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

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