PaperBLAST
PaperBLAST Hits for tr|G3XD87|G3XD87_PSEAE Respiratory nitrate reductase beta chain OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=narH PE=4 SV=1 (513 a.a., MKIRSQVGMV...)
Show query sequence
>tr|G3XD87|G3XD87_PSEAE Respiratory nitrate reductase beta chain OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=narH PE=4 SV=1
MKIRSQVGMVLNLDKCIGCHTCSITCKNVWTSREGMEYAWFNNVETKPGIGYPKEWENQE
KWKGGWVRAADGSIRPRIGGKFRVLANIFANPDLPEIDDYYEPFDFDYQHLHTAPKAEHQ
PVARPRSLVSGQRMEKIEWGPNWEEILGTEFAKRRKDKNFDQVQADIYGEYENTFMMYLP
RLCEHCLNPACVASCPSGAIYKREEDGIVLIDQDKCRGWRMCISGCPYKKIYFNWKSGKS
EKCIFCYPRIEAGQPTVCSETCVGRIRYLGVLLYDADRIHEVASCENERELYEKQLEIFL
DPFDPAVIAQARKDGVADSVIEAAQKSPVYKLAMDWKLALPLHPEYRTLPMVWYVPPLSP
IQNAAAEGHIGSDGVIPDVESLRIPVQYLANLLTAGDTAPVLLALKRLLAMRAYKRAEHV
EGRQDLEVLAKVGLSVEQVEEMYRYLAIANYEDRFVIPSAHREEALSDAFAERSGCGFSF
GNGCSGGSNSAVNLFGGKPTNRRDVIQVVQIQE
Running BLASTp...
Found 251 similar proteins in the literature:
PA3874 respiratory nitrate reductase beta chain from Pseudomonas aeruginosa PAO1
G3XD87 Respiratory nitrate reductase beta chain from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
NP_252563 respiratory nitrate reductase subunit beta from Pseudomonas aeruginosa PAO1
PA14_13800 respiratory nitrate reductase beta subuni from Pseudomonas aeruginosa UCBPP-PA14
100% identity, 100% coverage
- Sub-lethal concentration of a colloidal nanosilver formulation (Silversol®) triggers dysregulation of iron homeostasis and nitrogen metabolism in multidrug resistant Pseudomonas aeruginosa
Gajera, BMC microbiology 2023 - “...protein 2.6 0.05 8 24 PA3407 hasAp heme acquisition protein HasAp 2.59 0.05 0 25 PA3874 narH respiratory nitrate reductase beta chain 2.58 0.05 7 26 PA1942 NA hypothetical protein 2.57 0.05 2 Genes are arranged in decreasing order of Fold Change. Databases consulted for gene...”
- The Small RNA ErsA Impacts the Anaerobic Metabolism of Pseudomonas aeruginosa Through Post-Transcriptional Modulation of the Master Regulator Anr
Ferrara, Frontiers in microbiology 2021 - “...(and U in response to nitrate) Alvarez-Ortega and Harwood, 2007 ; Platt et al., 2008 PA3874 narH , respiratory nitrate reductase beta chain U 1.65 U (and U in response to nitrate) Alvarez-Ortega and Harwood, 2007 ; Platt et al., 2008 Transport PA3465 major facilitator superfamily...”
- Traditional Chinese Medicine Tanreqing Inhibits Quorum Sensing Systems in Pseudomonas aeruginosa
Yang, Frontiers in microbiology 2020 - “...+ Respiratory nitrate reductase gamma chain PA3873 narJ 1.8 + Respiratory nitrate reductase delta chain PA3874 narH 1.8 + Respiratory nitrate reductase beta chain PA3875 narG 2.2 + Respiratory nitrate reductase alpha chain PA2321 gntK 3.1 + GntK PA2516 xylZ 4.1 1.7 Toluate 1,2-dioxygenase electron transfer...”
- The Small RNA ErsA of Pseudomonas aeruginosa Contributes to Biofilm Development and Motility through Post-transcriptional Modulation of AmrZ
Falcone, Frontiers in microbiology 2018 - “...reductase gamma chain 3,080462 8,4588527 PA3873 narJ , respiratory nitrate reductase delta chain 2,190598 4,5649467 PA3874 narH , respiratory nitrate reductase beta chain 1,653484 3,1459244 Log 2 (FC) = log 2 of fold change calculated as ratio between gene expression of PAO1 wild-type vs. PAO1 ersA....”
- Protein complex formation during denitrification by Pseudomonas aeruginosa
Borrero-de, Microbial biotechnology 2017 - “...enzymes, enzymes involved in the tricarboxylic acid ( TCA )cycle. The nitrate reductase NarGH (PA3875; PA3874) subunits firmly interacted with NorCB, whereas membranespanning NarI (PA3872) was not found to be involved in the interaction. The nitrate/nitrite antiporter NarK2 (PA3876), responsible for nitrate import into the cytoplasm,...”
- Nitrate Sensing and Metabolism Inhibit Biofilm Formation in the Opportunistic Pathogen Burkholderia pseudomallei by Reducing the Intracellular Concentration of c-di-GMP
Mangalea, Frontiers in microbiology 2017 - “...subunit narI-1 Bp1026b_I1015 PA3872 64.50 Delta subunit narJ-1 Bp1026b_I1016 PA3873 72.54 Beta subunit narH-1 Bp1026b_I1017 PA3874 75.88 Alpha subunit narG-1 Bp1026b_I1018 PA3875 75.20 Nitrate/nitrite transporter narK-2 d Bp1026b_I1019 PA3876 73.90 Nitrate/nitrite transporter narK-1 d Bp1026b_I1020 PA3877 69.76 Nitric oxide reductase norB Bp1026b_I0974 PA0524 68.37 Nitrous oxide...”
- “...subunit narI-2 Bp1026b_II1222 PA3872 65.45 Delta subunit narJ-2 Bp1026b_II1223 PA3873 65.60 Beta subunit narH-2 Bp1026b_II1224 PA3874 78.55 Alpha subunit narG-2 Bp1026b_II1225 PA3875 74.14 Assimilatory nitrate reductase (2) Large subunit nasA-2 Bp1026b_II1316 PA1779 66.77 Assimilatory nitrite reductase (NAD(P)H) (2) Small subunit nirD-2 Bp1026b_II1317 PA1780 64.53 Large subunit...”
- The Atypical Response Regulator AtvR Is a New Player in Pseudomonas aeruginosa Response to Hypoxia and Virulence
Kaihami, Infection and immunity 2017 - “...PA3876 narK2 5.44 PA14_13780 PA3875 narG 10.23 PA14_13800 PA3874 narH 10.67 PA14_13810 PA3873 narJ 9.09 PA14_13830 PA3872 narI 9.61 PA14_13840 PA3871 PA14_13850...”
- GcsR, a TyrR-Like Enhancer-Binding Protein, Regulates Expression of the Glycine Cleavage System in Pseudomonas aeruginosa PAO1
Sarwar, mSphere 2016 - “...Glycine metabolism PA3516 2.53 Purine metabolism PA3628 2.3 Formaldehyde metabolism PA3629 adhC 2.46 Formaldehyde metabolism PA3874 narH 3 Nitrogen metabolism PA3875 narG 2.8 Nitrogen metabolism PA3876 narK2 2.85 Nitrogen metabolism PA3877 narK1 2.53 Nitrogen metabolism PA4153 2.58 Butanediol catabolic process PA4280.3 7.5 tRNA-Ala PA4704.1 prrF1 2.2...”
- More
- Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - Fosfomycin and tobramycin in combination downregulate nitrate reductase genes narG and narH, resulting in increased activity against Pseudomonas aeruginosa under anaerobic conditions.
McCaughey, Antimicrobial agents and chemotherapy 2013 - GeneRIF: Down-regulation of narG and narH expression increases the susceptibility of Pseudomonas aeruginosa towards antibiotics.
- PtsN in Pseudomonas aeruginosa Is Phosphorylated by Redundant Upstream Proteins and Impacts Virulence-Related Genes
Underhill, Journal of bacteriology 2023 (secret) - A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration
Kampers, BMC microbiology 2021 - “...2012 PF00384 PDC, T, Steen et al., 2012 PF01568 PDC, T, Steen et al., 2012 PA14_13800 PF13247 Nitrate reductase NarH -subunit, Energy metabolism PDC, T, Steen et al., 2012 PF14711 PDC, T, Steen et al., 2012 PA14_13810 PF02613 Nitrate reductase NarJ -chain, Energy metabolism PDC, T,...”
- The Atypical Response Regulator AtvR Is a New Player in Pseudomonas aeruginosa Response to Hypoxia and Virulence
Kaihami, Infection and immunity 2017 - “...PA14_13770 PA3876 narK2 5.44 PA14_13780 PA3875 narG 10.23 PA14_13800 PA3874 narH 10.67 PA14_13810 PA3873 narJ 9.09 PA14_13830 PA3872 narI 9.61 PA14_13840 PA3871...”
- BqsR/BqsS constitute a two-component system that senses extracellular Fe(II) in Pseudomonas aeruginosa
Kreamer, Journal of bacteriology 2012 - “...protein Hypothetical protein pdxH narH azu PA14_50800 PA14_13800 PA14_65000 PA1049 PA3874 PA4922 1.6 1.8 1.9 5.61E3 8.71E3 2.39E3 Pyridoxamine 5=-phosphate...”
narH / A4VHZ3 respiratory nitrate reductase α subunit from Stutzerimonas stutzeri (strain A1501) (see paper)
86% identity, 100% coverage
Q8Z7F8 Nitrate reductase subunit beta from Salmonella typhi
SPAB_01470 hypothetical protein from Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7
77% identity, 98% coverage
SARI_01191 hypothetical protein from Salmonella enterica subsp. arizonae serovar 62:z4,z23:--
77% identity, 100% coverage
ESA_01521 hypothetical protein from Enterobacter sakazakii ATCC BAA-894
78% identity, 98% coverage
FNX95_06390 nitrate reductase subunit beta from Klebsiella variicola
76% identity, 100% coverage
- Isolation of Anaerobic Bromate-Reducing Bacteria Using Different Carbon Sources and Transcriptomic Insights From Klebsiella variicola Glu3
Wang, Frontiers in microbiology 2022 - “...Miralles-Robledillo et al., 2019 ). Homologues of both the respiratory nitrate reductase encoding genes (FNX95_06385, FNX95_06390, FNX95_06395, and FNX95_06400) and the selenate reductase encoding gene (FNX95_09885) were present on the genome of strain K. variicola Glu3. In addition, the dimethylsulfoxide reductase encoding genes (FNX95_13385 and FNX95_13390),...”
- “...FNX95_25960 1.05 1.45 dsbA thiol:disulfide interchange protein FNX95_06385 4.85 2.58 narG nitrate reductase subunit alpha FNX95_06390 3.68 2.27 narH nitrate reductase subunit beta FNX95_06395 3.91 1.97 narJ nitrate reductase molybdenum cofactor assembly chaperone FNX95_06400 3.80 1.91 narI respiratory nitrate reductase subunit gamma FNX95_07655 3.90 2.85 sodB...”
SEN1276 respiratory nitrate reductase 1 beta chain from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
77% identity, 98% coverage
BHE81_08715 nitrate reductase subunit beta from Klebsiella sp. AqSCr
76% identity, 100% coverage
- Transcriptome Analysis Reveals Cr(VI) Adaptation Mechanisms in Klebsiella sp. Strain AqSCr
Lara, Frontiers in microbiology 2021 - “...(BHE81_08735 and BHE81_08740), a nitrate/nitrite transporter MFC type (BHE81_08730), the nitrate reductase complex (BHE81_08705, BHE81_08710, BHE81_08715, and BHE81_08720), the formate dehydrogenase N complex (nitrate-dependent) (BHE81_06840, BHE81_06845, and BHE81_06850), as well as several genes involved in menaquinone biosynthesis were downregulated ( Supplementary Table 6 ), suggesting Cr(VI)-induced...”
SMDB11_RS10590 nitrate reductase subunit beta from Serratia marcescens subsp. marcescens Db11
77% identity, 98% coverage
Smlt2773 putative respiratory nitrate reductase subunit from Stenotrophomonas maltophilia K279a
77% identity, 97% coverage
LMH90_000545 nitrate reductase subunit beta from Enterobacter hormaechei
76% identity, 98% coverage
AL518_10520 nitrate reductase subunit beta from Hafnia paralvei
75% identity, 98% coverage
- Isolation and identification of chlorate-reducing Hafnia sp. from milk
McCarthy, Microbiology (Reading, England) 2023 - “...the KEGG webpage ( https://www.genome.jp/pathway/hpar00910 ) and included genes encoding: nitrate reductase subunits narZHI (AL518_10515, AL518_10520, AL518_10530), nitrate reductase napAB (AL518_10920, AL518_10935) and nitrite reductase nirDB (AL518_06025, AL518_06030). Following this, strain level comparison was performed using Prokka [ 46 ] to annotate and Roary [ 47...”
WP_059179798 nitrate reductase subunit beta from Lelliottia sp. T2.26D-8
76% identity, 98% coverage
JHW33_RS04770 nitrate reductase subunit beta from Rahnella aceris
76% identity, 98% coverage
WP_202666064 nitrate reductase subunit beta from Lelliottia amnigena
76% identity, 98% coverage
WP_216981296 nitrate reductase subunit beta from Lelliottia amnigena
76% identity, 98% coverage
CH1034_220300 nitrate reductase subunit beta from Klebsiella pneumoniae
75% identity, 99% coverage
SPAB_01714 hypothetical protein from Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7
73% identity, 100% coverage
Z2002 nitrate reductase 1, beta subunit from Escherichia coli O157:H7 EDL933
75% identity, 100% coverage
ChlZ / b1467 nitrate reductase Z subunit β (EC 1.7.5.1) from Escherichia coli K-12 substr. MG1655 (see 6 papers)
narY / P19318 nitrate reductase Z subunit β (EC 1.7.5.1) from Escherichia coli (strain K12) (see 2 papers)
TC 5.A.3.1.2 / P19318 Respiratory nitrate reductase 2 beta chain (NarY), component of Anaerobic, respiratory, membrane-bound nitrate reductase, NarZYV from Escherichia coli (see 4 papers)
NP_415984 nitrate reductase Z subunit beta from Escherichia coli str. K-12 substr. MG1655
b1467 nitrate reductase 2 (NRZ), beta subunit from Escherichia coli str. K-12 substr. MG1655
74% identity, 100% coverage
- substrates: Electrons
- A Multiplex Enzymatic Machinery for Cellular Protein S-nitrosylation
Seth, Molecular cell 2018 - “...1.8 SerS Serine--tRNA ligase P0A8L1 2.7 1.7 1.6 NarY Respiratory nitrate reductase 2 beta chain P19318 3.9 2.5 1.6 PtsG PTS system glucose-specific EIICB component P69786 2.7 1.7 1.6 NapA Periplasmic nitrate reductase P33937 5.0 3.2 1.6 PyrG CTP synthase P0A7E5 3.3 2.1 1.6 Y GuaA...”
- Nitrate reductases of Escherichia coli: sequence of the second nitrate reductase and comparison with that encoded by the narGHJI operon.
Blasco, Molecular & general genetics : MGG 1990 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on complete protein
- Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding
Bonocora, PLoS genetics 2015 - “...- b1448 mnaT 2132 10.795 IS19 1535850 2 C TGGC ACTACCG TTGC A 1535858 - b1467 narY - b1466 narW 517 10.363 IS20 1615388 6 T TGG TGTGGCTT TTGC A 1615385 + b1528 ydeA + b1530 marR 1756 11.186 IS21 1662480 2 TA GG AATGGCTA TTGC...”
- Global transcriptomic analysis of an engineered Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system during shikimic acid production in rich culture medium
Cortés-Tolalpa, Microbial cell factories 2014 - “...phosphate-L-Ara4FN transferase Lipid metabolism 33.1058 yhiD b3508 Predicted Mg(2+) transport ATPase Lipid metabolism 52.2858 narY b1467 Nitrate reductase Z, subunit Other metabolic process 18.7104 narZ b1468 Nitrate reductase Z, subunit Other metabolic process 13.4094 yciE b1257 Conserved protein Other metabolic process 18.9020 ydiS b1699 Putative flavoprotein...”
- The sulfur carrier protein TusA has a pleiotropic role in Escherichia coli that also affects molybdenum cofactor biosynthesis
Dahl, The Journal of biological chemistry 2013 - “...b0895 b1222 b1223 b1224 b1225 b1226 b1227 b1465 b1466 b1467 b1468 b1469 b1476 b1587 b1673 b2203 b2204 b2205 b2206 b2207 b2208 b2469 b2881 b3892 b3893 b3894...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Gene cloning and biochemical characterization of a NAD(P)+ -dependent aldehyde dehydrogenase from Bacillus licheniformis
Lo, Molecular biotechnology 2010 (PubMed)- “...aldehyde dehydrogenase (ALDH) gene, ybcD (gene locus b1467), was identified in the genome sequence of Bacillus licheniformis ATCC 14580. B. licheniformis...”
- “...[33] allowed the identification of an open reading frame (b1467) coding for an ALDH. The derived amino acid sequence predicted a polypeptide of 488 residues...”
- Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
Lee, Applied and environmental microbiology 2009 - “...agp potB potA narY narZ b0384 b0405 b0871 b1002 b1125 b1126 b1467 b1468 7.5 4.3 6.1 6.1 4.0 4.6 6.1 8.0 2.5 2.6 1.6 4.9 2.5 2.5 3.2 4.3 Phosphate...”
- Conserved and variable functions of the sigmaE stress response in related genomes
Rhodius, PLoS biology 2006 - “...(b1466) just beyond our distance cut-off that was very close to the beginning of narY (b1467). We confirmed this promoter in vitro to give 44 promoters. (4) Two genetic screens [ 28 , 29 ] identified additional putative E - dependent promoters; we validated the five...”
- Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity
Weber, Journal of bacteriology 2005 - “...gene b1478 b1927 b3012 b2097 b2661 b1619 b2720 b0186 b1469 b1467 b0871 b4051 b2464 b1519 b2465 b3449 b0485 ybaY ycaC yfcF ygjG yhfW yjcS yjgB yncG b0453 b0897...”
- More
Z2245 cryptic nitrate reductase 2, beta subunit from Escherichia coli O157:H7 EDL933
74% identity, 100% coverage
ECO26_1741 nitrate reductase 1, beta subunit from Escherichia coli O26:H11 str. 11368
75% identity, 100% coverage
ChlC / b1225 nitrate reductase A subunit β (EC 1.7.5.1) from Escherichia coli K-12 substr. MG1655 (see 12 papers)
narH / P11349 nitrate reductase A subunit β (EC 1.7.5.1) from Escherichia coli (strain K12) (see 10 papers)
NARH_ECOLI / P11349 Respiratory nitrate reductase 1 beta chain; Nitrate reductase A subunit beta; Quinol-nitrate oxidoreductase subunit beta; EC 1.7.5.1 from Escherichia coli (strain K12) (see 2 papers)
P11349 nitrate reductase (quinone) (EC 1.7.5.1) from Escherichia coli (see 2 papers)
TC 5.A.3.1.1 / P11349 NarH aka B1225, component of Anaerobic, respiratory, membrane-bound nitrate reductase, NarGHI. Two protons are consumed in the cytoplasm while two protons are released in the periplasm, contributing to the pmf from Escherichia coli (see 13 papers)
narH / RF|NP_836920.1 respiratory nitrate reductase 1 beta chain; EC 1.7.99.4 from Escherichia coli K12 (see 13 papers)
NP_415743 nitrate reductase A subunit beta from Escherichia coli str. K-12 substr. MG1655
b1225 nitrate reductase 1, beta (Fe-S) subunit from Escherichia coli str. K-12 substr. MG1655
EC042_RS06745 nitrate reductase subunit beta from Escherichia coli 042
75% identity, 100% coverage
- function: The nitrate reductase enzyme complex allows E.coli to use nitrate as an electron acceptor during anaerobic growth. The beta chain is an electron transfer unit containing four cysteine clusters involved in the formation of iron-sulfur centers. Electrons are transferred from the gamma chain to the molybdenum cofactor of the alpha subunit
catalytic activity: nitrate + a quinol = a quinone + nitrite + H2O (RHEA:56144)
cofactor: [4Fe-4S] cluster (Binds 3 [4Fe-4S] clusters per subunit.)
cofactor: [3Fe-4S] cluster (Binds 1 [3Fe-4S] cluster per subunit.)
subunit: Dimer of heterotrimers each composed of an alpha, a beta and a gamma chain. Alpha and beta are catalytic chains; gamma chains are involved in binding the enzyme complex to the cytoplasmic membrane. - substrates: Electrons
- Biodistribution of 89Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
Li, Poultry science 2023 - “...transport and metabolism Cell membrane 314 P09152 NARG Energy production and conversion Cell membrane 315 P11349 NARH Energy production and conversion Cell membrane Cell inner membrane 316 P0ABA0 ATPF Energy production and conversion Cell inner membrane 317 P0ADZ7 YAJC Intracellular trafficking, secretion, and vesicular transport Cell...”
- Transcriptomic analysis of multi-drug resistant Escherichia coli K-12 strain in response to Lavandula angustifolia essential oil
Lai, 3 Biotech 2020 - “...Down-regulation Up-regulation 13 14 15 16 P38489 P19926 P11349 P11350 nfsB agp narH narI 2 1 1 1 Up-regulation Down-regulation Down-regulation Down-regulation...”
- Combinatorial modulation of initial codons for improved zeaxanthin synthetic pathway efficiency in Escherichia coli
Wu, MicrobiologyOpen 2019 - “...Fructosebisphosphate aldolase class 2 OS= Escherichia coli 33.73338241 24.5125 7 359 39.123 5.86 1.581 26.53024399 P11349 Respiratory nitrate reductase 1 beta chain OS= Escherichia coli 29.23611516 9.375 4 512 58.029 6.77 0.311 20.04963112 sp 007 CrtY 86.47902161 45.0777 16 386 43.604 8 3.962 63.83823073 P0A794 Pyridoxine...”
- “...Fructosebisphosphate aldolase class 2 OS= Escherichia coli 97.09414663 29.2479 11 359 39.123 5.86 3.437 53.46555638 P11349 Respiratory nitrate reductase 1 beta chain OS= Escherichia coli 86.5361797 24.6094 16 512 58.029 6.77 1.581 63.89301682 sp 007 CrtY 72.35807128 40.1237 12 386 43.604 8 3.276 51.25720981 P0A794 Pyridoxine...”
- A Multiplex Enzymatic Machinery for Cellular Protein S-nitrosylation
Seth, Molecular cell 2018 - “...2.3 2.0 Eno Enolase P0A6P9 2.1 1.2 1.8 NarH Respiratory nitrate reductase 1 beta chain P11349 7.1 3.9 1.8 Y NarZ Respiratory nitrate reductase 2 alpha chain P19319 4.4 2.5 1.8 SerS Serine--tRNA ligase P0A8L1 2.7 1.7 1.6 NarY Respiratory nitrate reductase 2 beta chain P19318...”
- Exploration of Nitrate Reductase Metabolic Pathway in Corynebacterium pseudotuberculosis
Almeida, International journal of genomics 2017 - “...531 79 89 S5Y1U5 Mycobacterium tuberculosis 538 64 75 A0A049E025 Escherichia coli 512 54 72 P11349 Nitrate reductase gamma subunit (NarI)259aa Corynebacterium diphtheriae 259 96 98 H2HVN2 Corynebacterium glutamicum 259 75 89 S5YHX1 Mycobacterium tuberculosis 241 48 68 Q7D8Q6 Escherichia coli 225 28 51 P11350 Nitrate...”
- ETMB-RBF: discrimination of metal-binding sites in electron transporters based on RBF networks with PSSM profiles and significant amino acid pairs
Ou, PloS one 2013 - “...Q56223 783 NADH-quinone oxidoreductase subunit 3 Unknown Thermus thermophilus electron carrier activity;NADH dehydrogenase (ubiquinone) activity; P11349 512 Respiratory nitrate reductase 1 beta chain Unknown Escherichia coli electron carrier activity;nitrate reductase activity; P07173 356 Cytochrome c558/c559 Unknown Rhodopseudomonas viridis electron carrier activity; P13272 274 Cytochrome b-c1 complex...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...EIICBA component 5.78/68,346.89 NagZ NarH P75949 P11349 Beta-hexosaminidase Respiratory nitrate reductase 1 beta chain 5.86/37,594.73 6.36/58,066.41 NarW P19317...”
- Protein crystallography reveals a role for the FS0 cluster of Escherichia coli nitrate reductase A (NarGHI) in enzyme maturation.
Rothery, The Journal of biological chemistry 2010 - GeneRIF: analysis of the role of the FS0 cluster of Escherichia coli nitrate reductase A (NarGHI) in enzyme maturation
- Structural and biochemical characterization of a quinol binding site of Escherichia coli nitrate reductase A.
Bertero, The Journal of biological chemistry 2005 (PubMed)- GeneRIF: molecular characterization of a quinol binding and oxidation site (Q-site) in NarGHI
- Roles of the narJ and narI gene products in the expression of nitrate reductase in Escherichia coli.
Sodergren, The Journal of biological chemistry 1988 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on complete protein
- Preliminary functional analysis of the subgingival microbiota of cats with periodontitis and feline chronic gingivostomatitis
Rodrigues, Scientific reports 2021 - “...v2.1.3. One gene was significantly different among groups: narH, nitrate reductase 1, beta subunit (Gene: b1225 narH; nitrate reductase A subunit beta [KO: K00371] [EC:1.7.5.1 1.7.99.-]) was found with a corrected P -value=0.00225 (Fig. 5 ). Interestingly, this function is related to respiration and was present...”
- The sulfur carrier protein TusA has a pleiotropic role in Escherichia coli that also affects molybdenum cofactor biosynthesis
Dahl, The Journal of biological chemistry 2013 - “...protein Molybdoenzymes b0285 b0894 b0895 b1222 b1223 b1224 b1225 b1226 b1227 b1465 b1466 b1467 b1468 b1469 b1476 b1587 b1673 b2203 b2204 b2205 b2206 b2207...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction
Oberto, PloS one 2009 - “...4.86 4.82 3.78 1 1.32 1.99 2.3 FA, FAec nitrate reductase 1, alpha subunit narH b1225 narGHJI 1 0.06 1.64 0.13 1 2.85 3.71 2.09 1 1.13 0.77 1.75 FA, FAec nitrate reductase 1, beta subunit narJ b1226 narGHJI 1 0.06 1.31 0.13 1 1.89 1.68...”
- Detecting clusters of mutations
Zhou, PloS one 2008 - “...is shown in yellow. The second example is the subunit of nitrate reductase A (NarH, b1225) in E. coli . The mutation cluster runs from position 133 to position 164, and is completely conserved within both E. coli and S. enterica ( Fig. 7 ). Among...”
- Global gene expression profiling of the asymptomatic bacteriuria Escherichia coli strain 83972 in the human urinary tract
Roos, Infection and immunity 2006 - “...b1796 b4209 b1223 ECs5443 b1797 Z2001 b1541 Z0893 b1227 b1225 b4013 b2941 b2552 c4141 b1475 b0873 b3240 b3556 b2732 b3437 b3242 b0872 c3046 c3973 c1382 b1445...”
- Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid
Ren, Applied and environmental microbiology 2005 - “...0.0079 5.4 0.0061 2.0 0.1754 1.5 0.0257 1.4 0.0428 narH b1225 1.6 0.0022 1.4 0.0281 pheM b1715 1.6 0.0106 pheP b0576 1.5 0.0210 1.1 0.4985 rimL b1427 1.5 0.0220...”
- Overexpression of the third H-NS paralogue H-NS2 compensates fitness loss in hns mutants of the enteroaggregative Escherichia coli strain 042
Prieto, Scientific reports 2020 - “...(A) EC042_RS06740 (nitrate reductase subunit alpha NarZ) 44.9 2.9 EC042_RS06735 (nitrate transporter NarK) 23.6 2.6 EC042_RS06745 (nitrate reductase subunit beta NarH) 21.0 3.2 EC042_RS06750 (nitrate reductase molybdenum cofactor assembly chaperone NarJ) 13.2 2.4 EC042_RS06755 (respiratory nitrate reductase subunit gamma NarI) 12.8 3.1 EC042_RS03510 (DUF1266 domain-containing protein)...”
NRG857_07280 nitrate reductase subunit beta from Escherichia coli O83:H1 str. NRG 857C
74% identity, 100% coverage
SPC_2160 respiratory nitrate reductase 2 beta chain from Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
73% identity, 100% coverage
- Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn
Liu, Plants (Basel, Switzerland) 2023 - “...(3.204-fold to 29.218-fold) ( p < 0.05): a respiratory nitrate reductase 2 beta chain ( SPC_2160 ), a respiratory nitrate reductase 2 alpha chain ( SPC_2161 ), a nitrite reductase large subunit ( SPC_3544 ), and a hydroxylamine reductase ( SPC_0939 ). Notably, the expression of...”
- “...SPC_3400 0.3 Glutamate synthase (NADPH) large chain precursor SPC_3401 0.421 Glutamate synthase (NADPH) small chain SPC_2160 3.204 Respiratory nitrate reductase 2 beta chain SPC_3544 6.181 Nitrite reductase large subunit SPC_2161 28.095 Respiratory nitrate reductase 2 alpha chain SPC_0939 29.218 Hydroxylamine reductase Pyruvate metabolism SPC_3776 0.04 Putative...”
c1686 Respiratory nitrate reductase 1 beta chain from Escherichia coli CFT073
75% identity, 100% coverage
3egwB / P11349 The crystal structure of the narghi mutant narh - c16a
75% identity, 100% coverage
- Ligands: fe3-s4 cluster; iron/sulfur cluster; protoporphyrin ix containing fe (3egwB)
BP1026B_II1224 nitrate reductase subunit beta from Burkholderia pseudomallei 1026b
75% identity, 99% coverage
BRA0298 respiratory nitrate reductase, beta subunit from Brucella suis 1330
74% identity, 99% coverage
- Brucella spp. are facultative anaerobic bacteria under denitrifying conditions
Freddi, Microbiology spectrum 2023 - “...Encoded protein Primers For 5'- > 3' Rev 5'- > 3' B. suis B. microti BRA0298 BMI_II292 NarH CATCCTCGCCAAGATTTTCG CCATTCGATCTTCTCCATCC BRA0260 BMI_II254 NirK GAAAGTGGAGCTGGTCGATC CCGCATCATCAATGACGATC BRA0249 BMI_II243 NorB GGAGCTTTACAGCACCAAGC TGAAGAAGGGCTGTTCAAGG BRA0274 BMI_II269 NosR AAGGGGAACGAGCTTCTAGG TTGGTATCAATGCCCACAAC Construction of a B. microti narG deletion mutant Inactivation of narG...”
Q2YJY3 Cytochrome c heme-binding site:4Fe-4S ferredoxin, iron-sulfur binding domain:Nitrate reductase, beta subunit from Brucella abortus (strain 2308)
BAB2_0905 Cytochrome c heme-binding site:4Fe-4S ferredoxin, iron-sulfur binding domain:Nitrate reductase, beta subunit from Brucella melitensis biovar Abortus 2308
BMI_II292 respiratory nitrate reductase, beta subunit from Brucella microti CCM 4915
74% identity, 99% coverage
BPSS1158 putative respiratory nitrate reductase subunit from Burkholderia pseudomallei K96243
75% identity, 99% coverage
- Transcriptomics Analysis Uncovers Transient Ceftazidime Tolerance in Burkholderia Biofilms
Chattagul, ACS infectious diseases 2021 - “...are associated with nitrosative stress response (BPSL2368), FeS homeostasis (BPSL2369), and nitrate respiration (BPSS1154 and BPSS1158). Additionally, five orthologous genes, BPSL2370BPSL2374, implicated in FeS cluster biogenesis, and another gene, BPSL2863, involved in DNA-binding of the stress protein ferritin, were shown to increase expression by RT-qPCR. The...”
- “...degrade PA as a sole carbon source for energy consumption. 29 Nitrate metabolism (e.g., BPSS1154, BPSS1158, BPSL2309, BPSL2312, and BPSL2313) was responsible for a partial adaptive response in anaerobic condition in biofilm. 30 , 31 This utilization of nitrate in microaerophilic and anaerobic condition may be...”
- Host-Adaptation of Burkholderia pseudomallei Alters Metabolism and Virulence: a Global Proteome Analysis
Mariappan, Scientific reports 2017 - “...hypothetical protein BPSS1107) were located at cytoplasmic region and two proteins (Hsp and hypothetical protein BPSS1158) were predicted to be present at unknown location. However, out of the 12 proteins which were found to be missing from Bp mouse-adapted , eight proteins (ClpB, KatG, Alededh, PcaF,...”
BMEII0951, BME_RS14810 nitrate reductase subunit beta from Brucella melitensis bv. 1 str. 16M
73% identity, 99% coverage
- Systems Biology Analysis of Temporal In vivo Brucella melitensis and Bovine Transcriptomes Predicts host:Pathogen Protein-Protein Interactions
Rossetti, Frontiers in microbiology 2017 - “...retroviral tranforming sequence Yes BSS T cell receptor signaling, Insulin signaling, ErbB signaling, Jak-STAT signaling BMEII0951 (BME_RS14810, narH) Nitrate reductase beta subunit 0.13 CRK v-crk sarcoma virus CT10 oncogene homolog Yes BSS Regulation of actin cytoskeleton, Insulin signaling, ErbB signaling, MAPK, Integrin-mediated cell adhesion BMEII1085 (BME_RS15470,...”
- “...tranforming sequence Yes BSS T cell receptor signaling, Insulin signaling, ErbB signaling, Jak-STAT signaling BMEII0951 (BME_RS14810, narH) Nitrate reductase beta subunit 0.13 CRK v-crk sarcoma virus CT10 oncogene homolog Yes BSS Regulation of actin cytoskeleton, Insulin signaling, ErbB signaling, MAPK, Integrin-mediated cell adhesion BMEII1085 (BME_RS15470, flgA)...”
PHG271 respiratory nitrate reductase subunit from Ralstonia eutropha H16
73% identity, 97% coverage
SGRAN_3847 nitrate reductase subunit beta from Sphingopyxis granuli
74% identity, 97% coverage
BPSL2310 respiratory nitrate reductase beta chain from Burkholderia pseudomallei K96243
71% identity, 96% coverage
BTH_I1853 nitrate reductase, beta subunit from Burkholderia thailandensis E264
71% identity, 96% coverage
BP1026B_I1017 nitrate reductase subunit beta from Burkholderia pseudomallei 1026b
71% identity, 96% coverage
CNX70_14405 nitrate reductase subunit beta from Janthinobacterium svalbardensis
71% identity, 97% coverage
- Complete Genome Sequence of a Psychrotolerant Denitrifying Bacterium, Janthinobacterium svalbardensis PAMC 27463
Cho, Genome announcements 2017 - “...nitrate transporters (CNX70_12890, CNX70_14170, CNX70_14385, CNX70_16780, and CNX70_16810) to nitrite using nitrate reductase proteins (CNX70_14400, CNX70_14405, CNX70_14410, and CNX70_14415). The produced nitrite can be reduced to nitric oxide by the nitrite reductase proteins NirK (CNX70_19440, CNX70_20610, and CNX70_25620) and NirS (CNX70_15420 and CNX70_15425, CNX70_17105 and CNX70_17110,...”
Tbd_1404 nitrate reductase, beta subunit from Thiobacillus denitrificans
63% identity, 97% coverage
BMB171_RS10505 nitrate reductase subunit beta from Bacillus thuringiensis BMB171
59% identity, 94% coverage
- NupR Responding to Multiple Signals Is a Nucleoside Permease Regulator in Bacillus thuringiensis BMB171
Qin, Microbiology spectrum 2022 - “.... The expression of -chain respiratory nitrate reductase (BMB171_RS10500, narG ), -chain respiratory nitrate reductase (BMB171_RS10505, narH ), -chain respiratory nitrate reductase (BMB171_RS10510, narJ ), -chain respiratory nitrate reductase (BMB171_RS10515, NarI ), small subunit nitrite reductase [NAD(P)H] (BMB171_RS10585), significant subunit nitrite reductase [NAD(P)H] (BMB171_RS10590), and nitrite...”
BC2119 Respiratory nitrate reductase beta chain from Bacillus cereus ATCC 14579
58% identity, 94% coverage
- Correction: SecDF as Part of the Sec-Translocase Facilitates Efficient Secretion of Bacillus cereus Toxins and Cell Wall-Associated Proteins
, PloS one 2014 - “...formate-lyase activating enzyme 0.15 7.7E-04 Respiration BC1939 Cytochrome d ubiquinol oxidase subunit II 6.31 2.3E-05 BC2119 Respiratory nitrate reductase beta chain 0.07 2.2E-04 BC2120 Respiratory nitrate reductase delta chain 0.20 3.2E-02 BC4792 Cytochrome d ubiquinol oxidase subunit I 0.14 8.6E-05 BC4793 Cytochrome d ubiquinol oxidase subunit...”
- SecDF as part of the Sec-translocase facilitates efficient secretion of Bacillus cereus toxins and cell wall-associated proteins
Vörös, PloS one 2014 - “...formate-lyase activating enzyme 0.15 7.7E-04 Respiration BC1939 Cytochrome d ubiquinol oxidase subunit II 6.31 2.3E-05 BC2119 Respiratory nitrate reductase beta chain 0.07 2.2E-04 BC2120 Respiratory nitrate reductase delta chain 0.20 3.2E-02 BC4792 Cytochrome d ubiquinol oxidase subunit I 0.14 8.6E-05 BC4793 Cytochrome d ubiquinol oxidase subunit...”
- “...(1.5<FC<5: BC1991, BC5239, Flagellin, cytK, hlbB, hlyII ) and highly differentially (FC>5: BC_p007, BC0862, BC1436, BC2119, ECF-type sigma factor, sigB ) expressed genes from the microarray experiment, in order to best mirror the expression pattern observed in the microarray experiments. Analysis of secreted proteins For the...”
- Comparative transcriptomic and phenotypic analysis of the responses of Bacillus cereus to various disinfectant treatments
Ceragioli, Applied and environmental microbiology 2010 - “...and conversion. Six of these downregulated genes (BC2118, BC2119, BC2120, BC2121, BC2136, and BC3439) coded for proteins involved in the reduction of nitrogen...”
KQ76_12500 nitrate reductase subunit beta from Staphylococcus aureus
57% identity, 96% coverage
SAR2485 nitrate reductase beta chain from Staphylococcus aureus subsp. aureus MRSA252
57% identity, 96% coverage
LI17339_03245 nitrate reductase subunit beta from Bacillus licheniformis LMG 17339
58% identity, 96% coverage
- Nitrous oxide emission by the non-denitrifying, nitrate ammonifier Bacillus licheniformis
Sun, BMC genomics 2016 - “...LI6934_11815 (contig19_3766_7449) LI7559_18375 (contig29_333921_330235) - respiratory nitrate reductase subunit beta narH1 LI6934_10235 (contig17_40515_39046) LI7559_10225 (contig17_112933_114483) LI17339_03245 (contig01_599120_597651) narH2 LI6934_11820 (contig19_7439_8989) LI7559_18370 (contig29_330245_328776) - respiratory nitrate reductase subunit delta narJ1 LI6934_10230 (contig17_39028_38486) LI7559_10230 (contig17_114470_115018) LI17339_03240 (contig01_597632_597090) narJ2 LI6934_11825 (contig19_8976_9524) LI7559_18365 (contig29_328758_328216) - respiratory nitrate reductase subunit gamma...”
NWMN_RS13205, SAUSA300_RS12930 nitrate reductase subunit beta from Staphylococcus aureus subsp. aureus USA300_FPR3757
SACOL2394 respiratory nitrate reductase, beta subunit from Staphylococcus aureus subsp. aureus COL
57% identity, 96% coverage
SA2184 nitrate reductase beta chain narH from Staphylococcus aureus subsp. aureus N315
57% identity, 96% coverage
- Sulfide Homeostasis and Nitroxyl Intersect via Formation of Reactive Sulfur Species in Staphylococcus aureus
Peng, mSphere 2017 - “...protein NWMN_2274 SA2162 13.6 Pyridine nucleotide-disulfide oxidoreductase (TrxB-like) Yes (3.4) NWMN_2282 SA2170 12.3 Hypothetical NWMN_2306 SA2184 32.0 Zinc-binding lipoprotein, AdcA-like Yes (12.1) NWMN_2359 SA2250 cntE 5.6 Major facilitator superfamily (MFS) Yes (66.1) NWMN_2360 SA2251 cntF 7.2 ABC transporter; cobalt-nickel Yes (108) NWMN_2361 SA2252 cntD 7.9 ABC...”
- VraT/YvqF is required for methicillin resistance and activation of the VraSR regulon in Staphylococcus aureus
Boyle-Vavra, Antimicrobial agents and chemotherapy 2013 - “...description Function USA300 N315 2.3 7.5 4 SA2184 This study 6.5 4.6 Nitrate/nitrite metabolism Nitrate/nitrite metabolism SAUSA300_2342 2.7 SAUSA300_2344...”
- Characterization of the oxygen-responsive NreABC regulon of Staphylococcus aureus
Schlag, Journal of bacteriology 2008 - “...SA0841 SA2083 SA2084 SA2085 SA2086 SA2149 SA2150 SA2176 SA2183 SA2184 SA2185 SA2186 SA2187 SA2188 SA2189 Product 7852 SCHLAG ET AL. J. BACTERIOL. TABLE 2. Genes...”
- “...SA0691 SA1225 SA1226 SA1227 SA1228 SA1229 SA1759 SA2176 SA2183 SA2184 SA2185 SA2186 SA2187 SA2188 SA2189 SA2384 Gene name VOL. 190, 2008 ROLE OF NreABC IN S....”
- Genome-wide analysis of ruminant Staphylococcus aureus reveals diversification of the core genome
Ben, Journal of bacteriology 2008 - “...specific SA0523 SAS0861 SA1848 SA2475 SA2476 SA0579 SA0581 SA2184 SA0171 SA1200 SA1201 SA2120 SA2189 SA2469 SA1324 SA0328 SA1538 SA1525 SAR1898 SA1145 SACOL0350...”
- Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover
Anderson, Journal of bacteriology 2006 - “...betB SA0251 SA1551 SA2180 SA2183 SA2184 SA2185 SA2186 SA2628 6-Phospho-beta-glucosidase Alpha-glucosidase 6-Phospho-beta-galactosidase Tagatose 1,6-diphosphate...”
- Multidrug resistance in Staphylococcus aureus due to overexpression of a novel multidrug and toxin extrusion (MATE) transport protein
Kaatz, Antimicrobial agents and chemotherapy 2005 - “...of California, Berkeley SA0095 SA0404 SA0405 SA0406 SA0757 SA1321 SA2184 SA2185 SA2186 SA2549 Gene VOL. 49, 2005 NOVEL S. AUREUS MATE MDR TRANSPORTER 1861 The...”
UH47_01710 nitrate reductase subunit beta from Staphylococcus pseudintermedius
59% identity, 94% coverage
P42176 Nitrate reductase beta chain from Bacillus subtilis (strain 168)
BSU37270 nitrate reductase (beta subunit) from Bacillus subtilis subsp. subtilis str. 168
59% identity, 94% coverage
R3M60_03335 nitrate reductase subunit beta from Bacillus subtilis
59% identity, 94% coverage
R5D67_10750 nitrate reductase subunit beta from Bacillus velezensis
58% identity, 94% coverage
MJ920_17830, RBIBE_34680 nitrate reductase subunit beta from Bacillus velezensis
58% identity, 94% coverage
- Complete genome sequence of biocontrol strain Bacillus velezensis YC89 and its biocontrol potential against sugarcane red rot
Xie, Frontiers in microbiology 2023 - “...reduction MJ920_17820 narI Nitrate reductase subunit gamma MJ920_17825 narJ Nitrate reductase molybdenum cofactor assembly chaperone MJ920_17830 narK Nitrate transporter NarK MJ920_01690 nirD Nitrite reductase small subunit NirD MJ920_01695 nasD NADPH-nitrite reductase MJ920_07485 ktrC Ktr system potassium transporter KtrC Potassium transporter MJ920_14795 yugO Potassium channel family protein...”
- Complete genome sequence data of chitin-degrading Bacillus velezensis RB.IBE29
Tran, Data in brief 2023 - “...reductase-like protein NarX RBIBE_34660 Nitrate reductase 1 alpha chain RBIBE_34690 Nitrate reductase 1 beta chain RBIBE_34680 Nitrate transporter NarK RBIBE_34730 NADPH-nitrite reductase RBIBE_02980 Nitrite reductase small subunit NirD RBIBE_02970 ACC biosynthesis Acyl-CoA dehydrogenase RBIBE_22770 Acyl-CoA dehydrogenase RBIBE_18460 Acyl-CoA dehydrogenase FadE RBIBE_30110 Acyl-CoA dehydrogenase family protein RBIBE_04320...”
narH / Q5HLK1 menaquinol:nitrate oxidoreductase subunit β (EC 1.7.5.1) from Staphylococcus epidermidis (strain ATCC 35984 / RP62A) (see paper)
SERP_RS09905 nitrate reductase subunit beta from Staphylococcus epidermidis RP62A
SERP1986 respiratory nitrate reductase, beta subunit from Staphylococcus epidermidis RP62A
57% identity, 96% coverage
- Mutation of gdpS gene induces a viable but non-culturable state in Staphylococcus epidermidis and changes in the global transcriptional profile
Zhu, BMC microbiology 2022 - “...narI respiratory nitrate reductase subunit gamma 1.24 SERP_RS09900 narJ respiratory nitrate reductase subunit delta 1.6 SERP_RS09905 narH respiratory nitrate reductase subunit beta 1.59 SERP_RS09910 narG respiratory nitrate reductase subunit alpha 1.54 SERP_RS09915 cobA uroporphyrinogen-III C-methyltransferase 1.15 SERP_RS09920 nirD nitrite reductase small subunit 1.26 SERP_RS09925 nirB nitrite...”
- Deciphering the Antibacterial Mode of Action of Alpha-Mangostin on Staphylococcus epidermidis RP62A Through an Integrated Transcriptomic and Proteomic Approach
Sivaranjani, Frontiers in microbiology 2019 - “...lyase activating enzyme 1.61 2.10 10 -13 SERP0244 Oxidoreductase, aldo/ketoreductase family 2.04 3.91 10 -13 SERP1986 narH Respiratory nitrate reductase, beta subunit 1.74 4.21 10 -12 SERP0245 YdfJ Transporter, putative 233 9.35 10 -12 SERP1783 Conserved hypothetical protein 1.66 1.21 10 -11 SERP2112 adh2 Alcohol dehydrogenase,...”
- Impact of the Staphylococcus epidermidis LytSR two-component regulatory system on murein hydrolase activity, pyruvate utilization and global transcriptional profile
Zhu, BMC microbiology 2010 - “...cytochrome d ubiquinol oxidase subunit II-like protein 13.85 SERP1985 narJ nitrate reductase delta chain 0.441 SERP1986 narH nitrate reductase beta chain 0.327 SERP1987 narG nitrate reductase alpha chain 0.324 SERP1990 nirB nitrite reductase nitrite reductase 0.354 SERP2168 mqo-2 malate:quinone oxidoreductase 0.317 SERP2169 hypothetical protein 0.0165 SERP2261...”
- AI-2-dependent gene regulation in Staphylococcus epidermidis
Li, BMC microbiology 2008 - “...Respiratory nitrate reductase, gamma subunit 2.57 0.47 SERP1985 Respiratory nitrate reductase, delta subunit 4.81 0.39 SERP1986 Respiratory nitrate reductase, beta subunit 3.93 0.47 SERP1989 Nitrite reductase 2.52 0.46 Other SERP0878 Portal protein, truncation 3.76 0.48 SERP2027 Antiholin-like protein LrgB 0.46 9.38 SERP2069 Major facilitator superfamily protein...”
MLD56_17965 nitrate reductase subunit beta from Paenibacillus peoriae
57% identity, 94% coverage
UE46_11975 nitrate reductase subunit beta from Listeria weihenstephanensis
59% identity, 91% coverage
- Complete Circular Genome Sequence and Temperature Independent Adaptation to Anaerobiosis of Listeria weihenstephanensis DSM 24698
Ferrari, Frontiers in microbiology 2017 - “...cgattgacgtctttacgaat UE46_10735_qRT_R caattttcgacatcaccttc UE46_11895, pdhB UE46_11895_qRT_F aaggtcttttgatctcagca UE46_11895_qRT_R ctttaccgatttcgattgtg UE46_11930, moaC UE46_11930_qRT_F tattaaagaagggcaaatcg UE46_11930_qRT_R actttcgtcgtcataattgg UE46_11975, narH UE46_11975_qRT_F caactggaaaacgaataagg UE46_11975_qRT_R cataaagcatcacaccaaga UE46_14170 UE46_14170_qRT_F attgcaccgaatatcttcac UE46_14170_qRT_R aaatgctttcgtcaaactgt UE46_14320 UE46_14320_qRT_F cgaataaaatcgacttcgtg UE46_14320_qRT_R cgaccgacttaatatccgta Results Complete genome sequence of L. weihenstephanensis DSM 24698 A key prerequisite for the analyses...”
cg1343 respiratory nitrate reductase oxidoreduct from Corynebacterium glutamicum ATCC 13032
58% identity, 87% coverage
- A pseudokinase version of the histidine kinase ChrS promotes high heme tolerance of Corynebacterium glutamicum
Krüger, Frontiers in microbiology 2022 - “...0.02 cg0446 sdhA , succinate dehydrogenase 0.40 0.00 cg0447 sdhB , succinate dehydrogenase 0.45 0.00 cg1343 narH , probable respiratory nitrate reductase oxidoreduct 0.49 0.03 cg1344 narG , nitrate reductase 2, alpha subunit 0.30 0.00 cg1487 leuC , isopropylmalate isomerase large subunit 0.29 0.01 cg1737 acn...”
- The Iron Deficiency Response of Corynebacterium glutamicum and a Link to Thiamine Biosynthesis
Küberl, Applied and environmental microbiology 2020 (secret) - The pupylation machinery is involved in iron homeostasis by targeting the iron storage protein ferritin
Küberl, Proceedings of the National Academy of Sciences of the United States of America 2016 - “...Locus tag Gene cg0310 cg0445 cg0446 cg0447 cg1341 cg1342 cg1343 cg1344 cg1345 cg1487 cg1488 cg1737 cg2636 cg3047 cg3048 katA sdhC sdhA sdhB narI narJ narH narG...”
- RosR (Cg1324), a hydrogen peroxide-sensitive MarR-type transcriptional regulator of Corynebacterium glutamicum
Bussmann, The Journal of biological chemistry 2010 - “...2017 cg0416 cg0415 cg1109 cg1324 cg1345 cg1344 cg1343 cg1342 cg1341 cg1382 cg1671 cg2136 cg2137 cg2138 cg2139 cg2649 cg2773 Gene H2O2-sensitive Transcriptional...”
- Two-component systems of Corynebacterium glutamicum: deletion analysis and involvement of the PhoS-PhoR system in the phosphate starvation response
Kocan, Journal of bacteriology 2006 - “...NCgl0776 cg0926 cg0927 cg0928 cg0957 cg1120 cg1121 cg1343 cg1344 cg1405 cg1412 cg1413 cg1418 cg1419 cg1447 NCgl0777 NCgl0778 NCgl0779 NCgl0802 NCgl0943 NCgl0944...”
- Global gene expression during stringent response in Corynebacterium glutamicum in presence and absence of the rel gene encoding (p)ppGpp synthase
Brockmann-Gretza, BMC genomics 2006 - “...cstA carbon starvation protein A T cg0994 0.62 0.41 rpmE 50S ribosomal protein L31 J cg1343 0.57 0.47 narH respiratory nitrate reductase oxireductase C cg1344 0.60 0.41 narG nitrate reductase 2 ( subunit) C cg1345 0.59 0.37 narK nitrate/nitrite transporter P cg1565 0.66 0.62 rplT 50S...”
WSS_RS29470 nitrate reductase subunit beta from Rhodococcus opacus M213
57% identity, 88% coverage
MAP_RS13360 nitrate reductase subunit beta from Mycobacterium avium subsp. paratuberculosis K-10
57% identity, 90% coverage
- Delineating transcriptional crosstalk between Mycobacterium avium subsp. paratuberculosis and human THP-1 cells at the early stage of infection via dual RNA-seq analysis
Park, Veterinary research 2022 - “...), were overexpressed. Likewise, four loci for Anaerobic respiration (MAP_RS10685, narK2 ; MAP_RS13350, narI ; MAP_RS13360, narH ; and MAP_RS13365, narG ) and two loci for Protease (MAP_RS02300 and MAP_RS09345, mpa ; MAP_RS04650, htrA/degP ) were upregulated, thereby contributing to their functional category being significantly enriched....”
Rv1162 PROBABLE RESPIRATORY NITRATE REDUCTASE (BETA CHAIN) NARH from Mycobacterium tuberculosis H37Rv
O06560 Probable respiratory nitrate reductase (Beta chain) NarH from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
BCG_1224 putative respiratory nitrate reductase subunit beta narH from Mycobacterium bovis BCG str. Pasteur 1173P2
56% identity, 87% coverage
- Aureolic Acid Group of Agents as Potential Antituberculosis Drugs
Bespyatykh, Antibiotics (Basel, Switzerland) 2020 - “...MSMEG_5137 narI - respiratory nitrate reductase subunit gamma - - Nitrogen metabolism 2.28108 MSMEG_5139 narH Rv1162 nitrate reductase subunit beta intermediary metabolism and respiration - - 2.0609 MSMEG_5392 kdpA Rv1029 potassium-transporting ATPase A cell wall and cell processes Inorganic ion transport and metabolism Signal transduction 3.84888...”
- Identification of Autophagy-Inhibiting Factors of Mycobacterium tuberculosis by High-Throughput Loss-of-Function Screening
Strong, Infection and immunity 2020 (secret) - Acid Fasting: Modulation of Mycobacterium tuberculosis Metabolism at Acidic pH
Baker, Trends in microbiology 2019 - “...ammonia secretion to neutralize acidic pH; attenuated in mice. [ 6 , 7 ] Rv1161, Rv1162 narGH Yes No Reduced survival at pH 5.5 and hypoxia. [ 34 ] Rv1221 sigE Yes No Reduced expression of PhoP and acidic pH induced genes; attenuated in mice. [...”
- Deciphering the metabolic response of Mycobacterium tuberculosis to nitrogen stress
Williams, Molecular microbiology 2015 - “...function(s) Genes Up u1 <0.001 6 1 Nitrite/nitrate reductase activity Rv0252, Rv0253, Rv0261, Rv0267, Rv1161, Rv1162, Rv1163, Rv1164, Rv1737, Rv2329, Rv2391 u2 <0.001 11 5 Citrate/oxaloacetate metabolism Rv0211, Rv0337, Rv0467, Rv0482, Rv0889, Rv0896, Rv1023, Rv1130, Rv1131, Rv1315, Rv1475, Rv1595, Rv1915, Rv3565 u3 0.01 1 1 Phthiocerol...”
- InbR, a TetR family regulator, binds with isoniazid and influences multidrug resistance in Mycobacterium bovis BCG
Yang, Scientific reports 2015 - “...13 BCG_1223 1.69 2.32 Rv1161 narG respiratory nitrate reductase (alpha chain) narG BCG_1224 1.12 1.64 Rv1162 narH respiratory nitrate reductase subunit beta narH Up BCG_1225 1.06 1.22 Rv1163 narJ respiratory nitrate reductase (delta chain) narJ 14 BCG_1249 1.06 Rv1187 rocA BCG_1250 1.40 Rv1188 Up BCG_1251 2.06...”
- Transcriptional profiling of Mycobacterium tuberculosis replicating ex vivo in blood from HIV- and HIV+ subjects
Ryndak, PloS one 2014 - “...pathway when aerobic respiration is inhibited e.g. Rv0392c ( ndhA ), Rv1854c ( ndh ), Rv1162 ( narH ) and Rv1164 ( narI ) were not affected. Another potential source of oxidative stress for M. tb is an environment which is high in free iron since...”
- Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis
Arnvig, PLoS pathogens 2011 - “...20.7 whole Rv0191 transporter II.C.5 56 0.9 3 end Rv1805c HP VI 55 46.9 whole Rv1162 narH I.B.6b 53 0.7 middle Rv3634c galE1 I.C.3 52 0.8 middle Rv0583c lpqN II.C.1 23 0.6 5 end Ranking of most abundant antisense transcripts during exponential growth. **antisense transcript extends...”
- Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions
Bordbar, Molecular systems biology 2010 - “...Fructose-bisphosphate aldolase Rv0946c pgi Glucose-6-phosphate isomerase Rv1099c Fructose-bisphosphatase Yes Rv1161 narG Nitrate reductase No a Rv1162 narH Nitrate reductase No a Rv1163 narJ Nitrate reductase No a Rv1164 narI Nitrate reductase No a Rv1475c acn Aconitase Rv2391 sirA Sulfite reductase Yes Table 3 Genes predicted to...”
- More
- Identification and Quantification of S-Sulfenylation Proteome of Mycobacterium tuberculosis under Oxidative Stress
Lu, Microbiology spectrum 2023 - “...the total SOH modified proteins as shown in Fig. S6. P9WQE7 , P9WGY9 , and O06560 have 10 modified sites, while O50431, A0A089QRB9, O53669, P9WIV9 , and I6Y231 have 9, 11, 12, 13, and 14 modified sites. Among these proteins, the SOH modification levels of 89...”
- InbR, a TetR family regulator, binds with isoniazid and influences multidrug resistance in Mycobacterium bovis BCG
Yang, Scientific reports 2015 - “...O-methyltransferase omt NA 13 BCG_1223 1.69 2.32 Rv1161 narG respiratory nitrate reductase (alpha chain) narG BCG_1224 1.12 1.64 Rv1162 narH respiratory nitrate reductase subunit beta narH Up BCG_1225 1.06 1.22 Rv1163 narJ respiratory nitrate reductase (delta chain) narJ 14 BCG_1249 1.06 Rv1187 rocA BCG_1250 1.40 Rv1188...”
MSMEG_5139 nitrate reductase, beta subunit from Mycobacterium smegmatis str. MC2 155
57% identity, 88% coverage
MAV_1304 nitrate reductase, beta subunit from Mycobacterium avium 104
57% identity, 90% coverage
- Adaptive Changes in Mycobacterium avium Gene Expression Profile Following Infection of Genetically Susceptible and Resistant Mice
Ignatov, Acta naturae 2010 - “...expression in the lungs of the I/St mice MAV_2015 MbtG; mycobactin lysine-N-oxygenase MAV_1696 Glutamate dehydrogenase MAV_1304 NarH; nitrate reductase, ?-subunit MAV_2379 MetH; vitamin B12-dependent methionine synthase MAV_2385 Mce protein MAV_2063 Mce protein MAV_2386 Mce protein MAV_0118 PPE protein MAV_3109 RifB; polyketide synthase 7 MAV_0880 3-Ketosteroid-?-1-dehydrogenase MAV_3000...”
- “...for the increase in its expression in the resistant mice is not quite clear. The MAV_1304 locus coding for the -subunit of nitrate reductase is of particular interest. This gene is orthologous to the narH gene of M. tuberculosis . Its product is a subunit of...”
DSY0335 nitrate reductase beta chain from Desulfitobacterium hafniense Y51
57% identity, 94% coverage
OCU_12110 nitrate reductase subunit beta from Mycobacterium intracellulare ATCC 13950
57% identity, 90% coverage
lp_1498 nitrate reductase, beta chain from Lactobacillus plantarum WCFS1
55% identity, 93% coverage
nfa45500 putative nitrate reductase beta subunit from Nocardia farcinica IFM 10152
54% identity, 85% coverage
SCO6534 nitrate reductase beta chain NarH from Streptomyces coelicolor A3(2)
58% identity, 88% coverage
ArtHe_11505 nitrate reductase subunit beta from Arthrobacter sp. Helios
54% identity, 89% coverage
SAOUHSC_02680 nitrate reductase, beta subunit from Staphylococcus aureus subsp. aureus NCTC 8325
Q2FVM2 Nitrate reductase, beta subunit from Staphylococcus aureus (strain NCTC 8325 / PS 47)
SAUSA300_2342 respiratory nitrate reductase, beta subunit from Staphylococcus aureus subsp. aureus USA300_FPR3757
55% identity, 89% coverage
- The roles of cell wall inhibition responsive protein CwrA in the pathogenicity of Staphylococcus aureus
Han, Virulence 2024 - “...nitrate reductase molybdenum cofactor assembly chaperone; NarJ 1.2 SAOUHSC_02684 nasD Assimilatory nitrite reductase; NasD 1.1 SAOUHSC_02680 narH Nitrate reductase beta chain; NarH 1.1 Well consistent with our finding that the cwrA mutant exhibited decreased levels of eDNA release in biofilm, the transcription levels of a critical...”
- Transcriptomic analyses reveal the potential antibacterial mechanism of citral against Staphylococcus aureus
Liao, Frontiers in microbiology 2023 - “...pflB formate acetyltransferase SAOUHSC_02685 5.845924926 2.22966E-93 sirohydrochlorin ferrochelatase SAOUHSC_02681 5.770892267 8.0905E-128 nitrate reductase subunit alpha SAOUHSC_02680 5.655444057 1.3733E-110 nitrate reductase subunit beta SAOUHSC_00131 5.423736733 3.31075E-51 YbaN family protein SAOUHSC_02679 5.263068749 3.38926E-75 respiratory nitrate reductase subunit delta SAOUHSC_02645 5.222935859 2.92178E-05 LytTR family DNA-binding domain-containing protein 3.2.3. Go...”
- Functional analysis of the EsaB component of the Staphylococcus aureus Type VII secretion system
Casabona, Microbiology (Reading, England) 2017 - “...metalloproteinase aureolysin ns SAOUHSC_01942 splA 16.4 Highly specific serine protease specific to S. aureus 5.4 SAOUHSC_02680 narH 15.7 Nitrate reductase subunit beta ns SAOUHSC_01944 14.3 Unknown, hypothetical protein 4.5 SAOUHSC_02681 narG 14.3 Nitrate reductase subunit alpha ns SAOUHSC_01121 hla 13.5 -hemolysin 4.1 SAOUHSC_02241 lukF 13.0 Unknown,...”
- The Staphylococcus aureus KdpDE two-component system couples extracellular K+ sensing and Agr signaling to infection programming
Xue, Infection and immunity 2011 - “...SAOUHSC_02282 SAOUHSC_02283 SAOUHSC_02671 SAOUHSC_02679 SAOUHSC_02680 SAOUHSC_02682 SAOUHSC_02684 SAOUHSC_02849 SAOUHSC_02945 SAOUHSC_02969 SAOUHSC_03011...”
- The mevalonate pathway of Staphylococcus aureus
Balibar, Journal of bacteriology 2009 - “...nitrate reductase subunits narJ (SAOUHSC_02679) and narH (SAOUHSC_02680), respectively. Therefore, for all further analyses we chose to compare transcriptional...”
- Antimicrobial Activity and Mechanism of Action of Dracocephalum moldavica L. Extracts Against Clinical Isolates of Staphylococcus aureus
Yu, Frontiers in microbiology 2019 - “...nitrate reductase gamma chain NarI 3.66 0.009594 Q2FY19 Zinc uptake regulation ZUR Zur 3.63 0.001459 Q2FVM2 Respiratory nitrate reductase beta chain NarH 3.60 0.000643 Q2G2U1 Sensor histidine kinase SaeS 3.53 0.002208 Q2G2M7 Serine acetyltransferase CysE 3.39 0.007534 Q2G0B7 Lysine decarboxylase family YvdD 3.12 0.000743 Q2FWD8 50S...”
- VraT/YvqF is required for methicillin resistance and activation of the VraSR regulon in Staphylococcus aureus
Boyle-Vavra, Antimicrobial agents and chemotherapy 2013 - “...This study 6.5 4.6 Nitrate/nitrite metabolism Nitrate/nitrite metabolism SAUSA300_2342 2.7 SAUSA300_2344 SA2186 This study 3.6 6.8 5.5 SA2187 This study 6.3 4...”
SCO4948 nitrate reductase beta chain NarH3 from Streptomyces coelicolor A3(2)
56% identity, 86% coverage
MLP_46650 nitrate reductase subunit beta from Microlunatus phosphovorus NM-1
55% identity, 87% coverage
- Deciphering the genome of polyphosphate accumulating actinobacterium Microlunatus phosphovorus
Kawakoshi, DNA research : an international journal for rapid publication of reports on genes and genomes 2012 - “...gene cluster that putatively encodes subunits of the membrane-bound respiratory nitrate reductase, NarG (MLP_46640), NarH (MLP_46650), NarJ (MLP_46660), and NarI (MLP_46670), linked to a NarK-type nitrate/nitrite transporter gene (MLP_46680). In addition, we found a gene that encodes another NarK-type nitrate/nitrite transporter (MLP_35250) located the downstream of...”
SiRe_0443 nitrate reductase subunit beta from Saccharolobus islandicus REY15A
54% identity, 91% coverage
PAE3612 nitrate reductase beta subunit (narH) from Pyrobaculum aerophilum str. IM2
53% identity, 91% coverage
- Microbe-Mineral Interaction and Novel Proteins for Iron Oxide Mineral Reduction in the Hyperthermophilic Crenarchaeon Pyrodictium delaneyi
Kashyap, Applied and environmental microbiology 2021 - “...molybdopterin oxidoreductase protein bands in silver-stained gels, a nitrate reductase from P. aerophilum (PAE3611 and PAE3612) and a thiosulfate reductase from P. islandicum (Pisl_0266), were identified by peptide mass fingerprinting and present in nitrate- and thiosulfate-grown cells, respectively, but were absent in Pyrobaculum cells grown on...”
- Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum
Cozen, Journal of bacteriology 2009 - “...a polycistronic operon that includes an iron-sulfur subunit (PAE3612), a cytochrome b-containing membrane subunit (PAE3613) (1), and a downstream ORF of unknown...”
- Characterization of dissimilatory Fe(III) versus NO3- reduction in the hyperthermophilic archaeon Pyrobaculum aerophilum
Feinberg, Journal of bacteriology 2006 - “...matched those for the nitrate reductase subunit (NarH, PAE3612). There was only one peptide match overlap between the two proteins. Both fragments are predicted...”
Nwi_0776 nitrate reductase, beta subunit from Nitrobacter winogradskyi Nb-255
51% identity, 92% coverage
norB / Q6R887 nitrite oxidoreductase β subunit from Nitrobacter winogradskyi (see 5 papers)
50% identity, 94% coverage
norB / Q51075 nitrite oxidoreductase β subunit from Nitrobacter hamburgensis (see 3 papers)
51% identity, 92% coverage
Nwi_0965 nitrate reductase, beta subunit from Nitrobacter winogradskyi Nb-255
50% identity, 92% coverage
Gmet_0330 Nitrate reductase, beta subunit from Geobacter metallireducens GS-15
50% identity, 94% coverage
NARH_BRASZ / P85098 Respiratory nitrate reductase beta chain; Respiratory membrane-bound nitrate reductase subunit beta; EC 1.7.5.1 from Bradyrhizobium sp.
58% identity, 56% coverage
- function: The nitrate reductase enzyme complex allows Bradyrhizobium sp. USDA 3045 to use nitrate as an electron acceptor during anaerobic growth. The beta chain is an electron transfer unit containing four cysteine clusters involved in the formation of iron-sulfur centers. Electrons are transferred from the gamma chain to the molybdenum cofactor of the alpha subunit.
catalytic activity: nitrate + a quinol = a quinone + nitrite + H2O (RHEA:56144)
cofactor: [4Fe-4S] cluster (Binds 3 [4Fe-4S] clusters per subunit.)
cofactor: [3Fe-4S] cluster (Binds 1 [3Fe-4S] cluster per subunit.)
subunit: Heterotrimer composed of an alpha, a beta and a gamma chain. Alpha and beta are catalytic chains; gamma chains are involved in binding the enzyme complex to the cytoplasmic membrane. - Mass spectrometry identification of membrane-bound respiratory nitrate reductase from Bradyrhizobium sp. (Lupinus)
Polcyn, Acta biochimica Polonica 2008 (PubMed)- “...and 52% of NarH sequence (266 aa) was assembled (UniProt KB acc. no. P85097 and P85098). This is the first unambiguous identification of an active NarGH-like NR in rhizobia. Moreover, arguments are provided here for the existence of a functional enzyme of this type also among...”
ddhB / Q8GPG3 dimethylsulfide dehydrogenase β subunit (EC 1.8.2.4) from Rhodovulum sulfidophilum (see paper)
DDHB_RHOSU / Q8GPG3 Dimethylsulfide dehydrogenase subunit beta; DMS DH subunit beta; DMS DH iron-sulfur subunit; Dimethyl sulfide:cytochrome c2 reductase subunit beta; Dimethylsulfide iron-sulfur subunit from Rhodovulum sulfidophilum (Rhodobacter sulfidophilus) (see paper)
Q8GPG3 dimethyl sulfide:cytochrome c2 reductase (EC 1.8.2.4) from Rhodovulum sulfidophilum (see paper)
37% identity, 81% coverage
- function: Electron transfer subunit of the dehydrogenase during anaerobic growth on dimethyl sulfide.
cofactor: [3Fe-4S] cluster (Binds 1 [3Fe-4S] cluster.)
cofactor: [4Fe-4S] cluster (Binds 3 [4Fe-4S] clusters.)
subunit: Heterotrimer of alpha, beta and gamma subunits.
NARH_HALMT / I3R9M8 Respiratory nitrate reductase subunit beta; Nitrate reductase beta chain; EC 1.7.5.1 from Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4) (Halobacterium mediterranei) (see 2 papers)
I3R9M8 ferredoxin-nitrate reductase (subunit 1/2) (EC 1.7.7.2); chlorate reductase (subunit 1/2) (EC 1.97.1.1) from Haloferax mediterranei (see paper)
37% identity, 76% coverage
- function: The respiratory membrane-bound nitrate reductase enzyme complex plays a role in generation of metabolic energy by using nitrate as a terminal electron acceptor during anaerobic conditions. The beta chain is an electron transfer unit containing four cysteine clusters involved in the formation of iron-sulfur centers.
catalytic activity: nitrate + a quinol = a quinone + nitrite + H2O (RHEA:56144)
cofactor: [4Fe-4S] cluster (Binds 3 [4Fe-4S] clusters per subunit.)
cofactor: [3Fe-4S] cluster (Binds 1 [3Fe-4S] cluster per subunit.)
subunit: Probable multiprotein complex; a catalytic heterodimer of an alpha and beta chain is proposed to associate with additional subunits involved in membrane attachment and electron transfer.
clrB / P60069 chlorate reductase β subunit (EC 1.97.1.1) from Ideonella dechloratans (see paper)
P60069 chlorate reductase (subunit 2/3) (EC 1.97.1.1) from Ideonella dechloratans (see paper)
TC 5.A.3.8.2 / P60069 Chlorate reductase beta subunit aka Chlorate reductase iron-sulfur subunit, component of Chlorate reductase, ClrABC from Ideonella dechloratans (see paper)
36% identity, 83% coverage
SERB_THASE / Q9S1G9 Selenate reductase subunit beta; SER subunit beta; Selenate reductase iron-sulfur subunit; EC 1.97.1.9 from Thauera selenatis (see 5 papers)
Q9S1G9 selenate reductase (subunit 2/3) (EC 1.97.1.9) from Thauera selenatis (see 2 papers)
TC 5.A.3.8.1 / Q9S1G9 Selenate reductase beta subunit aka Selenate reductase iron-sulfur subunit, component of Selenate reductase, SerABC from Thauera selenatis (see 3 papers)
36% identity, 83% coverage
- function: Component of the selenate reductase, which catalyzes the reduction of selenate to selenite and allows anaerobic growth with selenate as the sole terminal electron acceptor (PubMed:20388716, PubMed:20547201, PubMed:9295321). A c-type di-heme cytochrome of the cytc4 family was shown to donate electrons to the selenate reductase in vitro (PubMed:20388716). SerABC can also use reduced benzyl viologen or reduced methyl viologen as an electron donor (PubMed:20547201, PubMed:9295321). This subunit transfers electrons from SerC to SerA (Probable). The reductase is specific for selenate, and cannot reduce nitrate, nitrite, chlorate or sulfate (PubMed:9295321).
catalytic activity: selenite + 2 Fe(III)-[cytochrome c] + H2O = 2 Fe(II)- [cytochrome] + selenate + 2 H(+) (RHEA:80603)
cofactor: [3Fe-4S] cluster (Binds 1 [3Fe-4S] cluster.)
cofactor: [4Fe-4S] cluster (Binds 3 [4Fe-4S] clusters.)
subunit: Heterotrimer of alpha (SerA), beta (SerB) and gamma (SerC) subunits. - substrates: Electrons
- Identification, characterization, and classification of genes encoding perchlorate reductase
Bender, Journal of bacteriology 2005 (secret)
s25dB3 / H9NN90 steroid C25 dehydrogenase β3 subunit (EC 1.17.99.10) from Sterolibacterium denitrificans (see 8 papers)
H9NN90 steroid C-25 hydroxylase (subunit 2/3) (EC 1.17.99.10) from Sterolibacterium denitrificans (see paper)
SDENCHOL_20205 4Fe-4S dicluster domain-containing protein from Sterolibacterium denitrificans
34% identity, 81% coverage
ebdB / Q93PD1 EBDB subunit (EC 1.17.99.2) from Azoarcus sp. EB1 (see paper)
TC 5.A.3.9.1 / Q93PD1 Anaerobic ethylbenzene dehydrogenase subunit B, component of Anaerobic ethylbenzene dehydrogenase, EbdABC (see paper)
35% identity, 82% coverage
2ivfB / Q5P5I1 Ethylbenzene dehydrogenase from aromatoleum aromaticum (see paper)
35% identity, 82% coverage
- Ligands: fe3-s4 cluster; iron/sulfur cluster; protoporphyrin ix containing fe (2ivfB)
5ch7B / G8QM54 Crystal structure of the perchlorate reductase pcrab - phe164 gate switch intermediate - from azospira suillum ps (see paper)
35% identity, 73% coverage
- Ligands: fe3-s4 cluster; iron/sulfur cluster (5ch7B)
B2D1S5 Perchlorate reductase B from Azospira sp. KJ
Dsui_0148 4Fe-4S dicluster domain-containing protein from Azospira oryzae PS
35% identity, 73% coverage
pcrB / Q4G1W2 perchlorate reductase β subunit from Dechloromonas agitata (see paper)
Q4G1W2 chlorate reductase (EC 1.97.1.1) from Dechloromonas agitata (see paper)
35% identity, 69% coverage
PCRB_DECAR / Q47CW7 Perchlorate reductase subunit beta; Perchlorate reductase iron-sulfur subunit from Dechloromonas aromatica (strain RCB) (see paper)
34% identity, 73% coverage
- function: Component of the perchlorate reductase that catalyzes the reduction of perchlorate to chlorite and allows anaerobic growth on perchlorate as the sole electron acceptor. The beta subunit may be responsible for electron transfer to the catalytic alpha subunit PcrA (Probable).
cofactor: [3Fe-4S] cluster (Binds 1 [3Fe-4S] cluster.)
cofactor: [4Fe-4S] cluster (Binds 3 [4Fe-4S] clusters.)
subunit: Heterotrimer of alpha, beta and gamma subunits. - Peptide biomarkers as evidence of perchlorate biodegradation
Bansal, Applied and environmental microbiology 2011 (secret)
W01_12940, W01_14020, W01_16860 4Fe-4S dicluster domain-containing protein from Candidatus Nitrotoga sp. AM1P
31% identity, 69% coverage
- Effects of Co-existing Heterotrophs on Physiology of and Nitrogen Metabolism in Autotrophic Nitrite-oxidizing Candidatus Nitrotoga
Ide, Microbes and environments 2023 - “...). The transcript abundance of nitrite oxidoreductase genes ( nxrABC ) (W01_16870, W01_12950, W01_16860, W01_14020, W01_12940, and W01_14030) slightly increased. AM1P grown in the co-culture significantly increased the transcript levels of genes encoding the liposome protein (W01_22860) and cell division protein FtsH (W01_24700). These gene expression...”
- “...2 ). The transcript abundance of nitrite oxidoreductase genes ( nxrABC ) (W01_16870, W01_12950, W01_16860, W01_14020, W01_12940, and W01_14030) slightly increased. AM1P grown in the co-culture significantly increased the transcript levels of genes encoding the liposome protein (W01_22860) and cell division protein FtsH (W01_24700). These gene...”
- “...Fig. 2 ). The transcript abundance of nitrite oxidoreductase genes ( nxrABC ) (W01_16870, W01_12950, W01_16860, W01_14020, W01_12940, and W01_14030) slightly increased. AM1P grown in the co-culture significantly increased the transcript levels of genes encoding the liposome protein (W01_22860) and cell division protein FtsH (W01_24700). These...”
THTE_1508 4Fe-4S dicluster domain-containing protein from Thermogutta terrifontis
31% identity, 69% coverage
KsCSTR_07970 4Fe-4S dicluster domain-containing protein from Candidatus Kuenenia stuttgartiensis
31% identity, 76% coverage
- Effects of reducing, stabilizing, and antibiotic agents on "Candidatus Kuenenia stuttgartiensis"
Ude, Applied microbiology and biotechnology 2023 - “...nitrite reductase electron transfer iron-sulfur-cluster subunit (KsCSTR_46210); NirS, nitrite reductase (KsCSTR_33370); NXR, nitrite:nitrate oxidoreductase, (KsCSTR_08000, KsCSTR_07970, KsCSTR_07960); HOX, hydroxylamine oxidase (KsCSTR_43280); Cyt c, NapC/NirT family cytochrome c (KsCSTR_12840); HZS, hydrazine synthase (KsCSTR_28210, KsCSTR_28190, KsCSTR_12680); HDH, hydrazine dehydrogenase (KsCSTR_46980, KsCSTR_11820); HAO, putative hydroxylamine oxidoreductase HAO (KsCSTR_49490). Protein...”
- Comparative genomics in "Candidatus Kuenenia stuttgartiensis" reveal high genomic plasticity in the overall genome structure, CRISPR loci and surface proteins
Ding, BMC genomics 2020 - “...dehydrogenase gene KsCSTR_43280, and the alpha, beta and gamma subunits of nitrite:nitrate oxidoreductase (KsCSTR_08000 / KsCSTR_07970 / KsCSTR_07960). Just as strain KUST and strain MBR1, strain CSTR1 also contains four different types of ATPase genes, three complex III genes, a complete set of genes encoding the...”
7b04A / Q1PZD5 of Nitrite oxidoreductase (Nxr) from the anammox bacterium Kuenenia stuttgartiensis.
31% identity, 76% coverage
- Ligands: iron/sulfur cluster; fe3-s4 cluster; protoporphyrin ix containing fe (7b04A)
NITMOv2_4533 4Fe-4S dicluster domain-containing protein from Nitrospira moscoviensis
30% identity, 76% coverage
- Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated From a Drinking Water Treatment Plant
Fujitani, Frontiers in microbiology 2020 - “...NxrA (W02_21980 and W02_23210) are 3,438 and 3,447 bp, respectively. **Two of five nxrB genes (NITMOv2_4533 and 4537) are fused after genome deletion event. ***Two of five NxrC (NITMOv2_0740 and 3640) has C-terminal transmembrane helix besides N-terminal signal peptide recognized by the Sec pathway. (a) Koch...”
- Cultivation and Transcriptional Analysis of a Canonical Nitrospira Under Stable Growth Conditions
Mundinger, Frontiers in microbiology 2019 - “...genes based on mapping with 95% alignment identity were nxrA (NITMOv2_4538), nxrC (NITMOv2_3624), and nxrB (NITMOv2_4533) (log 2 -fold to median 8.1, 7.6, and 7.3, respectively), together with a conserved exported protein of unknown function (NITMOv2_2496, Supplementary Table S1 ), demonstrating the key role of the...”
W02_10680 4Fe-4S dicluster domain-containing protein from Nitrospira sp. KM1
29% identity, 26% coverage
NITMOv2_0254, NITMOv2_4032, NITMOv2_RS01125, NITMOv2_RS18530 4Fe-4S dicluster domain-containing protein from Nitrospira moscoviensis
30% identity, 76% coverage
- Cultivation and Transcriptional Analysis of a Canonical Nitrospira Under Stable Growth Conditions
Mundinger, Frontiers in microbiology 2019 - “...NXR alpha subunit 1 131.8 NITMOv2_0255 NITMOv2_RS01130 486 215 nxrB_1 NXR beta subunit 1 49.8 NITMOv2_0254 NITMOv2_RS01125 311 179 nxrA_2 NXR alpha subunit 2 131.6 NITMOv2_4028 NITMOv2_RS18515 179 76 nxrB_2 NXR beta subunit 2 49.8 NITMOv2_4027 NITMOv2_RS18510 59 46 nxrA_3 NXR alpha subunit 3 131.9 NITMOv2_4033...”
- “...NXR alpha subunit 3 131.9 NITMOv2_4033 NITMOv2_RS18535 19 7 nxrB_3 NXR beta subunit 3 49.8 NITMOv2_4032 NITMOv2_RS18530 9 11 nxrC_2 NXR gamma subunit 2 1 SP 34.2/30.5 NITMOv2_3624 NITMOv2_RS16660 20,365 2508 nxrC_1 NXR gamma subunit 1 1 SP 30.8/27.4 NITMOv2_3617 NITMOv2_RS16630 354 115 nxrC_3 NXR gamma...”
- “...alpha subunit 1 131.8 NITMOv2_0255 NITMOv2_RS01130 486 215 nxrB_1 NXR beta subunit 1 49.8 NITMOv2_0254 NITMOv2_RS01125 311 179 nxrA_2 NXR alpha subunit 2 131.6 NITMOv2_4028 NITMOv2_RS18515 179 76 nxrB_2 NXR beta subunit 2 49.8 NITMOv2_4027 NITMOv2_RS18510 59 46 nxrA_3 NXR alpha subunit 3 131.9 NITMOv2_4033 NITMOv2_RS18535...”
- “...alpha subunit 3 131.9 NITMOv2_4033 NITMOv2_RS18535 19 7 nxrB_3 NXR beta subunit 3 49.8 NITMOv2_4032 NITMOv2_RS18530 9 11 nxrC_2 NXR gamma subunit 2 1 SP 34.2/30.5 NITMOv2_3624 NITMOv2_RS16660 20,365 2508 nxrC_1 NXR gamma subunit 1 1 SP 30.8/27.4 NITMOv2_3617 NITMOv2_RS16630 354 115 nxrC_3 NXR gamma subunit...”
NITMOv2_4027, NITMOv2_RS18510 4Fe-4S dicluster domain-containing protein from Nitrospira moscoviensis
30% identity, 76% coverage
- Cultivation and Transcriptional Analysis of a Canonical Nitrospira Under Stable Growth Conditions
Mundinger, Frontiers in microbiology 2019 - “...NXR alpha subunit 2 131.6 NITMOv2_4028 NITMOv2_RS18515 179 76 nxrB_2 NXR beta subunit 2 49.8 NITMOv2_4027 NITMOv2_RS18510 59 46 nxrA_3 NXR alpha subunit 3 131.9 NITMOv2_4033 NITMOv2_RS18535 19 7 nxrB_3 NXR beta subunit 3 49.8 NITMOv2_4032 NITMOv2_RS18530 9 11 nxrC_2 NXR gamma subunit 2 1 SP...”
- “...alpha subunit 2 131.6 NITMOv2_4028 NITMOv2_RS18515 179 76 nxrB_2 NXR beta subunit 2 49.8 NITMOv2_4027 NITMOv2_RS18510 59 46 nxrA_3 NXR alpha subunit 3 131.9 NITMOv2_4033 NITMOv2_RS18535 19 7 nxrB_3 NXR beta subunit 3 49.8 NITMOv2_4032 NITMOv2_RS18530 9 11 nxrC_2 NXR gamma subunit 2 1 SP 34.2/30.5...”
DSY0894 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
46% identity, 20% coverage
DSY0887 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
46% identity, 20% coverage
Dsui_2508 sulfate reduction electron transfer complex DsrMKJOP subunit DsrO from Azospira oryzae PS
47% identity, 21% coverage
- Curated BLAST for Genomes
Price, mSystems 2019 - “...characterized protein. Curated BLAST also found another protein in the genome of A. oryzae , Dsui_2508, that has some similarity to perchlorate reductase. The alignment covers less than 50% of the perchlorate reductase subunit (38% cov), and the similarity is modest (43% id.), which suggests that...”
- “...entries about homologs of a protein of interest. Clicking on the PaperBLAST link shows that Dsui_2508 is 57% identical, over 85% of its length, to a subunit of a tetrathionate reductase, so Dsui_2508 is not likely to be involved in perchlorate reduction. As illustrated by this...”
DSY3061 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
42% identity, 20% coverage
DSY3057 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
43% identity, 20% coverage
TC 5.A.3.10.1 / Q7WMZ5 Tetrathionate reductase subunit B, component of Tetrathionate reductase, TtrABC from Bordetella bronchiseptica (Alcaligenes bronchisepticus) (see paper)
40% identity, 25% coverage
ttrB / Q7CQM9 tetrathionate reductase β subunit from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 3 papers)
TTRB_SALTY / Q7CQM9 Tetrathionate reductase subunit B; Tetrathionate reductase electron transport protein from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 3 papers)
ttrB / CAB37414.1 tetrathionate reductase subunit B (TtrB) from Salmonella enterica subsp. enterica serovar Typhimurium (see 2 papers)
NP_805056 tetrathionate reductase subunit B from Salmonella enterica subsp. enterica serovar Typhi Ty2
NP_460350, STM1385 tetrathionate reductase complex, subunit B from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
42% identity, 24% coverage
- function: Part of a membrane-bound tetrathionate reductase that catalyzes the reduction of tetrathionate to thiosulfate. TtrB is probably involved in transfer of electrons from TtrC to TtrA. During mice infection, the ability to use tetrathionate as an electron acceptor is a growth advantage for S.typhimurium over the competing microbiota in the lumen of the inflamed gut.
subunit: Probably composed of three subunits: TtrA, TtrB and TtrC. - Prediction of twin-arginine signal peptides
Bendtsen, BMC bioinformatics 2005 - “...of an arginine in the first position of the Tat signal peptide motif (Genbank AC: NP_805056) [ 11 ], was correctly and positively predicted by TatP if the regular expression was expanded with a lysine in the first position. TATFIND does not directly allow variations in...”
- Stress response, amino acid biosynthesis and pathogenesis genes expressed in Salmonella enterica colonizing tomato shoot and root surfaces
Han, Heliyon 2020 - “...STM0843 pyruvate formate lyase 1.2 0.004 ttrA STM1383 tetrathionate reductase subunit A 1.3 0.003 ttrB STM1385 tetrathionate reductase subunit B 1.2 0.005 ydiQ STM1354 Electron transfer flavoprotein; may play a role in electron transport between the anaerobic fatty acid oxidation pathway and the respiratory chain 1.0...”
- Signal peptide etiquette during assembly of a complex respiratory enzyme.
James, Molecular microbiology 2013 (PubMed)- GeneRIF: findings reveal that processing of TtrB Tat signal peptide is dependent on successful assembly of its partner protein, TtrA; data suggest both signals are active during assembly of the enzyme and imply a code of conduct exists between the signal peptides where one can compensate for inactivity in the other
- Abrogation of the twin arginine transport system in Salmonella enterica serovar Typhimurium leads to colonization defects during infection
Reynolds, PloS one 2011 - “...ycbK y b0926 ycbK y putative outer membrane protein STM1383 ttrA y tetrathionate reductase (SPI-2) STM1385 ttrB y ** tetrathionate reductase (SPI-2) STM1498 ynfF y b1588 ynfF y putative dimethyl sulfoxide reductase STM1499 ynfE b y b1587 ynfE y putative dimethyl sulfoxide reductase STM1539 hyaA c...”
K3G22_02680 sulfate reduction electron transfer complex DsrMKJOP subunit DsrO from Shewanella putrefaciens
45% identity, 19% coverage
Shew185_3734 4Fe-4S ferredoxin iron-sulfur binding domain protein from Shewanella baltica OS185
45% identity, 19% coverage
- Adaptation of the Marine Bacterium Shewanella baltica to Low Temperature Stress
Kloska, International journal of molecular sciences 2020 - “...only downregulated genes in the sulfur metabolic pathway were those encoding the tetrathionate reductase ttrB (Shew185_3734), and thiosulfate/3-mercaptopyruvate sulfurtransferase (Shew185_1160), i.e., enzymes playing a key role in tetrathionate and thiosulfate metabolism. Under anaerobic conditions there is a switch of sulfur metabolism to the dissimilatory pathway in...”
AMK58_24695 sulfate reduction electron transfer complex DsrMKJOP subunit DsrO from Azospirillum brasilense
38% identity, 27% coverage
VP2011 tetrathionate reductase, subunit B from Vibrio parahaemolyticus RIMD 2210633
VP_RS09775 sulfate reduction electron transfer complex DsrMKJOP subunit DsrO from Vibrio parahaemolyticus RIMD 2210633
47% identity, 19% coverage
WU75_13155 sulfate reduction electron transfer complex DsrMKJOP subunit DsrO from Vibrio parahaemolyticus
47% identity, 19% coverage
amb3289 Fe-S-cluster-containing hydrogenase components 1 from Magnetospirillum magneticum AMB-1
39% identity, 22% coverage
- A protease-mediated switch regulates the growth of magnetosome organelles in Magnetospirillum magneticum
Wan, Proceedings of the National Academy of Sciences of the United States of America 2022 - “...contrast, one magnetosome protein, MamD (also known as Mms7), and three proteins (Amb3286, Amb3288, and Amb3289) encoded by a putative operon outside of MAI were greatly enriched in magnetosomes from mamE pd ( Fig. 3 A ). Amb3286, Amb3288, and Amb3289 are annotated as tetrathionate reductase...”
- “...shows no noticeable differences between the two strains. MamE is slightly enriched, while Amb3286, Amb3288, Amb3289, and MamD are clearly enriched in purified magnetosomes from mamE pd . The mean values of peptides for each protein are from five distinct preparations of magnetosomes (see full dataset...”
- Simultaneously discrete biomineralization of magnetite and tellurium nanocrystals in magnetotactic bacteria
Tanaka, Applied and environmental microbiology 2010 - “...Amb2321, 1e63; and Amb1666, 1e41), trgB (Amb1307, 5e26), narH (Amb3289, 3e21; Amb3542, 2e18; Amb1649, 4e17; and Amb3377, 4e13) were found and presumed to be the...”
DSY3751 putative anaerobic DMSO reductase chain B iron-sulfur subunit from Desulfitobacterium hafniense Y51
37% identity, 26% coverage
DSY4904 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
44% identity, 20% coverage
AL038_09730, BLE401_14540 4Fe-4S dicluster domain-containing protein from Beggiatoa leptomitoformis
33% identity, 36% coverage
PMI1706 anaerobic dimethyl sulfoxide reductase chain B from Proteus mirabilis HI4320
47% identity, 18% coverage
YPTB2689 putative dimethyl sulfoxide reductase chain B protein from Yersinia pseudotuberculosis IP 32953
YPO2966 putative dimethyl sulfoxide reductase chain B protein from Yersinia pestis CO92
45% identity, 18% coverage
V6E02_08845 4Fe-4S dicluster domain-containing protein from Thiobacter aerophilum
38% identity, 28% coverage
VP1448 anaerobic dimethyl sulfoxide reductase, subunit B from Vibrio parahaemolyticus RIMD 2210633
VP_RS07025 DMSO/selenate family reductase complex B subunit from Vibrio parahaemolyticus RIMD 2210633
39% identity, 21% coverage
GSU0069 oxidoreductase, iron-sulfur cluster-binding subunit from Geobacter sulfurreducens PCA
42% identity, 22% coverage
GF1_03930 sulfate reduction electron transfer complex DsrMKJOP subunit DsrO from Desulfolithobacter dissulfuricans
47% identity, 18% coverage
JHW33_RS01730 DMSO/selenate family reductase complex B subunit from Rahnella aceris
38% identity, 23% coverage
YnfG / b1589 putative oxidoreductase YnfG (EC 1.97.1.9) from Escherichia coli K-12 substr. MG1655 (see paper)
ynfG / P0AAJ1 putative oxidoreductase YnfG (EC 1.97.1.9) from Escherichia coli (strain K12) (see 2 papers)
TC 5.A.3.3.1 / P0AAJ1 Probable anaerobic dimethyl sulfoxide reductase chain ynfG aka DMSO reductase iron-sulfur subunit, component of Anaerobic dimethylsulfoxide (DMSO) reductase, (YnfEFGH) from Escherichia coli (see 3 papers)
ECs2295 putative oxidoreductase Fe-S subunit from Escherichia coli O157:H7 str. Sakai
b1589 oxidoreductase, Fe-S subunit from Escherichia coli str. K-12 substr. MG1655
Z2577 putative oxidoreductase, Fe-S subunit from Escherichia coli O157:H7 EDL933
42% identity, 20% coverage
- substrates: Electrons
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...O157 2.30 2 ECs2670 yedK 2.55 2 ECs2292 - 3.22 2 ECs2693 - 2.62 2 ECs2295 ynfG -2.81 6 ECs2785 erfK 2.37 2 ECs2820 hisG -2.80 1 ECs3458 yfiO -2.61 1 ECs2821 hisD -2.57 1 ECs3465 yfiL 3.81 2 ECs2822 hisC -2.52 1 ECs3469 rplS -4.28...”
- A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli
Rodionova, Scientific reports 2022 - “...cspI Qin prophage cold shock protein CspI 6.3 5.6 b3370 frlA Fructoselysine/psicoselysine transporter 2.1 5.5 b1589 ynfG Putative oxidoreductase YnfG 87.0 5.5 b1890 motA Motility protein A 267.0 5.4 b1940 fliH Flagellar biosynthesis protein FliH 73.1 5.4 b0903 pflB Pyruvate formate-lyase 23,055.8 5.4 b4355 tsr Methyl-accepting...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction
Oberto, PloS one 2009 - “...1 4.96 4.83 0.14 1 0.32 0.3 2.08 FA, FAec putative oxidoreductase, major subunit ynfG b1589 ynfEFGH-dmsD 1 0.26 2.05 0.14 1 7.12 4.24 0.12 1 0.21 1.67 1.99 FA, FAec putative oxidoreductase, Fe-S subunit ynfH b1590 ynfEFGH-dmsD 1 0.64 1.48 0.87 1 5.19 3.77 0.67...”
- Activation of prophage eib genes for immunoglobulin-binding proteins by genes from the IbrAB genetic island of Escherichia coli ECOR-9
Sandt, Journal of bacteriology 2002 - “...that common to E. coli K-12 occurred within gene b1589, which is predicted to encode the Fe-S subunit of an oxidoreductase. Based on this relationship, we...”
- Comparative Whole Genome Analysis of Escherichia coli O157:H7 Isolates From Feedlot Cattle to Identify Genotypes Associated With the Presence and Absence of stx Genes
Jia, Frontiers in microbiology 2021 - “...stx insertion sites ( wrbA , sbcB , yehV , argW , yecE , and Z2577 ) were extracted from the whole genome sequence of E. coli O157:H7 strain Sakai ( Yokoyama et al., 2000 ; Hayashi et al., 2001 ; Ohnishi et al., 2002 ;...”
- “...stx insertion sites ( wrbA , sbcB , yehV , argW , yecE , and Z2577 ). All 10 strains carried all 6 stx insertion site genes. As shown in Table 4 , three of the stx insertion sites of wrbA , yehV , and sbcB...”
- Variability in the Occupancy of Escherichia coli O157 Integration Sites by Shiga Toxin-Encoding Prophages
Henderson, Toxins 2021 - “...It is therefore more likely that the Stx2a/2c prophages were integrated within the yecE or Z2577 insertion sites, which were not examined but were previously shown to be occupied by Stx prophages at low frequencies [ 22 ]. The same is true for the 59 additional...”
- Bacteriophages of Shiga Toxin-Producing Escherichia coli and Their Contribution to Pathogenicity
Rodríguez-Rubio, Pathogens (Basel, Switzerland) 2021 - “...function is unknown [ 32 ], sbcB encoding an exonuclease [ 17 , 53 ], Z2577 encoding an oxidoreductase [ 54 ], ssrA encoding a tmRNA [ 55 ], prfC encoding a peptide chain release factor [ 56 ], argW encoding a tRNA [ 57 ],...”
- Pathogenomes of Atypical Non-shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive Phylogenomic Analysis Using Closed Genomes
Nyong, Frontiers in microbiology 2020 - “...al., 2008 ), yecE of unknown function ( Shringi et al., 2012 ), and oxidoreductase (Z2577) ( Koch et al., 2003 ; Serra-Moreno et al., 2007 ). Unoccupied SBI were defined as those strains that showed undisrupted BLASTn alignments when queried ( Altschul et al., 1990...”
- Whole-Genome Sequence of Escherichia coli Serotype O157:H7 Strain ATCC 43888
Uhlich, Microbiology resource announcements 2019 - “...in the stx 2 insertion sites within the wrbA , sbcB , yecE , or Z2577 genes. An LEE pathogenicity island with 99.99% identity (100% coverage with no gaps) to the reference outbreak strain Sakai (GenBank accession number NC_002695 ) ( 4 ) was present. The...”
- Escherichia coli ST302: Genomic Analysis of Virulence Potential and Antimicrobial Resistance Mediated by Mobile Genetic Elements
Jarocki, Frontiers in microbiology 2019 - “...was found to have the following unoccupied: wrbA (2984895.2985491), yehV (1780350.1781081), yecE (2076464.2077282), sbcB (1921208.1922635), Z2577 (2354785.2354802) and the torS/torT intergenic region (2996339.2996467). Additionally, F2_18C possesses the lambda phage receptor gene LamB (4667691.4669028) required for lambda bacteriophage adsorption ( Bertozzi Silva et al., 2016 ). F2_18C...”
- Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli
González-Escalona, PloS one 2019 - “...have been described in STEC strains genes: wrbA , yehV , yecE , sbcB , Z2577 , ssrA , prfC , argW , torS-torT intergenic region. Delannoy et al. (2017) also described the presence of a Stx phage at a different insertion site yciD for O26:H11/H-...”
- Highly Pathogenic Clone of Shiga Toxin-Producing Escherichia coli O157:H7, England and Wales
Byrne, Emerging infectious diseases 2018 - “...an exonuclease; yecE , a gene of unknown function; the tRNA gene argW ; and Z2577, which encodes an oxidoreductase ( 5 ). We mapped short reads from the STEC O157:H7 genomes to intact reference sequences of these genes, and aligned them with BWA MEM (...”
- More
S1742 putative oxidoreductase, Fe-S subunit from Shigella flexneri 2a str. 2457T
42% identity, 20% coverage
- Distribution and characterization of Shiga toxin converting temperate phages carried by Shigella flexneri in Hispaniola
Fogolari, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018 - “...Haiti. In each instance, the insertion site in the bacterial genomes was identified as locus S1742 or a homologous gene. 3.2. Phylogenetic inference of POC-J13 phage sequences The phage POC-J13 sequences extracted from all stx -positive bacterial strains and the POC-J13 reference sequence from BS937 11...”
- Stx-Producing Shigella Species From Patients in Haiti: An Emerging Pathogen With the Potential for Global Spread
Gray, Open forum infectious diseases 2015 - “...primers Stx1R2/Phage_stxR2 and Phage_stx1F2/Stx1F2 [ 9 ]. The insertion site of the phage into locus S1742 or a homologous gene was determined by PCR using primers to the region upstream of S1742 and an early phage gene (primers S1742_up/Stx_phage_up) and by amplifying a late phage gene...”
- “...previous studies, we found that POC-J13 is inserted into the S flexneri chromosome at locus S1742. Polymerase chain reaction analysis using the primers from those studies demonstrated that the phage in the Stx-producing Haiti isolates was also inserted into S1742 or a homologous gene. Whole-genome sequencing...”
- Prevalence of Shiga toxin-producing Shigella species isolated from French travellers returning from the Caribbean: an emerging pathogen with international implications
Gray, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2015 - “...pairs Stx1R2/Phage_stxR2 and Phage_stx1F2/Stx1F2 [ 6 ]. The insertion site of the phage into locus S1742 or a homologous gene was determined by PCR using primers to the upstream region of S1742 and an early phage gene (primers S1742_up/Stx-_phage_up) and by amplifying a late phage gene...”
- “...our previous analysis showed that POC-J13 is inserted in the S. flexneri chromosome into locus S1742, which encodes a putative oxidoreductase. Based upon our primer sequences designed from POC-J13, we determined that the phage in each of the 12 stx -positive French isolates had also inserted...”
- Clinical isolates of Shiga toxin 1a-producing Shigella flexneri with an epidemiological link to recent travel to Hispañiola
Gray, Emerging infectious diseases 2014 - “...primer pairs Stx1R2/Phage_stxR2 and Phage_stx1F2/Stx1F2. The insertion site of the phage into S. flexneri locus S1742 was determined by amplifying the upstream region of S1742 and an early phage gene with primers S1742_up/Stx_phage_up and by amplifying a late phage gene and the downstream region of S1742...”
- “...study Phage_stxR2 GACGCCATACAAGGAGTC Stx1F2 ACGCCTGATTGTGTAACTGGAAA 1,333 This study Phage_stx1F2 CACTCGCGTCACTGTATG Stx_phage_up GACCGCACACTGTGCTATC 1,155 This study S1742 up CCGTGCGGGTATTTAACAATAATGG Stx_phage_dn AGTCAAACCGCGCTATTGG 1,224 This study S1742 dn TGCATGACAGAGGCAATAAACCCGAT RecAko-site1 GCTATCGACGAAAACAAACAGAAAGCGTTGGCGGCAGCACTGGGCCAGATTGTGTAGGCTGGAGCTGCTTC 1,609 This study RecAko-site2 AAAATCTTCGTTAGTTTCTGCTACTCCTTCGCTGTCATCTACAGAGAAATCCATATGAATATCCTCCTTA RecA-1 ACATATTGACTATCCGGTATTACCCGG 1,148, 1,701* This study RecA-3 GACCGTCCGTGCACACATTATCTATT *Amplicon sizes for wild-type recA...”
DSY4617 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
38% identity, 23% coverage
c1032 Anaerobic dimethyl sulfoxide reductase chain B from Escherichia coli CFT073
42% identity, 20% coverage
DmsB / b0895 dimethyl sulfoxide reductase subunit B (EC 1.8.5.3) from Escherichia coli K-12 substr. MG1655 (see 4 papers)
dmsB / P18776 dimethyl sulfoxide reductase subunit B (EC 1.8.5.3) from Escherichia coli (strain K12) (see paper)
TC 5.A.3.3.2 / P18776 Anaerobic dimethyl sulfoxide reductase chain B aka DMSO reductase iron-sulfur subunit (DmsB), component of Anaerobic dimethyl sulfoxide (DMSO) reductase, DmsABC from Escherichia coli (see 6 papers)
NP_415415 dimethyl sulfoxide reductase subunit B from Escherichia coli str. K-12 substr. MG1655
b0895 dimethyl sulfoxide reductase, anaerobic, subunit B from Escherichia coli str. K-12 substr. MG1655
42% identity, 20% coverage
- substrates: Electrons
- Nucleotide sequence of the dmsABC operon encoding the anaerobic dimethylsulphoxide reductase of Escherichia coli.
Bilous, Molecular microbiology 1988 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on mature peptide
- Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth
Franchini, PloS one 2015 - “...synthetase, beta subunit 4.4 moa b0781 molybdopterin biosynthesis, protein A -6.2 ** -7.4 ** dmsB b0895 anaerobic dimethyl sulfoxide reductase subunit B -7.4 ** -3.0 ** mgsA b0963 methylglyoxal synthase 5.5 nark b1223 nitrite extrusion protein 4.7 aldA c , f , g b1415 aldehyde dehydrogenase,...”
- The sulfur carrier protein TusA has a pleiotropic role in Escherichia coli that also affects molybdenum cofactor biosynthesis
Dahl, The Journal of biological chemistry 2013 - “...Molybdate transporter subunit ATP-binding protein Molybdoenzymes b0285 b0894 b0895 b1222 b1223 b1224 b1225 b1226 b1227 b1465 b1466 b1467 b1468 b1469 b1476 b1587...”
- The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction
Oberto, PloS one 2009 - “...1.78 0.14 1 1.04 0.61 1.03 FA, FAec anaerobic dimethyl sulfoxide reductase subunit A dmsB b0895 dmsABC 1 0.05 1.59 0.13 1 2.16 2.19 0.3 1 1.5 1.48 1.65 FA, FAec anaerobic dimethyl sulfoxide reductase subunit B narK b1223 narK 1 0.02 1.08 0.16 1 3.44...”
amb3542 Fe-S-cluster-containing hydrogenase components 1 from Magnetospirillum magneticum AMB-1
40% identity, 22% coverage
Z1241 anaerobic dimethyl sulfoxide reductase subunit B from Escherichia coli O157:H7 EDL933
42% identity, 20% coverage
PAE1263 molybdopterin oxidoreductase, iron-sulfur binding subunit from Pyrobaculum aerophilum str. IM2
44% identity, 19% coverage
DSY0549 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
40% identity, 20% coverage
ST1839 270aa long hypothetical thiosulfate reductase electron transport protein phsB from Sulfolobus tokodaii str. 7
46% identity, 16% coverage
FOKN1_0491 4Fe-4S dicluster domain-containing protein from Thiohalobacter thiocyanaticus
38% identity, 26% coverage
DSY0187 putative anaerobic DMSO reductase chain B iron-sulfur subunit from Desulfitobacterium hafniense Y51
44% identity, 19% coverage
2vpwF / Q72LA5 Polysulfide reductase with bound menaquinone (see paper)
43% identity, 20% coverage
- Ligand: iron/sulfur cluster (2vpwF)
Pcal_1599 4Fe-4S ferredoxin, iron-sulfur binding domain protein from Pyrobaculum calidifontis JCM 11548
43% identity, 19% coverage
AMK58_25705 4Fe-4S dicluster domain-containing protein from Azospirillum brasilense
38% identity, 25% coverage
TC 5.A.3.11.2 / O67279 SreB aka DmsB1 aka DMSO reductase chain B, component of The cytoplasmic sulfur/tetrathionate/polysulfide oxidoreductase, SreABC (Guiral et al., 2005) [While SreA and B most resemble 5.A.3.11.1, SreC most resembles 5.A.3.3.2.] from Aquifex aeolicus (see paper)
41% identity, 20% coverage
DSY1449 putative anaerobic DMSO reductase chain B iron-sulfur subunit from Desulfitobacterium hafniense Y51
43% identity, 19% coverage
DMSB_HALSA / Q9HR73 Putative dimethyl sulfoxide reductase iron-sulfur subunit B; DMSO reductase subunit B from Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halobacterium halobium) (see paper)
TC 5.A.3.3.3 / Q9HR73 DmsB (Gamma-1); aka Molybdopterin oxidoreductase, component of Anaerobic dimethylsulfoxide (DMSO)/trimethylamine-N-oxide (TMAO) reductase from Halobacterium salinarium (Halobacterium halobium) (see paper)
36% identity, 24% coverage
- function: Dimethyl sulfoxide (DMSO) reductase catalyzes the reduction of dimethyl sulfoxide (DMSO) to dimethyl sulfide (DMS) during anaerobic respiration; it can also use trimethylamine N-oxide (TMAO) as terminal electron acceptor. Subunit B is proposed to be involved in electron transfer
cofactor: [4Fe-4S] cluster (Binds 4 [4Fe-4S] clusters.)
subunit: Probable multiprotein complex that likely consists of DmsA, DmsB and DmsC - substrates: Electrons
SRDB_MESS1 / A0A0A8X5N4 Selenate reductase subunit B; Selenate reductase electron transport subunit; EC 1.97.1.14 from Mesobacillus selenatarsenatis (strain DSM 18680 / JCM 14380 / FERM P-15431 / SF-1) (see paper)
E9RFC9 selenate reductase (EC 1.97.1.9) from Mesobacillus selenatarsenatis (see paper)
35% identity, 20% coverage
- function: Component of the respiratory selenate reductase complex, which catalyzes the reduction of selenate to selenite (PubMed:21357486). This subunit probably transfers electrons from SrdC to SrdA (Probable).
catalytic activity: selenite + a quinone + H2O = selenate + a quinol (RHEA:51636)
cofactor: [4Fe-4S] cluster (Binds 4 [4Fe-4S] cluster.)
subunit: The complex is composed of three subunits: SrdA, SrdB and SrdC.
SSO2794 Oxydoreductase, putative from Sulfolobus solfataricus P2
31% identity, 32% coverage
HVO_B0364 molybdopterin oxidoreductase from Haloferax volcanii DS2
40% identity, 20% coverage
YP_001472099 anaerobic dimethyl sulfoxide reductase, subunit B from Shewanella sediminis HAW-EB3
32% identity, 28% coverage
- Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation
Zhao, PloS one 2010 - “...+ YP_001672640 + DmsA/YnfE family A subunit YP_001472091, 2100, 3046, 3143, 4658, + subunit B YP_001472099 + Note: , last four digits of accession number given; , CDS sets listed in Table 2 ; +, present. To adapt to the high osmotic pressure of seawater, S....”
Gmet_3519 Twin-arginine translocation pathway signal from Geobacter metallireducens GS-15
40% identity, 23% coverage
aq_067 dimethylsulfoxide reductase chain B from Aquifex aeolicus VF5
O66481 Dimethylsulfoxide reductase chain B from Aquifex aeolicus (strain VF5)
44% identity, 18% coverage
STM0965 anaerobic dimethyl sulfoxide reductase, subunit B from Salmonella typhimurium LT2
39% identity, 20% coverage
YPTB0806 anaerobic dimethyl sulfoxide reductase, subunit B from Yersinia pseudotuberculosis IP 32953
34% identity, 23% coverage
- IscR is essential for yersinia pseudotuberculosis type III secretion and virulence
Miller, PLoS pathogens 2014 - “...ribonucleotide reductase activating protein nrdG 2.6 YPTB0805 anaerobic dimethyl sulfoxide reductase, subunit A dmsA 2.3 YPTB0806 anaerobic dimethyl sulfoxide reductase, subunit B dmsB 2.1 YPTB2688 putative dimethyl sulfoxide reductase chain A protein dmsA 2.1 Regulatory Functions (3) YPTB0247 lysR-family transcriptional regulatory protein metR 2.0 YPTB0386 L-rhamnose...”
DSY3895 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
39% identity, 22% coverage
Moth_0451 4Fe-4S ferredoxin, iron-sulfur binding from Moorella thermoacetica ATCC 39073
38% identity, 22% coverage
DSY0598 putative anaerobic DMSO reductase chain B iron-sulfur subunit from Desulfitobacterium hafniense Y51
44% identity, 17% coverage
TC 5.A.3.11.1 / Q5P036 Molybdenum enzyme, medium subunit,related to phenylacetyl-CoA: acceptor oxidoreductase, component of Phenylacetyl-CoA:acceptor oxidoreductase (see paper)
38% identity, 20% coverage
Dde_0681 Oxidoreductase, iron-sulfur cluster-binding subunit from Desulfovibrio desulfuricans G20
35% identity, 23% coverage
FNX95_13385 DMSO/selenate family reductase complex B subunit from Klebsiella variicola
40% identity, 19% coverage
- Isolation of Anaerobic Bromate-Reducing Bacteria Using Different Carbon Sources and Transcriptomic Insights From Klebsiella variicola Glu3
Wang, Frontiers in microbiology 2022 - “...on the genome of strain K. variicola Glu3. In addition, the dimethylsulfoxide reductase encoding genes (FNX95_13385 and FNX95_13390), which is another member of the DMSOR family, were also present. However, transcription of those genes mentioned above was downregulated when 0.1mm or 0.5mm bromate was dosed (...”
- “...superoxide dismutase [Fe] FNX95_09885 2.20 1.30 NA molybdopterin-dependent oxidoreductase FNX95_13380 3.16 1.82 NA dimethylsulfoxide reductase FNX95_13385 3.89 2.21 dmsB dimethylsulfoxide reductase subunit B FNX95_13390 3.59 1.85 dmsA dimethylsulfoxide reductase subunit A FNX95_13975 1.73 1.27 moaE molybdopterin synthase catalytic subunit FNX95_13980 2.03 1.34 moaD molybdopterin synthase sulfur...”
STM4306 putative anaerobic dimethyl sulfoxide reductase, subunit B from Salmonella typhimurium LT2
SL1344_RS22110 DMSO/selenate family reductase complex B subunit from Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
38% identity, 19% coverage
- Nonredundant Dimethyl Sulfoxide Reductases Influence Salmonella enterica Serotype Typhimurium Anaerobic Growth and Virulence
Cruz, Infection and immunity 2023 (secret) - Effects of colonization-associated gene yqiC on global transcriptome, cellular respiration, and oxidative stress in Salmonella Typhimurium
Fan, Journal of biomedical science 2022 - “...tdcD Propionate kinase 3.106 0.001601 13 cadA cadA Lysine decarboxylase CadA 2.988 0.001601 14 SL1344_RS22110 STM4306 Dimethylsulfoxide reductase, chain B 2.979 0.001601 15 SL1344_RS22105 STM4305 Dimethyl sulfoxide reductase subunit A 2.883 0.001601 16 tdcC tdcC Threonine/serine transporter TdcC 2.869 0.001601 17 cadB cadB Arginine:agmatine antiporter 2.809...”
- Effects of indole on drug resistance and virulence of Salmonella enterica serovar Typhimurium revealed by genome-wide analyses
Nikaido, Gut pathogens 2012 - “...I), anaerobic isozyme 0.19 0.088 STM4305 Putative anaerobic dimethyl sulfoxide reductase, subunit A 0.14 0.082 STM4306 Putative anaerobic dimethyl sulfoxide reductase, subunit B 0.11 0.058 STM4452 nrdD Anaerobic ribonucleoside-triphosphate reductase 0.047 0.095 STM4465 Putative ornithine carbamoyltransferase 0.19 0.10 STM4466 Putative carbamate kinase 0.19 0.10 STM4467 Putative...”
- Salmonella serovar identification using PCR-based detection of gene presence and absence
Arrach, Journal of clinical microbiology 2008 - “...STM4102, STM4113, STM4115, STM4205, STM4261, STM4279, STM4306, STM4319, STM4373, STM4413, STM4420, STM4426, STM4445, STM4484, STM4486, STM4493, STM4499,...”
- A new experimental approach for studying bacterial genomic island evolution identifies island genes with bacterial host-specific expression patterns
Wilson, BMC evolutionary biology 2006 - “...two-component system with DcuR island genes STM4305 dmsA Putative anaerobic dimethyl sulfoxide reductase, subunit A STM4306 dmsB Putative anaerobic dimethyl sulfoxide reductase, subunit B STM4307 dmsC Putative anaerobic dimethyl sulfoxide reductase, subunit C STM4308 Putative component of anaerobic dehydrogenases STM4309 Putative periplasmic or exported protein STM4310...”
- Effects of colonization-associated gene yqiC on global transcriptome, cellular respiration, and oxidative stress in Salmonella Typhimurium
Fan, Journal of biomedical science 2022 - “...tdcD tdcD Propionate kinase 3.106 0.001601 13 cadA cadA Lysine decarboxylase CadA 2.988 0.001601 14 SL1344_RS22110 STM4306 Dimethylsulfoxide reductase, chain B 2.979 0.001601 15 SL1344_RS22105 STM4305 Dimethyl sulfoxide reductase subunit A 2.883 0.001601 16 tdcC tdcC Threonine/serine transporter TdcC 2.869 0.001601 17 cadB cadB Arginine:agmatine antiporter...”
soeB / D3RNN7 SoeB (EC 1.8.5.6) from Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D) (see paper)
SOEB_ALLVD / D3RNN7 Sulfite dehydrogenase subunit B; Sulfite dehydrogenase iron-sulfur subunit; Sulfite-oxidizing enzyme subunit B from Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D) (Chromatium vinosum) (see paper)
D3RNN7 sulfite dehydrogenase (quinone) (subunit 2/3) (EC 1.8.5.6) from Allochromatium vinosum (see paper)
Alvin_2490 4Fe-4S ferredoxin iron-sulfur binding domain protein from Allochromatium vinosum DSM 180
35% identity, 26% coverage
DSY3521 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
35% identity, 26% coverage
TC 5.B.12.1.1 / SFW35650 SFW35650.1 putative sulfite reductase-associated electron transfer protein DsrO, component of Transmembrane one electron carrier complex, DsrMJKOP from Desulfovibrio desulfuricans
41% identity, 18% coverage
- substrates: Electrons
tcdb comment: See family description for the properties of the 5 constituent proteins
DSY3723 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
38% identity, 20% coverage
STM2529 putative anaerobic dimethylsulfoxide reductase from Salmonella typhimurium LT2
40% identity, 18% coverage
SEN2509 putative anaerobic reductase component from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
40% identity, 18% coverage
amb1649 Fe-S-cluster-containing hydrogenase components 1 from Magnetospirillum magneticum AMB-1
40% identity, 18% coverage
NTHI1206 anaerobic dimethyl sulfoxide reductase chain B from Haemophilus influenzae 86-028NP
37% identity, 18% coverage
D11S_0494 anaerobic dimethyl sulfoxide reductase chain B from Aggregatibacter actinomycetemcomitans D11S-1
37% identity, 23% coverage
YP_001672640 Dimethylsulfoxide reductase chain B from Shewanella halifaxensis HAW-EB4
37% identity, 19% coverage
- Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation
Zhao, PloS one 2010 - “...TorT YP_001675621-5625 + + cytochrome c , TorC YP_001675619 + DMSO reductase YP_001675134, 5133 + YP_001672640 + DmsA/YnfE family A subunit YP_001472091, 2100, 3046, 3143, 4658, + subunit B YP_001472099 + Note: , last four digits of accession number given; , CDS sets listed in Table...”
DSY3409 putative anaerobic DMSO reductase chain B iron-sulfur subunit from Desulfitobacterium hafniense Y51
39% identity, 20% coverage
UWK_00239 sulfate reduction electron transfer complex DsrMKJOP subunit DsrO from Desulfocapsa sulfexigens DSM 10523
34% identity, 20% coverage
DET0103 molybdopterin oxidoreductase, iron-sulfur binding subunit, putative from Dehalococcoides ethenogenes 195
32% identity, 20% coverage
BCAM1175 putative dimethyl sulfoxide reductase subunit from Burkholderia cenocepacia J2315
40% identity, 18% coverage
Hflu203000517 COG0437: Fe-S-cluster-containing hydrogenase components 1 from Haemophilus influenzae R2866
37% identity, 18% coverage
Dshi_1237 4Fe-4S ferredoxin iron-sulfur binding domain protein from Dinoroseobacter shibae DFL 12
33% identity, 23% coverage
DSY1254 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
38% identity, 21% coverage
Theos_0750 4Fe-4S dicluster domain-containing protein from Thermus oshimai JL-2
39% identity, 20% coverage
AF0175 molybdopterin oxidoreductase, iron-sulfur binding subunit from Archaeoglobus fulgidus DSM 4304
33% identity, 20% coverage
DSY0528 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
38% identity, 20% coverage
Dpo_3c03820 4Fe-4S dicluster domain-containing protein from Desulfotignum phosphitoxidans DSM 13687
38% identity, 19% coverage
KKC1_RS05310 4Fe-4S dicluster domain-containing protein from Calderihabitans maritimus
35% identity, 22% coverage
Z3784 putative dimethyl sulfoxide reductase subunit B from Escherichia coli O157:H7 EDL933
38% identity, 19% coverage
PMI1205 anaerobic dimethyl sulfoxide reductase chain B from Proteus mirabilis HI4320
40% identity, 18% coverage
swp_3458 Anaerobic dimethyl sulfoxide reductase, B subunit from Shewanella piezotolerans WP3
40% identity, 18% coverage
- Condition-Specific Molecular Network Analysis Revealed That Flagellar Proteins Are Involved in Electron Transfer Processes of Shewanella piezotolerans WP3
Ding, Genetics research 2021 - “...1 9 0.58 3.49 E 04 Carbon metabolism swp_3663, swp_5025, swp_4312, swp_1239, swp_2139, swp_2142, swp_3875, swp_3458, swp_0182 2 9 0.50 9.74 E 04 Oxidative phosphorylation swp_4058, swp_0854, swp_4352, swp_3589, swp_4940, swp_1424, swp_1425, swp_0430, swp_0429 3 6 0.87 1.26 E 03 Flagellar assembly swp_1531, swp_3616, swp_1536, swp_1521,...”
DSY0356 putative anaerobic DMSO reductase chain B iron-sulfur subunit from Desulfitobacterium hafniense Y51
34% identity, 21% coverage
AF0157 molybdopterin oxidoreductase, iron-sulfur binding subunit from Archaeoglobus fulgidus DSM 4304
42% identity, 19% coverage
- Conserved signal peptide recognition systems across the prokaryotic domains
Coulthurst, Biochemistry 2012 - “...in Archaeoglobus fulgidus . (A) Schematic representation of the AF0157AF0161 operon from A. fulgidus . AF0157 (TtrB) is predicted to be an FeS protein, AF0158 (TtrC) is predicted to be an integral membrane protein with nine transmembrane domains, AF0159 (TtrA) is predicted to encode a Tat-dependent...”
- “...A. fulgidus encodes a putative tetrathionate reductase (Figure 1 A). The genes in question are Af0157 Af0159 , but for ease of understanding here, and in agreement with the Salmonella nomenclature, 31 these have been renamed ttrBCA here (Figure 1 A). A. fulgidus TtrA (1134 residues)...”
TSC_c10040 4Fe-4S dicluster domain-containing protein from Thermus scotoductus SA-01
42% identity, 16% coverage
A0KLW8 4Fe-4S binding domain protein from Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / BCRC 13018 / CCUG 14551 / JCM 1027 / KCTC 2358 / NCIMB 9240 / NCTC 8049)
AHA_2761 4Fe-4S binding domain protein from Aeromonas hydrophila subsp. hydrophila ATCC 7966
31% identity, 29% coverage
phsB / P0A1I1 thiosulfate reductase (quinone) β subunit (EC 1.8.5.5) from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 8 papers)
PHSB_SALTY / P0A1I1 Thiosulfate reductase electron transfer subunit PhsB; Thiosulfate reductase subunit beta from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 2 papers)
P0A1I1 thiosulfate reductase (quinone) (subunit 1/2) (EC 1.8.5.5) from Salmonella enterica subsp. enterica serovar Typhimurium (see 2 papers)
TC 5.A.3.5.1 / P0A1I1 Thiosulfate reductase electron transport protein PhsB, component of Thiosulfate reductase, PhsABC (Heinzinger et al., 1995). Menaquinone is the sole electron donor. The endoergonic reduction reaction is driven by the pmf by a reverse loop mechanism. The enzyme can catalyze oxidation of sulfide to sulfite and sulfite to thiosulfate in an exergonic reaction that is pmf-independent from Salmonella typhimurium (see 3 papers)
phsB thiosulfate reductase electron transport protein phsb from Salmonella enterica subsp. enterica serovar Typhimurium (see paper)
phsB / AAC36935.1 thiosulfate reductase from Salmonella enterica subsp. enterica serovar Typhimurium (see paper)
STM2064 Hydrogen sulfide production: iron- sulfur subunit; electron transfer from Salmonella typhimurium LT2
37% identity, 20% coverage
- function: Component of the PhsABC thiosulfate reductase that catalyzes the reduction of thiosulfate to sulfite and hydrogen sulfide, with menaquinol as the sole electron donor. Proton motive force (PMF) is required to drive transmembrane electron transfer within the reductase. The PhsB subunit transfers electrons between PhsC and PhsA.
cofactor: [4Fe-4S] cluster (Binds 4 [4Fe-4S] clusters per subunit.)
subunit: Composed of three subunits: PhsA, PhsB and PhsC. - substrates: Electrons
- Abrogation of the twin arginine transport system in Salmonella enterica serovar Typhimurium leads to colonization defects during infection
Reynolds, PloS one 2011 - “...pgpB y phosphatidylglycerophosphate phosphatase STM1786 hyaA c y b0972 hyaA y hydrogenase 1, small subunit STM2064 phsB n b1671 ydhX y putative oxidoreductase STM2065 phsA y hydrogen sulfide production STM2099 wcaM y b2043 wcaM y putative colanic acid biosynthesis STM2258 napG y b2205 napG y ferredoxin,...”
- Comparison of Salmonella enterica serovar Typhimurium LT2 and non-LT2 salmonella genomic sequences, and genotyping of salmonellae by using PCR
Kim, Applied and environmental microbiology 2006 - “...results of genome comparison, only 4 genes (STM0699, STM2064, STM2549, and STM3098) from 31 genes of group 1 overlapped with previously reported Salmonella...”
TDIS_RS03055 4Fe-4S dicluster domain-containing protein from Thermosulfurimonas dismutans
29% identity, 31% coverage
DSY4602 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
38% identity, 21% coverage
LGS26_01020 sulfate reduction electron transfer complex DsrMKJOP subunit DsrO from Dissulfurimicrobium hydrothermale
31% identity, 28% coverage
PM1755 DmsB from Pasteurella multocida subsp. multocida str. Pm70
41% identity, 18% coverage
VFMJ11_A0105 DMSO/selenate family reductase complex B subunit from Aliivibrio fischeri MJ11
VFMJ11_A0105 dimethylsulfoxide reductase, chain B from Vibrio fischeri MJ11
38% identity, 19% coverage
dsrO / Q72CJ6 DsrO from Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough) (see paper)
Q72CJ6 Reductase, iron-sulfur binding subunit, putative from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
DVU1287 Periplasmic (Tat), binds 2[4Fe-4S] from Desulfovibrio vulgaris Hildenborough
39% identity, 17% coverage
- Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough.
Marbehan, Frontiers in microbiology 2024 - “...complex, subunit P DsrP Q72CJ7 DVU_1286 43.5 Dissimilatory sulfite reductase, DsrMKJOP complex, subunit O DsrO Q72CJ6 DVU_1287 29.0 28 76 17 Dissimilatory sulfite reductase, DsrMKJOP complex, subunit J DsrJ Q72CJ5 DVU_1288 14.5 Dissimilatory sulfite reductase, DsrMKJOP complex, subunit K DsrK Q72CJ4 DVU_1289 60.7 40 54 20...”
- Proteomic and Isotopic Response of Desulfovibrio vulgaris to DsrC Perturbation
Leavitt, Frontiers in microbiology 2019 - “...bound DsrMKJOP complex that reduces the DsrC trisulfide and releases H 2 S, only DsrO (DVU1287) was detected in all replicates. DsrO was less abundant in the mutant (0.37 0.04) ( Figure 5 and Supplementary Figure S5 ). Energy Metabolism Proteins Interacting With DsrC In addition...”
- Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete
Gao, Applied and environmental microbiology 2016 - “...apsB dsrJ dsrA dsrB DVU0850 DVU1290 DVU1289 DVU1287 DVU1286 DVU1597 Lactate oxidation DVU3030 DVU3027 DVU3031 DVU3032 DVU3028 DVU3033 DVU0600 DVU2110 DVU2285...”
- Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough
Caffrey, Journal of bacteriology 2007 - “...DVU2796 DVU0846 DVU0847 DVU0848 DVU0849 DVU0850 DVU1286 DVU1287 DVU1288 DVU1289 DVU1290 DVU0774 DVU0775 DVU0776 DVU0777 DVU0778 DVU0779 DVU0780 DVU1056 DVU1057...”
- Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis
He, Applied and environmental microbiology 2006 - “...DVU0777 DVU0778 DVU0779 DVU0780 DVU0917 DVU0918 DVU1286 DVU1287 DVU1288 DVU1289 DVU1290 DVU1769 DVU1770 DVU2792 DVU2793 DVU2794 DVU2795 DVU2796 DVU2797 DVU2798...”
- Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough
Chhabra, Journal of bacteriology 2006 - “...DVU0847 DVU0849 DVU0850 DVU1067 DVU1069 DVU1070 DVU1286 DVU1287 DVU1288 DVU1289 DVU1290 DVU1568 DVU1636 DVU1867 DVU2108 DVU2310 DVU2735 DVU2776 DVU2825 DVU3183...”
- Physiological and gene expression analysis of inhibition of Desulfovibrio vulgaris hildenborough by nitrite
Haveman, Journal of bacteriology 2004 - “...and Dvu0850 qmoABC; and 8, Dvu1290, Dvu1289, Dvu1288, Dvu1287, and Dvu1286 dsrMKJOP. Downloaded from http://jb.asm.org/ on February 11, 2017 by University of...”
DVU0172 thiosulfate reductase (phsB) from Desulfovibrio vulgaris Hildenborough
44% identity, 17% coverage
cbdbA131 4Fe-4S dicluster domain-containing protein from Dehalococcoides mccartyi CBDB1
40% identity, 18% coverage
NP_311410 anaerobic dimethyl sulfoxide reductase chain B from Escherichia coli O157:H7 str. Sakai
ECs3383 putative anaerobic dimethyl sulfoxide reductase chain B from Escherichia coli O157:H7 str. Sakai
38% identity, 19% coverage
CJJ81176_1571 dimethylsulfoxide reductase, chain B from Campylobacter jejuni subsp. jejuni 81-176
32% identity, 28% coverage
DBT_RS08140 4Fe-4S dicluster domain-containing protein from Dissulfuribacter thermophilus
35% identity, 19% coverage
DET0112 [Ni/Fe] hydrogenase, iron-sulfur cluster-binding subunit, putative from Dehalococcoides ethenogenes 195
41% identity, 18% coverage
- Effects of Arsenic on Trichloroethene-Dechlorination Activities of Dehalococcoides mccartyi 195
Gushgari-Doyle, Environmental science & technology 2020 - “...variety of proteins in Dhc195 contain iron-sulfur units, including reductive dehalogenases 4 and formate dehydrogenase (DET0112), 57 the latter of which was upregulated under As(III)-amended conditions. Since As(III) and As(V) are otherwise known to act via different modes of toxicity, many of these shared gene expression...”
- Structural dynamics and transcriptomic analysis of Dehalococcoides mccartyi within a TCE-Dechlorinating community in a completely mixed flow reactor
Mao, Water research 2019 - “...2014 ). The Fdh-like oxidoreductase (DET0187) was shown to be associated with the Fdh-like protein DET0112 from the hup operon ( Mansfeldt et al. 2014 ) and a recent transcriptomic study of D. mccartyi -containing microbial communities indicated the expression pattern of the Hup and the...”
- Inferring Gene Networks for Strains of Dehalococcoides Highlights Conserved Relationships between Genes Encoding Core Catabolic and Cell-Wall Structural Proteins
Mansfeldt, PloS one 2016 - “...culture displayed inhibited growth (1) or not (0) 0.86 0.90 DET0111 [Ni/Fe] hydrogenase, small subunit DET0112 [Ni/Fe] hydrogenase, Fe-S cluster 0.86 0.74 DET0451 malate dehydrogenase, NAD-dependent DET0115 ABC transporter, permease protein 0.92 0.81 DET0610 hypothetical protein tRNA Cys-1 0.99 0.76 DET1111 ATP-binding protein DET0097 iron dependent...”
- “...findings. Two transcripts in the operon for the major periplasmic facing hydrogenase (Hup; DET0111 and DET0112) displayed a strong relationship with regards to the solvent toxicity/inhibition condition (f = 0.86). Both of these transcripts are down-regulated when the culture is inhibited by high chloroethene concentrations. Therefore,...”
- SPINE: SParse eIgengene NEtwork linking gene expression clusters in Dehalococcoides mccartyi to perturbations in experimental conditions
Mansfeldt, PloS one 2015 - “...oxidoreductases predicted to be involved in respiration including the following: the [NiFe]-hydrogenase FeS binding subunit (DET0112), a formate dehydrogenase like (Fdh-like) membrane subunit (DET0186), and a member of the NADH-ubiquinone oxidoreductase (DET0923). C 12 is also directly connected to the C 66 cluster. The C 66...”
- Meta-analyses of Dehalococcoides mccartyi strain 195 transcriptomic profiles identify a respiration rate-related gene expression transition point and interoperon recruitment of a key oxidoreductase subunit
Mansfeldt, Applied and environmental microbiology 2014 - “...these proteins did not migrate as a single complex, DET0112 (an FdhB-like protein encoded in the Hup operon) was found to comigrate with DET0187 rather than...”
- “...recruiting a subunit expressed from the Hup operon (DET0112). T he pervasiveness of recalcitrant halogenated organics in hazardous waste cleanup sites (1) makes...”
- Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195
Nonaka, Journal of bacteriology 2006 - “...DET1570 DET1571 DET1572 DET1573 DET1574 DET1575 DET0186 DET0112 DET0147 DET1431 DET1430 Continued on following page Downloaded from http://jb.asm.org/ on...”
Alvin_1318 4Fe-4S ferredoxin iron-sulfur binding domain protein from Allochromatium vinosum DSM 180
34% identity, 22% coverage
G4V39_RS07125 4Fe-4S dicluster domain-containing protein from Thermosulfuriphilus ammonigenes
31% identity, 24% coverage
K3767_RS01060 4Fe-4S dicluster domain-containing protein from Thermosulfurimonas sp. F29
28% identity, 31% coverage
APL_1675 anaerobic dimethyl sulfoxide reductase chain B from Actinobacillus pleuropneumoniae L20
37% identity, 18% coverage
SPO3558 4Fe-4S dicluster domain-containing protein from Ruegeria pomeroyi DSS-3
37% identity, 19% coverage
- An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3
Rivers, Standards in genomic sciences 2014 - “...protein sitA Function YP_168752 SPO3557 Sulfite dehydrogenase subunit SoeC; transmembrane sulfate transporter soeC Function YP_168753 SPO3558 Sulfite dehydrogenase iron-sulfur cluster-binding subunit SoeB; cytosolic protein soeB Function YP_168754 SPO3559 Sulfite dehydrogenase molybdopterin cofactor-binding subunit SoeA; cytosolic protein soeA Function YP_168755 SPO3560 Phosphate acetyltransferase pta Function YP_168757 SPO3562...”
FVE67_RS02285 4Fe-4S dicluster domain-containing protein from Thermosulfurimonas marina
28% identity, 31% coverage
DSY3726 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
38% identity, 20% coverage
GF1_30500 4Fe-4S dicluster domain-containing protein from Desulfolithobacter dissulfuricans
44% identity, 16% coverage
- Physiological and comparative proteomic characterization of Desulfolithobacter dissulfuricans gen. nov., sp. nov., a novel mesophilic, sulfur-disproportionating chemolithoautotroph from a deep-sea hydrothermal vent
Hashimoto, Frontiers in microbiology 2022 - “...subunit of thiosulfate reductase-type protein, PhsB, was also found in both TD and SR (PhsB-1, GF1_30500 and PhsB-2, GF1_10130; Supplementary Tables 6 , 7 ). Further, a full set of enzymes required for CO 2 fixation by the Wood-Ljungdhal pathway were detected in both TD and...”
NTHI1227 NrfC, Fe-S-cluster-containing hydrogenase component 1 from Haemophilus influenzae 86-028NP
30% identity, 27% coverage
SPO3558, YP_168753 iron-sulfur cluster-binding protein from Silicibacter pomeroyi DSS-3
37% identity, 19% coverage
- An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3
Rivers, Standards in genomic sciences 2014 - “...protein sitA Function YP_168752 SPO3557 Sulfite dehydrogenase subunit SoeC; transmembrane sulfate transporter soeC Function YP_168753 SPO3558 Sulfite dehydrogenase iron-sulfur cluster-binding subunit SoeB; cytosolic protein soeB Function YP_168754 SPO3559 Sulfite dehydrogenase molybdopterin cofactor-binding subunit SoeA; cytosolic protein soeA Function YP_168755 SPO3560 Phosphate acetyltransferase pta Function YP_168757 SPO3562...”
- “...periplasmic protein sitA Function YP_168752 SPO3557 Sulfite dehydrogenase subunit SoeC; transmembrane sulfate transporter soeC Function YP_168753 SPO3558 Sulfite dehydrogenase iron-sulfur cluster-binding subunit SoeB; cytosolic protein soeB Function YP_168754 SPO3559 Sulfite dehydrogenase molybdopterin cofactor-binding subunit SoeA; cytosolic protein soeA Function YP_168755 SPO3560 Phosphate acetyltransferase pta Function YP_168757...”
HI1067 nitrite reductase, Fe-S protein (nrfC) from Haemophilus influenzae Rd KW20
P45015 Protein NrfC homolog from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
30% identity, 27% coverage
- Comparison of transcription of the Haemophilus influenzae iron/heme modulon genes in vitro and in vivo in the chinchilla middle ear
Whitby, BMC genomics 2013 - “...+2.06 +1.66 +1.15 HI1066 Nitrite reductase complex, transmembrane protein NrfD +6.34 +2.24 +1.88 +3.84 ns HI1067 Nitrite reductase complex, Fe-S subunit NrfC +6.99 +1.70 +1.52 +2.98 +3.53 HI1068 Nitrite reductase complex, periplasmic cytochrome subunit NrfB +9.49 ns +2.00 +4.75 +3.81 HI1069 Nitrite reductase complex, periplasmic cytochrome...”
- “...as well as a glutathione-dependent formaldehyde dehydrogense (HI0185), two components of the nitrate reduction complex (HI1067 and HI1069), and a cytochrome C biogenesis gene (HI1094). Comparison of the 5 genome core, with the previously described 3 genome core A previous iteration of the FeHm-responsive core modulon...”
- Rubrerythrin and rubredoxin oxidoreductase in Desulfovibrio vulgaris: a novel oxidative stress protection system
Lumppio, Journal of bacteriology 2001 - “...Hi_NrfC, Haemophilus influenzae putative iron-sulfur protein (P45015); Sm_NosZ Sinorhizobium meliloti nitrous oxide reductase (Q59746); and Ps_NosZ, Pseudomonas...”
- The biochemical basis for the species difference in hepatic microsomal 4-vinylcyclohexene epoxidation between female mice and rats.
Smith, Carcinogenesis 1990 (PubMed) - Mouse liver P450Coh: genetic regulation of the pyrazole-inducible enzyme and comparison with other P450 isoenzymes.
Lang, Archives of biochemistry and biophysics 1989 (PubMed)
STY2774 putative anaerobic reductase component from Salmonella enterica subsp. enterica serovar Typhi str. CT18
38% identity, 18% coverage
- Temporal Genomic Phylogeny Reconstruction Indicates a Geospatial Transmission Path of Salmonella Cerro in the United States and a Clade-Specific Loss of Hydrogen Sulfide Production
Kovac, Frontiers in microbiology 2017 - “...sulfide metabolism ( asrA, asrC, cysJ, cysT, phsA, phsB, phsC, ttrA, ttrB, ttrC , and STY2774; all from S. enterica subsp. enterica serotype Typhimurium str. LT2 complete genome deposited on NCBI under gi 16763390). Hydrogen Sulfide Production The ability of S. Cerro isolates to produce hydrogen...”
- “...involved in the hydrogen sulfide metabolic pathway (i.e., asrC, cysJ, cyst, phsABC, ttrABC , and STY2774). Three isolates, FSL R9-1900, FSL R9-1904, and FSL R9-1902, did not carry phsA , which encodes thiosulfate reductase subunit A. The rest of the 10 isolates with impaired ability to...”
DSY3719 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
44% identity, 17% coverage
Dde_2274 Periplasmic (Tat), binds 2[4Fe-4S] from Desulfovibrio desulfuricans G20
31% identity, 32% coverage
- Shotgun proteomic analysis of nanoparticle-synthesizing Desulfovibrio alaskensis in response to platinum and palladium
Capeness, Microbiology (Reading, England) 2019 - “...protein relative to the control was the periplasmic Fe hydrogenase small subunit (Dde_2280); this and Dde_2274 are potential hydrogenases that appear not to be involved in the reduction of either platinum or palladium. This suggests that there might be a separate hydrogenase and other electron transfer...”
- “...(Dde_0584, Dde_1113, Dde_3240, Dde_2272 and Dde_1638), one ATPase subunit (Dde_0990) and the prokaryotic molybdopterin-containing oxidoreductase (Dde_2274). Table 2. Proteins significantly less abundant (<0.667-fold) in the presence of either platinum and palladium and their overlap between datasets Platinum and palladium Platinum only Palladium only Protein ID Annotation...”
APL_0102 nitrate reductase from Actinobacillus pleuropneumoniae L20
30% identity, 27% coverage
HD0349 nitrate reductase, Fe-S protein from Haemophilus ducreyi 35000HP
33% identity, 21% coverage
RM25_RS09690 DMSO/selenate family reductase complex B subunit from Propionibacterium freudenreichii subsp. freudenreichii
40% identity, 18% coverage
sreB / Q8NKT6 sulfur reductase FeS subunit (EC 1.12.98.4) from Acidianus ambivalens (see paper)
sreB / CAC86938.1 sulfur reductase FeS subunit from Acidianus ambivalens (see paper)
37% identity, 20% coverage
THER_1541 4Fe-4S dicluster domain-containing protein from Thermodesulfovibrio sp. N1
36% identity, 21% coverage
DSY3471 putative anaerobic DMSO reductase chain B iron-sulfur subunit from Desulfitobacterium hafniense Y51
DSY3467 putative anaerobic DMSO reductase chain B iron-sulfur subunit from Desulfitobacterium hafniense Y51
40% identity, 23% coverage
SO1430 anaerobic dimethyl sulfoxide and manganese oxide reductase, B subunit from Shewanella oneidensis MR-1
SO_1430 DMSO/selenate family reductase complex B subunit from Shewanella oneidensis MR-1
35% identity, 19% coverage
- Pyruvate accelerates palladium reduction by regulating catabolism and electron transfer pathway in Shewanella oneidensis
Cheng, Applied and environmental microbiology 2021 (secret) - Tracking Electron Uptake from a Cathode into Shewanella Cells: Implications for Energy Acquisition from Solid-Substrate Electron Donors
Rowe, mBio 2018 - “...38bp upstream of the mtrA sequence in pBBR1MCS-2 ( 65 ) 57.6 3.8 dmsB mutant SO1430 45 * Lacking the iron-sulfur cluster subunit of the Dms operon 93.5 1.2 dms- all mutant SO1427SO1432 This work Lacking the DMSO reductase operon ( dmsEFABGH ) 91.8 0.3 petABC...”
- Promotion of iron oxide reduction and extracellular electron transfer in Shewanella oneidensis by DMSO
Cheng, PloS one 2013 - “...deletion of SO1427 in in S. oneidensis MR-1 22 dmsB mutant with in-flame deletion of SO1430 in S. oneidensis MR-1 This study E.coli JM109 F traD36 proA + B + lacI q (lacZ)M15/(lac-proAB) glnV44 e14 gyrA96 recA1 relA1 endA1 thi hsdR17 Lab stock WM3064 thrB1004 pro...”
- Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1
Cruz-García, BMC microbiology 2011 - “...iron-sulfur cluster-binding protein SO1429 dmsA-1 0.43 ( 0.09) TGTGATACAATTCAAA anaerobic dimethyl sulfoxide reductase, A subunit SO1430 dmsB-1 0.29 ( 0.04) anaerobic dimethyl sulfoxide reductase, B subunit SO1490 adhB 0.28 ( 0.12) TGTGATCTAGATCGGT TTGGAACTAGATAACT alcohol dehydrogenase II SO1776 mtrB 0.22 ( 0.04) outer membrane protein precursor MtrB...”
- Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling
Zhang, Journal of proteome research 2010 - “...implicated in translocating the outer membrane proteins MtrC (SO1778), OmcA (SO1779), DmsA (SO1429) and DmsB (SO1430) across the bacterial outer membrane. 44 , 45 Our results revealed that gspD deletion significantly altered abundances of a group of membrane proteins specifically within the cell membrane envelop, including...”
- Extracellular respiration of dimethyl sulfoxide by Shewanella oneidensis strain MR-1
Gralnick, Proceedings of the National Academy of Sciences of the United States of America 2006 - “...DMSO reductase subunits (DmsA, SO1429 and SO4358; DmsB, SO1430 and SO4359), suggesting that reduction of DMSO in S. oneidensis is an extracellular Conflict of...”
- “...SO1429 and SO4358 are 59% and 52% similar to DmsA, and SO1430 and SO4357 are 67% and 72% similar to DmsB). Both homologs of DmsA in S. oneidensis (SO1429 and...”
- Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors
Beliaev, Journal of bacteriology 2005 - “...encode putative dimethyl sulfoxide reductases, dmsAB-1 (SO1429, SO1430) and dmsAB-2 (SO4358, SO4357), were significantly induced by DMSO. While the former...”
- Global transcriptional profiling of Shewanella oneidensis MR-1 during Cr(VI) and U(VI) reduction
Bencheikh-Latmani, Applied and environmental microbiology 2005 - “...(it should be dmsA). In MR-1, dmsA-1 (SO1429) and dmsB-1 (SO1430) were upregulated to a greater extent for U(VI) than for Cr(VI). Genes on both sides of dmsAB...”
- A dynamic periplasmic electron transfer network enables respiratory flexibility beyond a thermodynamic regulatory regime
Sturm, The ISME journal 2015 - “...SO_2913 SO_2915 SO_2916 SO_0027 SO_3720 SO_0845 SO_0848 SO_1428 SO_1429 SO_1430 lldG lldF lldE pflB pflA ackA pta hemG-2 hemG-3 napB napA dmsF dmsA dmsB 2.7 2.6...”
- Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling
Zhang, Journal of proteome research 2010 - “...DMSO requires surface localization of MtrC (SO_1778) and OmcA (SO_1779) or DmsA (SO_1429) and DmsB (SO_1430), respectively. The type II secretion system is directly involved in translocating MtrC and OmcA across the bacterial outer membrane. 44 Inactivation of the type II secretion system diminished the bacterial...”
- “...membrane decaheme cytochrome c, OmcA surface lipoprotein 11.71 15.16 11.02 13.65 8.40 15.10 14.63 0.06 SO_1430 dimethyl sulfoxide reductase, FeS subunit, DmsB Complexed with surface lipoprotein 15.22 19.71 23.09 28.59 6.50 11.68 19.99 0.42 SO_0404 zinc dependent metalloprotease domain lipoprotein lipoprotein 4.77 6.18 5.22 6.46 4.04...”
- Involvement of a membrane-bound class III adenylate cyclase in regulation of anaerobic respiration in Shewanella oneidensis MR-1
Charania, Journal of bacteriology 2009 - “...upstream of the DMSO reductase operon (dmsEFAB; SO_1427 to SO_1430), the fumarate reductase gene (fccA; SO_0970), cyaA, and cyaC were amplified by PCR using the...”
- “...CyaC-upregulated genes SO_0827 SO_1422 SO_1427 SO_1428 SO_1429 SO_1430 SO_1431 SO_1432 SO_1776 SO_1777 SO_1778 SO_1779 SO_3285 SO_3286 Gene VOL. 191, 2009...”
DSY0601 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
35% identity, 21% coverage
D11S_1987 cytochrome c nitrite reductase, Fe-S protein from Aggregatibacter actinomycetemcomitans D11S-1
29% identity, 27% coverage
DSY4782 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
36% identity, 20% coverage
THER_0568 4Fe-4S dicluster domain-containing protein from Thermodesulfovibrio sp. N1
36% identity, 19% coverage
SO4357, SO_4357 anaerobic dimethyl sulfoxide reductase, B subunit from Shewanella oneidensis MR-1
35% identity, 21% coverage
- The dmsEFABGH operon encodes an essential and modular electron transfer pathway for extracellular iodate reduction by Shewanella oneidensis MR-1
Hou, Microbiology spectrum 2024 - “...) dmsA so4358 dmsA and so4358 deletion mutant of S. oneidensis MR-1 This study dmsB so4357 dmsB and so4357 deletion mutant of S. oneidensis MR-1 This study dmsE so4360 dmsE and so4360 deletion mutant of S. oneidensis MR-1 This study dmsE cctA dmsE and cctA deletion...”
- “...This study pDmsH Recombinant pBBR1MCS-2 containing dmsH coding sequence This study pSO4357 Recombinant pBBR1MCS-2 containing so4357 coding sequence This study pSO4358 Recombinant pBBR1MCS-2 containing so4358 coding sequence This study pSO4359 Recombinant pBBR1MCS-2 containing so4359 coding sequence This study pSO4360 Recombinant pBBR1MCS-2 containing so4360 coding sequence This...”
- K-shell Analysis Reveals Distinct Functional Parts in an Electron Transfer Network and Its Implications for Extracellular Electron Transfer
Ding, Frontiers in microbiology 2016 - “...membrane proteins (DmsF, MtrB, MtrE, SO_1659, SO_4359) and extracellular proteins (DmsA, DmsB, MtrC, MtrF, OmcA, SO_4357, SO_4358) in this shell are mostly functionally important for EET, as indicated by previous studies ( Coursolle and Gralnick, 2010 , 2012 ). Furthermore, proteins in this shell are broadly...”
- “...TorA OM 5 DmsF, MtrB, MtrE, SO_1659, SO_4359 Ex 7 DmsA, DmsB, MtrC, MtrF, OmcA, SO_4357, SO_4358 Ex, extracellular; OM, outer membrane; Pe, periplasm; IM, inner membrane; Cy, cytoplasm. We found that the proteins in this shell can be categorized into several modules according to their...”
- Genomic plasticity enables a secondary electron transport pathway in Shewanella oneidensis
Schicklberger, Applied and environmental microbiology 2013 - “...Para mtrBSTREP mtrB suppressor strain mtrBS SO4358 SO4357 mtrBS SO4359 mtrBS mtrC mtrBS SO4359 pBAD_SO4359STREP mtrBS SO4359 SO4360 pBAD_SO4359STREP mtrBS...”
- “...Regions of 500 bp flanking mtrC (primers 17 to 20), SO4357 and SO4358 (primers 21 to 24), or SO4359 (primers 25 to 28) were amplified (Table 4). The resulting...”
- Bacterial decolorization of textile dyes is an extracellular process requiring a multicomponent electron transfer pathway
Brigé, Microbial biotechnology 2008 - “...clusters in addition to omcBmtrAB ( Gralnick etal. , 2006 ): dmsEFABGH (SO_1427 SO_1432) and SO_4357 SO_4362 both encode proteins with similarity to MtrA, MtrB and DMSO reductase subunits, yet only the former is involved in DMSO respiration ( Gralnick etal. , 2006 ). The mtrDEF...”
- Extracellular respiration of dimethyl sulfoxide by Shewanella oneidensis strain MR-1
Gralnick, Proceedings of the National Academy of Sciences of the United States of America 2006 - “...are 59% and 52% similar to DmsA, and SO1430 and SO4357 are 67% and 72% similar to DmsB). Both homologs of DmsA in S. oneidensis (SO1429 and SO4358) contain...”
- Shewanella oneidensis MR-1 uses overlapping pathways for iron reduction at a distance and by direct contact under conditions relevant for Biofilms
Lies, Applied and environmental microbiology 2005 - “...(ORFs SO1427 to SO1432 and ORFs SO4362 to SO4357). Protein localization prediction programs indicate that these redox-active lipoproteins may be localized to...”
- Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors
Beliaev, Journal of bacteriology 2005 - “...reductases, dmsAB-1 (SO1429, SO1430) and dmsAB-2 (SO4358, SO4357), were significantly induced by DMSO. While the former displayed 3- to 8-fold upregulation...”
LT988_06615 sulfate reduction electron transfer complex DsrMKJOP subunit DsrO from Thiocapsa bogorovii
41% identity, 16% coverage
Pyrde_0487 4Fe-4S dicluster domain-containing protein from Pyrodictium delaneyi
33% identity, 22% coverage
Dde_2934 Respiratory nitrate reductase, beta subunit (narH) from Desulfovibrio desulfuricans G20
31% identity, 23% coverage
DSY2331 putative anaerobic DMSO reductase chain B iron-sulfur subunit from Desulfitobacterium hafniense Y51
44% identity, 16% coverage
DSY4086 putative anaerobic DMSO reductase chain B iron-sulfur subunit from Desulfitobacterium hafniense Y51
34% identity, 24% coverage
swp_2142 4Fe-4S ferredoxin, iron-sulfur binding from Shewanella piezotolerans WP3
38% identity, 17% coverage
- Condition-Specific Molecular Network Analysis Revealed That Flagellar Proteins Are Involved in Electron Transfer Processes of Shewanella piezotolerans WP3
Ding, Genetics research 2021 - “...pathways Members 1 9 0.58 3.49 E 04 Carbon metabolism swp_3663, swp_5025, swp_4312, swp_1239, swp_2139, swp_2142, swp_3875, swp_3458, swp_0182 2 9 0.50 9.74 E 04 Oxidative phosphorylation swp_4058, swp_0854, swp_4352, swp_3589, swp_4940, swp_1424, swp_1425, swp_0430, swp_0429 3 6 0.87 1.26 E 03 Flagellar assembly swp_1531, swp_3616,...”
HCU62_RS07540 4Fe-4S dicluster domain-containing protein from Dissulfurirhabdus thermomarina
29% identity, 24% coverage
YP_910613 4Fe-4S ferredoxin, iron-sulfur binding domain protein from Chlorobium phaeobacteroides DSM 266
38% identity, 18% coverage
DSY3534 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
33% identity, 21% coverage
H1G3R8 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein ArxB from Ectothiorhodospira sp. PHS-1
28% identity, 22% coverage
E2348C_4395 cytochrome c nitrite reductase Fe-S protein from Escherichia coli O127:H6 str. E2348/69
27% identity, 27% coverage
- PerC Manipulates Metabolism and Surface Antigens in Enteropathogenic Escherichia coli
Mellies, Frontiers in cellular and infection microbiology 2017 - “...2.27 71.03 14.77 0.00 E2348C_4394 nrfB Nitrite reductase pentaheme subunit 4.39 2.13 21.93 5.00 0.07 E2348C_4395 nrfC Formate-dependent nitrite reductase NrfC 4Fe4S subunit 6.42 2.68 43.02 6.70 0.00 E2348C_4396 nrfD Formate-dependent nitrite reductase NrfD membrane subunit 5.81 2.54 34.06 5.86 0.00 E2348C_4397 nrfE Heme lyase for...”
swp_4116 4Fe-4S ferredoxin, iron-sulfur binding from Shewanella piezotolerans WP3
37% identity, 17% coverage
- Condition-Specific Molecular Network Analysis Revealed That Flagellar Proteins Are Involved in Electron Transfer Processes of Shewanella piezotolerans WP3
Ding, Genetics research 2021 - “...swp_2888, swp_2886, swp_2884, swp_1173, swp_2883 7 7 0.62 1.94 E 03 Multihaem cytochrome swp_4806, swp_2182, swp_4116, swp_2918, swp_2183, swp_3403, swp_0613 8 8 0.64 2.70 E 03 Lipopolysaccharide biosynthesis swp_3507, swp_3506, swp_0834, swp_3511, swp_3509, swp_3508, swp_3516, swp_3515 9 5 0.70 2.79 E 03 swp_3204, swp_3981, swp_0083, swp_3979,...”
UWK_01206 4Fe-4S dicluster domain-containing protein from Desulfocapsa sulfexigens DSM 10523
31% identity, 27% coverage
DSY0531 putative oxidoreductase iron-sulfur subunit from Desulfitobacterium hafniense Y51
37% identity, 18% coverage
YjcJ / b4072 putative menaquinol-cytochrome c reductase 4Fe-4S subunit (EC 7.1.1.8) from Escherichia coli K-12 substr. MG1655 (see paper)
Z5671 formate-dependent nitrite reductase; Fe-S centers from Escherichia coli O157:H7 EDL933
b4072 formate-dependent nitrite reductase, 4Fe4S subunit from Escherichia coli str. K-12 substr. MG1655
ECs5054 formate-dependent nitrite reductase NrfC from Escherichia coli O157:H7 str. Sakai
27% identity, 27% coverage
- Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents
Segura, BMC genomics 2018 - “...NDE 3.67 2.51E-14 Z4726 nirB Nitrite reductase (large subunit) NDE NDE NDE NDE 2.06 9.01E-07 Z5671 nrfC Nitrite reductase (formate-dependent) NDE NDE 5.35 1.49E-13 2.63 8.52E-04 5.20 7.59E-13 Z5673 nrfE Cytochrome c-type biogenesis protein NrfE NDE NDE 3.43 2.08E-06 NDE 3.35 3.59E-06 Z5674 nrfF Formate-dependent nitrite...”
- Characterization of Zn(II)-responsive ribosomal proteins YkgM and L31 in E. coli
Hensley, Journal of inorganic biochemistry 2012 - “...sdhB b0724 succinate dehydrogenase, iron sulfur protein 2.0E-05 6.3 CRP, ArcA [ 61 ] nrfC b4072 formate-dependent nitrite reductase; Fe-S centers 8.0E-04 6.2 FlhDC [ 64 ] sdhC b0721 succinate dehydrogenase, cytochrome b556 2.0E-05 6.1 CRP, ArcA [ 61 ] dppB b3543 dipeptide transport system permease...”
- The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction
Oberto, PloS one 2009 - “...1.51 1 4.71 3.62 2.6 FA, FAec formate-dependent nitrite reductase a penta-haeme cytochrome c nrfC b4072 nrfABCDEFG 1 0.14 2.19 0.15 1 2.8 1.3 0.84 1 1.76 1.62 0.69 FA, FAec formate-dependent nitrite reductase Fe-S centers yjdK b4128 yjdKO 1 0.03 1.63 0.32 1 1.06 1.65...”
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...6 ECs5052 nrfA periplasmic cytochrome c(552) 3.08 un ECs5053 nrfB formate-dependent nitrite reductase 2.86 6 ECs5054 nrfC formate-dependent nitrite reductase; Fe-S centers 2.96 un ECs5134 frdB fumarate reductase, anaerobic, iron-sulfur protein subunit 2.50 8 ECs5135 frdA fumarate reductase, anaerobic, flavoprotein subunit 2.11 8 ECs5214 nrdG anaerobic...”
PA14_63580 nitrate-inducible formate dehydrogenase, beta subunit from Pseudomonas aeruginosa UCBPP-PA14
37% identity, 19% coverage
PPECC33_RS22515 cytochrome c nitrite reductase Fe-S protein from Escherichia coli PCN033
27% identity, 27% coverage
- The Tat system and its dependent cell division proteins are critical for virulence of extra-intestinal pathogenic Escherichia coli
Liu, Virulence 2020 - “...oxidation 3 HybA PPECC33_RS16530 MNRRNFIKAASCGALLTGALPSVSHAA Hydrogen oxidation 4 NapG PPECC33_RS11870 MSRSAKPQNGRRRFLRDVVRTAGGLAAVGVALGLQQQTARA Nitrate reduction 5 NrfC PPECC33_RS22515 MTWSRRQFLTGVGVLAAVSGTAGRVVA Nitrite reduction 6 YagT PPECC33_RS01655 MSNQGEYPEDNRVGKHEPHDFSLTRRDLIKVSAATAATAVVYPHSTLAASVPA Aldehyde oxidoreductase 7 YdhX PPECC33_RS09020 MSFTRRKFVLGMGTVIFFTGSASSLLA Unknown 8 TorA* PPECC33_RS05440 MNNNDLFQASRRRFLAQLGGLTVAGMLGPSLLTPRRATAAQA TMAO reduction 9 TorZ* PPECC33_RS10195 MTLTRREFIKHSGIAAGALVVTSAAPLPAWA TMAO reduction 10 NapA* PPECC33_RS11875 MKLSRRSFMKANAVAAAAAAAGLSVPGVA...”
APL_0894 formate dehydrogenase, iron-sulfur subunit from Actinobacillus pleuropneumoniae L20
32% identity, 25% coverage
- Actinobacillus pleuropneumoniae genes expression in biofilms cultured under static conditions and in a drip-flow apparatus
Tremblay, BMC genomics 2013 - “...key enzymes for anaerobic metabolism were identified: glycerol-3-phosphate dehydrogenase (APL_0379 and APL_0381) and formate dehydrogenase (APL_0894 and APL_0895). The largest group of up-regulated genes were transport-related genes followed by genes associated with regulatory functions (Figure 3 A). Among the transport-related genes, two homologues for the transport...”
- “...APL_0449 APL_0626 macB APL_0627 cpxA APL_0629 cpxR APL_0840 tolC APL_0891 fdhD APL_0892 fdxG APL_0893 fdxG APL_0894 fdxH APL_0895 fdnI APL_0896 fdhE APL_0936 APL_0959 APL_1045 APL_1110 APL_1159 APL_1387 APL_1494 ftpA APL_1550 wecD APL_1552 wecB APL_1553 APL_1554 wecA APL_1674 dmsA APL_1675 dmsB APL_1676 dmsC APL_1875 APL_1921 pgaA APL_1922...”
- Comparative profiling of the transcriptional response to iron restriction in six serotypes of Actinobacillus pleuropneumoniae with different virulence potential
Klitgaard, BMC genomics 2010 - “...APL_0966 - Putative transport protein R -0.71 APL_0895 fdnI Formate dehydrogenase, gamma subunit C -1.15 APL_0894 + fdxH Formate dehydrogenase, iron-sulfur subunit C -1.17 APL_0893 + fdxG Formate dehydrogenase, nitrate-inducible, major subunit C -1.01 APL_0892 fdxG Formate dehydrogenase, nitrate-inducible, major subunit C -1.18 APL_0857 sdaA #...”
- Effects of growth conditions on biofilm formation by Actinobacillus pleuropneumoniae
Labrie, Veterinary research 2010 - “...3-hydroxyacid dehydrogenase 3.100 APL_0841 pntB NAD(P) transhydrogenase subunit beta 2.726 APL_1908 xylA Xylose isomerase 2.243 APL_0894 fdxH Formate dehydrogenase, iron-sulfur subunit 2.161 APL_1425 napC Cytochrome c-type protein NapC 2.159 APL_1799 torC Pentahemic c-type cytochrome 2.156 APL_0892 fdxG Formate dehydrogenase, nitrate-inducible, major subunit 2.116 APL_1798 torA Trimethylamine-N-oxide...”
- Host-pathogen interactions of Actinobacillus pleuropneumoniae with porcine lung and tracheal epithelial cells
Auger, Infection and immunity 2009 - “...APL_1555 Energy metabolism APL_1832 APL_0892 APL_0895 APL_0894 APL_0687 APL_0100 APL_0106 APL_0101 APL_1091 APL_1528 APL_1137 APL_1959 APL_1414 APL_1379...”
- “...metabolism APL_0434 APL_0892 APL_0771 APL_1379 APL_0983 APL_0894 APL_1251 APL_1450 APL_0181 APL_1925 APL_1091 APL_0688 APL_1011 APL_0772 APL_1137 APL_0486...”
AMETH_3398 4Fe-4S dicluster domain-containing protein from Amycolatopsis methanolica 239
34% identity, 20% coverage
- A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus
Tang, Synthetic and systems biotechnology 2016 - “...encoded by AMETH_3767 and formate dehydrogenase (EC: 1.2.1.2) encoded by AMETH_3397 ( fdh ) and AMETH_3398 ( fdoH ), respectively ( Fig.7 A). Though a glutathione-independent formaldehyde dehydrogenase (GD-FA1DH, EC: 1.2.1.46) is encoded by AMETH_1319 in the genome of A.methanolica strain 239 T , its activity...”
- “...oxidoreductase, K17067, EC:1.2.99.4/EC:1.1.99.37; AMETH_3767 NAD/mycothiol-dependent formaldehyde dehydrogenase, K00153, EC:1.1.1.306; AMETH_3397 formate dehydrogenase, K00123, EC:1.2.1.2, and AMETH_3398 formate dehydrogenase iron-sulfur subunit, K00124, EC:1.2.1.2. In panel B , Y denotes the identified genes, N denotes the unidentified genes in complete genomes, and ND denotes the genes that are...”
O67147 Formate dehydrogenase beta subunit from Aquifex aeolicus (strain VF5)
31% identity, 24% coverage
Swol_0798 formate dehydrogenase iron-sulfur subunit from Syntrophomonas wolfei subsp. wolfei str. Goettingen
SWOL_RS04030 4Fe-4S dicluster domain-containing protein from Syntrophomonas wolfei subsp. wolfei str. Goettingen G311
34% identity, 21% coverage
- Energy-Conserving Enzyme Systems Active During Syntrophic Acetate Oxidation in the Thermophilic Bacterium Thermacetogenium phaeum
Keller, Frontiers in microbiology 2019 - “...(Tph_c15400, Swol_0799) showed 56% similarity and FdhA2 (Tph_c15410, Swol_0800) showed 53%, the iron-sulfur subunit (Tph_c15390, Swol_0798) had 54%, the gamma subunit (Tph_c15380, Swol_0797) 46% and the formate accessory protein (Tph_c15370, Swol_0796) had only 28% identity. In contrast to the iron-sulfur subunit (Tph_c15390), its homolog in S....”
- A proteomic view at the biochemistry of syntrophic butyrate oxidation in Syntrophomonas wolfei
Schmidt, PloS one 2013 - “...in the gene cluster Swol_0799-0800 is also a membrane-bound iron-sulfur subunit (30 kDa) candidate gene (Swol_0798) and a membrane-bound cytochrome b (26 kDa) candidate gene (Swol_0797) [12] . The FDH iron-sulfur subunit gene (Swol_0798) was validly identified by the peptide fingerprint obtained from a second prominent,...”
- Membrane Complexes of Syntrophomonas wolfei Involved in Syntrophic Butyrate Degradation and Hydrogen Formation
Crable, Frontiers in microbiology 2016 - “...the S. wolfei genome encodes genes for two membrane-bound formate dehydrogenases, fdh2 (locus tags: SWOL_RS04025, SWOL_RS04030, SWOL_RS04035 and SWOL_RS04040) and fdh4 (locus tags: SWOL_RS05200, SWOL_RS05205, SWOL_RS05210, SWOL_RS05215, SWOL_RS05220, and SWOL_RS05225). Interestingly, the four subunits of Fdh2 were detected in axenic culture S. wolfei cell membrane preparations...”
NTHI0010 formate dehydrogenase, iron-sulfur subunit from Haemophilus influenzae 86-028NP
36% identity, 19% coverage
HI0007 formate dehydrogenase, beta subunit (fdxH) from Haemophilus influenzae Rd KW20
36% identity, 19% coverage
- Comparison of transcription of the Haemophilus influenzae iron/heme modulon genes in vitro and in vivo in the chinchilla middle ear
Whitby, BMC genomics 2013 - “...R2846 86-028NP HI0006m Formate dehydrogenase-N, alpha subunit FdnG +7.58 +8.36 not on d +1.44 +1.71 HI0007 Formate dehydrogenase-N, Fe-S beta subunit FdnH +7.49 +6.00 +3.40 +1.21 +1.73 HI0008 Formate dehydrogenase-N, cytochrome B556 gamma subunit, FdnI +7.47 +5.23 +3.20 ns +1.76 HI0009 Formate dehydrogenase-N, accessory protein FdnE...”
- “...malQ 2.36 10.27 -1.92 10.86 HI1369 8.94 30.26 5.15 30.63 HI1427 3.63 8.8 3.33 7.42 HI0007 fdnH -2.3 1.15 -3.84 1.81 HI0185 adhC -4.48 -1.42 -5.35 -1.42 HI0343 napD -1.38 1.56 1.00 12.4 HI0980 fis -1.05 1.26 -1.18 2.36 HI1069 nrfA -5.08 2.28 -5.06 9.69 HI1078...”
- The iron/heme regulated genes of Haemophilus influenzae: comparative transcriptional profiling as a tool to define the species core modulon
Whitby, BMC genomics 2009 - “...hxuC (HI0262). Genes selected for validation that were preferentially expressed under FeHm supplementation (FeHm+ve) were: HI0007 which encodes a putative formate dehydrogenase, HI0185 encoding alcohol dehydrogenase, HI0980 encoding the DNA architectural protein Fis, HI1384 encoding the ferritin subunit A1 and HI1706 which encodes the osmoprotection-related protein...”
- “...by Q-PCR NTHi R2866 Hib 10810 Gene Array a Q-PCR b Array a Q-PCR b HI0007 fdxI +7.49 +9.88 +6.00 +5.20 HI0017 yfiD -8.25 -10.72 -3.03 -3.34 HI0185 adhC +5.86 +7.65 +4.01 +6.52 HI0262 hxuC -24.69 -32.65 -4.03 -12.12 HI0502 rbsA ns +1.08 ns c +1.13...”
- The ArcA regulon and oxidative stress resistance in Haemophilus influenzae
Wong, Molecular microbiology 2007 - “...8.39E-10 9.4 1.53E-09 HI0008 Formate dehydrogenase, gamma subunit ( fdxI ) 9.7 5.42E-09 12 3.81E-09 HI0007 Formate dehydrogenase, beta subunit ( fdxH ) 7.8 1.12E-09 9.2 7.77E-10 HI1731 Conserved hypothetical protein 5.9 2.52E-09 6.2 4.67E-09 HI1444 5,10 methylenetetrahydrofolate reductase ( metF ) 5.6 4.91E-06 4.1 2.57E-05...”
- “...( HI0747 ) (5-ATGAAAAACGTCGTGATC and 5-ATGCAATTTTAATCTTGGTTTTAAATAAC), lldD ( HI1739.1 ) (5-ATGATTATTTCATCAGCTAG and 5-AAGTTTACTTAGATCAACC), fdxH ( HI0007 ) (5-ATGGCTGGAACTGCTCAAGGCG and 5-GAAACACGATCTACACAAAGAG), fdxI ( HI0008 ) (5-ATGAGTAAAATTGAAATTAGCAAC and 5-AGATACCAGTGAATAACATAAAAG), fdhE ( HI0009 ) (5-ATGAGTATCAAAATCTTATC and 5-TGCTTCTTCTGCAGGAAAAATAAATG), lldP ( HI1218 ) (5-ATGCTGTCTTTTATTCTAAG and 5-TAGATTATAAAATAAAGGTAC), sucB ( HI1661 ) (5-ATGGCAATCGAAATTCTTG...”
- Transcriptional profile of Haemophilus influenzae: effects of iron and heme
Whitby, Journal of bacteriology 2006 - “...lacked several of the predicted genes on the array. HI0007 to HI0009 were shown, by microarray, to be upregulated upon the addition of FeHm. The genes...”
- “...homolog (4). Comparison of RNA levels of HI0006m and HI0007 using Q-PCR confirmed that HI0006m is also repressed by addition of FeHm, consistent with the other...”
PA4811 nitrate-inducible formate dehydrogenase, beta subunit from Pseudomonas aeruginosa PAO1
39% identity, 16% coverage
- Differential transcription profiling of the phage LUZ19 infection process in different growth media
Brandão, RNA biology 2021 (secret) - A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm
Sigurdsson, PloS one 2012 - “...Table 2 Oxygen-sensitive genes . Subsystem Genes Amino acid catabolism FolD (PA1796), FdnI (P4810), FdnH (PA4811), FdnG (PA4812) Amino acid synthesis LysC (PA0904), Hom (PA3736), Ldh (PA3418), AruH (PA4976), GdhA (PA4588) Central metabolism Fda (PA0555), SdhC (PA1581), SdhD (PA1582), SdhA (PA1583), SdhB (PA1584), Fbp (PA5110), TktA...”
- Genomewide identification of genetic determinants of antimicrobial drug resistance in Pseudomonas aeruginosa
Dötsch, Antimicrobial agents and chemotherapy 2009 - “...PA4463 PA4490 PA4536 PA4600 PA4609 PA4733 PA4766 PA4781 PA4811 PA4838 PA4939 PA4942 PA4945 PA4946d PA4946d PA4974 PA5001 PA5003 PA5028 PA5037 PA5038 PA5094...”
- The Pseudomonas aeruginosa proteome during anaerobic growth
Wu, Journal of bacteriology 2005 - “...PA3886 PA3895 PA3913 PA3914* PA3915* PA3918* PA3958 PA4180 PA4811 PA4812 PA4868 PA4922 PA5005 PA5011 PA5012 PA5015 PA5064 PA5223 PA5296 Protein VOL. 187, 2005...”
- Cystic fibrosis sputum supports growth and cues key aspects of Pseudomonas aeruginosa physiology
Palmer, Journal of bacteriology 2005 - “...PA4471 PA4498 PA4514 PA4570 PA4633 PA4770 PA4771 PA4772 PA4811 PA4834 PA4835 PA4836 PA4837 PA4838 PA4929 PA5303 PA5532 PA5534 PA5535 PA5536 PA5538 PA5539 PA5540...”
- Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis
Wilderman, Proceedings of the National Academy of Sciences of the United States of America 2004 - “...ORF operon Gene Function PA2512 PA2513 PA2514 PA2511 PA2682 PA4811 PA4880 PA4236 PA1174 PA4366 PA1582 PA1583 PA1584 PA1581 PA3531 antA antB antC HUU HUU fdnH...”
- Transcriptome analysis of Pseudomonas aeruginosa after interaction with human airway epithelial cells
Frisk, Infection and immunity 2004 - “...PA3383 PA2491 PA2493 PA0697 PA1195 PA5180 PA2495 PA3219 PA4811 PA4881 PA3382 PA0696 PA2882 PA3368 PA0674 PA4623 PA2881 PA2331 PA4221 PA4225 PA4231 PA4220 PA4218...”
PP0490, PP_0490 formate dehydrogenase, iron-sulfur subunit from Pseudomonas putida KT2440
38% identity, 16% coverage
DSY3100 formate dehydrogenase beta subunit from Desulfitobacterium hafniense Y51
37% identity, 18% coverage
swp_4653 Formate-dependent nitrite reductase, nrfC protein from Shewanella piezotolerans WP3
34% identity, 19% coverage
- Condition-Specific Molecular Network Analysis Revealed That Flagellar Proteins Are Involved in Electron Transfer Processes of Shewanella piezotolerans WP3
Ding, Genetics research 2021 - “...4 0.67 1.01 E 02 swp_0059, swp_0060, swp_0056, swp_1586 6 5 0.50 1.42 E 02 swp_4653, swp_4654, swp_4652, swp_4657, swp_4655 7 7 0.52 2.19 E 02 swp_2623, swp_2495, swp_4933, swp_4301, swp_4936, swp_4935, swp_4940 8 4 0.50 2.89 E 02 Purine metabolism swp_1361, swp_4724, swp_2972, swp_2621 9...”
GM298_01155 formate dehydrogenase subunit beta from Enterobacter sp. HSTU-ASh6
37% identity, 17% coverage
APL_1332 hydrogenase-2 operon protein HybA precursor from Actinobacillus pleuropneumoniae L20
31% identity, 26% coverage
amb3377 Fe-S-cluster-containing hydrogenase components 1 from Magnetospirillum magneticum AMB-1
41% identity, 15% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory