Table 3 The functionally ratified protein homologues of DMS/DMSP cycling-related enzymes
From: Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans
Protein | Source of strain | Gene ID# | e-value cutoff | Identity cutoff | Method | Ref |
|---|---|---|---|---|---|---|
DsyB | Thalassobaculum salexigens DSM 19539 | 2523405058 | 1E− 67 | -- | HMMsearch | [10] |
Amorphus coralli DSM 19760 | 2517908241 | |||||
Oceanicola batsensis HTCC2597 | 638883374 | |||||
Sagittula stellata E-37 | 640641694 | |||||
Sediminimonas qiaohouensis DSM 21189 | 2523943366 | |||||
Labrenzia aggregata LZB033 | AOR83342.1 | |||||
Labrenzia aggregate IAM12614 | WP_075282486.1 | |||||
MmtN | Roseovarius indicus B108 | WP_143100449.1 | 1E− 50 | -- | HMMsearch | [11] |
Thalassospira profundimaris WP0211 | 2530549224 | |||||
Novosphingobium sp. MBES04 | 2631597816 | |||||
Nocardiopsis chromatogenes YIM90109 | 2554031325 | |||||
Streptomyces mobaraensis NBRC13819 | 2538966579 | |||||
DddD | Marinomonas sp. MWYL1 | WP_012071702.1 | 1E− 30 | -- | HMMsearch | [72] |
Sinorhizobium fredii NGR234 | AAQ87407.1 | |||||
Burkholderia ambifaria AMMD | WP_011659284.1 | |||||
Halomonas sp. HTNK1 | ACV84065.1 | |||||
Pseudomonas sp. J465 | ACY01992.1 | |||||
Psychrobacter sp. J466 | ACY02894.1 | |||||
Oceanimonas doudoroffii | AEQ39135.1 | |||||
DddL | Sulfitobacter sp. EE-36 | ADK55772.1 | 1E− 30 | -- | HMMsearch | [72] |
Rhodobacter sphaeroides 2.4.1 | Q3J6L0.1 | |||||
Thioclava pacifica | WP_051692700.1 | |||||
Puniceibacterium antarcticum SM1211 | WP_099909581.1 | |||||
DddY | Alcaligenes faecalis M3A | WP_123051132.1 | 1E− 30 | -- | HMMsearch | [72] |
Shewanella chilikensis | PYE57415.1 | |||||
Acinetobacter bereziniae NIPH 3 | 5Y4K_A | |||||
DddQ | Ruegeria pomeroyi DSS-3 | Q5LT18.1 | 1E− 30 | -- | HMMsearch | [72] |
Ruegeria lacuscaerulensis ITI-1157 | SHI35160.1 | |||||
DddK | Pelagibacter ubique HTCC1062 | WP_011281678.1 | 1E− 30 | -- | HMMsearch | this study |
Pelagibacteraceae bacterium BACL20 MAG-120920-bin64 | KRP06000.1 | |||||
Alpha proteobacterium HIMB5 | AFS47241.1 | |||||
Candidatus Pelagibacter ubique | WP_006997514.1 | |||||
DddW | Ruegeria pomeroyi DSS-3 | WP_011046214.1 | 1E− 30 | -- | HMMsearch | [72] |
Roseobacter sp. MED193 | EAQ44306.1 | |||||
DddP | Roseovarius nubinhibens ISM | A3SK19.1 | 1E− 30 | -- | HMMsearch | [72] |
Ruegeria pomeroyi DSS-3 | AAV95561.1 | |||||
Phaeobacter inhibens DSM 17395 | AFO91571.1 | |||||
Ruegeria lacuscaerulensis ITI-1157 | SHJ09750.1 | |||||
Oceanimonas doudoroffii DSM 7028 | AEQ39091.1 | |||||
Oceanimonas doudoroffii DSM 7028 | AEQ39103.1 | |||||
Aspergillus oryzae RIB40 | BAE62778.1 | |||||
DmdA | Ruegeria pomeroyi DSS-3 | AAV95190.1 | 1E− 50 | -- | HMMsearch | [73] |
Pelagibacter ubique HTCC1062 | Q4FP21.1 | |||||
Dinoroseobacter shibae DFL 12 | WP_012178987.1 | |||||
Marine gammaproteobacterium HTCC2080 | WP_007233625.1 | |||||
Granulosicoccus antarcticus IMCC3135 | ASJ73090.1 | |||||
DMSOR | Rhodobacter sphaeroides f. sp. denitrificans | BAA07615.1 | 1E− 50 | -- | HMMsearch | this study |
Rhodobacter capsulatus | Q52675.2 | |||||
Tmm | Roseovarius sp. 217 | EAQ26624.1 | 1E− 80 | -- | HMMsearch | [20] |
Ruegeria pomeroyi DSS-3 | AAV94838.1 | |||||
Methylophaga sp. SK1 | JC7986 | |||||
Methylocella silvestris BL2 | ACK52489 | |||||
Pelagibacter ubique HTCC1002 | EAS85405.1 | |||||
Pelagibacter ubique HTCC7211 | EDZ59919.1 | |||||
DsoB | Acinetobacter guillouiae strain 20B | BAA23331.1 | 1E− 30 | ≥ 40 | Blastp | this study |
DdhA | Sagittula stellata E-37 | EBA07058.1 | 1E− 50 | -- | HMMsearch | this study |
Rhodovulum sulfidophilum strain SH1 | AAN46632.1 | |||||
DmoA | Hyphomicrobium sulfonivorans | E9JFX9.1 | 1E− 30 | ≥ 40 | Blastp | [23] |
MddA | Pseudomonas deceptionensis M1 | AJE75769.1 | 1E− 30 | -- | HMMsearch | [72] |
Cyanothece sp. ATCC 51142 | WP_009545670.1 | |||||
Mycobacterium tuberculosis H37Rv | NP_217755.1 | |||||
Pseudomonas sp. GM41 | WP_008148420.1 | |||||
Bradyrhizobium diazoefficiens USDA 110 (Blr1218) | WP_011084036.1 | |||||
Bradyrhizobium diazoefficiens USDA 110 (Blr5741) | WP_011088485.1 | |||||
MTO | Hyphomicrobium sp. VS | ATJ26742.1 | 1E− 20 | -- | HMMsearch | [74] |
Ruegeria pomeroyi DSS-3 | WP_011242048.1 | |||||
Hyphomicrobium denitrificans ATCC 51888 | ADJ22562.1 | |||||
Pseudovibrio ascidiaceicola DSM 16392 | WP_093522951.1 | |||||
Methylococcus capsulatus str. Bath | AAU90430.1 |