 G 2116.9557 1058.9815 2099.9292 1050.4682 2098.9451 1049.9762 20

7 672.3199 336.6636 654.3093 327.6583 E 2059.9342 1030.4708 2042.9077 1021.9575 2041.9237 1021.4655 19

8 787.3468 394.1771 769.3363 385.1718 D 1930.8916 965.9495 1913.8651 957.4362 1912.8811 956.9442 18

9 884.3996 442.7034 866.3890 433.6982 P 1815.8647 908.4360 1798.8382 899.9227 1797.8541 899.4307 17

10 971.4316 486.2195 953.4211 477.2142 S 1718.8119 859.9096 1701.7854 851.3963 1700.8014 850.9043 16

11 1042.4687 521.7380 1024.4582 512.7327 A 1631.7799 816.3936 1614.7534 807.8803 1613.7693 807.3883 15

12 1171.5113 586.2593 1153.5008 577.2540 E 1560.7428 780.8750 1543.7162 772.3618 1542.7322 771.8698 14

13 1318.5798 659.7935 1300.5692 650.7882 F 1431.7002 716.3537 1414.6737 707.8405 1413.6896 707.3485 13

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:24 AM

14 1405.6118 703.3095 1387.6012 694.3042 S 1284.6318 642.8195 1267.6052 634.3063 1266.6212 633.8142 12

15 1518.6958 759.8516 1500.6853 750.8463 I 1197.5998 599.3035 1180.5732 590.7902 1179.5892 590.2982 11

16 1605.7279 803.3676 1587.7173 794.3623 S 1084.5157 542.7615 1067.4891 534.2482 1066.5051 533.7562 10

17 1702.7806 851.8940 1684.7701 842.8887 P 997.4837 499.2455 980.4571 490.7322 979.4731 490.2402 9

18 1789.8127 895.4100 1771.8021 886.4047 S 900.4309 450.7191 883.4044 442.2058 882.4203 441.7138 8

19 1904.8396 952.9234 1886.8290 943.9182 D 813.3989 407.2031 796.3723 398.6898 795.3883 398.1978 7

20 2001.8924 1001.4498 1983.8818 992.4445 P 698.3719 349.6896 681.3454 341.1763 680.3614 340.6843 6

21 2114.9764 1057.9919 2096.9659 1048.9866 L 601.3192 301.1632 584.2926 292.6499 583.3086 292.1579 5

22 2212.0292 1106.5182 2194.0186 1097.5130 P 488.2351 244.6212 471.2086 236.1079 470.2245 235.6159 4

23 2327.0561 1164.0317 2309.0456 1155.0264 D 391.1823 196.0948 374.1558 187.5815 373.1718 187.0895 3

24 2456.0987 1228.5530 2438.0882 1219.5477 E 276.1554 138.5813 259.1288 130.0681 258.1448 129.5761 2

25 K 147.1128 74.0600 130.0863 65.5468 1

NCBI BLAST search of TVEVGGEDPSAEFSISPSDPLPDEK

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

65.5 2601.1970 0.0165 TVEVGGEDPSAEFSISPSDPLPDEK

1.6 2601.2347 -0.0213 YSDRYSQPTSFVGTHTTDLEVAK

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:24 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of STTLVDQYPVK

Found in 2507075767 in 4G-BT-D, halTADL_1361 CRISPR-associated protein Csh1 domain protein [halophilic archaeon sp. True-ADL]

Match to Query 3394: 1249.655048 from(625.834800,2+) index(9920)

Title: Bernhad_31_5_13_680_1in2_rr.5136.5136.2.dta

Data file F:\MatrixScience\MGF\388 Bernhard-surface-3um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1249.6554

Ions Score: 42 Expect: 0.0058

Matches : 15/98 fragment ions using 22 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 88.0393 44.5233 70.0287 35.5180 S 11

2 189.0870 95.0471 171.0764 86.0418 T 1163.6307 582.3190 1146.6041 573.8057 1145.6201 573.3137 10

3 290.1347 145.5710 272.1241 136.5657 T 1062.5830 531.7951 1045.5564 523.2819 1044.5724 522.7899 9

4 403.2187 202.1130 385.2082 193.1077 L 961.5353 481.2713 944.5088 472.7580 943.5247 472.2660 8

5 502.2871 251.6472 484.2766 242.6419 V 848.4512 424.7293 831.4247 416.2160 830.4407 415.7240 7

6 617.3141 309.1607 599.3035 300.1554 D 749.3828 375.1951 732.3563 366.6818 731.3723 366.1898 6

7 745.3727 373.1900 728.3461 364.6767 727.3621 364.1847 Q 634.3559 317.6816 617.3293 309.1683 5

8 908.4360 454.7216 891.4094 446.2084 890.4254 445.7164 Y 506.2973 253.6523 489.2708 245.1390 4

9 1005.4888 503.2480 988.4622 494.7347 987.4782 494.2427 P 343.2340 172.1206 326.2074 163.6074 3

10 1104.5572 552.7822 1087.5306 544.2689 1086.5466 543.7769 V 246.1812 123.5942 229.1547 115.0810 2

11 K 147.1128 74.0600 130.0863 65.5468 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 7:10 AM

NCBI BLAST search of STTLVDQYPVK

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

42.1 1249.6554 -0.0004 STTLVDQYPVK

14.8 1249.6819 -0.0269 ITYKGWVLDR

11.3 1249.6013 0.0538 ASDDLCFVGVPK

9.2 1249.6085 0.0466 SNNSVMLERGK

8.6 1249.7435 -0.0884 LGTIVWVPVPAV

8.3 1249.6819 -0.0269 SSLWQFVAKGK

8.0 1249.6489 0.0062 RDVMGIFAVDK

7.6 1249.6554 -0.0004 DADTVYVLINK

7.2 1249.6336 0.0214 SRVTVEAMETK

7.0 1249.5357 0.1193 VNESNGCSLDR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 7:10 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of SGVTTFDTGAWDVAIYGENADDYENK

Found in lcl|featureId|224455862 in meta-bt-d, cell surface glycoprotein

Match to Query 7887: 2837.231448 from(1419.623000,2+) index(4195)

Title: Bernhad_31_5_13_681.7583.7583.2.dta

Data file F:\MatrixScience\MGF\389 Bernhard-surface-08um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 2837.2304

Ions Score: 70 Expect: 5.2e-006

Matches : 20/260 fragment ions using 32 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 88.0393 44.5233 70.0287 35.5180 S 26

2 145.0608 73.0340 127.0502 64.0287 G 2751.2057 1376.1065 2734.1791 1367.5932 2733.1951 1367.1012 25

3 244.1292 122.5682 226.1186 113.5629 V 2694.1842 1347.5957 2677.1577 1339.0825 2676.1736 1338.5905 24

4 345.1769 173.0921 327.1663 164.0868 T 2595.1158 1298.0615 2578.0892 1289.5483 2577.1052 1289.0562 23

5 446.2245 223.6159 428.2140 214.6106 T 2494.0681 1247.5377 2477.0416 1239.0244 2476.0575 1238.5324 22

6 593.2930 297.1501 575.2824 288.1448 F 2393.0204 1197.0139 2375.9939 1188.5006 2375.0099 1188.0086 21

7 708.3199 354.6636 690.3093 345.6583 D 2245.9520 1123.4796 2228.9255 1114.9664 2227.9414 1114.4744 20

8 809.3676 405.1874 791.3570 396.1821 T 2130.9251 1065.9662 2113.8985 1057.4529 2112.9145 1056.9609 19

9 866.3890 433.6982 848.3785 424.6929 G 2029.8774 1015.4423 2012.8508 1006.9291 2011.8668 1006.4371 18

10 937.4262 469.2167 919.4156 460.2114 A 1972.8559 986.9316 1955.8294 978.4183 1954.8454 977.9263 17

11 1123.5055 562.2564 1105.4949 553.2511 W 1901.8188 951.4130 1884.7923 942.8998 1883.8082 942.4078 16

12 1238.5324 619.7698 1220.5218 610.7646 D 1715.7395 858.3734 1698.7130 849.8601 1697.7289 849.3681 15

13 1337.6008 669.3041 1319.5903 660.2988 V 1600.7126 800.8599 1583.6860 792.3466 1582.7020 791.8546 14

14 1408.6379 704.8226 1390.6274 695.8173 A 1501.6441 751.3257 1484.6176 742.8124 1483.6336 742.3204 13

15 1521.7220 761.3646 1503.7114 752.3594 I 1430.6070 715.8072 1413.5805 707.2939 1412.5965 706.8019 12

16 1684.7853 842.8963 1666.7748 833.8910 Y 1317.5230 659.2651 1300.4964 650.7518 1299.5124 650.2598 11

17 1741.8068 871.4070 1723.7962 862.4018 G 1154.4596 577.7335 1137.4331 569.2202 1136.4491 568.7282 10

18 1870.8494 935.9283 1852.8388 926.9230 E 1097.4382 549.2227 1080.4116 540.7095 1079.4276 540.2174 9

19 1984.8923 992.9498 1967.8658 984.4365 1966.8818 983.9445 N 968.3956 484.7014 951.3690 476.1882 950.3850 475.6961 8

20 2055.9294 1028.4684 2038.9029 1019.9551 2037.9189 1019.4631 A 854.3527 427.6800 837.3261 419.1667 836.3421 418.6747 7

21 2170.9564 1085.9818 2153.9298 1077.4685 2152.9458 1076.9765 D 783.3155 392.1614 766.2890 383.6481 765.3050 383.1561 6

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:03 AM

22 2285.9833 1143.4953 2268.9568 1134.9820 2267.9727 1134.4900 D 668.2886 334.6479 651.2620 326.1347 650.2780 325.6427 5

23 2449.0466 1225.0270 2432.0201 1216.5137 2431.0361 1216.0217 Y 553.2617 277.1345 536.2351 268.6212 535.2511 268.1292 4

24 2578.0892 1289.5483 2561.0627 1281.0350 2560.0787 1280.5430 E 390.1983 195.6028 373.1718 187.0895 372.1878 186.5975 3

25 2692.1322 1346.5697 2675.1056 1338.0564 2674.1216 1337.5644 N 261.1557 131.0815 244.1292 122.5682 2

26 K 147.1128 74.0600 130.0863 65.5468 1

NCBI BLAST search of SGVTTFDTGAWDVAIYGENADDYENK

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

69.9 2837.2304 0.0010 SGVTTFDTGAWDVAIYGENADDYENK

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:03 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of ANEEEEEEEEDAEADK

Found in lcl|featureId|224481395 in meta-bt-d, hypothetical

Match to Query 4946: 1864.701048 from(933.357800,2+) index(5070)

Title: Bernhad_31_5_13_682_2.3534.3534.2.dta

Data file F:\MatrixScience\MGF\390 Bernhard-surface-01um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1864.6969

Ions Score: 92 Expect: 5.2e-008

Matches : 12/172 fragment ions using 15 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 72.0444 36.5258 A 16

2 186.0873 93.5473 169.0608 85.0340 N 1794.6672 897.8372 1777.6406 889.3240 1776.6566 888.8319 15

3 315.1299 158.0686 298.1034 149.5553 297.1193 149.0633 E 1680.6243 840.8158 1663.5977 832.3025 1662.6137 831.8105 14

4 444.1725 222.5899 427.1460 214.0766 426.1619 213.5846 E 1551.5817 776.2945 1534.5551 767.7812 1533.5711 767.2892 13

5 573.2151 287.1112 556.1885 278.5979 555.2045 278.1059 E 1422.5391 711.7732 1405.5125 703.2599 1404.5285 702.7679 12

6 702.2577 351.6325 685.2311 343.1192 684.2471 342.6272 E 1293.4965 647.2519 1276.4699 638.7386 1275.4859 638.2466 11

7 831.3003 416.1538 814.2737 407.6405 813.2897 407.1485 E 1164.4539 582.7306 1147.4273 574.2173 1146.4433 573.7253 10

8 960.3429 480.6751 943.3163 472.1618 942.3323 471.6698 E 1035.4113 518.2093 1018.3847 509.6960 1017.4007 509.2040 9

9 1089.3855 545.1964 1072.3589 536.6831 1071.3749 536.1911 E 906.3687 453.6880 889.3421 445.1747 888.3581 444.6827 8

10 1218.4281 609.7177 1201.4015 601.2044 1200.4175 600.7124 E 777.3261 389.1667 760.2996 380.6534 759.3155 380.1614 7

11 1333.4550 667.2311 1316.4285 658.7179 1315.4444 658.2259 D 648.2835 324.6454 631.2570 316.1321 630.2729 315.6401 6

12 1404.4921 702.7497 1387.4656 694.2364 1386.4816 693.7444 A 533.2566 267.1319 516.2300 258.6186 515.2460 258.1266 5

13 1533.5347 767.2710 1516.5082 758.7577 1515.5241 758.2657 E 462.2195 231.6134 445.1929 223.1001 444.2089 222.6081 4

14 1604.5718 802.7896 1587.5453 794.2763 1586.5613 793.7843 A 333.1769 167.0921 316.1503 158.5788 315.1663 158.0868 3

15 1719.5988 860.3030 1702.5722 851.7897 1701.5882 851.2977 D 262.1397 131.5735 245.1132 123.0602 244.1292 122.5682 2

16 K 147.1128 74.0600 130.0863 65.5468 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 7:00 AM

NCBI BLAST search of ANEEEEEEEEDAEADK

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

91.7 1864.6969 0.0041 ANEEEEEEEEDAEADK

5.5 1864.9530 -0.2520 KGYIVGGLATLSDEEASR

5.4 1864.8843 -0.1832 IFYVPEPGSVEDAASER

2.5 1864.8585 -0.1574 QCETASLRAETGEISDR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 7:00 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of TDFNLGTGAEGPINR

Found in lcl|featureId|224461294 in meta-bt-d, hypothetical protein HF2p103

Match to Query 2162: 1560.753448 from(781.384000,2+) index(4740)

Title: Bernhard-20130627-634neattest.5678.5678.2.dta

Data file F:\MatrixScience\MGF\393 Bernhard-5m-01um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1560.7532

Ions Score: 41 Expect: 0.0068

Matches : 18/152 fragment ions using 26 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 102.0550 51.5311 84.0444 42.5258 T 15

2 217.0819 109.0446 199.0713 100.0393 D 1460.7128 730.8601 1443.6863 722.3468 1442.7023 721.8548 14

3 364.1503 182.5788 346.1397 173.5735 F 1345.6859 673.3466 1328.6593 664.8333 1327.6753 664.3413 13

4 478.1932 239.6003 461.1667 231.0870 460.1827 230.5950 N 1198.6175 599.8124 1181.5909 591.2991 1180.6069 590.8071 12

5 591.2773 296.1423 574.2508 287.6290 573.2667 287.1370 L 1084.5745 542.7909 1067.5480 534.2776 1066.5640 533.7856 11

6 648.2988 324.6530 631.2722 316.1397 630.2882 315.6477 G 971.4905 486.2489 954.4639 477.7356 953.4799 477.2436 10

7 749.3464 375.1769 732.3199 366.6636 731.3359 366.1716 T 914.4690 457.7381 897.4425 449.2249 896.4585 448.7329 9

8 806.3679 403.6876 789.3414 395.1743 788.3573 394.6823 G 813.4213 407.2143 796.3948 398.7010 795.4108 398.2090 8

9 877.4050 439.2062 860.3785 430.6929 859.3945 430.2009 A 756.3999 378.7036 739.3733 370.1903 738.3893 369.6983 7

10 1006.4476 503.7274 989.4211 495.2142 988.4371 494.7222 E 685.3628 343.1850 668.3362 334.6717 667.3522 334.1797 6

11 1063.4691 532.2382 1046.4425 523.7249 1045.4585 523.2329 G 556.3202 278.6637 539.2936 270.1504 5

12 1160.5218 580.7646 1143.4953 572.2513 1142.5113 571.7593 P 499.2987 250.1530 482.2722 241.6397 4

13 1273.6059 637.3066 1256.5794 628.7933 1255.5953 628.3013 I 402.2459 201.6266 385.2194 193.1133 3

14 1387.6488 694.3281 1370.6223 685.8148 1369.6383 685.3228 N 289.1619 145.0846 272.1353 136.5713 2

15 R 175.1190 88.0631 158.0924 79.5498 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 7:03 AM

NCBI BLAST search of TDFNLGTGAEGPINR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

41.3 1560.7532 0.0002 TDFNLGTGAEGPINR

16.3 1560.8545 -0.1011 EMIVTLSVIGLNTR

13.2 1560.8009 -0.0474 EQHAAHVVVLTDSR

10.2 1560.8260 -0.0725 ESAIGDLFLVARDR

7.9 1560.7016 0.0519 DRDDADDEAGTIIR

7.8 1560.9252 -0.1718 APIVPIAAWQRAIR

6.8 1560.6587 0.0948 EGRTECTHAETDR

6.6 1560.9028 -0.1494 LGPLTAVSFQFLLR

6.5 1560.7315 0.0220 QGLGGGNTSCLGGDLGR

6.5 1560.8260 -0.0725 NSNKFEEVVNIIR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 7:03 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of TVDGATNDTSEIER

Found in 2507057432 in 4G-BT-D, HalDL1_3291 DNA repair exonuclease [Halobacterium sp. DL1]

Match to Query 5782: 1506.684848 from(754.349700,2+) index(869)

Title: Bernhad_31_5_13_680_2.3829.3829.2.dta

Data file F:\MatrixScience\MGF\388 Bernhard-surface-3um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1506.6798

Ions Score: 45 Expect: 0.003

Matches : 22/142 fragment ions using 50 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 102.0550 51.5311 84.0444 42.5258 T 14

2 201.1234 101.0653 183.1128 92.0600 V 1406.6394 703.8233 1389.6128 695.3101 1388.6288 694.8181 13

3 316.1503 158.5788 298.1397 149.5735 D 1307.5710 654.2891 1290.5444 645.7759 1289.5604 645.2838 12

4 373.1718 187.0895 355.1612 178.0842 G 1192.5440 596.7757 1175.5175 588.2624 1174.5335 587.7704 11

5 444.2089 222.6081 426.1983 213.6028 A 1135.5226 568.2649 1118.4960 559.7516 1117.5120 559.2596 10

6 545.2566 273.1319 527.2460 264.1266 T 1064.4855 532.7464 1047.4589 524.2331 1046.4749 523.7411 9

7 659.2995 330.1534 642.2729 321.6401 641.2889 321.1481 N 963.4378 482.2225 946.4112 473.7093 945.4272 473.2172 8

8 774.3264 387.6669 757.2999 379.1536 756.3159 378.6616 D 849.3949 425.2011 832.3683 416.6878 831.3843 416.1958 7

9 875.3741 438.1907 858.3476 429.6774 857.3636 429.1854 T 734.3679 367.6876 717.3414 359.1743 716.3573 358.6823 6

10 962.4061 481.7067 945.3796 473.1934 944.3956 472.7014 S 633.3202 317.1638 616.2937 308.6505 615.3097 308.1585 5

11 1091.4487 546.2280 1074.4222 537.7147 1073.4382 537.2227 E 546.2882 273.6477 529.2617 265.1345 528.2776 264.6425 4

12 1204.5328 602.7700 1187.5063 594.2568 1186.5222 593.7648 I 417.2456 209.1264 400.2191 200.6132 399.2350 200.1212 3

13 1333.5754 667.2913 1316.5488 658.7781 1315.5648 658.2861 E 304.1615 152.5844 287.1350 144.0711 286.1510 143.5791 2

14 R 175.1190 88.0631 158.0924 79.5498 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:46 AM

NCBI BLAST search of TVDGATNDTSEIER

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

44.6 1506.6798 0.0051 TVDGATNDTSEIER

5.7 1506.7426 -0.0578 ISENYREAIAADR

5.0 1506.6919 -0.0070 EALMDGICGQRNK

5.0 1506.7348 -0.0500 TVDKVTEVGMDGTR

4.3 1506.7790 -0.0942 EAQDLVGTLRSYR

4.0 1506.7314 -0.0466 EAVEDYIEDIRR

3.9 1506.6872 -0.0023 VTDEDVCIEEVTR

3.9 1506.7314 -0.0466 TDSAGELYVKPDGR

3.5 1506.7678 -0.0830 SLDVRSDTYNLPK

3.4 1506.7427 -0.0578 TDQRFSDLGVVDR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:46 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of ITALQNQFQETGTGR

Found in lcl|featureId|224454334 in meta-bt-d, PKD domain-containing protein

Match to Query 6498: 1662.832448 from(832.423500,2+) index(2595)

Title: Benni-20130617-633-1.5128.5128.2.dta

Data file F:\MatrixScience\MGF\392 Bernhard-5m-08um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1662.8326

Ions Score: 71 Expect: 6.7e-006

Matches : 18/154 fragment ions using 28 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 114.0913 57.5493 I 15

2 215.1390 108.0731 197.1285 99.0679 T 1550.7558 775.8815 1533.7292 767.3682 1532.7452 766.8762 14

3 286.1761 143.5917 268.1656 134.5864 A 1449.7081 725.3577 1432.6815 716.8444 1431.6975 716.3524 13

4 399.2602 200.1337 381.2496 191.1285 L 1378.6710 689.8391 1361.6444 681.3258 1360.6604 680.8338 12

5 527.3188 264.1630 510.2922 255.6498 509.3082 255.1577 Q 1265.5869 633.2971 1248.5604 624.7838 1247.5763 624.2918 11

6 641.3617 321.1845 624.3352 312.6712 623.3511 312.1792 N 1137.5283 569.2678 1120.5018 560.7545 1119.5178 560.2625 10

7 769.4203 385.2138 752.3937 376.7005 751.4097 376.2085 Q 1023.4854 512.2463 1006.4589 503.7331 1005.4748 503.2411 9

8 916.4887 458.7480 899.4621 450.2347 898.4781 449.7427 F 895.4268 448.2170 878.4003 439.7038 877.4163 439.2118 8

9 1044.5473 522.7773 1027.5207 514.2640 1026.5367 513.7720 Q 748.3584 374.6828 731.3319 366.1696 730.3478 365.6776 7

10 1173.5899 587.2986 1156.5633 578.7853 1155.5793 578.2933 E 620.2998 310.6536 603.2733 302.1403 602.2893 301.6483 6

11 1274.6375 637.8224 1257.6110 629.3091 1256.6270 628.8171 T 491.2572 246.1323 474.2307 237.6190 473.2467 237.1270 5

12 1331.6590 666.3331 1314.6325 657.8199 1313.6484 657.3279 G 390.2096 195.6084 373.1830 187.0951 372.1990 186.6031 4

13 1432.7067 716.8570 1415.6801 708.3437 1414.6961 707.8517 T 333.1881 167.0977 316.1615 158.5844 315.1775 158.0924 3

14 1489.7282 745.3677 1472.7016 736.8544 1471.7176 736.3624 G 232.1404 116.5738 215.1139 108.0606 2

15 R 175.1190 88.0631 158.0924 79.5498 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:18 AM

NCBI BLAST search of ITALQNQFQETGTGR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

70.8 1662.8326 -0.0001 ITALQNQFQETGTGR

57.1 1662.8689 -0.0365 ITALQNQFEKTGTGR

8.2 1662.9417 -0.1092 TLAIELTLPKAHSNR

5.7 1662.8498 -0.0174 ITACGEVSDGTLKLEK

5.4 1662.7560 0.0765 EVYVEYTSVGMGTGR

5.0 1663.0396 -0.2072 LTALVTVAVLLAGLPGR

3.2 1662.7640 0.0685 AQAKMECGQPQCTIR

2.6 1662.8213 0.0111 VEEREDGVLFSLDR

0.7 1662.8801 -0.0477 TLAIAPGEHGRSDALR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:18 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of LSGADLIAR

Found in lcl|featureId|224477033 in meta-bt-d, hypothetical protein Hlac_0909

Match to Query 888: 914.517848 from(458.266200,2+) index(2158)

Title: Bernhad_31_5_13_680_2.5326.5326.2.dta

Data file F:\MatrixScience\MGF\388 Bernhard-surface-3um\mascot_daemon_merge.mgf

Click mouse within plot area to zoom in by factor of two about that point

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Monoisotopic mass of neutral peptide Mr(calc): 914.5185

Ions Score: 45 Expect: 0.0035

Matches : 17/70 fragment ions using 48 most intense peaks (help)

# b b++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 114.0913 57.5493 L 9

2 201.1234 101.0653 183.1128 92.0600 S 802.4417 401.7245 785.4152 393.2112 784.4312 392.7192 8

3 258.1448 129.5761 240.1343 120.5708 G 715.4097 358.2085 698.3832 349.6952 697.3991 349.2032 7

4 329.1819 165.0946 311.1714 156.0893 A 658.3883 329.6978 641.3617 321.1845 640.3777 320.6925 6

5 444.2089 222.6081 426.1983 213.6028 D 587.3511 294.1792 570.3246 285.6659 569.3406 285.1739 5

6 557.2930 279.1501 539.2824 270.1448 L 472.3242 236.6657 455.2976 228.1525 4

7 670.3770 335.6921 652.3665 326.6869 I 359.2401 180.1237 342.2136 171.6104 3

8 741.4141 371.2107 723.4036 362.2054 A 246.1561 123.5817 229.1295 115.0684 2

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:07 AM

9 R 175.1190 88.0631 158.0924 79.5498 1

NCBI BLAST search of LSGADLIAR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

45.4 914.5185 -0.0007 LSGADLIAR

41.5 914.5549 -0.0370 ISKGEIIR

23.2 914.4359 0.0820 AEQGHFAR

20.6 914.5007 0.0171 LSLNCLPR

18.3 914.4821 0.0357 EALGDALAR

18.1 914.5661 -0.0483 TVGTRIIR

17.6 914.4093 0.1085 EAQEGEPR

17.3 914.5185 -0.0007 LSDQALLR

17.2 914.5549 -0.0370 ATALLSLAR

16.5 914.5185 -0.0006 EALKDLAR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:07 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of VVFDGSVSTAPDLSIEDYR

Found in lcl|featureId|224464122 in meta-bt-d, dge:Dgeo_3026 PKD domain containing protein

Match to Query 18416: 2069.015448 from(1035.515000,2+) index(26236)

Title: Bernhard-20130722-629repeat2.7027.7027.2.dta

Data file F:\MatrixScience\MGF\397 Bernhard-24m-3um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 2068.9953

Ions Score: 45 Expect: 0.0025

Matches : 15/170 fragment ions using 34 most intense peaks (help)

# b b++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 100.0757 50.5415 V 19

2 199.1441 100.0757 V 1970.9342 985.9707 1953.9076 977.4575 1952.9236 976.9654 18

3 346.2125 173.6099 F 1871.8658 936.4365 1854.8392 927.9232 1853.8552 927.4312 17

4 461.2395 231.1234 443.2289 222.1181 D 1724.7974 862.9023 1707.7708 854.3890 1706.7868 853.8970 16

5 518.2609 259.6341 500.2504 250.6288 G 1609.7704 805.3888 1592.7439 796.8756 1591.7598 796.3836 15

6 605.2930 303.1501 587.2824 294.1448 S 1552.7489 776.8781 1535.7224 768.3648 1534.7384 767.8728 14

7 704.3614 352.6843 686.3508 343.6790 V 1465.7169 733.3621 1448.6904 724.8488 1447.7064 724.3568 13

8 791.3934 396.2003 773.3828 387.1951 S 1366.6485 683.8279 1349.6220 675.3146 1348.6379 674.8226 12

9 892.4411 446.7242 874.4305 437.7189 T 1279.6165 640.3119 1262.5899 631.7986 1261.6059 631.3066 11

10 963.4782 482.2427 945.4676 473.2374 A 1178.5688 589.7880 1161.5422 581.2748 1160.5582 580.7828 10

11 1060.5310 530.7691 1042.5204 521.7638 P 1107.5317 554.2695 1090.5051 545.7562 1089.5211 545.2642 9

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:25 AM

12 1175.5579 588.2826 1157.5473 579.2773 D 1010.4789 505.7431 993.4524 497.2298 992.4684 496.7378 8

13 1288.6420 644.8246 1270.6314 635.8193 L 895.4520 448.2296 878.4254 439.7164 877.4414 439.2243 7

14 1375.6740 688.3406 1357.6634 679.3353 S 782.3679 391.6876 765.3414 383.1743 764.3573 382.6823 6

15 1488.7581 744.8827 1470.7475 735.8774 I 695.3359 348.1716 678.3093 339.6583 677.3253 339.1663 5

16 1617.8006 809.4040 1599.7901 800.3987 E 582.2518 291.6295 565.2253 283.1163 564.2413 282.6243 4

17 1732.8276 866.9174 1714.8170 857.9121 D 453.2092 227.1083 436.1827 218.5950 435.1987 218.1030 3

18 1895.8909 948.4491 1877.8804 939.4438 Y 338.1823 169.5948 321.1557 161.0815 2

19 R 175.1190 88.0631 158.0924 79.5498 1

NCBI BLAST search of VVFDGSVSTAPDLSIEDYR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

44.5 2068.9953 0.0201 VVFDGSVSTAPDLSIEDYR

8.2 2069.0290 -0.0136 TGTSNRAQFPTVQVGTSYR

5.1 2068.9921 0.0233 EMMRDSNAIDLPLTIYR

2.0 2069.0501 -0.0347 VLSAAGPGEDREAIAATAGASR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:25 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of VDGNAISAGDQTR

Found in lcl|featureId|224432368 in meta-bt-d, O29169|Y1096_ARCFU Uncharacterized protein AF_1096 - Archaeoglobus fulgidus

Match to Query 3867: 1302.616248 from(652.315400,2+) index(6727)

Title: Benni-20130617-633-2.3172.3172.2.dta

Data file F:\MatrixScience\MGF\392 Bernhard-5m-08um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1302.6164

Ions Score: 42 Expect: 0.0056

Matches : 11/134 fragment ions using 22 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 100.0757 50.5415 V 13

2 215.1026 108.0550 197.0921 99.0497 D 1204.5553 602.7813 1187.5287 594.2680 1186.5447 593.7760 12

3 272.1241 136.5657 254.1135 127.5604 G 1089.5283 545.2678 1072.5018 536.7545 1071.5178 536.2625 11

4 386.1670 193.5872 369.1405 185.0739 368.1565 184.5819 N 1032.5069 516.7571 1015.4803 508.2438 1014.4963 507.7518 10

5 457.2041 229.1057 440.1776 220.5924 439.1936 220.1004 A 918.4639 459.7356 901.4374 451.2223 900.4534 450.7303 9

6 570.2882 285.6477 553.2617 277.1345 552.2776 276.6425 I 847.4268 424.2170 830.4003 415.7038 829.4163 415.2118 8

7 657.3202 329.1638 640.2937 320.6505 639.3097 320.1585 S 734.3428 367.6750 717.3162 359.1617 716.3322 358.6697 7

8 728.3573 364.6823 711.3308 356.1690 710.3468 355.6770 A 647.3107 324.1590 630.2842 315.6457 629.3002 315.1537 6

9 785.3788 393.1930 768.3523 384.6798 767.3682 384.1878 G 576.2736 288.6404 559.2471 280.1272 558.2631 279.6352 5

10 900.4058 450.7065 883.3792 442.1932 882.3952 441.7012 D 519.2522 260.1297 502.2256 251.6164 501.2416 251.1244 4

11 1028.4643 514.7358 1011.4378 506.2225 1010.4538 505.7305 Q 404.2252 202.6162 387.1987 194.1030 386.2146 193.6110 3

12 1129.5120 565.2596 1112.4855 556.7464 1111.5014 556.2544 T 276.1666 138.5870 259.1401 130.0737 258.1561 129.5817 2

13 R 175.1190 88.0631 158.0924 79.5498 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:22 AM

NCBI BLAST search of VDGNAISAGDQTR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

42.4 1302.6164 -0.0002 VDGNAISAGDQTR

8.4 1302.7296 -0.1133 NAPSSLLIAVYR

7.1 1302.6892 -0.0729 NANVTIGETTRK

6.3 1302.6568 -0.0406 EFQDDVLGPKR

6.2 1302.6424 -0.0261 MNESICIIPAR

2.8 1302.7230 -0.1068 NLRWLTTLMR

1.6 1302.6052 0.0111 DNVGALDDTVER

1.5 1302.6276 -0.0114 RAQQTDEAQTR

1.5 1302.6754 -0.0592 AFEIGCLLANPR

1.2 1302.7659 -0.1497 QTILPIAYKTR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:22 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of NNSDDAASDVQR

Found in lcl|featureId|224481271 in meta-bt-d, hypothetical

Match to Query 1843: 1290.546048 from(646.280300,2+) index(376)

Title: Bernhad_31_5_13_682.3146.3146.2.dta

Data file F:\MatrixScience\MGF\390 Bernhard-surface-01um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1290.5436

Ions Score: 44 Expect: 0.0042

Matches : 24/122 fragment ions using 60 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 115.0502 58.0287 98.0237 49.5155 N 12

2 229.0931 115.0502 212.0666 106.5369 N 1177.5080 589.2576 1160.4814 580.7444 1159.4974 580.2523 11

3 316.1252 158.5662 299.0986 150.0529 298.1146 149.5609 S 1063.4651 532.2362 1046.4385 523.7229 1045.4545 523.2309 10

4 431.1521 216.0797 414.1256 207.5664 413.1415 207.0744 D 976.4330 488.7202 959.4065 480.2069 958.4225 479.7149 9

5 546.1790 273.5932 529.1525 265.0799 528.1685 264.5879 D 861.4061 431.2067 844.3795 422.6934 843.3955 422.2014 8

6 617.2162 309.1117 600.1896 300.5984 599.2056 300.1064 A 746.3791 373.6932 729.3526 365.1799 728.3686 364.6879 7

7 688.2533 344.6303 671.2267 336.1170 670.2427 335.6250 A 675.3420 338.1747 658.3155 329.6614 657.3315 329.1694 6

8 775.2853 388.1463 758.2588 379.6330 757.2747 379.1410 S 604.3049 302.6561 587.2784 294.1428 586.2944 293.6508 5

9 890.3122 445.6598 873.2857 437.1465 872.3017 436.6545 D 517.2729 259.1401 500.2463 250.6268 499.2623 250.1348 4

10 989.3807 495.1940 972.3541 486.6807 971.3701 486.1887 V 402.2459 201.6266 385.2194 193.1133 3

11 1117.4392 559.2233 1100.4127 550.7100 1099.4287 550.2180 Q 303.1775 152.0924 286.1510 143.5791 2

12 R 175.1190 88.0631 158.0924 79.5498 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 7:06 AM

NCBI BLAST search of NNSDDAASDVQR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

43.6 1290.5436 0.0024 NNSDDAASDVQR

15.3 1290.6350 -0.0890 MIATTADDARAR

14.4 1290.6793 -0.1332 QKHPIEAGQGAR

9.7 1290.6568 -0.1108 EVAKVEGFEGAR

9.2 1290.6350 -0.0889 EAIREMAATGAR

8.7 1290.6932 -0.1471 DLFLLGSEKNR

8.2 1290.5986 -0.0526 LDSNMDQANRK

8.0 1290.6456 -0.0995 EDAIAFLVEER

7.9 1290.5840 -0.0380 NDDFPDADVKR

7.7 1290.6316 -0.0856 AAEPRSYGGDLR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 7:06 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of TFGSNVTMGTNEGSNNAVR

Found in lcl|featureId|224481280 in meta-bt-d, hypothetical

Match to Query 5313: 1954.884248 from(978.449400,2+) index(6036)

Title: Bernhad_31_5_13_682_2.4772.4772.2.dta

Data file F:\MatrixScience\MGF\390 Bernhard-surface-01um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1954.8803

Ions Score: 55 Expect: 0.00023

Matches : 13/198 fragment ions using 17 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 102.0550 51.5311 84.0444 42.5258 T 19

2 249.1234 125.0653 231.1128 116.0600 F 1854.8399 927.9236 1837.8134 919.4103 1836.8293 918.9183 18

3 306.1448 153.5761 288.1343 144.5708 G 1707.7715 854.3894 1690.7449 845.8761 1689.7609 845.3841 17

4 393.1769 197.0921 375.1663 188.0868 S 1650.7500 825.8786 1633.7235 817.3654 1632.7395 816.8734 16

5 507.2198 254.1135 490.1932 245.6003 489.2092 245.1082 N 1563.7180 782.3626 1546.6914 773.8494 1545.7074 773.3574 15

6 606.2882 303.6477 589.2617 295.1345 588.2776 294.6425 V 1449.6751 725.3412 1432.6485 716.8279 1431.6645 716.3359 14

7 707.3359 354.1716 690.3093 345.6583 689.3253 345.1663 T 1350.6067 675.8070 1333.5801 667.2937 1332.5961 666.8017 13

8 838.3764 419.6918 821.3498 411.1785 820.3658 410.6865 M 1249.5590 625.2831 1232.5324 616.7699 1231.5484 616.2778 12

9 895.3978 448.2026 878.3713 439.6893 877.3873 439.1973 G 1118.5185 559.7629 1101.4919 551.2496 1100.5079 550.7576 11

10 996.4455 498.7264 979.4190 490.2131 978.4349 489.7211 T 1061.4970 531.2522 1044.4705 522.7389 1043.4865 522.2469 10

11 1110.4884 555.7479 1093.4619 547.2346 1092.4779 546.7426 N 960.4493 480.7283 943.4228 472.2150 942.4388 471.7230 9

12 1239.5310 620.2692 1222.5045 611.7559 1221.5205 611.2639 E 846.4064 423.7068 829.3799 415.1936 828.3959 414.7016 8

13 1296.5525 648.7799 1279.5259 640.2666 1278.5419 639.7746 G 717.3638 359.1856 700.3373 350.6723 699.3533 350.1803 7

14 1383.5845 692.2959 1366.5580 683.7826 1365.5740 683.2906 S 660.3424 330.6748 643.3158 322.1615 642.3318 321.6695 6

15 1497.6274 749.3174 1480.6009 740.8041 1479.6169 740.3121 N 573.3103 287.1588 556.2838 278.6455 5

16 1611.6704 806.3388 1594.6438 797.8256 1593.6598 797.3335 N 459.2674 230.1373 442.2409 221.6241 4

17 1682.7075 841.8574 1665.6809 833.3441 1664.6969 832.8521 A 345.2245 173.1159 328.1979 164.6026 3

18 1781.7759 891.3916 1764.7494 882.8783 1763.7653 882.3863 V 274.1874 137.5973 257.1608 129.0840 2

19 R 175.1190 88.0631 158.0924 79.5498 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 7:07 AM

NCBI BLAST search of TFGSNVTMGTNEGSNNAVR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

55.2 1954.8803 0.0039 TFGSNVTMGTNEGSNNAVR

13.1 1954.8479 0.0363 GEMNSTHYSYPTVNGNGK

9.9 1954.9791 -0.0948 LTLMQDGLTFVMMQRR

1.2 1954.9135 -0.0293 DPEFVVWMNQLFSTDK

0.6 1954.9636 -0.0794 GDTIDEASAYLLLSGQFR

0.5 1954.9791 -0.0948 LTLMQDGLTFVMMQRR

0.4 1955.0476 -0.1634 VLFLDEPSAGLDPLSARR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 7:07 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of SHEGATSTGPGEELR

Found in lcl|featureId|224493207 in meta-bt-d, hypothetical

Match to Query 9559: 1526.693848 from(764.354200,2+) index(6921)

Title: Benni-20130617-632-2.3435.3435.2.dta

Data file F:\MatrixScience\MGF\391 Bernhard-5m-3um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1526.6961

Ions Score: 40 Expect: 0.0083

Matches : 8/136 fragment ions using 13 most intense peaks (help)

# b b++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 88.0393 44.5233 70.0287 35.5180 S 15

2 225.0982 113.0527 207.0877 104.0475 H 1440.6714 720.8393 1423.6448 712.3260 1422.6608 711.8340 14

3 354.1408 177.5740 336.1302 168.5688 E 1303.6125 652.3099 1286.5859 643.7966 1285.6019 643.3046 13

4 411.1623 206.0848 393.1517 197.0795 G 1174.5699 587.7886 1157.5433 579.2753 1156.5593 578.7833 12

5 482.1994 241.6033 464.1888 232.5980 A 1117.5484 559.2778 1100.5218 550.7646 1099.5378 550.2726 11

6 583.2471 292.1272 565.2365 283.1219 T 1046.5113 523.7593 1029.4847 515.2460 1028.5007 514.7540 10

7 670.2791 335.6432 652.2685 326.6379 S 945.4636 473.2354 928.4371 464.7222 927.4530 464.2302 9

8 771.3268 386.1670 753.3162 377.1617 T 858.4316 429.7194 841.4050 421.2062 840.4210 420.7141 8

9 828.3482 414.6778 810.3377 405.6725 G 757.3839 379.1956 740.3573 370.6823 739.3733 370.1903 7

10 925.4010 463.2041 907.3904 454.1989 P 700.3624 350.6849 683.3359 342.1716 682.3519 341.6796 6

11 982.4225 491.7149 964.4119 482.7096 G 603.3097 302.1585 586.2831 293.6452 585.2991 293.1532 5

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:58 AM

12 1111.4651 556.2362 1093.4545 547.2309 E 546.2882 273.6477 529.2617 265.1345 528.2776 264.6425 4

13 1240.5077 620.7575 1222.4971 611.7522 E 417.2456 209.1264 400.2191 200.6132 399.2350 200.1212 3

14 1353.5917 677.2995 1335.5812 668.2942 L 288.2030 144.6051 271.1765 136.0919 2

15 R 175.1190 88.0631 158.0924 79.5498 1

NCBI BLAST search of SHEGATSTGPGEELR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

40.2 1526.6961 -0.0023 SHEGATSTGPGEELR

8.0 1526.7260 -0.0321 MRDVDTEVNHVGR

5.7 1526.7549 -0.0611 QSRPDDERAALNR

5.7 1526.8061 -0.1123 HSLKAMDQCLLLR

5.5 1526.8205 -0.1267 YKTVHTQSPPTIR

4.8 1526.8668 -0.1730 ITDGTVIAGDVVVIR

4.1 1526.7841 -0.0903 HSAADAYLKPALDR

3.8 1526.7841 -0.0903 KGELYEPTQGHLR

3.4 1526.8569 -0.1630 KKPNWILSPTTSR

3.2 1526.6750 0.0189 SAETEEFDHIGHR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:58 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of GQSIDSSTSAGAGETVR

Found in lcl|featureId|224423235 in meta-bt-d, hypothetical

Match to Query 3761: 1621.751048 from(811.882800,2+) index(735)

Title: Bernhad_31_5_13_682.3817.3817.2.dta

Data file F:\MatrixScience\MGF\390 Bernhard-surface-01um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1621.7544

Ions Score: 56 Expect: 0.00022

Matches : 15/182 fragment ions using 26 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 58.0287 29.5180 G 17

2 186.0873 93.5473 169.0608 85.0340 Q 1565.7402 783.3737 1548.7136 774.8604 1547.7296 774.3684 16

3 273.1193 137.0633 256.0928 128.5500 255.1088 128.0580 S 1437.6816 719.3444 1420.6550 710.8312 1419.6710 710.3392 15

4 386.2034 193.6053 369.1769 185.0921 368.1928 184.6001 I 1350.6496 675.8284 1333.6230 667.3151 1332.6390 666.8231 14

5 501.2304 251.1188 484.2038 242.6055 483.2198 242.1135 D 1237.5655 619.2864 1220.5390 610.7731 1219.5549 610.2811 13

6 588.2624 294.6348 571.2358 286.1216 570.2518 285.6295 S 1122.5386 561.7729 1105.5120 553.2596 1104.5280 552.7676 12

7 675.2944 338.1508 658.2679 329.6376 657.2838 329.1456 S 1035.5065 518.2569 1018.4800 509.7436 1017.4960 509.2516 11

8 776.3421 388.6747 759.3155 380.1614 758.3315 379.6694 T 948.4745 474.7409 931.4480 466.2276 930.4639 465.7356 10

9 863.3741 432.1907 846.3476 423.6774 845.3636 423.1854 S 847.4268 424.2170 830.4003 415.7038 829.4163 415.2118 9

10 934.4112 467.7093 917.3847 459.1960 916.4007 458.7040 A 760.3948 380.7010 743.3682 372.1878 742.3842 371.6958 8

11 991.4327 496.2200 974.4061 487.7067 973.4221 487.2147 G 689.3577 345.1825 672.3311 336.6692 671.3471 336.1772 7

12 1062.4698 531.7385 1045.4433 523.2253 1044.4592 522.7333 A 632.3362 316.6717 615.3097 308.1585 614.3257 307.6665 6

13 1119.4913 560.2493 1102.4647 551.7360 1101.4807 551.2440 G 561.2991 281.1532 544.2726 272.6399 543.2885 272.1479 5

14 1248.5339 624.7706 1231.5073 616.2573 1230.5233 615.7653 E 504.2776 252.6425 487.2511 244.1292 486.2671 243.6372 4

15 1349.5815 675.2944 1332.5550 666.7811 1331.5710 666.2891 T 375.2350 188.1212 358.2085 179.6079 357.2245 179.1159 3

16 1448.6500 724.8286 1431.6234 716.3153 1430.6394 715.8233 V 274.1874 137.5973 257.1608 129.0840 2

17 R 175.1190 88.0631 158.0924 79.5498 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 7:04 AM

NCBI BLAST search of GQSIDSSTSAGAGETVR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

55.7 1621.7544 -0.0033 GQSIDSSTSAGAGETVR

3.0 1621.8325 -0.0814 GQWRVVIAPDDNPR

1.9 1621.6679 0.0832 DTSFEPCPQGVDDR

1.7 1621.8862 -0.1351 VAVSFGQLTVVISMR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 7:04 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of DVTLDATALLDR

Found in lcl|featureId|224471491 in meta-bt-d, hma:pNG4049 cas3; CRISPR-associated protein

Match to Query 3686: 1301.682248 from(651.848400,2+) index(3526)

Title: Bernhard_20130712_674-test3.6922.6922.2.dta

Data file F:\MatrixScience\MGF\394 Bernhard-13m-3um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1301.6827

Ions Score: 59 Expect: 0.00013

Matches : 28/108 fragment ions using 44 most intense peaks (help)

# b b++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 116.0342 58.5207 98.0237 49.5155 D 12

2 215.1026 108.0550 197.0921 99.0497 V 1187.6630 594.3352 1170.6365 585.8219 1169.6525 585.3299 11

3 316.1503 158.5788 298.1397 149.5735 T 1088.5946 544.8009 1071.5681 536.2877 1070.5841 535.7957 10

4 429.2344 215.1208 411.2238 206.1155 L 987.5469 494.2771 970.5204 485.7638 969.5364 485.2718 9

5 544.2613 272.6343 526.2508 263.6290 D 874.4629 437.7351 857.4363 429.2218 856.4523 428.7298 8

6 615.2984 308.1529 597.2879 299.1476 A 759.4359 380.2216 742.4094 371.7083 741.4254 371.2163 7

7 716.3461 358.6767 698.3355 349.6714 T 688.3988 344.7030 671.3723 336.1898 670.3883 335.6978 6

8 787.3832 394.1953 769.3727 385.1900 A 587.3511 294.1792 570.3246 285.6659 569.3406 285.1739 5

9 900.4673 450.7373 882.4567 441.7320 L 516.3140 258.6606 499.2875 250.1474 498.3035 249.6554 4

10 1013.5514 507.2793 995.5408 498.2740 L 403.2300 202.1186 386.2034 193.6053 385.2194 193.1133 3

11 1128.5783 564.7928 1110.5677 555.7875 D 290.1459 145.5766 273.1193 137.0633 272.1353 136.5713 2

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 7:13 AM

12 R 175.1190 88.0631 158.0924 79.5498 1

NCBI BLAST search of DVTLDATALLDR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

58.5 1301.6827 -0.0004 DVTLDATALLDR

20.1 1301.6463 0.0359 AEDSIAVVDLDR

11.2 1301.6575 0.0247 VVETEEGRIDR

9.8 1301.7456 -0.0633 RGVDVLLFLDR

8.9 1301.6463 0.0359 GDDDALDLLTVR

8.6 1301.5459 0.1364 VDMGWGEHTDR

8.5 1301.6211 0.0611 AEDLIEAGNTGGR

8.3 1301.6939 -0.0117 LTLTDAEVERR

7.6 1301.7190 -0.0368 ESSIVAELAKQK

6.5 1301.7415 -0.0593 LTTTANGRITVR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 7:13 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of LENNLSDGFFGATLR

Found in lcl|featureId|224481056 in meta-bt-d, CRISPR-associated protein Csc3

Match to Query 6969: 1652.819448 from(827.417000,2+) index(7320)

Title: Bernhad_31_5_13_680_1in2_r.6535.6535.2.dta

Data file F:\MatrixScience\MGF\388 Bernhard-surface-3um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1652.8158

Ions Score: 56 Expect: 0.00023

Matches : 14/158 fragment ions using 28 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 114.0913 57.5493 L 15

2 243.1339 122.0706 225.1234 113.0653 E 1540.7390 770.8732 1523.7125 762.3599 1522.7285 761.8679 14

3 357.1769 179.0921 340.1503 170.5788 339.1663 170.0868 N 1411.6965 706.3519 1394.6699 697.8386 1393.6859 697.3466 13

4 471.2198 236.1135 454.1932 227.6003 453.2092 227.1082 N 1297.6535 649.3304 1280.6270 640.8171 1279.6430 640.3251 12

5 584.3039 292.6556 567.2773 284.1423 566.2933 283.6503 L 1183.6106 592.3089 1166.5841 583.7957 1165.6000 583.3037 11

6 671.3359 336.1716 654.3093 327.6583 653.3253 327.1663 S 1070.5265 535.7669 1053.5000 527.2536 1052.5160 526.7616 10

7 786.3628 393.6850 769.3363 385.1718 768.3523 384.6798 D 983.4945 492.2509 966.4680 483.7376 965.4839 483.2456 9

8 843.3843 422.1958 826.3577 413.6825 825.3737 413.1905 G 868.4676 434.7374 851.4410 426.2241 850.4570 425.7321 8

9 990.4527 495.7300 973.4262 487.2167 972.4421 486.7247 F 811.4461 406.2267 794.4196 397.7134 793.4355 397.2214 7

10 1137.5211 569.2642 1120.4946 560.7509 1119.5105 560.2589 F 664.3777 332.6925 647.3511 324.1792 646.3671 323.6872 6

11 1194.5426 597.7749 1177.5160 589.2617 1176.5320 588.7696 G 517.3093 259.1583 500.2827 250.6450 499.2987 250.1530 5

12 1265.5797 633.2935 1248.5531 624.7802 1247.5691 624.2882 A 460.2878 230.6475 443.2613 222.1343 442.2772 221.6423 4

13 1366.6274 683.8173 1349.6008 675.3040 1348.6168 674.8120 T 389.2507 195.1290 372.2241 186.6157 371.2401 186.1237 3

14 1479.7114 740.3594 1462.6849 731.8461 1461.7009 731.3541 L 288.2030 144.6051 271.1765 136.0919 2

15 R 175.1190 88.0631 158.0924 79.5498 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 7:11 AM

NCBI BLAST search of LENNLSDGFFGATLR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

55.5 1652.8158 0.0036 LENNLSDGFFGATLR

8.3 1652.8304 -0.0110 VTVEQNRYGAMTLR

6.6 1652.8807 -0.0613 TLFSELLEGMKITR

5.4 1652.7828 0.0366 AADNPDSTSKTIFMR

2.9 1652.8046 0.0149 IEPAEAAEYYKVDR

2.9 1652.8305 -0.0110 TLLGHCVQIDAGDVR

2.3 1652.7174 0.1020 MIQQVEDMFPDER

1.9 1652.8053 0.0141 HVMSGKLGTSNHVDR

1.4 1652.7307 0.0888 YPHWRWGMAYDR

0.8 1652.9209 -0.1015 IDRPITLAGEGAATIR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 7:11 AM

Mascot Search Results

Peptide View

MS/MS Fragmentation of AVDLLDSIDAIQIR

Found in 2507057443 in 4G-BT-D, HalDL1_3302 Catalase (peroxidase I) [Halobacterium sp. DL1]

Match to Query 9742: 1540.845048 from(771.429800,2+) index(11300)

Title: Benni-20130617-632-2.8312.8312.2.dta

Data file F:\MatrixScience\MGF\391 Bernhard-5m-3um\mascot_daemon_merge.mgf

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Monoisotopic mass of neutral peptide Mr(calc): 1540.8461

Ions Score: 58 Expect: 0.00013

Matches : 20/120 fragment ions using 27 most intense peaks (help)

# b b++ b* b*++ b0 b0++ Seq. y y++ y* y*++ y0 y0++ #

1 72.0444 36.5258 A 14

2 171.1128 86.0600 V 1470.8162 735.9118 1453.7897 727.3985 1452.8057 726.9065 13

3 286.1397 143.5735 268.1292 134.5682 D 1371.7478 686.3775 1354.7213 677.8643 1353.7373 677.3723 12

4 399.2238 200.1155 381.2132 191.1103 L 1256.7209 628.8641 1239.6943 620.3508 1238.7103 619.8588 11

5 512.3079 256.6576 494.2973 247.6523 L 1143.6368 572.3220 1126.6103 563.8088 1125.6262 563.3168 10

6 627.3348 314.1710 609.3243 305.1658 D 1030.5528 515.7800 1013.5262 507.2667 1012.5422 506.7747 9

7 714.3668 357.6871 696.3563 348.6818 S 915.5258 458.2665 898.4993 449.7533 897.5152 449.2613 8

8 827.4509 414.2291 809.4403 405.2238 I 828.4938 414.7505 811.4672 406.2373 810.4832 405.7452 7

9 942.4779 471.7426 924.4673 462.7373 D 715.4097 358.2085 698.3832 349.6952 697.3991 349.2032 6

10 1013.5150 507.2611 995.5044 498.2558 A 600.3828 300.6950 583.3562 292.1817 5

11 1126.5990 563.8032 1108.5885 554.7979 I 529.3457 265.1765 512.3191 256.6632 4

12 1254.6576 627.8324 1237.6311 619.3192 1236.6470 618.8272 Q 416.2616 208.6344 399.2350 200.1212 3

13 1367.7417 684.3745 1350.7151 675.8612 1349.7311 675.3692 I 288.2030 144.6051 271.1765 136.0919 2

14 R 175.1190 88.0631 158.0924 79.5498 1

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

1 of 2 3/17/2015 6:44 AM

NCBI BLAST search of AVDLLDSIDAIQIR

(Parameters: blastp, nr protein database, expect=20000, no filter, PAM30)

Other BLAST web gateways

All matches to this query

Score Mr(calc) Delta Sequence

58.2 1540.8461 -0.0010 AVDLLDSIDAIQIR

17.1 1540.8759 -0.0309 ALVLDKMNAIGQIR

10.1 1540.8825 -0.0374 TVSQLIQNTTPLVK

9.6 1540.8224 0.0226 LAWYMYGGALIRK

8.5 1540.8977 -0.0526 GPILLDFELKQIR

8.3 1540.7845 0.0605 ASEQEPLDVERIR

8.3 1540.8838 -0.0388 LDVAHGVVVHVAGLR

6.5 1540.7522 0.0929 NEAITAFAYDTGLR

6.1 1540.8283 0.0168 SAGSLIYISSMRIK

5.9 1540.8110 0.0340 SARVDWIPAANVSR

Mascot: http://www.matrixscience.com/

Mascot Search Results: Peptide View http://129.94.63.146/mascot/cgi/peptide_view.pl?file=D:/data/20150227...

2 of 2 3/17/2015 6:44 AM

Table S2: Taxonomic composition and abundance of all proteins and just cell surface proteins in the Deep Lake metaproteome.

All Detected Proteins Cell Surface Proteins Taxonomic Group Number

of Proteins

Spectrum Count

Number of

Proteins

Percentage of Proteins

for Taxonomic

Group

Spectrum Count

Percentage of Spectra for Taxonomic

Group

tADL (100%) 429 11362 24 6 2155 19 tADL variants 178 4572 18 10 1120 24 DL31 (100%) 143 2344 9 6 110 5 DL31 variants 6 908 3 50 749 82 Hrr. lacusprofundi (100%) 88 1277 8 9 189 15 Hrr. lacusprofundi variants 7 204 5 71 202 99 DL1 (100%) 6 138 3 50 103 75 DL1 variants 3 46 1 33 28 62 Other Halobacteriaceae 91 1890 28 31 1127 60 Other Archaea 4 176 2 50 168 95 Bacteria 36 518 8 22 199 38 Dunaliella sp. 6 216 0 0 0 0 Viruses 25 1144 0 0 0 0 Protein families 86 604 3 3 4 0.6 Ambiguous 1 0.4 0 0 0 0 Lake total 1109 25399 112 10 6154 24

Table S5. Proteins identified in the Deep Lake metaproteome inferred to be of viral origin. Contigs targeted by CRISPR spacers in either the four genomes db or the metagenome db (see Table S10) are underlined. Full contig details are given in Table S11. * Designates an ambiguous match (protein family).

Protein # (metaproteome) Identification Sequence identity Contig name Contig identity Spectral count

433 prohead protease 33% match to prohead protease [119] [Halovirus HVTV-1]

deg7180000395111

HCTV-1-like type head-tail virus

10.6

5 major capsid protein 64% match to major capsid protein [120] [Halovirus HVTV-1] 433.1

166 hypothetical protein 45% match to hypothetical protein [114] [Halovirus HCTV-1] 39.1

892 hypothetical protein 49% match to hypothetical protein [123] [Halovirus HVTV-1] 1.4

880 hypothetical protein

47% match to hypothetical protein [121] [Halovirus HCTV-1]

ctg7180000406861

HCTV-1-like type head-tail virus 1.5

881 51% match to hypothetical protein [121] [Halovirus HCTV-1]

ctg7180000406863

HCTV-1-like type head-tail virus

1.5

38 hypothetical protein 43% match to hypothetical protein [121] [Halovirus HCTV-5] 116.4

24 major capsid protein 68% match to major capsid protein [119] [Halovirus HCTV-5] 147.4

634 prohead protease 35% match to prohead protease [118] [Halovirus HCTV-5] 4.4

90 major capsid protein 31% match to major capsid protein [HALG_00004] [Halorubrum phage CGphi46] deg7180000401097

head-tail viruses CGΦ46 & BJ1; also homologs in haloarchaeal genomes

65.8

174 major capsid protein 34% match to major capsid protein [HALG_00004] [Halorubrum phage CGphi46]

37.6

167 major capsid protein 45% match to major capsid protein [21] [Halovirus HHTV-1]

deg7180000413894

head-tail virus HHTV-1

39.0

340 major capsid protein 43% match to major capsid protein [21] [Halovirus HHTV-1] 15.9

582 hypothetical protein 34% match to hypothetical protein [20] [Halovirus HHTV-1] 5.4

91 major capsid protein (Hlac_0260 homolog)

32% match to major capsid protein [Hlac_0760] [Hrr. lacusprofundi ACAM34] deg7180000409203

head-tail virus Hlac-Pro1 provirus & HCTV-5; also homologs in haloarchaeal genomes

65.1

425 major capsid protein (Hlac_0260 homolog)

32% match to major capsid protein [Hlac_0760] [Hrr. lacusprofundi ACAM34]

10.8

367 hypothetical protein 34% match to hypothetical protein [VPGG_00035] [Vibrio phage VBM1] ctg7180000427076

head-tail virus VBM1 (vibriophage)

14.0

520 major capsid protein 41% match to major capsid protein [VPGG_00034] [Vibrio phage VBM1] 7.4

452 major capsid protein 54% match to major capsid protein [33] [Halovirus HCTV-2] deg7180000398907

head-tail virus HCTV-2

9.7

127 major capsid protein 51% match to major capsid protein [33] [Halovirus HCTV-2] 48.4

104 major capsid protein 42% match to uncharacterized protein [OSG_eHP12_00035] [Environmental Halophage eHP-12]

ctg7180000408321

head-tail virus eHP-12/eHP-6; also homologs in haloarchaeal genomes

55.5

726 scaffold protein 59% match to hypothetical protein [12] [Halovirus HRTV-7] ctg7180000410975

head-tail HRTV-7; also homologs in haloarchaeal genomes

3.0

879 hypothetical protein 54% match to hypothetical protein [122] [Halovirus HCTV-5] ctg7180000399498 HCTV-1-like type

head-tail virus 1.5

358 adhesion pilus (halTADL1885 homolog) 61% match to adhesion pilus [PilA] [tADL] ctg7180000459513

haloarchaeal genomes & pleolipovirus HRPV-3

14.6

824 cell surface protein? 38% to Halorubrum kocurii [C468_14103]; 31% match to hypothetical protein ctg7180000403008 haloarchaeal genomes,

Halorubrum virus 1.8

[HAPG_00095] [Halorubrum phage GNf2] GNf2 & bacteriophage ORF

147 hypothetical protein 66% match to hypothetical protein [EL22_00080] [Halostagnicola sp. A56] deg7180000399274

haloarchaeal genomes & head-tail virus HGTV-1

43.0

720 linocin M18 bacteriocin 82% match to linocin M18 bacteriocin [EL22_00075] [Halostagnicola sp. A56] 3.0

1090* cell surface protein?

39%/42% to Haloferax gibbonsii [C454_02855]; 38% match to hypothetical protein [HAPG_00095] [Halorubrum phage GNf2]

ctg7180000446992 haloarchaeal genomes & Halorubrum virus GNf2

0.4

551 linocin M18 bacteriocin 85% identity to linocin_M18 bacteriocin [C472_12565] [Halorubrum tebenquichense DSM 14210]

ctg7180000411793

haloarchaeal genomes & head-tail virus HGTV-1

6.6

Table S6. CRISPR-associated (Cas) proteins identified in the Deep Lake metaproteome. * Designates an ambiguous match (protein family).

Protein # (metaproteome)

Identification Sequence identity Source Spectral count

214 Cas7 (= Csh2) (type I-B) 100% match to halTADL_1360 [Halohasta litchfieldiae tADL] tADL 30.9

595* Cas8b (=Csh1) (type I-B) 82/100% match to halTADL_1361 [Halohasta litchfieldiae tADL]

tADL 5.2

627 Cas7 (= Csh2) (type I-B) 100% match to Hlac_3331 [Hrr. lacusprofundi ACAM34] Hrr. lacusprofundi 4.6

914 Cas10d (=Csc3) (type I-D) 100% match to Hlac_3573 [Hrr. lacusprofundi ACAM34] Hrr. lacusprofundi 1.2

626 Csc2 (type I-D) 100% match to Hlac_3574 [Hrr. lacusprofundi ACAM34] Hrr. lacusprofundi 4.6

827 Cas7 (= Csh2) (subtype I-B) 100% match to HalDL1_3062 [Halobacterium sp. DL1] DL1 1.7

913

Cas7 (= Csh2) (subtype I-B) 68% match to [Cas7] [Haloquadratum walsbyi C23] unknown haloarchaeon 1.2

Table S7. CRISPR loci for tADL, DL31, Hrr. lacusprofundi and DL1.

Taxon CRISPR locus

Position No. spacers Repeat sequence (consensus) Comments

tADL

1 tADL replicon 1305778..1311449

86 GTTTCAGACGAACTCTCGTGAGGTTGAAGC Adjacent to type I-B cas gene cluster (halTADL_1355 to _haltADL_1362)

2 tADL replicon 1320912..1321203

4 GTTTCAGACGAACGCTTGTGCGGTTGAAGC In intergenic region between halTADL_1362 & halTADL_1363 (transposase)

3 tADL replicon 1474449..1475583

17 GTTTCAGACCAACCCTCGTGGGGTCGGAGG In intergenic region between halTADL_1520 (transposase) & halTADL_1521

4 tADL replicon 2597028..2598626

24 GTTTCAGACGAACTCTCGTGAGGTTGAAGC In intergenic region between halTADL_2674 (fragments) & halTADL_2675

DL31

1 DL31 replicon 1 190284..194678

60 GTTTCAATCCCGTTCTGGGTTTTCTGGGTGTCGCGAC Adjacent to type I-D cas gene cluster (Halar_0915 to Halar_0923)

2 DL31 replicon 1 1876825..1877379

8 GTTTCAGACGTACCCTTGTGGGGTTGAAGC In intergenic region between Halar_2656 & Halar_2657

Hrr. lacusprofundi

1 Hlac replicon 3 67425..76153

131 CTTTCAGCCGAACCCCTCGTGGGTTTGAAGC Adjacent to type I-B cas gene cluster (Hlac_3326 to Hlac_3333)

2 Hlac replicon 3 333645..339403

79 GTTTCAATCCCGTGCTGGGTTTTCTGAGTGTCTCGAC Adjacent to type I-D cas gene cluster (Hlac_3572 to Hlac_3579)

DL1 1 DL1 Contig37 17051..20676

55 GTTTCAGACGTACCCTCGTGGGGTTGAAGT Adjacent to type I-B cas gene cluster (HalDL1_3060 to HalDL1_3067)

Table S8. Cas genes identified in Deep Lake metagenome contigs that could not be assigned to tADL, DL31, Hrr. lacusprofundi or DL1. Encoded proteins detected in the Deep Lake metaproteome are shown (Identification; bold font).

Identification Sequence identity Contig name Repeat

Cas6 74% match to Cas6 [Haloferax sp. ATCC BAA-645]

ctg7180000278686 GTTTCAGACGCACCCTTGTGGGGTTGAAGT (=’unknown haloarchaeon #1’ in Table S10)

Cas8b 47% match to Cas8b [Haloquadratum walsbyi (strain DSM 16854 / JCM 12705 / C23)]

Cas7 68% match to Cas7 [Haloquadratum walsbyi (strain DSM 16854 / JCM 12705 / C23)]

Cas5 55% match to Cas5 [Haloquadratum walsbyi (strain DSM 16854 / JCM 12705 / C23)]

Cas3 48% match to Cas3 [Haloquadratum walsbyi (strain DSM 16854 / JCM 12705 / C23)]

Cas4 76% match to Cas4 [HalDL1_3065] [Halobacterium sp. DL1]

Cas1 73% match to Cas1 [Natrialba chahannaoensis JCM 10990]

Cas2 79% match to Cas2 [HalDL1_3067] [Halobacterium sp. DL1]

Cas3 78% match to Cas3 [Halar_0918] [DL31]

ctg7180000293457 not contained on contig

Cas4 90% match to Cas4 [Halar_0917] [DL31]

Cas1 91% match to Cas1 Halar_0916 [DL31]

Cas2 86% match to Cas2 [Halar_0915] [DL31]

Cas2 70% match to Cas2 [Halobiforma lacisalsi AJ5]

ctg7180000441522 not contained on contig

Cas1 84% match to Cas1 [Halobiforma lacisalsi AJ5]

Cas4 74% match to Cas4 [Halobiforma lacisalsi AJ5]

Cas3 64% match to Cas3 [Halobiforma lacisalsi AJ5]

Cas5 81% match to Cas5 [Halobiforma lacisalsi AJ5]

Cas7 77% match to Cas7 [Halobiforma lacisalsi AJ5]

Cas8b 70% match to Cas8b [Halobiforma lacisalsi AJ5]

Cas6 82% match to Cas6 [Halobiforma lacisalsi AJ5]

Cas6 71% match to CRISPR-associated protein Cas6 [HalDL1_3060] [Halobacterium sp. DL1]

ctg7180000459074 not contained on contig

Cas8b 68% match to Csh1 (Cas8b) family - uncharacterized protein [Haloferax sp. ATCC BAA-644]

Cas7 76% match to Csh2 (Cas7) family CRISPR-associated protein [Haloferax sp. ATCC BAA-644]

Cas5 72% match to CRISPR-associated protein Cas5 [Haloferax sp. ATCCBAA-644]

Cas3 53% match to CRISPR-associated helicase Cas3 [Haloferax sp. ATCC BAA-644]

Cas6 86% match to CRISPR-associated protein Cas6 [Haloarcula hispanica N601]

Cas6 93% match to Cas6 [C443_03094] [Haloarcula argentinensis DSM 12282] ctg7180000459076 GTTTCAGACGAACGCTCGTGCGGTTGAAGC (same as tADL locus 2)

Cas8b 82% match to Cas8b [halTADL_1361] [True-ADL]

Cas7 90% match to Cas7 [halTADL_1360] [True-ADL]

Cas5 83% match to Cas5 [halTADL_1359] [True-ADL]

Cas3 73% match to Cas3 [halTADL_1358] [True-ADL]

Cas4 91% match to Cas4 [halTADL_1357] [True-ADL]

Cas1 94% match to Cas1 [halTADL_1356] [True-ADL]

Cas2 94% match to Cas2 [halTADL_1355] [True-ADL]

Cas8b 81% match to CRISPR-associated protein, Csh1 family [C443_03089] [Haloarcula argentinensis DSM 12282] ctg7180000277681

not contained on contig

Cas6 92% match to CRISPR-associated protein Cas6 [C443_03094] [Haloarcula argentinensis DSM 12282]

Cas3 38% match to Cas3 [Natronobacterium gregoryi (strain ATCC 43098 / CCM 3738 / NCIMB 2189 / SP2)]

ctg7180000287417 not contained on contig

Cas5 47% match to Cas5 [Haloquadratum walsbyi (strain DSM 16854 / JCM 12705 / C23)]

Cas7 61% match to Cas7 [Haloterrigena thermotolerans DSM 11522]

Cas8b 34% match to Cas8b [Haloterrigena thermotolerans DSM 11522]

Cas6 54% match to Cas6 [Halorhabdus utahensis (strain DSM 12940 / JCM 11049 / AX-2)]

Cas5 69% match to Cas5 [Hlac_3575] [Halorubrum lacusprofundi ACAM34] ctg7180000295653 not contained on contig

Cas7 79% match to Cas7 [Hlac_357] [Halorubrum lacusprofundi ACAM34]

Cas10d 77% match to Cas10d [Hlac_3573] [Halorubrum lacusprofundi ACAM34]

Cas10d 74% match to Cas10d [Hlac_3573] [Halorubrum lacusprofundi ACAM34]

Cas10d 84% match to Cas10 [Halarchaeum acidiphilum MH1-52-1]

ctg7180000298318 not contained on contig

Cas10d 95% match to Cas10 [Halarchaeum acidiphilum MH1-52-1]

Cas2 75% match to Cas2 [Halomonas sp. BC04]

ctg7180000292244 not contained on contig

Cas1 74% match to Cas1 [Halomonas sp. BC04]

Cas1 80% match to Cas1 [Acidovorax sp. NO-1]

Cas5 68% match to Cas5 [Halomonas sp. BC04]

Cas7 72% match to Cse4 [Acidovorax sp. NO-1]

Cas6e 65% match to Cse3 [Acidovorax sp. NO-1]

Cse2 60% match to Cse2 [Halomonas sp. BC04]

Cse1 64% match to Cse1 [Acidovorax sp. NO-1]

Cse1 60% match to Cse1 [Acidovorax sp. NO-1]

Cas3 55% match to Cas3 [Acidovorax sp. NO-1]

Table S9. BREX clusters in Hrr. lacusprofundi and DL31. Protein sequence identity between the Hrr. lacusprofundi and DL31 homologues is given in percent. Metagenome fragment recruitment (FR) coverage of genes is given as rpkm (reads per kilobase per 1000000 recruited reads) values.

1 FR coverage is not shown for the transposase as coverage is uncertain due to multiple copies of the gene being present in Hrr. lacuprofundi and other Deep Lake genomes.

Annotation Hrr. lacusprofundi locus tag

DL31 locus tag

Sequence identity

Hrr. lacusprofundi FR coverage

DL31 FR coverage

brxHII Hlac_3187 Halar_0263 99% 3322 3886 pglZ Hlac_3188 Halar_0262 92% 2929 3772 Hypothetical - Halar_0261 - - 723 pglX Hlac_3189 Halar_0260

(AA 281 – 1402)

66% 1458 871

Transposase Hlac_3190 - - Not shown1 - pglX Hlac_3191 Halar_0260

(AA 1 – 287)

92% 2993 3984

Toxin/antitoxin system Hlac_3192 Halar_0259 99% 6044 7247 Toxin/antitoxin system Hlac_3193 Halar_0258 100% 4574 5626 brxC/pglY Hlac_3194 Halar_0257 95% 2889 3251 brxB Hlac_3195 Halar_0256 85% 3739 4529 brxC/pglY Hlac_3196 Halar_0255 95% 2804 3500 brxA Hlac_3197 Halar_0254 100% 3687 4313 Complete BREX clusters Hlac_3187 to

Hlac_3197 Halar_0254 to Halar_0263

2367 2796

Table S10. The species identified as the source of the spacers present in CRISPR loci identified in the genomes of tADL, DL31, Hrr. lacusprofundi, DL1 and metagenome contigs. For Hrr. lacusprofundi, which has two separate CRISPR systems, the two possible types (I-B and I-D) are given. Contig descriptions outline the evidence for the inferred sources of the spacers. Some contigs match to spacers from more than one source (CRISPR spacer source; shaded in gray), and some contigs encoded proteins detected in the Deep Lake metaproteome (Contig or genome name; bold text). Detailed descriptions of each contig are provided in Table S11. Cdc6, cell division control protein 6; PLD, Phospholipase D Active site domain; PQQ/WD-40, pyrrolo-quinoline quinone repeat; UspA, universal stress protein A; VP, virion protein; VWA, von Willebrand factor type A domain.

CRISPR spacer source # spacers in genome or metagenome

Contig or genome name Contig description Target of spacers

Hrr. lacusprofundi (I-D) (locus 2) metagenome (1) ctg7180000261785 homologs to haloarchaeal & Halorubrum phage GNf2 ORFs

(unknown function). no identifiable ORF

Hrr. lacusprofundi (I-D) (locus 2)

genome (1), metagenome (1) ctg7180000266221 all homologs to pleolipovirus HRPV-1 ORFs (incl. VP8). hypothetical protein;

VP8 protein tADL (locus 1 or 4 & 2) metagenome (1,1) ctg7180000268294 homologs to haloarchaeal ORFs (incl. winged helix-turn-helix

DNA-binding protein). hypothetical protein; no identifiable ORF

DL1 (locus 1) genome (1) ctg7180000271318 homologs to haloarchaeal ORFs (incl. RepH, replication

protein). RepH

tADL (locus 1 or 4)

metagenome (1) ctg7180000271658 ORFs with no known homologs.

no identifiable ORF

Hrr. lacusprofundi (I-B) (locus 1) & (1-D) (locus 2) metagenome (2,3) hypothetical protein; no

identifiable ORF Hrr. lacusprofundi (I-B) (locus 1) & (1-D) (locus 2) metagenome (1,3) ctg7180000271717

homolog to head-tail virus HSTV-2/HRTV-7 ORF (unknown function) & ORF with no known homolog.

hypothetical protein; no identifiable ORF

tADL (locus 2) metagenome (1) ctg7180000277369

homologs to haloarchaeal ORFs (incl. PadR-like transcriptional regulator) & BJ1 head-tail virus ORF (PhiH-like repressor).

no identifiable ORF

DL31 (locus 1) genome (2) ctg7180000296261

homolog to ORF of possible surface protein (PQQ/WD-40 repeat protein).

hypothetical protein (WD-40)

unknown haloarchaeon #1 metagenome (1) hypothetical protein (WD-40)

bacterial (Halomonas?) metagenome (1) ctg7180000297164 homologs to bacterial (Halomonas sp.) ORFs (unknown function) & bacteriophage ORFs (incl. tail fiber protein). no identifiable ORF

bacterial (Halomonas?) metagenome (1) ctg7180000447433 homologs to bacteriophage (rhizobial) ORF, & ORF with no known homolog. hypothetical protein

Hrr. lacusprofundi (I-B) (locus 1) & (I-D) (locus 2) metagenome (1,1) ctg7180000396713

homologs to haloarchaeal ORFs (incl. methyltransferase, other unknown function) & head-tail virus BJ1 ORF (unknown function).

hypothetical protein (same)

Hrr. lacusprofundi (I-B) genome (1) ctg7180000396891 homolog to Halar_0011 (putative DNA primase). DNA primase

(locus 1) tADL (locus 1 or 4) metagenome (1)

ctg7180000403008 homologs to haloarchaeal ORFs (unknown function) + Halorubrum phage GNf2 ORF (cell surface, unknown function).

hypothetical protein

Hrr. lacusprofundi (1-B) (locus 1) & (1-D) (locus 2)

genome (1), metagenome (1)

hypothetical protein (cell surface)

tADL (locus 1) metagenome (1) ctg7180000403010

homologs to haloarchaeal ORFs (unknown function).

hypothetical protein

Hrr. lacusprofundi (I-B) (locus 1) metagenome (1) hypothetical protein

Hrr. lacusprofundi (I-B) (locus 1) genome (1) ctg7180000405763

segment of DL31 genome (Halar_2946-_2949): transposase, Cdc6-like protein, signal peptidase, aminopeptidase

Halar_2947: Cdc6-like protein

DL1 (locus 1) genome (2) ctg7180000408317 homologs to ORFs from head-tail viruses eHP-6/eHP-12

(unknown function) hypothetical proteins

DL1 (locus 1) genome (2) ctg7180000408318 homologs to ORFs from head-tail viruses eHP-12 & HGTV-1

(incl. tail proteins). hypothetical protein; no identifiable ORF

tADL (locus 4 genome; locus 1 or 4 metagenome)

genome (2), metagenome (2, same as genome)

ctg7180000408321 homologs to ORFs from head-tail virus eHP-12/eHP-6 & Halomonas (ATP-dependent zinc metalloprotease [FtsH])

FtsH; hypothetical protein

tADL (locus 4 genome; locus 1 or 4 metagenome)

genome (1), metagenome (1, same as genome) ctg7180000408328

homologs to head-tail virus eHP-36 ORF (unknown function), haloarchaeal ORF (terminase), & Natrialba phage ΦCh1 ORF (unknown function)

terminase B

unknown haloarchaeon #2 metagenome (1) ctg7180000411793 homologs to haloarchaeal ORFs (incl. linocin) & head-tail virus HGTV-1 ORF (prohead protease) no identifiable ORF

DL1 (locus 1) genome (1)

ctg7180000414238

homologs to ORFs from head-tail viruses eHP-32/eHP-36 (unknown function) & haloarchaeal ORF (nucleic acid binding protein).

hypothetical protein (virus)

DL31 (locus 2)

metagenome (1) hypothetical protein

unknown haloarchaeon #2 metagenome (1) nucleic acid-binding protein

Hrr. lacusprofundi (I-B) (locus 1) genome (1) ctg7180000417783

segment of tADL genome (halTADL_0207-_0211): incl. DNA methylase N4/N6 domain protein, endonuclease, DUF1524/RloF, other hypothetical proteins.

DNA methylase-like protein (tADL)

Hrr. lacusprofundi (I-B) (locus 1) genome (1) ctg7180000424023 homologs to haloarchaeal ORFs (unknown function); ORFs

homologous to those on ctg7180000464057 hypothetical protein

unknown haloarchaeon #1 metagenome (1) ctg7180000428629 all homologs to head-tail virus HSTV-2/HRTV-7 ORFs (unknown function)

hypothetical protein (virus)

Hrr. lacusprofundi (I-D) (locus 2) metagenome (1) ctg7180000435415

homologs of haloarchaeal ORFs (incl. transcription initiation factor IIB, translation initiation factor IF-2, histone-like protein)

no identifiable ORF

Hrr. lacusprofundi (I-D) (locus 2) metagenome (1) ctg7180000436748

homologs to haloarchaeal ORFs (PadR transcriptional regulator, protein of unknown function) & ORFs with no known homologs

transcriptional regulator

tADL (locus 1 or 4) metagenome (1) ctg7180000438477 homologs of haloarchaeal ORFs (UspA domain protein,

otherwise unknown function). hypothetical protein

Hrr. lacusprofundi (I-B) metagenome (1) ctg7180000438795 homologs of haloarchaeal ORFs (helicase domain protein, hypothetical protein

(locus 1) Phospholipase D Active site motif domain protein, DNA-cytosine methyltransferase, A/G-specific DNA glycosylase, & proteins of unknown function).

tADL (locus 1 or 4) metagenome (4) ctg7180000439875

homologs to head-tail virus HSTV-2/HRTV-7 ORFs (unknown function), haloarchaeal ORF (VWA domain-like/ATPase protein), & mycobacterial phage ORF (unknown function).

hypothetical protein (phage); hypothetical protein (VWA); no identifiable ORF

Hrr. lacusprofundi (I-B) (locus 1)

genome (1), metagenome (1)

hypothetical protein (phage)

Hrr. lacusprofundi (I-B) (locus 1) genome (1) ctg7180000440486 homologs to haloarchaeal ORF (unknown function) &

methanogen ORF (AsnC transcriptional regulator). hypothetical protein

tADL (locus 1 genome; locus 1 or 4 metagenome)

genome (2), metagenome (1) ctg7180000446992 homologs of haloarchaeal ORFs (unknown function) &

Halorubrum phage GNf2 (cell surface, unknown function).

hypothetical protein (cell surface); hypothetical protein

Hrr. lacusprofundi (I-B) (locus 1) genome (2) ctg7180000447311 homologs to haloarchaeal ORFs (unknown function). hypothetical protein

unknown haloarchaeon #2 metagenome (1) ctg7180000450146 homolog to haloarchaeal ORF (DNA primase). DNA primase

tADL (locus 1 or 4) metagenome (1) ctg7180000452388

homologs to haloarchaeal ORFs (zinc finger SWIM domain protein, ribosomal L36-like protein, membrane protein of unknown function)

hypothetical protein (membrane)

tADL (locus 1 or 4) metagenome (1) ctg7180000454867 homologs to haloarchaeal ORFs (haltADL_0529, _0533,

_0534, all unknown function). no identifiable ORF

tADL (locus 1) genome (1) ctg7180000455053 homologs of haloarchaeal ORFs (GTP-binding protein, XRE

transcriptional regulator), & ORFs with no known homologs no identifiable ORF

tADL (locus 3) metagenome (1) ctg7180000456477

homologs of haloarchaeal ORFs (PRC-barrel domain protein, helicase), bacteriophage ORF (unknown function), & ORF with no known homolog.

helicase

tADL (locus 1 genome; locus 1 or 4 metagenome)

genome (3, but 2 identical), metagenome (2, same as genome) ctg7180000459513

homologs of pleolipovirus HRPV-3 ORF (ORF6 - unknown function) & haloarchaeal ORFs (incl. adhesion pilus [haltADL_1885 homolog] & integrase).

hypothetical protein; no identifiable ORF

Hrr. lacusprofundi (I-B) (locus 1) metagenome (1) integrase

Hrr. lacusprofundi (I-B) (locus 1) genome (1) ctg7180000464057 homologs to haloarchaeal ORFs (unknown function); ORFs

homologous to those on ctg7180000424023. hypothetical protein

DL1 (locus 1) genome (1) ctg7180000475061

homologs to haloarchaeal ORFs (unknown function) & Haloarcula phage (halosphaerovirus) SH1 ORF (unknown function)

hypothetical protein

tADL (locus 1 genome; locus 1 or 4 metagenome)

genome (1), metagenome (1, same as genome)

deg7180000395624 homologs to Firmicutes ORFs (immunoglobulin [Ig]-binding regulator A family protein, Ig-binding regulator B family protein, acetyltransferase-like protein).

Ig-binding regulator A family protein

Hrr. lacusprofundi (I-B) (locus 1) metagenome (2)

Ig-binding regulator A family protein; Ig-binding regulator B family protein

DL1 (locus 1) genome (1) Ig-binding regulator A

family protein DL31 genome (1) deg7180000398860 homologs of haloarchaeal ORF (unknown function), head-tail TerL

(locus 2) virus HSTV-1 ORF (large terminase [TerL]), & head-tail virus BJ1 ORF (unknown function).

DL1 (locus 1) metagenome (1) TerL

DL31 (locus 1) metagenome (1) deg7180000398907 homologs of head-tail virus HCTV-2 ORFs (incl. major

capsid protein & prohead protease). major capsid protein

DL31 (locus 2)

genome (1), metagenome (1) deg7180000398909

homologs of head-tail virus HCTV-2/HHTV-2 ORFs (incl. tail tube, tail assembly protein, tape measure protein) & Firmicutes (Streptococcus sp.) phage ORFs.

hypothetical protein

Hrr. lacusprofundi (I-D) (locus 2) genome (1) deg7180000399274

homologs to haloarchaeal ORFs (incl. linocin M18 bacteriocin), head-tail HGTV-1 ORF (prohead protease), & ORF with no known homolog.

linocin

tADL (locus 3) metagenome (1) deg7180000401097

homologs to Halorubrum phages (head-tail viruses) CGΦ46 & BJ1 ORFs (incl. major capsid protein) & Natrialba phage ΦCh1 (unknown function).

no identifiable ORF

DL31 (locus 1) genome (1) deg7180000401099 homologs to Halorubrum phages (head-tail viruses) CGΦ46

& BJ1 ORFs (unknown function). hypothetical protein (virus?)

tADL (locus 1 or 4) metagenome (1) deg7180000413894 homologs to head-tail virus HHTV-1 ORFs (incl. major

capsid protein) & ORFs with no known homologs. major capsid protein

unknown haloarchaeon #1 metagenome (1) deg7180000422908 homologs to haloarchaeal ORFs (helicase, phage/plasmid primase). helicase

Hrr. lacusprofundi (I-B) (locus 1) genome (1) DL31 genome DL31 replicon 1 – same as ctg7180000405763 (above). Halar_2947: Cdc6-like

protein Hrr. lacusprofundi (I-B) (locus 1)

genome (1), metagenome (1) DL1 genome DL1 replicon (“Contig37”). HalDL1_3267:

hypothetical protein

Hrr. lacusprofundi (I-B) (locus 1) genome (1) tADL genome tADL single replicon –

same as ctg7180000417783 (above). halTADL_0211: DNA methylase N-4/N-6

DL1 (locus 1) genome (1) DL1 genome DL1 replicon (“Contig38”).

HalDL1_0747: Peptidase MA superfamily protein

tADL (locus 1 or 4) metagenome (1) tADL genome tADL single replicon. halTADL_1427:

hypothetical protein

unknown haloarchaeon #2 metagenome (1) DL31 genome DL31 replicon 3. Halar_0011: DNA primase

Table S11. Complete annotations for known ORFs on Deep Lake metagenome contigs utilized in this study. The best matches are given for all proteins encoded on the contigs. For certain proteins, no homologs were identified (= no matches). Proteins detected in the Deep Lake metaproteome are shown in bold font with protein number in brackets.

Contig name ORF coordinates ORF identifier Sequence identity

Best matches (database) Annotation

ctg7180000261785 0..176 Reverse 224424980 50% 44%

Uncharacterized protein [C454_02750] [Haloferax gibbonsii ATCC 33959] Uncharacterized protein [HAPG_00091] [Halorubrum phage GNf2]

integrase

591..2984 Forward 224424988 - no matches

3026..3250 Forward 224424995 43% 41%

Uncharacterized protein [C486_18934] [Natrinema gari JCM 14663] Uncharacterized protein [C462_10737] [Halorubrum arcis JCM 13916]

hypothetical protein

ctg7180000266221

0..683 Reverse 224421870 60% 53% 49%

Uncharacterized protein [C438_13414] [Haloferax denitrificans ATCC 35960] Virion protein 8 (VP8) [ORF8] [Halorubrum pleomorphic virus 1 (HRPV-1)] Gp7 [Haloarcula hispanica pleomorphic virus 2]

virion protein VP8

824..1645 Reverse 224421885 37% 35% 34% 34%

Gp6 [Haloarcula hispanica pleomorphic virus 2] ORF7 [ORF7] [Halorubrum pleomorphic virus 2] ORF6 [ORF6] [Halorubrum pleomorphic virus 6] Uncharacterized protein 7 [ORF7] [Halorubrum pleomorphic virus 1 (HRPV-1)]

hypothetical protein

1642..2154 Reverse 224421894 35% 34% 29%

Gp5 [Haloarcula hispanica pleomorphic virus 2] ORF6 [ORF6] [Halorubrum pleomorphic virus 6] Uncharacterized protein 6 precursor [ORF6] [Halorubrum pleomorphic virus 1 (HRPV-1)]

hypothetical protein

ctg7180000268294 227..496 Forward 224424137 50% 50%

Uncharacterized protein [C472_04803] [Halorubrum tebenquichense DSM 14210] Uncharacterized protein [C468_14033] [Halorubrum kocurii JCM 14978]

hypothetical protein

493..2019 Forward 224424150 69% 68%

Uncharacterized protein [C470_03671] [Halorubrum litoreum JCM 13561] Uncharacterized protein [C462_04165] [Halorubrum arcis JCM 13916]

hypothetical protein

ctg7180000271318 0..128 Reverse 224453749 - no matches

250..2154 Reverse 224453755 43% 43%

Uncharacterized protein [C451_04551] [Halococcus thailandensis JCM 13552] PNRC100 replication protein H-like protein [C471_09485] [Halorubrum saccharovorum DSM 1137]

plasmid replication protein RepH

ctg7180000271658 1060..1308 Forward 224449635 - no matches

1451..1819 Forward 224449637 - no matches

ctg7180000271717 2..634 Reverse 224449653 35% 34%

Uncharacterized protein [104] [Halovirus HSTV-2] Uncharacterized protein [106] [Halovirus HRTV-7]

hypothetical protein

823..1191 Reverse 224449655 - no matches

ctg7180000277369 230..754 Forward 224448726 37% Uncharacterized protein [BN903_430] [Halorubrum sp. AJ67]

hypothetical protein

1690..2484 Forward 224448733 27% M20 family peptidase PepV [WT2_00409] [Weissella thailandensis fsh4-2]

peptidase

2513..3109 Forward 224448740 - no matches

3270..3578 Reverse 224448747 64% Transcriptional regulator, PadR-like family protein [C472_09266] [Halorubrum sp. AJ67]

transcriptional regulator

3934..4254 Forward 224448751 64% 62%

Uncharacterized protein [Archaeal BJ1 virus] PhiH1 repressor-like protein [Hmuk_0443] [Halomicrobium mukohataei (strain ATCC 700874 / DSM 12286 / JCM 9738 / NCIMB 13541) (Haloarcula mukohataei)]

PhiH1 repressor-like protein

ctg7180000296261 0..59 Forward

224480153 - no matches

314..1678 Forward 224480157 27% 25%

Pyrrolo-quinoline quinone repeat-containing protein halTADL_0404 [halophilic archaeon True-ADL] Pyrrolo-quinoline quinone [Huta_1990] [Halorhabdus utahensis (strain DSM 12940 / JCM 11049 / AX-2)]

PQQ/WD-40 repeat protein

2072..2926 Forward 224480161 27% 27%

WD-40 repeat protein [ARTHRO_740065] [Arthrospira sp. PCC 8005] NB-ARC domain protein [RoseRS_4025] [Roseiflexus sp. (strain RS-1)]

PQQ/WD-40 repeat protein

ctg7180000297164

0..533 Reverse 224470664 68% 51%

Uncharacterized protein [Q671_08045] [Halomonas sp. PBN3] Gp18 protein [Vibrio phage VP58.5]

hypothetical protein

546..869 Reverse 224470675 39% 38%

Uncharacterized protein [AT59_23010] [Aeromonas hydrophila AD9] Uncharacterized protein [Q671_08050] [Halomonas sp. PBN3]

hypothetical protein

880..1758 Reverse 224470684 61% 69%

Uncharacterized protein [Q671_08055] [Halomonas sp. PBN3] Phage tail protein [AK33_05805] [Mannheimia haemolytica serotype A1/A6 str. PKL10]

tail protein

1771..2214 Reverse 224470694 67% 39%

Uncharacterized protein [Q671_08060] [Halomonas sp. PBN3] Putative tail fiber protein [nvie-Pro1-24] [Nitrososphaera phage Pro-Nvie1]

tail protein

2227..2499 Reverse 224470701 37% Tail protein [Q671_08065] [Halomonas sp. PBN3]

tail protein

ctg7180000447433 1..99 Reverse 224462392 - no matches

194..2311 Reverse 224462407 29% 26%

p023 [16-3p023] [Rhizobium phage 16-3 (Bacteriophage 16-3)] Uncharacterized protein [BN406_06039] [Sinorhizobium meliloti Rm41]

hypothetical protein

ctg7180000396713

649..1005 Forward 224429490 - no matches

1751..2365 Forward 224429492 32% Uncharacterized protein [BN903_363] [Halorubrum sp. AJ67]

hypothetical protein

2362..3333 Forward 224429494 46% 29%

Uncharacterized protein [BN903_354] [Halorubrum sp. AJ67] Uncharacterized protein [C484_00850] [Natrialba taiwanensis DSM 12281]

DNA methylase

3583..4077 Forward 224429496 28% 29%

Uncharacterized protein [Archaeal BJ1 virus] Phage EaA protein [ECRM13514_2726] [Escherichia coli O145:H28 str. RM13514]

hypothetical protein

4233..4733 Forward 224429498 34% 34%

Uncharacterized protein [BN903_276] [Halorubrum sp. AJ67] Uncharacterized protein [BN595_01238] [Clostridium sp. CAG:302]

hypothetical protein

4772..5005 Forward 224429500 - no matches

5002..5142 Forward 224429502 - no matches

ctg7180000396891 65..3346 Forward 224443408 68% 42%

Halar_0011 hypothetical protein [halophilic archaeon DL31] Putative DNA primase/helicase [OSG_eHP11_00130] [Environmental Halophage eHP-11]

DNA primase

ctg7180000399277

1..1236 Reverse 224422439 79% 52%

Uncharacterized protein [C461_03073] [Halorubrum aidingense JCM 13560] Terminase large subunit [1] [Halovirus HSTV-1]

terminase, large subunit (TerL)

1220..1714 Reverse 224422455 52% 38%

Uncharacterized protein [HacjB3_05495] [Halalkalicoccus jeotgali (strain DSM 18796 / CECT 7217 / JCM 14584 / KCTC 4019 / B3)] Putative uncharacterized protein [Natrialba phage PhiCh1]

hypothetical protein

1938..2246 Reverse 224422460 80% 32%

Uncharacterized protein [Natgr_3426] [Natronobacterium gregoryi (strain ATCC 43098 / CCM 3738 / NCIMB 2189 / SP2)] Uncharacterized protein [HacjB3_05510] [Halalkalicoccus jeotgali (strain DSM 18796 / CECT 7217 / JCM 14584 / KCTC 4019 / B3)]

hypothetical protein

ctg7180000403008

129..1631 Forward 224476272 36% 31%

Uncharacterized protein [C467_07852] [Halorubrum hochstenium ATCC 700873] Uncharacterized protein [HAPG_00095] [Halorubrum phage GNf2]

hypothetical protein (cell surface) (#824)

1631..2017 Forward 224476278 35%

30% Uncharacterized protein [C468_14098] [Halorubrum kocurii JCM 14978] Uncharacterized protein [C467_07847] [Halorubrum hochstenium ATCC 700873]

hypothetical protein (multiple transmembrane helices)

2024..2395 Forward 224476284 25% Uncharacterized protein [C475_14528] [Halosimplex carlsbadense 2-9-1]

hypothetical protein

2388..2864 Forward 224476290 25% 34%

Uncharacterized protein [C468_14088] [Halorubrum kocurii JCM 14978] Uncharacterized protein [C467_07837] [Halorubrum hochstenium ATCC 700873]

hypothetical protein

2861..3139 Forward 224476296 31% 39%

Marine sediment metagenome DNA, contig: S03H2_L02786 (Fragment) [S03H2_15438] [marine sediment metagenome] RarD protein [rarD] [Pseudomonas fluorescens Q2-87]

hypothetical protein (multiple transmembrane helices)

3213..3854 Forward 224476302 31% 30%

Uncharacterized protein [C468_14078] [Halorubrum kocurii JCM 14978] Uncharacterized protein [C467_07827] [Halorubrum hochstenium ATCC 700873]

hypothetical protein

ctg7180000403010 2..1699 Forward 224476308 31% 30%

Uncharacterized protein [C472_05723] [Halorubrum tebenquichense DSM 14210] Uncharacterized protein [C468_14068] [Halorubrum kocurii JCM 14978]

hypothetical protein

1689..2522 Forward 224476313 46% 44%

Uncharacterized protein [C472_05728] [Halorubrum tebenquichense DSM 14210] Uncharacterized protein [C468_14063] [Halorubrum kocurii JCM 14978]

hypothetical protein

2519..3685 Forward 224476318 45% 46%

Uncharacterized protein [C472_05733] [Halorubrum tebenquichense DSM 14210] Uncharacterized protein [C468_14058] [Halorubrum kocurii JCM 14978]

hypothetical protein

ctg7180000405763

0..239 Reverse

224464682 100% 95%

Transposase and inactivated derivatives [Halar_2946 ] [halophilic archaeon DL31] Transposase, IS605 OrfB family [Halar_2119] [halophilic archaeon DL31]

transposase

1188..2846 Forward 224464692 100% 78%

Cell division control protein 6-like protein [Halar_2947 ] [halophilic archaeon DL31] ORC1-type DNA replication protein [HSB1_20890] [Halogranum salarium B-1]

Cdc6-like protein

2974..3885 Reverse 224464702 100% 59%

Peptidase S26B, signal peptidase [Halar_2948] [halophilic archaeon DL31] Uncharacterized protein [HSB1_20880] [Halogranum salarium B-1]

signal peptidase

3982..4395 Forward 224464712 100% 56%

Dipeptidyl aminopeptidase/acylaminoacyl peptidase [Halar_2949 ] [halophilic archaeon DL31] Peptidase S9 prolyl oligopeptidase active site domain protein [HSB1_21530] [Halogranum salarium B-1]

peptidase

ctg7180000408317

0..485 Reverse 224436900 39% 37%

Uncharacterized protein [OSG_eHP16_00005] [Environmental Halophage eHP-16] Uncharacterized protein [OSG_eHP6_00070] [Environmental Halophage eHP-6]

hypothetical protein

490..1473 Reverse 224436902 37% Uncharacterized protein [OSG_eHP6_00065] [Environmental Halophage eHP-6] hypothetical protein

36% Uncharacterized protein [OSG_eHP12_00080] [Environmental Halophage eHP-12]

1474..1860 Reverse 224436904 42% 41%

Uncharacterized protein [OSG_eHP12_00075] [Environmental Halophage eHP-12] Uncharacterized protein [OSG_eHP6_00060] [Environmental Halophage eHP-6]

hypothetical protein

1867..3579 Reverse 224436906 51% 33%

Uncharacterized protein [C437_14012] [Haloarcula vallismortis ATCC 29715] Uncharacterized protein [OSG_eHP12_00070] [Environmental Halophage eHP-12]

hypothetical protein

ctg7180000408318 2..565 Reverse 224436908 52% 31%

Uncharacterized protein [C437_14012] [Haloarcula vallismortis ATCC 29715] Uncharacterized protein [OSG_eHP12_00070] [Environmental Halophage eHP-12]

hypothetical protein

715..1182 Reverse 224436910 24% 25%

Uncharacterized protein [OSG_eHP12_00065] [Environmental Halophage eHP-12] Uncharacterized protein [19] [Halovirus HGTV-1]

hypothetical protein

1247..1627 Reverse 224436912 25% 25%

Uncharacterized protein [OSG_eHP12_00060] [Environmental Halophage eHP-12] Uncharacterized protein [OSG_eHP6_00045] [Environmental Halophage eHP-6]

hypothetical protein

1634..2974 Reverse 224436914 37% 32%

Tail sheath [17] [Halovirus HGTV-1] Uncharacterized protein [OSG_eHP12_00055] [Environmental Halophage eHP-12]

tail sheath protein

3008..3604 Reverse 224436916 42% 27%

Uncharacterized protein [OSG_eHP12_00050] [Environmental Halophage eHP-12] Uncharacterized protein [16] [Halovirus HGTV-1]

hypothetical protein

3601..4074 Reverse 224436918 47% 44%

Tail component protein [OSG_eHP12_00045] [Environmental Halophage eHP-12] Tail component protein [OSG_eHP6_00030] [Environmental Halophage eHP-6]

tail component protein

4071..4391 Reverse 224436920 58% 58%

Uncharacterized protein [OSG_eHP12_00040] [Environmental Halophage eHP-12] Uncharacterized protein [OSG_eHP6_00025] [Environmental Halophage eHP-6]

hypothetical protein

ctg7180000408321 0..248 Reverse 224436922 41% ATP-dependent zinc metalloprotease FtsH (EC 3.4.24.-) [ftsH] [Halomonas sp. A3H3]

FtsH ATPase

255..1082 Reverse 224436924 42% 42%

Uncharacterized protein [OSG_eHP12_00035] [Environmental Halophage eHP-12] Uncharacterized protein [OSG_eHP6_00020] [Environmental Halophage eHP-6]

major capsid protein (#104)

1122..1523 Reverse 224436926 54% 55%

Uncharacterized protein [OSG_eHP12_00030] [Environmental Halophage eHP-12] Uncharacterized protein [OSG_eHP6_00015] [Environmental Halophage eHP-6]

hypothetical protein

1523..2074 Reverse 224436928 35% 42%

Uncharacterized protein [OSG_eHP12_00025] [Environmental Halophage eHP-12] Uncharacterized protein [OSG_eHP6_00020] [Environmental Halophage eHP-6]

hypothetical protein

ctg7180000408328

1..237 Reverse 224436936 57% 57%

Uncharacterized protein (Fragment) [OSG_eHP36_00220] [Environmental Halophage eHP-36]

hypothetical protein

Uncharacterized protein [OSG_eHP12_00010] [Environmental Halophage eHP-12]

244..423 Reverse 224436938 - no matches

426..2087 Reverse 224436940 56% 56%

Uncharacterized protein [C482_15301] [Natrialba chahannaoensis JCM 10990] Uncharacterized protein [Nmag_1649] [Natrialba magadii (strain ATCC 43099 / DSM 3394 / NCIMB 2190 / MS3) (Natronobacterium magadii)]

terminase, large subunit?

2093..2614 Reverse 224436942 46% 48%

Putative uncharacterized protein [Natrialba phage PhiCh1] Uncharacterized protein [Nmag_1650] [Natrialba magadii (strain ATCC 43099 / DSM 3394 / NCIMB 2190 / MS3) (Natronobacterium magadii)]

hypothetical protein

ctg7180000411793 54..1706 Forward 224463840 58% 31%

Uncharacterized protein [C472_12555] [Halorubrum tebenquichense DSM 14210] Prohead protease [11] [Halovirus HGTV-1]

prohead protease

1715..2200 Forward 224463851 80% 83%

Uncharacterized protein [C472_12560] [Halorubrum tebenquichense DSM 14210] Uncharacterized protein [C464_06240] [Halorubrum coriense DSM 10284]

hypothetical protein

2202..3368 Forward 224463862 85% 84%

Linocin_M18 bacteriocin protein [C472_12565] [Halorubrum tebenquichense DSM 14210] Linocin_M18 bacteriocin protein [C461_03098] [Halorubrum aidingense JCM 13560]

linocin M18 bacteriocin

3380..3775 Forward 224463873 46% 62%

Uncharacterized protein [C472_12570] [Halorubrum tebenquichense DSM 14210] Uncharacterized protein [EL22_00070] [Halostagnicola sp. A56]

hypothetical protein

ctg7180000414061 651..1343 Forward 0 224457133 43% 33%

Uncharacterized protein [C461_04527] [Halorubrum sp. AJ67] DSBA oxidoreductase [C467_12741] [Halorubrum hochstenium ATCC 700873]

protein-disulfide isomerase

1383..1736 Forward 0 224457137 39% 33%

Uncharacterized protein [BN903_336] [Halorubrum sp. AJ67] RNA-dependent RNA polymerase [Potato mop-top virus]

RNA polymerase

1758..2195 Reverse 1 224457141 44% Uncharacterized protein [BN903_228] [Halorubrum sp. AJ67]

hypothetical protein

2560..2913 Forward 1 224457145 - no matches

3030..3284 Forward 0 224457149 38% 32%

Uncharacterized protein [BN903_288] [Halorubrum sp. AJ67] Putative uncharacterized protein [uncultured virus]

hypothetical protein

ctg7180000414238

0..266 Forward 224457311 - no matches

257..685 Reverse 224457315 32% 22%

Nucleic acid binding OB-fold tRNA/helicase-type [C471_01900] [Halorubrum saccharovorum DSM 1137] Subtilisin-like serine protease precursor [Natgr_1499] [Natronobacterium gregoryi (strain

nucleic acid-binding protein

ATCC 43098 / CCM 3738 / NCIMB 2189 / SP2)]

692..1939 Reverse 224457319 39% 33% 33%

Uncharacterized protein [OSG_eHP32_00095] [Environmental Halophage eHP-32] Uncharacterized protein [OSG_eHP36_00050] [Environmental Halophage eHP-36] Uncharacterized protein [C481_11035] [Halorubrum sp. AJ67]

hypothetical protein

1936..2115 Reverse 224457323 - no matches

2131..2667 Reverse 224457326 46% 43%

Uncharacterized protein [OSG_eHP36_00045] [Environmental Halophage eHP-36] Uncharacterized protein [OSG_eHP32_00090] [Environmental Halophage eHP-32]

hypothetical protein

2661..3062 Reverse 224457330 36% 30%

Uncharacterized protein [OSG_eHP32_00085] [Environmental Halophage eHP-32] Uncharacterized protein [OSG_eHP36_00040] [Environmental Halophage eHP-36]

hypothetical protein

3064..3411 Reverse 224457334 50% 50% 37%

Uncharacterized protein [OSG_eHP36_00035] [Environmental Halophage eHP-36] Uncharacterized protein [OSG_eHP32_00080] [Environmental Halophage eHP-32] Uncharacterized protein [C481_11050] [Halorubrum sp. AJ67]

hypothetical protein

ctg7180000417783 1..420 Reverse 224478897 100% 58%

halTADL_0211 DNA methylase N-4/N-6 domain protein [halophilic archaeon True-ADL] DNA methylase (Fragment) [J07HB67_00853] [halophilic archaeon J07HB67]

hypothetical protein

643..903 Forward 224478902 99% 37%

halTADL_0210 hypothetical protein [halophilic archaeon True-ADL] Transcriptional regulator, Acidobacterial, PadR-family [B857_00610] [Bacillus isronensis B3W22]

hypothetical protein

1006..1797 Forward 224478909 100% 33%

halTADL_0209 endonuclease [halophilic archaeon True-ADL] Marine sediment metagenome DNA, contig: S03H2_S00463 (Fragment) [S03H2_28057] [marine sediment metagenome]

endonuclease

1864..2052 Forward 224478921 100% 46%

halTADL_0208 hypothetical protein [halophilic archaeon True-ADL] Uncharacterized protein [Nmag_0254] [Natrialba magadii (strain ATCC 43099 / DSM 3394 / NCIMB 2190 / MS3) (Natronobacterium magadii)]

hypothetical protein

2069..2140 Reverse 224478927 100% 90%

halTADL_0207 protein of unknown function DUF1524 RloF [halophilic archaeon True-ADL] Uncharacterized protein [C463_05800] [Halorubrum californiensis DSM 19288]

DUF1524 RloF

ctg7180000424023 0..164 Reverse 224483007 - no matches

154..1524 Reverse 224483019 89% 83%

Uncharacterized protein [C472_00404] [Halorubrum tebenquichense DSM 14210] Uncharacterized protein [C465_05206] [Halorubrum distributum JCM 9100]

hypothetical protein

1521..2291 Reverse 224483031 80% 73%

Uncharacterized protein [C472_00409] [Halorubrum tebenquichense DSM 14210] Uncharacterized protein [C466_09897] [Halorubrum distributum JCM 10118]

hypothetical protein

2284..3477 Reverse 224483043 69% 65%

Uncharacterized protein [C472_00414] [Halorubrum tebenquichense DSM 14210] Uncharacterized protein [C466_09892] [Halorubrum distributum JCM 10118]

hypothetical protein

ctg7180000428629 1..552 Reverse 224435257 59% 59%

Uncharacterized protein [58] [Halovirus HRTV-7] Uncharacterized protein [59] [Halovirus HSTV-2]

hypothetical protein

806..2056 Reverse 224435269 66% 66%

Uncharacterized protein [61] [Halovirus HSTV-2] DNA polymerase II small subunit [60] [Halovirus HRTV-7]

hypothetical protein

2134..3237 Reverse 224435282 73% 72%

Uncharacterized protein [62] [Halovirus HSTV-2] Uncharacterized protein [61] [Halovirus HRTV-7]

hypothetical protein

ctg7180000435415 32..1111 Reverse 224464624 47% 44%

HalDL1_0844 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Halobacterium sp. DL1] Transcription initiation factor IIB [tfbA5] [Halorubrum sp. AJ67]

hypothetical protein

1108..1470 Reverse 224464632 27% Probable translation initiation factor IF-2 [infB] [Halogranum salarium B-1] hypothetical protein

1672..1839 Forward 224464640 87% 89%

halTADL_1708 Core histone H2A/H2B/H3/H4. [halophilic archaeon True-ADL] Uncharacterized protein [J07HN6_00174] [Halonotius sp. J07HN6]

hypothetical protein

1954..2331 Reverse 224464648 26% 23%

Uncharacterized protein [C454_12983] [Haloferax gibbonsii ATCC 33959] Uncharacterized protein [C455_08137] [Haloferax larsenii JCM 13917]

hypothetical protein

ctg7180000436748 83..463 Forward 224490970 55% 54%

halTADL_2483 transcriptional regulator PadR family protein [halophilic archaeon True-ADL] PadR family transcriptional regulator [C484_13076] [Natrialba taiwanensis DSM 12281]

transcriptional regulator PadR

460..780 Forward 224490976 - no matches

767..1003 Forward 224490982 - no matches

1000..1122 Forward 224490989 - no matches

1119..1580 Forward 224490996 37% 36%

Uncharacterized protein [C489_05178] [Natrinema versiforme JCM 10478] Uncharacterized protein [C440_07552] [Haloferax mucosum ATCC BAA-1512]

hypothetical protein

1812..2003 Forward 224491002 - no matches

ctg7180000438477 230..631 Reverse 224491799 81% 76%

Uncharacterized protein [C459_05971] [Haloferax sp. ATCC BAA-645] Uncharacterized protein domain protein [C460_02974] [Halorubrum sp. AJ67]

hypothetical protein

881..1750 Forward 224491805 80% 78%

Universal stress protein UspA related nucleotide-binding protein [J07HQX50_01805] [Haloquadratum sp. J07HQX50] UspA domain-containing protein [C452_02090] [Haloferax alexandrinus JCM 10717]

UspA domain protein

1814..2260 Forward 224491809 66% 67%

Uncharacterized protein [C480_19097] [Natrialba aegyptia DSM 13077] Uncharacterized protein [C482_03256] [Natrialba chahannaoensis JCM 10990]

hypothetical protein

ctg7180000438795

4..1482 Forward 224491845 97% 66%

Helicase domain protein [Nmlp_2188] [Halorubrum sp. AJ67] Helicase domain protein [Nmlp_2188] [Natronomonas moolapensis (strain DSM 18674 / JCM 14361 / 8.8.11)]

helicase domain protein

1485..3434 Forward 224491849 98% 52%

Uncharacterized protein [Nmlp_2187] [Halorubrum sp. AJ67] Uncharacterized protein [Nmlp_2187] [Natronomonas moolapensis (strain DSM 18674 / JCM 14361 / 8.8.11)]

hypothetical protein

3431..4318 Forward 224491853 90% 51%

Phospholipase D Active site motif domain protein [C464_16647] [Halorubrum sp. AJ67] Phospholipase D Active domain protein [Nmlp_2186] [Natronomonas moolapensis (strain DSM 18674 / JCM 14361 / 8.8.11)]

phospholipase D Active site motif domain protein

4525..5532 Forward 224491857 30% 29%

HalDL1_3325 hypothetical protein [Halobacterium sp. DL1] Uncharacterized protein [C438_05222] [Haloferax denitrificans ATCC 35960]

hypothetical protein

5525..6289 Forward 224491861 41% 41%

Uncharacterized protein [C453_00900] [Haloferax elongans ATCC BAA-1513] Uncharacterized protein [C438_05217] [Haloferax denitrificans ATCC 35960]

hypothetical protein

6297..6923 Reverse 224491865 92% 91%

Uncharacterized protein [HSB1_39200] [Halorubrum sp. AJ67] Uncharacterized protein [HSB1_39200] [Halogranum salarium B-1]

hypothetical protein

6988..8025 Reverse 224491869 91% 86%

Uncharacterized protein [HSB1_39190] [Halorubrum sp. AJ67] Uncharacterized protein [HSB1_39190] [Halogranum salarium B-1]

hypothetical protein

8022..9926 Reverse 224491873 92% 89%

Uncharacterized protein [HalDL1DRAFT_3150] [Halorubrum sp. AJ67] Uncharacterized protein [HALDL1_01045] [Halobacterium sp. DL1]

helix-turn-helix DNA-binding domain

10118..11233 Forward 224491877 94% 90%

DNA-cytosine methyltransferase (EC 2.1.1.37) [HalDL1DRAFT_3151] [Halorubrum sp. AJ67] DNA-cytosine methyltransferase [HSB1_39170] [Halogranum salarium B-1]

DNA methylase

11242..11748 Forward 224491881 84% 59%

A/G-specific DNA glycosylase [Halru_3020] [Halorubrum sp. AJ67] Uncharacterized protein [HSB1_39140] [Halogranum salarium B-1]

A/G-specific DNA glycosylase

12041..12457 Forward 224491885 90% 93%

Uncharacterized protein [HalDL1DRAFT_3154] [Halorubrum sp. AJ67] Uncharacterized protein [HALDL1_01030] [Halobacterium sp. DL1]

hypothetical protein

ctg7180000439875

28..384 Reverse 224492094 40% 40%

Uncharacterized protein [106] [Halovirus HRTV-7] Uncharacterized protein [104] [Halovirus HSTV-2]

hypothetical protein

416..712 Reverse 224492101 51% 55%

Uncharacterized protein [106] [Halovirus HRTV-7] Uncharacterized protein [104] [Halovirus HSTV-2]

hypothetical protein

709..1011 Reverse 224492109 32% ATPase AAA containing von Willebrand factor type A (VWA) domain-like protein [C483_14815] [Natrialba hulunbeirensis JCM 10989]

von Willebrand factor type A (VWA) domain-like protein

1292..1906 Reverse 224492117 36% 26%

Uncharacterized protein [C495_03677] [Natronorubrum sulfidifaciens JCM 14089] Gp110 [110] [Mycobacterium phage Pio]

hypothetical protein

1923..2009 Reverse 224492125 - no matches

ctg7180000440486 233..1471 Forward 224492518 30% 51%

Uncharacterized protein [C492_00484] [Natronococcus jeotgali DSM 18795] Uncharacterized protein (Fragment) [C451_00110] [Halococcus thailandensis JCM 13552]

hypothetical protein

1549..1788 Reverse 224492527 40% 37%

AsnC family transcriptional regulator [Mcup_1017] [Metallosphaera cuprina (strain Ar-4)] Hth domain-containing protein [C436_09281] [Haloarcula sinaiiensis ATCC 33800]

transcriptional regulator AsnC

ctg7180000446992 0..1439 Reverse 224458665 39% 38%

Uncharacterized protein [C454_02855] [Haloferax gibbonsii ATCC 33959] Uncharacterized protein [HAPG_00095] [Halorubrum phage GNf2]

hypothetical protein (#1090)

1436..1576 Reverse 224458669 - no match

1573..1947 Reverse 224458673 46% Uncharacterized protein [C468_14108] [Halorubrum kocurii JCM 14978]

hypothetical protein

ctg7180000447311 0..758 Forward 224461969 41% 30%

Uncharacterized protein [C454_02855] [Haloferax gibbonsii ATCC 33959] Uncharacterized protein [HAPG_00095] [Halorubrum phage GNf2]

hypothetical protein

762..1214 Forward 224461977 45% 44%

Uncharacterized protein [HFX_0911] [Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4) (Halobacterium mediterranei)] Uncharacterized protein [C454_02850] [Haloferax gibbonsii ATCC 33959]

hypothetical protein

1216..1563 Forward 224461983 42% 39%

Uncharacterized protein [C454_02845] [Haloferax gibbonsii ATCC 33959] Uncharacterized protein [HFX_0912] [Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4) (Halobacterium mediterranei)]

hypothetical protein

1560..1982 Forward 224461989 34% 42%

Uncharacterized protein [C454_02840] [Haloferax gibbonsii ATCC 33959] Uncharacterized protein [HFX_0913] [Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4) (Halobacterium mediterranei)]

hypothetical protein

1979..2230 Forward 224461997 30%

34% Uncharacterized protein [C454_02835] [Haloferax gibbonsii ATCC 33959] Uncharacterized protein [HFX_0914] [Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4) (Halobacterium mediterranei)]

hypothetical protein

2280..2702 Forward 224462001 37% 37%

Uncharacterized protein [C454_02830] [Haloferax gibbonsii ATCC 33959] Uncharacterized protein [HFX_0915] [Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4) (Halobacterium mediterranei)]

hypothetical protein

ctg7180000450146 95..5110 Reverse 224460325 45% 59%

Uncharacterized protein [C448_05923] [Halococcus morrhuae DSM 1307] Uncharacterized protein [C450_05200] [Halococcus salifodinae DSM 8989]

DNA primase?

ctg7180000452388 647..1072 Forward 224484136 87% 67%

Hlac_3421 zinc finger SWIM domain protein [Halorubrum lacusprofundi ATCC 49239] Zinc finger SWIM domain protein [C474_13749] [Halosarcina pallida JCM 14848]

zinc finger SWIM domain protein

2218..2469 Reverse 224484143 - no matches

2542..3231 Reverse 224484151 42% 37%

Uncharacterized protein [Nmag_1794] [Natrialba magadii (strain ATCC 43099 / DSM 3394 / NCIMB 2190 / MS3) (Natronobacterium magadii)] 60S ribosomal protein L36-like protein [C493_13628] [Natronolimnobius innermongolicus JCM 12255]

hypothetical protein

3541..3927 Reverse 224484163 92% 80%

Uncharacterized protein [halTADL_1427] [halophilic archaeon True-ADL] Uncharacterized protein [C459_05971] [Haloferax sp. ATCC BAA-645]

hypothetical protein (multiple transmembrane helices)

ctg7180000454867 705..1154 Reverse 224479766 92% 77%

halTADL_0534 hypothetical protein [halophilic archaeon True-ADL] Uncharacterized protein [HSB1_47410] [Halogranum salarium B-1]

hypothetical protein

1162..1725 Reverse 224479779 93% 77%

halTADL_0533 hypothetical protein [halophilic archaeon True-ADL] Uncharacterized protein [HSB1_47390] [Halogranum salarium B-1]

hypothetical protein

2346..3101 Reverse 224479789 80% 81%

halTADL_0529 hypothetical protein [halophilic archaeon True-ADL] Uncharacterized protein [C494_08827] [Natronorubrum bangense JCM 10635]

hypothetical protein

ctg7180000455053 135..311 Forward 224481050 - no matches

366..2021 Reverse 224481069 60% 63%

halTADL_3394 protein synthesis factor GTP-binding [halophilic archaeon True-ADL] Translation elongation factor aEF-1 subunit alpha-like protein [C455_11823] [Haloferax larsenii JCM 13917]

GTP-binding/aEF-1-like protein

2124..3197 Forward 224481086 - no matches

3199..3609 Reverse 224481103 - no matches

3656..4156 Reverse 224481117 33% 31%

Transcriptional regulator, XRE family [Halar_3398] [halophilic archaeon DL31] DNA binding domain-containing protein [C437_16036] [Haloarcula vallismortis ATCC 29715]

transcriptional regulator, XRE family

ctg7180000456477 47..367 Forward 224474852 - no matches

371..673 Reverse 224474856 47% 45%

halTADL_2525 PRC-barrel domain protein [halophilic archaeon True-ADL] Uncharacterized conserved protein (Uncharacterized protein) [Hbor_15200] [Halogeometricum borinquense (strain ATCC 700274 / DSM 11551 / JCM 10706 / PR3)]

PRC-barrel domain protein

780..3227 Reverse 224474860 36% 47%

Helicase / DNA excision repair protein ERCC-2 [C455_03169] [Haloferax larsenii JCM 13917] Helicase [C452_03963] [Haloferax alexandrinus JCM 10717]

helicase domain protein

3288..3854 Reverse 224474864 34% 32%

Uncharacterized protein [M079_4752] [Bacteroides fragilis str. 3996 N(B) 6] Uncharacterized protein [My1_077] [Pectobacterium phage My1]

hypothetical protein

ctg7180000459513 6..305 Reverse 224467993 63% 57%

Integrase [C480_04701] [Natrialba aegyptia DSM 13077] Integrase [C489_09146] [Natrinema versiforme JCM 10478]

integrase

499..1284 Reverse 224467995 46% 45%

Uncharacterized protein [C486_00305] [Natrinema gari JCM 14663] Uncharacterized protein [C489_16640] [Natrinema versiforme JCM 10478]

hypothetical

1474..1839 Forward 224467997 69% 69%

halTADL_1885 flagellin domain protein [halophilic archaeon True-ADL] Uncharacterized protein [C468_00270] [Halorubrum kocurii JCM 14978]

pilin

1805..1990 Forward 224467999 61% 56%

halTADL_1885 flagellin domain protein [halophilic archaeon True-ADL] Archaeal flagellin N-terminal-like domain protein [A07HR60_01245] [uncultured archaeon A07HR60]

Pilin (#358)

2129..2320 Forward 224468001 87% 81%

Uncharacterized protein [Halorubrum sp. T3] Uncharacterized protein [C473_11139] [Halorubrum terrestre JCM 10247]

hypothetical protein

2334..2528 Forward 224468003 53% 46%

ORF6 [ORF6] [Halorubrum pleomorphic virus 3] Uncharacterized protein [HALLA_17520] [Halostagnicola larsenii XH-48]

ORF6

ctg7180000464057 2..1051 Reverse 224476108 87% 88%

Uncharacterized protein [C472_00404] [Halorubrum tebenquichense DSM 14210] Uncharacterized protein [C466_09902] [Halorubrum distributum JCM 10118]

hypothetical protein

1048..1848 Reverse 224476114 63% 63%

Uncharacterized protein [C472_00409] [Halorubrum tebenquichense DSM 14210] Uncharacterized protein [C466_09897] [Halorubrum distributum JCM 10118]

hypothetical protein

1811..2053 Reverse 224476120 43% 68%

Uncharacterized protein [C472_00414] [Halorubrum tebenquichense DSM 14210] Uncharacterized protein [C461_04722] [Halorubrum aidingense JCM 13560]

hypothetical protein

ctg7180000467184 572..832 Forward 224474813 28% 28%

Uncharacterized protein [106] [Halovirus HRTV-7] Uncharacterized protein [104] [Halovirus HSTV-2]

802..975 Forward 224474821 - no matches

hypothetical protein

ctg7180000475061 1..321 Reverse 2 224437146 51% 46%

Uncharacterized protein [rrnAC0604] [Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809) (Halobacterium marismortui)] Uncharacterized protein [C469_15538] [Halorubrum lipolyticum DSM 21995]

hypothetical protein

321..617 Reverse 224437149 35% 34%

Uncharacterized protein [C442_08766] [Haloarcula amylolytica JCM 13557] Uncharacterized protein [C436_14484] [Haloarcula sinaiiensis ATCC 33800]

hypothetical protein

712..867 Reverse 224437153 45% 45%

Uncharacterized protein [Natoc_0261] [Natronococcus occultus SP4] Uncharacterized protein [C491_05721] [Natronococcus amylolyticus DSM 10524]

hypothetical protein

843..1667 Reverse 224437157 50% 25%

Uncharacterized protein [Hmuk_1723] [Halomicrobium mukohataei (strain ATCC 700874 / DSM 12286 / JCM 9738 / NCIMB 13541) (Haloarcula mukohataei)] ORF 17 [Haloarcula phage SH1]

hypothetical protein

1671..1958 Reverse 224437161 - no matches

1958..2110 Reverse 224437164 - no matches

deg7180000395624 1..441 Reverse 224494910 62% 57%

Putative immunoglobulin-binding regulator B [HMPREF0083_04675] [Aneurinibacillus aneurinilyticus ATCC 12856] Putative immunoglobulin-binding regulator B [HMPREF1548_03108] [Clostridium sp. KLE 1755]

IgB-binding regulator-like protein

714..1037 Reverse 224494918 35% 36%

Acetyltransferase-like protein [ERIC2_c23940] [Paenibacillus larvae subsp. larvae DSM 25430] Marine sediment metagenome DNA, contig: S03H2_C00527 [S03H2_01725] [marine sediment metagenome]

acetyltransferase-like protein

968..1396 Reverse 224494924 50% 46%

Immunoglobulin-binding regulator A family protein [HMPREF0083_04674] [Aneurinibacillus aneurinilyticus ATCC 12856] Putative immunoglobulin-binding regulator A [HMPREF1548_03106] [Clostridium sp. KLE 1755]

IgA-binding regulator-like protein

1626..2471 Reverse 224494932 59% 56%

Immunoglobulin-binding regulator A family protein [HMPREF0083_04674] [Aneurinibacillus aneurinilyticus ATCC 12856] Putative immunoglobulin-binding regulator A [HMPREF1548_03106] [Clostridium sp. KLE

IgA-binding regulator-like protein

1755]

deg7180000398860 2..157 Forward 224479357 - no matches

501..2009 Forward 224479368 49% 45% 42%

Uncharacterized protein [C451_19456] [Halococcus thailandensis JCM 13552] Terminase large subunit [1] [Halovirus HSTV-1] Uncharacterized protein [Archaeal BJ1 virus]

terminase, large subunit (TerL)

deg7180000398907 117..1715 Forward 224479418 33% 31% 27%

Prohead protease [32] [Halovirus HCTV-2] Prohead protease [38] [Halovirus HHTV-2] Structural protein [OSG_eHP28_00115] [Environmental Halophage eHP-28]

prohead protease

1715..2029 Forward 224479426 - no matches

2026..2523 Forward 224479435 54% 48% 41% 35%

Major capsid protein [33] [Halovirus HCTV-2] Major capsid protein [39] [Halovirus HHTV-2] Capsid protein [14] [Halovirus HSTV-1] Uncharacterized protein [OSG_eHP28_00125] [Environmental Halophage eHP-28]

major capsid protein (#452)

2541..2918 Forward 224479443 51% 50% 31% 29%

Major capsid protein [33] [Halovirus HCTV-2] Major capsid protein [39] [Halovirus HHTV-2] Uncharacterized protein [OSG_eHP28_00125] [Environmental Halophage eHP-28] Capsid protein [14] [Halovirus HSTV-1]

major capsid protein (#127)

2932..3195 Forward 224479475 44% Uncharacterized protein [34] [Halovirus HCTV-2]

hypothetical protein

3300..4130 Forward 224479486 31% 29% 33% 20%

Uncharacterized protein [35] [Halovirus HCTV-2] Uncharacterized protein [42] [Halovirus HHTV-2] Uncharacterized protein [117] [Halovirus HCTV-1] Uncharacterized protein [125] [Halovirus HVTV-1]

hypothetical protein

4130..4684 Forward 224479500 43% 43% 43% 40%

Uncharacterized protein [36] [Halovirus HCTV-2] Uncharacterized protein [125] [Halovirus HCTV-5] Uncharacterized protein [126] [Halovirus HVTV-1] Uncharacterized protein [43] [Halovirus HHTV-2]

hypothetical protein

4687..5112 Forward 224479510 30% 28%

Uncharacterized protein [37] [Halovirus HCTV-2] Uncharacterized protein [44] [Halovirus HHTV-2]

hypothetical protein

deg7180000398909 43..1062 Forward 224479521 44% 39% 38%

Tail tube [46] [Halovirus HHTV-2] Uncharacterized protein [128] [Halovirus HVTV-1] Tail tube [127] [Halovirus HCTV-5]

tail tube protein

1132..1674 Forward 224479533 22% Tail assembly chaperone [41] [Halovirus HCTV-2] tail assembly chaperone

1728..2165 Forward 224479544 34% Tail assembly chaperone [41] [Halovirus HCTV-2]

tail assembly chaperone

2165..3013 Forward 224479556 30% 28%

Tape measure [49] [Halovirus HHTV-2] Tape measure [42] [Halovirus HCTV-2]

tail tape measure protein

2944..3462 Forward 224479569 28% 23%

Uncharacterized protein [SAG0343_07310] [Streptococcus agalactiae GB00874] Phage protein [K710_0916] [Streptococcus iniae SF1]

hypothetical protein

3468..5360 Forward 224479582 40% 39%

Uncharacterized protein [133] [Halovirus HVTV-1] Uncharacterized protein [132] [Halovirus HCTV-5]

hypothetical protein

5491..6138 Forward 224479594 40% 37%

Uncharacterized protein [134] [Halovirus HVTV-1] Uncharacterized protein [133] [Halovirus HCTV-5]

hypothetical protein

6140..6409 Forward 224479604 50% 50%

Uncharacterized protein [134] [Halovirus HCTV-5] Uncharacterized protein [135] [Halovirus HVTV-1]

hypothetical protein

deg7180000399274 0..176 Reverse 224481657 76% 74%

Uncharacterized protein [C478_10486] [Haloterrigena thermotolerans DSM 11522] Uncharacterized protein [EL22_00065] [Halostagnicola sp. A56]

hypothetical protein

269..502 Reverse 224481671 - no matches

511..846 Reverse 224481685 81% 82%

Linocin_M18 bacteriocin protein [C478_10476] [Haloterrigena thermotolerans DSM 11522] Bacteriocin [EL22_00075] [Halostagnicola sp. A56]

linocin M18 bacterocin (#720)

1668..2165 Reverse 224481699 64% 68%

Uncharacterized protein [C478_10471] [Haloterrigena thermotolerans DSM 11522] Uncharacterized protein [EL22_00080] [Halostagnicola sp. A56]

hypothetical protein (#147)

2251..2637 Reverse 224481714 60% 55%

Uncharacterized protein [C478_10466] [Haloterrigena thermotolerans DSM 11522] Uncharacterized protein [EL22_00085] [Halostagnicola sp. A56]

hypothetical protein

3027..3491 Reverse 224481729 76% 65% 37%

Uncharacterized protein [C478_10466] [Haloterrigena thermotolerans DSM 11522] Uncharacterized protein [EL22_16955] [Halostagnicola sp. A56] Prohead protease [11] [Halovirus HGTV-1]

prohead protease

deg7180000401097 239..472 Forward 224482874 81% 54%

Uncharacterized protein [C443_17953] [Haloarcula argentinensis DSM 12282] Uncharacterized protein [HALG_00005] [Halorubrum phage CGphi46]

hypothetical protein

405..740 Forward 224482887 65% 63%

Uncharacterized protein [HALG_00005] [Halorubrum phage CGphi46] Uncharacterized protein [Archaeal BJ1 virus]

hypothetical protein

737..1465 Forward 224482899 47%

41% Uncharacterized protein [HALG_00005] [Halorubrum phage CGphi46] Uncharacterized protein [Archaeal BJ1 virus]

hypothetical protein

1465..1791 Forward 224482911 42% 31%

Phage major capsid protein, HK97 family [Asulf_01513] [Archaeoglobus sulfaticallidus PM70-1] Uncharacterized protein [HALG_00004] [Halorubrum phage CGphi46]

major capsid protein (#90)

1749..2252 Forward 224482923 40% 34%

Phage major capsid protein, HK97 family [Asulf_01513] [Archaeoglobus sulfaticallidus PM70-1] Uncharacterized protein [HALG_00004] [Halorubrum phage CGphi46]

major capsid protein (#174)

2392..2715 Forward 224482935 30% Uncharacterized protein [OG2516_17595] [Oceanicola granulosus HTCC2516]

hypothetical protein

2715..2882 Forward 224482946 40% 40%

Putative uncharacterized protein [Natrialba phage PhiCh1] Uncharacterized protein [Nmag_4261] [Natrialba magadii (strain ATCC 43099 / DSM 3394 / NCIMB 2190 / MS3) (Natronobacterium magadii)]

hypothetical protein

deg7180000401099 2..196 Forward 2 224482954 60% 52%

Uncharacterized protein [HALG_00010] [Halorubrum phage CGphi46] Uncharacterized protein [OSG_eHP9_00180] [Environmental Halophage eHP-9]

hypothetical protein

200..940 Forward 2 224482962 61% 51%

Uncharacterized protein [C443_17938] [Haloarcula argentinensis DSM 12282] Uncharacterized protein [HALG_00002] [Halorubrum phage CGphi46]

hypothetical protein

940..1404 Forward 1 224482973 51% 48%

Uncharacterized protein [HALG_00054] [Halorubrum phage CGphi46] Uncharacterized protein [Archaeal BJ1 virus]

hypothetical protein

1412..1897 Forward 2 224482982 45% 33%

Uncharacterized protein [C482_15346] [Natrialba chahannaoensis JCM 10990] Uncharacterized protein [HALG_00053] [Halorubrum phage CGphi46]

hypothetical protein

1947..2396 Forward 0 224482994 35% 24%

Uncharacterized protein [C443_17898] [Haloarcula argentinensis DSM 12282] Uncharacterized protein [HALG_00052] [Halorubrum phage CGphi46]

hypothetical protein

deg7180000413894 1..72 Reverse 224482759 - no matches

76..534 Reverse 224482770 32% Uncharacterized protein [22] [Halovirus HHTV-1]

hypothetical protein

254..932 Forward - - tRNA-Thr

tRNA-Thr

541..1143 Reverse 224482784 45% Major capsid protein [21] [Halovirus HHTV-1]

major capsid protein (#167)

1092..1679 Reverse 224482795 43% Major capsid protein [21] [Halovirus HHTV-1]

major capsid protein (#340)

1692..2147 Reverse 224482803 34% Uncharacterized protein [20] [Halovirus HHTV-1]

hypothetical protein (#582)

2150..2863 Reverse 224482814 - no matches

deg7180000422908 17..2155 Reverse 224442380 36% 33%

Uncharacterized protein [C441_04514] [Haloferax sulfurifontis ATCC BAA-897] Phage/plasmid primase, P4 family [Htur_5275] [Haloterrigena turkmenica (strain ATCC 51198 / DSM 5511 / NCIMB 13204 / VKM B-1734) (Halococcus turkmenicus)]

DNA primase

2145..2771 Reverse 224442384 39% 40%

ATP-dependent DNA helicase PcrA protein (EC 3.6.4.12) (Repair helicase) [HLRTI_001350] [Halorhabdus tiamatea SARL4B] DNA/RNA helicase, superfamily I [Hbor_37910] [Halogeometricum borinquense (strain ATCC 700274 / DSM 11551 / JCM 10706 / PR3)]

DNA helicase

deg7180000395111 1..348 Forward 224493170 33% 33% 31%

Uncharacterized protein [118] [Halovirus HCTV-5] Prohead protease [119] [Halovirus HVTV-1] Uncharacterized protein [111] [Halovirus HCTV-1]

prohead protease (#433)

364..1719 Forward 224493180 64% 64% 64%

Major capsid protein [112] [Halovirus HCTV-1] Major capsid protein [120] [Halovirus HVTV-1] Major capsid protein [119] [Halovirus HCTV-5]

major capsid protein (#5)

1850..2140 Forward 224493190 43% 43% 40%

Uncharacterized protein [120] [Halovirus HCTV-5] Uncharacterized protein [121] [Halovirus HVTV-1] Uncharacterized protein [113] [Halovirus HCTV-1]

hypothetical protein

2144..2461 Forward 224493199 45% 42% 41%

Uncharacterized protein [114] [Halovirus HCTV-1] Uncharacterized protein [122] [Halovirus HVTV-1] Uncharacterized protein [121] [Halovirus HCTV-5]

hypothetical protein (#166)

2468..2662 Forward 224493207 48% 49% 40%

Uncharacterized protein [122] [Halovirus HCTV-5] Uncharacterized protein [123] [Halovirus HVTV-1] Uncharacterized protein [115] [Halovirus HCTV-1]

hypothetical protein (#892)

ctg7180000406863 1..513 Reverse 224481280 51% 38% 32%

Uncharacterized protein [121] [Halovirus HCTV-1] Uncharacterized protein [OSG_eHP27_00035] [Environmental Halophage eHP-27] Uncharacterized protein [OSG_eHP18_00080] [Environmental Halophage eHP-18]

hypothetical protein (#881)

530..799 Reverse 224481290 32% Uncharacterized protein [120] [Halovirus HCTV-1]

hypothetical protein

868..1386 Reverse 224481300 49% 28%

Uncharacterized protein [119] [Halovirus HCTV-1] Uncharacterized protein [OSG_eHP18_00055] [Environmental Halophage eHP-18]

hypothetical protein

1390..1851 Reverse 224481310 - no matches

1832..2602 Reverse 224481320 43% 43% 43%

Uncharacterized protein [117] [Halovirus HCTV-1] Uncharacterized protein [124] [Halovirus HCTV-5] Uncharacterized protein [125] [Halovirus HVTV-1]

hypothetical protein

2605..2895 Reverse 224481361 41% 43% 43%

Uncharacterized protein [116] [Halovirus HCTV-1] Uncharacterized protein [123] [Halovirus HCTV-5] Uncharacterized protein [124] [Halovirus HVTV-1]

hypothetical protein

2899..3207 Reverse 224481368 36% 36% 30%

Uncharacterized protein [122] [Halovirus HCTV-5] Uncharacterized protein [123] [Halovirus HVTV-1] Uncharacterized protein [115] [Halovirus HCTV-1]

hypothetical protein

3308..3592 Reverse 224481376 40% 43% 36%

Uncharacterized protein [114] [Halovirus HCTV-1] Uncharacterized protein [121] [Halovirus HCTV-5] Uncharacterized protein [122] [Halovirus HVTV-1]

hypothetical protein

3607..3966 Reverse 224481383 39% 39% 35%

Uncharacterized protein [120] [Halovirus HCTV-5] Uncharacterized protein [121] [Halovirus HVTV-1] Uncharacterized protein [113] [Halovirus HCTV-1]

hypothetical protein

3988..5358 Reverse 224481388 68% 68% 65%

Major capsid protein [120] [Halovirus HVTV-1] Major capsid protein [119] [Halovirus HCTV-5] Major capsid protein [112] [Halovirus HCTV-1]

major capsid protein (#24)

5359..5724 Reverse 224481395 35% 35% 38%

Uncharacterized protein [118] [Halovirus HCTV-5] Prohead protease [119] [Halovirus HVTV-1] Uncharacterized protein [111] [Halovirus HCTV-1]

prohead protease (#634)

ctg7180000406861 2..325 Reverse 224481212 - no matches

394..1509 Reverse 224481221 19% Uncharacterized protein [125] [Halovirus HCTV-1]

hypothetical protein

1659..2207 Reverse 224481262 41% 39%

Tail assembly chaperone [122] [Halovirus HCTV-1] Tail assembly chaperone [123] [Halovirus HCTV-1]

tail assembly chaperone

2231..3172 Reverse 224481271 47% 31% 28%

Uncharacterized protein [121] [Halovirus HCTV-1] Uncharacterized protein [OSG_eHP27_00035] [Environmental Halophage eHP-27] Uncharacterized protein [OSG_eHP18_00080] [Environmental Halophage eHP-18]

hypothetical protein (#880)

deg7180000409203 0..431 Reverse 224480691 - no matches

496..1545 Forward 224480706 45% 44%

Uncharacterized protein [Hlac_0758] [Halorubrum lacusprofundi (strain ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34)] Uncharacterized protein [C453_12931] [Haloferax elongans ATCC BAA-1513]

hypothetical protein

1542..2489 Forward 224480724 32% 31%

Uncharacterized protein [Hlac_0760] [Halorubrum lacusprofundi (strain ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34)] Uncharacterized protein [C453_12941] [Haloferax elongans ATCC BAA-1513]

major capsid protein (#91)

2437..2817 Forward 224480742 37% 30% 29%

Uncharacterized protein [Hlac_0760] [Halorubrum lacusprofundi (strain ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34)] Major capsid protein [120] [Halovirus HVTV-1] Major capsid protein [119] [Halovirus HCTV-5]

major capsid protein (#425)

2822..3484 Forward 224480760 47% 50%

Uncharacterized protein [Hlac_0762] [Halorubrum lacusprofundi (strain ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34)] Uncharacterized protein [C453_12951] [Haloferax elongans ATCC BAA-1513]

hypothetical protein

ctg7180000427076 1..276 Forward 224433999 58% Uncharacterized protein [VPGG_00036] [Vibrio phage VBM1]

hypothetical protein

279..719 Forward 224434012 34% Uncharacterized protein [VPGG_00035] [Vibrio phage VBM1]

hypothetical protein (#367)

731..1684 Forward 224434023 41% Uncharacterized protein [VPGG_00034] [Vibrio phage VBM1]

major capsid protein (#520)

1732..1959 Forward 224434035 - no matches

1963..2310 Forward 224434047 46% Uncharacterized protein [VPGG_00032] [Vibrio phage VBM1]

hypothetical protein

2376..2456 Forward 224434059 - no matches

ctg7180000410975 2..100 Forward 224461268 - no matches

104..1249 Forward 224461277 67% 67% 45%

Uncharacterized protein [10] [Halovirus HSTV-2] Prohead protease [10] [Halovirus HRTV-7] Uncharacterized protein [Halorubrum phage HF2]

hypothetical protein

1265..1750 Forward 224461287 66% 66% 43%

Uncharacterized protein [11] [Halovirus HSTV-2] Uncharacterized protein [11] [Halovirus HRTV-7] Uncharacterized protein [Halorubrum phage HF2]

hypothetical protein

1769..2314 Forward 224461294 60% 59% 41% 31%

Scaffold protein [12] [Halovirus HSTV-2] Uncharacterized protein [12] [Halovirus HRTV-7] Uncharacterized protein [C494_07760] [Natronorubrum bangense JCM 10635] Uncharacterized protein [Halorubrum phage HF2]

scaffold protein (#726)

2353..3336 Forward 224461304 77% 70% 44% 41%

Capsid protein [13] [Halovirus HSTV-2] Major capsid protein [13] [Halovirus HRTV-7] Uncharacterized protein [Halorubrum phage HF2] Uncharacterized protein [C494_07760] [Natronorubrum bangense JCM 10635]

major capsid protein

ctg7180000399498 0..185 Forward 224423212 48% 46%

Dihydrofolate reductase (EC 1.5.1.3) [Hmuk_3007] [Halomicrobium mukohataei (strain ATCC 700874 / DSM 12286 / JCM 9738 / NCIMB 13541) (Haloarcula mukohataei)] Dihydrofolate reductase [C445_15901] [Halobiforma lacisalsi AJ5]

dihydrofolate reductase

365..3286 Forward 224423224 66% 77%

Ribonucleoside-diphosphate reductase [21] [Halovirus HVTV-1] Ribonucleoside-diphosphate reductase (EC 1.17.4.1) [nrdA_2] [Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4) (Halobacterium mediterranei]

ribonucleoside-diphosphate reductase

3323..3592 Forward 224423235 53% 53% 41%

Uncharacterized protein [122] [Halovirus HCTV-5] Uncharacterized protein [123] [Halovirus HVTV-1] Uncharacterized protein [115] [Halovirus HCTV-1]

hypothetical protein (#879)

ctg7180000397348 1..1770 Reverse 224439563 96% halTADL_2902 aconitate hydratase [halophilic archaeon True-ADL]

aconitate hydratase

1950..2414 Forward 224439567 85% halTADL_2901 deoxyUTP pyrophosphatase [halophilic archaeon True-ADL]

deoxyUTP pyrophosphatase

2421..3035 Reverse 224439571 82% halTADL_2900 hypothetical protein [halophilic archaeon True-ADL]

hypothetical protein

3456..4466 Forward 224439575 44% halTADL_0413 integrase [halophilic archaeon True-ADL]

integrase

4564..4821 Forward 224439579 - no matches

5332..5595 Forward 224439583 - no matches

5667..8597 Reverse 224439587 69% 61%

Type I restriction-modification system methyltransferase subunit [Natgr_3510 [Natronobacterium gregoryi (strain ATCC 43098 / CCM 3738 / NCIMB 2189 / SP2)] N-6 DNA methylase [Halorubrum tebenquichense DSM 14210]

DNA methylase

8731..8925 Forward 224439590 - no matches

9500..9682 Forward 224439594 - no matches

9679..9915 Forward 224439598 58% 54%

Uncharacterized protein [EL22_25330] [Halostagnicola sp. A56] Uncharacterized protein [C464_08175] [Halorubrum coriense DSM 10284]

hypothetical protein

9908..10180 Forward 224439602 - no matches

10490..10879 Forward 224439606 - no matches

10876..11034 Forward 224439610 64% Uncharacterized protein [C453_17239] [Haloferax elongans ATCC BAA-1513]

hypothetical protein

11059..11454 Reverse 224439614 - no matches

11717..12007 Forward 224439618 - no matches

11991..12617 Forward 224439622 40% 40%

Putative phage integrase [C440_07957] [Haloferax mucosum ATCC BAA-1512] Integrase (Putative phage integrase) [HFX_6119 [Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4) (Halobacterium mediterranei)]

integrase

12630..12851 Reverse 224439626 - no matches

13004..13663 Forward 224439630 - no matches

14091..14312 Reverse 224439634 - no matches

14309..14605 Reverse 224439638 - no matches

14602..14958 Reverse 224439642 42% 31% 27%

Uncharacterized protein [C470_03611] [Halorubrum litoreum JCM 13561] Uncharacterized protein HALG_00029 [Halorubrum phage CGphi46] Uncharacterized protein [19] [Halovirus HCTV-2]

hypothetical protein

15254..15688 Reverse 224439646 - no matches

15868..16113 Forward 224439651 41% 50%

Uncharacterized protein [Hlac_2951] [Halorubrum lacusprofundi (strain ATCC 49239 / DSM 5036 / JCM 8891 / ACAM 34)] Uncharacterized protein [C489_06133 ] [Natrinema versiforme JCM 10478]

hypothetical protein