Nitrosopumilus maritimus genome reveals unique - de la Torre ...

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0.5 A. B. Thermoplasma volcanium GSS1 [rusticyanin; gi13542283] Acidithiobacillus ferrooxidans [rusticyanin; gi3282064] Thermobaculum terrenum ATCC BAA-798 [plastocyanin; gi227373287] Sphaerobacter thermophilus DSM 20745 [plastocyanin; gi229876615] Streptomyces sp. AA4 [hypothetical protein; gi256667890] Burkholderia cenocepacia PC184 [plastocyanin; gi254250279] 95 Catenulispora acidiphila DSM 44928 [blue (type 1) copper domain protein; gi256391720] Mycobacterium intracellulare ATCC 13950 [hypothetical protein; gi254819204] 83 Mycobacterium avium subsp. avium ATCC 25291 [copper-binding protein; gi254776845] 99 Mycobacterium avium 104 [copper-binding protein; gi118462975] Nmar0747 96 Nmar0361 Candidatus Koribacter versatillis [plastocyanin-like protein; gi94968815] Nmar0902 Chromobacterium violaceum ATCC 12472 [hypothetical protein; gi34498952] Methylocella silvestris BL2 [blue (type 1) copper domain protein; gi217976580] Methylobacterium nodulans ORS [blue (type 1) copper domain protein; gi220920817] Methylocella silvestris BL2 [blue (type 1) copper domain protein; gi217976580] 61 Nitrobacter hamburgensis X14 [blue (type 1) copper domain protein; gi92118183] Bradyrhizobium japonicum USDA 110 [putative Amicyanin precursor; gi27378126] Paracoccus denitrificans PD1222 [amicyanin; gi119387457] Nmar0190 Methanosarcina mazei Go1 [hypothetical protein; gi21226177] 64 Methanosarcina acetivorans C2A [hypothetical protein; gi20090537] C. symbiosum A [copper-binding protein; gi118575216] 99 Nmar0167 99 Nmar0621 Methanosarcina mazei Go1 [copper-binding protein; gi21228445] Methanosarcina acetivorans C2A [plastocyanin/azurin family copper-binding protein; gi20090218] 62 Methanosarcina mazei Go1 [copper-binding protein; gi21228446] 100 Methanosarcina acetivorans C2A [plastocyanin/azurin family copper-binding protein; gi20090219] Jannaschia sp. CCS1 [blue (type 1) copper domain protein; gi89056161] Nmar0718 Thermobaculum terrenum ATCC BAA-798 [plastocyanin; gi227373254] Deinococcus deserti VCD115 [copper-binding protein; gi226356528] Synechococcus sp. WH 8102 [plastocyanin; gi33866031] 91 Prochlorococcus marinus MIT 9312 [plastocyanin; gi78778966] 88 Anabaena variabilisATCC 29413 [plastocyanin; gi75908957] 79 Gloeobacter violaceus PCC 7421 [plastocyanin; gi35212909] Methanococcus maripaludis C7 [copper-binding protein; gi150402166] 82 Methanococcus maripaludis S2 [copper-binding protein; gi45358560] Nmar1913 82 Nmar1789 Nmar0300 Nmar0762 C. symbiosum A [copper-binding protein; gi118576966] 100 C. symbiosum A [copper-binding protein; gi118576965] Nmar0516 Nmar1087 C. symbiosum A [hypothetical protein; gi118575848] 98 C. symbiosum A [hypothetical protein; gi118575831] C. symbiosum A [copper-binding protein; gi118575244] 79 Nmar0121 uncultured marine Crenarchaeote [putative copper-binding protein; gi167045254] 100 uncultured marine Crenarchaeote [putative copper-binding protein; gi167044521] 100 uncultured marine Crenarchaeote [putative copper-binding protein; gi167042919] C. symbiosum A [copper-binding protein; gi118575724] 100 Nmar0273 Nmar0732 Nmar0121 Nmar0324 79 Nmar0167 80 C. symbiosum A [copper-binding protein; gi118576967] Nmar0190 Nmar0273 Nmar0300 Nmar0324 Nmar0361 Nmar0516 Nmar0621 Nmar0718 Nmar0732 Nmar0747 Nmar0762 Nmar1087 Nmar1789 Nmar1913 100 aa 0.1 Bacillus subtilis subsp. subtilis str. 168 [BdbD thiol-disulfide oxidoreductase; gi 16080401] Bacillus amyloliquefaciens FZB42 [BdbD; gi 154687467] Paenibacillus larvae subsp. larvae BRL-230010 [disulfide dehydrogenase D; gi 167461952] Deinococcus geothermalis DSM 11300 [DsbA oxidoreductase; gi 94984799] Thermobaculum terrenum ATCC BAA-798 [protein-disulfide isomerase; gi 227374421] 100 C. 100 87 82 75 Gemmatimonas aurantiaca T-27 [putative oxidoreductase; gi 226228008] Sphaerobacter thermophilus DSM 20745 [protein-disulfide isomerase; gi 229876989] Thermomicrobium roseum DSM 5159 [DsbA oxidoreductase; gi 221635547] Thermus aquaticus Y51MC23 [DsbA oxidoreductase; gi 218295130] Thermobifida fusca YX [protein-disulfide isomerase; gi 72161925] Mycobacterium kansasii ATCC 12478 [DsbA oxidoreductase; gi 240169146] Rubrobacter xylanophilus DSM 9941 [DsbA oxidoreductase; gi 108804655] Streptomyces coelicolor A3(2) [hypothetical protein SCO5993; gi 21224330] 100 Streptomyces ghanaensis ATCC 14672 [hypothetical protein SghaA1_08748; gi 239928300] Symbiobacterium thermophilum IAM 14863 [hypothetical protein STH2058; gi 51893196] Roseiflexus castenholzii DSM 13941 [DsbA oxidoreductase; gi 156741642] 100 99 100 Chloroflexus aggregans DSM 9485 [DsbA oxidoreductase; gi 219849651] Chloroflexus aggregans DSM 9485 [DsbA oxidoreductase; gi 219847445] Marinobacter algicola DG893 [DsbA oxidoreductase; gi 149377658] Vibrio harveyi HY01 [DsbA oxidoreductase; gi 153832115] Vibrio parahaemolyticus RIMD 2210633 [hypothetical protein VPA0994; gi 28900849] Moritella sp. PE36 [putative membrane protein; gi 149908466] 99 Shewanella benthica KT99 [hypothetical protein KT99_10483; gi 163751466] Roseiflexus castenholzii DSM 13941 [protein-disulfide isomerase-like protein; gi 156741356] 75 Roseiflexus castenholzii DSM 13941 [DsbA oxidoreductase; gi 156743646] Chloroflexus aurantiacus J-10-fl [DsbA oxidoreductase; gi 163848707] Herpetosiphon aurantiacus ATCC 23779 [DsbA oxidoreductase; gi 159896786] 72 100 Chloroflexus aurantiacus J-10-fl [DsbA oxidoreductase; gi 163845898] Chloroflexus aggregans DSM 9485 [DsbA oxidoreductase; gi 219850456] Stigmatella aurantiaca DW4/3-1 [conserved hypothetical protein; gi 115374845] Solibacter usitatus Ellin6076 [DsbA oxidoreductase; gi 116625220] Solibacter usitatus Ellin6076 [DsbA oxidoreductase; gi 116624599] 82 Syntrophobacter fumaroxidans MPOB [DsbA oxidoreductase; gi 116751066] Anaeromyxobacter dehalogenans 2CP-1 [DsbA oxidoreductase; gi 220919173] 100 Myxococcus xanthus DK 1622 [putative lipoprotein; gi 108762810] Stigmatella aurantiaca DW4/3-1 [disulfide interchange protein; gi 115379912] Archaeoglobus fulgidus DSM 4304 [hypothetical protein AF1354; gi 11498950] Cenarchaeum symbiosum A [protein-disulfide isomerase; gi 118575694] Nmar0752 93 91 Nmar0179 Nmar0218 73 79 Nmar0740 Nmar0175 Natrialba magadii ATCC 43099 ]DsbA oxidoreductase; gi 224823141] Nmar1863 90 Cenarchaeum symbiosum A [protein-disulfide isomerase; gi 118576454] Nmar1805 67 100 Cenarchaeum symbiosum A [protein-disulfide isomerase; gi 118576169] Nmar1606 72 63 88 Nmar0164 Nmar0169 Nmar1590 Cenarchaeum symbiosum A [protein-disulfide isomerase; gi 118575427] Fig. S1. Phylogeny of plastocyanin-like protein sequences. Sequences with significant matches to COG3794 (PetE: Plastocyanin [Energy production and conversion]) were used to query the non-redundant protein sequence database from NCBI. Sequences from the top 20–30 non-N. maritimus hits were retrieved and their match to the above conserved domain model verified. Sequences from experimentally characterized proteins were obtained from the available literature and included, aligned with ClustalW and then curated manually. Distance-based phylogenies were inferred in Phylip using the Neighbor- Joining algorithm and 100 bootstrap replicates. Bootstrap support values >60% are displayed. Nodes with
Fig. S2. Archaeal ammonia monooxygenase AmoB sequence mapped onto the crystal structure of the particulate methane monooxygenase (PDB accession code 1YEW). The pmoA subunit is shown in dark gray, the pmoC subunit in light gray, and the pmoB subunit in red and pink. The red part represents the region of pmoB conserved in the predicted N. maritimus AmoB. The transmembrane helix and C-terminal cupredoxin domain shown in pink are missing in the predicted N. maritimus AmoB. Cyan spheres represent copper ions. The grey sphere represents a zinc ion. Walker et al. www.pnas.org/cgi/content/short/0913533107 3of5
Page 1 and 2: Nitrosopumilus maritimus genome rev
Page 3 and 4: ammonia oxidation. There are two hy
Page 5 and 6: Fig. 3. Comparison of N. maritimus
Page 7: Supporting Information Walker et al
Page 11 and 12: A. 0.1 B. 100 90 52 Other Supportin
Page 13 and 14: Supplemental Table 2: Predicted coo
Page 15 and 16: Supplemental Table 3: Gene predicti
Page 17 and 18: Nmar_tR26 1,630,610 1,630,537 ProGG
Page 19 and 20: Supplemental Table 4: Gene predicti
Page 21 and 22: Nmar_0258 CENSYa_1705 82 227,624 22
Page 29 and 30: Nmar_1303 CENSYa_0131 86 1,193,261
Page 35 and 36: Molybdopterin-guanine dinucleotide
Page 37 and 38: Nmar0935 DeepAntEC39 f 815,847 816,
Page 39 and 40: Nmar0101 EQ085329 r 91,543 93,711 A
Page 41 and 42: Nmar0436 EQ085799 f 386,930 387,319
Page 43 and 44: Nmar0982 EP710054 r 859,116 859,526
Page 45 and 46: Nmar1297 EQ086682 f 1,187,165 1,188

Nitrosopumilus maritimus genome reveals unique - de la Torre ...

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