PaperBLAST
PaperBLAST Hits for reanno::Phaeo:GFF2923 D-lactate dehydrogenase, iron-sulfur subunit GlcF (EC 1.1.99.6) (Phaeobacter inhibens DSM 17395) (444 a.a., MQTTFSEKQL...)
Show query sequence
>reanno::Phaeo:GFF2923 D-lactate dehydrogenase, iron-sulfur subunit GlcF (EC 1.1.99.6) (Phaeobacter inhibens DSM 17395)
MQTTFSEKQLRDPGTQRANEILRSCVHCGFCTATCPTYQVLGDELDSPRGRIYLIKDMLE
NERVPDAKTVKHIDRCLSCLACMTTCPSGVHYMHLVDHARAYIDKHYNRPWSDRALRWLL
ARILPYPGRFRLALIGAKLAQPFKRLVPDARLRAMLDMAPRHIPPVSRNDDPQSFAAKAP
RRKRVALMTGCAQKALNTDINDATIRLLTRLGCEVVVAAGAGCCGALTHHMGREEESHAT
AAKNIRAWTDEIDGQGLDAIVINTSGCGTTVKDYGHMFRNDALAEDAARVSAIAMDISEL
LMQLDLPEGEDKETTVAYHAACSLQHGQQIKTHPKTLLKRAGFTVVEPADSHLCCGSAGT
YNLLQPEISAELKARKVTSLEARQPDLIAAGNIGCMMQIGSATDIPILHTVELLDWATGG
PKPRALVAGGPGADPRAGEIPILR
Running BLASTp...
Found 151 similar proteins in the literature:
PGA1_c29700 D-lactate dehydrogenase, iron-sulfur subunit GlcF (EC 1.1.99.6) from Phaeobacter inhibens DSM 17395
100% identity, 100% coverage
- mutant phenotype: Specifically important for: Sodium D,L-Lactate; Sodium D-Lactate.
SPO3480 glycolate oxidase subunit GlcF from Ruegeria pomeroyi DSS-3
83% identity, 100% coverage
- Diel investments in metabolite production and consumption in a model microbial system
Uchimiya, The ISME journal 2022 - “...glycolate oxidase, GlcD subunit 18.6 [ 25 ] SPO3479 glcE glycolate oxidase, GlcE subunit 19.9 SPO3480 glcF glycolate oxidase, iron-sulfur subunit 21.6 Phosphonate Phosphonate SPO0780 phnC ABC transporter, ATP-binding 32.4 SPO0781 phnD ABC transporter, periplasmic phosphonate-binding 18.6 SPO0782 phnE-1 ABC transporter, permease 38.3 SPO0783 phnE-2 ABC...”
SMc00926 D-lactate dehydrogenase, iron-sulfur subunit GlcF (EC 1.1.99.6) from Sinorhizobium meliloti 1021
65% identity, 96% coverage
- mutant phenotype: Specifically important for: Sodium D,L-Lactate. This is the first step in D-lactate oxidation.
RL0866 putative glycolate oxidase iron-sulfur subunit from Rhizobium leguminosarum bv. viciae 3841
63% identity, 96% coverage
- Rhizobium leguminosarum Glutathione Peroxidase Is Essential for Oxidative Stress Resistance and Efficient Nodulation
Hu, Frontiers in microbiology 2021 - “...oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (GFO/IDH/MocA) dehydrogenase 38.70 0.76 0.0091 RL0802 Cytoplasmic Deoxygenase 31.23 0.8 0.0469 RL0866 glcF Cytoplasmic Glycolate oxidase iron-sulfur subunit 46.87 0.79 0.0089 pRL80022 Cytoplasmic Alpha/beta hydrolase 35.12 0.78 0.0461 RL3549 glnII Cytoplasmic Glutamine synthetase 38.76 0.64 0.0118 RL1559 acpP Cytoplasmic Acyl carrier protein...”
- “...Four genes RL4392 , pRL90175 , RL0644 , and RL2323 code for dehydrogenases. RL0802 , RL0866 , and pRL80022 code for a deoxygenase, an oxidase and a hydrolase, respectively. Many of the differentially expressed genes display similarity to genes known to be involved in cellular metabolism...”
- Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics
Ramachandran, Genome biology 2011 - “...to the pea rhizosphere Increased expression of genes encoding enzymes of the glyoxylate cycle (RL0054, RL0866) only occurred in the pea rhizosphere. RL0054 (malate synthase) forms malate from glyoxylate and acetyl CoA while GlcF (RL0866) probably converts glycolate to glyoxylate (Figure 2 ). Thus, while C2...”
Atu0667 glycolate oxidase iron-sulfur subunit from Agrobacterium tumefaciens str. C58 (Cereon)
63% identity, 96% coverage
NGR_c03950 glycolate oxidase subunit GlcF from Sinorhizobium fredii NGR234
NGR_c03950 glycolate oxidase, iron-sulphur subunit from Rhizobium sp. NGR234
65% identity, 96% coverage
BMEII1061 (S)-2-HYDROXY-ACID OXIDASE SUBUNIT GLCF from Brucella melitensis 16M
61% identity, 97% coverage
- Integrated Bioinformatics-Based Subtractive Genomics Approach to Decipher the Therapeutic Drug Target and Its Possible Intervention against Brucellosis
Khan, Bioengineering (Basel, Switzerland) 2022 - “...like: malate synthase G, involved in the glycolate utilization (glcB); aconitate hydratase (BMEI1855), (BMEII0009), (BMEI1952), (BMEII1061), (BMEI1939), (BMEII1060), (BMEII1062), (BMEII1064); and ureidoglycolate lyase (allA) and (BMEI0799). The PPI results showed that isocitrate lyase had a total number of nodes 11, average node numbers 7.09, average local...”
bll7540 glycolate oxidase iron-sulfur subunit from Bradyrhizobium japonicum USDA 110
56% identity, 95% coverage
F6476_01175 glycolate oxidase subunit GlcF from Pseudomonas umsongensis
45% identity, 94% coverage
A9762_17965 glycolate oxidase subunit GlcF from Pandoraea sp. ISTKB
44% identity, 93% coverage
AFE_1663 glycolate oxidase subunit GlcF from Acidithiobacillus ferrooxidans ATCC 23270
45% identity, 93% coverage
YghL / b4467 glycolate dehydrogenase, putative iron-sulfur subunit (EC 1.1.99.14) from Escherichia coli K-12 substr. MG1655 (see 5 papers)
glcF / P52074 glycolate dehydrogenase, putative iron-sulfur subunit (EC 1.1.99.14) from Escherichia coli (strain K12) (see 4 papers)
GLCF_ECOLI / P52074 Glycolate oxidase iron-sulfur subunit; Glycolate dehydrogenase subunit GlcF; Glycolate oxidase subunit GlcF; EC 1.1.99.14 from Escherichia coli (strain K12) (see 4 papers)
glcF / RF|YP_026190.1 glycolate oxidase, iron-sulfur subunit from Escherichia coli K12 (see paper)
glcF / AAB02532.1 glycolate oxidase subunit, (Fe-S)protein from Escherichia coli (see paper)
A0A140N897 Glycolate oxidase iron-sulfur subunit from Escherichia coli (strain B / BL21-DE3)
b4467 glycolate oxidase iron-sulfur subunit from Escherichia coli str. K-12 substr. MG1655
43% identity, 94% coverage
- function: Component of a complex that catalyzes the oxidation of glycolate to glyoxylate (PubMed:4557653, PubMed:8606183). Is required for E.coli to grow on glycolate as a sole source of carbon (PubMed:8606183). Is also able to oxidize D-lactate ((R)-lactate) with a similar rate (PubMed:4557653). Does not link directly to O(2), and 2,6-dichloroindophenol (DCIP) and phenazine methosulfate (PMS) can act as artificial electron acceptors in vitro, but the physiological molecule that functions as a primary electron acceptor during glycolate oxidation is unknown (PubMed:4557653).
catalytic activity: glycolate + A = glyoxylate + AH2 (RHEA:21264)
catalytic activity: (R)-lactate + A = pyruvate + AH2 (RHEA:15089)
cofactor: [4Fe-4S] cluster (Binds 2 [4Fe-4S] clusters.)
subunit: The glycolate oxidase likely consists of three subunits, GlcD, GlcE and GlcF.
disruption phenotype: Abolishes glycolate oxidase activity. Is unable to grow on glycolate as the sole source of carbon, in contrast to wild type. - Omics analysis coupled with gene editing revealed potential transporters and regulators related to levoglucosan metabolism efficiency of the engineered Escherichia coli
Chang, Biotechnology for biofuels and bioproducts 2022 - “...domain protein A0A140N975 ydeM 2.14 1.05 Iron-containing alcohol dehydrogenase A0A140N5B5 yqhD 3.08 2.71 Uncharacterized protein A0A140N897 glcF 1.93 1.42 Amino acid transport and metabolismrelated proteins Extracellular solute-binding protein family 1 A0A140NBZ6 ydcS 1.49 1.62 Extracellular solute-binding protein family 3 A0A140N2V7 yhdW 2.19 1.89 Tryptophanase A0A140NGF8 tnaA...”
- More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coli
Göhler, BMC systems biology 2011 - “...b0091 murC $ -0.030 5.958 b0114 aceE * 2.250 5.866 b0115 aceF * 2.008 5.883 b4467 glcF $ 2.181 0.275 b0114 aceE * 2.250 5.866 b0115 aceF * 2.008 5.883 b0088 murD $ -0.013 5.623 b2579 yfiD * 1.973 0.805 b0090 murG $ -0.015 4.773 b2979...”
D1792_12360 glycolate oxidase subunit GlcF from Escherichia coli CFT073
43% identity, 94% coverage
Psest_3839 D-lactate/glycolate dehydrogenase, iron-sulfur subunit GlcF (EC 1.1.99.6; EC 1.1.99.14) from Pseudomonas stutzeri RCH2
43% identity, 93% coverage
- mutant phenotype: Specifically important for: Glycolic Acid; Sodium D-Lactate. This is the first step in both D-lactate and glycolate oxidation.
Bphy_5641 glycolate oxidase subunit GlcF from Paraburkholderia phymatum STM815
Bphy_5641 glycolate oxidase iron-sulfur subunit from Burkholderia phymatum STM815
43% identity, 94% coverage
RR42_RS17315 D-lactate dehydrogenase, iron-sulfur subunit GlcF (EC 1.1.99.6) from Cupriavidus basilensis FW507-4G11
43% identity, 94% coverage
- mutant phenotype: Important on D-lactate
MCA_RS07375 glycolate oxidase subunit GlcF from Methylococcus capsulatus str. Bath
44% identity, 91% coverage
cce_3708 (Fe-S)-binding protein from Crocosphaera subtropica ATCC 51142
cce_3708 glycolate oxidase subunit (Fe-S) protein from Cyanothece sp. ATCC 51142
39% identity, 89% coverage
PP_3747 glycolate oxidase, iron-sulfur subunit from Pseudomonas putida KT2440
43% identity, 95% coverage
- Genome analysis of the metabolically versatile Pseudomonas umsongensis GO16: the genetic basis for PET monomer upcycling into polyhydroxyalkanoates
Narancic, Microbial biotechnology 2021 - “...Glycolate oxidase FADbinding subunit 100 72 PP_3746 glcF F6476_01175 Glycolate oxidase FeS subunit 100 77 PP_3747 glcG F6476_01170 Uncharacterized protein 90 73 PP_3748 glcB F6476_01165 Malate synthase 99 63 PP_0356 glcA F6476_01160 Glycolate permease 100 81 PP_4735 maeB F6476_01155 Malate dehydrogenase/malic enzyme 98 71 PP_5085 John...”
- The Cellular Response to Lanthanum Is Substrate Specific and Reveals a Novel Route for Glycerol Metabolism in Pseudomonas putida KT2440
Wehrmann, mBio 2020 - “...hydroperoxide reductase subunit F 3.13 3.08 PP_3745 GlcD Glycolate oxidase, putative FAD-linked subunit 3.12 3.32 PP_3747 GlcF Glycolate oxidase, iron-sulfur subunit 2.67 3.50 PP_3746 GlcE Glycolate oxidase, putative FAD-binding subunit 2.64 2.98 PP_4922 ThiC Phosphomethylpyrimidine synthase 2.21 3.84 PP_3748 GlcG Conserved hypothetical protein 2.06 3.71 PP_3622...”
- “...downstream of the calA (PP_2426), garK (PP_3178), glpFKRD (PP_1076 to PP_1973), and glcDEF (PP_3745 to PP_3747) genes were amplified from genomic DNA of P. putida KT2440 using primer pairs PcalA1/2 and PcalA3/4, PgarK1/2 and PgarK3/4, Pglp1/2 and Pglp3/4, and MWH03/04 and MWH05/06, respectively ( TableS2 )....”
- Light Response of Pseudomonas putida KT2440 Mediated by Class II LitR, a Photosensor Homolog
Sumi, Journal of bacteriology 2020 (secret)
BP2903 glycolate oxidase iron-sulfur subunit from Bordetella pertussis Tohama I
41% identity, 93% coverage
sll1831 glycolate oxidase subunit (Fe-S) protein from Synechocystis sp. PCC 6803
39% identity, 87% coverage
PA5353 glycolate oxidase subunit GlcF from Pseudomonas aeruginosa PAO1
44% identity, 95% coverage
SYNW0163 putative glycolate oxidase subunit (Fe-S) protein from Synechococcus sp. WH 8102
35% identity, 92% coverage
A9WF32 Glycolate oxidase iron-sulfur subunit from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)
Caur_2135 protein of unknown function DUF224 cysteine-rich region domain protein from Chloroflexus aurantiacus J-10-fl
35% identity, 85% coverage
- Deciphering the functional role of hypothetical proteins from Chloroflexus aurantiacs J-10-f1 using bioinformatics approach
Thakur, Molecular biology research communications 2020 - “...tRNAthreonylcarbamoyl adenosine modification protein TsaE A9WEL0 Small GTPase superfamily, ARF/SAR type A9WEX4 Immunoglobulin like fold A9WF32 Glycolate oxidase, iron sulphur subunit A9WFR2 Epimerase family protein SDR39U1 A9WGG2 Rhamnose/fucosemutarotase A9WDH7 Photosynthetic complex assembly protein 2, putative A9WDG5 P loop containing nucleoside triphosphate hydrolase A9WCP0 FAD binding, type...”
- “...9.51 14440 37.55 stable 98.92 -0.044 A9WEX4 735 78497.61 4.3 86430 24.92 stable 70.76 -0.151 A9WF32 466 50442.28 8.62 33890 41.79 unstable 90.94 -0.044 A9WFR2 317 34356.5 7.76 53525 37.01 stable 97.29 -0.003 A9WGG2 107 12495.26 5.11 23950 57.52 unstable 75.7 -0.324 A9WDH7 254 28099.11 8.63...”
- Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus
Tang, BMC genomics 2011 - “...L, actL , Caur_2134), a Cys-rich protein with Fe-S binding motifs (component M, actM , Caur_2135), components B ( actB , Caur_2136), E ( actE , Caur_2137), A ( actA , Caur_2138), and G ( actG , Caur_2139) in the C p ACIII operon, an electron...”
- “...(Caur_0173), mct (Caur_0174), meh (Caur_0180) Glycolate assimilation and glyoxylate cycle glcDEF (Caur_1144 - 1145, Caur_2133, Caur_2135), glyr (Caur_0825), icl (Caur_3889) and mas (Caur_2969) Cobalamin biosynthesis cobS (Caur_1198), cobQ / cbiP (Caur_2560), N -transferase (Caur_2561), cobP / cobU (Caur_2562), cobB/cbiA (Caur_2563), cobA (Caur_2564, Caur_0687), cobJ (Caur_2565), cobM...”
Cagg_1528 protein of unknown function DUF224 cysteine-rich region domain protein from Chloroflexus aggregans DSM 9485
34% identity, 86% coverage
Bcer98_1017 protein of unknown function DUF224 cysteine-rich region domain protein from Bacillus cereus subsp. cytotoxis NVH 391-98
32% identity, 89% coverage
- Divergence of the SigB regulon and pathogenesis of the Bacillus cereus sensu lato group
Scott, BMC genomics 2012 - “...carrier protein bID_Cluster_2625 8 Bcer98_0499 malate dehydrogenase, putative bID_Cluster_3344 9 Bcer98_0651 hypothetical protein bID_Cluster_2017 10 Bcer98_1017 hypothetical protein bID_Cluster_6230 11 Bcer98_1200 two component transcriptional regulator, ResD bID_Cluster_857 11 Bcer98_1201 multi-sensor signal transduction histidine kinase, ResE bID_Cluster_9721 12 Bcer98_3007 ferric uptake regulator family protein bID_Cluster_3378 13 Bcer98_3102...”
IT6_09370 (Fe-S)-binding protein from Methylacidiphilum caldifontis
32% identity, 89% coverage
- Verrucomicrobial methanotrophs grow on diverse C3 compounds and use a homolog of particulate methane monooxygenase to oxidize acetone
Awala, The ISME journal 2021 - “...detail. Genes in the cluster (Fig. 5 ) were predicted as follows: (i) lactate dehydrogenase (IT6_09370 and 09375), ( ii ) glucose-methanol-choline (GMC) oxidoreductase (IT6_09380 and IT6_09385), (iii) lactoylglutathione lyases (IT6_09390), (iv) pmoCAB3 operon (IT6_0939509405) with an additional pmoD gene (IT6_09410), (v) phosphoenolpyruvate (PEP) synthase (IT6_09415),...”
- “...distantly from the C3-upregulated cluster, and their expression was not differential. The two upregulated genes (IT6_09370 and 09375) containing Fe-S- and FAD-binding motifs, respectively, comprise an annotated lactate dehydrogenase [ 92 ]. PEP synthetase (IT6_09415) is required for the synthesis of precursor metabolites for cellular carbon...”
NCTC12103_00751 (Fe-S)-binding protein from Mammaliicoccus sciuri
29% identity, 89% coverage
GSU1624 glycolate oxidase iron-sulfur subunit, putative from Geobacter sulfurreducens PCA
31% identity, 88% coverage
GSU3297 iron-sulfur cluster-binding protein from Geobacter sulfurreducens PCA
28% identity, 91% coverage
AYM39_RS04895 (Fe-S)-binding protein from Methylomonas sp. DH-1
29% identity, 88% coverage
Dde_3245 Iron-sulfur cluster binding protein from Desulfovibrio desulfuricans G20
Dde_3245 L-lactate dehydrogenase (quinone) large subunit LdhH from Oleidesulfovibrio alaskensis G20
28% identity, 56% coverage
- Transcriptome-wide marker gene expression analysis of stress-responsive sulfate-reducing bacteria
Jawaharraj, Scientific reports 2023 - “...producing cell materials 59 . In this study, the GO term related to lactate oxidation (Dde_3245, Dde_1843) was down-regulated in EC-2 (P-Cu) whereas the same was up-regulated in SLG-Cu (EC-3) with z-scores -0.04 and 0.04, respectively. This confirms that the lactate oxidation pathway was activated in...”
- Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes
Meyer, Journal of bacteriology 2013 - “...redox pair) Gene locus tag(s) Dde_1207-Dde_1213 Dde_3523-Dde_3530 Dde_3245 Dde_0312 Dde_3540 M. maripaludis M. hungatei M. maripaludis M. hungatei Mutant growth...”
- “...the lactate dehydrogenase (LdhB-1, Dde_3240, and LdhB-2, Dde_3245) showed no growth in coculture on lactate, confirming their essential function during...”
- Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth
Meyer, Journal of bacteriology 2013 - “...putative iron-sulfur subunits (LdhB-1/2, Dde_3240 and Dde_3245), two phosphate acetyltransferases (Pta, Dde_3241 and Dde_3243), an acetate kinase (Ack,...”
- “...is significantly upregulated during syntrophy (Dde_3239-40 and Dde_3245). This cytoplasmic lactate dehydrogenase, LdhAB, is not homologous to the previously...”
Dde_3240 Glycolate oxidase iron-sulfur subunit. {escherichia, putative from Desulfovibrio desulfuricans G20
26% identity, 91% coverage
- Shotgun proteomic analysis of nanoparticle-synthesizing Desulfovibrio alaskensis in response to platinum and palladium
Capeness, Microbiology (Reading, England) 2019 - “...less-abundant dataset are proteins involved in energy production and metabolism, such as oxidoreductases (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...”
- “...membrane-bound oxidoreductase 0.5 Dde_2670 Ferrous iron transporter component feoA 0.54 Dde_1111 Quinone-interacting membrane-bound oxidoreductase 0.64 Dde_3240 Protein of unknown function DUF224 0.55 Dde_1633 Gamma-glutamyl phosphate reductase 0.55 Dde_3604 d -lactate dehydrogenase (cytochrome) 0.65 Dde_2272 Hdr menaquinol oxidoreductase 0.56 Dde_2979 Carbonic anhydrase 0.57 Dde_2201 Polyprenyl synthetase 0.65...”
- New model for electron flow for sulfate reduction in Desulfovibrio alaskensis G20
Keller, Applied and environmental microbiology 2014 - “...Ab Dde_0182 Dde_0312 Dde_0750 Dde_1087 Dde_3238 Dde_3239 Dde_3240 GlcD COG-GlcD LdlD COG-GlcD LldP GlcD LdhB (S)-2-Hydroxy acid oxidase FAD/FMN-containing...”
- Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes
Meyer, Journal of bacteriology 2013 - “...beta subunits of the lactate dehydrogenase (LdhB-1, Dde_3240, and LdhB-2, Dde_3245) showed no growth in coculture on lactate, confirming their essential...”
- Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth
Meyer, Journal of bacteriology 2013 - “...two HdrD-like putative iron-sulfur subunits (LdhB-1/2, Dde_3240 and Dde_3245), two phosphate acetyltransferases (Pta, Dde_3241 and Dde_3243), an acetate...”
D2S426 4Fe-4S ferredoxin-type domain-containing protein from Geodermatophilus obscurus (strain ATCC 25078 / DSM 43160 / JCM 3152 / CCUG 61914 / KCC A-0152 / KCTC 9177 / NBRC 13315 / NRRL B-3577 / G-20)
28% identity, 95% coverage
DVU_3033 / Q726S3 quinone-dependent L-lactate dehydrogenase large subunit (EC 1.1.2.3) from Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough) (see 4 papers)
Q726S3 Iron-sulfur cluster-binding protein from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
DVU3033 iron-sulfur cluster-binding protein from Desulfovibrio vulgaris Hildenborough
25% identity, 55% 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 - “...dehydrogenase subunit A LldG Q726S4 DVU_3032 22.6 21 63 11 L-lactate dehydrogenase subunit B LldH Q726S3 DVU_3033 79.6 106 63 43 Lactate dehydrogenase P62051 DVU_0600 32.2 2 13 2 D-lactate dehydrogenase subunit A (Dld-II family) Q72DV3 DVU_0826 47.4 2 4 2 D-lactate dehydrogenase subunit B (Dld-II...”
- Key Enzymes for Anaerobic Lactate Metabolism in Geobacter sulfurreducens
Ueki, Applied and environmental microbiology 2021 (secret) - Proteomic and Isotopic Response of Desulfovibrio vulgaris to DsrC Perturbation
Leavitt, Frontiers in microbiology 2019 - “...Ldh1a belongs to a gene cluster found in the organic acid oxidation region (DVU3025 to DVU3033), previously identified in the genomes of D. vulgaris and Desulfo vibrio alaskensis G20 ( Pereira et al., 2007 ; Wall et al., 2008 ), and recently named as the luo...”
- A stable genetic polymorphism underpinning microbial syntrophy
Großkopf, The ISME journal 2016 - “...to encode for a sigma-54 dependent response regulator that controls the downstream operon (DVU3025 - DVU3033), which includes the genes lactate permease and pyruvate decarboxylase. Notably, both enzymes are involved in the lactate oxidation pathway, with the first enzyme catalyzing the lactate uptake and the second...”
- Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete
Gao, Applied and environmental microbiology 2016 - “...Lactate oxidation DVU3030 DVU3027 DVU3031 DVU3032 DVU3028 DVU3033 DVU0600 DVU2110 DVU2285 DVU2451 DVU2683 DVU3026 DVU3029 DVU1569 DVU1570 DVU3025 DVU0577...”
- The primary pathway for lactate oxidation in Desulfovibrio vulgaris
Vita, Frontiers in microbiology 2015 - “...Table S1 ). The two 500 bp regions upstream and downstream of the DVU3032 and DVU3033 genes, respectively, were cloned into the pNOTCm, which produced pNOTCm32-33, and the mutagenic plasmid was transferred into Dv H by electrotransformation. Briefly, cells grown in 80 mL medium C (OD...”
- “...histidine conserved in enzymes that bind lactate ( Griffin et al., 1992 ). DVU3032 and DVU3033 were annotated as a conserved hypothetical protein and iron sulfur cluster-binding protein, respectively. However, their amino-acid sequences shared 26% amino acid sequence identity with the three subunits of the non-flavin...”
- The electron transfer system of syntrophically grown Desulfovibrio vulgaris
Walker, Journal of bacteriology 2009 - “...transcription of genes in a predicted operon (DVU3024 to DVU3033) coding for lactate uptake and oxidation. The enzymes in this pathway are predicted to produce...”
DVU_3028 / Q726S8 quinone-dependent D-lactate dehydrogenase iron-sulfur subunit (EC 1.1.2.5) from Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough) (see 3 papers)
Q726S8 Glycolate oxidase iron-sulfur subunit from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
DVU3028 iron-sulfur cluster-binding protein from Desulfovibrio vulgaris Hildenborough
25% identity, 86% 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 - “...dehydrogenase subunit A D-LdII-A Q726S9 DVU_3027 49.3 85 81 32 D-lactate dehydrogenase subunit B D-LdII-B Q726S8 DVU_3028 45.9 32 45 16 Phosphate acetyl transferase Pta Q726S7 DVU_3029 76.8 121 75 41 Acetate kinase Ack Q726S6 DVU_3030 44.1 77 60 28 Conserved hypothetical protein Q726S5 DVU_3031 39.0...”
- Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes
Denise, Microbial genomics 2023 - “...DVU3027 are each in an operon with a gene encoding their iron-sulphur subunits, DVU0826, and DVU3028, respectively ( Fig. 5 , panel B). DVU0390 is in an operon with genes encoding a putative amino acid transporter. DVU0253 and DVU0371 are multidomain proteins with additional FAD-binding and...”
- Key Enzymes for Anaerobic Lactate Metabolism in Geobacter sulfurreducens
Ueki, Applied and environmental microbiology 2021 (secret) - Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature
Kempher, mBio 2020 - “...DVU0426), a leucyl-tRNA synthetase gene ( leuS ; DVU1196), and an iron-sulfur cluster-binding protein gene (DVU3028). Only one phage-related tail fiber gene (DVU1486) was mutated in both the EC-T and ES-T populations. The genes that acquired mutations in populations from two or more groups in phase...”
- Proteomic and Isotopic Response of Desulfovibrio vulgaris to DsrC Perturbation
Leavitt, Frontiers in microbiology 2019 - “...experiments. The putative Fe-S lactate dehydrogenase, Ldh1a, was less abundant in the mutant than wildtype (DVU3028, 1.52 0.25). Ldh1a belongs to a gene cluster found in the organic acid oxidation region (DVU3025 to DVU3033), previously identified in the genomes of D. vulgaris and Desulfo vibrio alaskensis...”
- Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete
Gao, Applied and environmental microbiology 2016 - “...genes DVU3026 for lactate permease, DVU3027, DVU3028, DVU3032, and DVU03033 for lactate dehydrogenase subunits, DVU3025 for pyruvate-ferredoxin oxidoreductase,...”
- “...DVU1597 Lactate oxidation DVU3030 DVU3027 DVU3031 DVU3032 DVU3028 DVU3033 DVU0600 DVU2110 DVU2285 DVU2451 DVU2683 DVU3026 DVU3029 DVU1569 DVU1570 DVU3025...”
- The primary pathway for lactate oxidation in Desulfovibrio vulgaris
Vita, Frontiers in microbiology 2015 - “...D , L -lactate permease DVU3027 Glycolate oxidase, subunit GlcD D -lactate dehydrogenase subunit dldII-A DVU3028 Iron-sulfur cluster-binding protein D -lactate dehydrogenase subunit dldII-B DVU3029 Phosphate acetyltransferase (pta) Phosphate acetyltransferase pta DVU3030 Acetate kinase (ack) Acetate kinase ack DVU3031 Conserved hypothetical protein Unknown DVU3032 Conserved hypothetical...”
- “...respectively) and do not display the ShineDalgarno (SD) sequence upstream of the start codon. For DVU3028 , another start codon was observed 27 nucleotides upstream of the previously reported ( Heidelberg et al., 2004 ) and proposed codon ( Price et al., 2011 ). Products were...”
- Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation
He, Applied and environmental microbiology 2010 - “...in the operon containing DVU3025, DVU3026, DVU3027, DVU3028, DVU3029, and DVU3030, which encode a putative pyruvate-ferredoxin oxi- Downloaded from...”
- The electron transfer system of syntrophically grown Desulfovibrio vulgaris
Walker, Journal of bacteriology 2009 - “...by a putative lactate dehydrogenase (DVU3027 and DVU3028), which likely functions primarily during syntrophic growth. The extracted electrons reduce an...”
- “...oxidase of E. coli (DVU3027 and DVU3028), a monomeric pyruvate:ferredoxin oxidoreductase (DVU3025), phosphate acetyltransferase (DVU3029), and acetate kinase...”
- More
Q362_RS0100810, WP_028317114 L-lactate dehydrogenase (quinone) large subunit LdhH from Desulfobulbus elongatus DSM 2908
26% identity, 54% coverage
- Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle
Detman, Biotechnology for biofuels 2018 - “...Acetobacterium woodii DSM 1030 genome NC_016894; l -lactate utilization protein LutB containing FeS oxidoreductase WP_028317114 (Q362_RS0100810) from Desulfobulbus elongatus DSM 2908 assembly ASM62114v1; [FeFe]-hydrogenase large subunit Fe, Fe_hydrog_A WP_012939287 (ACFER_RS10010) from Acidaminococcus fermentans DSM 20731 genome NC_013740; Ni, Fe-hydrogenase III large subunit WP_075074147 (LARV_RS13630) from Longilinea...”
- “...from Acetobacterium woodii DSM 1030 genome NC_016894; l -lactate utilization protein LutB containing FeS oxidoreductase WP_028317114 (Q362_RS0100810) from Desulfobulbus elongatus DSM 2908 assembly ASM62114v1; [FeFe]-hydrogenase large subunit Fe, Fe_hydrog_A WP_012939287 (ACFER_RS10010) from Acidaminococcus fermentans DSM 20731 genome NC_013740; Ni, Fe-hydrogenase III large subunit WP_075074147 (LARV_RS13630) from...”
Dred_0690 protein of unknown function DUF162 from Desulfotomaculum reducens MI-1
27% identity, 55% coverage
Cj0991c putative oxidoreductase ferredoxin-type electron transport protein from Campylobacter jejuni subsp. jejuni NCTC 11168
24% identity, 87% coverage
- In Campylobacter jejuni, a new type of chaperone receives heme from ferrochelatase
Zamarreño, Frontiers in genetics 2023 - “...gene is part of a gene cluster that also encodes a ferredoxin-type electron transport protein (Cj0991c), the hypothetical protein Cj0993c, an ornithine carbamoyltransferase ArgF (Cj0994c), and the delta-aminolevulinic acid dehydratase HemB/PbgS (Cj0995c). Genes cj0363c and cj0580c are scattered throughout the genome and not located near any...”
THER_0617 L-lactate dehydrogenase (quinone) large subunit LdhH from Thermodesulfovibrio sp. N1
23% identity, 57% coverage
GSU1620 iron-sulfur cluster binding protein, putative from Geobacter sulfurreducens PCA
25% identity, 55% coverage
AF0506 iron-sulfur binding reductase from Archaeoglobus fulgidus DSM 4304
26% identity, 82% coverage
MMP1067 Succinate dehydrogenase/fumarate reductase iron-sulfur subunit // Methanosarcina type heterodisulfide reductase subunit D from Methanococcus maripaludis S2
23% identity, 80% coverage
lutA / O07020 iron-sulfur oxidase subunit used in L-lactate utilization (EC 1.1.1.27) from Bacillus subtilis (strain 168) (see 2 papers)
LUTA_BACSU / O07020 Lactate utilization protein A from Bacillus subtilis (strain 168) (see paper)
24% identity, 52% coverage
- function: Is essential for L-lactate degradation and allows cells to grow with lactate as the sole carbon source. May also allow cells to utilize an alternative carbon source during biofilm formation, since it contributes to the formation of architecturally complex communities when lactate is present.
disruption phenotype: Cells lacking this gene are unable to grow on minimal medium with L-lactate as the sole carbon source. Cells lacking the lutABC operon exhibit little or no defect in biofilm formation on MSgg medium, but form small colonies that almost completely lacked surface architecture when glycerol is replaced with L-lactate in the MSgg medium.
cg2543 glycolate oxidase FAD-linked subunit oxidoreductase from Corynebacterium glutamicum ATCC 13032
25% identity, 41% coverage
- Physiology and Transcriptional Analysis of (p)ppGpp-Related Regulatory Effects in Corynebacterium glutamicum
Ruwe, Frontiers in microbiology 2019 - “...1.25 1.64564E61 cg1665 putative secreted protein 1.09 6.95957E12 cg1784 ocd putative ornithine cyclodeaminase 1.44 5.2046E16 cg2543 glcD putative (S)-2-hydroxy-acid oxidase 1.66 1.09228E47 cg2545 putative secreted or membrane protein 1.34 1.85048E09 cg2546 putative secondary C4-dicarboxylate transporter, tripartite ATP-independent transporter (TRAP-T) family 1.46 1.04406E29 cg3113 cysY sirohydrochlorin ferrochelatase...”
A9762_26930 (Fe-S)-binding protein from Pandoraea sp. ISTKB
29% identity, 52% coverage
HP0666 anaerobic glycerol-3-phosphate dehydrogenase, subunit C (glpC) from Helicobacter pylori 26695
22% identity, 89% coverage
Dred_0433 CoB--CoM heterodisulfide reductase from Desulfotomaculum reducens MI-1
23% identity, 55% coverage
D9Q9T4 (Fe-S)-binding protein from Corynebacterium pseudotuberculosis (strain C231)
CpC231_0829 (Fe-S)-binding protein from Corynebacterium pseudotuberculosis C231
28% identity, 52% coverage
- Changes in protein abundance are observed in bacterial isolates from a natural host
Rees, Frontiers in cellular and infection microbiology 2015 - “...lutB CpC231_0828 Lactate utilization protein B 0.234 1.888 * 2.065 * Energy production and conversion D9Q9T4 lutA CpC231_0829 Lactate utilization protein A 0.239 1.848 * 2.476 * Energy production and conversion D9Q9Y9 CpC231_0884 CpC231_0884 Uncharacterized protein 1.794 * D9QAC0 cobG CpC231_1019 Precorrin-3B synthase 0.773 * 1.959...”
- Changes in protein abundance are observed in bacterial isolates from a natural host
Rees, Frontiers in cellular and infection microbiology 2015 - “...Lactate utilization protein B 0.234 1.888 * 2.065 * Energy production and conversion D9Q9T4 lutA CpC231_0829 Lactate utilization protein A 0.239 1.848 * 2.476 * Energy production and conversion D9Q9Y9 CpC231_0884 CpC231_0884 Uncharacterized protein 1.794 * D9QAC0 cobG CpC231_1019 Precorrin-3B synthase 0.773 * 1.959 * 1.946...”
- “...were associated with metabolism. This includes three lactate utilization proteins encoded by genes CpC231_0827 to CpC231_0829, which demonstrated increased abundance in all three field isolates in contrast to the reference strain. CpC231_0829 is lactate utilization protein A (LutA), CpC231_0828 is lactate utilization protein B (LutB) while...”
LUTA_BACCR / Q81GA5 Lactate utilization protein A from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711) (see paper)
BC1303 (S)-2-hydroxy-acid oxidase, iron-sulfur chain from Bacillus cereus ATCC 14579
24% identity, 52% coverage
- function: Is involved in L-lactate degradation and allows cells to grow with lactate as the sole carbon source.
- SigB modulates expression of novel SigB regulon members via Bc1009 in non-stressed and heat-stressed cells revealing its alternative roles in Bacillus cereus
Yeak, BMC microbiology 2023 - “...Protein dltD precursor 2.1 M 45 BC1403 LeuD 3-isopropylmalate dehydratase small subunit 2.1 E 46 BC1303 YvfV (S)-2-hydroxy-acid oxidase, iron-sulfur chain 2.0 2.1 C 47 BC4463 BC4463 Stage II sporulation protein B 2.0 S 48 BC3980 YkuR putative N-acetyldiaminopimelate deacetylase, peptidoglycan synthesis 2.0 1.9 R 49...”
- “...cutC 3.6 3.1 P 7 BC2752 YpeB hypothetical Membrane Spanning Protein 3.5 3.5 S 8 BC1303 YvfV (S)-2-hydroxy-acid oxidase, iron-sulfur chain 3.5 3.0 C 9 BC5077 hypothetical protein 3.4 3.2 S 10 BC4830 ABC transporter permease protein 3.3 1.0 V 11 BC0544 iron-sulfur cluster-binding protein 3.0...”
YkgE / b0306 putative lactate utilization oxidoreductase YkgE from Escherichia coli K-12 substr. MG1655 (see 3 papers)
P77252 Uncharacterized protein YkgE from Escherichia coli (strain K12)
b0306 predicted oxidoreductase from Escherichia coli str. K-12 substr. MG1655
27% identity, 52% coverage
SCO5966 oxidase from Streptomyces coelicolor A3(2)
27% identity, 39% coverage
BAS1216 conserved hypothetical protein from Bacillus anthracis str. Sterne
25% identity, 52% coverage
H16_RS06900 (Fe-S)-binding protein from Cupriavidus necator H16
27% identity, 49% coverage
Dde_0312 Oxidoreductase, putative from Desulfovibrio desulfuricans G20
24% identity, 34% coverage
O24951 Conserved hypothetical secreted protein from Helicobacter pylori (strain ATCC 700392 / 26695)
HP0139 conserved hypothetical secreted protein from Helicobacter pylori 26695
26% identity, 49% coverage
- Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors
Wei, ACS omega 2022 - “...O25762 HP_1143 218 P56106 pyrH 219 O25998 HP_1462 220 P56459 aspS 221 O25068 Fla 222 O24951 HP_0139 223 P66637 rpsI 224 O25036 Omp8 225 P56191 ddl 226 P56052 rpmC 227 O25087 hugZ 228 P48370 gyrA 229 O25080 pgdA 230 O25276 Cag22 231 O25157 HP_0396 232 O25773...”
- “...O25684 HP_1043 259 P56041 rplP 260 O25288 HP_0564 261 P56039 rplN 262 O25930 BamD 263 O24951 HP_0139 264 O25089 HP_0322 265 O25426 HP_0726 266 O25116 pyrG 267 O25256 HP_0519 268 P94844 dapB 269 P66052 rplK 270 O25573 FrpB 271 O25856 NQO3 272 O25713 HP_1081 273 O25276...”
- Identification of the genes that contribute to lactate utilization in Helicobacter pylori
Iwatani, PloS one 2014 - “...hp1222 :: aph3 This study pSI05 TOPO vector with 2.8 kb fragment containing hp0137 - hp0139 This study pSI06 pSI05 derivative with hp01370139 :: cat This study *Cm r , chloramphenicol resistance; Kan r , kanamycin resistance; Zeo r , zeocin resistance; Amp r , ampicillin...”
- “...one nucleotide substitution (A>T) so as to introduce a termination codon in 5 region of hp0139 . The PCR fragment was then cloned into TOPO vector (pSI05), and pSI05 was used in inverse PCR with hp137-F0/hp139-R0 primers to amplify the complete plasmid excluding the first codon...”
- Proteomic analysis of the sarcosine-insoluble outer membrane fraction of Helicobacter pylori strain 26695
Baik, Journal of bacteriology 2004 - “...HP0706 HP0706 HP0706 HP0073 HP0073 HP0671 HP1469 HP1469 HP0139 HP0325 HP1563 HP1107 HP0606 HP0512 HP1173 HP1173 HP1173 HP1376 29,000 29,000 29,000 29,000 28,500...”
- “...five hypothetical proteins (HP0205, HP1349, HP0052, HP1173, and HP0139). These proteins are not theoretically OMPs, and their localization is unclear. HP1173 is...”
EF1108 oxidoreductase, putative from Enterococcus faecalis V583
24% identity, 52% coverage
Rru_A3606 Protein of unknown function DUF224, cysteine-rich region from Rhodospirillum rubrum ATCC 11170
28% identity, 54% coverage
- Investigation of candidate genes involved in the rhodoquinone biosynthetic pathway in Rhodospirillum rubrum
Campbell, PloS one 2019 - “...15.2 -18.3 Peptidase/amidohydrolase Rru_A2553 13.5 -5.1 Ubiquinone/menaquinone biosynthesis methyltransferase Rru_A2106 7.7 -68.4 16QF5 Hypothetical protein Rru_A3606 7.1 -31.8 16RW4 Hypothetical protein Rru_A1729 6.9 -35.2 16YKK Hypothetical protein Rru_A3004 4.5 -73.4 16Q21 Class I and Class II aminotransferases Rru_A3121 3.2 -170.0 Asparagine synthase Rru_A3231 3.0 -57.0 1748D...”
- “.... rubrum , which were in direct correlation to RQ levels. For example, deletion of Rru_A3606 resulted in a higher production of both Q and RQ under anaerobic conditions, while under semi-aerobic conditions, the amounts were consistent with the WT control. These data suggest the Rru_A3606...”
D351_01409 (Fe-S)-binding protein from Enterococcus faecalis WKS-26-18-2
24% identity, 52% coverage
PMI3046 oxidoreductase (cysteine-rich protein) from Proteus mirabilis HI4320
26% identity, 52% coverage
trd_1165 glycolate oxidase subunit from Thermomicrobium roseum DSM 5159
27% identity, 41% coverage
HVO_1540 glycerol-3-phosphate dehydrogenase subunit C from Haloferax volcanii DS2
25% identity, 89% coverage
Q88DT2 D-2-hydroxyacid dehydrogenase (quinone) (EC 1.1.5.10); D-lactate dehydrogenase (quinone) (EC 1.1.5.12) from Pseudomonas putida (see paper)
PP4737, PP_4737 D-lactate dehydrogenase, putative from Pseudomonas putida KT2440
27% identity, 38% coverage
llmg_1915 putative Fe-S oxidoreductase from Lactococcus lactis subsp. cremoris MG1363
24% identity, 52% coverage
- Early adaptation to oxygen is key to the industrially important traits of Lactococcus lactis ssp. cremoris during milk fermentation
Cretenet, BMC genomics 2014 - “...COG1053 C frdC fumarate reductase flavoprotein subunit 4.24 llmg_0993 COG0634 F hprT hypoxanthine-guanine phosphoribosyltransferase 2.01 llmg_1915 COG0247 C llmg_1915 putative Fe-S oxidoreductase 3.61 llmg_0447 COG0674 C nifJ Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, alpha subunit 11.19 llmg_1514 COG2344 R rex Redox-sensing transcriptional repressor rex. 2.73 llmg_0640...”
- “...hydrogen peroxide to water, were over-expressed at 1h. Conversely, oxygen-sensitive genes such as nifJ and llmg_1915 were found to be under-expressed at 1h. Transport proteins were also under-expressed: cadA coding for a cation transporting ATPase, dtpT and eriC coding for di-/tri-peptide transporter and for chloride transporter...”
APL_0446 putative dehydrogenase subunit from Actinobacillus pleuropneumoniae L20
24% identity, 52% coverage
MSMEG_0595 glycolate oxidase from Mycobacterium smegmatis str. MC2 155
29% identity, 53% coverage
- Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress
Hillion, Scientific reports 2017 - “...6,4 34,1 MSMEG_1977 MSMEG_1977 Alcohol DH, zinc-containing 39* B 22,8 14,5 30,0 11,9 12,6 27,5 MSMEG_0595 MSMEG_0595 Fe-S oxidoreductase 142* B 13,9 12,4 23,4 7,6 30,2 37,8 MSMEG_0690 MSMEG_0690 Fe-S oxidoreductase 637* B 11,5 22,7 38,8 8,2 38,5 45,2 MSMEG_0768 MSMEG_0768 Rhodanese domain protein 83* B...”
PM1853 unknown from Pasteurella multocida subsp. multocida str. Pm70
25% identity, 52% coverage
Q72B55 Cysteine-rich domain protein from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
DVU1783 cysteine-rich domain protein from Desulfovibrio vulgaris Hildenborough
26% identity, 50% 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 - “...DVU_1781 23.9 L-lactate dehydrogenase (LldH family) Q72B56 DVU_1782 52.6 4 8 4 Lactate permeases, putative Q72B55 DVU_1783 27.4 3 14 2 Q72A87 DVU_2110 57.9 5 9 3 Q729R4 DVU_2285 53.0 5 13 5 Q725Z0 DVU_3284 57.7 Sulfate reduction Sulfate permeases Q72FD5 DVU_0279 60.6 9 21 8...”
- The primary pathway for lactate oxidation in Desulfovibrio vulgaris
Vita, Frontiers in microbiology 2015 - “...into two groups according to their expression level. The first group included the genes DVU0253, DVU1783 , and DVU2784 , which exhibited a high expression level under these conditions similar to that of the genes belonging to the operon luo. The second group, which included all...”
- Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution
Zhou, The ISME journal 2013 - “...II) DVU0384 DVU2451 DVU2683 DVU1780 DVU1781 DVU1782 DVU1783 DVU2286 DVU2287 DVU2288 DVU2289 DVU2290 DVU2291 DVU2292 DVU2293 Annotation Cytochrome c family...”
- Genetics and molecular biology of the electron flow for sulfate respiration in desulfovibrio
Keller, Frontiers in microbiology 2011 - “...2.6 fold upon entering stationary phase presumably because of carbon and electron donor limitation, DVU0600, DVU1783, and the complex DVU30273028. Of the three, only the latter complex had more abundant transcripts than the average gene. This complex is also part of a nine gene operon that...”
PfGW456L13_5118 D-lactate dehydrogenase (quinone), FeS subunit (EC 1.1.5.12) from Pseudomonas fluorescens GW456-L13
27% identity, 38% coverage
- mutant phenotype: Specific phenotype: utilization of D-Lactate, Glycerol. The phenotype on glycerol is not explained (is there is a side pathway via glycerate?)
Cj0075c putative oxidoreductase iron-sulfur subunit from Campylobacter jejuni subsp. jejuni NCTC 11168
YP_002343537 oxidoreductase iron-sulfur subunit from Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
25% identity, 52% coverage
- Defining the metabolic requirements for the growth and colonization capacity of Campylobacter jejuni
Hofreuter, Frontiers in cellular and infection microbiology 2014 - “...oxidized by C. jejuni to pyruvate by the membrane-associated NAD-independent respiratory lactate dehydrogenase complex (L-iLDH; Cj0075c, Cj0074c; Cj0073c) though inactivation of these genes in C. jejuni NCTC 11168 did not abolish the growth of respective mutants with lactate (Thomas et al., 2011 ). However, a second...”
- “...responsible for the observed redundancy in the catabolism of L-lactate. Only a double mutation inactivating cj0075c and cj1585c abolished the growth of C. jejuni NCTC 11168 with 20 mM L-lactate as a carbon source but it did not affect in the utilization of D-lactate. The gene...”
- Insights into the mode of action of benzyl isothiocyanate on Campylobacter jejuni
Dufour, Applied and environmental microbiology 2013 - “...frdB frdC Cj0414 Cj0415 Cj1476c Cj0265c Cj0037c Cj1153 Cj0074c Cj0075c Cj1514c Cj0264c Cj0559 oorA oorB acnB aspA dcuA glnA IlvD gapA fba atpE atpA atpD atpG...”
- Mutational and transcriptomic changes involved in the development of macrolide resistance in Campylobacter jejuni
Hao, Antimicrobial agents and chemotherapy 2013 - “...and frdABC), respiration (gpsA, Cj1357c, Cj1358c, Cj0074c, Cj0075c, Cj0265c, fdxA, and napAGH), central intermediary metabolism (ppa, gltB, aspA, and uxaA),...”
- Nutrient acquisition and metabolism by Campylobacter jejuni
Stahl, Frontiers in cellular and infection microbiology 2012 - “...through one of several pathways. The first involves three genes, cj0073c , cj0074c , and cj0075c ( lldEFG/lutABC ). These three genes code for a non-flavin ironsulfur containing oxidoreductase complex that demonstrate NAD-independent, l -lactate dehydrogenase activity ( l -iLDH), thereby converting l -lactate to pyruvate...”
- “...and demonstrated d -iLDH activity. However, d -lactate metabolism was not significantly affected in the cj0075c or cj1585c mutants and no other transporters or pathways have been identified as responsible for this phenotype (Thomas et al., 2011 ). Citric acid cycle intermediates Campylobacter jejuni depends heavily...”
- Two respiratory enzyme systems in Campylobacter jejuni NCTC 11168 contribute to growth on L-lactate
Thomas, Environmental microbiology 2011 (PubMed)- “...as well as wild-type on this substrate, while a cj0075c cj1585c double mutant showed no L-lactate oxidase activity and did not utilize or grow on L-lactate;...”
- “...donor was barely detectable in the cj0073c, cj0074c and cj0075c mutants when compared with a rate of 28 4 nmol min-1 mg protein-1 in wild-type C. jejuni...”
- In vivo and in silico determination of essential genes of Campylobacter jejuni
Metris, BMC genomics 2011 - “..."metabolic genes" according to the different techniques Technique Essential genes FBA only cj0024, cj0026c, cj0066c, cj0075c, cj0127c, cj0146c, cj0172c, cj0187c, cj0194, cj0196c, cj0197c, cj0205, cj0227, cj0237, cj0240c, cj0273, cj0274, cj0286c, cj0288c, cj0296c, cj0297c, cj0298c, cj0306c, cj0307, cj0321, cj0326, cj0332c, cj0360, cj0384c, cj0405, cj0432c, cj0433c, cj0434, cj0435,...”
- Identification of Campylobacter jejuni genes contributing to acid adaptation by transcriptional profiling and genome-wide mutagenesis
Reid, Applied and environmental microbiology 2008 - “...growth at low pH are pldA (phospholipase A), Cj0075c (oxidoreductase), gltA (citrate synthase), and gltB (Glu synthase). The sdhA gene (succinate dehydrogenase...”
- Two respiratory enzyme systems in Campylobacter jejuni NCTC 11168 contribute to growth on L-lactate.
Thomas, Environmental microbiology 2011 (PubMed)- GeneRIF: A cj0075c cj1585c double mutant showed no L-lactate oxidase activity and did not utilize or grow on L-lactate; D-lactate-dependent growth was unaffected.
HSERO_RS19500 Putative phosphoglycerate dehydrogenase (EC:1.1.1.95) from Herbaspirillum seropedicae SmR1
HSERO_RS19500 DUF3683 domain-containing protein from Herbaspirillum seropedicae SmR1
22% identity, 28% coverage
- mutant phenotype: The annotation of this essential protein is based on its homology to BPHYT_RS03150. Orthologs in Acidovorax sp. GW300-3H11 (Ac3H11_4791) and Dechlorosoma suillum PS (Dsui_0736) are also essential. HSERO_RS21555 is another plausible candidate for this reaction, but it has little phenotype and its ortholog in Cupriavidus basilensis 4G11 (RR42_RS20535) seems to be involved in cell wall synthesis. (essential)
- Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics
Price, PLoS genetics 2018 - “...We propose that another oxidase provides this missing activity: BPHYT_RS03150 in B . phytofirmans or HSERO_RS19500 in H . seropedicae . These two proteins are very similar (76% amino acid identity) and both were originally annotated as FAD-linked oxidase. They contain an N-terminal DUF3683 domain, FAD-binding...”
- “...also at low abundance in our mutant pool, so the poor viability of mutants in HSERO_RS19500 is consistent with a role in serine synthesis. To look for other candidates for this step, we collected fitness data for H . seropedicae in minimal media with and without...”
CJJ81176_0112 cysteine-rich domain protein from Campylobacter jejuni subsp. jejuni 81-176
25% identity, 52% coverage
HD1221 conserved putative dehydrogenase subunit from Haemophilus ducreyi 35000HP
23% identity, 52% coverage
MSMEG_2492 D-lactate dehydrogenase from Mycobacterium smegmatis str. MC2 155
28% identity, 21% coverage
VM_17045 anaerobic glycerol-3-phosphate dehydrogenase subunit GlpC from Vibrio mimicus
21% identity, 90% coverage
RR42_RS21295 L-lactate dehydrogenase, LutA subunit from Cupriavidus basilensis FW507-4G11
26% identity, 54% coverage
- mutant phenotype: Specifically important for utilization of L-lactate or D,L-lactate. (Also important on various nitrogen sources with lactate as the carbon source.) This is related to the LutABC system from Bacillus subtilis (PMC3347220, PMC2668416).
ZMO0022 hypothetical protein from Zymomonas mobilis subsp. mobilis ZM4
26% identity, 53% coverage
- Elucidation of Zymomonas mobilis physiology and stress responses by quantitative proteomics and transcriptomics
Yang, Frontiers in microbiology 2014 - “...2.45 ZMO0094 Biotin synthase 1.18 0.70 ZMO0080 CheD, stimulates methylation of MCP proteins 0.70 0.90 ZMO0022 Protein of unknown function 1.01 1.05 ZMO0013 Purine NTP pyrophosphatase, rdgB/HAM1 family 0.74 0.80 Gene Product A190 P190 14 UNIQUE TRANSCRIPTOMICSPROTEOMICS PAIRS IDENTIFIED ONLY IN 190 h ZMO0017 Fmu 0.73...”
- Insights into acetate toxicity in Zymomonas mobilis 8b using different substrates
Yang, Biotechnology for biofuels 2014 - “...I, J (ZMO0005, 8, 9) and individual genes are involved in stress response: Fe-S oxidoreductase (ZMO0022), aldo/keto reductase (Dkg, ZMO1344), and catalase (ZMO0918). Other upregulated genes encode the TonB-dependent receptor (ZMO0031), glucan biosynthesis protein D (ZMO0905), L-sorbose reductase (ZMO1449), and a potential alanine/aspartate transporter (ZMO1681) (Figure...”
- Transcriptome profiling of Zymomonas mobilis under ethanol stress
He, Biotechnology for biofuels 2012 - “...chain genes were shown to be more abundant under stress condition, including putative Fe-S oxidoreductase (ZMO0022, 1.09-fold), cytochrome bd-type quinol oxidase subunits 1(ZMO1571, 1.52-fold), cytochrome bd-type quinol oxidase subunits 2 (ZMO1572, 1.09-fold), Fe-S-cluster redox enzyme (ZMO1032, 1.04-fold), cytochrome c -type biogenesis protein (ZMO1255, ZMO1256, 1.07-fold), ubiquinone...”
- Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations
Yang, BMC genomics 2009 - “...). A number of other respiratory genes were also down-regulated under these conditions. These included ZMO0022, ZMO1571, ZMO1572 and ZMO1844 encoding a putative Fe-S oxidoreductase, NADH dehydrogenase, cytochrome bd-type quinol oxidase subunits 1 and 2, and oxidoreductase genes, respectively (see Additional file 4 ). The stimulation...”
Dde_1842 protein of unknown function DUF224 cysteine-rich region domain protein from Desulfovibrio desulfuricans G20
26% identity, 46% coverage
VCA0749 anaerobic glycerol-3-phosphate dehydrogenase, subunit C from Vibrio cholerae O1 biovar eltor str. N16961
21% identity, 90% coverage
SCO7572 oxidoreductase from Streptomyces coelicolor A3(2)
23% identity, 40% coverage
- Effects of carbon ion beam-induced mutagenesis for the screening of RED production-deficient mutants of Streptomyces coelicolor JCM4020
Yanagisawa, PloS one 2022 - “...195G>T S hypothetical protein JCM4020_47210 SCO4587 99.5 5 Mt 204003 8,370,142 843C>T S oxidoreductase JCM4020_75780 SCO7572 99.7 6,935,841 379_381delCGC del_Arg127 D hypothetical protein JCM4020_63500 SCO6192 99.7 2,858,275 555G>T Gln185His M chitinase precursor JCM4020_26770 SCO2503 98.7 2,828,233 G>T UTR 2,240,012 783C>T S hydrolase JCM4020_21170 SCO1968 99.6 305,254...”
RSc0454 PUTATIVE OXIDOREDUCTASE PROTEIN from Ralstonia solanacearum GMI1000
22% identity, 26% coverage
- Metagenomic and Culturomics Analysis of Microbial Communities within Surface Sediments and the Prevalence of Antibiotic Resistance Genes in a Pristine River: The Zaqu River in the Lancang River Source Region, China
Yan, Microorganisms 2024 - “...]. The most prevalent pathogen genes included RpoB (belonging to Acinetobacter baumannii ), followed by RSc0454 and speC ( Ralstonia solanacearum ), as well as CcoN2 and rmlA ( Pseudomonas aeruginosa ). Among the pathogens carrying the most diverse genes, the top 10 species were Xanthomonas...”
- Involvement of a FAD-Linked Oxidase RSc0454 for Expression of the Type III Secretion System and Pathogenicity in Ralstonia solanacearum
Chen, Molecular plant-microbe interactions : MPMI 2021 (PubMed)- “...Ralstonia solanacearum RSc0454 is predicted as a FAD-linked oxidase based on protein homologies, while it contains distinct domains of lactate dehydrogenase and succinate dehydrogenase. A previous study demonstrated that RSc0454 exhibits lactate dehydrogenase...”
- “...substrates, and is essential for pathogenicity of R. solanacearum. Here, we genetically characterized involvement of RSc0454 on bacterial growth and expression of genes for the type III secretion system (T3SS, a pathogenicity determinant) in R. solanacearum. The RSc0454 mutant grew normally in rich medium but grew...”
- The RSc0454-Encoded FAD-Linked Oxidase Is Indispensable for Pathogenicity in Ralstonia solanacearum GMI1000
Hu, Molecular plant-microbe interactions : MPMI 2019 (PubMed)- “...agent of bacterial wilt disease. Here, we report that a large FAD-linked oxidase encoded by RSc0454 in GMI1000 is required for pathogenicity. The FAD-linked oxidase encoded by RSc0454 is composed of 1,345 amino acids, including DUF3683, lactate dehydrogenase (LDH), and succinate dehydrogenase (SDH) domains. The RSc0454...”
- “...LDH and SDH activities. To investigate its role in pathogenicity, a deletion mutant of the RSc0454 gene was constructed in GMI1000, which was impaired in its ability to cause bacterial wilt disease in tomato. A single DUF3683, LDH, or SDH domain was insufficient to restore bacterial...”
A9762_00290 DUF3683 domain-containing protein from Pandoraea sp. ISTKB
22% identity, 28% coverage
Msil_2429 protein of unknown function DUF224 cysteine-rich region domain protein from Methylocella silvestris BL2
27% identity, 45% coverage
- Genome Scale Metabolic Model of the versatile methanotroph Methylocella silvestris
Bordel, Microbial cell factories 2020 - “...metabolized via its transformation into pyruvate by a putative lactate dehydrogenase present in the genome (Msil_2429, 2430, 2431). However, the enzymes involved in the transformation of acetone to 2-oxopropanal remain to be elucidated. Proteomics has revealed strong overexpression of the gene Msil_1641, induced by propane. This...”
TFRB_METTM / D9PUX5 Fumarate reductase (CoM/CoB) subunit B; Thiol:fumarate reductase subunit B; EC 1.3.4.1 from Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg) (Methanobacterium thermoautotrophicum) (see 2 papers)
28% identity, 48% coverage
- function: Catalyzes the reduction of fumarate with reduced coenzyme M (CoM-S-H) and coenzyme B (CoB-S-H). In vitro, is able to reduces fumarate with reduced benzyl viologen, oxidize CoM-S-H and CoB-S-H to CoM-S-S-CoB with methylene blue, and reduce CoM-S-S-CoB with reduced benzyl viologen. The enzyme has specificity for the two thiol compounds as the CoB--CoM heterodisulfide reductase. The enzyme is very sensitive to oxygen.
catalytic activity: coenzyme B + coenzyme M + fumarate = coenzyme M-coenzyme B heterodisulfide + succinate (RHEA:40235)
cofactor: [2Fe-2S] cluster (Binds 1 [2Fe-2S] cluster per subunit.)
cofactor: [4Fe-4S] cluster (Binds 2 [4Fe-4S] clusters per subunit.)
subunit: Subunit B of the heterodimeric fumarate reductase of methanogenic Archaea, composed of subunits A (TfrA) and B (TfrB).
BPHYT_RS03150 Phosphoglycerate dehydrogenase (EC:1.1.1.95) from Burkholderia phytofirmans PsJN
21% identity, 26% coverage
- mutant phenotype: Auxotrophic, and rescued by L-serine or gly-glu. Glycine could yield serine via hydroxymethyltransferase, so this is consistent with a role in serine synthesis. BPHYT_RS31960 is also a possibility but gene context suggests that has a role in catabolism and has little phenotype; BPHYT_RS01425 is a possibility, but fitness data suggests it is cell wall related (auxotroph)
HP15_4088 L-lactate dehydrogenase, LutA subunit from Marinobacter adhaerens HP15
25% identity, 60% coverage
- mutant phenotype: Specifically important for utilization of L-lactate or D,L-lactate. This is related to the LutABC system from Bacillus subtilis (PMC3347220, PMC2668416).
STM2286 sn-glycerol-3-phosphate dehydrogenase (anaerobic), K-small subunit from Salmonella typhimurium LT2
SEN2268 anaerobic glycerol-3-phosphate dehydrogenase subunit C from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
24% identity, 90% coverage
FZF21_17655 anaerobic glycerol-3-phosphate dehydrogenase subunit GlpC from Enterobacter sp. LU1
24% identity, 89% coverage
DR_1907 (Fe-S)-binding protein from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
DR1907 fumarate reductase-related protein from Deinococcus radiodurans R1
25% identity, 49% coverage
- Essentiality of threonylcarbamoyladenosine (t(6)A), a universal tRNA modification, in bacteria
Thiaville, Molecular microbiology 2015 - “...1 DR_A0018 5-nucleotidase (EC 3.1.3.5) 2.5 5.20E-03 1 DR_0459 FIG00578356: hypothetical protein 2.3 1.01E-03 1 DR_1907 Predicted L-lactate dehydrogenase, Fe-S oxidoreductase subunit YkgE 2.3 7.41E-03 1 DR_B0014 Vitamin B12 ABC transporter, B12-binding component BtuF 2.2 1.25E-02 DR_1277 ABC-type probable sulfate transporter, periplasmic binding protein 2.0 2.14E-03...”
- A novel OxyR sensor and regulator of hydrogen peroxide stress with one cysteine residue in Deinococcus radiodurans
Chen, PloS one 2008 - “...Conserved membrane protein 3.770361 0.000821 DR0203 Membrane protein, similar to gi|1653436 of Synechocystis 3.729993 0.022306 DR1907 Fe-S subunit of glycolate oxidase, YKGE 3.728085 0.007343 10.1371/journal.pone.0001602.t005 Table 5 The 36 most highly induced genes in MOxyR. Locus Annotation Induction fold p value DRA0211 HTH transcriptional regulator, GntR...”
- “...in E coli 20.82 0.001641 7.19 0.001764 DR1799 Initiation factor IF-2 2.53 0.002127 2.36 0.069017 DR1907 Fe-S subunit of glycolate oxidase, YKGE 3.73 0.007343 5.66 0.003095 DR2470 Related to biothin biosysnthesis protein BioY 2.51 0.027048 2.62 0.029802 DR2524 Ribosomal protein L28 2.47 0.005166 2.11 0.01617 DRA0157...”
BFV67_RS15220 anaerobic glycerol-3-phosphate dehydrogenase subunit GlpC from Enterobacter roggenkampii
25% identity, 90% coverage
NJ56_05160 anaerobic glycerol-3-phosphate dehydrogenase subunit GlpC from Yersinia ruckeri
25% identity, 89% coverage
DVU0826 glycolate oxidase, iron-sulfur subunit, putative from Desulfovibrio vulgaris Hildenborough
Q72DV3 Glycolate oxidase, iron-sulfur subunit, putative from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
26% identity, 51% coverage
- Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough
Trotter, Frontiers in microbiology 2023 - “...medium that lacks pyridoxal phosphate (vitamin B 6 ), we identified a putative two-subunit dehydrogenase (DVU0826 and DVU0827) that is required for pyridoxal phosphate biosynthesis ( Figure 4A ). The genes for both subunits have nearly identical fitness patterns (high cofitness) as pdxA (DVU2241), which encodes...”
- “...)). This evidence supports a role for the dehydrogenase in pyridoxal phosphate biosynthesis. Figure 4 DVU0826 and DVU0827 are required for vitamin B 6 synthesis. (A) Comparison of gene fitness values across 757 experiments between pdxA (DVU2241) and either DVU0826 (left) or DVU0827 (right). Experiments performed...”
- Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes
Denise, Microbial genomics 2023 - “...( DVU2241 ) and pdxJ ( DVU1908 ) in conditions of B 6 limitation are DVU0826 and DVU0827 (Fig. S5), annotated as encoding the two subunits of the glycolate oxidase complex, the iron-sulphur subunit (GlcF), and the FAD-dependent subunits respectively (GlcD). This co-fitness is conserved in...”
- “...DVU0827 and DVU3027 are each in an operon with a gene encoding their iron-sulphur subunits, DVU0826, and DVU3028, respectively ( Fig. 5 , panel B). DVU0390 is in an operon with genes encoding a putative amino acid transporter. DVU0253 and DVU0371 are multidomain proteins with additional...”
- Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium
Trotter, 2021 - Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough.
Marbehan, Frontiers in microbiology 2024 - “...43 Lactate dehydrogenase P62051 DVU_0600 32.2 2 13 2 D-lactate dehydrogenase subunit A (Dld-II family) Q72DV3 DVU_0826 47.4 2 4 2 D-lactate dehydrogenase subunit B (Dld-II family) Q72DV2 DVU_0827 50.1 7 22 6 D-lactate dehydrogenase (Dld-II family) Q72F25 DVU_0390 48.2 25 51 17 D-lactate dehydrogenase (Dld-II...”
MPF_0946 (Fe-S)-binding protein from Methanohalophilus portucalensis FDF-1
21% identity, 89% coverage
BPHYT_RS26975 L-lactate dehydrogenase, LldE subunit from Burkholderia phytofirmans PsJN
26% identity, 53% coverage
- mutant phenotype: Specifically important for utilization of L-lactate and D,L-lactate as well as L-rhamnose and L-fucose, which are catabolized via L-lactate.
GlpC / b2243 anaerobic glycerol-3-phosphate dehydrogenase subunit C (EC 1.1.5.3) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
glpC / P0A996 anaerobic glycerol-3-phosphate dehydrogenase subunit C (EC 1.1.5.3) from Escherichia coli (strain K12) (see 4 papers)
NP_416746 anaerobic glycerol-3-phosphate dehydrogenase subunit C from Escherichia coli str. K-12 substr. MG1655
P0A996 Anaerobic glycerol-3-phosphate dehydrogenase subunit C from Escherichia coli (strain K12)
P0A997 Anaerobic glycerol-3-phosphate dehydrogenase subunit C from Escherichia coli O157:H7
b2243 sn-glycerol-3-phosphate dehydrogenase (anaerobic), small subunit from Escherichia coli str. K-12 substr. MG1655
EcolC_1408 glycerol-3-phosphate dehydrogenase, anaerobic, C subunit from Escherichia coli C str. ATCC 8739
Z3501 sn-glycerol-3-phosphate dehydrogenase (anaerobic), K-small subunit from Escherichia coli O157:H7 EDL933
ECs3128 anaerobic sn-glycerol-3-phosphate dehydrogenase K-small subunit from Escherichia coli O157:H7 str. Sakai
24% identity, 89% coverage
- Discovery of glpC, an organic solvent tolerance-related gene in Escherichia coli, using gene expression profiles from DNA microarrays.
Shimizu, Applied and environmental microbiology 2005 - GeneRIF: remarkably increased the tolerance to organic solvents
- Nucleotide sequence and gene-polypeptide relationships of the glpABC operon encoding the anaerobic sn-glycerol-3-phosphate dehydrogenase of Escherichia coli K-12.
Cole, Journal of bacteriology 1988 - GeneRIF: N-terminus verified by Edman degradation on complete protein
- Biodistribution of 89Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
Li, Poultry science 2023 - “...metabolism Cell inner membrane 527 P0AF98 LPTF General function prediction only Cell inner membrane 528 P0A996 GLPC Energy production and conversion Cell inner membrane 529 P06974 FLIM Cell motility Cell inner membrane 530 P0AA86 DSBE Function unknown Cell inner membrane 531 P0AB12 YCCF Function unknown Cell...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...dehydrogenase subunit B 5.75/45,357.24 GlpC P0A996 Anaerobic glycerol-3-phosphate dehydrogenase subunit C 8.78/44,108.04 GlpD P13035 Aerobic...”
- Use of Acetic Acid to Partially Replace Lactic Acid for Decontamination against Escherichia coli O157:H7 in Fresh Produce and Mechanism of Action
Wang, Foods (Basel, Switzerland) 2021 - “...glucan phosphorylase 0.41 Q8X6X8 glgX Glycogen debranching enzyme 0.34 Glycerophospholipid metabolism and major intrinsic proteins P0A997 glpC Anaerobic glycerol-3-phosphate dehydrogenase subunit C 0.59 P0A6F4 glpK Glycerol kinase 0.55 P0A9C1 glpA Anaerobic glycerol-3-phosphate dehydrogenase subunit A 0.69 A0A0H3JI74 glpD Glycerol-3-phosphate dehydrogenase 0.60 P0A6S9 gpsA Glycerol-3-phosphate dehydrogenase [NAD(P)+]...”
- BasS/BasR Two-Component System Affects the Sensitivity of Escherichia coli to Plantaricin BM-1 by Regulating the Tricarboxylic Acid Cycle
Liu, Frontiers in microbiology 2022 - “...glycerol-3-phosphate dehydrogenase subunit A 0.64914 0.571328 b2242 GlpB Anaerobic glycerol-3-phosphate dehydrogenase subunit B 0.707122 0.667276 b2243 GlpC Anaerobic glycerol-3-phosphate dehydrogenase subunit C 0.611355 0.498009 b3829 MetE 5-methyltetrahydropteroyltriglutamatehomocysteine S-methyltransferase 0.829016 0.729757 b3113 RidA Enamine/imine deaminase 0.803088 0.800797 b3114 PflD 2-ketobutyrate formate-lyase/pyruvate formate-lyase 0.713731 0.764876 b4122 FumA Class...”
- Comparison on extreme pathways reveals nature of different biological processes
Xi, BMC systems biology 2014 - “...factors. For example, two redundant ExPas shown in Figure 4 stimulate the expression of gene b2243 in the same environment, but they employ the regulatory rules of ' CRP_noRIB AND Fnr AND NOT(GlpR) ' and ' CRP_noRIB AND ArcA AND NOT(GlpR) ', respectively. From Figure 3...”
- Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD
Kim, Environmental microbiology 2010 - “...1.5 Anaerobic glycerol-3-phosphate dehydrogenase subunit A glpB b2242 1.3 4.9 1.7 sn-glycerol-3-phosphate dehydrogenase (anaerobic) glpC b2243 1.4 7.5 1.8 sn-glycerol-3-phosphate dehydrogenase (anaerobic), K-small subunit glpD b3426 1.1 10.6 1.2 sn-glycerol-3-phosphate dehydrogenase (aerobic) glpK b3926 1.1 4.0 1.3 Glycerol kinase glpF b3927 1.0 5.3 1.1 Facilitated diffusion...”
- The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction
Oberto, PloS one 2009 - “...0.96 0.24 1 0.28 0.29 0.54 FA, FAec sn-glycerol-3-phosphate dehydrogenase (anaerobic), membrane anchor subunit glpC b2243 glpABC 1 0.54 1.24 0.31 1 1.2 1.17 0.27 1 0.26 0.33 0.51 FA, FAec sn-glycerol-3-phosphate dehydrogenase (anaerobic), K-small subunit uraA b2497 upp-uraA 1 0.42 1.03 0.49 1 0.66 0.07...”
- Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
Stepanova, Journal of bacteriology 2007 - “...aldolase 1 glpB glpC b2242 b2243 2.7 3.5 sn-Glycerol-3-phosphate dehydrogenase (anaerobic), membrane anchor subunit sn-Glycerol-3-phosphate dehydrogenase...”
- DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
Polen, Applied and environmental microbiology 2003 - “...0.75 0.68 1.39 1.39 b2241 b2242 b2243 glpA glpB glpC 2 2 2 sn-Glycerol-3-phosphate dehydrogenase sn-Glycerol-3-phosphate dehydrogenase sn-Glycerol-3-phosphate...”
- In silico Design for Systems-Based Metabolic Engineering for the Bioconversion of Valuable Compounds From Industrial By-Products
Tafur, Frontiers in genetics 2021 - “...Exp 3 Log2 FC evolved 01540 glpD EcolC_0288 Aerobic glycerol-3-phosphate dehydrogenase 1.69 1.21 07540 glpC EcolC_1408 Anaerobic glycerol-3-phosphate dehydrogenase subunit C 2.61 3.59 07545 glpB EcolC_1409 Anaerobic glycerol-3-phosphate dehydrogenase subunit B 2.87 3.74 07550 glpA EcolC_1410 Sn-glycerol-3-phosphate dehydrogenase subunit A 1.28 2.00 07555 glpT EcolC_1411 Glycerol-3-phosphate...”
- Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents
Segura, BMC genomics 2018 - “...glpB Glycerol 3-phosphate dehydrogenase (b subunit) 4.33 4.60E-06 NDE 5.01 1.05E-07 2.20 3.19E-02 3.77 1.06E-04 Z3501 glpC Glycerol 3-phosphate dehydrogenase (c subunit) 3.91 2.15E-05 NDE 3.84 4.04E-05 NDE 2.51 1.03E-02 Z4786 glpD Glycerol 3-phosphate dehydrogenase 3.62 8.99E-05 2.65 7.55E-03 4.98 4.13E-08 4.75 1.79E-07 4.23 4.61E-06 Z5472...”
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...ECs3125 glpT 1.65 -2.22 4 ECs3126 glpA 3.61 -2.78 3 ECs3127 glpB 2.59 -2.15 3 ECs3128 glpC 2.92 -2.94 un ECs3142 yfbF -2.54 1.59 12 ECs3143 yfbG -2.50 1.03 5 ECs3144 yfbH -2.66 0.98 5 ECs3299 yfeU 2.39 -0.89 3 ECs3300 yfeV 2.28 -0.99 3 ECs3305...”
BCAL2486 putative iron-sulphur oxidoreductase from Burkholderia cenocepacia J2315
26% identity, 52% coverage
- Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment
O'Grady, Frontiers in cellular and infection microbiology 2011 - “...chromate transport protein 1.6 BCAL1789 ExbB, iron-transport protein 1.7 BCAL2485 Putative ironsulfur cluster-binding electron 2.1 BCAL2486 Putative ironsulfur oxidoreductase 2.1 BCAM0447 Putative exported multicopper oxidase 13.0 BCAM1187 TonB-dependent siderophore receptor 1.7 BCAM1527 Putative cation efflux protein 1.8 BCAM2007 TonB-dependent siderophore receptor 1.6 BCAS0028 Succinylglutamate desuccinylase/aspartoacylase 2.8...”
- “...is a putative outer membrane porin (OmpC) and is in the same predicted operon as BCAL2486 and BCAL2485, which are ironsulfur oxidoreductase and ironsulfur electron transport proteins, respectively. All three genes are induced at least twofold in vivo (Table 4 ). Although ornibactin biosynthesis and uptake...”
C7391_RS01355 (Fe-S)-binding protein from Methanimicrococcus blatticola
21% identity, 82% coverage
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...1 ). In addition, a membrane-bound heterodisulfide reductase consisting of the subunits HdrDE was detected (C7391_RS01355, C7391_RS01360). No genes encoding for an F 420 H 2 dehydrogenase (Fpo complex) or an Ech/Eha/Ehb hydrogenase could be identified which often plays a role in regenerating F 420 and...”
NTHI0805 sn-glycerol-3-phosphate dehydrogenase subunit C from Haemophilus influenzae 86-028NP
21% identity, 92% coverage
BPSL0634 putative oxidoreductase from Burkholderia pseudomallei K96243
22% identity, 29% coverage
BCAL0870 putative oxidoreductase from Burkholderia cenocepacia J2315
22% identity, 26% coverage
- Common duckweed (Lemna minor) is a versatile high-throughput infection model for the Burkholderia cepacia complex and other pathogenic bacteria
Thomson, PloS one 2013 - “...BDSF signalling [ 41 ] Limited to B. cenocepacia ET-12 epidemic lineage 62F12 ~5x10 5 bcal0870 Putative oxidoreductase, identified as an essential gene in B. cenocepacia H111 [ 43 ] Ubiquitous a S.E., standard error of the mean, included where applicable b n.d., not determined. Because...”
- “...pathway [ 41 ]; bcal1124 (mutant 46B2), a hypothetical protein encoded on a genomic island; bcal0870 (mutant 62F12), encoding a putative oxidoreductase; and bcal2159 (mutant 16A11), which is located near the recently characterized suhB gene, bcal2157 . Elimination of SuhB Bc , which encodes an inositol...”
FH974_06490 anaerobic glycerol-3-phosphate dehydrogenase subunit GlpC from Photobacterium ganghwense
22% identity, 89% coverage
YPO3824 sn-glycerol-3-phosphate dehydrogenase subunit C from Yersinia pestis CO92
23% identity, 89% coverage
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...YPO3929 phosphoenolpyruvate carboxylase 0.678 (0.045) YPTB0118 YPO3917 putative pyridine nucleotide-disulphide oxidoreductase 1.559 (0.016) YPTB0211 (glpC) YPO3824 anaerobic glycerol-3-phosphate dehydrogenase subunit C 0.49 (0.003) YPTB0374 (qor) YPO0319 quinone oxidoreductase 1.393 (0.04) YPTB0410 (frdD) YPO0357 fumarate reductase hydrophobic protein 0.393 (0.001) YPTB0411 (frdC) YPO0358 fumarate reductase hydrophobic protein...”
YPTB0211 anaerobic glycerol-3-phosphate dehydrogenase subunit C from Yersinia pseudotuberculosis IP 32953
23% identity, 89% coverage
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...YPTB0108 (ppc) YPO3929 phosphoenolpyruvate carboxylase 0.678 (0.045) YPTB0118 YPO3917 putative pyridine nucleotide-disulphide oxidoreductase 1.559 (0.016) YPTB0211 (glpC) YPO3824 anaerobic glycerol-3-phosphate dehydrogenase subunit C 0.49 (0.003) YPTB0374 (qor) YPO0319 quinone oxidoreductase 1.393 (0.04) YPTB0410 (frdD) YPO0357 fumarate reductase hydrophobic protein 0.393 (0.001) YPTB0411 (frdC) YPO0358 fumarate reductase...”
PST_3340 D-lactate dehydrogenase, putative from Pseudomonas stutzeri A1501
24% identity, 37% coverage
HVO_A0271 glycerol-3-phosphate dehydrogenase subunit C from Haloferax volcanii DS2
22% identity, 82% coverage
KP13_00964 anaerobic glycerol-3-phosphate dehydrogenase subunit GlpC from Klebsiella pneumoniae subsp. pneumoniae Kp13
25% identity, 89% coverage
VF_A0248 sn-glycerol-3-phosphate dehydrogenase subunit C from Vibrio fischeri ES114
21% identity, 89% coverage
- Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes
Thompson, Environmental microbiology 2017 - “...7.7 E-03 outer membrane phospholipase A glpD (VF_A0239) 3.1 1.3 E-04 glycerol-3-phosphate (G3P) dehydrogenase glpC (VF_A0248) 0.5 0.69 anaerobic G3P dehydrogenase subunit C glpB (VF_A0249) 2.3 8.4 E-03 anaerobic G3P dehydrogenase subunit B glpA (VF_A0250) 1.7 1.8 E-02 anaerobic G3P dehydrogenase subunit A glpQ (VF_A0958) 3.2...”
- TfoX-based genetic mapping identifies Vibrio fischeri strain-level differences and reveals a common lineage of laboratory strains
Brooks, Journal of bacteriology 2015 - “...The region of chromosome II from VF_A0219 through VF_A0248 is shown. Transposon insertions in ES114 that were transformed into ES114-L, conferring a glycerol...”
- Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis
Wier, Proceedings of the National Academy of Sciences of the United States of America 2010 - “...VF_0072; squares, VF_A0235; triangles, VF_A0236; diamonds, VF_A0248; hexagons, VF_A0249; trapezoids, VF_A0250; and pentagons, VF_A0958. The relatively small,...”
HDRD_METTT / A0A0E3NEE1 Dihydromethanophenazine:CoB--CoM heterodisulfide reductase subunit D; CoB--CoM heterodisulfide reductase iron-sulfur subunit D; Coenzyme B:coenzyme M:methanophenazine oxidoreductase subunit D; EC 1.8.98.1 from Methanosarcina thermophila (strain ATCC 43570 / DSM 1825 / OCM 12 / VKM B-1830 / TM-1) (see 3 papers)
22% identity, 83% coverage
- function: Part of a complex that catalyzes the reversible reduction of CoM-S-S-CoB to the thiol-coenzymes H-S-CoM (coenzyme M) and H-S-CoB (coenzyme B) (PubMed:11034998, PubMed:9654152, PubMed:9665708). Electrons probably transfer from phenazine to the high potential 4Fe cluster in HdrD subunit, then to the low potential heme in HdrE subunit and finally to CoM-S-S-CoB (PubMed:11034998).
catalytic activity: methanophenazine + coenzyme B + coenzyme M = dihydromethanophenazine + coenzyme M-coenzyme B heterodisulfide (RHEA:18085)
cofactor: [4Fe-4S] cluster (Binds 2 [4Fe-4S] cluster.)
subunit: The dihydromethanophenazine:CoB--CoM heterodisulfide reductase is composed of two subunits; HdrD and HdrE.
lldE / Q8EGS4 L-lactate dehydrogenase LldE subunit (EC 1.1.2.3) from Shewanella oneidensis (strain MR-1) (see paper)
SO1520 conserved hypothetical protein from Shewanella oneidensis MR-1
SO_1520 (Fe-S)-binding protein from Shewanella oneidensis MR-1
24% identity, 53% coverage
- Transcriptional analysis of Shewanella oneidensis MR-1 with an electrode compared to Fe(III)citrate or oxygen as terminal electron acceptor
Rosenbaum, PloS one 2012 - “...2.487641 SO1490 alcohol dehydrogenase II 0.0001 Ethanol metabolism 1.4943 SO1495 putative glycosyl hydrolase 0.0005 3.021139 SO1520 Fe-S oxidoreductase, L-lactate dehydrogenase 0.0296 Lactate metabolism 1.413225 SO1521 D-lactate dehydrogenase (dld) 0.0035 Lactate metabolism 1.487265 SO1538 isocitrate dehydrogenase 0.0000 TCA-cycle 1.61607 SO1678 methylmalonate-semialdehyde dehydrogenase 0.0132 1.572969 SO1748 hypothetical protein...”
- “...the biofilm at the electrode ( Figure 1 Cellular Processes). Two recently identified lactate dehydrogenases (SO1520 and SO1521) [39] also showed higher expression with the electrode than with soluble iron(III) as electron acceptor, as did many of the core enzymes of the TCA-cycle (see Table 2...”
- Shewanella oneidensis MR-1 sensory box protein involved in aerobic and anoxic growth
Sundararajan, Applied and environmental microbiology 2011 - “...D-lactate, and it was hypothesized that SO1518 to SO1520 encodes an L-lactate dehydrogenase and SO1521 encodes a D-lactate dehydrogenase (40). In our study,...”
- “...(frdB) SO0583 (bfd) SO0768 SO1329 (cyaA) SO1427 SO1519 SO1520 SO1521 SO1522 SO1927 (sdhC) SO1928 (sdhA) SO1929 (sdhB) SO1930 (sucA) SO1931 (sucB) SO1932 (sucC)...”
- Genomic analysis of carbon source metabolism of Shewanella oneidensis MR-1: Predictions versus experiments
Serres, Journal of bacteriology 2006 - “...We note that two genes, designated by locus tags SO1520 and SO1521, are located adjacent to the lactate permease gene. One codes for an ironsulfur protein, and...”
- Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations
Kolker, Proceedings of the National Academy of Sciences of the United States of America 2005 - “...ID no. Annotation category COG no. COG category SO0311 SO0363 SO1007 SO1309 SO1520 SO1622 3 2 3 3 3 3 1032 1210 1757 1629 0247 0716 C M C P C C SO2512 SO2523 3...”
- “...reannotated as FeS center-containing oxidoreductases (SO0311 and SO1520; Table 4). For SO1520, an upstream regulatory binding site was also detected (Table...”
- Supplementation with Amino Acid Sources Facilitates Fermentative Growth of Shewanella oneidensis MR-1 in Defined Media
Ikeda, Applied and environmental microbiology 2023 (secret) - CRP Regulates D-Lactate Oxidation in Shewanella oneidensis MR-1
Kasai, Frontiers in microbiology 2017 - “...In this strain, L -LDH is comprised of three subunits encoded by the lldEFG genes (SO_1520 to SO_1518), whereas D -LDH is encoded by the dld gene (SO_1521), a distant homolog of a FAD-dependent LDH gene in yeast ( Pinchuk et al., 2009 ). A previous...”
- Regulation of Gene Expression in Shewanella oneidensis MR-1 during Electron Acceptor Limitation and Bacterial Nanowire Formation
Barchinger, Applied and environmental microbiology 2016 - “...Energy metabolism SO_0101 SO_0102 SO_0103 SO_1483 SO_1484 SO_1520 SO_1521 SO_2098 SO_2099 SO_2912 SO_2913 SO_3920 SO_3921 SO_4508 SO_4509 SO_4510 SO_4511 fdnG...”
- Catabolic and regulatory systems in Shewanella oneidensis MR-1 involved in electricity generation in microbial fuel cells
Kouzuma, Frontiers in microbiology 2015 - “...in yeast, whereas L -LDH is predicted to be comprised three subunits encoded by lldEGF (SO_1520 to SO_1518). Genetic and biochemical characterization confirmed that dld -II and lldEFG encode functional D - and L -LDHs, respectively ( Pinchuk et al., 2009 ). Although these enzymes represent...”
- A dynamic periplasmic electron transfer network enables respiratory flexibility beyond a thermodynamic regulatory regime
Sturm, The ISME journal 2015 - “...Gene name Fold change Dcrp DcyaC SO_1518 SO_1519 SO_1520 SO_2912 SO_2913 SO_2915 SO_2916 SO_0027 SO_3720 SO_0845 SO_0848 SO_1428 SO_1429 SO_1430 lldG lldF lldE...”
PA4772 probable ferredoxin from Pseudomonas aeruginosa PAO1
26% identity, 38% coverage
- The Effects of Sub-inhibitory Antibiotic Concentrations on Pseudomonas aeruginosa: Reduced Susceptibility Due to Mutations
Ramsay, Frontiers in microbiology 2021 - “...1.0 DUN-036-1 Ceftazidime 1 1.5 Ciprofloxacin 1 1.0 Meropenem 1 ^ 6.3 PA2441 (P233H (CCCCAC); PA4772 (+1bp, bp 6) Tobramycin 1 2.0 * Fold change of MIC over time; Average value of up to three Etest replicates. ^ Etest performed in replicate. # Etest performed in...”
- The AraC-Type Transcriptional Regulator GliR (PA3027) Activates Genes of Glycerolipid Metabolism in Pseudomonas aeruginosa
Kotecka, International journal of molecular sciences 2021 - “...kinase/response regulator 19 intra 25,030 PA4610 3.03 2.56 5,276,490 HUU copper transporter 20 term 26,025 PA4772 1.83 3.09 5,480,812 EM FAD-binding oxidoreductase 21 intra 28,310 PA5208 3.54 3.28 5,982,827 HUU TIGR00153 family protein 22 intra 28,490 PA5243 1.56 3.49 6,024,153 BCPGC porphobilinogen synthase 23 prom 28,760...”
- Structural and Molecular Mechanism of CdpR Involved in Quorum-Sensing and Bacterial Virulence in Pseudomonas aeruginosa
Zhao, PLoS biology 2016 - “...binds to some selected target regions in vitro. The chosen promoter regions (for opdC , PA4772 , PA4087 , PA0440 , PA3388 , cysG , recC , pscC , PA5146 , and PA1271valS , PA0159 , PA4541 , selB , serS , PA3992 , PA5114 ,...”
- Dissection of the cis-2-decenoic acid signaling network in Pseudomonas aeruginosa using microarray technique
Rahmani-Badi, Frontiers in microbiology 2015 - “...rubB napCF, nuoD, aer, ubiA, ercS, norD, etfB, hemE, PA0510, PA0516, PA0918, PA1779, PA3025, PA3491, PA4772, PA5491 Bacteriophage production PA0616-PA0623, PA0627, PA063 Tricarboxylic acid (TCA) cycle fumC1, acnA N -AHLs and PQS QS-dependent genes and Virulence lasIR, rhlI, qscR, rsaL, vfr, pqsR (mvfR), pchR, gacA,pqsBCDEH, antAB,...”
- Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains
Kwon, Journal of proteome research 2014 - “...binding protein component of ABC transporter PA4771| lldD 10.5 29.6 709.5 1772.5 l -lactate dehydrogenase PA4772 0.7 10.8 933.5 2008.0 probable ferredoxin PA4778 0.0 9.7 266.5 1392.5 probable transcriptional regulator PA5261| algR 6.6 1.1 207.0 100.0 alginate biosynthesis regulatory protein AlgR PA5289 5.0 0.0 655.0 190.5...”
- Transcriptome profiling defines a novel regulon modulated by the LysR-type transcriptional regulator MexT in Pseudomonas aeruginosa
Tian, Nucleic acids research 2009 - “...protein PA4770 lldP 43 46 l -lactate permease PA4771 lldD 28 70 l -lactate dehydrogenase PA4772 7.0 19 Probable ferredoxin PA4881 751 <2 Hypothetical protein a Gene number from the Pseudomonas Genome Project ( http://www.pseudomonas.com ). b Fold change in gene expression of PAO1 (pME6032- mexT...”
- Cystic fibrosis sputum supports growth and cues key aspects of Pseudomonas aeruginosa physiology
Palmer, Journal of bacteriology 2005 - “...PA4231 PA4471 PA4498 PA4514 PA4570 PA4633 PA4770 PA4771 PA4772 PA4811 PA4834 PA4835 PA4836 PA4837 PA4838 PA4929 PA5303 PA5532 PA5534 PA5535 PA5536 PA5538 PA5539...”
DSY1713 hypothetical protein from Desulfitobacterium hafniense Y51
23% identity, 46% coverage
PA14_63100 putative ferredoxin from Pseudomonas aeruginosa UCBPP-PA14
25% identity, 38% coverage
- Transcriptional profiling of Pseudomonas aeruginosa and Staphylococcus aureus during in vitro co-culture
Tognon, BMC genomics 2019 - “...second lactate dehydrogenase operon including lldD , the adjacent lldP lactate permease gene (3-fold) and PA14_63100 coding for a cytochrome type lactate dehydrogenase (Table 3 and Additionalfile 4 : Table S2), strongly suggests that P. aeruginosa takes up lactate secreted by S. aureus to use it...”
- “...RNA RNA synthesis/modif. PA14_62060 5.05 23S ribosomal RNA RNA synthesis/modif. PA14_61830 4.88 tRNA-Met RNA synthesis/modif. PA14_63100 4.38 cytochrome type D-lactate DH (4Fe-4S) metabolism narK1 3.95 nitrite extrusion protein I transport PA14_24780 3.87 Amoonium transporter transport lldD 3.64 L-lactate dehydrogenase metabolism PA14_60150 3.26 tRNA-Lys RNA synthesis/modif. popN...”
- The Pseudomonas aeruginosa Complement of Lactate Dehydrogenases Enables Use of d- and l-Lactate and Metabolic Cross-Feeding
Lin, mBio 2018 - “...lactate dehydrogenases. PA14 contains four genes with the following annotation: ldhA (PA14_52270), lldD (PA14_63090), lldE (PA14_63100), and lldA (PA14_33860) ( Fig.1 ). ldhA encodes a lactate dehydrogenase that reduces pyruvate to lactate during anaerobic pyruvate fermentation ( 7 ) ( Fig.1 ). According to computational prediction...”
MCP_0282 putative CoB--CoM heterodisulfide reductase iron-sulfur subunit D from Methanocella paludicola SANAE
24% identity, 72% coverage
H16_B0093 Fe-S oxidoreductase from Ralstonia eutropha H16
H16_B0093, H16_RS19190 (Fe-S)-binding protein from Cupriavidus necator H16
25% identity, 44% coverage
- (R/S)-lactate/2-hydroxybutyrate dehydrogenases in and biosynthesis of block copolyesters by Ralstonia eutropha
Ishihara, Applied microbiology and biotechnology 2023 - “..._ B1817 del This study pK18ms-A3091ud980 pK18ms derivative; h16_A3091 del This study pK18ms-B0093-B0092-B0091ud980 pK18ms derivative; h16_B0093 - B0092 - B0091 del This study pK18ms-A1681-A1682ud900 pK18ms derivative; h16_A1681 - A1682 del This study pBBR1MCS-2 Broad host range plasmid; Km r , mob , P lac , lacZ...”
- “...was conducted by removing both h16_A1681 and h16_A1682 along with the intergenic region. The genes h16_B0093 , h16_B0092 , and h16_B0091 , sharing 44.2%, 26.0%, and 40.1% identities to lutA , lutC , and lutB derived from Bacillus subtilis , respectively, are a homolog set of...”
- Identification and characterization of L- and D-lactate-inducible systems from Escherichia coli MG1655, Cupriavidus necator H16 and Pseudomonas species
Augustiniene, Scientific reports 2022 - “...compounds are investigated. We demonstrate that the inducible systems Ec LldR/P lldP and Cn GntR/P H16_RS19190 respond only to the L-lactate, exhibiting approximately 19- and 24-fold induction, respectively. Despite neither of the examined bacteria possess the D-lactate-specific inducible system, the Pa PdhR/P lldP and Pf PdhR/P...”
- “...utilization operon identified in C. necator H16 is controlled by potential inducible system Cn GntR/P H16_RS19190 . Iron-sulfur cluster-binding protein (locus tag H16_RS19180 ) and (Fe-S)-binding protein (locus tag H16_RS19190 ) encoded by genes of this operon exhibit 40% and 40.5% sequence identity, respectively, with the...”
NMB1436 hypothetical protein from Neisseria meningitidis MC58
Q9JYT8 Cysteine-rich domain-containing protein from Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)
24% identity, 49% coverage
- Interplay Between Virulence and Variability Factors as a Potential Driver of Invasive Meningococcal Disease
Siena, Computational and structural biotechnology journal 2018 - “...Stress response iga NMB0700 Yes [ 15 , 54 ] Iron-sulphur protein Stress response NEIS1371 NMB1436 Iron-sulphur protein Stress response NEIS1372 NMB1437 Iron-sulphur protein Stress response NEIS1373 NMB1438 Catalase Stress response katA NMB0216 Endonuclease Stress response nth NMB0533 Manganese transport system Stress response mntA NMB0588 Manganese...”
- Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence
Ampattu, BMC genomics 2017 - “...n.d. n.d. NMB1343 - Hypothetical protein NMB1343 1.29 n.s. n.s. n.s. 1.50 n.s. 2.01 1.85 NMB1436 - Hypothetical protein n.s. n.s. n.s. n.s. 2.60 n.s. 2.81 2.18 NMB1437 - Hypothetical protein 0.87 n.s. n.s. n.s. n.s. n.s. n.s. n.s. NMB1438 - Hypothetical protein 1.26 n.s. n.s....”
- How the Knowledge of Interactions between Meningococcus and the Human Immune System Has Been Used to Prepare Effective Neisseria meningitidis Vaccines
Gasparini, Journal of immunology research 2015 - “...in nutritional immunity, supplying energy to the pathogen [ 93 ] Uncharacterized proteins (NGO1686, NMB0741, NMB1436, NMB1437, NMB1438, and NMB1828) They protect from nonoxidative factors, but their mechanisms are still not understood; NMB1436, NMB1437, and NMB1438 are putatively involved in iron metabolism [ 122 , 195...”
- A bacterial siren song: intimate interactions between Neisseria and neutrophils
Criss, Nature reviews. Microbiology 2012 - “...proteins that protect bacteria from antimicrobial peptides 139 NMB1436, NMB1437 and NMB1438 N. meningitidis * Protect against killing by neutrophils 119 NspA N....”
- Transcriptional profiling of serogroup B Neisseria meningitidis growing in human blood: an approach to vaccine antigen discovery
Hedman, PloS one 2012 - “...0.991 1.064 0.712 0.734 NMB1312 clpP 0.961 0.794 0.715 1.472 NMB1428 clpX 0.782 0.627 0.823 NMB1436 0.866 1.017 1.259 0.642 NMB1437 1.324 1.309 1.626 1.025 0.896 NMB1438 1.254 1.344 1.487 1.118 Candidate vaccine antigen genes: identification of up-regulated genes encoding surface exposed proteins Differential gene expression...”
- Fur-mediated global regulatory circuits in pathogenic Neisseria species
Yu, Journal of bacteriology 2012 - “...nitrite reductase EM, FP 23, 44 NGO1276 NMB0884 NMB0216 NMB1436 to -1438 sodB, superoxide dismutase kat, catalase Hypothetical proteins EM 44 EM 44 EM, FP 22,...”
- Regulatory role of the MisR/S two-component system in hemoglobin utilization in Neisseria meningitidis
Zhao, Infection and immunity 2010 - “...Fur-dependent regulation. Another Fur-dependent and iron-induced gene, NMB1436, which codes for a putative protein involved in oxidative stress protection (14),...”
- “...was also analyzed. As expected, the levels of the NMB1436 transcript were reduced in the absence of iron, and no significant changes were detected in the misS...”
- The Hfq-dependent small noncoding RNA NrrF directly mediates Fur-dependent positive regulation of succinate dehydrogenase in Neisseria meningitidis
Metruccio, Journal of bacteriology 2009 - “...high-affinity binding sites upstream of the Fur-activated norB, nmb1436 and nuo promoters (6, 11) and significantly higher than that of other Fur-repressed...”
- “...labeled probes for nuoA, norB, pan1, and nmb1436 promoters we verified that the previously reported Fur-mediated positive regulation of these genes...”
- More
- Towards New Drug Targets? Function Prediction of Putative Proteins of Neisseria meningitidis MC58 and Their Virulence Characterization
Shahbaaz, Omics : a journal of integrative biology 2015 - “...15. 16. 17. 18. Q9K1J7 Q9K146 Q9K0W9 Q9JZM5 Q9JZL3 P0A0Z0 Q9JYT8 Q9JYC7 Q7DD45 Q9K1M3 Q9JXG7 19. 20. 21. Q7DD54 P67217 Q9JZZ2 22. 23. 24. 25. 26. 27. 28. 29....”
VCA0985 oxidoreductase/iron-sulfur cluster-binding protein from Vibrio cholerae O1 biovar eltor str. N16961
24% identity, 42% coverage
- Regulatory Effects of CsrA in Vibrio cholerae
Butz, mBio 2021 - “...iron-containing proteins, such as ferritin (VC0078), ferredoxin (VC0311), and iron-sulfur cluster-containing proteins (VC1512, VC2088, and VCA0985), were repressed. This suggests that CsrA may be critical for restricting the influx of free, unchelated iron during stationary phase growth, while sequestering any excess intracellular iron. Another significantly overrepresented...”
- Transcriptomics reveals a cross-modulatory effect between riboflavin and iron and outlines responses to riboflavin biosynthesis and uptake in Vibrio cholerae
Sepúlveda-Cisternas, Scientific reports 2018 - “...1.135 VCA0968 hypothetical protein 1.527 1.190 VCA0979 methyl-accepting chemotaxis protein 1.006 VCA0981 hypothetical protein 1.008 VCA0985 oxidoreductase/iron-sulfur cluster-binding protein 1.381 VCA0988 methyl-accepting chemotaxis protein 1.119 VCA1006 organic hydroperoxide resistance protein putative 1.130 VCA1007 hypothetical protein 1.064 VCA1009 hypothetical protein 1.260 VCA1010 conserved hypothetical protein 3.403 VCA1014...”
- Genes induced late in infection increase fitness of Vibrio cholerae after release into the environment
Schild, Cell host & microbe 2007 - “...family 3.0 7.6 10.1 17.3 5.8 1.7 2.3 VCA0985 VCA09845 oxidoreductase-iron-sulfur cluster-binding protein 13.0 22.3 43.3 88.0 6.7 2.0 3.9 Early infection-induced...”
D2S272 4Fe-4S ferredoxin-type domain-containing protein from Haloterrigena turkmenica (strain ATCC 51198 / DSM 5511 / JCM 9101 / NCIMB 13204 / VKM B-1734 / 4k)
23% identity, 54% coverage
HMPREF1322_RS00720, PG_RS05185 (Fe-S)-binding protein from Porphyromonas gingivalis W50
PG1171 oxidoreductase, putative from Porphyromonas gingivalis W83
25% identity, 52% coverage
- Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis
Costeira, mSystems 2023 - “...15 DMAs was observed in a genomic region (NZ_AJZS01000011.1 1220 kb) containing the (Fe-S)-binding protein HMPREF1322_RS00720, lactate utilization protein HMPREF1322_RS00725, hypothetical protein HMPREF1322_RS00730, PaaI family thioesterase HMPREF1322_RS00735, and ABC transporter ATP-binding protein HMPREF1322_RS00740 ( Fig. 5 top panel, purple; Fig. 6 ). In annotating DMAs to...”
- “...). Four DMAs were located within 1 kb of a gene encoding a (Fe-S)-binding protein (HMPREF1322_RS00720). In a sensitivity analysis considering only adenines with at least 100 coverage (85,090 adenines), 20 DMAs were identified at FDR = 5% ( Table S6 ), and all 20 were...”
- Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...PG0564 Hypothetical protein 4.3 4.4923E-10 PG_RS04540 PG1031 IS 5 family transposase 2.0 1.5145E-08 to 0.0002 PG_RS05185 to 90 PG1171 to 72 (Fe-S)-binding protein, lactate utilization protein 2.6 0.044 PG_RS05275 PG1197 IS 5 family transposase 1.9 0.0007 nrdG PG_RS05545 PG1259 Anaerobic ribonucleoside-triphosphate reductase activating protein 2.0 0.139...”
- Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis
Costeira, 2022 - Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...4.3 4.4923E-10 PG_RS04540 PG1031 IS 5 family transposase 2.0 1.5145E-08 to 0.0002 PG_RS05185 to 90 PG1171 to 72 (Fe-S)-binding protein, lactate utilization protein 2.6 0.044 PG_RS05275 PG1197 IS 5 family transposase 1.9 0.0007 nrdG PG_RS05545 PG1259 Anaerobic ribonucleoside-triphosphate reductase activating protein 2.0 0.139 PG_RS06340 PG1445 RteC...”
- Metabolome variations in the Porphyromonas gingivalis vimA mutant during hydrogen peroxide-induced oxidative stress
McKenzie, Molecular oral microbiology 2015 - “...protein PG1055 3.923686 Thiol protease PG1085 3.189495 Hypothetical protein PG1151 2.33 Alcohol dehydrogenase iron containing PG1171 2.14 Oxidoreductase putative PG1208 5.291382 dnaK protein PG1240 2.75 Transcription regulator tetR PG1286 3.566204 Ferritin PG1326 2.50 Hemagglutinin putative PG1372 2.04 Hypothetical protein PG1491 5.03 Hypothetical protein PG1492 5.335137 Hypothetical...”
- Nitric oxide stress resistance in Porphyromonas gingivalis is mediated by a putative hydroxylamine reductase
Boutrin, Journal of bacteriology 2012 - “...upregulated genes (PG1858, dps, PG0777, PG0776, PG1172, PG1171, PG1239, hcp, PG2034, PG0108, PG0616, and PG0195) that were differentially expressed following NO...”
- HcpR of Porphyromonas gingivalis is required for growth under nitrosative stress and survival within host cells
Lewis, Infection and immunity 2012 - “...PG1129 PG1321 PG0456 PG0931 PG2167 PG2132 PG0313 PG1171 PG2164 PG1759 PG0055 PG1012 PG0705 PG0758 PG1340 PG0722 Prismane protein Thioredoxin, putative...”
CV_3030 probable oxidoreductase iron-sulfur subunit from Chromobacterium violaceum ATCC 12472
25% identity, 44% coverage
PGN_1268 putative oxidoreductase from Porphyromonas gingivalis ATCC 33277
25% identity, 52% coverage
- Porphyromonas gingivalis genes conferring fitness in a tobacco-rich environment
Hutcherson, Molecular oral microbiology 2020 - “...PGN_0534 nicotinate-nucleotide pyrophosphorylase PGN_0564 Superoxide dismutase Fe-Mn PGN_0604 Ferritin PGN_0709 Indolepyruvate ferredoxin oxidoreductase, beta subunit PGN_1268 oxidoreductase PGN_2073 a oxidoreductase PGN_2077 a 2Fe-2S binding protein Annotated functions of CSE-essential genes (>500 reads on input, >50 fold change, p < 0.05) were annotated using KEGG. a Annotation...”
NGFG_00825 (Fe-S)-binding protein from Neisseria gonorrhoeae MS11
24% identity, 49% coverage
ETAE_3113 sn-glycerol-3-phosphate dehydrogenase subunit C from Edwardsiella tarda EIB202
24% identity, 90% coverage
Q5F885 L-lactate dehydrogenase (subunit 3/3) (EC 1.1.1.27) from Neisseria gonorrhoeae (see paper)
NGO0904 hypothetical protein from Neisseria gonorrhoeae FA 1090
24% identity, 49% coverage
- Global Network Analysis of Neisseria gonorrhoeae Identifies Coordination between Pathways, Processes, and Regulators Expressed during Human Infection
McClure, mSystems 2020 - “...Fur binds to their promoter regions) contained Fur binding sites by our analysis. These included NGO0904 ( 15 ), aniA (NGO1276), and tbpB (NG1496). We also found an additional seven genes within this network neighborhood that contained Fur binding sites in their promoter regions ( Fig.5B...”
- Fur-mediated activation of gene transcription in the human pathogen Neisseria gonorrhoeae
Yu, Journal of bacteriology 2012 - “...4). Lower Fur binding affinities were observed for NGO1430, NGO0904, NGO0794, NGO0076, and NGO0233 (nspA) than for the fur promoter, with KDs of 45.9 15.8 nM,...”
- “...5, gonococcal Fur. For the fur, NGO0711, NGO0794, NGO0904, NGO1205, NGO1275/NGO1276, NGO1430, NGO1751, NGO1851, and NGO2116 probes, the Fur protein was added at...”
- Fur-mediated global regulatory circuits in pathogenic Neisseria species
Yu, Journal of bacteriology 2012 - “...proteins EM 44 EM 44 EM, FP 22, 44 NGO0904 to -0906 NGO1317 Transcription/ regulation NGO0199 NGO1851 Hypothetical NMB0298 Hypothetical protein EM EM, FP, 53,...”
- Transcriptional and functional analysis of the Neisseria gonorrhoeae Fur regulon
Jackson, Journal of bacteriology 2010 - “...(NGO1317), the ATP binding protein NGO2116, and NGO0904, a Fe-S oxidoreductase, was increased by growth under iron-replete conditions. NGO0711 (an alcohol...”
- Comparison of the RpoH-dependent regulon and general stress response in Neisseria gonorrhoeae
Gunesekere, Journal of bacteriology 2006 - “...NGO1473 NGO1234 NGO1233 NGO0233 NGO1980 NGO1415 NGO1449 NGO0563 NGO0904 NGO1406 Gene ilvH ilvI mdaB ilvC nsgA yojH nqrC gcvT Fold changeb Proposed functionc...”
TTX_1318 (Fe-S)-binding protein from Thermoproteus tenax Kra 1
38% identity, 18% coverage
WP_019177711, WYS_RS08335 CoB--CoM heterodisulfide reductase subunit B from Methanomassiliicoccus luminyensis B10
24% identity, 54% coverage
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...HdrD WYS_RS12230 WP_019178460 FpoNMLKJJIHDCBA WYS_RS00365-420 WP_019176172-83 HdrABC MvhAGD WYS_RS07030, WYS_RS08335, WYS_RS08340, WYS_RS07015, WYS_RS07020, WYS_RS07025 WP_026068905, WP_019177711, WP_026068956, WP_019177457, WP_026068904, WP_019177459 Methanosphaera stadtmanae H 2 +MeOH EhbA-P, EhbQ Msp_1457-42, Msp_1436 ABC57827-12, ABC57807 HdrA1B1C1 Msp_1476, Msp_1013, Msp_1014 ABC57846, ABC57401, ABC57402 HdrA2B2C2 Msp_0127-25 ABC56545-43 MvhDGA Msp_0314-16 ABC56724-26 FrhADGB Msp_1302-05...”
- “...identifier Methanomassilicoccus luminyensis H 2 +MeOH HdrD WYS_RS12230 WP_019178460 FpoNMLKJJIHDCBA WYS_RS00365-420 WP_019176172-83 HdrABC MvhAGD WYS_RS07030, WYS_RS08335, WYS_RS08340, WYS_RS07015, WYS_RS07020, WYS_RS07025 WP_026068905, WP_019177711, WP_026068956, WP_019177457, WP_026068904, WP_019177459 Methanosphaera stadtmanae H 2 +MeOH EhbA-P, EhbQ Msp_1457-42, Msp_1436 ABC57827-12, ABC57807 HdrA1B1C1 Msp_1476, Msp_1013, Msp_1014 ABC57846, ABC57401, ABC57402 HdrA2B2C2 Msp_0127-25...”
YP_002344954 oxidoreductase from Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Cj1585c putative oxidoreductase from Campylobacter jejuni subsp. jejuni NCTC 11168
22% identity, 43% coverage
- Two respiratory enzyme systems in Campylobacter jejuni NCTC 11168 contribute to growth on L-lactate.
Thomas, Environmental microbiology 2011 (PubMed)- GeneRIF: A cj0075c cj1585c double mutant showed no L-lactate oxidase activity and did not utilize or grow on L-lactate; D-lactate-dependent growth was unaffected.
- Phylogenetic Association and Genetic Factors in Cold Stress Tolerance in Campylobacter jejuni
Hur, Microbiology spectrum 2022 - “...domain-containing protein cj1420c Class I SAM-dependent methyltransferase Energy production and conversion cj0490 ald Aldehyde dehydrogenase cj1585c FAD-binding oxidoreductase Nucleotide transport and metabolism cj0766 Pseudogene Putative arylsulfate sulfotransferase cj0381c pyrF Orotidine-5-phosphate decarboxylase General function prediction only cj0054c TIGR00730 family Rossman fold protein cj1555c NAD(P)-dependent oxidoreductase Lipid transport...”
- A Genome-Wide Association Study to Identify Diagnostic Markers for Human Pathogenic Campylobacter jejuni Strains
Buchanan, Frontiers in microbiology 2017 - “...1.21E-15 Cj1255 Putative isomerase 11168_01309 5.30E-15 1.04E-11 Cj1365c Putative secreted serine protease 11168_01519 4.29E-10 8.39E-07 Cj1585c Putative oxidoreductase 11168_01610 4.29E-10 8.38E-07 Cj1679 Hypothetical protein 06_2866_00597 6.89E-28 1.36E-24 Di-/tripeptide transporter 06_7515_00723 4.19E-16 8.24E-13 Prophage Lp2 protein 6 07_0675_00227 2.62E-11 5.15E-08 tetO Elongation factor G 1 p -value...”
- A Bacterial Multidomain NAD-Independent d-Lactate Dehydrogenase Utilizes Flavin Adenine Dinucleotide and Fe-S Clusters as Cofactors and Quinone as an Electron Acceptor for d-Lactate Oxidization
Jiang, Journal of bacteriology 2017 - “...respectively, while the purified enzyme from C. jejuni (Cj1585c) exhibited higher activity with D-lactate than with L-lactate (17, 18). In the case of P....”
- “...purified Fe-S D-iLDH. In accordance with the results using Cj1585c, Fe-S D-iLDH from P. putida KT2440 exhibits activity with both D- and L-lactate, although the...”
- [Multilocus Sequence Typing analysis of human Campylobacter coli in Granada (Spain)]
Carrillo-Ávila, Revista espanola de quimioterapia : publicacion oficial de la Sociedad Espanola de Quimioterapia 2016 (PubMed)- “...strains of Campylobacter coli. Nineteen genetic markers were amplified for MLST analysis: AnsB, DmsA, ggt, Cj1585c, CJJ81176-1367/1371, Tlp7, cj1321-cj1326, fucP, cj0178, cj0755/cfrA, ceuE, pldA, cstII, cstIII. After comparing the obtained sequences with the Campylobacter MLST database, the allele numbers, sequence types (STs) and clonal complexes (CCs)...”
- Genomic insights from whole genome sequencing of four clonal outbreak Campylobacter jejuni assessed within the global C. jejuni population
Clark, BMC genomics 2016 - “...A A G secreted serine protease Cj1365c 1515973 A A A A C D-lactate dehydrogenase Cj1585c 1630514 C C C C T 2-isopropylmalate synthase Cj1719c Fig. 3 Phylogenetic tree of C. jejuni sequenced in this study compared with publicly available C. jejuni . The tree was...”
- Defining the metabolic requirements for the growth and colonization capacity of Campylobacter jejuni
Hofreuter, Frontiers in cellular and infection microbiology 2014 - “...respective mutants with lactate (Thomas et al., 2011 ). However, a second L-iLDH, the oxidoreductase Cj1585c, was identified and demonstrated to be responsible for the observed redundancy in the catabolism of L-lactate. Only a double mutation inactivating cj0075c and cj1585c abolished the growth of C. jejuni...”
- “...source but it did not affect in the utilization of D-lactate. The gene locus of cj1585c is not conserved in C. jejuni (Hofreuter et al., 2006 ) and is replaced by a dimethyl sulfoxide reductase ( dmsABC ) gene cluster encoding for an anaerobic dimethyl sulfoxide...”
- Identification of the genes that contribute to lactate utilization in Helicobacter pylori
Iwatani, PloS one 2014 - “...the stereoisomer specificity of this enzyme is somewhat controversial as the orthologue in C. jejuni (Cj1585c) was identified as L-iLDH but not D-iLDH [17] . Cj1585c is one of the highly similar orthologues of HP1222 sharing ca. 50% identity with each other. This similarity may explain...”
- Discrimination of multilocus sequence typing-based Campylobacter jejuni subgroups by MALDI-TOF mass spectrometry
Zautner, BMC microbiology 2013 - “...combination of MLST with isolate-profiling for sixteen genetic markers: ansB , dmsA , ggt , cj1585c , cjj81176-1367/71 ( cj1365c ), tlp7 m+c ( cj0951c plus cj0952c ), cj1321-cj1326 , fucP , cj0178 , cj0755/cfrA , ceuE , pldA , cstII , and cstIII lead to...”
- “...major clusters, the overall majority of isolates is positive for the marker genes cj1365c , cj1585c , cj1321-6 , fucP , cj0178 , and cj0755 positive but dmsA -, ansB - and ggt -negative (different shades of yellow); B1 : one cluster of dmsA + ,...”
- More
MA4410 hypothetical protein (multi-domain) from Methanosarcina acetivorans C2A
20% identity, 38% coverage
- Deconstructing Methanosarcina acetivorans into an acetogenic archaeon
Schöne, Proceedings of the National Academy of Sciences of the United States of America 2022 - “...activity ( SI Appendix , Fig. S6 ). Instead, its genome contains two conspicuous loci, MA4410 and MA4630-MA4631, which could be responsible for the anabolic requirement of CoM-S-S-CoB. The loci encode putative enzymes consisting of a (N-terminal domain of a) FAD/FMN-containing dehydrogenase (COG0277) and a (C-terminal...”
- “...reaction in which the thiols HS-CoM and HS-CoB serve as electron donors for fumarate reduction, MA4410 and/or MA4630-MA4631 would use CoM-S-S-CoB as an electron acceptor for an oxidation reaction. Using CoM-S-S-CoB both as the terminal catabolic as well as an anabolic electron acceptor offers a simple...”
TTX_1191 (Fe-S)-binding protein from Thermoproteus tenax Kra 1
40% identity, 14% coverage
MA0526 heterodisulfide reductase, subunit D from Methanosarcina acetivorans C2A
24% identity, 53% coverage
- Rerouting Cellular Electron Flux To Increase the Rate of Biological Methane Production
Catlett, Applied and environmental microbiology 2015 - “...is cytoplasmic and does not conserve energy. M. acetivorans also expresses genes encoding HdrD2 ( MA0526 ), HdrA2 and polyferredoxin ( MA2867-MA2868 ), and HdrC2B2 ( MA4236-MA4237 ), all of which are constitutively expressed ( 8 ). The physiological roles of the hdrD2 , hdrA2 ,...”
- “...encoding the membrane-bound HdrED ( MA0687-MA0688 ) are essential. M. acetivorans also expresses hdrD2 ( MA0526 ), hdrA2 , polyferredoxin genes ( MA2867-MA2868 ), and hdrC2B2 ( MA4236-MA4237 ), which are constitutively expressed. We assayed CoM-S-S-CoB-dependent methyl viologen oxidation in clarified cell extracts to minimize HdrED...”
- A multienzyme complex channels substrates and electrons through acetyl-CoA and methane biosynthesis pathways in Methanosarcina
Lieber, PloS one 2014 - “...complexes M. acetivorans has a close homolog of HdrD1, HdrD2, which is encoded by gene MA0526. HdrD2 is 31% identical, 47% similar to HdrD1 by primary amino acid sequence. Unlike HdrD1, expression of HdrD2 is not essential for growth [11] . However, we hypothesized that HdrD1...”
A9WD59 4Fe-4S ferredoxin-type domain-containing protein from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)
21% identity, 53% coverage
- Deciphering the functional role of hypothetical proteins from Chloroflexus aurantiacs J-10-f1 using bioinformatics approach
Thakur, Molecular biology research communications 2020 - “...A9WBU0 Glycoside hydrolase superfamily A9WCD7 Peptidase C11, clostripain A9WCF4 PDZ superfamily A9WD37 Putative zincin peptidase A9WD59 4Fe4S_Fe-S-bd, NarG like superfamily,Cys_rich_dom, A9WE09 Cellulose synthase BcsB, bacterial A9WEE4 tRNAthreonylcarbamoyl adenosine modification protein TsaE A9WEL0 Small GTPase superfamily, ARF/SAR type A9WEX4 Immunoglobulin like fold A9WF32 Glycolate oxidase, iron sulphur...”
- “...HC-HPs role as the member of photosynthetic complex. Four HC-HPs with accession number: A9WC42, A9WC74, A9WD59 and A9WDH7 were found to the members of photosynthesis complex. For instance, A9WC42 showed 88.96% identity with (Fe-S)-binding protein of Chloroflexus aggregans and A9WC74 was 88.77% identical to carotenoid biosynthesis...”
AF0867 reductase, putative from Archaeoglobus fulgidus DSM 4304
23% identity, 50% coverage
HDRB_METTM / Q50755 H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B; CoB--CoM heterodisulfide reductase subunit B; EC 1.8.98.5 from Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg) (Methanobacterium thermoautotrophicum) (see 4 papers)
Q50755 ferredoxin:CoB-CoM heterodisulfide reductase (EC 1.8.7.3); dihydromethanophenazine:CoB-CoM heterodisulfide reductase (EC 1.8.98.1); H2:CoB-CoM heterodisulfide,ferredoxin reductase (EC 1.8.98.5) from Methanothermobacter marburgensis (see 3 papers)
hdrB CoB--CoM heterodisulfide reductase subunit B; EC 1.8.98.1 from Methanothermobacter marburgensis str. Marburg (see 4 papers)
25% identity, 55% coverage
- function: Part of a complex that catalyzes the reversible reduction of CoM-S-S-CoB to the thiol-coenzymes H-S-CoM (coenzyme M) and H-S-CoB (coenzyme B).
catalytic activity: coenzyme B + coenzyme M + 2 reduced [2Fe-2S]-[ferredoxin] + 2 H(+) = coenzyme M-coenzyme B heterodisulfide + 2 H2 + 2 oxidized [2Fe-2S]-[ferredoxin] (RHEA:55748)
subunit: The heterodisulfide reductase is composed of three subunits; HdrA, HdrB and HdrC. It forms a complex with the F420-non-reducing hydrogenase (Mvh), which provides the reducing equivalents to the heterodisulfide reductase.
Q726N5 Oxidoreductase, FAD/iron-sulfur cluster-binding domain protein from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
DVU3071 oxidoreductase, FAD/iron-sulfur cluster-binding domain protein from Desulfovibrio vulgaris Hildenborough
23% identity, 33% coverage
- Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes.
Denise, Microbial genomics 2023 - “...(UniProt ID Q72F25), DVU0827 (UniProt ID Q72DV2), DVU3027 (UniProt ID Q72659), and DVU3071 (UniProt ID Q726N5). The genes encoding DVU0827 and DVU3027 are each in an operon with a gene encoding their iron-sulphur subunits, DVU0826, and DVU3028, respectively ( Fig. 5 , panel B). DVU0390 is...”
- “...DVU0390 (UniProt ID Q72F25); magenta node, DVU0253 (UniProt ID Q72FG1); cyan node, DVU03071 (UniProt ID Q726N5). Panel (b). Genome context () for the paralogs in Desulfovibrio vulgaris str. Hildenborough (NC_002937.3), colour coding for five paralogs conserved between the two panels. AA_Transporter_ATP, Amino Acid ABC transporter ATPase...”
- Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes
Denise, Microbial genomics 2023 - “...ID Q72FG1), DVU0390 (UniProt ID Q72F25), DVU0827 (UniProt ID Q72DV2), DVU3027 (UniProt ID Q72659), and DVU3071 (UniProt ID Q726N5). The genes encoding DVU0827 and DVU3027 are each in an operon with a gene encoding their iron-sulphur subunits, DVU0826, and DVU3028, respectively ( Fig. 5 , panel...”
- The primary pathway for lactate oxidation in Desulfovibrio vulgaris
Vita, Frontiers in microbiology 2015 - “...classify these orthologs into several groups ( Table 4 ). The first group included DVU0826-27, DVU3071, DVU0390, and DVU0253, which are paralogs of DVU3027-28 in the Dld-II family. The second group included DVU1781-82-83, which is a paralog of DVU3032-33 in the LldEFG family. A schematic representation...”
- “...protein (3028) DVU0826-27 Glycolate oxidase, iron-sulfur subunit, putative (0826) Glycolate oxidase, subunit GlcD, putative (0827) DVU3071 Oxidoreductase, FAD/iron-sulfur cluster-binding domain protein DVU0390 Glycolate oxidase, subunit GlcD, putative Dld-II DVU0253 Oxidoreductase, FAD/iron-sulfur cluster-binding domain protein L -lactate dehydrogenase DVU3032-33 Conserved hypothetical protein (3032) Iron-sulfur cluster-binding protein (3033)...”
- Identification of key components in the energy metabolism of the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus by transcriptome analyses
Hocking, Frontiers in microbiology 2014 - “...AF0809, may facilitate a multimeric complex that functions as monomeric homologs encoded in other species (Dvu3071, Figures 3 , 5 ). The presence of a gene cluster with identical arrangement in the lactate utilizing A. sulfaticallidus and A. fulgidus , supports a potential role of the...”
CCO0259 probable oxidoreductase Cj1585c from Campylobacter coli RM2228
22% identity, 43% coverage
- Differences in the Transcriptomic Response of Campylobacter coli and Campylobacter lari to Heat Stress
Riedel, Frontiers in microbiology 2020 - “...Category Up-regulated Down-regulated Energy production and conversion aspA , cydA , hydA2 , ldh , CCO0259, CCO0482, CCO1660 fliI Amino acid transport and metabolism bisZ , dapA , glnA , hisH , potA , proB , serB , CCO1002, CCO1668 ilvE , proC , CCO0338, CCO0845,...”
Q39TW0 Iron-sulfur cluster-binding oxidoreductase, CCG domain pair-containing, putative benzoyl-CoA reductase electron transfer protein from Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15)
Gmet_2085 protein of unknown function DUF224, cysteine-rich region from Geobacter metallireducens GS-15
22% identity, 79% coverage
Dde_3604 FAD-binding and (Fe-S)-binding domain-containing protein from Oleidesulfovibrio alaskensis G20
Dde_3604 Oxidoreductase/iron-sulfur cluster-binding protein from Desulfovibrio desulfuricans G20
22% identity, 37% coverage
- Influence of Copper on Oleidesulfovibrio alaskensis G20 Biofilm Formation
Thakur, Microorganisms 2024 - “...energy to support cell growth through anaerobic respiration. In addition, lactate dehydrogenases ( ldh , Dde_3604) had the highest expression level (log2FC = 2.642) in 15 M-biofilm samples. Ldh allow Desulfovibrio sp. to maintain energy balance and metabolic flexibility, enabling the bacteria to adapt to the...”
- Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria
Saxena, Frontiers in microbiology 2023 - “...(shown in Figure 4A ). The enriched genes (dde_0276, dde_0528, dde_1112, dde_1258, dde_2115, dde_2271, dde_3081, dde_3604, cysQ , and sucD ) were not only unconstrained to sulfate metabolism but a strong network to three other pathways- cysteine and methionine metabolism, selenocompound metabolism, and secondary metabolite synthesis...”
- “...dde_1109, dde_1110, dde_0527, dde_0526, dde_2271, dde_3081, dde_1112, dde_2115, dde_2265, dde_3080, and dde_0528 dde_1789, sucD , dde_3604, and, dde_1258 dde_0123, dde_0276 12 4 2 18 Ribosome synthesis rpsM, rpsE, rpsD, fbp, rpsR, rpsK, bamD, rpmJ, rplO, rplQ, rpmD, rplS, rpsP, rplF, polA, rplR, rpsH, secY, tsaD, rplI,...”
- Shotgun proteomic analysis of nanoparticle-synthesizing Desulfovibrio alaskensis in response to platinum and palladium
Capeness, Microbiology (Reading, England) 2019 - “...membrane-bound oxidoreductase 0.64 Dde_3240 Protein of unknown function DUF224 0.55 Dde_1633 Gamma-glutamyl phosphate reductase 0.55 Dde_3604 d -lactate dehydrogenase (cytochrome) 0.65 Dde_2272 Hdr menaquinol oxidoreductase 0.56 Dde_2979 Carbonic anhydrase 0.57 Dde_2201 Polyprenyl synthetase 0.65 Dde_0990 H + transporting two-sector ATPase B/B' subunit 0.56 Dde_3520 Molybdate-transporting ATPase...”
- Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes
Meyer, Journal of bacteriology 2013 - “.../ / / / Dde_0750 / / / / Dde_3604 Dde_0182 Dde_1681 / / / / / / / / / Dde_1842-Dde_1844 Dde_3239-Dde_3240 Dde_1085-Dde_1087 Dde_3241 Dde_3242 Dde_1273...”
Q0ZAZ1 D-lactate dehydrogenase (cytochrome) from Chlamydomonas reinhardtii
22% identity, 32% coverage
GYD1 / A8J2E9 glycolate dehydrogenase (EC 1.1.99.14) from Chlamydomonas reinhardtii (see 4 papers)
A8J2E9 D-lactate dehydrogenase (cytochrome) from Chlamydomonas reinhardtii
22% identity, 32% coverage
CV_3027 probable ferredoxin from Chromobacterium violaceum ATCC 12472
Q7NTM7 D-lactate dehydrogenase (cytochrome) from Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)
23% identity, 43% coverage
- GeLC-MS-based proteomics of Chromobacterium violaceum: comparison of proteome changes elicited by hydrogen peroxide
Lima, Scientific reports 2016 - “...NADH + that will feed the oxidative phosphorylation increasing the production of ATP. The ORF CV_3027, which is annotated as a likely ferredoxin, decreased its abundance in 3.7 fold, being the most reduced expression ( Table 2 ). In the C. violaceum genome, it appears to...”
- “...Q7P1P4 fad H 3, 1 2,4-dienoyl-CoA reductase FadH1 Q7NYM4 CV_1250 3, 4 UPF0246 protein Q7NTM7 CV_3027 3, 7 Probable ferredoxin These proteins presented the most significant changes in their abundance (p<0.01). A positive fold change indicates a higher abundancy in the treatment condition....”
- GeLC-MS-based proteomics of Chromobacterium violaceum: comparison of proteome changes elicited by hydrogen peroxide
Lima, Scientific reports 2016 - “...dehydrogenase Q7P1P4 fad H 3, 1 2,4-dienoyl-CoA reductase FadH1 Q7NYM4 CV_1250 3, 4 UPF0246 protein Q7NTM7 CV_3027 3, 7 Probable ferredoxin These proteins presented the most significant changes in their abundance (p<0.01). A positive fold change indicates a higher abundancy in the treatment condition....”
AL538_RS14635 succinate dehydrogenase iron-sulfur subunit from Vibrio harveyi
25% identity, 22% coverage
VpaChn25_0841 succinate dehydrogenase iron-sulfur subunit from Vibrio parahaemolyticus
25% identity, 22% coverage
WU75_19780 succinate dehydrogenase iron-sulfur subunit from Vibrio parahaemolyticus
25% identity, 22% coverage
- Identification of Antibacterial Components and Modes in the Methanol-Phase Extract from a Herbal Plant Potentilla kleiniana Wight et Arn
Tang, Foods (Basel, Switzerland) 2023 - “...0.133-fold, 0.134-fold, and 0.16-fold) ( p < 0.05). Moreover, the DEGs ( sdhABCD, WU75_19775 , WU75_19780 , WU75_19765, and WU75_19770 ) encoding a succinate dehydrogenase were also highly repressed (0.144-fold to 0.199-fold) ( p < 0.05), which links two essential energy-producing processes, the citrate cycle and...”
- “...synthetase subunit beta WU75_19800 sucD 0.16 Succinyl-CoA synthetase subunit alpha WU75_19770 sdhD 0.199 Succinate dehydrogenase WU75_19780 sdhB 0.157 Succinate dehydrogenase WU75_19765 sdhC 0.182 Succinate dehydrogenase WU75_13785 fumA 0.497 Fumarate hydratase WU75_09605 icd 0.179 Isocitrate dehydrogenase WU75_19775 sdhA 0.144 Succinate dehydrogenase WU75_06430 mdh 0.177 Malate dehydrogenase WU75_16530...”
LOC105668392 uncharacterized protein from Linepithema humile
30% identity, 18% coverage
- Social environment affects the transcriptomic response to bacteria in ant queens
Viljakainen, Ecology and evolution 2018 - “...d arabinitol dehydrogenase 1like (LOC105671469) 2.22 1.99E04 3.56E02 LOC105673823 Glucose dehydrogenase [FAD 2.16 4.39E06 2.31E03 LOC105668392 Succinate dehydrogenase [ubiquinone] ironsulfur subunit 2.16 1.30E04 2.67E02 LOC105669349 Uncharacterized LOC105669349 (LOC105669349) 2.15 1.24E04 2.60E02 LOC105669805 Facilitated trehalose transporter Tret12 homolog (LOC105669805) 2.08 5.43E04 8.40E02 LOC105667792 Synaptotagmin6 (LOC105667792) 2.00 1.08E04...”
SMUL_0787 FAD-binding and (Fe-S)-binding domain-containing protein from Sulfurospirillum multivorans DSM 12446
21% identity, 37% coverage
BA5590 ferredoxin, 4Fe-4S from Bacillus anthracis str. Ames
25% identity, 28% coverage
SMDB11_RS02550 succinate dehydrogenase iron-sulfur subunit from Serratia marcescens subsp. marcescens Db11
24% identity, 22% coverage
- RNA‑seq analyses of antibiotic resistance mechanisms in Serratia marcescens
Li, Molecular medicine reports 2019 - “...13 SMDB11_RS23570 1013.2664 SMDB11_RS23335 0.028103517 SMDB11_RS00625 13 SMDB11_RS21855 1010 SMDB11_RS14910 0.028103517 SMDB11_RS02545 13 SMDB11_RS01845 915.4805 SMDB11_RS02550 0.028097836 SMDB11_RS14100 13 SMDB11_RS05590 890.28687 SMDB11_RS00615 0.028080808 SMDB11_RS14095 12 SMDB11_RS03340 874.0195 SMDB11_RS00620 0.028075136 SMDB11_RS22005 10 SMDB11_RS14915 855.25476 SMDB11_RS00600 0.028075136 SMDB11_RS22020 10 SMDB11_RS02545 767.4091 SMDB11_RS02555 0.028075136 SMDB11_RS14105 10 SMDB11_RS00590 710.21094 SMDB11_RS15030...”
PMI0568 succinate dehydrogenase iron-sulfur protein from Proteus mirabilis HI4320
23% identity, 23% coverage
- Pathogenesis of <i>Proteus mirabilis</i> Infection
Armbruster, EcoSal Plus 2018 (secret) - Proteus mirabilis and Urinary Tract Infections
Schaffer, Microbiology spectrum 2015 - “...distances between rings of swarming and consolidation; TCA cycle mutations ( fumC PMI1296 and sdhB PMI0568) had decreased distances, and pentose phosphate pathway mutants ( gnd PMI0655 and talB PMI0006) had increased distances. Mutations in glycolysis ( pfkA PMI3203 and tpiA PMI3205) resulted in reduced swarming...”
- “...57 ) fumC PMI1296 fumarate hydratase, class II NR cr NR ( 134 ) sdhB PMI0568 succinate dehydrogenase iron-sulfur protein NR cr NR ( 134 ) gnd PMI0655 6-phosphogluconate dehydrogenase, decarboxylating NR cr NR ( 134 ) talB PMI0006 transaldolase B NR cr NR ( 134...”
VC_2088 succinate dehydrogenase iron-sulfur subunit from Vibrio cholerae O1 biovar El Tor str. N16961
VC2088 succinate dehydrogenase, iron-sulfur protein from Vibrio cholerae O1 biovar eltor str. N16961
24% identity, 22% coverage
- Genomic analysis of pathogenic isolates of Vibrio cholerae from eastern Democratic Republic of the Congo (2014-2017)
Irenge, PLoS neglected tropical diseases 2020 - “...515 stop_gained p.Glu241 2 I:2127275_A/G VC_1975 (2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase/2-oxoglutarate decarboxylase) c.457T>C 69 missense_variant p.Ser153Pro I:2249832_C/T VC_2088 (Succinate dehydrogenase, iron-sulfur protein) c.428G>A 69 missense_variant p.Gly143Asp I:2431057_A/G VC_2276 (Conserved hypothetical protein) c.229T>C 515 missense_variant p.Ser77Pro I:2433926_A/G VC_2279 (Aminoacyl-histidine Dipeptidase) c.4A>G 69 missense_variant p.Thr2Ala II:189289_C/A VC_A0172 (Conserved hypothetical protein)...”
- Regulatory Effects of CsrA in Vibrio cholerae
Butz, mBio 2021 - “...iron-binding, and iron-containing proteins, such as ferritin (VC0078), ferredoxin (VC0311), and iron-sulfur cluster-containing proteins (VC1512, VC2088, and VCA0985), were repressed. This suggests that CsrA may be critical for restricting the influx of free, unchelated iron during stationary phase growth, while sequestering any excess intracellular iron. Another...”
- MerR and ChrR mediate blue light induced photo-oxidative stress response at the transcriptional level in Vibrio cholerae
Tardu, Scientific reports 2017 - “...and down-regulated DEGs (VC0837, VC0943, VC1118, VC1248, VC1263, VC1359, VC1392, VC1484, VC1570, VC1643, VC1814, VC1922, VC2088, VC2301, VCA0055, VCA0615, VCA0782, VCA0798, VCA0809, VCA0957, VCA1087), designated as Set2 DEGs, were selected to validate the RNA-seq results. Among the selected DEGs, 12 were from 12 different operons while...”
- “...BL exposure resulted in increased transcript levels of genes encoding the succinate dehydrogenase ironsulfur subunit (VC2088), the succinate dehydrogenase flavoprotein subunit (VC2089), the succinate dehydrogenase hydrophobic membrane anchor protein (VC2090), and the succinate dehydrogenase cytochrome b556 large membrane subunit (VC2091). Succinate dehydrogenase (complex II) is a...”
RB5701 FAD-binding and (Fe-S)-binding domain-containing protein from Rhodopirellula baltica SH 1
21% identity, 38% coverage
OA238_160p0460 succinate dehydrogenase iron-sulfur subunit from Octadecabacter arcticus 238
31% identity, 20% coverage
- Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments
Dziewit, Frontiers in microbiology 2014 - “...(OA238_160p0470; EC 4.2.1.3), responsible for the bidirectional conversion of citrate into isocitrate, and succinate dehydrogenase (OA238_160p0460; EC 1.3.5.1), catalyzing the bidirectional transformation of succinate into fumarate; (iii) alpha-ketoglutarate-dependent taurine dioxygenase TauD (OA238_160p0180; EC 1.14.11.17), responsible for taurine utilization under sulfur starvation conditions, resulting in the release...”
RB5701 putative oxidase from Pirellula sp. 1
21% identity, 37% 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