PaperBLAST

PaperBLAST Hits for sp|Q9I0J7|NUOF_PSEAE NADH-quinone oxidoreductase subunit F OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=nuoF PE=3 SV=1 (448 a.a., MTLTSIGPAN...)

Show query sequence

>sp|Q9I0J7|NUOF_PSEAE NADH-quinone oxidoreductase subunit F OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=nuoF PE=3 SV=1
MTLTSIGPANRMARSAETHPLTWRLREDAQPVWLEEYQSKDGYAAARKALTQMAQDDIVQ
TVKDSGLKGRGGAGFPTGVKWGLMPKDESLNIRYLLCNADEMEPNTWKDRMLMEQLPHLL
VEGMLISARALKAYRGYIFLRGEYVDAARNLNRAIDEAKAAGLLGKNILGSGFDFELFVH
TGAGRYICGEETALINSLEGRRANPRSKPPFPAAVGVWGKPTCVNNVETLCNVPAIVGNG
VDWYKTLARPGSEDMGTKLMGFSGKVKNPGLWELPFGVSARELFEDYAGGMRDGFQLKAW
QPGGAGTGFLLPEHLDAQMFAGGIAKVGTRMGTGLAMAVDDSINMVSLLRNMEEFFARES
CGWCTPCRDGLPWSVKLLRALERGEGQPGDLETLEQLVNFLGPGKTFCAHAPGAVEPLGS
ALKYFRAEFEAGISRQPSAAPRPATVGA

Running BLASTp...

Found 250 similar proteins in the literature:

NP_251331 NADH dehydrogenase I subunit F from Pseudomonas aeruginosa PAO1
PA2641 NADH dehydrogenase I chain F from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage

• Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions
  Hu, Frontiers in microbiology 2024
  • “...1782 nuoD NADH:-quinone oxidoreductase subunit C/D PA2640 NP_251330 501 nuoE NADH-quinone oxidoreductase subunit E PA2641 NP_251331 1,347 nuoF NADH dehydrogenase I subunit F PA2642 NP_251332 2,718 nuoG NADH-quinone oxidoreductase subunit G PA2643 NP_251333 996 nuoH NADH-quinone oxidoreductase subunit H PA2644 NP_251334 549 nuoI NADH-quinone oxidoreductase subunit...”
• Identification of complex III, NQR, and SDH as primary bioenergetic enzymes during the stationary phase of Pseudomonas aeruginosa cultured in urine-like conditions
  Hu, Frontiers in microbiology 2024
  • “...NP_251329 1782 nuoD NADH:-quinone oxidoreductase subunit C/D PA2640 NP_251330 501 nuoE NADH-quinone oxidoreductase subunit E PA2641 NP_251331 1,347 nuoF NADH dehydrogenase I subunit F PA2642 NP_251332 2,718 nuoG NADH-quinone oxidoreductase subunit G PA2643 NP_251333 996 nuoH NADH-quinone oxidoreductase subunit H PA2644 NP_251334 549 nuoI NADH-quinone oxidoreductase...”
• The Pseudomonas aeruginosa RpoH (σ³²) Regulon and Its Role in Essential Cellular Functions, Starvation Survival, and Antibiotic Tolerance
  Williamson, International journal of molecular sciences 2023
  • “...3.2 1.1 10 2 PA2640 nuoE NADH dehydrogenase I chain E 3.1 1.5 10 2 PA2641 nuoF NADH dehydrogenase I chain F 2.9 2.8 10 3 PA2642 nuoG NADH dehydrogenase I chain G 3.7 3.5 10 3 PA2643 nuoH NADH dehydrogenase I chain H 6.3 2.4...”
• CRISPRi-Mediated Gene Suppression Reveals Putative Reverse Transcriptase Gene PA0715 to Be a Global Regulator of Pseudomonas aeruginosa
  Zhou, Infection and drug resistance 2022
  • “...nuoD NADH:-quinone oxidoreductase 1.595 Down Subunit C/D PA2640 nuoE NADH-quinone oxidoreductase 1.4195 Down Subunit E PA2641 nuoF NADH dehydrogenase I subunit F 1.4948 Down PA2642 nuoG NADH-quinone oxidoreductase 1.7562 Down subunit G PA2643 nuoH NADH-quinone oxidoreductase 1.802 Down Subunit H PA2644 nuoI NADH-quinone oxidoreductase subunit I...”
• Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics
  Yung, NPJ biofilms and microbiomes 2019
  • “...NR NR NR NuoE PA2640 NADH-quinone oxidoreductase subunit E NR NR NR NR NR NuoF PA2641 NADH dehydrogenase I subunit F NR NR o NR NR NuoG PA2642 NADH-quinone oxidoreductase subunit G NR NR NR NR NR NuoI PA2644 NADH-quinone oxidoreductase subunit I NR NR NR...”
• Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions
  Yan, Journal of applied genetics 2017
  • “...association with PAH degradation genes are as follows: PA2638 with PA1210, PA2639 with PA0231, both PA2641 and PA2647 with PA4125, PA2643 and PA2644 with PA2513, both PA2645 and PA2646 with both PA2009 and PA4091, and PA2648 with PA0247. These associations are reasonable because NADH dehydrogenase I...”
• Genomewide identification of genetic determinants of antimicrobial drug resistance in Pseudomonas aeruginosa
  Dötsch, Antimicrobial agents and chemotherapy 2009
  • “...PA14_57080 PA14_57210 PA14_57260 PA14_57540 PA2532 PA2561 PA2571 PA2641 PA2643 PA2644 PA2645 PA2647d PA2647d PA2691 PA2693 PA2700 PA2797 PA2871 PA2951 PA2953...”
• Identification of Pseudomonas aeruginosa genes involved in virulence and anaerobic growth
  Filiatrault, Infection and immunity 2006
  • “...5 4 2 7 6 nirQ norC norB norD PA1850 PA2637 PA2638 PA2639 PA2641 PA2642 PA2644 PA2645 PA2646 PA2648 PA2649 PA3164 1 1 2 2 1 4 2 1 1 5 1 1 PA3912 PA3913 PA3918...”
  • “...PA0525 PA1006 PA1544 PA1546 PA1850 PA2637 PA2638 PA2639 PA2641 PA2642 PA2644 PA2645 PA2646 PA2648 PA2649 PA3164 PA3912 PA3913 PA3918 PA4049 PA5497 Gene...”
• Defining the Pseudomonas aeruginosa SOS response and its role in the global response to the antibiotic ciprofloxacin
  Cirz, Journal of bacteriology 2006
  • “...PA5558 PA5559 PA5560 PA5561 PA2637 PA2638 PA2639 PA2640 PA2641 PA2642 PA2643 PA2644 PA2645 PA2646 PA2647 PA2648 PA2649 PAO1 P. AERUGINOSA SOS RESPONSE VOL. 188,...”

PA14_29970 NADH dehydrogenase I chain F from Pseudomonas aeruginosa UCBPP-PA14
93% identity, 100% coverage

• Gene Expression Profiling of <i>Pseudomonas aeruginosa</i> Upon Exposure to Colistin and Tobramycin
  Cianciulli, Frontiers in microbiology 2021
  • “...NADH dehydrogenase subunit H 10 4.88 nuoG PA14_29940 NADH dehydrogenase subunit G 46.39 8.11 nuoF PA14_29970 NADH dehydrogenase I subunit F 13.36 8.16 nuoE PA14_29980 NADH dehydrogenase subunit E 13.55 5.35 icd PA14_30190 Iisocitrate dehydrogenase 3.09 ND sucD PA14_43940 Succinyl-CoA synthetase subunit alpha 9.39 3.27 sucC...”
• Genomewide identification of genetic determinants of antimicrobial drug resistance in Pseudomonas aeruginosa
  Dötsch, Antimicrobial agents and chemotherapy 2009
  • “...PAO1 ortholog PA14_31810 PA14_31400 PA14_30840 PA14_29970 PA14_29930 PA14_29920 PA14_29900 PA14_29880 PA14_29880 PA14_29320 PA14_29290 PA14_29220 PA14_27950...”

nuoF / Q88FH3 NADH-quinone oxidoreductase subunit F (EC 7.1.1.2) from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) (see 2 papers)
PP4123 NADH dehydrogenase I, F subunit from Pseudomonas putida KT2440
89% identity, 98% coverage

• The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: highlights from a multi-level omics approach
  Poblete-Castro, Microbial cell factories 2012
  • “...4.5 36 0.90 n.s. Succinate dehydrogenase PP4191 SdhA 3.9 23 2.8 n.s. NADH dehydrogenase I PP4123 NuoF 2.9 15 2.4 n.s. Glycosyl hydrolase PP4053 2.6 21 3.0 n.s. Phosphoenolpyruvate synthase PP2082 PpsA 2.4 24 1.5 n.s. Acetoin dehydrogenase -sub PP0554 AcoB only in C 23 -4.0...”

Psyr_3201 NADH-quinone oxidoreductase, F subunit from Pseudomonas syringae pv. syringae B728a
88% identity, 99% coverage

• Gene Expression Profiling in Viable but Nonculturable (VBNC) Cells of Pseudomonas syringae pv. syringae
  Postnikova, Frontiers in microbiology 2015
  • “...Psyr_3404 1.87 acnA, aconitate hydratase Energy generation Psyr_3204 1.02 NADH dehydrogenase subunit I Energy generation Psyr_3201 1.03 NADH dehydrogenase I subunit F Energy generation Psyr_3198 1.08 NADH dehydrogenase subunit B Energy generation Psyr_3202 1.10 NADH dehydrogenase subunit G Energy generation Psyr_3200 1.11 NADH dehydrogenase subunit E...”

Q3KA59 NADH-quinone oxidoreductase subunit F from Pseudomonas fluorescens (strain Pf0-1)
87% identity, 99% coverage

• Sulfur-34S stable isotope labeling of amino acids for quantification (SULAQ34) of proteomic changes in Pseudomonas fluorescens during naphthalene degradation
  Herbst, Molecular & cellular proteomics : MCP 2013 (secret)

H78_04192 NADH-quinone oxidoreductase subunit NuoF from Pseudomonas protegens
87% identity, 99% coverage

• The global regulator Hfq exhibits far more extensive and intensive regulation than Crc in Pseudomonas protegens H78
  Wang, Molecular plant pathology 2021
  • “...0.95 H78_04190 nuoC Protein NuoC 4.73 1.22 H78_04191 nuoE NADH dehydrogenase subunit E 4.67 1.24 H78_04192 nuoF NADH dehydrogenase subunit I F 4.35 1.19 H78_04193 nuoG NADH dehydrogenase subunit G 4.84 1.12 H78_04194 nuoH NADHquinone oxidoreductase subunit H 4.83 1.05 H78_04195 nuoI NADH dehydrogenase subunit I...”

SO_1017 NADH-quinone oxidoreductase subunit NuoF from Shewanella oneidensis MR-1
SO1017 NADH dehydrogenase I, F subunit from Shewanella oneidensis MR-1
87% identity, 94% coverage

• Electrochemically active bacteria sense electrode potentials for regulating catabolic pathways
  Hirose, Nature communications 2018
  • “...2.46 SO_1015 nuoH NADH-ubiquinone oxidoreductase subunit H 2.89 SO_1016 nuoG NADH-ubiquinone oxidoreductase subunit G 2.61 SO_1017 nuoF NADH-ubiquinone oxidoreductase subunit F 2.46 SO_1018 nuoE NADH-ubiquinone oxidoreductase subunit E 1.78 SO_1019 nuoCD NADH-ubiquinone oxidoreductase subunit CD 1.90 ATP synthesis SO_4746 atpC ATP synthase F1 epsilon subunit 2.19...”
  • “...the target genes, SO_0577 ( arcS ), SO_2912 ( pflB ), SO_0424 ( aceE ), SO_1017 ( nuoF ), SO_3517 ( ndh ), SO_0907 ( nqrF-1 ), and SO_1108 ( nqrF-2 ), are listed in Supplementary Table 2 . The amplified fusion product was ligated into...”
• Conserved synteny at the protein family level reveals genes underlying Shewanella species' cold tolerance and predicts their novel phenotypes
  Karpinets, Functional & integrative genomics 2010
  • “...Complex1_24kDa; Complex1_30kDa; Complex1_49kDa; Complex1_51K; NADHdh; Oxidored_q1; Oxidored_q1_N; Oxidored_q3; Oxidored_q4; Oxidored_q1; Oxidored_q1_N; Oxidored_q2 SO_1011; SO_1013; SO_1015; SO_1017; SO_1018; SO_1019; SO_1021; SO_1009SO_1012 nqr-2 operon: nuo ABCDIFGHIJKLMN Na(+)-transporting NADH: ubiquinone oxidoreductase nqr-2 operon (Mrazek et al. 2006 ) SO_1008 is ISSod20 transposase, TnpA_ISSod20 S. benthica and S. woodyi 5,...”
• Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1
  Gao, BMC genomics 2006
  • “...reductase flavoprotein subunit +3.409 0.711 * SO0399 frdB fumarate reductase iron-sulfur protein +1.895 0.336 ** SO1017 nuoF NADH dehydrogenase I, F subunit +9.606 2.178 * SO2098 hyaB quinone-reactive Ni/Fe hydrogenase, large subunit +3.506 0.937 ** SO2361 ccoP cytochrome c oxidase, cbb3-type, subunit III -2.079 0.036 *****...”

KPN_02674 NADH dehydrogenase I chain F from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
80% identity, 95% coverage

• Functional Genomic Screen Identifies Klebsiella pneumoniae Factors Implicated in Blocking Nuclear Factor κB (NF-κB) Signaling
  Tomás, The Journal of biological chemistry 2015
  • “...KPN_01924 Y/Y P035C5 Uncharacterized protein conserved KpST66_3673 KPN_02456 Y/Y P018C10 NADH-quinone oxidoreductase subunit F KpST66_3892 KPN_02674 Y/Y P006E12 Putative uncharacterized protein KpST66_0795 KPN_03309 Y/Y P026H10 cueO KpST66_4209 KPN_00131 Y/Y Carbohydrates P036D12 NADPH-dependent preQ0 reductase KpST66_3564 Unknown function Y/Y P043B5 N -Acetylmuramic acid 6-phosphate etherase KpST66_2662 KPN_01553...”

Entcl_1445 NADH-quinone oxidoreductase subunit NuoF from [Enterobacter] lignolyticus SCF1
81% identity, 95% coverage

• Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1
  Deangelis, Frontiers in microbiology 2013
  • “...2.5 9.2e-04 LIGNIN AS ELECTRON ACCEPTOR Entcl_1442 NADH:quinone oxidoreductase B subunit Electron transport 4.5 4.2e-03 Entcl_1445 NADH:quinone oxidoreductase F subunit Electron transport 3.1 1.8e-04 Entcl_1446 NADH:quinone oxidoreductase G subunit Electron transport 4.7 3.6e-22 Entcl_0986 NADH dehydrogenase (ubiquinone) Electron transport 2.4 2.3e-04 Entcl_0361 Nitrite reductase [NAD(P)H)] Electron...”
  • “...unamended growth on xylose minimal media. We found three NADH-quinone oxidoreductase proteins (Entcl_1446, Entcl_1442, and Entcl_1445) significantly up-regulated in lignin amended samples (Figure 2C ). These proteins are integral in electron transport chain (Brandt, 2006 ) and are involved in transfer of electron from NADH to...”

SG1597 NADH dehydrogenase I subunit F from Sodalis glossinidius str. 'morsitans'
80% identity, 94% coverage

• Identification of overexpressed genes in Sodalis glossinidius inhabiting trypanosome-infected self-cured tsetse flies
  Hamidou, Frontiers in microbiology 2014
  • “...protein kinase 1.3 SOD_P7410 SG1659 Hypothetical protein 1.3 SOD_P1886 SG0301__dipZ Thiol:disulfide interchange protein 1.2 SOD_P7169 SG1597 NADH dehydrogenase I subunit F 1.4 SOD_P7309 SG1632 Lipoprotein precursor 1.3 SOD_P4186 SG0858__nagB Glucosamine-6-phosphate deaminase 1.6 SOD_P4186 SG0858__nagB Glucosamine-6-phosphate deaminase 1.7 SOD_P324 pSG1GP_81_triE triE protein 1.6 SOD_P4134 SG0845 Phage tail...”
  • “...which were 1.5- and 1.7-fold over-represented in refractory flies. Oxidative respiration complex enzyme NADH dehydrogenase (SG1597) appears to be 1.4-fold overexpressed in refractory flies. In resistant flies, we also found overexpressed genes involved in the exonucleolytic cleavage of DNA, synthesis of amino acids and lipoproteins, as...”

Q8XCX1 NADH-quinone oxidoreductase subunit F from Escherichia coli O157:H7
ECs3168 NADH dehydrogenase I chain F from Escherichia coli O157:H7 str. Sakai
80% identity, 95% coverage

• Yeast Mannan-Rich Fraction Modulates Endogenous Reactive Oxygen Species Generation and Antibiotic Sensitivity in Resistant E. coli
  Smith, International journal of molecular sciences 2022
  • “...P0AFC9 NUOB 2 2 12 6 1.41 0.01 1.33 0.09 4.43 0.09 MRF + AMP Q8XCX1 NUOF 2 2 11 5 0.44 0.03 0.19 0.03 0.3 0.03 MRF + AMP Q8XCX2 NUOG 7 7 34 9 0.03 0.83 0.07 0.91 1.65 0.03 MRF + AMP P0ABJ0...”
• Physiological Response of Escherichia coli O157:H7 Sakai to Dynamic Changes in Temperature and Water Activity as Experienced during Carcass Chilling
  King, Molecular & cellular proteomics : MCP 2016
  • “...involved in aerobic respiration ( ECs3161 , ECs3162 , ECs3163 , ECs3164 , ECs3166 , ECs3168 , ECs3169 , nuoC / ECs3170 , nuoB / ECs3171 ), oxidative phosphorylation ( cydA / ECs0768 , ECs0769 , ECs3161 , ECs3162 , ECs3163 , ECs3164 , ECs3166 ,...”
  • “..., ECs2308 , nuoB / ECs3171 , ECs3166 , cydA / ECs0768 , ECs3162 , ECs3168 , ECs1031 , ycbY / ECs1032 , nuoC / ECs3170 ). These results correlate with the T-profiler analysis of the transcriptomic data ( supplemental Table S14 ), with significant downregulation...”

7p61F / P31979 Complex i from e. Coli, ddm-purified, with nadh, resting state (see paper)
80% identity, 95% coverage

• Ligands: iron/sulfur cluster; flavin mononucleotide; 1,4-dihydronicotinamide adenine dinucleotide (7p61F)

NuoF / b2284 NADH:quinone oxidoreductase subunit F from Escherichia coli K-12 substr. MG1655 (see 15 papers)
nuoF / P31979 NADH:quinone oxidoreductase subunit F from Escherichia coli (strain K12) (see 15 papers)
TC 3.D.1.1.1 / P31979 NUOF aka B2284, component of NADH dehydrogenase I, NuoA-N from Escherichia coli (see 7 papers)
NP_416787 NADH:quinone oxidoreductase subunit F from Escherichia coli str. K-12 substr. MG1655
b2284 NADH:ubiquinone oxidoreductase, chain F from Escherichia coli str. K-12 substr. MG1655
80% identity, 95% coverage

• substrates: H+
  tcdb comment: NuoL probably comprises part of the proton pathway (Nakamaru-Ogiso et al. 2010). NuoL (ND5), NuoM (ND4) and NuoN (ND2) are all homologous to proton:sodium antiporters and may all play reoles in pumping protons using a similar mechanism (Sato et al. 2013)
• Real-time optical studies of respiratory Complex I turnover.
  Belevich, Biochimica et biophysica acta 2014 (PubMed)
  • GeneRIF: Data indicate that the NADH:ubiquinone oxidoreductase chain F (NuoF) E95Q variant of Complex I shows that the single amino acid replacement in the catalytic site caused a strong decrease of NADH binding.
• Stress-induced evolution of Escherichia coli points to original concepts in respiratory cofactor selectivity.
  Auriol, Proceedings of the National Academy of Sciences of the United States of America 2011
  • GeneRIF: Data show that both NuoF mutations E183A and E183G having NADH and NADPH oxidizing ability.
• Spin labeling of the Escherichia coli NADH ubiquinone oxidoreductase (complex I).
  Pohl, Biochimica et biophysica acta 2010 (PubMed)
  • GeneRIF: Study determined the distance between a MTSL labeled complex I variant and the bound quinone by continuous-wave (cw) EPR allowing an inference on the location of the quinone binding site.
• Amino acid residues associated with cluster N3 in the NuoF subunit of the proton-translocating NADH-quinone oxidoreductase from Escherichia coli.
  Velazquez, FEBS letters 2005 (PubMed)
  • GeneRIF: two distinct Electron Spin Resonance Spectroscopy, arising from a [4Fe-4S] cluster (g(x,y,z)=1.90, 1.95, and 2.05) in NuoF
• Adenosine diphosphate sugar pyrophosphatase prevents glycogen biosynthesis in Escherichia coli.
  Moreno-Bruna, Proceedings of the National Academy of Sciences of the United States of America 2001
  • GeneRIF: N-terminus verified by Edman degradation on complete protein
• Heterocyclic Diaryliodonium-Based Inhibitors of Carbapenem-Resistant Acinetobacter baumannii
  Kumari, Microbiology spectrum 2023
  • “...( A. aeolicus ; UniProtKB ID number O66841 ; E. coli ; UniProtKB ID number P31979 ) were obtained from the UniProt database. The unweighted sequence alignments between NuOE and NuOF from A. aeolicus and E. coli were performed using T-coffee at the European Bioinformatics Institute...”
• Mutations in respiratory complex I promote antibiotic persistence through alterations in intracellular acidity and protein synthesis
  Van, Nature communications 2022
  • “...we modeled the protein structure of the cytoplasmic domain (nuoBCDEFGI; uniprot IDs: P0AFC7, P33599, P0AFD1, P31979, P33602, P0AFD6) and membrane arm (nuoAHJKLMN; uniprot IDs: P0AFC3, P0AFD4, P0AFE0, P0AFE4, P33607, P0AFE8, P0AFF0) using the online SWISS modeling server ( https://swissmodel.expasy.org/ ) 130 with 6g2j and 4he8 PDB...”
  • “...available in the NCBI nucleotide database (NC_000913.3, NC_007946.1, NC_007941.1), Uniprot database (P0AFC3, P0AFC7, P33599, P0AFD1, P31979, P33602, P0AFD4, P0AFD6, P0AFE0, P0AFE4, P33607, P0AFE8, P0AFF0), PDB database (6g2j, 4he8) and PubChem database (135398637). Source data are provided with this paper. Competing interests The authors declare no competing...”
• Exposure to microwave irradiation at constant culture temperature slows the growth of Escherichia coli DE3 cells, leading to modified proteomic profiles
  Mazinani, RSC advances 2019
  • “...Bifunctional protein HldE P76658 5 2 51.0/5.4 5.41 7 1.5 (0.006) NADH-quinone oxidoreductase subunit F P31979 12 5 49.3/6.9 49.9/6.6 6.86 8 1.9 (<0.001) Aspartate aminotransferase P00509 17 7 43.5/5.8 43.3/5.3 5.77 NADPH-dependent curcumin reductase P76113 7 2 37.6/5.8 5.82 Aminomethyltransferase P27248 5 2 40.1/5.6 5.57...”
• Functional states of the genome-scale Escherichia coli transcriptional regulatory system
  Gianchandani, PLoS computational biology 2009
  • “...including the absence of ArcA and Fnr as well as their target genes, such as b2284 ( nuoF , which expresses a subunit of NADH ubiquinone oxidoreductase) (not shown). Therefore, the dominant modes of the column space of R* capture the components of the TRS that...”
• Involvement of NADH:acceptor oxidoreductase and butyryl coenzyme A dehydrogenase in reversed electron transport during syntrophic butyrate oxidation by Syntrophomonas wolfei
  Müller, Journal of bacteriology 2009
  • “...oxidoreductase complex I in Escherichia coli (locus tag b2284; 40% id-aa). In the genome sequence, this attributed gene (Swol_1018) was part of an apparent...”
• Identification of genome-scale metabolic network models using experimentally measured flux profiles
  Herrgård, PLoS computational biology 2006
  • “...nuoM (b2277), nuoL (b2278), nuoK (b2279), nuoJ (b2280), nuoI (b2281), nuoH (b2282), nuoG (b2283), nuoF (b2284), nuoE (b2285), nuoC (b2286), nuoB (b2287), nuoA (b2288), fdoI (b3892), fdoH (b3893), fdoG (b3894), fdhF (b4079), frdD (b4151), frdC (b4152), frdB (b4153), frdA (b4154), deoC (b4381), and deoB (b4383). We...”
• Effect of RyhB small RNA on global iron use in Escherichia coli
  Massé, Journal of bacteriology 2005
  • “...b1778 b2113 b2276 b2277 b2278 b2279 b2280 b2281 b2282 b2283 b2284 b2285 b2286 b2287 b2288 b2522 b2523 b2524 b2525 b2526 4.4 2.1 6.1 6.1 4.0 5.1 1.9 1.7 3.8...”

STM2324 NADH dehydrogenase I chain F from Salmonella typhimurium LT2
79% identity, 95% coverage

• Analysis of the ArcA regulon in anaerobically grown Salmonella enterica sv. Typhimurium
  Evans, BMC microbiology 2011
  • “...STM2892 invJ 5'-TTGCTATCGTCTAAAAATAGGC-3' 5'-TTGATATTATCGTCAGAGATTCC-3' 128 surface presentation of antigens; secretory proteins 0.855 1.010 -0.2 0.0 STM2324 nuoF 5'-GGATATCGAGACACTTGAGC-3' 5'-GATTAAATGGGTATTACTGAACG-3' 163 NADH dehydrogenase I chain F 0.380 1.706 -1.4 0.8 STM0650 STM0650 5'-CAACAGCTTATTGATTTAGTGG-3' 5'-CTAACGATTTTTCTTCAATGG-3' 130 putative hydrolase C-terminus 0.274 0.123 -1.9 -3.0 STM2787 STM2787 5'-AAGCGAATACAGCTATGAACC-3' 5'-ATTAGCTTTTGCAGAACATGG-3' 144...”
• Salmonella enterica serovar typhimurium colonizing the lumen of the chicken intestine grows slowly and upregulates a unique set of virulence and metabolism genes
  Harvey, Infection and immunity 2011
  • “...and conversion STM2320 STM2321 STM2255 STM0440 STM4340 STM2325 STM2324 STM0441 STM0740 nuoJ nuoI napC cyoD frdD nuoE nuoF cyoC cydA NADH dehydrogenase I chain...”
• FNR is a global regulator of virulence and anaerobic metabolism in Salmonella enterica serovar Typhimurium (ATCC 14028s)
  Fink, Journal of bacteriology 2007
  • “...secretory proteins 0.246 0.182 2.0 2.5 STM2324 nuoF 5-GGATATCGAGACACTTGAGC-3 5-GATTAAATGGGTATTACTGAA CG-3 163 NADH-dehydrogenase I, chain F 2.894 2.600...”

ETAE_2381 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit from Edwardsiella tarda EIB202
78% identity, 95% coverage

• Genome-Wide Identification of Fitness Factors in Seawater for Edwardsiella piscicida
  Wei, Applied and environmental microbiology 2019
  • “...nuoK nuoJ nuoI ETAE_2379 ETAE_2380 nuoH nuoG ETAE_2381 ETAE_2382 ETAE_2383 ETAE_2384 nuoF nuoE nuoD nuoB ETAE_2385 ETAE_0147 ETAE_2337 ETAE_2944 nuoA ubiE...”

plu3085 NADH dehydrogenase I chain F (NADH-ubiquinone oxidoreductase chain 6) (NUO6) from Photorhabdus luminescens subsp. laumondii TTO1
77% identity, 95% coverage

• Influence of the Photorhabdus luminescens phosphomannose isomerase gene, manA, on mannose utilization, exopolysaccharide structure, and biofilm formation
  Amos, Applied and environmental microbiology 2011
  • “...-- plu2360 plu4799 plu0934 plu4004 plu2728 plu2728 plu3085 plu3085 plu1849 plu1850 plu1919 plu1920 plu1851 plu4890 plu2203 plu2209 plu3559 plu0499 plu2244...”

A1S_0756 NADH dehydrogenase I chain F from Acinetobacter baumannii ATCC 17978
61% identity, 86% coverage

• Insights Into Mechanisms of Biofilm Formation in Acinetobacter baumannii and Implications for Uropathogenesis
  Colquhoun, Frontiers in cellular and infection microbiology 2020
  • “...pathway 2.2 AB5075_UW Penesyan et al., 2019 2.37 ATCC 17978 Kentache et al., 2017 nuoF A1S_0756 NADH dehydrogenase I chain F 2.62 AB5075_UW Penesyan et al., 2019 2.75 ATCC 17978 Kentache et al., 2017 hisZ A1S_1178 ATP phosphoribosyltransferase 2.01 AB5075_UW Penesyan et al., 2019 2.94 ATCC...”
• Mucin acts as a nutrient source and a signal for the differential expression of genes coding for cellular processes and virulence factors in Acinetobacter baumannii
  Ohneck, PloS one 2018
  • “...2.187429899 0.003373818 NADH:ubiquinone oxidoreductase subunit C/D A1S_0755 2.307700992 0.001117444 NADH dehydrogenase I E subunit E A1S_0756 2.469437059 0.000653644 NADH dehydrogenase I subunit F A1S_0757 2.366086417 0.002066849 NADH dehydrogenase subunit G A1S_0758 2.287136558 0.003517374 NADH dehydrogenase subunit H A1S_0759 2.275271124 0.003174267 NADH dehydrogenase subunit I A1S_0761 2.403445757...”

Caur_2901 NADH-quinone oxidoreductase, F subunit from Chloroflexus aurantiacus J-10-fl
49% identity, 90% coverage

• Temporal metatranscriptomic patterning in phototrophic Chloroflexi inhabiting a microbial mat in a geothermal spring
  Klatt, The ISME journal 2013
  • “...Caur_1976 Caur_2896 Caur_2897 Caur_2898 Caur_2899 Caur_2900 Caur_2901 Caur_2902 Caur_2904 Caur_2905 Caur_2906 Caur_2907 Caur_2908 Caur_2909 NOT FOUND Night...”

P56913 NADH-quinone oxidoreductase subunit F 2 from Rhizobium meliloti (strain 1021)
50% identity, 90% coverage

• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “...REFSEQ:ZP_00943355.1, Rhizobium loti Swiss-Prot: Q98BW8 , Swiss-Prot: Q98KR0 , Rhizobium meliloti Swiss-Prot: P56912 , Swiss-Prot: P56913 , Rhodobacter capsulatus Swiss-Prot: O07948 , Rhodococcus opacus Swiss-Prot: P72304 , Rhodoferax ferrireducens T118 REFSEQ:YP_525088.1, Rickettsia prowazekii Swiss-Prot: Q9ZE33 , Solanum tuberosum Swiss-Prot: Q43840 , Streptomyces avermitilis MA-4680 REFSEQ:NP_823011.1, Synechococcus...”

SSGG_04170 NADH-quinone oxidoreductase subunit NuoF from Streptomyces filamentosus NRRL 15998
49% identity, 87% coverage

• Transcriptional analysis of the effect of exogenous decanoic acid stress on Streptomyces roseosporus
  Liao, Microbial cell factories 2013
  • “...SSGG_04165 NuoA 2.55 SSGG_04166 NuoB 2.91 SSGG_04167 NuoC 3.36 SSGG_04168 NuoD 4.09 SSGG_04169 NuoE 5.37 SSGG_04170 NuoF 3.37 SSGG_04171 NuoG 3.07 SSGG_04172 NuoH 4.33 SSGG_04173 NuoI 2.60 SSGG_04174 NuoJ 3.20 SSGG_04176 NuoL 2.61 SSGG_04178 NuoN 2.91 SSGG_03413 CydA 1.20 SSGG_03414 CydB 1.19 SSGG_04984 F0F1 ATP synthase...”

Rv3150 PROBABLE NADH DEHYDROGENASE I (CHAIN F) NUOF (NADH-UBIQUINONE OXIDOREDUCTASE CHAIN F) from Mycobacterium tuberculosis H37Rv
47% identity, 92% coverage

• Association of mutations in Mycobacterium tuberculosis complex (MTBC) respiration chain genes with hyper-transmission
  Li, BMC genomics 2024
  • “...Rv2196 ( qcrB , G1250T), Rv3145 ( nuoA , C35T), Rv3149 ( nuoE , G121C), Rv3150 ( nuoF , G700A), Rv3151 ( nuoG , A1810G), Rv3152 ( nuoH , G493A), and Rv3157 ( nuoM , A1243G). Furthermore, our results showed that the SNPs of atpH C73G,...”
  • “...Rv2196 ( qcrB , G1250T), Rv3145 ( nuoA , C35T), Rv3149 ( nuoE , G121C), Rv3150 ( nuoF , G700A), Rv3151 ( nuoG , C668T, A1810G), Rv3152 (nuoH, G493A), and Rv3157 ( nuoM , A1243G). To build up tree decision models, we adopted random forest and...”
• Genome-wide identification of the context-dependent sRNA expression in Mycobacterium tuberculosis
  Ami, BMC genomics 2020
  • “...expression in the iron limiting conditions (P value <2.2e-16) (Fig. 6 ). Genes Rv3003c, Rv1924c, Rv3150, Rv1937, Rv1728c, Rv1626, Rv1308, Rv0544c, Rv0532 and Rv1526c are the predicted targets for this sRNA (Additional file 11 : Table S5b). Subsequent gene expression analysis revealed that the predicted targets...”
• Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis
  Puniya, Scientific reports 2016
  • “...14 genes ( Rv0082 , Rv3145 , Rv3146 , Rv3147 , Rv3148 , Rv3149 , Rv3150 , Rv3152 , Rv3153 , Rv3154 , Rv3155 , Rv3156 , Rv3157 , Rv3158 ). These genes form 91 pairs and 78 (85.71%) of these had positive correlations (TO in...”
• Oxygen Modulates the Effectiveness of Granuloma Mediated Host Response to Mycobacterium tuberculosis: A Multiscale Computational Biology Approach
  Sershen, Frontiers in cellular and infection microbiology 2016
  • “...O2 = NAD + 2H Rv3145 AND Rv3146 AND Rv3147 AND Rv3148 AND Rv3149 AND Rv3150 AND Rv3151 AND Rv3152 AND Rv3153 AND Rv3154 AND Rv3155 AND Rv3156 AND Rv3157 AND Rv3158 NADH reductase (Non-proton translocating, NDH) 1 NADH + 0.5 O2 = 1 NAD Rv1854c...”
• Deciphering the metabolic response of Mycobacterium tuberculosis to nitrogen stress
  Williams, Molecular microbiology 2015
  • “...Rv2928 d10 0.041 1 1 NADH dehydrogenase demethylmenaquinone 8 Rv0082, Rv3145, Rv3146, Rv3147, Rv3148, Rv3149, Rv3150, Rv3152, Rv3153, Rv3154, Rv3155, Rv3156, Rv3157, Rv3158 d11 0.041 1 1 NADH dehydrogenase (ubiquinol) Rv0082, Rv3145, Rv3146, Rv3147, Rv3148, Rv3149, Rv3150, Rv3152, Rv3153, Rv3154, Rv3155, Rv3156, Rv3157, Rv3158 d12 0.041...”
• Functional genomics reveals extended roles of the Mycobacterium tuberculosis stress response factor sigmaH
  Mehra, Journal of bacteriology 2009
  • “...0.009 0.004 0.018 0.046 Energy metabolism Rv3053c Rv3146 Rv3147 Rv3150 Rv3153 Rv3154 Rv3155 Rv3158 nrdH nuoB nuoC nuoF nuoI nuoJ nuoK nuoN 1.126 0.003 0.917...”

SCO4567 NuoF, NADH dehydrogenase subunit from Streptomyces coelicolor A3(2)
48% identity, 91% coverage

• Comparative analysis of non-coding RNAs in the antibiotic-producing Streptomyces bacteria
  Moody, BMC genomics 2013
  • “...protein sco4137 sav4077 sven3895 Pit-accessory protein (phosphate transport) sco4440 sav3782 sven3077 Hypothetical protein sco4566 - sco4567 sav4841 - sav4842 sven4269 - sven4270 NuoF / NuoE sco4606 - sco4607 sav4888 - sav4889 sven4315 - sven4316 NuoL2 / NuoM2 sco4829 sav3433 sven0126 Putative oxidoreductase sco4848 sav3412 sven4521 Putative...”
• Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture
  Thomas, Molecular & cellular proteomics : MCP 2012
  • “...subunits (SCO1081 and SCO1082, respectively), three subunits (SCO4567, SCO4568, and SCO4573 or NuoF, NuoG, and NuoL, respectively) from an NADH dehydrogenase...”

NQO1_THET8 / Q56222 NADH-quinone oxidoreductase subunit 1; NADH dehydrogenase I chain 1; NDH-1 subunit 1; EC 7.1.1.- from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see 2 papers)
TC 3.D.1.3.1 / Q56222 Nqo1, component of NADH Dehydrogenase, NDH (Baradaran et al. 2013).  The x-ray structures of various complexes have been solved, and a coupling mechanism involving long range conformational changes has been proposed from Thermus thermophilus (see 3 papers)
TTHA0089 NADH-quinone oxidoreductase chain 1 from Thermus thermophilus HB8
47% identity, 92% coverage

• function: NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP. The Nqo1 subunit contains the NADH-binding site and the primary electron acceptor FMN.
  catalytic activity: a quinone + NADH + 5 H(+)(in) = a quinol + NAD(+) + 4 H(+)(out) (RHEA:57888)
  cofactor: FMN (Binds 1 FMN per subunit.)
  cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster per subunit. This [4Fe-4S] cluster is referred to as N3.)
  subunit: NDH-1 is composed of 15 different subunits, Nqo1 to Nqo15. The complex has a L-shaped structure, with the hydrophobic arm (subunits Nqo7, Nqo8 and Nqo10 to Nqo14) embedded in the membrane and the hydrophilic peripheral arm (subunits Nqo1 to Nqo6, Nqo9 and Nqo15) protruding into the bacterial cytoplasm. The hydrophilic domain contains all the redox centers.
• substrates: H+
• Determination and Dissection of DNA-Binding Specificity for the Thermus thermophilus HB8 Transcriptional Regulator TTHB099
  Moncja, International journal of molecular sciences 2020
  • “...+1.255 6.43 10 3 5 TTHA0088 NADH-quinone oxidoreductase subunit 2 +0.693 4.43 10 2 6 TTHA0089 NADH-quinone oxidoreductase subunit 1 +1.249 4.68 10 3 7 TTHA0090 NADH-quinone oxidoreductase subunit 3 +1.248 5.76 10 3 8 TTHA0091 NADH-quinone oxidoreductase subunit 8 +1.490 3.62 10 3 9 TTHA0092...”
• Lysine propionylation is a prevalent post-translational modification in Thermus thermophilus
  Okanishi, Molecular & cellular proteomics : MCP 2014
  • “...Metabolism Energy production and conversion TTHA0027 TTHA0089 TTHA0185 TTHA0206 TTHA0229 TTHA0230 TTHA0232 TTHA0233 TTHA0278 TTHA0287 TTHA0288 TTHA0466 TTHA0506...”
• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “..., Thermotoga maritima Swiss-Prot: O52682 , Swiss-Prot: Q9WXM5 , Swiss-Prot: Q9WY70 , Thermus thermophilus Swiss-Prot: Q56222 , Thiobacillus denitrificans ATCC 25259 REFSEQ:YP_314905.1, Trypanosoma brucei REFSEQ:XP_824451.1, Trypanosoma cruzi GenBank: EAN82122.1 , uncultured archaeon GZfos26D6 GenBank: AAU83054.1 , Yarrowia lipolytica Swiss-Prot: Q9UUU2 ] Multivariate Comparative Analysis The codon...”

4hea1 / Q56222 Crystal structure of the entire respiratory complex i from thermus thermophilus (see paper)
47% identity, 92% coverage

• Ligands: iron/sulfur cluster; flavin mononucleotide (4hea1)

LA_0890 NADH dehydrogenase (ubiquinone) chain F from Leptospira interrogans serovar lai str. 56601
Q8F7Q4 NADH-quinone oxidoreductase subunit F from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)
45% identity, 94% coverage

• Use of an Integrated Multi-Omics Approach To Identify Molecular Mechanisms and Critical Factors Involved in the Pathogenesis of Leptospira
  Kavela, Microbiology spectrum 2023
  • “...VagC vagC , LA_1002 3.40 2.34 Q8F7Q4 NADH-quinone oxidoreductase subunit F (EC 7.1.1.) nuoF , LA_0890 1.42 1.54 Q8F7R5 Uncharacterized protein LA_0879 4.21 4.29 Q8F7X6 Response regulator containing a signal receiver domain and a DNA-binding domain citB , LA_0816 3.72 2.26 Q8F7X9 PINc domain-containing protein LA_0813...”
• Use of an Integrated Multi-Omics Approach To Identify Molecular Mechanisms and Critical Factors Involved in the Pathogenesis of Leptospira
  Kavela, Microbiology spectrum 2023
  • “...lipoprotein LA_1004 2.81 1.71 + + Q8F7E3 Virulence-associated protein VagC vagC , LA_1002 3.40 2.34 Q8F7Q4 NADH-quinone oxidoreductase subunit F (EC 7.1.1.) nuoF , LA_0890 1.42 1.54 Q8F7R5 Uncharacterized protein LA_0879 4.21 4.29 Q8F7X6 Response regulator containing a signal receiver domain and a DNA-binding domain citB...”

AFE_2625 NADH-quinone oxidoreductase subunit NuoF from Acidithiobacillus ferrooxidans ATCC 23270
47% identity, 90% coverage

• Extending the models for iron and sulfur oxidation in the extreme acidophile Acidithiobacillus ferrooxidans
  Quatrini, BMC genomics 2009
  • “...nuoD NADH-quinone oxidoreductase, D subunit -0,5 0,64 AFE_2626 nuoE NADH-quinone oxidoreductase, E subunit -1,1 0,05 AFE_2625 nuoF NADH-quinone oxidoreductase, F subunit 0,4 0,01 AFE_2624 nuoG NADH-quinone oxidoreductase, G subunit -0,2 0,24 AFE_2623 nuoH NADH-quinone oxidoreductase, H subunit -0,7 0,00 AFE_2622 nuoI NADH-quinone oxidoreductase, I subunit 1,4...”

Mflv_4486 NADH-quinone oxidoreductase, F subunit from Mycobacterium flavescens PYR-GCK
49% identity, 92% coverage

• Energy metabolism in Mycobacterium gilvum PYR-GCK: insights from transcript expression analyses following two states of induction
  Badejo, PloS one 2014
  • “...subunit C 2.107 Mflv_4484 NADH dehydrogenase subunit D 1.900 Mflv_4485 NADH dehydrogenase subunit E 2.254 Mflv_4486 NADH-quinone oxidoreductase, F subunit 1.197 Mflv_4487 NADH dehydrogenase subunit G 2.478 Mflv_4488 NADH dehydrogenase subunit H 1.742 Mflv_4489 NADH dehydrogenase subunit I 2.110 Mflv_4490 NADH dehydrogenase subunit J 2.345 Mflv_4491...”

DR_RS07680 NADH-quinone oxidoreductase subunit NuoF from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
DR1500 NADH dehydrogenase I, F subunit from Deinococcus radiodurans R1
49% identity, 89% coverage

• Spatial chromosome organization and adaptation of the radiation-resistant extremophile Deinococcus radiodurans
  Qiu, The Journal of biological chemistry 2025
  • “...subunit NuoI 2.60 DR_RS07670 1,513,512 1,514,705 subunit NuoH 2.61 DR_RS07675 1,514,705 1,516,897 subunit NuoG 2.52 DR_RS07680 1,517,019 1,518,353 subunit NuoF 2.86 DR_RS07685 1,518,350 1,518,973 subunit NuoE 3.08 DR_RS07690 1,518,940 1,519,416 hypothetical protein 2.94 DR_RS07695 1,519,446 1,520,651 subunit D 2.89 DR_RS07700 1,520,648 1,521,322 subunit C 2.54 DR_RS07705...”
• A Mur regulator protein in the extremophilic bacterium Deinococcus radiodurans
  Ul, PloS one 2014
  • “...dr1498 NADH dehydrogenase I subunit H 2.28 DR1499 dr1499 NADH dehydrogenase I subunit G 1.57 DR1500 dr1500 NADH dehydrogenase I subunit F 1.99 DR1501 dr1501 NADH dehydrogenase I subunit E 1.76 DR1503 dr1503 NADH dehydrogenase I subunit D 2.59 DR1504 dr1504 NADH dehydrogenase I subunit C...”

MSMEG_2058 NADH-quinone oxidoreductase, F subunit from Mycobacterium smegmatis str. MC2 155
46% identity, 96% coverage

• Expression of a novel mycobacterial phosphodiesterase successfully lowers cAMP levels resulting in reduced tolerance to cell wall-targeting antimicrobials
  Thomson, The Journal of biological chemistry 2022
  • “...encoding subunits G, F, E, D, C, and B ofthetype I NADH:menaquinone oxidoreductase (Nuo) (MSMEG_2057, MSMEG_2058, MSMEG_2059, MSMEG_2060, MSMEG_2061, and MSMEG_2062) with log2 fold changes ( p < 0.05) of 1.62, 1.26, 1.42, 1.49, 1.01, and 1.77, respectively, as well as in four of the five...”

RSP_0104 Respiratory-chain NADH dehydrogenase, 51 kDa subunit from Rhodobacter sphaeroides 2.4.1
47% identity, 93% coverage

• Convergence of the transcriptional responses to heat shock and singlet oxygen stresses
  Dufour, PLoS genetics 2012
  • “...Mainrole Subrole Locus RpoHI/II regulon (45 genes) Energy metabolism Electron transport RSP_0100, RSP_0101, RSP_0102, RSP_0103, RSP_0104, RSP_0105, RSP_0106, RSP_0107, RSP_2805 Other RSP_0472 Protein synthesis/fate Degradation of proteins, peptides, and glycopeptides RSP_0665, RSP_1076, RSP_1174, RSP_2710, RSP_2806 Other RSP_1825 Protein folding and stabilization RSP_1207 Ribosomal proteins: synthesis and...”

Q9WY70 NADP-reducing hydrogenase, subunit C from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
TM0228 NADP-reducing hydrogenase, subunit C from Thermotoga maritima MSB8
44% identity, 77% coverage

• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “...Thermococcus kodakarensis KOD1 DDBJ: BAD85803.1 , Thermotoga maritima Swiss-Prot: O52682 , Swiss-Prot: Q9WXM5 , Swiss-Prot: Q9WY70 , Thermus thermophilus Swiss-Prot: Q56222 , Thiobacillus denitrificans ATCC 25259 REFSEQ:YP_314905.1, Trypanosoma brucei REFSEQ:XP_824451.1, Trypanosoma cruzi GenBank: EAN82122.1 , uncultured archaeon GZfos26D6 GenBank: AAU83054.1 , Yarrowia lipolytica Swiss-Prot: Q9UUU2 ]...”
• Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex
  Ravcheev, Journal of bacteriology 2012
  • “...TM0201, TM0983, TM1586 (A); TRQ2-0578 (1), TRQ2-0578 (2), TM0228 (B); TM1420, TM0423, TM0686, TM1400 (C); TM0179, TM0379, TM1814 (D). As a negative control, the...”

8e9hF / A0QU31 Mycobacterial respiratory complex i, fully-inserted quinone (see paper)
46% identity, 96% coverage

• Ligands: flavin mononucleotide; zinc ion; iron/sulfur cluster (8e9hF)

SPV1_13739 NADH-quinone oxidoreductase, F subunit from Mariprofundus ferrooxydans PV-1
46% identity, 87% coverage

• Mariprofundus ferrooxydans PV-1 the first genome of a marine Fe(II) oxidizing Zetaproteobacterium
  Singer, PloS one 2011
  • “...electron transport chain through a bc 1 and NADH-Q oxidoreductase complex ( e.g. SPV1_03858, SPV1_03863, SPV1_13739, SPV1_13744), as shown in Thiobacillus ferrooxidans [61] . Since the genome of PV-1 appears to encode for a complete set of genes required for the uptake and conversion of poly...”

NGO1746 NuoF from Neisseria gonorrhoeae FA 1090
45% identity, 88% coverage

• Transcriptional profiling identifies the metabolic phenotype of gonococcal biofilms
  Falsetta, Infection and immunity 2009
  • “...no.) Downregulated genes meeting a 2.0-fold cutoff NGO1746 NGO0182 NGO0752 NGO0023 Downregulated genes not meeting a 2.0-fold cutoff NGO0189 NGO0190 NGO0138...”

K0B622 formate dehydrogenase (NAD+, ferredoxin) (subunit 2/4) (EC 1.17.1.11) from Gottschalkia acidurici (see paper)
Curi_c29400 NADH-quinone oxidoreductase subunit NuoF from Gottschalkia acidurici 9a
44% identity, 66% coverage

• Energy Conservation in the Acetogenic Bacterium Clostridium aceticum
  Wiechmann, Microorganisms 2021
  • “...are both similar (around 30%) to the first 180 amino acids of HylB (encoded by Curi_c29400). HydB2 (encoded by CACET_c32730) and HydB3 (encoded by CACET_c32700) in C. aceticum share 82% identity and are both similar to HylB of G. acidurici . HydC2 (encoded by CACET_c32720) of...”

lpp2831 NADH dehydrogenase I chain F from Legionella pneumophila str. Paris
44% identity, 94% coverage

• Two small ncRNAs jointly govern virulence and transmission in Legionella pneumophila
  Sahr, Molecular microbiology 2009
  • “...lpp3032 Major outer membrane protein 4.22 7.52 lpp2835 NADH dehydrogenase I chain B 3.84 2.37 lpp2831 NADH dehydrogenase I chain F 2.35 1.69 lpp2830 NADH dehydrogenase I chain G 3.14 - lpp2828 NADH-quinone oxidoreductase chain I 1.99 - lpp2827 NADH-quinone oxidoreductase chain J 2.42 - lpp2768...”

Q9WXM5 NADP-reducing hydrogenase, subunit C from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
43% identity, 67% coverage

• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “...GenBank: EAR96899.1 , Thermococcus kodakarensis KOD1 DDBJ: BAD85803.1 , Thermotoga maritima Swiss-Prot: O52682 , Swiss-Prot: Q9WXM5 , Swiss-Prot: Q9WY70 , Thermus thermophilus Swiss-Prot: Q56222 , Thiobacillus denitrificans ATCC 25259 REFSEQ:YP_314905.1, Trypanosoma brucei REFSEQ:XP_824451.1, Trypanosoma cruzi GenBank: EAN82122.1 , uncultured archaeon GZfos26D6 GenBank: AAU83054.1 , Yarrowia lipolytica...”

PTH_2011 NADH:ubiquinone oxidoreductase, NADH-binding 51 kD subunit from Pelotomaculum thermopropionicum SI
41% identity, 74% coverage

• Membrane Potential-requiring Succinate Dehydrogenase Constitutes the Key to Propionate Oxidation and Is Unique to Syntrophic Propionate-oxidizing Bacteria
  Kosaka, Microbes and environments 2023
  • “...and Complex1_51K (PF01512). These domains containing genes include PTH_1405 (NAD_binding_1); PTH_0267, PTH_0595, and PTH_0596 (Oxidored_FMN); PTH_2011, PTH_1378, and PTH_2648 (Complex1_51K) ( Table S2 ). The appropriate gene cannot be identified by the presence of a domain; however, the genes in P. thermopropionicum may be coupled to...”
• Concerted Metabolic Shifts Give New Insights Into the Syntrophic Mechanism Between Propionate-Fermenting Pelotomaculum thermopropionicum and Hydrogenotrophic Methanocella conradii
  Liu, Frontiers in microbiology 2018
  • “...Coculture P. thermopropionicum Fe-hydrogenase (Fe-H 2 ase III) PTH_2010 1.49 12.05 13.51 Hypothetical hydrogenase subunit PTH_2011 nuoF 1.19 11.62 12.79 NADH: ubiquinone oxidoreductase, NADH-binding 51 kD subunit PTH_2012 nuoE 1.68 11.23 12.88 NADH: ubiquinone oxidoreductase, 24 kD subunit Formate dehydrogenase (Fdh II) PTH_2645 4.26 7.20 11.53...”

SYN_RS05185 NADH-quinone oxidoreductase subunit NuoF from Syntrophus aciditrophicus SB
SYN_01369 NADH-quinone oxidoreductase chain F from Syntrophus aciditrophicus SB
43% identity, 67% coverage

• Enoyl-Coenzyme A Respiration via Formate Cycling in Syntrophic Bacteria
  Agne, mBio 2021
  • “...NuoF-like gene products in the genome of S. aciditrophicus . The HydB subunit of [Fe-Fe]-hydrogenase (SYN_RS05185) served as query sequence during BLAST application. Download TableS1, DOCX file, 0.02 MB . Copyright 2022 Agne et al. 2022 Agne et al. https://creativecommons.org/licenses/by/4.0/ This content is distributed under the...”
• The Beta Subunit of Non-bifurcating NADH-Dependent [FeFe]-Hydrogenases Differs From Those of Multimeric Electron-Bifurcating [FeFe]-Hydrogenases
  Losey, Frontiers in microbiology 2020
  • “...A DNA sequence encoding the genes for the S. aciditrophicus dimeric [FeFe]-hydrogenase HydAB (Locus Tags: SYN_01369 and SYN_01370, Genome Genbank ID: CP000252) was ordered from Integrated DNA Technologies (Coralville, IA, United States) and delivered in a plasmid for recombinant protein expression, including a T7 promoter region...”
  • “...2018 ). Results Purification and Characterization of S. aciditrophicus Hydrogenase HydAB The protein products of SYN_01369 and SYN_01370 were recombinantly produced in E. coli and purified using nickel-affinity chromatography and molecular mass cut off filters. Recombinant HydAB was purified 36-fold with a 62% yield and a...”

CACET_c32730 NADH-quinone oxidoreductase subunit NuoF from Clostridium aceticum
42% identity, 69% coverage

• Energy Conservation in the Acetogenic Bacterium Clostridium aceticum
  Wiechmann, Microorganisms 2021
  • “...30%) to the first 180 amino acids of HylB (encoded by Curi_c29400). HydB2 (encoded by CACET_c32730) and HydB3 (encoded by CACET_c32700) in C. aceticum share 82% identity and are both similar to HylB of G. acidurici . HydC2 (encoded by CACET_c32720) of C. aceticum is 62%...”

FCKEOINB_00346 NADH-quinone oxidoreductase subunit NuoF from Nitrosomonas sp.
42% identity, 96% coverage

• Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome
  Beach, mSystems 2021
  • “...the CRP family ANR (FCKEOINB_00121), which was not detected in our initial analyses; NADH-quinone oxidoreductase (FCKEOINB_00346) involved in respiration; and a chaperone involved in photosystem 1 formation in other organisms (JNIBNLAF_02096). Among the FNR-controlled genes in Nitrosomonas with higher expression under aerobic conditions (cluster 6 in...”

NITMOv2_4064 NADH-quinone oxidoreductase subunit NuoF from Nitrospira moscoviensis
43% identity, 94% coverage

• Cultivation and Transcriptional Analysis of a Canonical Nitrospira Under Stable Growth Conditions
  Mundinger, Frontiers in microbiology 2019
  • “..., and nuoF genes and contains an enlarged nuoG homolog. Interestingly, a separate nuoF gene (NITMOv2_4064) together with genes encoding a ferredoxin and an ironsulfur cluster insertion protein forms a highly expressed gene cluster. This NuoF might interact with Cl_1 and could be involved in the...”

TC 3.D.1.2.1 / P29913 NQO1, component of NADH dehydrogenase I from Paracoccus denitrificans (see 3 papers)
AAA25585.1 NADH dehydrogenase from Paracoccus denitrificans (see paper)
43% identity, 88% coverage

• substrates: H+
• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “...Nitrosospira multiformis ATCC 25196 REFSEQ:YP_411791.1, REFSEQ:YP_412360.1, Nyctotherus ovalis BA GenBank: AY608627 , Paracoccus denitrificans Swiss-Prot: P29913 , Psychromonas ingrahamii 37 REFSEQ:ZP_01348563.1, Ralstonia eutropha GenBank: AAC06140 , Ralstonia eutropha JMP134 GenBank: AAZ60345.1 , Ralstonia metallidurans CH34 REFSEQ:YP_583087.1, Ralstonia solanacearum EMBL: CAD15764.1 , Ralstonia solanacearum UW551 REFSEQ:ZP_00943355.1, Rhizobium...”

8qbyF / A1B491 Respiratory complex i from paracoccus denitrificans in msp2n2 nanodiscs
43% identity, 88% coverage

• Ligands: flavin mononucleotide; iron/sulfur cluster (8qbyF)

A1B491 NADH-quinone oxidoreductase subunit F from Paracoccus denitrificans (strain Pd 1222)
43% identity, 88% coverage

• Exploring the Denitrification Proteome of Paracoccus denitrificans PD1222
  Olaya-Abril, Frontiers in microbiology 2018
  • “...the respiratory electron transport chain like proteins belonging to complex I-NADH-quinone oxidoreductase (A1B481, A1B486, A1B489, A1B491, A1B495, A1B496), complex II-succinate dehydrogenase (A1AZJ0, A1AZI7) and the cytochrome cbb 3 -type cytochrome c oxidase (A1B348 and A1B350) were detected under denitrifying conditions (Supplementary Table S1 ). Fourthly, several...”

BB3836 respiratory-chain NADH dehydrogenase, 51 kDa subunit from Bordetella bronchiseptica RB50
44% identity, 90% coverage

• Conservation of Ancient Genetic Pathways for Intracellular Persistence Among Animal Pathogenic Bordetellae
  Rivera, Frontiers in microbiology 2019
  • “...L BB3834 nuoH 1.7 1.3E-07 NADH-quinone oxidoreductase subunit H BB3835 nuoG 1.9 3.7E-08 NADH-quinone oxidoreductase BB3836 nuoF 2.0 5.7E-09 NADH-quinone oxidoreductase subunit F Cell division BB4188 2.2 2.4E-08 Uncharacterized protein BB4193 ftsZ 2.5 4.3E-10 Cell division protein FtsZ BB4194 ftsA 3.4 3.3E-09 Cell division protein FtsA...”
  • “..., ftsW , and murD . Similarly, expression of a large gene locus (BB3827 to BB3836) encoding the oxidative respiratory chain was significantly downregulated, including NADH dehydrogenase genes nuoN , nuoM , nuoL , and nuoH . Taken together, B. bronchiseptica responded to internalization by macrophages...”

PHATR_43944 predicted protein from Phaeodactylum tricornutum CCAP 1055/1
40% identity, 86% coverage

• Examination of metabolic responses to phosphorus limitation via proteomic analyses in the marine diatom Phaeodactylum tricornutum
  Feng, Scientific reports 2015
  • “...catalysts that plays an essential role in citric acid cycle 56 . Moreover, ubiquinone oxidoreductase (PHATR_43944) and ATP synthase mitochondrial subunit (PHATRDRAFT_54086) involved in the oxidative phosphorylation pathway was downregulated except a vacuolar ATP synthase subunit b (PHATRDRAFT_24978). These results showed that most of the proteins...”

RSP_2518 NADH dehydrogenase-ubiquinone oxidoreductase, chain F from Rhodobacter sphaeroides 2.4.1
43% identity, 87% coverage

• Regulation of Reactive Oxygen Species Promotes Growth and Carotenoid Production Under Autotrophic Conditions in Rhodobacter sphaeroides
  Lee, Frontiers in microbiology 2022
  • “...production and conversion 2.0 RSP_2516 nuoE NADH dehydrogenase subunit E Energy production and conversion 1.1 RSP_2518 nuoF NADH-quinone oxidoreductase subunit F Energy production and conversion 1.1 RSP_2779 katE Catalase Inorganic ion transport and metabolism 2.2 RSP_2380 katC Catalase Inorganic ion transport and metabolism 2.2 RSP_1796 sodC...”

GSU2721 NAD-reducing hydrogenase, alpha subunit from Geobacter sulfurreducens PCA
42% identity, 72% coverage

• Genome sequence of a dissimilatory Fe(III)-reducing bacterium Geobacter soli type strain GSS01(T)
  Yang, Standards in genomic sciences 2015
  • “...SE37_01575= GSU0734 ; second complex: SE37_01780= GSU2718 , SE37_01775= GSU2719 , SE37_01770= GSU2720 , SE37_01765= GSU2721 , SE37_01760= GSU2722 ) that predicted to participate the hydrogen cycling [ 31 ]. In addition, at least two hydrogenases (SE37_02470 and SE37_02475) in G. soli genome have no orthologs...”

HM1_1028 NADH dehydrogenase conserved domain protein, nuoe and nuof from Heliobacterium modesticaldum Ice1
42% identity, 45% coverage

• Energy metabolism of Heliobacterium modesticaldum during phototrophic and chemotrophic growth
  Tang, BMC microbiology 2010
  • “...( hupS (HM1_1478) and hupL (HM1_1479), subunits of uptake nickel-iron ([NiFe])-hydrogenase ( hupSL ); nuoEFG (HM1_1028 - HM1_1029), encoding [FeFe]-hydrogenase; and hymD (HM1_1590), encoding the Hymd subunit of Fe-only dehydrogenase). (C) Pyruvate metabolism is either active or up-regulated in darkness As shown in Figure 4 ,...”
• The genome of Heliobacterium modesticaldum, a phototrophic representative of the Firmicutes containing the simplest photosynthetic apparatus
  Sattley, Journal of bacteriology 2008
  • “...are shown schematically in Fig. 3A. These genes, nuoEF (HM1_1028) and nuoG (hydA; HM1_ 1029), showed levels of sequence identity of 79 and 81%, respectively, to...”

Halsa_1863 NADH-quinone oxidoreductase subunit NuoF from Halanaerobium hydrogeniformans
42% identity, 68% coverage

• Going from microbial ecology to genome data and back: studies on a haloalkaliphilic bacterium isolated from Soap Lake, Washington State
  Mormile, Frontiers in microbiology 2014
  • “...for iron hydrogenases. Halsa_1862 is part of a putative operon that includes a NADH dehydrogenase (Halsa_1863), a ferredoxin-like protein (Halsa_1864), a histidine kinase (Halsa_1865), NADH-quinone oxidoreductase subunit E (Halsa_1866), PHP domain-containing protein (Halsa_1867), an iron-sulfur binding hydrogenase (Halsa_1868), an iron-sulfur cluster domain-containing protein (Halsa_1869), an anti-sigma...”

Tph_c08050 NADH-quinone oxidoreductase subunit NuoF from Thermacetogenium phaeum DSM 12270
42% identity, 68% coverage

• Energy-Conserving Enzyme Systems Active During Syntrophic Acetate Oxidation in the Thermophilic Bacterium Thermacetogenium phaeum
  Keller, Frontiers in microbiology 2019
  • “...(Tph_c08060) is located in a gene cluster together with genes of a NADH:quinone oxidoreductase (Tph_c08040- Tph_c08050) was present during growth with formate. The electrons derived in this reaction could be coupled via a quinone pool to the reduction of methylene-THF ( Figure 5 ). However, at...”

Q9ZE33 NADH-quinone oxidoreductase subunit F from Rickettsia prowazekii (strain Madrid E)
44% identity, 86% coverage

• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “...Swiss-Prot: O07948 , Rhodococcus opacus Swiss-Prot: P72304 , Rhodoferax ferrireducens T118 REFSEQ:YP_525088.1, Rickettsia prowazekii Swiss-Prot: Q9ZE33 , Solanum tuberosum Swiss-Prot: Q43840 , Streptomyces avermitilis MA-4680 REFSEQ:NP_823011.1, Synechococcus elongatus PCC 6301 EMBL: CAA73873.1 , Syntrophus aciditrophicus SB REFSEQ:YP_461127.1, Tetrahymena thermophila SB210 GenBank: EAR96899.1 , Thermococcus kodakarensis KOD1...”

7t2rB / I4BYB5 Structure of electron bifurcating ni-fe hydrogenase complex hydabcsl in fmn-free apo state (see paper)
43% identity, 92% coverage

• Ligands: iron/sulfur cluster; fe2/s2 (inorganic) cluster (7t2rB)

CD3406 putative iron-only hydrogenase,electron-transferring subunit from Clostridium difficile 630
41% identity, 66% coverage

• Vegetative Cell and Spore Proteomes of Clostridioides difficile Show Finite Differences and Reveal Potential Protein Markers
  Abhyankar, Journal of proteome research 2019
  • “...synthases/CO dehydrogenases (CD0174, CD0176, and CD0727), formate dehydrogenases (CD2179), and iron-only hydrogenases (CD0893, CD3258, and CD3406). Enzymes CD0174 and CD0176 synthesize the key metabolite acetyl-CoA from CO, methyl corrinoid, and CoASH. The formate dehydrogenases can be seleno (CD3317) or nonseleno (CD0769 and CD2179) enzymes. Protein CD2179,...”

HNDC_SOLFR / Q46507 NADP-reducing hydrogenase subunit HndC; Hydrogen dehydrogenase (NADP(+)); EC 1.12.1.3 from Solidesulfovibrio fructosivorans (Desulfovibrio fructosivorans) (see 2 papers)
42% identity, 84% coverage

• function: Catalyzes the reduction of NADP in the presence of molecular H2 to yield NADPH.
  catalytic activity: H2 + NADP(+) = NADPH + H(+) (RHEA:18637)
  subunit: Heterotetramer composed of HndA, HndB, HndC and HndD subunits. HndC is probably the reducing subunit.
  disruption phenotype: Disruption completely abolishes the NADP reductase activity.

CACET_c32700 NADH-quinone oxidoreductase subunit NuoF from Clostridium aceticum
40% identity, 72% coverage

• Energy Conservation in the Acetogenic Bacterium Clostridium aceticum
  Wiechmann, Microorganisms 2021
  • “...amino acids of HylB (encoded by Curi_c29400). HydB2 (encoded by CACET_c32730) and HydB3 (encoded by CACET_c32700) in C. aceticum share 82% identity and are both similar to HylB of G. acidurici . HydC2 (encoded by CACET_c32720) of C. aceticum is 62% similar to HylC of G....”
• The Complete Genome Sequence of Clostridium aceticum: a Missing Link between Rnf- and Cytochrome-Containing Autotrophic Acetogens
  Poehlein, mBio 2015
  • “...acting formate dehydrogenase is required. C.aceticum contains a non-selenocysteine-containing paralog (CACET_c07250) and a selenocysteine-containing paralog (CACET_c32700); the latter one is directly associated with a gene cluster coding for an iron-only hydrogenase (CACET_c32700-CACET_c32740). The genome of C.aceticum contains three additional iron-only hydrogenase gene clusters comparable to those...”

Dtur_0919 NADH dehydrogenase (quinone) from Dictyoglomus turgidum DSM 6724
42% identity, 69% coverage

• The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor
  Brumm, Frontiers in microbiology 2016
  • “...The proton gradient needed for ATP generation is produced by NADH oxidoreductase (Dtur_0558; Dtur_0559; Dtur_0916; Dtur_0919, and Dtur_1091), and succinate dehydrogenase (Dtur_0445). ATP is generated by proton translocation via an F0F1-type ATP synthase (Dtur_129 through Dtur_135). D . turgidum also possesses a V-type ATP synthase (Dtur_1499...”

A9762_09275 NADH-quinone oxidoreductase subunit NuoF from Pandoraea sp. ISTKB
43% identity, 90% coverage

• Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB
  Kumar, Biotechnology for biofuels 2018
  • “...I 1.983 13 54.6 18.63 1.26E66 A0A1E3LC99 A9762_26255 Oxidoreductase 1.46342 9 62.5 26.21 1.99E100 A0A1E3LAC9 A9762_09275 NADH oxidoreductase (quinone) subunit F 0.86275 19 70.7 47.093 5.72E135 A0A1E3LMK8 A9762_03120 NADP oxidoreductase 0.82498 10 55.5 32.458 3.02E38 A0A1E3LHK5 A9762_23470 FAD-dependent oxidoreductase 0.33833 3 14.7 38.458 4.28E15 A0A1E3LLW4 A9762_03220...”

Pcar_2708 NADH dehydrogenase I, F subunit from Pelobacter carbinolicus str. DSM 2380
42% identity, 83% coverage

• The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features
  Aklujkar, BMC genomics 2012
  • “...P . carbinolicus (Pcar_1772, Pcar_2602) and next to an NADPH oxidoreductase ( hndC - 5 Pcar_2708) with ~75% sequence identity to the hydrogenase-associated HndC proteins. These arrangements suggest that electron transfer to arsenate by P . carbinolicus may be mechanistically similar to hydrogen production. A third...”

PAAG_02656 NADH-ubiquinone oxidoreductase 51 kDa subunit from Paracoccidioides lutzii Pb01
42% identity, 75% coverage

• Interaction of Isocitrate Lyase with Proteins Involved in the Energetic Metabolism in Paracoccidioides lutzii
  Freitas, Journal of fungi (Basel, Switzerland) 2020
  • “...8694.258 PAAG_05031 NADH-ubiquinone oxidoreductase 40 kDa subunit 7284.236 PAAG_05735 NADH-ubiquinone oxidoreductase 49 kDa subunit 8447.485 PAAG_02656 NADH-ubiquinone oxidoreductase 51 kDa subunit 9802.509 PAAG_07791 NADH-ubiquinone oxidoreductase 8821.187 PAAG_08916 LYR family protein 7664.982 PAAG_04820 ATPase alpha subunit 7938.354 Respiration PAAG_08037 ATP synthase subunit beta 7580.651 PAAG_05576 ATP synthase...”
• Transcriptional and proteomic responses to carbon starvation in Paracoccidioides
  Lima, PLoS neglected tropical diseases 2014
  • “...riboflavin synthase alpha chain # biosynthesis of riboflavin PAAG_04443 spermidine synthase # B complex vitamins PAAG_02656 NADH-ubiquinone oxidoreductase 51 kDa subunit # ubiquinone ENERGY Glycolysis and gluconeogenesis PAAG_01583 6-phosphofructokinase subunit beta # glycolysis PAAG_06172 glucokinase # glycolysis Tricarboxylic-acid pathway PAAG_00588 fumarate hydratase # TCA cycle PAAG_04597...”

CND04070 NADH-ubiquinone oxidoreductase 51 kDa subunit from Cryptococcus neoformans var. neoformans JEC21
43% identity, 71% coverage

• Importance of mitochondria in survival of Cryptococcus neoformans under low oxygen conditions and tolerance to cobalt chloride
  Ingavale, PLoS pathogens 2008
  • “.../+ 69G9 CNE00180 t-RNA Lysine /+ /+ 92D9 CNJ01940 Dihydrofolate reductase /+ +/ /+ 135G10 CND04070 NADHubiquinone oxidoreductase /+ 161B3 CNM01080 ATPADP antiporter /+ +/ + +/ Vesicular Transport 132H6 CNF00890 Importin beta-4 subunit /+ Ts /+ /+ 155B3 CNA06920 V ATPase subunit H 252C2 CNC07180...”
  • “...a Complex I CNH02730 1.54 NADH-ubiquinone oxidoreductase (subunit D) CNB01310 2.10 NADH-ubiquinone oxidoreductase (subunit G) CND04070 1.93 NADH-ubiquinone oxidoreductase 51 kDa subunit (NuoF) CNF03360 1.45 NADH-ubiquinone oxidoreductase 30.4 kDa subunit, putative CND01070 1.61 NADH dehydrogenase (ubiquinone) CNC07090 1.91 NADH dehydrogenase (subunit E) putative CNE03960 1.62 NADH...”

CNAG_01287 NADH-ubiquinone oxidoreductase 51 kDa subunit, mitochondrial from Cryptococcus neoformans var. grubii H99
43% identity, 76% coverage

• The interplay between electron transport chain function and iron regulatory factors influences melanin formation in Cryptococcus neoformans
  Xue, mSphere 2024
  • “...( Fig. 3B ). The differential regulation of representative genes encoding ETC components (e.g., genes CNAG_01287, CNAG_05041, and CNAG_07491) was confirmed by qRT-PCR (Fig. S6). We also noted the transcript levels of genes encoding Cir1, HapX, or Rim101 were not differentially expressed in the RNA-Seq analysis...”
• HapX positively and negatively regulates the transcriptional response to iron deprivation in Cryptococcus neoformans
  Jung, PLoS pathogens 2010
  • “...annotation Fold change (Low-iron) b hap3 vs WT hapX vs WT cir1 vs WT 163.m06475 CNAG_01287 NADH-ubiquinone oxidoreductase 51 kDa subunit 16.09 8.18 1.20 * 163.m06504 CNAG_01323 ubiquinol-cytochrome-c reductase 5.68 5.24 1.00 * 167.m03416 CNAG_02266 NADH ubiqionone oxidoreductase chain B 1.24 * 1.41 * 1.67 *...”

hymB / GI|14250934 protein HymB from Eubacterium acidaminophilum (see paper)
40% identity, 72% coverage

8a6tB / A0A097ATG4 Cryo-em structure of the electron bifurcating fe-fe hydrogenase hydabc complex from thermoanaerobacter kivui in the reduced state (see paper)
TKV_c19590 NADH-quinone oxidoreductase subunit NuoF from Thermoanaerobacter kivui
41% identity, 65% coverage

• Ligands: flavin mononucleotide; iron/sulfur cluster; zinc ion; fe2/s2 (inorganic) cluster; nadp nicotinamide-adenine-dinucleotide phosphate (8a6tB)
• Electron carriers involved in autotrophic and heterotrophic acetogenesis in the thermophilic bacterium Thermoanaerobacter kivui
  Katsyv, Extremophiles : life under extreme conditions 2021
  • “...A). These molecular masses correspond well with the expected sizes for HydA (TKV_c19600, 64kDa), HydB (TKV_c19590, 68kDa) and HydC (TKV_c19580, 18kDa) of T. kivui . Analytical size exclusion chromatography revealed a molecular mass of 348kDa for the purified complex, which is consistent with HydABC being a...”
• A genome-guided analysis of energy conservation in the thermophilic, cytochrome-free acetogenic bacterium Thermoanaerobacter kivui
  Hess, BMC genomics 2014
  • “...identity to the corresponding subunits of M.thermoacetica and A.woodii , respectively. The identities for HydB (TKV_c19590) to the homologous proteins of M.thermoacetica and A.woodii are 54% and 59%, the ones for HydC (TKV_c19600) amount 42% and 47%, respectively. Apart from HydA2 of the HDCR and the...”

Pcar_1634 NADP-reducing hydrogenase chain C from Pelobacter carbinolicus str. DSM 2380
42% identity, 85% coverage

• Degradation of acetaldehyde and its precursors by Pelobacter carbinolicus and P. acetylenicus
  Schmidt, PloS one 2014
  • “...(Pcar_1501, likely responsible for ammonia uptake) and two subunits of a putative hydrogenase (Pcar_1633 and Pcar_1634). To link activity and protein identification, we applied our recently described activity staining method [38] to cytoplasmic fractions of ethanol-grown P. carbinolicus cells (see S3 Fig ., Table S1 )....”

XP_026737816 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Trichoplusia ni
45% identity, 80% coverage

• Stress-induced premature senescence in high five cell cultures: a principal factor in cell-density effects
  Min, Bioresources and bioprocessing 2024
  • “...fold: mitochondrial cytochrome b-c1 complex subunit 6 (QCR6, XP_026740563), NADH dehydrogenase [ubiquinone] flavoprotein 1 (NDUFV1, XP_026737816), NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 (NDUFA6, XP_026734396), NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 (NDUFA12, XP_026742056) (Fig. 5 f). QCR6 is a subunit of the cytochrome...”

FTH_1761 NADH dehydrogenase (ubiquinone) from Francisella tularensis subsp. holarctica OSU18
42% identity, 92% coverage

• Use of magnetic hydrazide-modified polymer microspheres for enrichment of Francisella tularensis glycoproteins
  Horák, Soft matter 2012
  • “...F0 sector subunit a) 30.00/6.22 CM cyt FTH_1760 NADH dehydrogenase (ubiquinone) 87.36/5.09 cyt, MLS cyt FTH_1761 NADH dehydrogenase (ubiquinone) 46.8/5.61 cyt, MLS cyt FTH_1763 NADH dehydrogenase (ubiquinone) 47.59/7.06 cyt, MLS cyt FTH_1824 Conserved hypothetical protein 20.32/6.64 CM TMH FTH_1830 Cell division protein FtsZ 39.8/4.76 cyt, MLS...”
  • “...FTH_1735 H(+)-transporting two-sector ATPase 19.20/6.11 cyt cyt FTH_1760 NADH dehydrogenase (ubiquinone) 87.36/5.09 cyt, MLS cyt FTH_1761 NADH dehydrogenase (ubiquinone) 46.28/5.55 cyt, MLS cyt FTH_1762 NADH dehydrogenase (ubiquinone) 18.17/5.00 cyt cyt FTH_1763 NADH dehydrogenase (ubiquinone) 47.59/7.06 cyt, MLS cyt FTH_1764 NADH-quinone oxidoreductase subunit C 25.20/6.95 cyt, MLS...”
• Multimethodological approach to identification of glycoproteins from the proteome of Francisella tularensis, an intracellular microorganism
  Balonova, Journal of proteome research 2010
  • “...- CM - 26,27,28 FTH_1167 SNA 69.4 4.88 3 ERN 417 TT PP - 32 FTH_1761 SNA 46.8 5.61 2 - cyt - 33 FTH_0516 MAA 30.8 6.85 0 - cyt - 34 FTH_1021 MAA 29.6 9.04 4 - OM SPII 35 FTH_1721 MAA PNA 27.2...”
  • “...DEN 68 IT cyt - FTH_0257 ConA, DSA, SBA 16.78 10.72 1 - ? - FTH_1761 ConA, DSA, SBA 46.28 5.55 2 - cyt - FTH_0604 ConA, DSA, SBA 32.98 6.51 4 - ? - FTH_1855 ConA, DSA, SBA 33.82 5.74 2 - ? SPI FTH_0172...”

DMR38_03370 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region domain-containing protein from Clostridium sp. AWRP
38% identity, 70% coverage

• Metabolic changes of the acetogen Clostridium sp. AWRP through adaptation to acetate challenge
  Kwon, Frontiers in microbiology 2022
  • “...2 to formate ( Wang et al., 2013 ; Mock et al., 2015 ): hytB (DMR38_03370; encoding flavin mononucleotide protein), hytD (DMR38_03375; ironsulfur protein), and hytE1 (DMR38_03380; ironsulfur protein), all of which are likely to be involved in electron transfer during enzyme reaction. The mutation in...”
  • “...Locus tag Annotation Mutation Amino acid change Predicted domain in which the mutation is located DMR38_03370 NADP + -dependent electron-bifurcating hydrogenase subunit B G1261T V421F None DMR38_03375 NADP + -dependent electron-bifurcating hydrogenase subunit D C422T T141I [4Fe-4S] ferredoxin-type, ironsulfur binding domain (IPR017896) DMR38_03380 NADP + -dependent...”

FGSG_09250 NADH dehydrogenase flavoprotein 1 from Fusarium graminearum PH-1
42% identity, 80% coverage

• Edeine B₁ produced by Brevibacillus brevis reduces the virulence of a plant pathogenic fungus by inhibiting mitochondrial respiration
  Kim, mBio 2024
  • “...differentially expressed in response to EB 1 ( Fig. 5C ). In particular, two genes FGSG_09250 encoding NADH dehydrogenase flavoprotein 1 in mitochondrial respiratory chain complex I and FGSG_07074 encoding mitochondrial pyruvate carrier 1 were assigned to the oxidative phosphorylation pathway (fgr00190) and mitochondrial biogenesis (fgr03029)...”

Gmet_2080 Respiratory-chain NADH dehydrogenase domain, 51 kDa subunit from Geobacter metallireducens GS-15
Q39TW5 Benzoyl-CoA reductase electron transfer protein, putative from Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15)
40% identity, 67% coverage

• Detrimental impact of the Geobacter metallireducens type VI secretion system on direct interspecies electron transfer
  Smith, Microbiology spectrum 2023
  • “...genes with the greatest increase in abundance of transcripts in DIET- versus QUIET-grown cells were Gmet_2080 and Gmet_2078, annotated as T6SS needle tube protein TssD and T6SS protein ImpB. Transcripts for other T6SS proteins were also much more abundant in DIET- versus QUIET-grown G. metallireducens (...”
• Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site
  Butler, BMC genomics 2007
  • “...3-hydroxyacyl-CoA dehydrogenase Gmet_2074 50.7 bamN^ Thiolase Gmet_2075 19.1 bamM* Acyl-CoA dehydrogenase Gmet_2077 21.8 bamK N-acetyltransferase Gmet_2080 36.1 bamH^ NAD(P) diaphorase, HoxF Gmet_2081 27.5 bamG NAD(P) diaphorase, HoxU Gmet_2083 27.3 bamF^ hydrogenase, delta subunit; HTH mo Gmet_2084 20.6 bamE* 4Fe-4S binding, FAD binding Gmet_2085 27 bamD^ 4Fe-4S...”
• Adaptation of Carbon Source Utilization Patterns of Geobacter metallireducens During Sessile Growth
  Marozava, Frontiers in microbiology 2020
  • “...4.2 3.1 Q39TP5 Cyclohexa-1,5-dienecarbonyl-CoA hydratase 2.0 1.3 1.0 Q39TV8 Benzoyl-CoA reductase, putative 1.6 1.4 1.4 Q39TW5 Benzoyl-CoA reductase electron transfer protein 1.5 1.9 2.0 Q39TW0 Iron-sulfur cluster-binding oxidoreductase 1.5 1.5 1.6 Q39TY0 Electron transfer flavoprotein-associated cytochrome b 1.1 2.6 2.5 Q39TQ2 Benzoatecoenzyme A ligase 1.1 9.1...”

PXO_RS16440 NADH-quinone oxidoreductase subunit NuoF from Xanthomonas oryzae pv. oryzae PXO99A
43% identity, 93% coverage

• Transcriptional responses of Xanthomonas oryzae pv. oryzae to type III secretion system inhibitor ortho-coumaric acid
  Fan, BMC microbiology 2019
  • “...PXO_RS16455 NADH-quinone oxidoreductase subunit C PXO_RS16450 NADH-quinone oxidoreductase subunit D PXO_RS16445 NADH-quinone oxidoreductase subunit NuoE PXO_RS16440 NADH-quinone oxidoreductase subunit F PXO_RS16435 NADH dehydrogenase (quinone) subunit G PXO_RS16430 NADH-quinone oxidoreductase subunit H PXO_RS16425 NADH-quinone oxidoreductase subunit I V PXO_RS10645 succinate dehydrogenase, cytochrome b556 subunit PXO_RS10650 succinate dehydrogenase,...”

Atu1275 NADH ubiquinone oxidoreductase chain F from Agrobacterium tumefaciens str. C58 (Cereon)
A9CJA6 NADH-quinone oxidoreductase subunit F from Agrobacterium fabrum (strain C58 / ATCC 33970)
42% identity, 88% coverage

• Agrobacterium tumefaciens Type IV and Type VI Secretion Systems Reside in Detergent-Resistant Membranes
  Czolkoss, Frontiers in microbiology 2021
  • “...chain G 0.17 0.002 NuoE atu1274 A9CJA7 NADH ubiquinone oxidoreductase chain E 0.13 0.011 NuoF atu1275 A9CJA6 NADH ubiquinone oxidoreductase chain F DSM only 0.008 FtsA atu2087 P0A331 Cell division protein FtsA DSM only 0.035 DctP atu5268 A9CLG5 ABC transporter, substrate binding protein 0.33 0.031 Atu2281...”
• Agrobacterium tumefaciens Type IV and Type VI Secretion Systems Reside in Detergent-Resistant Membranes
  Czolkoss, Frontiers in microbiology 2021
  • “...G 0.17 0.002 NuoE atu1274 A9CJA7 NADH ubiquinone oxidoreductase chain E 0.13 0.011 NuoF atu1275 A9CJA6 NADH ubiquinone oxidoreductase chain F DSM only 0.008 FtsA atu2087 P0A331 Cell division protein FtsA DSM only 0.035 DctP atu5268 A9CLG5 ABC transporter, substrate binding protein 0.33 0.031 Atu2281 atu2281...”

7zm7B / G0SA46 Cryoem structure of mitochondrial complex i from chaetomium thermophilum (inhibited by ddm) (see paper)
42% identity, 85% coverage

• Ligands: iron/sulfur cluster; flavin mononucleotide (7zm7B)

ACU12_RS13380 NADH-quinone oxidoreductase subunit NuoF from Xanthomonas oryzae pv. oryzicola
43% identity, 93% coverage

• Antagonistic transcriptome profile reveals potential mechanisms of action on Xanthomonas oryzae pv. oryzicola by the cell-free supernatants of Bacillus velezensis 504, a versatile plant probiotic bacterium
  Zhou, Frontiers in cellular and infection microbiology 2023
  • “...24 hpi ( Figure4D ). The expression pattern of ctaD ( ACU12_RS18730 ), nuoF ( ACU12_RS13380 ), and nuoL ( ACU12_RS13350 ) by qRT-PCR analysis was coincident with the RNA-Seq data ( Figures5EG ). After B. velezensis 504 CFSs treatment, DEGs were mainly enriched in flagellar...”

nuoF / CAA71232.1 complex I 51kDa subunit from Rhodobacter capsulatus (see paper)
O07948 NADH-quinone oxidoreductase subunit F from Rhodobacter capsulatus
42% identity, 87% coverage

• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “..., Swiss-Prot: Q98KR0 , Rhizobium meliloti Swiss-Prot: P56912 , Swiss-Prot: P56913 , Rhodobacter capsulatus Swiss-Prot: O07948 , Rhodococcus opacus Swiss-Prot: P72304 , Rhodoferax ferrireducens T118 REFSEQ:YP_525088.1, Rickettsia prowazekii Swiss-Prot: Q9ZE33 , Solanum tuberosum Swiss-Prot: Q43840 , Streptomyces avermitilis MA-4680 REFSEQ:NP_823011.1, Synechococcus elongatus PCC 6301 EMBL: CAA73873.1...”

LOC100282384 NADH-ubiquinone oxidoreductase 51 kDa subunit from Zea mays
B6T6U3 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Zea mays
43% identity, 77% coverage

• Comparative proteomics of chloroplasts envelopes from bundle sheath and mesophyll chloroplasts reveals novel membrane proteins with a possible role in c4-related metabolite fluxes and development
  Manandhar-Shrestha, Frontiers in plant science 2013
  • “...eight proteins of unknown function were also found. Two of the proteins (putative NADH dehydrogenase LOC100282384, Hyp 3) were not found in the mesophyll envelope samples. Hyp3, however, was only identified in one of the samples, suggesting it is either in very low abundance or a...”
• Qualitative and quantitative evaluation of thylakoid complexes separated by Blue Native PAGE
  Sárvári, Plant methods 2022
  • “...17,250 1834 a A0A1D6NDN3 Z.m FS7 13,933 3128 a,x A0A3L6G2J2 Z.m FV1 55,160 6878 a B6T6U3 Z.m FV1 55,146 1864 x B4FPX5 Z.m FV2 35,177 1867 a Q6R9J9 Z.m nad2 53,634 1035 a Q6R9H4 Z.m nad5 74,440 2815 a Q5K097 Z.m nad9 22,916 12347 a,x K7USN8...”

TC 3.D.1.6.2 / P24917 51 (NuoF), component of The fungal H+ translocating NADH dehydrogenase (NDH) complex (38 subunits; 35 included here) from Neurospora crassa (see 3 papers)
NCU04044 NADH2 dehydrogenase flavoprotein 1 from Neurospora crassa OR74A
42% identity, 79% coverage

• substrates: H+
  tcdb comment: The high resolution (3.6 - 3.9 Å) structure of the mitochondrial Yarrowia lipolytica enzyme, showing all central subunits that execute the bioenergetic functions, has been solved (see discussion for TC# 3.A.1 and Zickermann et al. 2015)
• RNAseq and targeted metabolomics implicate RIC8 in regulation of energy homeostasis, amino acid compartmentation, and asexual development in <i>Neurospora crassa</i>
  Quinn, mBio 2024
  • “...NCU05299 nuo29.9 1.0 1.4 2.9 NCU04074 nuo30.4 1.0 1.4 2.3 NCU02534 nuo49 1.0 1.5 2.4 NCU04044 nuo51 1.0 1.2 2.0 NCU00160 nuo6.6 1.0 1.5 2.4 NCU01765 nuo78 1.0 1.3 2.3 NCU00670 nuo9.5 1.0 1.7 2.8 NCU04781 nuo9.8 1.0 1.5 2.6 Complex IV NCU01808 cyc-1 1.0 1.4...”
• Characterization of apoptosis-related oxidoreductases from Neurospora crassa
  Carneiro, PloS one 2012
  • “...R- CCTCGCCCGATGACACGCCGTTTG amid-2 NCU12058 F- GAGCGACTGAGCGAGATCATCAAG R- CCCTCCACCACACTCCCATCC aif NCU05850 F- TCAACACCACGACGGGCGATATTG R- CCACCACCGACAACAACCACTCTG nuo-51 NCU04044 F- TGAACGCCACCGCTGCCTACATC R- GCTGGTCTCCTCGCCGCACAC actin NCU04173 F- GGCATCACACCTTCTACAACGAG R- ATGTCAACACGGGCAATGGC F-forward; R-reverse. 10.1371/journal.pone.0034270.t003 Table 3 Type II NAD(P)H:quinone oxidoreductases and AIF-like oxidoreductases used in the dendogram of Fig. 1B ....”
• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “..., Neisseria gonorrhoeae FA 1090 REFSEQ:YP_208779.1, Neisseria meningitidis Z2491 EMBL: CAB83334.1 , Neurospora crassa Swiss-Prot: P24917 , Nitrosococcus oceani ATCC 19707 GenBank: ABA59013.1 , Nitrosomonas europaea ATCC 19718 EMBL: CAD85683.1 , Nitrosomonas eutropha C71 REFSEQ:ZP_00669832.1, Nitrosospira multiformis ATCC 25196 REFSEQ:YP_411791.1, REFSEQ:YP_412360.1, Nyctotherus ovalis BA GenBank: AY608627...”

XAC2699 NADH-ubiquinone oxidoreductase NQO1 subunit from Xanthomonas axonopodis pv. citri str. 306
42% identity, 95% coverage

• Insights into xanthomonas axonopodis pv. citri biofilm through proteomics
  Zimaro, BMC microbiology 2013
  • “...45.0/6.0 47/43% 1.9 422 NADH-ubiquinone oxidoreductase 40 Q3BRN4_XANC5 X . c . pv . vesicatoria XAC2699 48.8/6.32 33.0/4.4 8/18% 3.9 11 Transcription 11.04 RNA processing 153 Polynucleotide phosphorylase 137 PNP_XANAC X . a . pv . citri XAC2683 75.5/5.47 28.0/5.9 6/3% 1.5 12 Protein synthesis 12.01...”
  • “...generation, such as ATP-synthase (XAC3649, spot 76), phosphoglycerate kinase (XAC3347, spot 442) and NADH-ubiquinone oxidoreductase (XAC2699, spot 422). Phosphoglycerate kinase enzyme is involved in later reactions of the glycolytic pathway; therefore its inhibition should lead to an increased pool of glycolytic intermediates in the early steps...”

U3BG69 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Callithrix jacchus
45% identity, 82% coverage

• PrimPol is required for replication reinitiation after mtDNA damage.
  Torregrosa-Muñumer, Proceedings of the National Academy of Sciences of the United States of America 2017

8b9zF / Q9VMI3 Drosophila melanogaster complex i in the active state (dm1) (see paper)
43% identity, 85% coverage

• Ligands: flavin mononucleotide; iron/sulfur cluster (8b9zF)

KUL73_08085 NADH-quinone oxidoreductase subunit NuoF from Rhodospirillum rubrum
44% identity, 86% coverage

• Cultivation driven transcriptomic changes in the wild-type and mutant strains of Rhodospirillum rubrum
  Jureckova, Computational and structural biotechnology journal 2024
  • “...oxidoreductase subunit C KUL73_08070 -0.33 3.31E-02 0.54 2.38E-04 -1.08 2.95E-13 nuoF NADH-quinone oxidoreductase subunit NuoF KUL73_08085 0.66 6.42E-04 2.15 5.34E-31 1.51 3.40E-15 NADH-quinone oxidoreductase subunit J KUL73_08105 -0.84 7.79E-03 1.00 1.18E-03 3.49 4.78E-25 nuoL NADH-quinone oxidoreductase subunit L KUL73_08115 -1.36 2.39E-09 0.61 8.42E-03 1.98 2.17E-17 NADH-quinone...”
  • “...NADP-dependent isocitrate dehydrogenase KUL73_01875 -2.10 3.10E-50 -1.24 1.05E-18 -1.75 1.80E-28 nuoF NADH-quinone oxidoreductase subunit NuoF KUL73_08085 0.41 3.86E-02 2.17 2.66E-31 0.45 2.96E-02 Finally, GO enrichment analysis between KO AY and WT AY identified 21 BP and 6 MF enriched terms. The main BP terms belonged to...”

TC 3.D.1.5.1 / Q74GA3 NuoF aka GSU0343, component of Proton-translocating NADH dehydrogenase I from Geobacter sulfurreducens (see paper)
GSU0343 NADH dehydrogenase I, F subunit from Geobacter sulfurreducens PCA
42% identity, 69% coverage

• substrates: H+
• Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes
  Butler, BMC genomics 2010
  • “...protein 39995271 GSU0160 0.91 dihydrodipicolinate reductase 39995450 GSU0341 0.91 NADH dehydrogenase I, D subunit 39995452 GSU0343 0.91 NADH dehydrogenase I, F subunit 39998388 GSU3299 0.91 carboxyl transferase domain protein 39996631 GSU1531 0.90 phosphoribosyl-AMP cyclohydrolase 39996591 GSU1491 0.90 type IV pilus biogenesis protein PilB 39997632 GSU2537 0.90...”

hytB / S5YUD3 hydrogenase (NADP⁺,ferredoxin) β subunit from Clostridium autoethanogenum DSM 10061 (see paper)
CAETHG_2795, CLAU_RS13685 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region domain-containing protein from Clostridium autoethanogenum DSM 10061
38% identity, 70% coverage

• Clostridium autoethanogenum alters cofactor synthesis, redox metabolism, and lysine-acetylation in response to elevated H₂:CO feedstock ratios for enhancing carbon capture efficiency
  Davin, Biotechnology for biofuels and bioproducts 2024
  • “...transcriptional repressor Rex 0.625 0.04 CAETHG_2794 Electron-bifurcating FeFe-hydrogenase dependent on TPN subunit C 0.468 0.13 CAETHG_2795 Electron-bifurcating FeFe-hydrogenase dependent on TPN subunit B 0.629 0.07 CAETHG_2796 4Fe-4S ferredoxin, iron-sulfur binding domain-containing protein 0.002* 0.65 CAETHG_2797 4Fe-4S ferredoxin, iron-sulfur binding domain-containing protein 0.005* 0.92 CAETHG_2798 Hydrogenase, Fe-only...”
• Genome-Scale Mining of Acetogens of the Genus Clostridium Unveils Distinctive Traits in [FeFe]- and [NiFe]-Hydrogenase Content and Maturation
  Di, Microbiology spectrum 2022
  • “...3,639.00 2,423.00 1,494.00 2,004.00 CLAU_RS13680 CAETHG_2794 2,976.28 3,669.1405 4,436.60 312.00 2,558.00 1,604.00 853.00 1,214.00 CLAU_RS13685 CAETHG_2795 4,073.53 3,117.7735 3,826.21 312.00 1,743.00 941.00 520.00 845.00 CLAU_RS13690 CAETHG_2796 5,372.79 3,721.7915 4,575.29 312.00 2,559.00 1,405.00 798.00 1,438.00 CLAU_RS13695 CAETHG_2797 7,373.13 4,108.917 5,225.86 405.00 2,610.00 1,612.00 968.00 1,383.00 CLAU_RS13705 CAETHG_2799...”
  • “...and ferredoxin-dependent hydrogenase HytABCDE 1 E 2 . CLAU_RS13700 encodes the catalytic subunit HytA, while CLAU_RS13685 encodes the iron-sulfur flavoprotein HytB, which was predicted to harbor the site binding the redox cofactor. CLAU_RS13680, CLAU_RS13690, CLAU_RS13695, and CLAU_RS13705 encode the Fe-S subunits HytC, HytD, HytE 1 ,...”
  • “...405.00 3,639.00 2,423.00 1,494.00 2,004.00 CLAU_RS13680 CAETHG_2794 2,976.28 3,669.1405 4,436.60 312.00 2,558.00 1,604.00 853.00 1,214.00 CLAU_RS13685 CAETHG_2795 4,073.53 3,117.7735 3,826.21 312.00 1,743.00 941.00 520.00 845.00 CLAU_RS13690 CAETHG_2796 5,372.79 3,721.7915 4,575.29 312.00 2,559.00 1,405.00 798.00 1,438.00 CLAU_RS13695 CAETHG_2797 7,373.13 4,108.917 5,225.86 405.00 2,610.00 1,612.00 968.00 1,383.00 CLAU_RS13705...”

W5PUX0 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Ovis aries
43% identity, 87% coverage

• Protein profiles of enzymatically isolated rumen epithelium in sheep fed a fibrous diet
  Bond, Journal of animal science and biotechnology 2019
  • “...30.01 6 2 W5PB27 ENSOARP00000007638 NDUFS3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 140.41 32 9 W5PUX0 ENSOARP00000014252 NDUFV1 NADH dehydrogenase [ubiquinone] flavoprotein 1 91.04 14 8 W5NRY1 ENSOARP00000000921 NDUFV2 NADH-ubiquinone oxidoreductase core subunit V2 113.11 27 6 W5QAH8 ENSOARP00000019723 NDUFA2 NADH dehydrogenase [ubiquinone] 1 alpha subunit...”
• Purification of Ovine Respiratory Complex I Results in a Highly Active and Stable Preparation
  Letts, The Journal of biological chemistry 2016
  • “...68.0 81.6 79.1 69.1 75.4 74.4 87.8 65.6 Uniprot no. W5PUX0 (78) Uniprot no. W5NRY1 (78) Uniprot no. W5QB34 (78) Uniprot no. W5PJ73 (78) Uniprot no. W5PB27 (78)...”

LOC408367 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Apis mellifera
42% identity, 82% coverage

• Support for the reproductive ground plan hypothesis of social evolution and major QTL for ovary traits of Africanized worker honey bees (Apis mellifera L.)
  Graham, BMC evolutionary biology 2011
  • “...factor related LOC408354, which is differentially expressed in female larval development [ 46 ] and LOC408367, the ortholog of a NADH dehydrogenase and three unidentified transcripts that all differ in expression between worker and queen developing ovaries (Klaus Hartfelder, pers. commun.). We consider the ortholog of...”

Swol_1018 NADH dehydrogenase (quinone) from Syntrophomonas wolfei subsp. wolfei str. Goettingen
SWOL_RS05170 NADH-quinone oxidoreductase subunit NuoF from Syntrophomonas wolfei subsp. wolfei str. Goettingen G311
38% identity, 93% coverage

• A proteomic view at the biochemistry of syntrophic butyrate oxidation in Syntrophomonas wolfei
  Schmidt, PloS one 2013
  • “...from butyrate-grown S. wolfei cells which was identified to derive from gene (IMG locus tag) Swol_1018 annotated as NADH-binding subunit gene of the HYD-1 hydrogenase complex (see above), i.e., located in the Swol_1017-19 gene cluster. Interestingly, the other two components of the HYD-1 complex, Swol_1017 and...”
  • “...and E16 ( Fig. 2AB ). The previously identified NADH dehydrogenase (NDH) subunit encoded by Swol_1018 [14] was represented by spot E5, and is inferred to receive electrons via NADH from the 3-hydroxybutyryl-CoA dehydrogenase for further transfer to the hydrogenase/formate dehydrogenase subunits (see Discussion ). For...”
• Involvement of NADH:acceptor oxidoreductase and butyryl coenzyme A dehydrogenase in reversed electron transport during syntrophic butyrate oxidation by Syntrophomonas wolfei
  Müller, Journal of bacteriology 2009
  • “...A3 in Fig. 3C) was attributed to predicted gene Swol_1018 (derived 44.4 kDa; see Table 4), which was annotated as the NADH-binding subunit gene of a [FeFe]...”
  • “...16,181 68,811 68,798 82,333 Swol_0785 Swol_0786 Swol_1017 Swol_1018 Swol_0768 Swol_2479 Swol_0316 Swol_0783 Swol_1019 Swol_1933 Swol_2052 Swol_0698 84 60 70 85...”
• Syntrophomonas wolfei Uses an NADH-Dependent, Ferredoxin-Independent [FeFe]-Hydrogenase To Reoxidize NADH
  Losey, Applied and environmental microbiology 2017
  • “...for NADH reoxidation. The S. wolfei genes for the multimeric [FeFe]-hydrogenase ( hyd1ABC ; SWOL_RS05165, SWOL_RS05170, SWOL_RS05175) and [FeFe]-hydrogenase maturation proteins (SWOL_RS05180, SWOL_RS05190, SWOL_RS01625) were coexpressed in Escherichia coli , and the recombinant Hyd1ABC was purified and characterized. The purified recombinant Hyd1ABC was a heterotrimer with...”
  • “...the S. wolfei genome identified a multimeric [FeFe]-hydrogenase encoded by genes ( hyd1ABC ; SWOL_RS05165, SWOL_RS05170, SWOL_RS05175) that shared a sequence identity similar to those of confurcating [FeFe]-hydrogenases ( 4 , 10 , 11 ), a NADPH-linked [FeFe]-hydrogenase ( 12 ), and NADH-dependent formate dehydrogenases (...”

NDUV1_BOVIN / P25708 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial; NDUFV1; Complex I-51kD; CI-51kD; NADH dehydrogenase flavoprotein 1; NADH-ubiquinone oxidoreductase 51 kDa subunit; EC 7.1.1.2 from Bos taurus (Bovine) (see 4 papers)
TC 3.D.1.6.1 / P25708 51 (NuoF), component of The vertebrate H+-translocating NADH dehydrogenase (NDH) complex (45 subunits) from Bos taurus (Bovine) (see 2 papers)
44% identity, 86% coverage

• function: Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. Part of the peripheral arm of the enzyme, where the electrons from NADH are accepted by flavin mononucleotide (FMN) and then passed along a chain of iron-sulfur clusters by electron tunnelling to the final acceptor ubiquinone. Contains FMN, which is the initial electron acceptor.
  catalytic activity: a ubiquinone + NADH + 5 H(+)(in) = a ubiquinol + NAD(+) + 4 H(+)(out) (RHEA:29091)
  cofactor: FMN (Binds 1 FMN.)
  cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster.)
  subunit: Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits (PubMed:10852722, PubMed:18721790). This is a component of the flavoprotein-sulfur (FP) fragment of the enzyme (PubMed:10852722, PubMed:18721790). Interacts with RAB5IF (By similarity).
• substrates: H+
  tcdb comment: The 3-d structure of the 44 subunit complex (14 core subunits present in bacteria, plus 30 additional subunits) with a molecular weight of 1 MDa, has been solved at 5 Å resolution by single particle electron cryo-microscopy (Vinothkumar et al. 2014).The core subunits contain eight iron-sulphur clusters and 60 transmembrane helices. The structures of many of the supernumerary subunits were determined or modeled. The structure provided insight into the roles of the supernumerary subunits in regulation, assembly and homeostasis. One such subunit, GRIM-19 or NDUFA13, (Q9P0J0 of the human homologue) is essential for membrane potential formation and NADH assembly (Lu and Cao 2008). Stroud et al. 2016 showed that 25 of the 31 accessory subunits in the 45 subunit human NADH dehydrogenase complex are required for assembly of a functional complex, and 1 subunit is essential for cell viability. Quantitative proteomic analysis revealed that loss of each subunit affects the stability of other subunits residing in the same structural module (Stroud et al. 2016). Leber's hereditary optic neuropathy (LHON) in humans is associated with combinations of individually non-pathogenic missense mitochondrial DNA (mtDNA) variants, affecting the MT-ND4, MT-ND4L and MT-ND6 subunit genes of Complex I (Caporali et al. 2018)
• Integrated Left Ventricular Global Transcriptome and Proteome Profiling in Human End-Stage Dilated Cardiomyopathy.
  Colak, PloS one 2016
  • “...0.023 Q9LKR3 4.010 0.035 MYH3 116176 -2.067 0.021 P13541 2.072 0.002 NDUFV1 183186 1.994 0.038 P25708 3.120 0.011 PDHB 171509 1.922 0.027 P11966 2.237 0.000 SLC25A11 110914 9.392 0.045 P22292 2.113 0.001 SLC25A13 * 121335 -2.053 0.031 Q9QXX4 3.263 0.021 TPP1 158867 4.918 0.038 O14773 -1.563...”
• Characterization of clinically identified mutations in NDUFV1, the flavin-binding subunit of respiratory complex I, using a yeast model system
  Varghese, Human molecular genetics 2015
  • “..., Bos taurus and Y. lipolytica . The accession codes are P49821 ( Hs ), P25708 ( Bt ) and Q9UUU2 ( Yl ), and the sequences shown include the mitochondrial target peptides (gray) that are removed to form the mature proteins. The sequences are colored...”
• Adaptation of phenylalanine and tyrosine catabolic pathway to hibernation in bats.
  Pan, PloS one 2013
  • “...212 8 99.00 16.14 1.11* 1.19 41 Q5EA20 4-hydroxyphenylpyruvate dioxygenase 44832.04/6.25 26 48.22 1.47** 42 P25708 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial 48499.21/7.08 38 40.30 - O09173 Homogentisate 1,2-dioxygenase g 49959.92/6.85 9 11.91 - 43 O09173 Homogentisate 1,2-dioxygenase g 49959.92/6.85 19 30.34 3.35** 44 Q8CI38 Homogentisate...”

SYNPCC7002_A0196 hydrogenase large diaphorase subunit F from Synechococcus sp. PCC 7002
41% identity, 75% coverage

• Transcription Profiling of the Model Cyanobacterium Synechococcus sp. Strain PCC 7002 by Next-Gen (SOLiD™) Sequencing of cDNA
  Ludwig, Frontiers in microbiology 2011
  • “...0.72 Short-chain alcohol dehydrogenase family SYNPCC7002_A0195 0.30 6.62 16.39 2.47 1.24 hoxE Hydrogenase subunit E SYNPCC7002_A0196 0.26 7.23 4.78 0.66 1.06 hoxF Hydrogenase large diaphorase subunit F SYNPCC7002_A0197 0.33 4.88 2.15 0.44 0.76 hoxU Hydrogenase small diaphorase subunit U SYNPCC7002_A0198 0.37 4.32 0.99 0.23 1.05 hoxY...”

Cthe_0341 NADH dehydrogenase (quinone) from Clostridium thermocellum ATCC 27405
40% identity, 69% coverage

• Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production
  Roberts, BMC systems biology 2010
  • “...Q2S6E8 1.00E-22 6.3.4.1 GMP synthase Cthe_0375 GMP synthase, large subunit A2C5P2 4.00E-176 1.2.1.2 formate dehydrogenase Cthe_0341 NADH dehydrogenase (quinone) B5IPC7 6.00E-126 5.3.3.2 isopentenyl-diphosphate Delta-isomerase Cthe_1022 Glycerol-3-phosphate dehydrogenase A8VXT5 2.00E-94 2.5.1.29 farnesyltranstransferase Cthe_0831 Polyprenyl synthetase B2J443 4.00E-69 2.5.1.33 trans-pentaprenyltranstransferase Cthe_0564 Trans-hexaprenyltranstransferase Q6KZR8 3.00E-25 3.2.1.108 lactase Cthe_0212 Beta-glucosidase...”

B9HTA1 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Populus trichocarpa
43% identity, 80% coverage

• Proteomics of Homeobox7 Enhanced Salt Tolerance in Mesembryanthemum crystallinum.
  Zhang, International journal of molecular sciences 2021
  • “...cells [ 55 ]. Surprisingly, several proteins that were related to oxidative phosphorylation like AOA078JRB4, B9HTA1, and I1J2V1 were identified in OE plants and the abundances of these proteins were increased compared to WT. This indicates McHB7 might function as a stress response TF induced by...”

DET0146 [Fe] hydrogenase, HymB subunit, putative from Dehalococcoides ethenogenes 195
40% identity, 93% coverage

• Effects of Sulfate Reduction on Trichloroethene Dechlorination by Dehalococcoides-Containing Microbial Communities
  Mao, Applied and environmental microbiology 2017
  • “...However, the downregulated genes include Hym [Fe]-hydrogenase (DET0146 to DET0148), ATP synthase (DET0558 to DET0565), and genes related to biosynthesis (see...”
• Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation
  Lee, Applied and environmental microbiology 2012
  • “...38.1 1.5 ND ND ND Downregulated DET0017 DET0022 DET0146 DET0178 DET0185 DET0341 DET0343 DET0345 DET0374 DET0381 DET0421 DET0528 DET0545 DET0614 DET0624 DET0636...”

LOC107436591 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Parasteatoda tepidariorum
44% identity, 79% coverage

• Dataset on gene expressions affected by simultaneous knockdown of Hedgehog and Dpp signaling components in embryos of the spider Parasteatoda tepidariorum
  Oda, Data in brief 2020
  • “...0.561 S7_d1_18_F06 2 10933 0.545 S7_d1_19_D06 2 3648 0.576 S7_d1_20_H05* IABY01019901 2 5931 0.583 S7_d1_21_H03 LOC107436591 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial 2 1902 0.597 S7_d1_29_B03 LOC107437456 cytochrome P450 302a1, mitochondrial 2 6935 0.480 S7_d1_30_G04 2 11999 0.528 S7_d1_33_A05 LOC107437124 lipoyltransferase 1, mitochondrial-like 2 9564 0.540...”

PITG_06815 NADH dehydrogenase flavoprotein 1, mitochondrial precursor from Phytophthora infestans T30-4
43% identity, 79% coverage

• Switchable Nitroproteome States of Phytophthora infestans Biology and Pathobiology
  Izbiańska, Frontiers in microbiology 2019
  • “...Putative uncharacterized protein 137 PITG_12490 Signal transduction S10 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial 60 PITG_06815 Pathogenesis S11 Glyceraldehyde-3-phosphate dehydrogenase 95 PITG_01938 Carbohydrate metabolism / energy metabolism S12 Putative uncharacterized protein Actin-like protein 152 78 PITG_06853 PITG_15078 Endonuclease activity / protein metabolism Cytoskeleton organization S13 Xanthine...”
  • “...proteins seems to be a promising signpost for further analysis. NADH dehydrogenase [ubiquinone] flavoprotein 1 (PITG_06815) was one of the pathogenicity-related proteins that were more abundant in both isolates growing in planta . Moreover, another putative pathogenicity related protein included actin like protein (PITG_15078), playing an...”
• Quantitative proteomics links metabolic pathways to specific developmental stages of the plant-pathogenic oomycete Phytophthora capsici
  Pang, Molecular plant pathology 2017 (secret)

CtherDRAFT_2978 NADH dehydrogenase (quinone) from Clostridium thermocellum DSM 4150
40% identity, 78% coverage

• Linking genome content to biofuel production yields: a meta-analysis of major catabolic pathways among select H2 and ethanol-producing bacteria
  Carere, BMC microbiology 2012
  • “...D M2e C. thermocellum DSM 4150 CtherDRAFT_2162-CtherDRAFT_2173 CtherDRAFT_1101-CtherDRAFT_1103 A8 TR(M3) CtherDRAFT_1098-CtherDRAFT_1099 CD(M2f) Yes B CtherDRAFT_0369-CtherDRAFT_0375 CtherDRAFT_2978 A1 TR(M3) Ta. pseudethanolicus 39E Teth39_0221 CD(M2f) Teth39_2119-Teth39_2124 Teth39_1456- Teth39_1458 A1 TR(M3) Teth39_1463 D M2e G. thermoglucosidasius C56-YS93 B. cereus ATCC 14579 A Group D M2e hydrogenases are poorly characterized...”

8oh5B / A0A0U1KYM9 Cryo-em structure of the electron bifurcating transhydrogenase stnabc complex from sporomusa ovata (state 2) (see paper)
42% identity, 71% coverage

• Ligands: zinc ion; fe2/s2 (inorganic) cluster; flavin mononucleotide; iron/sulfur cluster; nicotinamide-adenine-dinucleotide (8oh5B)

Dtur_0559 NADH dehydrogenase (quinone) from Dictyoglomus turgidum DSM 6724
40% identity, 64% coverage

• The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor
  Brumm, Frontiers in microbiology 2016
  • “...and Dtur_1717). The proton gradient needed for ATP generation is produced by NADH oxidoreductase (Dtur_0558; Dtur_0559; Dtur_0916; Dtur_0919, and Dtur_1091), and succinate dehydrogenase (Dtur_0445). ATP is generated by proton translocation via an F0F1-type ATP synthase (Dtur_129 through Dtur_135). D . turgidum also possesses a V-type ATP...”

hydB / Q8RBC9 NADH-dependent hydrogenase β subunit (EC 1.12.1.2) from Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (see 2 papers)
TTE0893 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit from Thermoanaerobacter tengcongensis MB4
43% identity, 68% coverage

• Involvement of NADH:acceptor oxidoreductase and butyryl coenzyme A dehydrogenase in reversed electron transport during syntrophic butyrate oxidation by Syntrophomonas wolfei
  Müller, Journal of bacteriology 2009
  • “...components, e.g., HydB in Thermoanaerobacter tengcongensis (33) (TTE0893; 55%), HndC in Desulfovibrio fructosovorans (7) (U07229; 50%), and HydB in Thermotoga...”

Q43840 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Solanum tuberosum
42% identity, 79% coverage

• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “...Swiss-Prot: P72304 , Rhodoferax ferrireducens T118 REFSEQ:YP_525088.1, Rickettsia prowazekii Swiss-Prot: Q9ZE33 , Solanum tuberosum Swiss-Prot: Q43840 , Streptomyces avermitilis MA-4680 REFSEQ:NP_823011.1, Synechococcus elongatus PCC 6301 EMBL: CAA73873.1 , Syntrophus aciditrophicus SB REFSEQ:YP_461127.1, Tetrahymena thermophila SB210 GenBank: EAR96899.1 , Thermococcus kodakarensis KOD1 DDBJ: BAD85803.1 , Thermotoga maritima...”

7v2cA / A0A4X1SZP7 Active state complex i from q10 dataset (see paper)
43% identity, 89% coverage

• Ligands: iron/sulfur cluster; flavin mononucleotide (7v2cA)

XP_003452502 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Oreochromis niloticus
44% identity, 80% coverage

• Plasticity of gene expression according to salinity in the testis of broodstock and F1 black-chinned tilapia, Sarotherodon melanotheron heudelotii
  Avarre, PeerJ 2014
  • “...512 0 0 Reference genes R1 291 20 PREDICTED: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial-like XP_003452502 5.14723E58 8 R2 299 20 PREDICTED: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial-like XP_004571622 7.27748E52 6 R3 265 20 PREDICTED: tubulin beta-4B chain XP_004005609 1.57111E59 21 R4 323...”

Q98KR0 NADH-quinone oxidoreductase subunit F from Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
43% identity, 87% coverage

• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin.
  Boxma, BMC evolutionary biology 2007
  • “...Ralstonia solanacearum EMBL: CAD15764.1 , Ralstonia solanacearum UW551 REFSEQ:ZP_00943355.1, Rhizobium loti Swiss-Prot: Q98BW8 , Swiss-Prot: Q98KR0 , Rhizobium meliloti Swiss-Prot: P56912 , Swiss-Prot: P56913 , Rhodobacter capsulatus Swiss-Prot: O07948 , Rhodococcus opacus Swiss-Prot: P72304 , Rhodoferax ferrireducens T118 REFSEQ:YP_525088.1, Rickettsia prowazekii Swiss-Prot: Q9ZE33 , Solanum tuberosum...”

G3V0I5 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Homo sapiens
44% identity, 83% coverage

• Synergistic Interactions of Cannabidiol with Chemotherapeutic Drugs in MCF7 Cells: Mode of Interaction and Proteomics Analysis of Mechanisms.
  Alsherbiny, International journal of molecular sciences 2021
  • “...Q15036 SNX17 Sorting nexin-17 2.22 O75306 NDUFS2 NADH dehydrogenase [ubiquinone] ironsulfur protein 2_ mitochondrial 2.17 G3V0I5 NDUFV1 NADH dehydrogenase [ubiquinone] flavoprotein 1_ mitochondrial 2.12 A0A590UJ21 CUL1 Cullin-1 1.97 Q00534 CDK6 Cyclin-dependent kinase 6 1.96 Q9P1A6 DLGAP2 Disks large-associated protein 2 1.95 K7EJV0 SEPTIN9 Septin-9 1.92 E7EN73...”
• Anti-parasite drug ivermectin can suppress ovarian cancer by regulating lncRNA-EIF4A3-mRNA axes
  Li, The EPMA journal 2020
  • “...cancer-associated gene 2 protein OVCA2 5 40.10 24.42 227 0 8 22,175,000 92,294,000 0.34 32.53 G3V0I5 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial NDUFV1 4 12.30 50.05 457 0 9 25,550,000 98,424,000 0.34 50.52 J3QLR8 28S ribosomal protein S23, mitochondrial MRPS23 3 19.70 17.52 152 0 8...”
• Quantitative proteomics revealed energy metabolism pathway alterations in human epithelial ovarian carcinoma and their regulation by the antiparasite drug ivermectin: data interpretation in the context of 3P medicine.
  Li, The EPMA journal 2020
• Proteomics analyses for the global proteins in the brain tissues of different human prion diseases
  Shi, Molecular & cellular proteomics : MCP 2015
  • “...P02647, P01877, P68871, P02042 11 Parkinson's disease 0.0228 31 O75251, C9JKQ2, P25705, P12235, O95168, P24539, G3V0I5, P09669, D6R9H7, P15954, P56556, P28331, P10606, O75947, Q16718, E7EPV7, P07919, P10176, Q08752, P30049, P14927, O75380, P18859, C9JFR7, O14561, P20674, O43181, Q99497, P68036, P56181, C9JSN6 12 Leishmaniasis 0.0314 9 B3KR49, B4DLJ8,...”
  • “...P01859, P49006, P01877 13 Alzheimer's disease 0.0442 35 P25705, P16615, G5E9P1, B3KR49, O95168, P24539, H0YEH5, G3V0I5, P09669, D6R9H7, P15954, P56556, P28331, Q99714, P07384, P10606, O75947, H7C0V9, Q16718, E7EPV7, P07919, P10176, P30049, P14927, O75380, P18859, C9JFR7, O14561, P20674, O43181, F6U1T9, P56181, P62158, C9JSN6, E7ENA9 14 Fc epsilon...”

NDUFV1 / P49821 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Homo sapiens (see 4 papers)
NDUV1_HUMAN / P49821 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial; NDUFV1; Complex I-51kD; CI-51kD; NADH dehydrogenase flavoprotein 1; NADH-ubiquinone oxidoreductase 51 kDa subunit; EC 7.1.1.2 from Homo sapiens (Human) (see 5 papers)
NP_009034 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial isoform 1 precursor from Homo sapiens
43% identity, 84% coverage

• function: Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor (PubMed:28844695). Part of the peripheral arm of the enzyme, where the electrons from NADH are accepted by flavin mononucleotide (FMN) and then passed along a chain of iron-sulfur clusters by electron tunnelling to the final acceptor ubiquinone (PubMed:28844695). Contains FMN, which is the initial electron acceptor as well as one iron-sulfur cluster (PubMed:28844695).
  catalytic activity: a ubiquinone + NADH + 5 H(+)(in) = a ubiquinol + NAD(+) + 4 H(+)(out) (RHEA:29091)
  cofactor: FMN (Binds 1 FMN.)
  cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster.)
  subunit: Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits (PubMed:12611891, PubMed:28844695). This is a component of the flavoprotein-sulfur (FP) fragment of the enzyme (PubMed:12611891). Interacts with RAB5IF (PubMed:31536960).
• Intracellular CYTL1, a novel tumor suppressor, stabilizes NDUFV1 to inhibit metabolic reprogramming in breast cancer.
  Xue, Signal transduction and targeted therapy 2022
  • GeneRIF: Intracellular CYTL1, a novel tumor suppressor, stabilizes NDUFV1 to inhibit metabolic reprogramming in breast cancer.
• Compound heterozygous mutations of NDUFV1 identified in a child with mitochondrial complex I deficiency.
  Tang, Genes & genomics 2022 (PubMed)
  • GeneRIF: Compound heterozygous mutations of NDUFV1 identified in a child with mitochondrial complex I deficiency.
• Evaluation of mitochondrial bioenergetics, dynamics, endoplasmic reticulum-mitochondria crosstalk, and reactive oxygen species in fibroblasts from patients with complex I deficiency.
  Leipnitz, Scientific reports 2018
  • GeneRIF: Mutations in the ND6, NDUFV1 or ACAD9 genes are responsible for the mitochondrial complex I deficiency.
• Genetic diversity of NDUFV1-dependent mitochondrial complex I deficiency.
  Srivastava, European journal of human genetics : EJHG 2018
  • GeneRIF: Biallelic missense variants in NDUFV1 were identified in two cases of mitochondrial complex I deficiency.
• Using extended pedigrees to identify novel autism spectrum disorder (ASD) candidate genes.
  Woodbury-Smith, Human genetics 2015 (PubMed)
  • GeneRIF: small number of putative de novo variants were transmitted from BAP parents to their ASD offspring, and evidence emerged for a rare duplication CNV at 11p13.3 harboring two putative developmental/neuropsychiatric susceptibility gene(s), GSTP1 and NDUFV1.
• Broad phenotypic variability in patients with complex I deficiency due to mutations in NDUFS1 and NDUFV1.
  Björkman, Mitochondrion 2015 (PubMed)
  • GeneRIF: The presented clinical courses of NDUFV1 and NDUFS1 mutation-based complex I deficiencies are characterized by leukoencephalopathy or early death and expand the already heterogeneous phenotypic spectrum.
• Characterization of clinically identified mutations in NDUFV1, the flavin-binding subunit of respiratory complex I, using a yeast model system.
  Varghese, Human molecular genetics 2015
  • GeneRIF: we have used a yeast model system to study the molecular consequences of 16 single amino acid substitutions, classified as pathogenic, in the NDUFV1 subunit of complex I
• Leigh syndrome associated with mitochondrial complex I deficiency due to novel mutations In NDUFV1 and NDUFS2.
  Marin, Gene 2013 (PubMed)
  • GeneRIF: study describes clinical, radiological, biochemical and molecular data of 6 patients with Leigh syndrome with novel mutations in NDUFV1 and NDUFS2; 2 siblings were homozygous for previously undescribed R386C mutation in NDUFV1
• More
• Combined High-Throughput Proteomics and Random Forest Machine-Learning Approach Differentiates and Classifies Metabolic, Immune, Signaling and ECM Intra-Tumor Heterogeneity of Colorectal Cancer
  Contini, Cells 2024
  • “...( HAPLN3) HPLPN3 ND in D 0.0009 C9JLW8 ( MCRIP1) MCRIP1 ND in S 0.0001 P49821 ( NDUFV1) NDUFV1 ND in S/D 0.0003 WB, enzyme assay [ 84 ] Q96IQ7 ( VSIG2 ) VSIG2 0.0015 WGCNA [ 85 ] O75312 (ZPR1) Zinc finger protein ZPR1 (ZPR1)...”
• Novel Genetic and Biochemical Insights into the Spectrum of NEFL-Associated Phenotypes.
  Della, Journal of neuromuscular diseases 2024
  • “...Myosin-9 (MYH9_HUMAN) 1.82 0.017 P10809 4 60 kDa heat shock protein, mitochondrial (CH60_HUMAN) 1.80 0.002 P49821 4 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (NDUV1_HUMAN) 1.79 0.016 P05091 3 Aldehyde dehydrogenase, mitochondrial (ALDH2_HUMAN) 1.79 0.015 P30048 6 Thioredoxin-dependent peroxide reductase, mitochondrial (PRDX3_HUMAN) 1.75 0.013 P00505 17 Aspartate...”
• Antitumor Effect of Poplar Propolis on Human Cutaneous Squamous Cell Carcinoma A431 Cells
  Zhang, International journal of molecular sciences 2023
  • “...0.003479756 down E7EPT4 NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial 0.003643833 down P18827 Syndecan-1 0.004028676 up P49821 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial 0.004095327 down A8K0B9 rRNA adenine N(6)-methyltransferase 0.004645847 down A0A3B3ISF9 Endothelin-converting enzyme 1 0.004659358 down Q96PU5 E3 ubiquitin-protein ligase NEDD4-like 0.004703096 down Q9NX12 cDNA FLJ20496...”
• Distinct or Overlapping Areas of Mitochondrial Thioredoxin 2 May Be Used for Its Covalent and Strong Non-Covalent Interactions with Protein Ligands.
  Ntallis, Antioxidants (Basel, Switzerland) 2023
  • “...10.3 2800 NC 2 P30048 Peroxiredoxin-3 5jcg (chain A) 49.26 2vocAB 7.9 1500 C 3 P49821 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial 5xtb (chain A) 48.13 2i7dAB 7.7 2200 NC 4 P07237 Protein disulfide isomerase 6i7s (chain A) 47.77 1uvzEF 9.1 190 NC 5 P07195 L-lactate...”
• Mitochondria-derived vesicles and their potential roles in kidney stone disease.
  Chaiyarit, Journal of translational medicine 2023
  • “...1 beta subcomplex subunit 5, mitochondrial (Complex I-SGDH) (CI-SGDH) (NADH-ubiquinone oxidoreductase SGDH subunit) 151 NDUFV1 P49821 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 7.1.1.2) (Complex I-51kD) (CI-51kD) (NADH dehydrogenase flavoprotein 1) (NADH-ubiquinone oxidoreductase 51kDa subunit) 152 NDUFV2 P19404 NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (EC 7.1.1.2)...”
• Reticulon-1A mediates diabetic kidney disease progression through endoplasmic reticulum-mitochondrial contacts in tubular epithelial cells.
  Xie, Kidney international 2022
  • “...1 (VDAC1) P21796 31 kDa 7 37 4.3 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (NDUFV1) P49821 51 kDa 0 6 4.0 DnaJ homolog subfamily C member 11 (DNAJC11) Q9NVH1 63 kDa 0 6 4.0 Voltage-dependent anion-selective channel protein 2 (VDAC2) P45880 32 kDa 4 20 3.7...”
• Isoform-specific dysregulation of AMP-activated protein kinase signaling in a non-human primate model of Alzheimer's disease.
  Wang, Neurobiology of disease 2021
  • “...0.65 Destrin DSTN P60981 18.5 5.00 3.33 0.67 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial NDUFV1 P49821 50.8 19.33 13.33 0.69 MICOS complex subunit MIC60 IMMT Q16891 83.6 23.33 17.00 0.73 ATP-citrate synthase ACLY P53396 120.8 11.67 8.67 0.74 2-iminobutanoate/2-iminopropanoate deaminase HRSP12 P52758 14.5 7.33 5.67 0.77...”
• Secretory Carrier Membrane Protein 3 Interacts with 3A Viral Protein of Enterovirus and Participates in Viral Replication.
  Lu, Microbiology spectrum 2021
  • “...O75380 NDUFS6 NADH dehydrogenase (ubiquinone) iron-sulfur protein 6, mitochondrial 13.7 117.9 2 2 3 21.77 P49821 NDUFV1 NADH dehydrogenase (ubiquinone) flavoprotein 1, mitochondrial 50.8 259.1 6 6 8 13.36 P01111 NRAS GTPase NRas 21.2 636.1 4 6 18 39.15 Q8WUM0 NUP133 Nuclear pore complex protein Nup133...”
• More

alr0752 hydrogenase subunit from Nostoc sp. PCC 7120
40% identity, 76% coverage

• Calcium impacts carbon and nitrogen balance in the filamentous cyanobacterium Anabaena sp. PCC 7120
  Walter, Journal of experimental botany 2016
  • “...0.4 0.2 0.015 3 hoxE alr0751 Bidirectional hydrogenase, diophorase subunit 0.8 0.5 0.000 3 hoxF alr0752 Bidirectional hydrogenase subunit 0.8 0.6 0.136 3 Other proteins alr0198 alr0198 Hypothetical protein 1.1 0.6 0.000 2 alr0199 alr0199 Hypothetical protein 1.1 0.3 0.000 2 alr3715 alr3715 Hypothetical protein 1.7...”
• Hydrogenases and hydrogen metabolism of cyanobacteria
  Tamagnini, Microbiology and molecular biology reviews : MMBR 2002
  • “...NP (27)d (ATCC 29133) (150) (150) X79285 (173) AB057405 alr0752 NP (27)d X79285 (173) AB057405 alr0762 NP (27)d X79285 (173) AB057405 alr0764 NP (194)d X79285...”

Caur_1185 NADH dehydrogenase (quinone) from Chloroflexus aurantiacus J-10-fl
40% identity, 77% coverage

• Temporal metatranscriptomic patterning in phototrophic Chloroflexi inhabiting a microbial mat in a geothermal spring
  Klatt, The ISME journal 2013
  • “...homolog Chloroflexus expression categorya Caur_1184 Caur_1185 Caur_1987 Caur_1986 Caur_1985 Caur_1984 Caur_1983 Caur_1982 Caur_1981 Caur_1980 Caur_1979...”
• Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus
  Tang, BMC genomics 2011
  • “...nuoA to nuoN (Caur_2896 to Caur_2909) nuoA (Caur_1987), nuoB (Caur_1986), muoC (Caur_1985), nuoDE (Caur_1984), nuoF (Caur_1185), nuoH (Caur_1982), nuoI (Caur_1983), nuoJ (Caur_1981), nuoK (Caur_1980), nuoL (Caur_1979), nuoM (Caur_1977 and Caur_1978) and nuoN (Caur_1976) The proposed C r ACIII operon contains 12 genes (Caur_2133 to 2144) encoding...”

TC 3.D.1.6.4 / Q6V9B2 50 (NuoF), component of The green algal H+ translocating NADH dehydrogenase (NDH) complex (42 subunits; 33 included here) from Chlamydomonas reinhardtii
42% identity, 80% coverage

• substrates: H+

AZC_1672 NADH-quinone oxidoreductase F subunit protein from Azorhizobium caulinodans ORS 571
42% identity, 89% coverage

• Respiratory membrane endo-hydrogenase activity in the microaerophile Azorhizobium caulinodans is bidirectional
  Sprecher, PloS one 2012
  • “...Nqo5 HyqG(N-term.) AZC_4356 23 57 NuoD AZC_1670 Nqo4 HyqG(C-term.) 26 62 NuoE AZC_1671 Nqo2 NuoF AZC_1672 Nqo1 NuoG AZC_1674 Nqo3 NuoI AZC_1676 Nqo9 L O subcomplex (membrane-integral) NuoA AZC_1667 Nqo7 NuoH AZC_1675 Nqo8 HyqC AZC_4359 23 58 NuoJ AZC_1677 Nqo10 HyqE AZC_4358 18 54 NuoK AZC_1678...”

P56912 NADH-quinone oxidoreductase subunit F 1 from Rhizobium meliloti (strain 1021)
NP_385376 NADH DEHYDROGENASE I CHAIN F TRANSMEMBRANE PROTEIN from Sinorhizobium meliloti 1021
40% identity, 90% coverage

• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “...Ralstonia solanacearum UW551 REFSEQ:ZP_00943355.1, Rhizobium loti Swiss-Prot: Q98BW8 , Swiss-Prot: Q98KR0 , Rhizobium meliloti Swiss-Prot: P56912 , Swiss-Prot: P56913 , Rhodobacter capsulatus Swiss-Prot: O07948 , Rhodococcus opacus Swiss-Prot: P72304 , Rhodoferax ferrireducens T118 REFSEQ:YP_525088.1, Rickettsia prowazekii Swiss-Prot: Q9ZE33 , Solanum tuberosum Swiss-Prot: Q43840 , Streptomyces avermitilis...”
• 'Ca. Liberibacter asiaticus' proteins orthologous with pSymA-encoded proteins of Sinorhizobium meliloti: hypothetical roles in plant host interaction
  Kuykendall, PloS one 2012
  • “...YP_003065269 4E-24 169 53 NP_385375 3E-22 NADH-quinone oxidoreductase subunit E NP_436075.1 YP_003065271 1E-104 420 64 NP_385376 1E-105 NADH dehydrogenase I subunit F NP_436074.1 YP_003065272 2E-62 410 54 NP_385378* 2E-65 NADH dehydrogenase subunit G NP_436071.1 YP_003065273 1E-51 311 55 NP_385379 2E-54 NADH dehydrogenase subunit H NP_436072.1 YP_003065274...”

LOC106772405 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Vigna radiata var. radiata
43% identity, 79% coverage

• Atomic structure of a mitochondrial complex I intermediate from vascular plants
  Maldonado, eLife 2020
  • “...arm N NDUS1 LOC106757688 A0A1S3TQ85 75 kDa At5g37510 NDUFS1 NDUFS1 NDUFS1 NUAM Nqo3 N NDUV1 LOC106772405 A0A1S3V7V2 51 kDa At5g08530 NDUFV1 NDUFV1 NDUFV1 NUBM Nqo1 N NDUV2 LOC106762461 A0A1S3U769 24 kDa At4g02580 NDUFV2 NDUFV2 NDUFV2 NUHM Nqo2 Q NDUS2 nad7 E9KZN6 Nad7 AtMg00510 NDUFS2 NDUFS2 NDUFS2...”

Q4WPZ9 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)
40% identity, 78% coverage

• The proteomic signature of Aspergillus fumigatus during early development
  Cagas, Molecular & cellular proteomics : MCP 2011
  • “...Q4WU32 Q4WN66 O43099 Q96X30 Q4WXU5 Q6J9U0 Q4WPZ9 Q4W9X3 Q4WJM1 Q4WCM7 Q4X1V2 Q4WTZ9 AFUA_4G07690 AFUA_6G06340 AFUA_1G14220 AFUA_2G16880 AFUA_1G07280...”

Cthe_0429 NADH-quinone oxidoreductase subunit NuoF from Acetivibrio thermocellus ATCC 27405
Cthe_0429 NADH dehydrogenase (quinone) from Clostridium thermocellum ATCC 27405
42% identity, 64% coverage

• Utilization of Monosaccharides by Hungateiclostridium thermocellum ATCC 27405 through Adaptive Evolution
  Ha-Tran, Microorganisms 2021
  • “...highly expressed genes in both [NiFe] and [FeFe] hydrogenases (i.e., Cthe_3013, Cthe_3014, Cthe_3018, Cthe_3020, Cthe_0428, Cthe_0429, Cthe_0430), ammonia assimilation genes (Cthe_01970199), porphyrin biosynthesis gene (Cthe_2525, Cthe_2527, Cthe_2528, Cthe_2529), and sulfate transport (Cthe_2533). The results suggest that FAs1 and GAs1 did not suffer much from redox imbalance...”
• Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress
  Wilson, Biotechnology for biofuels 2013
  • “...affected by the three stress treatments with possible redox balance functions included two NADH dehydrogenases (Cthe_0429, Cthe_3023) and an annotated CO dehydrogenase (Cthe_2801). The CO dehydrogenase formed a putative operon with an ABC transporter of unknown function (Cthe_2802-2804) and was affected by all stress treatments. Genes...”

NDUV1_MOUSE / Q91YT0 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial; NDUFV1; Complex I-51kD; CI-51kD; NADH-ubiquinone oxidoreductase 51 kDa subunit; EC 7.1.1.2 from Mus musculus (Mouse) (see 3 papers)
NP_598427 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial precursor from Mus musculus
44% identity, 82% coverage

• function: Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor. Part of the peripheral arm of the enzyme, where the electrons from NADH are accepted by flavin mononucleotide (FMN) and then passed along a chain of iron-sulfur clusters by electron tunnelling to the final acceptor ubiquinone. Contains FMN, which is the initial electron acceptor as well as one iron-sulfur cluster.
  catalytic activity: a ubiquinone + NADH + 5 H(+)(in) = a ubiquinol + NAD(+) + 4 H(+)(out) (RHEA:29091)
  cofactor: FMN (Binds 1 FMN.)
  cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster.)
  subunit: Core subunit of respiratory chain NADH dehydrogenase (Complex I) which is composed of 45 different subunits (PubMed:29915388, PubMed:38575788). This is a component of the flavoprotein-sulfur (FP) fragment of the enzyme (PubMed:29915388). Interacts with RAB5IF (PubMed:31536960).
• NDUFV1 attenuates renal ischemia-reperfusion injury by improving mitochondrial homeostasis.
  Li, Journal of cellular and molecular medicine 2023
  • GeneRIF: NDUFV1 attenuates renal ischemia-reperfusion injury by improving mitochondrial homeostasis.
• Mitochondrial complex I deficiency enhances skeletal myogenesis but impairs insulin signaling through SIRT1 inactivation.
  Hong, The Journal of biological chemistry 2014
  • GeneRIF: NDUFV1 knockdown-induced blockage of insulin signaling was released by protein-tyrosine phosphatase 1B knockdown in C2C12 myotubes, and NDUFV1 or SIRT1 knockdown did not affect mitochondria biogenesis during C2C12 myogenesis. myogenesis.
• Molecular base of biochemical complex I deficiency.
  Hoefs, Mitochondrion 2012 (PubMed)
  • GeneRIF: The authors provide an overview of the function and assembly of human complex I, also known as NADH dehydrogenase (ubiquinone) 1 alpha subcomplex. They discuss its role in oxidative phosphorylation and the implications of complex I deficiency in disease.
• Subunit-specific incorporation efficiency and kinetics in mitochondrial complex I homeostasis.
  Dieteren, The Journal of biological chemistry 2012
  • GeneRIF: The authors use green fluorescent-tagged complex I subunits to determine the kinetics of assembly. Tagged human NDUFV1 can replace endogenous protein in the holo-complex I protein and was also found in complex I subassemblies, suggesting that NDUFV1 may directly incorporate into the holo-enzyme and may also assemble into smaller complexes or in a monomer pool.
• Cloning of the human mitochondrial 51 kDa subunit (NDUFV1) reveals a 100% antisense homology of its 3'UTR with the 5'UTR of the gamma-interferon inducible protein (IP-30) precursor: is this a link between mitochondrial myopathy and inflammation?
  Schuelke, Biochemical and biophysical research communications 1998 (PubMed)
  • GeneRIF: The authors clone and characterize the human NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial protein, also known as NDUFV1. They identify transcription factor binding sites as well as consensus motifs for NADH, flavin mononucleotide, and iron-sulfur binding sites. The human ortholog has high homology to the cow NDUFV1 protein.
• Changes in protein fluxes in skeletal muscle during sequential stages of muscle regeneration after acute injury in male mice.
  Bizieff, Scientific reports 2024
  • “...14.8126.971% 7.4363.237% 2.8630.368% 83 Sarcalumenin Q7TQ48 Cytoplasm 13.0377.622% 6.7882.051%* 1.8610.849% 84 NADH dehydrogenase flavoprotein 1 Q91YT0 OxPhos 13.3586.28% 8.1202.029%* 2.6380.931% 85 Keratin, type II cytoskeletal 1 P04104 Cytoplasm 12.7812.845% 8.5233.349% 6.1562.426% 86 Voltage-dependent anion-selective channel protein 2 Q60930 Mitochondria 17.96910.852% 16.6229.964%* 1.1720.341% 87 2-oxoglutarate dehydrogenase Q60597...”
• A Murine Model of Maternal Micronutrient Deficiencies and Gut Inflammatory Host-microbe Interactions in the Offspring.
  Holani, Cellular and molecular gastroenterology and hepatology 2024
  • “...4.5456137025968E-06 0.007213888946021120 Down-regulated P62889 Rpl30 0.38498391842565500 1.98783985519615E-05 0.031050058538163900 Up-regulated Q9DC16 Ergic1 0.7290496384786000 1.17047415233173E-07 1.89148623016808E-04 Down-regulated Q91YT0 Ndufv1 1.3020189692086000 2.33146903187949E-05 0.03627765813604490 Down-regulated E9Q616 Ahnak 0.94758354213423000 1.21340442893264E-05 0.019086851667110500 Up-regulated E9Q9C6 Fcgbp 1.2391346856646700 8.8119032098072E-07 0.0014090233232481700 Up-regulated Q91VS7 Mgst1 0.5169999137432440 1.71667750067879E-05 0.026866002885623100 Up-regulated O35074 Ptgis 1.0277880624131500 1.43606521713443E-07 2.31780926045498E-04 Down-regulated O35295...”
  • “...Effect size (log2) P -value q-value Direction of change Q60605 Myl6 1.2370989878864900 2.01281730362787E-05 0.028883928307060000 Up-regulated Q91YT0 Ndufv1 0.8433293806317380 1.40842026326072E-05 0.020323504398852200 Down-regulated E9Q509 Pklr 1.1300153338196000 1.40375777454968E-07 2.05790889748983E-04 Down-regulated Q6ZWZ6 Rps12 0.698585731327696 1.85930237916802E-07 2.72387798548114E-04 Up-regulated F8VPQ6 Alpi 4.004047567210490 1.83343230426363E-05 0.02632808788922580 Down-regulated F8VPT3 Lct 4.202408985704460 2.06092072667672E-06 0.0029986396573146300 Down-regulated G3UZP7...”
• Effects of Hyperoxia and Hyperoxic Oscillations on the Proteome of Murine Lung Microvascular Endothelium
  Tiboldi, Antioxidants (Basel, Switzerland) 2022
  • “...Species Protein Name P51410 Rpl9 0.045581 1 . 461 21,881.6 MOUSE 60S ribosomal protein L9 Q91YT0 Ndufv1 0.02777 1.369 50,834.7 MOUSE NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Q9R0Y5 Ak1 0.00099 1 . 269 21,539.8 MOUSE Adenylate kinase isoenzyme 1 P62911 Rpl32 0.03549 1 . 164 15,859.9...”
  • “...# Gene Name t -Test p -Value log(2) [Fold Change] Protein MW Species Protein Name Q91YT0 Ndufv1 0.01774 2 . 093 50,834.7 MOUSE NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Q9DBR7 Ppp1r12a 0.02466 2 . 034 114,997.2 MOUSE Protein phosphatase 1 regulatory subunit 12A Q53WR6 Glg1 0.01798...”
• Dynamic Interplay between Copper Toxicity and Mitochondrial Dysfunction in Alzheimer's Disease
  Tassone, Life (Basel, Switzerland) 2021
  • “...(Cu-Treatment Versus Control) Reference Mice Cortex 3xTg-AD Mice Hippocampus NADH dehydrogenase [ubiquinone] flavoprotein 1 (CI-51kD) Q91YT0 NDUFV1 [ 33 ] Cytochrome b-c1 complex subunit 2 (CIII-s2) Q9DB77 UQCRC2 [ 33 ] ATP synthase subunit d (ATPase-d) Q9DCX2 ATP5PD [ 33 , 34 ] 75 kDa glucose-regulated...”
• Protein expression alteration in hippocampus upon genetic repression of AMPKα isoforms.
  Yang, Hippocampus 2021
  • “...Q8BGH2 1.644 EF-hand domain-containing protein D2 + Q9D8Y0 1.589 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Q91YT0 1.556 + Up-regulated also in AMPK1 cKO mice Table 3 List of down-regulated proteins in hippocampus of AMPK1 cKO mice. Description Accession Fold change 116 kDa U5 small nuclear ribonucleoprotein...”
• Proteomic analysis reveals ginsenoside Rb1 attenuates myocardial ischemia/reperfusion injury through inhibiting ROS production from mitochondrial complex I.
  Jiang, Theranostics 2021
  • “...NADH dehydrogenase [ubiquinone] iron-sulfur protein 6 Ndufs6 6 1.074 0.896 0.834 -0.178 0.022 0.005 0.000 Q91YT0 NADH dehydrogenase [ubiquinone] flavoprotein 1 Ndufv1 18 1.090 0.967 0.887 -0.123 0.009 0.336 0.012 Q9D6J6 NADH dehydrogenase [ubiquinone] flavoprotein 2 Ndufv2 11 1.075 0.949 0.883 -0.126 0.010 0.269 0.043 Q9CQ54...”
• Arachidyl amido cholanoic acid improves liver glucose and lipid homeostasis in nonalcoholic steatohepatitis via AMPK and mTOR regulation.
  Fernández-Ramos, World journal of gastroenterology 2020
  • “...subcomplex subunit 9 mitochondrial GN = Ndufa9 PE = 1 SV = 2 1.26E-02 1.54 Q91YT0 NADH dehydrogenase (ubiquinone) flavoprotein 1 mitochondrial GN = Ndufv1 PE = 1 SV = 1 1.92E-03 1.58 O09111 NADH dehydrogenase (ubiquinone) 1 beta subcomplex subunit 11 mitochondrial GN = Ndufb11...”
• Modulation of Proteome Profile in AβPP/PS1 Mice Hippocampus, Medial Prefrontal Cortex, and Striatum by Palm Oil Derived Tocotrienol-Rich Fraction
  Hamezah, Journal of Alzheimer's disease : JAD 2019
  • “...Fructose-bisphosphate aldolase ALDOA P03911 NADH-ubiquinone oxidoreductase chain 4 MTND4 Q9Z0J4 Nitric oxide synthase, brain NOS1 Q91YT0 NADH dehydrogenase [ubiquinone] flavoprotein 1 NDUFV1 Q8CGC7 Bifunctional glutamate/prolinetRNA ligase EPRS Q80UP3 Diacylglycerol kinase zeta DGKZ P62814 V-type proton ATPase subunit B, brain isoform ATP6V1B2 Q61753 D-3-phosphoglycerate dehydrogenase PHGDH Q9Z1B3...”
  • “...NDUFB10 Q9Z1B3 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1 PLCB1 Q91WD5 NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 NDUFS2 Q91YT0 NADH dehydrogenase [ubiquinone] flavoprotein 1 NDUFV1 P11352 Glutathione peroxidase 1 GPX1 Q7TMF3 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 NDUFA12 Q62108 Disks large homolog 4 DLG4 P56480 ATP synthase...”
• More

GRMZM2G024484 uncharacterized protein LOC100273176 from Zea mays
43% identity, 75% coverage

• Genome-wide association studies of grain yield and quality traits under optimum and low-nitrogen stress in tropical maize (Zea mays L.)
  Ndlovu, TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 2022
  • “...7 124403566 1.04E-05 0.34 0.14 GRMZM2G007249 1-Aminocyclopropane-1-carboxylate oxidase activity S7_170251419 7 170251419 2.39E-05 0.23 0.14 GRMZM2G024484 NADH dehydrogenase (ubiquinone) activity S7_174752436 7 174752436 1.05E-05 0.08 0.24 GRMZM2G108166 DNA binding and helicase activity Protein content under optimum N S1_17679954 1 17679954 9.57E-06 0.14 0.13 GRMZM2G410623 Shoot apex...”

BOV_RS04000 NADH-quinone oxidoreductase subunit NuoF from Brucella ovis ATCC 25840
41% identity, 90% coverage

• Mining the Flavoproteome of Brucella ovis, the Brucellosis Causing Agent in Ovis aries
  Minjárez-Sáenz, Microbiology spectrum 2022
  • “...FMN 1UM0 (42) 44 7.1.1.2 NADH-quinone oxidoreductase subunit F (H + translocating) Complex1_51K (PF01512) 47-216 BOV_RS04000 (nuoF) ABQ60521.1 6Q9C _D (46) SLBB (PF10531) 242-292 FMN NADH 4Fe-4S NADH_4Fe-4S (PF10589) 332-414 45 Electron transferring flavoprotein alpha subunit (ETFa) ETF (PF01012) 44-210 BOV_RS09295 (etfA) ABQ61011.1 1EFP _A (69)...”

V7BMQ3 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Phaseolus vulgaris
43% identity, 80% coverage

• Comprehensive Proteomic Analysis of Common Bean (<i>Phaseolus vulgaris</i> L.) Seeds Reveal Shared and Unique Proteins Involved in Terminal Drought Stress Response in Tolerant and Sensitive Genotypes
  Subramani, Biomolecules 2024
  • “...Proteasome subunit alpha type V7AHS3 0.691908505 0.71020376 NADH dehydrogenase (ubiquinone) flavoprotein 1, mitochondrial (EC 7.1.1.2) V7BMQ3 0.62391639 0.597474222 Alpha-galactosidase (EC 3.2.1.22) (Melibiase) V7B2C4 0.757427659 0.755447862 Epimerase domain-containing protein V7BF01 0.685465562 0.648430837 Mitochondrial Rho GTPase (EC 3.6.5.-) V7BIE7 1.397530527 1.285438844 CYTOSOL_AP domain-containing protein V7AYA6 0.699524201 0.726445174 biomolecules-14-00109-t002_Table...”

B2M23_RS16055 NADH-quinone oxidoreductase subunit NuoF from Eubacterium limosum
38% identity, 72% coverage

• Tungsten is utilized for lactate consumption and SCFA production by a dominant human gut microbe Eubacterium limosum
  Putumbaka, Proceedings of the National Academy of Sciences of the United States of America 2025
  • “...(B2M23_RS16035) and Wor2S (B2M23_RS04630) each contain four [4Fe-4S] clusters (yellow). Wor1A (purple; B2M23_RS16060), Wor1B (green; B2M23_RS16055), and Wor1C (blue; B2M23_RS16050) are the subunits enabling electron bifurcation. In this study, the goal was to determine how E. limosum generates SCFAs from lactate by elucidating the pathways and...”

DMR_02470 NADH-quinone oxidoreductase chain F from Desulfovibrio magneticus RS-1
42% identity, 84% coverage

• Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria
  Nakazawa, Genome research 2009
  • “...and another set in two separate gene regions (DMR_02470, DMR_27770-27880). The presence of nuo genes in strain RS-1 is therefore a unique characteristic in...”

D3Z1U9 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Mus musculus
44% identity, 83% coverage

• A Quantitative Proteomics Approach to Gain Insight into NRF2-KEAP1 Skeletal Muscle System and Its Cysteine Redox Regulation
  Abu, Genes 2021
  • “...Q9QUH0 Glrx 2.68731 a (-).MAQEFVNCK.[I] Q9CZU6 Cs 1.34429 b [R].GYSIPECQK.[LM] Q3TG92 Actc1 1.99585 a [R].CPETLFQPSFIGMESAGIHETTYNSIMK.[C] D3Z1U9 Ndufv1 1.42557 b [K].NACGSDYDFDVFVVR.[G] A0A0F7QZE4 HC 1.87462 b [K].CPAPNLEGGPSVFIFPPNIK.[D] E9Q1X8 Cacna2d1 1.18133 a [K].SYDYQSVCDPGAAPK.[Q] Q3TG92 Actc1 1.89048 a [R].CPETLFQPSFIGMESAGIHETTYNSIMK.[C] D3Z041 Acsl1 1.59049 b [R].GIQVSNNGPCLGSR.[K] Q3TID4 Psap 1.39122 b [K].SLPCDICK.[T] P17751...”

SYN_RS00435 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region domain-containing protein from Syntrophus aciditrophicus SB
41% identity, 68% coverage

• Syntrophus aciditrophicus uses the same enzymes in a reversible manner to degrade and synthesize aromatic and alicyclic acids
  James, Environmental microbiology 2019
  • “...were the most abundant of the BamBCDEF subunits detected. Two NADH dehydrogenase subunits (SYN_RS00430 and SYN_RS00435 gene products) were detected under all growth conditions ( Fig. 3 ), but are encoded by genes not linked to any of the bamBCDE genes ( Fig. S6 ). ATP...”

hydB / O52682 hydrogenase β subunit (EC 1.12.1.4) from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see 2 papers)
HYDB_THEMA / O52682 Bifurcating [FeFe] hydrogenase beta subunit; Hydrogenase (NAD(+), ferredoxin) beta subunit; Iron-hydrogenase beta subunit; EC 1.12.1.4 from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see 2 papers)
TM1425 Fe-hydrogenase, subunit beta from Thermotoga maritima MSB8
41% identity, 64% coverage

• function: Catalyzes the oxidation of the physiological electron carriers NADH and reduced ferredoxin, coupled to the production of H(2) (PubMed:19411328). Acts as a bifurcating [FeFe] hydrogenase, which uses the exergonic oxidation of reduced ferredoxin to drive the unfavorable oxidation of NADH to produce H(2) (PubMed:19411328). The beta subunit contains flavin- and NAD-binding sites and is potentially the site for NADH oxidation, with the subsequent shuttling of electrons to the alpha subunit (PubMed:19411328).
  catalytic activity: 2 H2 + 2 oxidized [2Fe-2S]-[ferredoxin] + NAD(+) = 2 reduced [2Fe-2S]-[ferredoxin] + NADH + 3 H(+) (RHEA:30279)
  cofactor: [2Fe-2S] cluster (May bind 1 [2Fe-2S] cluster per subunit.)
  cofactor: [4Fe-4S] cluster (May bind 3 [4Fe-4S] cluster per subunit.)
  cofactor: FMN (Binds 1 FMN per subunit.)
  subunit: Heterotrimer composed of HydA (alpha subunit), HydB (beta subunit) and HydC (gamma subunit) (PubMed:10482784). Near neutral and acidic pH conditions favor oligomerization of the heterotrimeric holoenzyme (PubMed:10482784).
• The iron-hydrogenase of Thermotoga maritima utilizes ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production
  Schut, Journal of bacteriology 2009
  • “...centers, termed beta (TM1424 protein) and gamma (TM1425 protein). These contain four Downloaded from http://jb.asm.org/ on February 13, 2017 by University...”
• Involvement of NADH:acceptor oxidoreductase and butyryl coenzyme A dehydrogenase in reversed electron transport during syntrophic butyrate oxidation by Syntrophomonas wolfei
  Müller, Journal of bacteriology 2009
  • “...(7) (U07229; 50%), and HydB in Thermotoga maritima (30) (TM1425; 46%). Notably, the Swol_1018 sequence lacked the N-terminal part (141 amino acids) of the HydB...”
• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “...Tetrahymena thermophila SB210 GenBank: EAR96899.1 , Thermococcus kodakarensis KOD1 DDBJ: BAD85803.1 , Thermotoga maritima Swiss-Prot: O52682 , Swiss-Prot: Q9WXM5 , Swiss-Prot: Q9WY70 , Thermus thermophilus Swiss-Prot: Q56222 , Thiobacillus denitrificans ATCC 25259 REFSEQ:YP_314905.1, Trypanosoma brucei REFSEQ:XP_824451.1, Trypanosoma cruzi GenBank: EAN82122.1 , uncultured archaeon GZfos26D6 GenBank: AAU83054.1...”

cbdbA684 NADH-quinone oxidoreductase subunit NuoF from Dehalococcoides mccartyi CBDB1
40% identity, 66% coverage

• Syntrophic Partners Enhance Growth and Respiratory Dehalogenation of Hexachlorobenzene by Dehalococcoides mccartyi Strain CBDB1
  Chau, Frontiers in microbiology 2018
  • “...dehydrogenase complexes and two oxidoreductase complexes. Three hydrogenases, VhuA, HymB, and HymC, encoded by cbdbA597, cbdbA684, and cbdbA685, respectively, were found to be marginally more abundant in syntrophic growth than in the isolate (Table S2 ). The co-culture also possessed 16 ribosomal proteins that were detected...”
• Organic cofactors in the metabolism of Dehalococcoides mccartyi strains
  Schipp, Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013
  • “...(FMN), e.g. for a HymB subunit [47] (cbdbA684, DET0729, DehalGT_0622, DehaBAV1_0661, DhcVS_635, Dehly_624) which is genetically linked with the Ech hydrogenase...”

WD0976 NADH dehydrogenase I, F subunit, putative from Wolbachia endosymbiont of Drosophila melanogaster
40% identity, 88% coverage

• wMel Wolbachia alters female post-mating behaviors and physiology in the dengue vector mosquito Aedes aegypti
  Osorio, Communications biology 2023
  • “...Ammonium transporter NUOD_WOLPM nuoD NADH-quinone oxidoreductase subunit D Q73HV3_WOLPM sdhA Succinate dehydrogenase flavoprotein subunit Q73GH8_WOLPM WD0976 NADH-quinone oxidoreductase subunit F ATPA_WOLPM atpA ATP synthase subunit alpha RPOBC_WOLPM rpoBC Bifunctional DNA-directed RNA polymerase subunit beta-beta HTPG_WOLPM htpG Chaperone protein HtpG Q73GV1_WOLPM cutA Periplasmic divalent cation tolerance protein...”
• Parasitism and mutualism in Wolbachia: what the phylogenomic trees can and cannot say
  Bordenstein, Molecular biology and evolution 2009
  • “...of the 21 genes following a Bonferroni correction (WD0976, putative NADH dehydrogenase, P , 0.001). No recombination was evident when outgroups were included,...”

7p8nB / O52682 Tmhydabc- t. Maritima hydrogenase with bridge closed (see paper)
41% identity, 65% coverage

• Ligands: iron/sulfur cluster; flavin mononucleotide; fe2/s2 (inorganic) cluster; zinc ion (7p8nB)

7arcF / A0A7S0V3A3 Cryo-em structure of polytomella complex-i (peripheral arm) (see paper)
42% identity, 86% coverage

• Ligands: flavin mononucleotide; iron/sulfur cluster (7arcF)

O66841 NADH-quinone oxidoreductase subunit F from Aquifex aeolicus (strain VF5)
44% identity, 91% coverage

• Heterocyclic Diaryliodonium-Based Inhibitors of Carbapenem-Resistant Acinetobacter baumannii
  Kumari, Microbiology spectrum 2023
  • “...; UniProtKB ID number P0AFD1 ) and NuOF ( A. aeolicus ; UniProtKB ID number O66841 ; E. coli ; UniProtKB ID number P31979 ) were obtained from the UniProt database. The unweighted sequence alignments between NuOE and NuOF from A. aeolicus and E. coli were...”
• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “...the 51 kDa subunit/NuoF/hoxU sequences are [ Agrobacterium tumefaciens Swiss-Prot: Q8U6U9 , Aquifex aeolicus Swiss-Prot: O66841 , Arabidopsis thaliana Swiss-Prot: Q8LAL7 , Aspergillus niger Swiss-Prot: Q92406 , Bos taurus GenBank: AF092131 , Bradyrhizobium japonicum DDBJ: BAC48402 , DDBJ: BAC50177 , Burkholderia xenovorans LB400 REFSEQ:YP_555778.1, Candida tropicalis...”

7q4vB / H6LFG4 Electron bifurcating hydrogenase - hydabc from a. Woodii (see paper)
Awo_c26980 NADH-quinone oxidoreductase subunit NuoF from Acetobacterium woodii DSM 1030
41% identity, 69% coverage

• Ligands: fe2/s2 (inorganic) cluster; iron/sulfur cluster; zinc ion; flavin mononucleotide (7q4vB)
• A new metabolic trait in an acetogen: Mixed acid fermentation of fructose in a methylene-tetrahydrofolate reductase mutant of Acetobacterium woodii
  Moon, Environmental microbiology reports 2023
  • “...complex protein RnfC1 4844 11,125 1.19 Awo_c26970 Iron hydrogenase HydA1 Bifurcating hydrogenase 63,435 56,607 0.17 Awo_c26980 Iron hydrogenase HydB 68,393 49,927 0.45 Awo_c26990 Iron hydrogenase HydD 7064 5220 0.43 Awo_c27000 Sensory transduction histidine kinase HydE 12,305 8710 0.5 Awo_c27010 Iron hydrogenase HydC 4010 4073 0.02 Awo_c02140...”
• It does not always take two to tango: "Syntrophy" via hydrogen cycling in one bacterial cell
  Wiechmann, The ISME journal 2020
  • “...enzyme [ 22 ]. To delete the genes coding for the two major subunits HydB (Awo_c26980) and HydA (Awo_c26970) of the electron-bifurcating hydrogenase encoded by the hydCEDBA operon (Awo_c27010-Awo_c26970), the suicide plasmid pMTL_AW_KO2 was generated. The plasmid contains homologous flanking regions of ~480bp upstream and downstream...”

Q6AZA2 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Danio rerio
43% identity, 79% coverage

• Reintroduction of DJ-1 in Müller Cells Inhibits Retinal Degeneration in the DJ-1 Deficient Retina.
  Gharbi, Antioxidants (Basel, Switzerland) 2021
  • “...23 *** * * 0.4 0.4 0.5 25.75 0.07 24.50 0.05 24.56 0.44 24.73 0.37 Q6AZA2 ndufv1 14 14 156 * * * 0.5 0.6 0.6 28.20 0.12 27.08 0.47 27.46 0.27 27.42 0.25 Q6PBX8 ndufv2 5 5 57 * * * 0.5 0.6 0.6 26.77...”

BAB1_0827 Respiratory-chain NADH dehydrogenase, 51 kDa subunit from Brucella melitensis biovar Abortus 2308
BMEI1153 NADH-QUINONE OXIDOREDUCTASE CHAIN F from Brucella melitensis 16M
40% identity, 90% coverage

• Iron-dependent reconfiguration of the proteome underlies the intracellular lifestyle of Brucella abortus
  Roset, Scientific reports 2017
  • “...NO 0.62 0.10 GI:82699683 BAB1_0826 nuoE NADH dehydrogenase subunit E C NO 0.57 0.04 GI:82615785 BAB1_0827 nuoF NADH dehydrogenase subunit F C NO 0.50 0.08 GI:82699685 BAB1_0828 nuoG NADH dehydrogenase subunit G C NO 0.56 0.09 Cytochrome b-c1 complex (Complex III) GI:82616452 BAB1_1559 petA Rieske iron-sulfur...”
  • “...We found that all the subunits of the dehydrogenase domain (NuoE, NuoF and NuoG) (BAB1_0826, BAB1_0827, and BAB1_0828, respectively) and one subunit of the connecting domain (NuoD, BAB1_0825) of Nuo Complex I were down-regulated (Table 2 and Fig. 4 ). Interestingly NuoE, NuoF and NuoG possess...”
• RNA-seq reveals the critical role of OtpR in regulating Brucella melitensis metabolism and virulence under acidic stress
  Liu, Scientific reports 2015
  • “...were differentially expressed from each functional group, e.g. , BMEI0655 belonging to ABC transporter system, BMEI1153 involved to oxidative phosphorylation, BMEI1325 belonging to a two-component system, and BMEII0704 associated with cell division. (ii) Virulence factor role. We purposely chose many important virulence-related genes out of the...”
  • “...0.014 BMEI0747 lsp ,lsu ribosomal protein l10p 0.022 BMEI1016 aerobic ,fumarate hydratase class i 0.012 BMEI1153 NADH-quinone oxidoreductase chain f 0.019 BMEI1325 Sensory transduction protein kinase 0.039 BMEI1464 pif , protoheme ix farnesyltransferase 0.014 BMEI1652 Urease alpha subunit 0.022 BMEI1758 blxR, transcriptional activator 0.043 BMEI1855 aconitate...”

BS1330_I0803 NADH-quinone oxidoreductase subunit NuoF from Brucella suis 1330
41% identity, 90% coverage

• Comparative genomic analysis between newly sequenced Brucella suis Vaccine Strain S2 and the Virulent Brucella suis Strain 1330
  Di, BMC genomics 2016
  • “...1 b YH hypothetical protein (found) 12 BS1330_I0775 1 b KT hypothetical protein (found) 13 BS1330_I0803 1 b VA nuo F (paper) 14 BS1330_I0912 1 b RQ penicillin-binding protein 1A (unknown) 15 BS1330_I1054 1 b HR acetyl-CoA hydrolase/transferase family protein (surface) 16 BS1330_I1203 1 b PS...”

Q8H2T7 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Oryza sativa subsp. japonica
43% identity, 75% coverage

• Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development.
  Deluc, BMC genomics 2007
  • “...21 2.42 1612005_s_at CB004075 TC64671 Q68S01 NADH dehydrogenase Complex 1 3 2.27 1610869_at CF515388 TC56269 Q8H2T7 NADH dehydrogenase subunit Complex 1 16 2.23 1610347_s_at CF202826 CF202826 Q0ZIW2 NAD(P)H-quinone oxidoreductase Complex 1 10 2.1 1609391_s_at CF404650 TC53103 Q41001 Copper Binding Protein Copper ion binding 2 26.11 1620588_at...”

CAETHG_3570, CLAU_RS17445 NADH-quinone oxidoreductase subunit NuoF from Clostridium autoethanogenum DSM 10061
40% identity, 65% coverage

• Genome-Scale Mining of Acetogens of the Genus Clostridium Unveils Distinctive Traits in [FeFe]- and [NiFe]-Hydrogenase Content and Maturation
  Di, Microbiology spectrum 2022
  • “...1,953.00 2,398.00 FeFe A3 CLAU_RS17440 CAETHG_3569 2.18 4.9865 4.92 2.00 4.00 4.00 6.00 7.00 CLAU_RS17445 CAETHG_3570 0.67 1.666 1.76 2.00 1.00 1.00 2.00 2.00 CLAU_RS17450 CAETHG_3571 0.76 0.459 0.33 2.00 0.00 0.00 0.00 0.00 FeFe A4 CLAU_RS18770 CAETHG_3841 72.40 28.644 22.24 9.00 15.00 15.00 14.00 25.00...”
  • “...which is predicted to operate in electron bifurcation mode. CLAU_RS17440 encodes the catalytic subunit, while CLAU_RS17445 encodes the redox cofactor-binding subunit and CLAU_RS17450 encodes a thioredoxin. The genes encoding this hydrogenase (CAETHG_3569 to 3571) were also identified in reference 9 . This work reported an additional...”
  • “...3,066.00 1,953.00 2,398.00 FeFe A3 CLAU_RS17440 CAETHG_3569 2.18 4.9865 4.92 2.00 4.00 4.00 6.00 7.00 CLAU_RS17445 CAETHG_3570 0.67 1.666 1.76 2.00 1.00 1.00 2.00 2.00 CLAU_RS17450 CAETHG_3571 0.76 0.459 0.33 2.00 0.00 0.00 0.00 0.00 FeFe A4 CLAU_RS18770 CAETHG_3841 72.40 28.644 22.24 9.00 15.00 15.00 14.00...”

Wbm0474 NADH:ubiquinone oxidoreductase, NADH-binding, chain F from Wolbachia endosymbiont strain TRS of Brugia malayi
40% identity, 87% coverage

• Effects of doxycycline on gene expression in Wolbachia and Brugia malayi adult female worms in vivo
  Rao, Journal of biomedical science 2012
  • “...production and conversion BMX14457 w Bm0689 0.09 8.65E-05 Down F0F1-type ATP synthase, beta subunit BMX14240 wBm0474 3.16 1.49E-03 Up NADH:ubiquinone oxidoreductase Metabolism & Transport BMX14214 w Bm0448 0.14 1.40E-04 Down Succinate dehydrogenase flavoprotein subunit, SdhA BMX13916 w Bm0146 0.23 1.38E-04 Down Kef-type K+ transport system, membrane...”

THTE_2882 FAD-dependent oxidoreductase from Thermogutta terrifontis
41% identity, 38% coverage

• Sugar Metabolism of the First Thermophilic Planctomycete Thermogutta terrifontis: Comparative Genomic and Transcriptomic Approaches
  Elcheninov, Frontiers in microbiology 2017
  • “...Vignais and Billoud, 2007 ) THTE_4311-4313 and/or [FeFe]-hydrogenases ( Vignais and Billoud, 2007 ) THTE_2884, THTE_2882, THTE_2881, THTE_3842-THTE_3844. On the other hand, according to our analysis, all the genomes of planctomycetes, available in the IMG database (34 genomes of planctomycetes with assigned genus and species names....”

E1ZJQ8 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (Fragment) from Chlorella variabilis
42% identity, 85% coverage

• Metabolic Insights Into Infochemicals Induced Colony Formation and Flocculation in Scenedesmus subspicatus Unraveled by Quantitative Proteomics
  Roccuzzo, Frontiers in microbiology 2020
  • “...Top 1% PCA contributors to dimension 1. Entry Protein names Organism Gene ontology (biological process) E1ZJQ8 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 1.6.5.3) (EC 1.6.99.3) (Fragment) Chlorella variabilis (Green alga) Electron transport, respiratory chain D8U1R3 Uncharacterized protein Volvox carteri f. nagariensis Protein metabolic process [GO:0019538]...”

DET0729 [Fe] hydrogenase, HymB subunit, putative from Dehalococcoides ethenogenes 195
40% identity, 66% coverage

• Organic cofactors in the metabolism of Dehalococcoides mccartyi strains
  Schipp, Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013
  • “...e.g. for a HymB subunit [47] (cbdbA684, DET0729, DehalGT_0622, DehaBAV1_0661, DhcVS_635, Dehly_624) which is genetically linked with the Ech hydrogenase...”
• Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation
  Lee, Applied and environmental microbiology 2012
  • “...DET0545 DET0614 DET0624 DET0636 DET0638 DET0645 DET0655 DET0729 DET0730 DET0734 DET0844 DET1008 DET1127 DET1193 DET1203 DET1258 DET1301 DET1372 DET1434 DET1468...”
• Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses
  Men, The ISME journal 2012
  • “...VhuA, HymB, HymC and Ech encoded by DET0615, DET0729, DET0730 and DET0866, respectively, were also found to be significantly up-regulated in the co-culture...”

CTN_RS05290 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region domain-containing protein from Thermotoga neapolitana DSM 4359
42% identity, 64% coverage

• CO₂-Induced Transcriptional Reorganization: Molecular Basis of Capnophillic Lactic Fermentation in Thermotoga neapolitana
  d'Ippolito, Frontiers in microbiology 2020
  • “...porD ( aka PFOR ) CTN_RS03950 2.74 L -lactate dehydrogenase CTN_RS05285 1.78 Fe-hydrogenase alpha subunit CTN_RS05290 1.27 Fe-hydrogenase beta subunit CTN_RS05295 NDE Fe-hydrogenase gamma subunit CTN_RS02020 1.16 Acetate kinase CTN_RS07210 1.78 Phosphate acetyltransferase Putative energy sustaining enzymes CTN_RS04025 1.50 NFN ( NADH-dependent Reduced Ferredoxin:NADP Oxidoreductase )...”

Q92406 NADH-ubiquinone oxidoreductase 51 kDa subunit, mitochondrial from Aspergillus niger
40% identity, 78% coverage

• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “...Q8U6U9 , Aquifex aeolicus Swiss-Prot: O66841 , Arabidopsis thaliana Swiss-Prot: Q8LAL7 , Aspergillus niger Swiss-Prot: Q92406 , Bos taurus GenBank: AF092131 , Bradyrhizobium japonicum DDBJ: BAC48402 , DDBJ: BAC50177 , Burkholderia xenovorans LB400 REFSEQ:YP_555778.1, Candida tropicalis Swiss-Prot: Q96UX4 , Caulobacter crescentus Swiss-Prot: Q9A6X9 , Chromobacterium violaceum...”

Mchl_1209 NADH dehydrogenase I subunit F from Methylobacterium chloromethanicum CM4
41% identity, 92% coverage

• The 380 kb pCMU01 plasmid encodes chloromethane utilization genes and redundant genes for vitamin B12- and tetrahydrofolate-dependent chloromethane metabolism in Methylobacterium extorquens CM4: a proteomic and bioinformatics study
  Roselli, PloS one 2013
  • “...n.d. n.d. 139 57 65 n.d. n.d. n.d. NuoF, NADH-quinone oxidoreductase, chain F (EC 1.6.5.3) Mchl_1209 nuoF CH 3 Cl 47.4 6.4 n.d. n.d. n.d. 217 30 49 n.d. n.d. n.d. PntAA, NAD(P)+ transhydrogenase, subunit alpha part 1 (EC 1.6.1.2) Mchl_2986 pntAA CH 3 Cl/+++ f...”

Q5XIH3 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Rattus norvegicus
NP_001006973 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Rattus norvegicus
43% identity, 82% coverage

• Targeted proteomic analysis reveals that crocodile oil from Crocodylus siamensis may enhance hepatic energy metabolism in rats.
  Fungfuang, Experimental animals 2023
  • “...CIGDLKMLAK Mitochondrial ATP synthesis coupled proton transport M0R3X7 Hexokinase-4 (HK4) Gck ARGVQDTDVVNR Glycolysis, glucose homeostasis Q5XIH3 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Ndufv1 AMGARAAYIYIRGEFYNEASNLQVAIR Mitochondrial ATP synthesis coupled electron transport P21643 Tryptophan 2,3-dioxygenase Tdo2, Tdo EEQMAEFRK Tryptophan catabolic process to acetyl-CoA B5LSW7 Cysteine sulfinic acid decarboxylase...”
• Fluoxetine Enhances Synaptic Vesicle Trafficking and Energy Metabolism in the Hippocampus of Socially Isolated Rats.
  Filipović, International journal of molecular sciences 2022
  • “...10 Pyruvate kinase PKM P11980 Pkm 1.61 34 4 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Q5XIH3 Ndufv1 1.60 4 4 Pck2 protein B2RYG2 Pck2 1.60 12 12 Ubiquitin-like modifier-activating enzyme 1 Q5U300 Uba1 1.60 16 14 14-3-3 protein epsilon P62260 Ywhae 1.60 18 15 Heat shock...”
• Quantitative proteomic analysis of intracerebral hemorrhage in rats with a focus on brain energy metabolism.
  Liu, Brain and behavior 2018
  • “...10.48 12.45 7 Th Tyrosine 3monooxygenase 0.65 B5DEN4 34.63 64.46 37 RGD1562690 Llactate dehydrogenase 0.66 Q5XIH3 35.39 58.84 31 Ndufv1 NADH dehydrogenase (Ubiquinone) flavoprotein 1 0.67 D4A830 12.09 27.63 8 Ppa2 Pyrophosphatase (inorganic) 2 0.70 Q6P7A9 19.16 19.41 14 Gaa Lysosomal alphaglucosidase 0.70 Q9JMC1 5.37 7.79...”
• Global Proteome Changes in the Rat Diaphragm Induced by Endurance Exercise Training
  Sollanek, PloS one 2017
  • “...alpha, mitochondrial F1LNF7 Idh3a 75.2 5 83.3 6.4 11 0.015 NADH dehydrogenase (Ubiquinone) flavoprotein 1 Q5XIH3 Ndufv1 102.7 8.6 114.1 9.8 11 0.023 Secreted Proteins Fibrinopeptide A P14480 Fgb 2.6 0.4 3.2 0.5 24 0.014 Serine protease inhibitor A3K P05545 Serpina3k 16.8 2.1 20.6 3.8 23...”
• Proteomics Analysis of Dorsal Striatum Reveals Changes in Synaptosomal Proteins following Methamphetamine Self-Administration in Rats
  Bosch, PloS one 2015
  • “...P17764 45 30.11 14.47 8 6 0.013 0.5 -2.0 NADH dehydrogenase (Ubiquinone) flavoprotein 1 Ndufv1 Q5XIH3 51 21.80 7.72 6 5 0.0071 0.4 -2.5 Dihydrolipoyl dehydrogenase, mitochondrial Dld Q6P6R2 54 21.80 7.72 6 2 0.0071 0.4 -2.5 Cytochrome b-c1 complex subunit Rieske, mitochondrial Uqcrfs1 P20788 29...”
• Regulation of postsynaptic function by the dementia-related ESCRT-III subunit CHMP2B
  Chassefeyre, The Journal of neuroscience : the official journal of the Society for Neuroscience 2015 (secret)
• Proteomic responses of skeletal and cardiac muscle to exercise.
  Burniston, Expert review of proteomics 2011
  • “...dehydrogenase (ubiquinone) alpha subcomplex Q561S0 [ 36 , 56 ] NADH dehydrogenase (ubiquinone) flavoprotein 1 Q5XIH3 [ 36 ] ATP synthase D-chain P31399 [ 50 ] ATP synthase O-subunit Q06647 [ 63 ] ATP synthase subunit alpha * P15999 [ 56 ] Electron transfer flavoprotein subunit...”
• Protective effects and potential mechanisms of Pien Tze Huang on cerebral chronic ischemia and hypertensive stroke
  Zhang, Chinese medicine 2010
  • “...precursor P62260 NP_113791 1433E -2.40 296 14-3-3 protein epsilon; Mitochondrial import stimulation factor L subunit Q5XIH3 NP_001006973 NDUV1 -2.00 236 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial precursor P63039 NP_071565 CH60 +2.63 595 60 kDa heat shock protein, mitochondrial precursor P08461 NP_112287 ODP2 +3.20 178 Dihydrolipoyllysine-residue acetyltransferase...”
• More
• Protective effects and potential mechanisms of Pien Tze Huang on cerebral chronic ischemia and hypertensive stroke
  Zhang, Chinese medicine 2010
  • “...P62260 NP_113791 1433E -2.40 296 14-3-3 protein epsilon; Mitochondrial import stimulation factor L subunit Q5XIH3 NP_001006973 NDUV1 -2.00 236 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial precursor P63039 NP_071565 CH60 +2.63 595 60 kDa heat shock protein, mitochondrial precursor P08461 NP_112287 ODP2 +3.20 178 Dihydrolipoyllysine-residue acetyltransferase component...”
  • “...P value Benjamini * Proteins DAVID Hippocampus Mitochondrion 0.0000185 0.01497 NP_036629, NP_112287 *, NP_071565 *, NP_001006973, NP_001006971, NP_001008888. Cerebellum Mitochondrial inner membrane 0.0000317 0.02553 NP_075581, NP_001006971, NP_036702, NP_114039, NP_037309. GOTM Hippocampus Mitochondrial membrane part 0.000000279 Nil NP_001006973, NP_071565 *, NP_001008888, NP_001006971. Cerebellum Mitochondrial inner membrane 0.0016...”
• Proteins altered by elevated levels of palmitate or glucose implicated in impaired glucose-stimulated insulin secretion
  Sol, Proteome science 2009
  • “...Hnrpa3 Q6URK4 NP_444493 23 105 Lonp1, Lon, Prss15 Q924S5 NP_596895 15 18 143 Ndufv1 Q5XIH3 NP_001006973 17 37 194 Pgk1, Pgk-1 P16617 NP_445743 15 52 131 Psmc5 O35050 BAA22935 17 41 190 Rab2 P05712 EDM11646 9 55 108 RGD1561681_predict. XP_001054125 27 58 257 Tcp1, Cct1, Ccta...”

Q54I90 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Dictyostelium discoideum
39% identity, 85% coverage

• Dictyostelium discoideum as a non-mammalian biomedical model
  Martín-González, Microbial biotechnology 2021
  • “...name ( Dictyostelium ) UniProt ( Dictyostelium ) abpC P13466 ndufs8 Q86K57 cap P54654 ndufv1 Q54I90 cluA O15818 ndufv2 Q54F10 DDB_G0267514 Q55GU0 piaA O77203 DDB_G0267552 Q55GR1 pkbA P54644 DDB_G0275973 Q552K6 raptor Q55BR7 DDB_G0279405 Q54WW7 rasD, gefE, NS gefL P03967, Q8IS18, B0M0P8 DDB_G0291852 Q54E48 rblA Q54FX2 DDB_G0292722...”

at5g08530 / Q9FNN5 NADH-ubiquinone oxidoreductase 51 kDa subunit (EC 7.1.1.2) from Arabidopsis thaliana (see paper)
TC 3.D.1.6.3 / Q9FNN5 53.5 (NuoF), component of The higher plant H+ translocating NADH dehydrogenase (NDH) complex (41 subunits; 23 included here) from Arabidopsis thaliana (Mouse-ear cress) (see paper)
NP_196470 51 kDa subunit of complex I from Arabidopsis thaliana
AT5G08530 CI51 (51 kDa subunit of complex I); 4 iron, 4 sulfur cluster binding / FMN binding / NAD or NADH binding / NADH dehydrogenase (ubiquinone)/ oxidoreductase, acting on NADH or NADPH from Arabidopsis thaliana
42% identity, 78% coverage

• substrates: H+
• Integrative Omics Analysis of Three Oil Palm Varieties Reveals (Tanzania × Ekona) TE as a Cold-Resistant Variety in Response to Low-Temperature Stress
  Saand, International journal of molecular sciences 2022
  • “...stress [ 63 ]. Furthermore, three respiratory electron transport chain proteins, NADH dehydrogenase [ubiquinone] O49313, Q9FNN5, and Q9FJW4, were reduced in BE only. The O49313 was suppressed in coconut, and several NADH dehydrogenase [ubiquinone] proteins were suppressed in the root proteomic analysis of Brassica in response...”
• Proteomic changes associated with expression of a gene (ipt) controlling cytokinin synthesis for improving heat tolerance in a perennial grass species
  Xu, Journal of experimental botany 2010
  • “...Cytoplasm 62237/6.96 195 P49105 192 0.4 NADH dehydrogenase [ Arabidopsis thaliana ] Mitochondrion 53504/8.46 526 Q9FNN5 196 0.2 NADH dehydrogenase [ Arabidopsis thaliana ] Mitochondrion 53504/8.46 551 Q9FNN5 244 0.9 Fructose-bisphosphate aldolase [ Oryza sativa ] Cytoplasm 38719/6.55 545 Q40676 252 0.6 0.7 NAD-dependent isocitrate dehydrogenase...”
• Complete Mitochondrial Complex I Deficiency Induces an Up-Regulation of Respiratory Fluxes That Is Abolished by Traces of Functional Complex I.
  Kühn, Plant physiology 2015
  • GeneRIF: Data show no major differences in the mitochondrial proteomes, cellular metabolomes, or transcriptomes between ndufv1 (At5g08530) and ndufs4 (At5g67590) mutants.
• Mitochondrial gene defects in Arabidopsis can broadly affect mitochondrial gene expression through copy number
  Ayabe, Plant physiology 2023
  • “...numbers in the TAIR library for Arabidopsis genes and Uniprot database for other plants: AtNDUFV1 (AT5G08530), AtWTF9 (AT2G39120), AtOTP87 (AT1G74600), AtPolIA (AT1G50840), AtPolIB (AT3G20540), AtRpoTmp (AT5G15700), AtrPPR5 (AT2G37230), AtCRS1 (AT5G16180), AtOTP51 (AT2G15820), AtSLO3 (AT3G61360), AtNDA2 (AT2G29990), AtNDB2 (AT4G05020), AtAOX1a (AT3G22370), AtNAD7 (ATMG00510), AtCOX2 (ATMG00160), AtATP6-1 (ATMG00410),...”
• FRIENDLY (FMT) is an RNA binding protein associated with cytosolic ribosomes at the mitochondrial surface
  Hemono, The Plant journal : for cell and molecular biology 2022
  • “...RISP subunit in complex III (Li etal., 2019 ), and two complex I subunits, CI51 (AT5G08530) and CI7.5 (AT1G67785) (Klodmann & Braun, 2011 ). In addition, in A. thaliana , a wellstudied targeted mRNA is VDAC3 (AT5G15090). The VDAC3 gene has previously been shown to be...”
  • “...only corresponds to the long mRNA isoform]; CIIIRISP, RISP subunit in complex III (AT5G13430); CI51 (AT5G08530) and CI7.5 (AT1G67785), 51 and 7.5kDa proteins in complex I. As reported previously (Michaud etal., 2014 ), VDAC short and long isoforms differ in their association with mitochondria. The three...”
• LC-MS Based Draft Map of the Arabidopsis thaliana Nuclear Proteome and Protein Import in Pattern Triggered Immunity
  Ayash, Frontiers in plant science 2021
  • “...nucleus. Name Initial part of protein sequence Transit peptide Fifty-one kilodalton subunit of complex I (AT5G08530) 1 30 52 130 MAPVRGILGLQRAVSIWKESNRLTPALRS F STQAASTSTTPQPPPPPPPPEK NAD-dependent malic enzyme 2 (AT4G00570) 1 24 37 124 MMWKNIAGLS KAAAAARTHGSRRC FSTAIPGPCIVHK Identified peptides are underlined. Transit peptides are in green. Arrow denotes...”
• Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening
  Nilo-Poyanco, BMC genomics 2021
  • “...alpha subcomplex subunit 12 AT3G03100 Prupe.1G231900 1 3 Up_O1 NADH dehydrogenase (ubiquinone) flavoprotein 1 (NDUFV1) AT5G08530 Prupe.2G281900 0.998 2 Up_O1 ENOLASE AT2G36530 Prupe.3G056600 1 10 Up_O1 6-PHOSPHOFRUCTOKINASE 1-RELATED AT4G26270 Esters Catabolism Prupe.1G439300 0.998 2 Up_O1 CARBOXYLESTERASE 2-RELATED AT1G47480 Prupe.8G121500 0.976 1 Up_O1 CARBOXYLESTERASE 12-RELATED AT3G48700 Hormones...”
• Phylogenomic proof of Recurrent Demipolyploidization and Evolutionary Stalling of the "Triploid Bridge" in Arundo (Poaceae)
  Jike, International journal of molecular sciences 2020
  • “...pa 3.79 9.98 0.009 AT2G01680 NA Ankyrin repeat family protein OG0018204 adf 4.73 6.09 0.028 AT5G08530 CI51 51 kDa subunit of mitochondrial complex I OG0018205 mc 9.25 15.13 0 AT3G15140 ERI-1 Ribonuclease H-like superfamily functioning as siRNA exonuclease. It affects post-transcriptional gene silencing and growth rate...”
• Atomic structure of a mitochondrial complex I intermediate from vascular plants
  Maldonado, eLife 2020
  • “...A0A1S3TQ85 75 kDa At5g37510 NDUFS1 NDUFS1 NDUFS1 NUAM Nqo3 N NDUV1 LOC106772405 A0A1S3V7V2 51 kDa At5g08530 NDUFV1 NDUFV1 NDUFV1 NUBM Nqo1 N NDUV2 LOC106762461 A0A1S3U769 24 kDa At4g02580 NDUFV2 NDUFV2 NDUFV2 NUHM Nqo2 Q NDUS2 nad7 E9KZN6 Nad7 AtMg00510 NDUFS2 NDUFS2 NDUFS2 NUCM Nqo4 Q NDUS3...”
• Nitric Oxide Regulates Seedling Growth and Mitochondrial Responses in Aged Oat Seeds
  Mao, International journal of molecular sciences 2018
  • “...1.24 ns V4LNR7 AT3G52300 ATP synthase subunit d, mitochondrial Eutrema salsugineum ns ns 0.70 A0A1J3KAQ0 AT5G08530 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Noccaea caerulescens ns 0.72 0.72 W5I0L9 AT3G03070 NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial Triticum aestivum ns ns 0.68 Q9SKT7 AT5G13430 External alternative NAD(P)H-ubiquinone...”
• Ectopic RING zinc finger gene from hot pepper induces totally different genes in lettuce and tobacco
  Kesawat, Molecular breeding : new strategies in plant improvement 2018
  • “...45 0.12 1.34 0.83 2.65 At5g48300 Glucose-1-phosphate adenylyltransferase small subunit (ADG1) 0.02 0.26 0.41 2.79 At5g08530 NADH dehydrogenase (ubiquinone) flavoprotein 1(CI51) 0.02 1.22 1.53 3.02 At3g03890 FMN binding protein 1.39 1.59 2.08 3.12 At4g10120 Sucrose-phosphate synthase 0 0 0 2.44 At5g66230 Chalcone-flavanone isomerase family protein 0...”
• More

7aqrF / Q9FNN5 Cryo-em structure of arabidopsis thaliana complex-i (peripheral arm) (see paper)
42% identity, 84% coverage

• Ligands: flavin mononucleotide; iron/sulfur cluster (7aqrF)

Q9A6X9 NADH-quinone oxidoreductase subunit F from Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)
41% identity, 91% coverage

• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “...DDBJ: BAC50177 , Burkholderia xenovorans LB400 REFSEQ:YP_555778.1, Candida tropicalis Swiss-Prot: Q96UX4 , Caulobacter crescentus Swiss-Prot: Q9A6X9 , Chromobacterium violaceum ATCC 12472 REFSEQ:NP_900616.1, Dechloromonas aromatica RCB GenBank: AAZ45735.1 , Dictyostelium discoideum REFSEQ:XP_636489.1, Eubacterium acidaminophilum EMBL: CAC39230.1 , Euplotes sp. GenBank: AY608636 , Hahella chejuensis KCTC 2396 REFSEQ:YP_431454.1,...”

SWOL_RS05200 NADH-quinone oxidoreductase subunit NuoF from Syntrophomonas wolfei subsp. wolfei str. Goettingen G311
Swol_1024 NADH dehydrogenase (quinone) from Syntrophomonas wolfei subsp. wolfei str. Goettingen
39% identity, 93% coverage

• Membrane Complexes of Syntrophomonas wolfei Involved in Syntrophic Butyrate Degradation and Hydrogen Formation
  Crable, Frontiers in microbiology 2016
  • “...membrane-bound formate dehydrogenases, fdh2 (locus tags: SWOL_RS04025, SWOL_RS04030, SWOL_RS04035 and SWOL_RS04040) and fdh4 (locus tags: SWOL_RS05200, SWOL_RS05205, SWOL_RS05210, SWOL_RS05215, SWOL_RS05220, and SWOL_RS05225). Interestingly, the four subunits of Fdh2 were detected in axenic culture S. wolfei cell membrane preparations (Bands A6 and A10, Supplementary Figure S1 ;...”
• Involvement of NADH:acceptor oxidoreductase and butyryl coenzyme A dehydrogenase in reversed electron transport during syntrophic butyrate oxidation by Syntrophomonas wolfei
  Müller, Journal of bacteriology 2009
  • “...three sequences derived from paralog genes in S. wolfei (Swol_1024, 1828, and 0784, with 76, 73, and 64% amino acid identity [id-aa], respectively), and to a...”

cce_2318 NADH dehydrogenase I chain F from Cyanothece sp. ATCC 51142
40% identity, 74% coverage

• Effect of continuous light on diurnal rhythms in Cyanothece sp. ATCC 51142
  Elvitigala, BMC genomics 2009
  • “...the dark (Table 1 ). Figure 2a shows the distribution of vectors for the gene cce_2318 , which encodes HoxF, one of the subunits of the bidirectional hydrogenase, as an example of circadian gene expression. All vectors corresponding to individual light and dark periods are well...”
  • “..., and the 3 rd time points within a 12 hour period. (a) The gene cce_2318 shows a cyclic expression profile under alternating light and dark conditions and does not reveal significant changes during the subjective dark period. (b) The expression of the gene cce_1063 alters...”

XF0310 NADH-ubiquinone oxidoreductase, NQO1 subunit from Xylella fastidiosa 9a5c
40% identity, 97% coverage

• Whole-genome analysis of transporters in the plant pathogen Xylella fastidiosa
  Meidanis, Microbiology and molecular biology reviews : MMBR 2002
  • “...NDH NDH NDH NDH QCR QCR 3.D.1.1.1 XF0908 XF0909 XF0315 XF0310 XF0309 XF0308 XF0307 XF0306 XF0311 XF0313 XF0305 XF0314 XF0312 XF0317 XF0316 XF0318 1 8 1 0 0 0...”

sll1221 hydrogenase subunit from Synechocystis sp. PCC 6803
40% identity, 75% coverage

• CyAbrB2 is a nucleoid-associated protein in Synechocystis controlling hydrogenase expression during fermentation
  Kariyazono, eLife 2024
  • “...genes. Operon Oxidoreductase sll0741 nifJ /pyruvate-ferredoxin/flavodoxin oxidoreductase TU3296 sll0743 Hypothetical protein sll0744 Dihydroorotate dehydrogenase (fumarate) sll1221 hoxF /bidirectional [NiFe] hydrogenase diaphorase subunit TU1714 sll1222 Unknown protein sll1223 hoxU /bidirectional [NiFe] hydrogenase diaphorase subunit sll1224 hoxY /NAD-reducing hydrogenase small subunit sll1225 Unknown protein sll1226 hoxH /NAD-reducing hydrogenase...”
• Culturing Synechocystis sp. Strain PCC 6803 with N2 and CO2 in a Diel Regime Reveals Multiphase Glycogen Dynamics with Low Maintenance Costs
  Angermayr, Applied and environmental microbiology 2016
  • “...hoxF, hoxU, hoxY, and hoxH, which are sll1220, sll1221, sll1223, sll1224, and sll1226) that encode the bidirectional NiFe-hydrogenase, as well as hydrogenase...”
• The Flavodiiron Protein Flv3 Functions as a Homo-Oligomer During Stress Acclimation and is Distinct from the Flv1/Flv3 Hetero-Oligomer Specific to the O2 Photoreduction Pathway
  Mustila, Plant & cell physiology 2016
  • “...The isiA transcription was not disturbed in the mutants. In addition, the mRNA level for sll1221 ( hoxF ), which encodes a diaphorase subunit of bidirectional hydrogenase, was elevated in both flv mutants. Analysis of the flv mutants in relation to the WT from the FL...”
• RNA-seq Profiling Reveals Novel Target Genes of LexA in the Cyanobacterium Synechocystis sp. PCC 6803
  Kizawa, Frontiers in microbiology 2016
  • “...HYDROGENASE sll1220 hoxE Diaphorase subunit of the bidirectional hydrogenase 100.28 48.94 0.49 62.85 32.54 0.52 sll1221 hoxF Diaphorase subunit of the bidirectional hydrogenase 64.58 31.77 0.49 49.47 31.90 0.64 sll1223 hoxU Diaphorase subunit of the bidirectional hydrogenase 96.63 49.39 0.51 68.18 47.23 0.69 sll1224 hoxY Hydrogenase...”
• The AbrB2 autorepressor, expressed from an atypical promoter, represses the hydrogenase operon to regulate hydrogen production in Synechocystis strain PCC6803
  Dutheil, Journal of bacteriology 2012
  • “...the eight-gene hox operon, namely, sll1220 (hoxE), sll1221 (hoxF), sll1222, sll1223 (hoxU), sll1224 (hoxY), ssl2420, sll1225, and sll1226 (hoxH). Therefore,...”
• Genetic engineering of group 2 sigma factor SigE widely activates expressions of sugar catabolic genes in Synechocystis species PCC 6803
  Osanai, The Journal of biological chemistry 2011
  • “...slr1239 slr1437 sll0611 sll1222 slr0473 ssl1533 slr1241 slll0830 slr1829 sll1221 sll1236 tal gnd hoxE pntA cph1 fus phaE hoxF a b Gene function Ratio (GOX50/GT)...”
• Hydrogenases and hydrogen metabolism of cyanobacteria
  Tamagnini, Microbiology and molecular biology reviews : MMBR 2002
  • “...30) X97797 (29, 30) X97797 (29, 30) sll1220,b X97610 sll1221, X97610 sll1223, X97610 sll1224, X97610 sll1226, X97610 (12, 95, 144) (12, 95, 144) (12, 95, 144.)...”

B7PNX4 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Ixodes scapularis
42% identity, 81% coverage

• Midgut proteome of an argasid tick, Ornithodoros erraticus: a comparison between unfed and engorged females.
  Oleaga, Parasites & vectors 2015
  • “...[ubiquinone] iron-sulfur protein Ir7 4 iron, 4 sulfur cluster binding 2 - 0.2 - Unfed B7PNX4 IscW_ISCW005985 NADH:ubiquinone oxidoreductase, NDUFV1/51kDa subunit, Ir8 4 iron, 4 sulfur cluster binding 2 - 0.13 - Unfed B7PBH7 IscW_ISCW003299 NADH-ubiquinone reductase Ir9 Iron-sulfur cluster binding 2 - 0.22 - Unfed...”

TTHERM_00193910 NADH-ubiquinone oxidoreductase flavoprotein from Tetrahymena thermophila SB210
41% identity, 81% coverage

• Gene network landscape of the ciliate Tetrahymena thermophila
  Xiong, PloS one 2011
  • “...electron transport, it should have many partners in the oxidative phosphorylation pathway. The Tetrahymena ortholog (TTHERM_00193910) of the human NDUFV1 gene has 347 partners in TGN. GO enrichment analysis results show these genes are involved in oxidative phosphorylation related terms: oxidation reduction, electron transport chain, tricarboxylic...”

8gymv1 / Q23KE4 8gymv1 (see paper)
41% identity, 86% coverage

• Ligands: iron/sulfur cluster; flavin mononucleotide (8gymv1)

PP2184 formate dehydrogenase, beta subunit, putative from Pseudomonas putida KT2440
40% identity, 81% coverage

• Redundancy of enzymes for formaldehyde detoxification in Pseudomonas putida
  Roca, Journal of bacteriology 2009
  • “...glutathione independent PP3970 PP0489 PP0490 PP0491 PP0492 PP2183 PP2184 PP2185 PP2186 fdhB fmdA fmdB fmdC fmdD fmdE fmdF fmdG fmdH Formaldehyde dehydrogenase,...”
  • “...fdhA (PP0328) PRCC fdhE (PP0492) PRCC fmdF (PP2184) AR0489 AR3970 AR2184/0489 AR0328/3970 Plasmids pCHESIKmGm pAR0489 pAR3970 pMP220 pMP0328 pMP0489 pMP2183...”
• Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology
  Puchałka, PLoS computational biology 2008
  • “...or PP4012 l -Serine 22.41 23.01 6.66 10.67 Formate dehydrogenase PP0490 or PP0491 PP2183 or PP2184 or PP2185 or PP2186 4 Citrate synthase PP4194 l -Valine 21.85 0.83 1.00 2-Methylcitrate dehydratase PP2338 5 Glycine hydroxymethyl transferase PP0322 l -Leucine, l -lysine, l -phenylalanine 16.75 3.33 4.00...”

PP_2184 formate dehydrogenase beta subunit from Pseudomonas putida KT2440
40% identity, 82% coverage

• Gene expression reprogramming of Pseudomonas alloputida in response to arginine through the transcriptional regulator ArgR
  Molina-Henares, Microbiology (Reading, England) 2024
  • “...PP_0328 fdhA formaldehyde dehydrogenase + PP_1088 argG arginine synthesis + PP_1741 betX choline/betaine/carnitine transport + PP_2184 formate dehydrogenase subunit beta + PP_0103 cytochrome c oxidase subunit (aa3) PP_0711 ycaC-I putative hydrolase PP_0806 lapF adhesin PP_2359 putative Type one pili subunit PP_2362 usher protein PP_2572 hypothetical protein...”

nubm / CAB65520.1 NUBM protein from Yarrowia lipolytica (see paper)
Q9UUU2 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Yarrowia lipolytica
40% identity, 77% coverage

• Characterization of clinically identified mutations in NDUFV1, the flavin-binding subunit of respiratory complex I, using a yeast model system
  Varghese, Human molecular genetics 2015
  • “...lipolytica . The accession codes are P49821 ( Hs ), P25708 ( Bt ) and Q9UUU2 ( Yl ), and the sequences shown include the mitochondrial target peptides (gray) that are removed to form the mature proteins. The sequences are colored as in Figure 2 to...”
• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “...REFSEQ:XP_824451.1, Trypanosoma cruzi GenBank: EAN82122.1 , uncultured archaeon GZfos26D6 GenBank: AAU83054.1 , Yarrowia lipolytica Swiss-Prot: Q9UUU2 ] Multivariate Comparative Analysis The codon usage of the genes investigated in this study was subjected to a multivariate analysis by means of Principal Component Analysis (PCA) to visualise the...”

NP_496376 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Caenorhabditis elegans
41% identity, 80% coverage

• Riboflavin enhances the assembly of mitochondrial cytochrome c oxidase in C. elegans NADH-ubiquinone oxidoreductase mutants.
  Grad, Biochimica et biophysica acta 2006 (PubMed)
  • GeneRIF: catalytic deficiency of complexes I & IV in nuo-1 mutants are due to impaired assembly or stability; mutants have reduced levels of fully assembled complex I & assembly intermediates; riboflavin stabilizes steady-state levels of NUO-1
• Caenorhabditis elegans development requires mitochondrial function in the nervous system.
  Ndegwa, Biochemical and biophysical research communications 2004 (PubMed)
  • GeneRIF: Results indicate that nuo-1 and mitochondrial respiratory chain function in the nervous system is needed to send and receive signals that control larval development and exit from dauer.

7b0nF / Q9UUU2 3.7-angstrom structure of Yarrowia lipolytica complex I with an R121M mutation in NUCM. (see paper)
40% identity, 82% coverage

• Ligands: flavin mononucleotide; iron/sulfur cluster (7b0nF)

MSMEG_0160 formate dehydrogenase, beta subunit from Mycobacterium smegmatis str. MC2 155
40% identity, 79% coverage

• Small RNA F6 Provides Mycobacterium smegmatis Entry into Dormancy
  Grigorov, International journal of molecular sciences 2021
  • “...MSMEG_0157 Oxalyl-CoA decarboxylase 54.1 MSMEG_0158 Formyl-coenzyme A transferase 45.5 MSMEG_0159 Formate dehydrogenase subunit gamma 29.8 MSMEG_0160 Formate dehydrogenase subunit beta 38.5 MSMEG_0161 Formate dehydrogenase subunit alpha 35.6 MSMEG_0162 NAD-dependent formate dehydrogenase subunit delta 30.3 MSMEG_0168 Formyl-coenzyme A transferase 19.3 MSMEG_4640 Hypothetical protein 14.2...”
• Mycobacterium smegmatis RoxY is a repressor of oxyS and contributes to resistance to oxidative stress and bactericidal ubiquitin-derived peptides
  Daugherty, Journal of bacteriology 2011
  • “...Further analysis of our microarray data revealed that msmeg_0160 and msmeg_0166 were upregulated in three out of four samples. We did not identify any...”

XP_001321469 hydrogenosomal NADH dehydrogenase 51 kDa subunit from Trichomonas vaginalis G3
40% identity, 85% coverage

• The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites
  Tanifuji, PloS one 2018
  • “...- - GCSH * XP_001299513 - GCSL * XP_001330332 - NuoE XP_001312168 - NuoF * XP_001321469 - Anaerobic ATP synthesis ME * AAA92714 XP_001707581 PFO * AAA85495 EET01691 ferredoxin XP_001324407 ABV81956 Hydrogenase * XP_001305709 EFO64299 HydE * XP_001326754 - HydF * XP_001309182 - HydG * XP_001313153...”

A4XKL3 NADH dehydrogenase (Quinone) from Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)
41% identity, 69% coverage

• Part I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2
  Andrews, Analytical and bioanalytical chemistry 2010
  • “...synthase II 9 A4XJY3 Putative, probable phosphoenolpyruvate carboxykinase 2 5 A4XKI0 6-phosphofructokinase 11 3 1 A4XKL3 NADH dehydrogenase 10 11 6 A4XKL4 Hydrogenase, Fe-only 2 1 1 A4XKR2 SYI Isoleucyl-tRNA synthetase 2 11 4 14 A4XKR7 Putative, probable peptidase M56 8 20 A4XKV0 ENO Enolase 19...”
• Part II: defining and quantifying individual and co-cultured intracellular proteomes of two thermophilic microorganisms by GeLC-MS2 and spectral counting
  Andrews, Analytical and bioanalytical chemistry 2010
  • “...3-oxoacyl-[acyl-carrier-protein] synthase II x A4XJY3 Putative, probable phophoenolpyruvate carboxykinase x Throughout 2nd half A4XK10 6-phosphofructokinase A4XKL3 NADH dehydrogenase A4XKL4 Hydrogenase, Fe-only A4XKR2 SYI Isoleucyl-tRNA synthetase Throughout 2nd half A4XKV2 Phosphoglycerate kinase/triosephosphate isomerase A4XKV3 Glyceraldehyde-3-phosphate dehydrogenase Throughtout 2nd half A4XKV5 Pyruvate phospahte dikinase A4XKX0ATPB ATP synthase subunit...”

PTH_2648 NADH:ubiquinone oxidoreductase, NADH-binding 51 kD subunit from Pelotomaculum thermopropionicum SI
42% identity, 68% coverage

• Membrane Potential-requiring Succinate Dehydrogenase Constitutes the Key to Propionate Oxidation and Is Unique to Syntrophic Propionate-oxidizing Bacteria
  Kosaka, Microbes and environments 2023
  • “...These domains containing genes include PTH_1405 (NAD_binding_1); PTH_0267, PTH_0595, and PTH_0596 (Oxidored_FMN); PTH_2011, PTH_1378, and PTH_2648 (Complex1_51K) ( Table S2 ). The appropriate gene cannot be identified by the presence of a domain; however, the genes in P. thermopropionicum may be coupled to FRD. Furthermore, cytoplasmic...”
• Concerted Metabolic Shifts Give New Insights Into the Syntrophic Mechanism Between Propionate-Fermenting Pelotomaculum thermopropionicum and Hydrogenotrophic Methanocella conradii
  Liu, Frontiers in microbiology 2018
  • “...dehydrogenase PTH_2646 4.42 7.06 11.57 Hypothetical formate dehydrogenase PTH_2647 4.45 7.00 11.53 Hypothetical membrane protein PTH_2648 nuoF 4.59 6.90 11.56 NADH: ubiquinone oxidoreductase, NADH-binding 51 kD subunit PTH_2649 nuoE 4.70 5.75 10.54 NADH: ubiquinone oxidoreductase 24 kD subunit Putative Fix complex I b PTH_0016 fixA 1.57...”

9fdvB / O66841 Crystal structure of reduced nuoef variant r66g(nuof) from aquifex aeolicus (see paper)
44% identity, 89% coverage

• Ligands: iron/sulfur cluster; 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydro-2h-benzo[g]pteridin-1-id-10(5h)-yl)-5-o-phosphonato-d-ribitol (9fdvB)

F7O84_RS09545 NADH-quinone oxidoreductase subunit NuoF from Candidatus Galacturonibacter soehngenii
41% identity, 64% coverage

• "Candidatus Galacturonibacter soehngenii" Shows Acetogenic Catabolism of Galacturonic Acid but Lacks a Canonical Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase Complex
  Valk, Frontiers in microbiology 2020
  • “...13 Electron transport complex protein E 7.2.1.2 F7O84_RS03285 143 9 Ferredoxin hydrogenase subunit A 1.12.7.2 F7O84_RS09545 196 100 Ferredoxin hydrogenase subunit B 1.12.7.2 F7O84_RS09550 356 32 Ferredoxin hydrogenase subunit C 1.12.7.2 F7O84_RS04820 124 86 N.d., not detected. Homologs of Rnf cluster (F7O84_03275-3295; EC 7.2.1.2) and hydrogenase...”

Q96UX4 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial from Candida tropicalis
40% identity, 75% coverage

• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “...Bradyrhizobium japonicum DDBJ: BAC48402 , DDBJ: BAC50177 , Burkholderia xenovorans LB400 REFSEQ:YP_555778.1, Candida tropicalis Swiss-Prot: Q96UX4 , Caulobacter crescentus Swiss-Prot: Q9A6X9 , Chromobacterium violaceum ATCC 12472 REFSEQ:NP_900616.1, Dechloromonas aromatica RCB GenBank: AAZ45735.1 , Dictyostelium discoideum REFSEQ:XP_636489.1, Eubacterium acidaminophilum EMBL: CAC39230.1 , Euplotes sp. GenBank: AY608636 ,...”

B5IPC7 Formate dehydrogenase, beta subunit from Cyanobium sp. PCC 7001
40% identity, 67% coverage

• Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production.
  Roberts, BMC systems biology 2010
  • “...synthase Cthe_0375 GMP synthase, large subunit A2C5P2 4.00E-176 1.2.1.2 formate dehydrogenase Cthe_0341 NADH dehydrogenase (quinone) B5IPC7 6.00E-126 5.3.3.2 isopentenyl-diphosphate Delta-isomerase Cthe_1022 Glycerol-3-phosphate dehydrogenase A8VXT5 2.00E-94 2.5.1.29 farnesyltranstransferase Cthe_0831 Polyprenyl synthetase B2J443 4.00E-69 2.5.1.33 trans-pentaprenyltranstransferase Cthe_0564 Trans-hexaprenyltranstransferase Q6KZR8 3.00E-25 3.2.1.108 lactase Cthe_0212 Beta-glucosidase P09848 3.00E-89 3.5.1.19 nicotinamidase...”

8x9vC / A0A0K0GM91 Crystal structure of xanthomonas oryzae pv. Oryzae nadh-quinone oxidoreductase subunits nuoe and nuof
41% identity, 93% coverage

• Ligand: flavin mononucleotide (8x9vC)

NDH51 NADH-quinone oxidoreductase chain F from Candida albicans (see 4 papers)
40% identity, 75% coverage

• CharProtDB CGD description: Subunit of nicotinamide adenine dinucleotide dehydrogenase complex I, of the mitochondrial electron transport chain; required for wild-type filamentous growth; alkaline downregulated

SWOL_RS03960 NADH-quinone oxidoreductase subunit NuoF from Syntrophomonas wolfei subsp. wolfei str. Goettingen G311
36% identity, 90% coverage

• Syntrophomonas wolfei Uses an NADH-Dependent, Ferredoxin-Independent [FeFe]-Hydrogenase To Reoxidize NADH
  Losey, Applied and environmental microbiology 2017
  • “...wolfei Hyd1ABC was previously found to copurify with a multimeric formate dehydrogenase encoded by SWOL_RS03955, SWOL_RS03960, SWOL_RS03965, and SWOL_RS03970 ( 47 ). The copurification of Hyd1ABC with an apparent formate dehydrogenase suggested a possible formate dehydrogenase-hydrogenase complex, although an alternative would be that Hyd1 and the...”

PTH_1378 NADH:ubiquinone oxidoreductase, NADH-binding 51 kD subunit from Pelotomaculum thermopropionicum SI
39% identity, 62% coverage

• Membrane Potential-requiring Succinate Dehydrogenase Constitutes the Key to Propionate Oxidation and Is Unique to Syntrophic Propionate-oxidizing Bacteria
  Kosaka, Microbes and environments 2023
  • “...Complex1_51K (PF01512). These domains containing genes include PTH_1405 (NAD_binding_1); PTH_0267, PTH_0595, and PTH_0596 (Oxidored_FMN); PTH_2011, PTH_1378, and PTH_2648 (Complex1_51K) ( Table S2 ). The appropriate gene cannot be identified by the presence of a domain; however, the genes in P. thermopropionicum may be coupled to FRD....”

6vw7D / Q0KDY2 Formate dehydrogenase fdsabg subcomplex fdsbg from c. Necator - nadh bound (see paper)
42% identity, 78% coverage

• Ligands: flavin mononucleotide; iron/sulfur cluster; 1,4-dihydronicotinamide adenine dinucleotide (6vw7D)

LT988_09425 NADH-quinone oxidoreductase subunit NuoF from Thiocapsa bogorovii
40% identity, 75% coverage

• The Complete Genome of a Novel Typical Species Thiocapsa bogorovii and Analysis of Its Central Metabolic Pathways
  Petushkova, Microorganisms 2024
  • “...]. The Hox1 hydrogenase consists of the HoxYH hydrogenase (LT988_09435 and LT988_09445) and HoxFU diaphorase (LT988_09425 and LT988_09430). HoxE (LT988_09420) is a fifth subunit that is thought to be involved in an electron transfer, followed by a gene (LT988_09450) encoding the hydrogenase maturation protein, namely HoxW....”

PFL_0330 formate dehydrogenase, beta subunit from Pseudomonas fluorescens Pf-5
41% identity, 77% coverage

• The effect of iron limitation on the transcriptome and proteome of Pseudomonas fluorescens Pf-5
  Lim, PloS one 2012
  • “...Genes Annotated functions Iron-deprived (-FeCl 2 ) Iron-deprived (-FeCl 3 ) Transcript Protein Transcript Protein PFL_0330 formate dehydrogenase subunit beta FdsB NS 1.85 0.62 1.68 PFL_1208 ferredoxin FdxA NS 1.97 NS 2.21 PFL_1241 ferredoxin-NADP reductase Fpr_1 0.65 1.44 NS 0.88 PFL_1666 flagellar synthesis regulator FleN NS...”

8iufV1 8iufV1 (see paper)
40% identity, 74% coverage

• Ligands: flavin mononucleotide; iron/sulfur cluster (8iufV1)

Q84FW2 formate dehydrogenase (EC 1.17.1.9) from Methylorubrum extorquens (see paper)
39% identity, 80% coverage

HPODL_04625 NADH-ubiquinone oxidoreductase subunit, mitochondrial from Ogataea parapolymorpha DL-1
40% identity, 76% coverage

• Physiological relevance, localization and substrate specificity of the alternative (type II) mitochondrial NADH dehydrogenases of <i>Ogataea parapolymorpha</i>
  Juergens, Frontiers in microbiology 2024
  • “...kanR resistance cassette using pUD801, IMX2197 was constructed from IMX1978 by additional deletion of NUBM (HPODL_04625) ( Juergens et al., 2020 ) with a pat resistance cassette using pUD1036, and IMX2167 was constructed from IMX2017 by additional deletion of GUT2 (HPODL_00581) with a pat resistance cassette...”
• Contribution of Complex I NADH Dehydrogenase to Respiratory Energy Coupling in Glucose-Grown Cultures of Ogataea parapolymorpha
  Juergens, Applied and environmental microbiology 2020
  • “...reading frame (ORF) encoding the complex I NUBM 51-kDa subunit ( OpNUBM , locus tag HPODL_04625; GenBank accession number XM_014080963.1 ) was identified. OpNUBM was found via a homology search (blastn [ https://blast.ncbi.nlm.nih.gov ]) in the O. parapolymorpha CBS11895 (DL-1) RefSeq assembly (NCBI accession number GCF_000187245.1)...”

PATL70BA_2847 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region domain-containing protein from Petrocella atlantisensis
39% identity, 40% coverage

• Hydrostatic Pressure Helps to Cultivate an Original Anaerobic Bacterium From the Atlantis Massif Subseafloor (IODP Expedition 357): Petrocella atlantisensis gen. nov. sp. nov
  Quéméneur, Frontiers in microbiology 2019
  • “...a 4Fe-4S dicluster domain-containing, poorly characterized, periplasmic hydrogenase found in many anaerobic Firmicutes , and PATL70BA_2847, another homolog of the hndA subunit gene. Besides, the genes encoding a [FeFe] hydrogenase maturase (HydEFG), involved in the synthesis and incorporation of the di-iron center, were identified. The genome...”

Q98BW8 NAD-dependent formate dehydrogenase beta subunit from Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
37% identity, 83% coverage

• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin.
  Boxma, BMC evolutionary biology 2007
  • “...metallidurans CH34 REFSEQ:YP_583087.1, Ralstonia solanacearum EMBL: CAD15764.1 , Ralstonia solanacearum UW551 REFSEQ:ZP_00943355.1, Rhizobium loti Swiss-Prot: Q98BW8 , Swiss-Prot: Q98KR0 , Rhizobium meliloti Swiss-Prot: P56912 , Swiss-Prot: P56913 , Rhodobacter capsulatus Swiss-Prot: O07948 , Rhodococcus opacus Swiss-Prot: P72304 , Rhodoferax ferrireducens T118 REFSEQ:YP_525088.1, Rickettsia prowazekii Swiss-Prot: Q9ZE33...”

MPNT_310010 formate dehydrogenase beta subunit from Candidatus Methylacidithermus pantelleriae
39% identity, 80% coverage

• Metagenome Assembled Genome of a Novel Verrucomicrobial Methanotroph From Pantelleria Island
  Picone, Frontiers in microbiology 2021
  • “...dehydrogenase MPNT_130014 1.17.1.9 fdh 77.2 C. sequanensis Formate dehydrogenase MPNT_310008 1.2.1.2 fdsA 77.3 N. kurashikiensis MPNT_310010 fdsB 69.1 M. ishizawai MPNT_310011 fdsC 62.1 Rhizobium MPNT_310006 fdsD 54.8 Burkholderiales bacterium The second step in methane oxidation is the conversion of methanol to formaldehyde or formate. Two types...”

ABD05_RS10755 formate dehydrogenase beta subunit from Burkholderia pyrrocinia
37% identity, 84% coverage

• The peanut root exudate increases the transport and metabolism of nutrients and enhances the plant growth-promoting effects of burkholderia pyrrocinia strain P10
  Han, BMC microbiology 2023
  • “...rfbD dTDP4-dehydro- rhamnose reductase 1.11 ABD05_RS18190 ywkA D-malate dehydrogenase 1.56 ABD05_RS27705 echA15 Enoyl-CoA hydratase 1.55 ABD05_RS10755 fdxH Formate dehydrogenase 1.05 ABD05_RS25365 ackA Acetate kinase 1.45 ABD05_RS29405 Gluconate 2-dehydrogenase 2.28 ABD05_RS17755 catB Muconate cycloisomerase 1.69 ABD05_RS21650 araG L-arabinose transport system ATP-binding protein 1.65 ABD05_RS27815 dmpE 2-Oxopent4-enoate/ cis2-oxohex4-enoate...”
  • “...transport system permease protein 1.66 ABD05_RS24050 purU Formyltetrahydrofolate deformylase 3.24 ABD05_RS00140 aceA Isocitrate lyase 1.30 ABD05_RS10755 fdxH Formate dehydrogenase 1.05 ABD05_RS30705 argH Argininosuccinate lyase 1.47 ABD05_RS19015 hipO Hippurate hydrolase 2.22 ABD05_RS19795 gabD Glutarate-/succinate- semialdehyde dehydrogenase 1.89 ABD05_RS23060 phnW 2-aminoethylphosphonate-pyruvate transaminase 2.15 Quantitative real-time polymerase chain reaction...”

B4DE93 NADH:ubiquinone oxidoreductase core subunit V1 from Homo sapiens
43% identity, 77% coverage

• Identification of proteins interacting with the mitochondrial small heat shock protein Hsp22 of Drosophila melanogaster: Implication in mitochondrial homeostasis
  Dabbaghizadeh, PloS one 2018
  • “...Putative ribosome-binding factor A, mitochondrial (Q8N0V3) 0.2 0.05 0 0 NADH dehydrogenase flavoprotein 1, mitochondrial (B4DE93) 0.18 0 0 0 Dimethyladenosine transferase 1, mitochondrial (Q8WVM0) 0.2 0.05 0 0 Long-chain-fatty-acid-CoA ligase 3 (O95573) 0.185 0.02 1.18 0.1 0.19 Synaptic vesicle membrane protein VAT-1 homolog (Q99536) 0.17...”

bll3137 NADH dehydrogenase I chain F from Bradyrhizobium japonicum USDA 110
40% identity, 77% coverage

• Influence of elevated atmospheric carbon dioxide on transcriptional responses of Bradyrhizobium japonicum in the soybean rhizoplane
  Sugawara, Microbes and environments 2013
  • “...1.5 Alpha-ketoglutarate dehydrogenase blr2316 1.7 Probable NADH-ubiquinone oxidoreductase chain F blr2524 1.6 Electrotransfer ubiquinone oxidoreductase bll3137 nuoF 2.1 NADH dehydrogenase I chain F bll4906 nuoL 1.6 NADH ubiquinone oxidoreductase chain L bll4909 nuoI 1.8 1.6 NADH ubiquinone oxidoreductase chain I bll4917 nuoC 1.6 NADH ubiquinone oxidoreductase...”

fdsB / GI|3724144 NAD-dependent formate dehydrogenase, beta subunit from Ralstonia eutropha H16 (see 2 papers)
fdsB / CAA11234.1 NAD-dependent formate dehydrogenase beta subunit from Cupriavidus necator (see paper)
41% identity, 79% coverage

IALB_0530 NADH-quinone oxidoreductase subunit NuoF from Ignavibacterium album JCM 16511
36% identity, 66% coverage

• Complete Genome of Ignavibacterium album, a Metabolically Versatile, Flagellated, Facultative Anaerobe from the Phylum Chlorobi
  Liu, Frontiers in microbiology 2012
  • “...et al., 2004 ). Additionally, the HydB subunits of the two predicted hydrogenases are different; IALB_0530 has an N-terminal [2Fe-2S] and two C-terminal [4Fe-4S] clusters other than the NuoF-like FMN and NAD(P)(H) binding domain like HydB of T. maritima and T. tengcongensis hydrogenases, but IALB_0256 does...”

IALB_0256 NADH-quinone oxidoreductase subunit F from Ignavibacterium album JCM 16511
40% identity, 92% coverage

• Complete Genome of Ignavibacterium album, a Metabolically Versatile, Flagellated, Facultative Anaerobe from the Phylum Chlorobi
  Liu, Frontiers in microbiology 2012
  • “...FMN and NAD(P)(H) binding domain like HydB of T. maritima and T. tengcongensis hydrogenases, but IALB_0256 does not have these extra Fe-S clusters (Figure 9 ). The exact enzymatic activities of these two hydrogenases are unclear, but it seems safe to assume they use NAD(P)(H) as...”

BTH_I1623 formate dehydrogenase, beta subunit from Burkholderia thailandensis E264
39% identity, 77% coverage

• Choline Catabolism in Burkholderia thailandensis Is Regulated by Multiple Glutamine Amidotransferase 1-Containing AraC Family Transcriptional Regulators
  Nock, Journal of bacteriology 2016
  • “...BTH_I0959 BTH_I1406 BTH_I1620 BTH_I1621 BTH_I1622 BTH_I1623 BTH_I1624 BTH_I1625 BTH_I3016 BTH_I3017 BTH_II0001 BTH_II0643 BTH_II0694 BTH_II0695 BTH_II0964...”

RL4392 putative NAD-dependent formate dehydrogenase beta subunit from Rhizobium leguminosarum bv. viciae 3841
39% identity, 80% coverage

• Rhizobium leguminosarum Glutathione Peroxidase Is Essential for Oxidative Stress Resistance and Efficient Nodulation
  Hu, Frontiers in microbiology 2021
  • “...0.0076 RL3066 Periplasmic Transmembrane protein 17.22 0.69 0.0083 RL2554 Periplasmic Exported protein 12.42 0.65 0.0291 RL4392 fdsB Cytoplasmic NAD-dependent formate dehydrogenase beta subunit 54.75 0.82 0.0485 pRL90175 bdhA Cytoplasmic D-beta-hydroxybutyrate dehydrogenase like protein 27.21 0.82 0.0473 RL0644 rbtD Cytoplasmic Ribitol 2-dehydrogenase 25.73 0.8 0.0419 RL2323 Periplasmic...”
  • “...and RL2554 code for membrane transport proteins, of which four were ABC-type transporters. 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...”

SMc02525 PUTATIVE NAD-DEPENDENT FORMATE DEHYDROGENASE BETA SUBUNIT PROTEIN from Sinorhizobium meliloti 1021
39% identity, 77% coverage

• Formate-dependent autotrophic growth in Sinorhizobium meliloti
  Pickering, Journal of bacteriology 2008
  • “...fds (consisting of smc02524, smc03086, smc03085, smc04444, smc02525, and smc02524), in S. meliloti affect formate-dependent growth. Moreover, we show that, in...”

Cenrod_0976 NAD(P)H-dependent oxidoreductase subunit E from Candidatus Symbiobacter mobilis CR
39% identity, 62% coverage

• Genomic analysis reveals key aspects of prokaryotic symbiosis in the phototrophic consortium "Chlorochromatium aggregatum"
  Liu, Genome biology 2013
  • “...bi-directional group 3d NiFe hydrogenase (Cenrod_0973 and Cenrod_0974) with an associated diaphorase complex (Cenrod_0975 and Cenrod_0976) and a group 3c Mvh hydrogenase (Cenrod_2144, Cenrod_2145, and Cenrod_2148) with an associated heterodisulfide reductase (Cenrod_2147). The diaphorase moiety of the group 3d NiFe hydrogenase should enable the reversible coupling...”

6tg9B / D5AQH1 Cryo-em structure of nadh reduced form of NAD+-dependent formate dehydrogenase from rhodobacter capsulatus (see paper)
40% identity, 81% coverage

• Ligands: flavin mononucleotide; iron/sulfur cluster; 1,4-dihydronicotinamide adenine dinucleotide (6tg9B)

A9762_24625 formate dehydrogenase beta subunit from Pandoraea sp. ISTKB
38% identity, 78% coverage

• Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB
  Kumar, Biotechnology for biofuels 2018
  • “...1.414862 16 34.2 90.668 3.91E102 A0A1E3LDS6 A9762_24610 Formate dehydrogenase 0.761355 2 57.1 8.7799 3.84E22 A0A1E3LE53 A9762_24625 Formate dehydrogenase 1.257519 9 30 56.957 3.45E62 A0A1E3LG97; A0A1E3LF08 A9762_24620 Formate dehydrogenase subunit alpha 1.020855 21 34 104.98 1.29E121 A0A1E3LL63 A9762_15395 NADH dehydrogenase 0.064345 9 60.8 21.897 5.70E49 A0A1E3LPJ3 A9762_01450...”

WP_041793924 NAD(P)H-dependent oxidoreductase subunit E from Pararhodospirillum photometricum DSM 122
40% identity, 64% coverage

• Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes
  Degli, Biology direct 2016
  • “...a , formerly CAG:977 Entamoeba invadens Trichomonas vaginalis Protein Fds/NuoE-like CAC39229, HymA WP_051228661 CCG42368, HoxS WP_041793924, HoxS ? CDB53275 MH0030_GL0011535, CCZ22624 absent AAV65813 Fds/NuoF-like CAC39230, HymB WP_026791755 ? CDB53276 MH0276_GL0125578,CCZ22625 absent AAV65812 Fds/NuoG-like, type M3 [FeFe]-hydrogenase CAC39231, HymC WP_026791754, WP_036838588 CCG42367, CCG40656 WP_051013609 ? CDB53277 MH0030_GL0047537,...”

blr2316 blr2316 from Bradyrhizobium japonicum USDA 110
39% identity, 67% coverage

• Induction by Bradyrhizobium diazoefficiens of Different Pathways for Growth in D-mannitol or L-arabinose Leading to Pronounced Differences in CO₂ Fixation, O₂ Consumption, and Lateral-Flagellum Production
  Cogo, Frontiers in microbiology 2018
  • “...- Ara catabolic pathway bll1188 Q89V68 atpB ATP synthase subunit a. - In only Ara blr2316 Q89ST4 Probable NADH-ubiquinone oxidoreductase chain F. In only Ara - blr2929 Q89R43 Hydroxypyruvate isomerase. NS In only Ara blr2974 Q89QZ8 Dehydratase. Similar to a putative D -galactarate dehydratase. -1.2323 -...”
• Influence of elevated atmospheric carbon dioxide on transcriptional responses of Bradyrhizobium japonicum in the soybean rhizoplane
  Sugawara, Microbes and environments 2013
  • “...Malonate carrier protein blr1278 mdcM 2.0 Malonate transporter TCA cycle bll0452 sucA 1.5 Alpha-ketoglutarate dehydrogenase blr2316 1.7 Probable NADH-ubiquinone oxidoreductase chain F blr2524 1.6 Electrotransfer ubiquinone oxidoreductase bll3137 nuoF 2.1 NADH dehydrogenase I chain F bll4906 nuoL 1.6 NADH ubiquinone oxidoreductase chain L bll4909 nuoI 1.8...”

LT988_16210 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region domain-containing protein from Thiocapsa bogorovii
37% identity, 61% coverage

• The Complete Genome of a Novel Typical Species Thiocapsa bogorovii and Analysis of Its Central Metabolic Pathways
  Petushkova, Microorganisms 2024
  • “...and characterized [ 13 ], is encoded by the genes Hox2YH (LT988_16220 and LT988_16225), Hox2FU (LT988_16210 and LT988_16215), and Hox2W (LT988_18265). HydSL, HupSLC, and Hox1 enzymes have been identified and described in Alc. vinosum DSM 180 T [ 32 ]; however, in contrast to T. bogorovii...”

SAR11_0680 NAD-dependent formate dehydrogenase beta subunit from Candidatus Pelagibacter ubique HTCC1062
37% identity, 71% coverage

• Proteomic and transcriptomic analyses of "Candidatus Pelagibacter ubique" describe the first PII-independent response to nitrogen limitation in a free-living Alphaproteobacterium
  Smith, mBio 2013
  • “...SAR11_0750 mmuM Homocysteine S -methyltransferase 1.62 0.76 b SAR11_0504 cycM Cytochrome c 2.30 0.74 a SAR11_0680 fdsB Formate dehydrogenase 1.58 0.64 b SAR11_1143 grlA Glutaredoxin 1.82 0.61 b SAR11_0171 Rhodanese-related sulfur transferase 1.62 0.57 b a q value of 0.05. No changes in mRNA abundance were...”
• One carbon metabolism in SAR11 pelagic marine bacteria
  Sun, PloS one 2011
  • “...in the methyl-THF linked oxidation pathway ( Fig. 2A ). The genes fdhF (SAR11_0679), fdsB (SAR11_0680) and fdhD (SAR11_0681; Fig. 1A ) are predicted to encode subunits of formate dehydrogenase (FDH), which catalyzes the final step in the pathway, the oxidation of formate to CO 2...”

hoxF / P22317 α subunit from Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337) (see paper)
P22317 hydrogen dehydrogenase (EC 1.12.1.2) from Cupriavidus necator (see paper)
PHG088 NAD-reducing hydrogenase diaphorase moiety large subunit from Ralstonia eutropha H16
PHG088 bidirectional NAD-reducing hydrogenase diaphorase subunit HoxF from Cupriavidus necator H16
39% identity, 54% coverage

• Construction of Cupriavidus necator displayed with superoxide dismutases for enhanced growth in bioelectrochemical systems
  Chen, Bioresources and bioprocessing 2023
  • “...subunits: HoxH (PHG091, 54.9 kD), HoxY (PHG090, 22.9 kD), HoxU (PHG089, 59.6 kD), and HoxF (PHG088, 66.7 kD), which deliver protons and electrons to NAD + to synthesize NADH for cell growth and biosynthetic reactions. Compared with H16, CMS strengthens the promoter of MBH and SH...”
• Global changes in the proteome of Cupriavidus necator H16 during poly-(3-hydroxybutyrate) synthesis from various biodiesel by-product substrates
  Sharma, AMB Express 2016
  • “...assembly protein HypD1 1.79 2.13 ND PHG021 Regulatory [NiFe] hydrogenase large subunit 1.98 3.13 0.84 PHG088 NAD-reducing hydrogenase diaphorase moiety large 4.55 5.59 ND PHG095 [NiFe] hydrogenase nickel incorporation-associated protein HypB2 2.06 2.53 ND PHG013 [NiFe] hydrogenase nickel incorporation-associated protein HypB1 3.23 4.99 0.36 PHG091 NAD-reducing...”
• An innovative cloning platform enables large-scale production and maturation of an oxygen-tolerant [NiFe]-hydrogenase from Cupriavidus necator in Escherichia coli
  Schiffels, PloS one 2013
  • “...Locus tag Gene Locus tag Gene Locus tag Gene Locus tag Gene Diaphorase large subunit PHG088 hoxF Diaphorase small subunit PHG089 hoxU H 2 ase small subunit PHG090 hoxY H 2 ase large subunit PHG091 hoxH Diaphorase-associated dimer with NADPH activation site PHG093 hoxI Nickel storage...”

CAP2UW1_1001 Respiratory-chain NADH dehydrogenase domain 51 kDa subunit from Candidatus Accumulibacter phosphatis clade IIA str. UW-1
36% identity, 63% coverage

• Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
  Oyserman, The ISME journal 2016
  • “...activation enzymes (CAP2UW1_1002, CAP2UW1_3266), a potassium transporter (CAP2UW1_2100), and an operon containing the cytoplasmic hydrogenase (CAP2UW1_1001- CAP2UW1_0998). These observations provide yet additional evidence for the co-regulation of hydrogen gas production with acetate uptake and PHA synthesis. Therefore, we hypothesize that this group of genes may represent...”

Saro_0733 NADH dehydrogenase (quinone) from Novosphingobium aromaticivorans DSM 12444
37% identity, 77% coverage

• Catabolism of β-5 linked aromatics by Novosphingobium aromaticivorans
  Metz, mBio 2024
  • “...S-glutathione hydrolases (Saro_2822) ( 35 ) and the subunits of a formate dehydrogenase complex (Saro_0732, Saro_0733, and Saro_0735) ( 36 ). Metabolic pathway diagram depicts the degradation of DC-A to vanillin, highlighting key intermediates (DC-L, DC-C, DC-S-C, 5-CF, 5-FF, PDC, ferulic acid) and enzymes (FdhA, FerD,...”

P72304 NAD-reducing hydrogenase alpha subunit from Rhodococcus opacus
40% identity, 52% coverage

• The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
  Boxma, BMC evolutionary biology 2007
  • “...UW551 REFSEQ:ZP_00943354.1, Rattus norvegicus Swiss-Prot: P19234 , Rhodobacter sphaeroides ATCC 17029 REFSEQ:ZP_00918830.1, Rhodococcus opacus Swiss-Prot: P72304 , Rhodoferax ferrireducens T118 REFSEQ:YP_525088.1, Streptomyces avermitilis MA-4680 REFSEQ:NP_823011.1, Syntrophus aciditrophicus SB REFSEQ:YP_461127.1, Tetrahymena thermophila Swiss-Prot: Q23LJ5 , Thermoanaerobacter tengcongensis GenBank: AAM24146 , Thermococcus kodakarensis KOD1 DDBJ: BAD85803.1 , Thermotoga...”
  • “...meliloti Swiss-Prot: P56912 , Swiss-Prot: P56913 , Rhodobacter capsulatus Swiss-Prot: O07948 , Rhodococcus opacus Swiss-Prot: P72304 , Rhodoferax ferrireducens T118 REFSEQ:YP_525088.1, Rickettsia prowazekii Swiss-Prot: Q9ZE33 , Solanum tuberosum Swiss-Prot: Q43840 , Streptomyces avermitilis MA-4680 REFSEQ:NP_823011.1, Synechococcus elongatus PCC 6301 EMBL: CAA73873.1 , Syntrophus aciditrophicus SB REFSEQ:YP_461127.1,...”

MCA2577 dehydrogenase subunit, putative from Methylococcus capsulatus str. Bath
36% identity, 70% coverage

• Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707
  Klotz, Applied and environmental microbiology 2006
  • “...MCA1525, 1528 to MCA1530 MCA2891 MCA2576 to MCA2577 MCA1208 to MCA1210 DH, dehydrogenase. classical denitrification capacity through dissimilatory nitrite...”

NDUV1_SCHPO / O94500 NADH-ubiquinone oxidoreductase 51 kDa subunit homolog SPBC18E5.10, mitochondrial; EC 1.6.-.- from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
34% identity, 82% coverage

• cofactor: FMN (Binds 1 FMN.)
  cofactor: [4Fe-4S] cluster (Binds 1 [4Fe-4S] cluster.)

Rmet_1522 Respiratory-chain NADH dehydrogenase domain, 51 kDa subunit from Ralstonia metallidurans CH34
Rmet_1522 NAD(P)H-dependent oxidoreductase subunit E from Cupriavidus metallidurans CH34
35% identity, 57% coverage

• The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments
  Janssen, PloS one 2010
  • “...the SH, contains one partial hox gene denoted hoxV (Rmet_1534), nine intact hox genes hoxFUYHWINXA (Rmet_1522 through Rmet_1527, Rmet_1533, and Rmet_1541-42), and six genes hypA 2 B 2 F 2 C 2 D 2 E 2 (Rmet_1535 through Rmet_1540) all on genomic island CMGI-3. The latter...”

fdh1B / Q8KTI8 NAD-dependent formate dehydrogenase β subunit (EC 1.17.1.9) from Methylorubrum extorquens (see 2 papers)
Q8KTI8 formate dehydrogenase (EC 1.17.1.9) from Methylorubrum extorquens (see paper)
35% identity, 73% coverage

7vw6B / C5ATT6 Cryo-em structure of formate dehydrogenase 1 from methylorubrum extorquens am1 (see paper)
35% identity, 70% coverage

• Ligands: fe2/s2 (inorganic) cluster; iron/sulfur cluster; flavin mononucleotide (7vw6B)

5xfaA / A0A077L6X8 Crystal structure of NAD+-reducing [nife]-hydrogenase in the h2- reduced state (see paper)
38% identity, 65% coverage

• Ligand: iron/sulfur cluster (5xfaA)

Rmet_4300 NADH-quinone oxidoreductase subunit F from Cupriavidus metallidurans CH34
Rmet_4300 NADH:ubiquinone oxidoreductase complex I, chain F from Ralstonia metallidurans CH34
37% identity, 83% coverage

• The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments
  Janssen, PloS one 2010
  • “...NAD-dependent epimerase/dehydratase, and by Rmet_4310 as a FAD-dependent pyridine nucleotide-disulphide oxidoreductase. We also discerned the Rmet_4300 gene that apparently codes for a NuoF homologue (NADH ubiquinone oxidoreductase, chain F). Other membrane-associated protein complexes that may be important to the electron transport chain in strain CH34 are...”

nuoB / AAA53584.1 NADH ubiquinone oxidoreductase subunit, partial from Escherichia coli (see paper)
74% identity, 24% coverage

MAP4_RS15540 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region domain-containing protein from Mycobacterium avium subsp. paratuberculosis MAP4
30% identity, 84% coverage

• Viable Mycobacterium avium subsp. paratuberculosis Colonizes Peripheral Blood of Inflammatory Bowel Disease Patients
  Estevinho, Microorganisms 2023
  • “...which has been isolated from human breast milk and is annotated in the Genbank as MAP4_RS15540. 4. Discussion The identification of pathobionts with a role in IBD is of importance to understand the complex multifactorial process of this disease [ 37 , 38 , 39 ]....”

MAV_0925 respiratory-chain NADH dehydrogenase 51 kd subunit family protein from Mycobacterium avium 104
30% identity, 85% coverage

• The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium
  Yano, BMC genomics 2019
  • “...and EA2) tended to cluster at one node in the trees of MAH_0766 (Mah104 locus_tag MAV_0925; product name of NADH dehydrogenase), MAH_0771 (Mah104 locus_tag MAV_0930; product name of amidohydrolase), MAH_0788 (Mah104 locus_tag MAV_0940; cinA gene, product name of 1,8-cineole 2-endo-monooxygenase or cytochrome P-450), and MAH_0809 (Mah104...”

MAH_0766 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region domain-containing protein from Mycobacterium avium subsp. hominissuis TH135
29% identity, 84% coverage

• The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium
  Yano, BMC genomics 2019
  • “...identified five marker gene candidates, including orthologs of strain TH135 gene MAH_0771 (TH135 coordinate 772,960), MAH_0766 (TH135 coordinate 767,567), MAH_0788 (TH135 coordinate 795,348), MAH_0809 (TH135 coordinate 813,897), and MAH_2714 (TH135 coordinate: 2,965,182). Members of each of the five major lineages (SC1, SC2 plus SC4, SC3, EA1,...”
  • “...(Mah104 locus_tag MAV_0960, product name of hypothetical protein), but not in MAH_2714 (Additionalfile 3 ). MAH_0766, MAH_0771, MAH_0788 are located in the recombination-cold region at chromosome coordinates 683,022 to 799,327 ( Hi : 4.6 to 2.0) (Fig. 2 d). SC2 and SC4 share an allele in...”

E9PQP1 NADH:ubiquinone oxidoreductase core subunit V1 (Fragment) from Homo sapiens
50% identity, 28% coverage

• Postsynaptic Proteome of Non-Demented Individuals with Alzheimer's Disease Neuropathology.
  Zolochevska, Journal of Alzheimer's disease : JAD 2018
  • “...5.5 13 13 237 3.21 1.44 4.62 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (Fragment) NDUFV1 E9PQP1 8.51 8.26 51 46 105 2.77 1.47 1.88 Neurofilament medium polypeptide NEFM E7EMV2 4.76 5.4 79 50 210 1.28 1.50 1.17 Profilin-2 PFN2 C9J0J7 9.26 5.76 10 14 126 1.80...”

7zc6C / A0A923IZ11 Na+ - translocating ferredoxin: NAD+ reductase (rnf) of c. Tetanomorphum (see paper)
24% identity, 63% coverage

• Ligands: iron/sulfur cluster; flavin mononucleotide (7zc6C)

Cphy_1185 Respiratory-chain NADH dehydrogenase domain 51 kDa subunit from Clostridium phytofermentans ISDg
27% identity, 53% coverage

• High-quality-draft genome sequence of the fermenting bacterium Anaerobium acetethylicum type strain GluBS11^T (DSM 29698)
  Patil, Standards in genomic sciences 2017
  • “...with NADH. 1,2-propanediol is then disproportionated in microcompartments to propionate and propanol by 1,2-propanediol oxidoreductase (Cphy_1185, Ga0116910_1005154), 1,2-propanediol dehydratase (Cphy_1174, Ga0116910_100557 - Ga0116910_100559 in a different area of the genome), propionaldehyde dehydrogenase (Cphy_1178, Ga0116910_1005146), phosphate propanoyl transferase (Cphy_1183, Ga0116910_1005152), acetate/propionate kinase (Cphy_1327, Ga0116910_104214, Ga0116910_1001586, or Ga0116910_103636)...”
• Characterization of a planctomycetal organelle: a novel bacterial microcompartment for the aerobic degradation of plant saccharides
  Erbilgin, Applied and environmental microbiology 2014
  • “...(C. phytofermentans) 4; Cphy_1176, 1; Cphy_1186 1; Cphy_1184 Cphy_1185 Cphy_1180, Cphy_1181, Cphy_1182 2; pvmD, -E 0 3; pvmH, -K, None -M Experimentally...”
• Involvement of a bacterial microcompartment in the metabolism of fucose and rhamnose by Clostridium phytofermentans
  Petit, PloS one 2013
  • “...49.4 32.7 Cphy_1184 ABC25535 (83) PduN (60) - - EutN_CcmL shell protein (PF03319) 37.2 22.5 Cphy_1185 ABC25536 (67) PduS (58) - - Propanediol oxidoreductase 31.7 20.6 Cphy_1186 ABC25537 (78) PduT (66.3) - - BMC shell protein (PF00936) 25.6 15.7 Cphy_1187 ABC25538 (69) PocR (nd) Escherichia coli...”

rnfC / H6LC32 Rnf complex RnfC subunit (EC 7.2.1.2) from Acetobacterium woodii (strain ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1) (see 12 papers)
RNFC_ACEWD / H6LC32 Na(+)-translocating ferredoxin:NAD(+) oxidoreductase complex subunit C; Rnf electron transport complex subunit C; EC 7.2.1.2 from Acetobacterium woodii (strain ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1) (see 3 papers)
H6LC32 ferredoxin-NAD+ oxidoreductase (Na+-transporting) (subunit 4/6) (EC 7.2.1.2) from Acetobacterium woodii (see paper)
TC 3.D.6.1.2 / C4N8U0 RnfC, component of The Rnf-type NADH dehydrogenase, RnfABCDEG (Imkamp et al., 2007). Note: RnfD may be truncated as almost all homologues have 300-330aas with 6-7 TMSs from Acetobacterium woodii (see 2 papers)
AWO_RS11370, Awo_c22060, WP_014356580 electron transport complex subunit RsxC from Acetobacterium woodii DSM 1030
27% identity, 54% coverage

• function: Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane. Couples electron transfer from reduced ferredoxin to NAD(+) with electrogenic movement of Na(+) out of the cell. Involved in caffeate respiration.
  catalytic activity: 2 reduced [2Fe-2S]-[ferredoxin] + Na(+)(in) + NAD(+) + H(+) = 2 oxidized [2Fe-2S]-[ferredoxin] + Na(+)(out) + NADH (RHEA:46800)
  cofactor: [4Fe-4S] cluster (Binds 2 [4Fe-4S] clusters per subunit.)
  subunit: The complex is composed of six subunits: RnfA, RnfB, RnfC, RnfD, RnfE and RnfG.
• substrates: H+
  tcdb comment: This system has been shown to pump Na+ out of the cell when reducing NAD+ with reduced ferredoxin, and dependent on the smf for reduction of ferredoxin with NADH2 (Hess et al. 2013)
• Looking for the mechanism of arsenate respiration of Fusibacter sp. strain 3D3, independent of ArrAB
  Acosta-Grinok, Frontiers in microbiology 2022
  • “...Alkaliphilus metalliredigens A6TQH4 4 10 160 RnfC Electron transport complex protein RnfC WP_069873483 Acetobacterium woodii H6LC32 7 10 158 RnfD Electron transport complex protein RnfD WP_069873485 Acetobacterium woodii H6LC31 1 10 118 RnfE Electron transport complex protein RnfE WP_069873489 Acetobacterium woodii H6LC32 3 10 92 RnfG...”
• A new metabolic trait in an acetogen: Mixed acid fermentation of fructose in a methylene-tetrahydrofolate reductase mutant of Acetobacterium woodii
  Moon, Environmental microbiology reports 2023
  • “...complex protein RnfG 1666 4351 1.38 Awo_c22050 Electron transport complex protein RnfD 2939 9086 1.62 Awo_c22060 Electron transport complex protein RnfC1 4844 11,125 1.19 Awo_c26970 Iron hydrogenase HydA1 Bifurcating hydrogenase 63,435 56,607 0.17 Awo_c26980 Iron hydrogenase HydB 68,393 49,927 0.45 Awo_c26990 Iron hydrogenase HydD 7064 5220...”
• Obligate autotrophy at the thermodynamic limit of life in a new acetogenic bacterium
  Frolov, Frontiers in microbiology 2023
  • “...T and/or the proteins of T.kivui . The RnfD and RnfC queries were Awo_c22050 and Awo_c22060 from Acetobacterium woodii . For convenience of further analysis of gene co-occurrence and co-location, the queries were usually concatenated (up to 17 subqueries separated by strings of 100 x letters)....”
• Genome-Scale Analysis of Acetobacterium woodii Identifies Translational Regulation of Acetogenesis
  Shin, mSystems 2021
  • “...the bifurcating hydrogenase gene cluster (Awo_c26970 to Awo_c27010), the Rnf complex gene cluster (Awo_c22010 to Awo_c22060), F 1 F o ATP synthase (Awo_c02140 to Awo_c02240), phage-related genes, transmembrane genes, and genes encoding putative transcriptional regulators. We analyzed the translational dynamics for phage-related genes, where two large...”
• The Rnf Complex Is an Energy-Coupled Transhydrogenase Essential To Reversibly Link Cellular NADH and Ferredoxin Pools in the Acetogen Acetobacterium woodii
  Westphal, Journal of bacteriology 2018 (secret)
• Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle
  Detman, Biotechnology for biofuels 2018
  • “...flavoprotein subunit alpha WP_014355266 (AWO_RS04415) (EtfA), FAD/FMN-containing dehydrogenase WP_014355267 (AWO_RS04420) (GlcD), electron transporter RnfC WP_014356580 (AWO_RS11370) all 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...”
  • “...transfer flavoprotein subunit alpha WP_014355266 (AWO_RS04415) (EtfA), FAD/FMN-containing dehydrogenase WP_014355267 (AWO_RS04420) (GlcD), electron transporter RnfC WP_014356580 (AWO_RS11370) all 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,...”

WP_069873483 electron transport complex subunit RsxC from Fusibacter sp. 3D3
27% identity, 53% coverage

• Looking for the mechanism of arsenate respiration of Fusibacter sp. strain 3D3, independent of ArrAB
  Acosta-Grinok, Frontiers in microbiology 2022
  • “...protein RnfB GAU77413 Alkaliphilus metalliredigens A6TQH4 4 10 160 RnfC Electron transport complex protein RnfC WP_069873483 Acetobacterium woodii H6LC32 7 10 158 RnfD Electron transport complex protein RnfD WP_069873485 Acetobacterium woodii H6LC31 1 10 118 RnfE Electron transport complex protein RnfE WP_069873489 Acetobacterium woodii H6LC32 3...”

TM0244 electron transport complex protein, putative from Thermotoga maritima MSB8
25% identity, 54% coverage

• Linking genome content to biofuel production yields: a meta-analysis of major catabolic pathways among select H2 and ethanol-producing bacteria
  Carere, BMC microbiology 2012
  • “...CD(M2f) Tpet_0723 TTH Tpet_0675-Tpet_0680 T. maritima MSB8 TM1424- TM1426 TTH TM1420- TM1422 CD(M2f) TM0201 TTH TM0244- TM0249 Cal.subterraneus subsp. tengcongensis MB4 TTE0123- TTE0134 TTE0892- TTE0894 A1 TR(M3) TTE0887 D M2e TTE0697 CD(M2f) E. harbinense YUAN-3 T Ethha_2614- Ethha_2616 A8 TR(M3) Ethha_0052 CD(M2f) Ethha_2293 A7 D(M3) Ethha_0031...”

THEMA_RS03485 electron transport complex subunit RsxC from Thermotoga maritima MSB8
25% identity, 55% coverage

• A Cytoplasmic NAD(P)H-Dependent Polysulfide Reductase with Thiosulfate Reductase Activity from the Hyperthermophilic Bacterium Thermotoga maritima
  Liang, Microbiology spectrum 2022
  • “...were also analyzed by qRT-PCR. Besides the nsr gene, mbxA (THEMA_RS08165), yeeE (THEMA_RS09360), and rnfC (THEMA_RS03485) genes were upregulated in the presence of S 0 or thiosulfate. There were more significant transcription level changes in these genes in the presence of thiosulfate ( Fig.3 ). The...”
  • “...(THEMA_RS08165), subunit A of putative membrane-bound sulfur oxidoreductase; yeeE (THEMA_RS09360), a putative thiosulfate transferase; rnfC (THEMA_RS03485), subunit C of reduced ferredoxin:NAD + oxidoreductase Rnf. The yeeE gene is annotated to encode a membrane protein YeeE, which reportedly mediates thiosulfate uptake in E. coli and Spirochaeta thermophila...”

Teth514_0079 electron transport complex, RnfABCDGE type, C subunit from Thermoanaerobacter ethanolicus X514
28% identity, 36% coverage

• Complete genome sequence of the chromate-reducing bacterium Thermoanaerobacter thermohydrosulfuricus strain BSB-33
  Bhattacharya, Standards in genomic sciences 2015
  • “...WP_006569864.1, WP_003869957.1- WP_003869960.1, WP_003869962.1- WP_003869964.1, WP_004399468.1, WP_039929512.1, Oxidoreductase activity Electron transport complex, RnfABCDGE Na(+) translocating Teth514_0079 - Teth514_0084 Electron carrier activity and oxidoreductase activity Fig. 5 Comparison of candidate chromate reductase genes in Thermoanaerobacter thermohydrosulfuricus BSB-33, T. wiegelii Rt8.B1, T. siderophilus SR4 and T. sp X514...”

CLOSPO_00573 hypothetical protein from Clostridium sporogenes ATCC 15579
26% identity, 59% coverage

• Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites
  Liu, Nature microbiology 2022
  • “...genomes for homologs of the C. sporogenes Rnf gene cluster ( rnfCDGEAB , CLOSPO_00568 to CLOSPO_00573) with default settings. The results were manually curated to identify organisms harboring complete gene clusters. Coding sequences for the 16S rRNA genes were retrieved for these organisms from the Joint...”

F7O84_RS03275 electron transport complex subunit RsxC from Candidatus Galacturonibacter soehngenii
26% identity, 55% coverage

• "Candidatus Galacturonibacter soehngenii" Shows Acetogenic Catabolism of Galacturonic Acid but Lacks a Canonical Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase Complex
  Valk, Frontiers in microbiology 2020
  • “...Electron transport complex protein B 7.2.1.2 F7O84_RS03300 261 40 Electron transport complex protein C 7.2.1.2 F7O84_RS03275 329 22 Electron transport complex protein DG 7.2.1.2 F7O84_RS03290 101 13 Electron transport complex protein E 7.2.1.2 F7O84_RS03285 143 9 Ferredoxin hydrogenase subunit A 1.12.7.2 F7O84_RS09545 196 100 Ferredoxin hydrogenase...”

CLNEO_01350 electron transport complex subunit RsxC from Anaerotignum neopropionicum
24% identity, 70% coverage

• Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum
  Benito-Vaquerizo, Microbial cell factories 2022
  • “...neopropionicum harbours a complete rnf cluster, composed of the genes rnfA (CLNEO_01390), rnfB (CLNEO_01400), rnfC (CLNEO_01350), rnfD (CLNEO_01360), rnfE (CLNEO_01380) and rnfG (CLNEO_01370). With ethanol as substrate, our assumption is that the Rnf complex of A. neopropionicum operates in reverse, generating Fd 2- . The endergonic...”

D8DXV6 Ion-translocating oxidoreductase complex subunit C from Segatella baroniae B14
26% identity, 56% coverage

• Occurrence and Function of the Na+-Translocating NADH:Quinone Oxidoreductase in Prevotella spp.
  Deusch, Microorganisms 2019
  • “...Uniprot Accession No. Identity (%) NDH-I Subunit Uniprot Accession No. Identity (%) NqrA D8DWC1 RnfC D8DXV6 25.22 NuoH D8DWN8 18.44 NqrB D8DWC0 RnfD D8DXV5 30.28 NuoK D8DWN5 26.88 NqrC D8DWB9 RnfG D8DYE1 27.05 NuoI D8DWN7 26.83 NqrD D8DWB8 RnfE D8DXV3 37.36 NuoN D8DX02 19.08 NqrE D8DWB7...”

E3PRL8 Ion-translocating oxidoreductase complex subunit C from Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / CCUG 9281 / NCIMB 10654 / HF)
32% identity, 26% coverage

• First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile.
  Serrano, Standards in genomic sciences 2017
  • “...4 10 -160 A6TQH4 rnfC Electron transport complex protein RnfC 52/2097 Clostridium sticklandii 64 0 E3PRL8 rnfD Electron transport complex protein RnfD 52/2098 Eubacterium acidaminophilum 64 5 10 -135 W8T3U4 rnfE Electron transport complex protein RnfE 52/2100 Clostridium bartlettii CAG:1329 70 5 10 -92 R5Y4N2 rnfG...”

CSPO_9c00100 proline reductase-associated electron transfer protein PrdC from Clostridium sporogenes
27% identity, 52% coverage

• Genome sequence of Clostridium sporogenes DSM 795(T), an amino acid-degrading, nontoxic surrogate of neurotoxin-producing Clostridium botulinum
  Poehlein, Standards in genomic sciences 2015
  • “...PrdB (CSPO_9c00070), and PrdC, a protein with high sequence homology to the C-subunit of Rnf-complex (CSPO_9c00100). The cluster shows a similar organization as in C. sticklandii [ 73 , 74 ], except for the additional presence of a transposase (CSPO_9c00150), a second copy of PrdH2 (CSPO_9c00160)...”

Dtur_1091 electron transport complex, RnfABCDGE type, C subunit from Dictyoglomus turgidum DSM 6724
28% identity, 34% coverage

• The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor
  Brumm, Frontiers in microbiology 2016
  • “...gradient needed for ATP generation is produced by NADH oxidoreductase (Dtur_0558; Dtur_0559; Dtur_0916; Dtur_0919, and Dtur_1091), and succinate dehydrogenase (Dtur_0445). ATP is generated by proton translocation via an F0F1-type ATP synthase (Dtur_129 through Dtur_135). D . turgidum also possesses a V-type ATP synthase (Dtur_1499 through Dtur_1506),...”

Pcar_2503 pyridine nucleotide-disulphide oxidoreductase from Pelobacter carbinolicus str. DSM 2380
38% identity, 12% coverage

• The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features
  Aklujkar, BMC genomics 2012
  • “...gene are genes for a hydrogenase ( hndD 1 Pcar_2502) and an NADPH oxidoreductase subunit (Pcar_2503) similar to SfrB of Geobacteraceae [ 40 ] that together may dispose of electrons from glycerol and 1,3-propanediol. The glycerol dehydratase gene cluster and the 1,3-propanediol dehydrogenase gene cluster share...”
  • “...of the glycerol/1,3-propanediol oxidation pathway, may receive electrons from this pathway via an SfrB-like protein (Pcar_2503) as its NADPH-oxidizing partner. Hydrogenases HndD-2 and HndD-3 may each form a complex with a three-subunit NADPH oxidoreductase encoded next to them ( hndA 2 B 2 C 2 ,...”

CD630_11370, CDIF630erm_01284 electron transport complex subunit RsxC from Clostridioides difficile
CD1137 electron transport complex protein from Clostridium difficile 630
28% identity, 25% coverage

• Iron Regulation in Clostridioides difficile
  Berges, Frontiers in microbiology 2018
  • “...CDIF630erm_03542 Surface protein -1.35 -2.85 CD630_32470 CDIF630erm_03544 prdC Electron transfer protein 4.62 -0.96 4.78 -0.90 CD630_11370 CDIF630erm_01284 rnfC Electron transport complex protein RnfC 2.64 -0.73 2.91 -0.49 CD630_11380 CDIF630erm_01285 rnfD Electron transport complex protein RnfD 2.01 -1.19 3.58 -0.62 CD630_11390 CDIF630erm_01286 rnfG Electron transport complex protein...”
  • “...Surface protein -1.35 -2.85 CD630_32470 CDIF630erm_03544 prdC Electron transfer protein 4.62 -0.96 4.78 -0.90 CD630_11370 CDIF630erm_01284 rnfC Electron transport complex protein RnfC 2.64 -0.73 2.91 -0.49 CD630_11380 CDIF630erm_01285 rnfD Electron transport complex protein RnfD 2.01 -1.19 3.58 -0.62 CD630_11390 CDIF630erm_01286 rnfG Electron transport complex protein RnfG...”
  • “...proline reductase ( prdFEDBARC , CDIF630erm_03533 03544) and Rnf complex encoding operons ( rnfCDGEAB , CDIF630erm_01284 01289) were induced in C. difficile (Table 1 ). Correspondingly, the highest increase in metabolite concentration was observed for 5-aminovalerate, the product of up-regulated proline utilization, when the lower biomass...”
• Is there a Function for a Sex Pheromone Precursor?
  Vasieva, Journal of integrative bioinformatics 2019
  • “...(a.k.a. CD630_24830, YP_001088997.1, AM180355, FAD:protein FMN transferase), rnfC Electron transport complex protein (a.k.a. CD630_11370, YP_001087628.1, CD1137, Electron transport complex protein), rnfD Electron transport complex protein (a.k.a. CD630_11380, YP_001087629.1, CD1138, Electron transport complex protein), rnfG Electron transport complex protein (a.k.a. CD630_11390, YP_001087630.1, CD1139, Electron transport complex protein),...”
• Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile
  Antunes, Nucleic acids research 2012
  • “...CD0854 d oppC 5.7 1029471 CD0853CD0856 AAGAAAACCTTATCTA 77 CD1116 36 1312695 GAGAAAAGGTTTCCAA 167 NR + CD1137 5.2 1336232 CD1136CD1137 GAAAAAATGTTTTTTT 37 NR NR CD1170 5.9 1368750 CD1170CD1173 ND ND + NR CD1214 e spo0A e 1.5 1412498 TGTAAAAAGTTTAGTT 42 CD1321 d 1.6 1531839 AGGAAATAGTTAACTT 24 CD1336...”

Hore_14350 electron transport complex, RnfABCDGE type, C subunit from Halothermothrix orenii H 168
22% identity, 89% coverage

• Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii
  Mavromatis, PloS one 2009
  • “...the organism on lactate has not been observed [3] . A cluster of genes (Hore_14300 Hore_14350) exhibiting similarity to the Rnf electron transport complex found in other genomes from anaerobic organisms is present. This system is similar to a Na + -dependent NADHubiquinone oxidoreductase [22] ....”

B5RBP3 Propanediol utilization ferredoxin from Salmonella gallinarum (strain 287/91 / NCTC 13346)
29% identity, 53% coverage

• Using the Yeast Three-Hybrid System to Identify Proteins that Interact with a Phloem-Mobile mRNA.
  Cho, Frontiers in plant science 2012
  • “...motifs (RRMs; Figure 3 ). The most frequently identified clone from the Y3H screening, StLSH10 (B5RBP3), was also included (Table A3 in Appendix). Each of these proteins induced -galactosidase activity in an interaction with the bait RNA to levels much higher than the negative controls and,...”
  • “...the regulation of alternative splicing, ribosome function, and RNA metabolism (Wachter et al., 2012 ). B5RBP3 is alight-dependent short hypocotyl (LSH10, AT2G42610) protein with a Domain of Unknown Function (DUF640, Figure 3 ). In Arabidopsis , there are 10 LSH genes and in potato, 15 (Figure...”

lmo1142 similar to Salmonella enterica PduS protein from Listeria monocytogenes EGD-e
24% identity, 70% coverage

• Pyruvate carboxylase plays a crucial role in carbon metabolism of extra- and intracellularly replicating Listeria monocytogenes
  Schär, Journal of bacteriology 2010
  • “...lmo1044b lmo1045b lmo1046b lmo1047 lmo1048b lmo1049 lmo1097 lmo1142 lmo1143 lmo1144 lmo1145 lmo1146 lmo1150 lmo1172b lmo1254d lmo1255d lmo1306 lmo1339 lmo1349b...”
  • “...the fruRBA operon (lmo2335 to lmo2337), the pdu genes (lmo1142 to lmo1150), and the panBCD genes (lmo1900 to lmo1902), as well as lmo0769 and lmo0865, encoding...”
• Glycerol metabolism and PrfA activity in Listeria monocytogenes
  Joseph, Journal of bacteriology 2008
  • “...lmo0979 lmo1034 lmo1057 lmo1097 lmo1099 cadA lmo1103 lmo1142 lmo1143 lmo1151 lmo1152 lmo1154 lmo1155 lmo1157 lmo1159 lmo1160 lmo1161 Similar to transaldolase...”
• Identification of Listeria monocytogenes genes contributing to intracellular replication by expression profiling and mutant screening
  Joseph, Journal of bacteriology 2006
  • “...10 genes within the 55-kb gene cluster ranging from lmo1142 (pduS) to lmo1208 (cbiP), which encode the factors for coenzyme B12 synthesis and for the vitamin...”

t1325 putative NADH reducing dehydrogenase from Salmonella enterica subsp. enterica serovar Typhi Ty2
25% identity, 63% coverage

• A whole-genome screen identifies Salmonella enterica serovar Typhi genes involved in fluoroquinolone susceptibility
  Turner, The Journal of antimicrobial chemotherapy 2020
  • “...associated gor glutathione reductase 2.95 6.5 10 158 trxB thioredoxin reductase 1.62 8.04 10 24 t1325 putative NADH reducing dehydrogenase 1.48 1.8 10 52 gshB glutathione synthetase 1.42 7.99 10 10 t1326 putative ferredoxin-like protein, cytoplasmic membrane 1.41 2.27 10 17 Nucleoid associated parC topoisomerase IV...”

CACET_c16320 electron transport complex subunit RsxC from Clostridium aceticum
31% identity, 22% coverage

• Energy Conservation in the Acetogenic Bacterium Clostridium aceticum
  Wiechmann, Microorganisms 2021
  • “...for a membrane-bound complex potentially consisting of monomers of each subunit. The first one is CACET_c16320 coding for RnfC, followed by CACET_c16330 coding for RnfD, CACET_c16340 coding for RnfG, CACET_c16350 coding for RnfE, CACET_c16360 coding for RnfA and CACET_c16370 coding for RnfB. The operon is flanked...”

pduS / Q9XDM9 cob(II)alamin reductase from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 3 papers)
PDUS_SALTY / Q9XDM9 Cobalamin reductase PduS; Propanediol utilization protein PduS from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 4 papers)
NP_460998 propanediol utilization protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
29% identity, 53% coverage

• function: A protein that aids in conversion of cob(III)alamin to cob(II)alamin and then to cob(I)alamin in the bacterial microcompartment (BMC) dedicated to 1,2-propanediol (1,2-PD) degradation (PubMed:15817784, PubMed:20656910). The latter step requires PduO. No free cob(I)alamin is released, suggesting a complex is formed with PduO that finishes conversion to adenosylcobalamin. PduS and PduO allow regeneration of the adenosylcobalamin cofactor within the BMC (PubMed:15817784). Another study showed reduction of cob(II)alamin to cob(I)alamin in the absence of PduO. Both reactions require NADH. Cyanocobalamin (CN-Cbl) is not a substrate for the first reaction (PubMed:20656910). Cobalamin reduction probably occurs spontaneously in the presence of free reduced flavin nucleotides, this protein may be involved in electron transfer for this reduction (Probable).
  function: The 1,2-PD-specific bacterial microcompartment (BMC) concentrates low levels of 1,2-PD catabolic enzymes, concentrates volatile reaction intermediates thus enhancing pathway flux and keeps the level of toxic, mutagenic propionaldehyde low.
  cofactor: [4Fe-4S] cluster (Binds 2 [4Fe-4S] clusters (By similarity). The two centers are coupled but must possess different redox potentials (By similarity).)
  cofactor: FMN (Binds one FMN non-covalently per monomer.)
  subunit: Monomeric when purified anaerobically, dimeric under aerobic conditions (PubMed:20656910). Forms a complex with PduO (PubMed:15817784, PubMed:20656910). Interacts with PduT, probably via the N-terminus of PduS (By similarity).
  disruption phenotype: Grows more slowly and to a lower cell density than wild-type.
• Characterization of the PduS cobalamin reductase of Salmonella enterica and its role in the Pdu microcompartment.
  Cheng, Journal of bacteriology 2010
  • GeneRIF: Studies further characterize PduS, an unusual MCP-associated cobalamin reductase, and, in conjunction with prior results, indicate that the Pdu MCP encapsulates a complete cobalamin assimilation system.

Tph_c07030 4Fe-4S dicluster domain-containing protein from Thermacetogenium phaeum DSM 12270
24% identity, 69% coverage

• Alternative Pathways of Acetogenic Ethanol and Methanol Degradation in the Thermophilic Anaerobe Thermacetogenium phaeum
  Keller, Frontiers in microbiology 2019
  • “...cluster does not contain genes for a phosphate acetyltransferase (eutD). A gene annotated as rnfC (Tph_c07030) and encoding a soluble protein containing ironsulfur clusters was expressed as well, however no potential function and no relation of this single gene to a membrane-bound Rnf-complex that usually consists...”
  • “...Bertsch et al., 2015 ). It remains pure speculation whether the wrongly annotated rnfC gene (Tph_c07030) located elsewhere in the genome is a possible homolog of the third methylene-THF reductase subunit in A. woodii , wrongly annotated as electron transport complex protein RnfC2. The latter is...”

BT_RS03050 electron transport complex subunit RsxC from Bacteroides thetaiotaomicron VPI-5482
BT0618 Na+-transporting NADH:ubiquinone oxidoreductase, Electron transport complex protein rnfC from Bacteroides thetaiotaomicron VPI-5482
29% identity, 23% coverage

• Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
  Lewis, Microbiology spectrum 2023
  • “...beta 2.96 0.014 BT_RS02775 BT0566, BT_0566 Hypothetical protein 3.4 to 2.6 1E-05 to 0.007 rsxC, BT_RS03050 BT0618 to 22 Electron transport complex subunit rsxc, rnfabcdge type electron transport complex sub D, rnfabcdge type electron transport complex sub G, electron transport complex subunit E, electron transport complex...”
• Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
  Lewis, Microbiology spectrum 2023
  • “...2.96 0.014 BT_RS02775 BT0566, BT_0566 Hypothetical protein 3.4 to 2.6 1E-05 to 0.007 rsxC, BT_RS03050 BT0618 to 22 Electron transport complex subunit rsxc, rnfabcdge type electron transport complex sub D, rnfabcdge type electron transport complex sub G, electron transport complex subunit E, electron transport complex subunit...”
  • “...encoding iron-dependent metabolic mechanisms, including the succinate dehydrogenase/fumarate reductase (BT3055) and RnfABCDGE electron transport complex (BT0618 to BT0622), were downregulated by 2.5- to 3.4-fold, depending on the gene. A gene encoding asparagine biosynthesis (BT0551) was downregulated by 2.5-fold and a locus coding for glutamate synthase (BT0552...”

RNFC_RHOCA / Q52716 Ion-translocating oxidoreductase complex subunit C; Nitrogen fixation protein RnfC; Rnf electron transport complex subunit C; EC 7.-.-.- from Rhodobacter capsulatus (Rhodopseudomonas capsulata) (see 2 papers)
RNFC_RHOCB / D5ARZ1 Ion-translocating oxidoreductase complex subunit C; Nitrogen fixation protein RnfC; Rnf electron transport complex subunit C; EC 7.-.-.- from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (see paper)
TC 3.D.6.1.1 / Q52716 RnfC, component of NADH:ferredoxin oxidoreductase from Rhodobacter capsulatus (Rhodopseudomonas capsulata) (see 3 papers)
26% identity, 34% coverage

• function: Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane (By similarity). Required for nitrogen fixation. Involved in electron transfer to nitrogenase (PubMed:8264535).
  cofactor: [4Fe-4S] cluster (Binds 2 [4Fe-4S] clusters per subunit.)
  subunit: The complex is composed of six subunits: RnfA, RnfB, RnfC, RnfD, RnfE and RnfG.
• function: Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane (By similarity). Required for nitrogen fixation. Stabilizes RnfB (PubMed:9154934).
  cofactor: [4Fe-4S] cluster (Binds 2 [4Fe-4S] clusters per subunit.)
  subunit: The complex is composed of six subunits: RnfA, RnfB, RnfC, RnfD, RnfE and RnfG.
• substrates: H+

DR76_3209 electron transport complex subunit RsxC from Escherichia coli ATCC 25922
31% identity, 18% coverage

• Chemogenomic Screen for Imipenem Resistance in Gram-Negative Bacteria
  El, mSystems 2019
  • “...b , c K. pneumoniae b C COG4656 Na + -translocating ferredoxin:NAD + oxidoreductase Rnf DR76_3209 (2) DR88_4075 (2) rnfC G COG2814 Predicted arabinose efflux permease DR76_1590 (2) nanT DR76_1762 (2) DR76_4561 (2) araJ DR88_690 (3) J COG0445 tRNA U34 5-carboxymethylaminomethy modifying enzyme MnmG/GidA DR76_727 (4)...”

YdgN / b1629 SoxR [2Fe-2S] reducing system protein RsxC from Escherichia coli K-12 substr. MG1655 (see paper)
RSXC_ECOLI / P77611 Ion-translocating oxidoreductase complex subunit C; Rsx electron transport complex subunit C; EC 7.-.-.- from Escherichia coli (strain K12) (see paper)
b1629 electron transport complex protein RnfC from Escherichia coli str. K-12 substr. MG1655
31% identity, 18% coverage

• function: Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane (By similarity). Required to maintain the reduced state of SoxR. Probably transfers electron from NAD(P)H to SoxR (PubMed:12773378).
  cofactor: [4Fe-4S] cluster (Binds 2 [4Fe-4S] clusters per subunit.)
  subunit: The complex is composed of six subunits: RsxA, RsxB, RsxC, RsxD, RsxE and RsxG.
• BEAN and HABAS: Polyphyletic insertions in the DNA-directed RNA polymerase
  Alvarez-Carreño, Protein science : a publication of the Protein Society 2024
  • “...cytochrome f (A2BPU4), peptidase M23 (A0A0E3QUJ6), RND (A0A1T5M7J5), BCC (O59021), OGDCE2 (P0AFG6), NusG (C5CGE4), rsxC (P77611) and uD5 (P11512). The structurederived multiple sequence alignment and the structure superimposition are colored by Scorecons conservation. Residues below 0.4 are gray. The location and number of b/lineagespecific insertions define...”
• Combinatorial modulation of initial codons for improved zeaxanthin synthetic pathway efficiency in Escherichia coli
  Wu, MicrobiologyOpen 2019
  • “...control sensor protein ArcB OS= Escherichia coli 4.008818242 1.41388 1 778 87.928 5.1 0.058 3.146479845 P77611 Electron transport complex subunit RsxC OS= Escherichia 7.615976868 7.2973 2 740 80.122 8.63 0.105 4.493131638 John Wiley & Sons, Ltd Table A8 The protein mass spectrometry result for the determination...”
  • “...control sensor protein ArcB OS= Escherichia coli 4.97510404 1.41388 1 778 87.928 5.1 0.058 3.045333862 P77611 Electron transport complex subunit RsxC OS= Escherichia 3.865271223 4.86486 2 740 80.122 8.63 0.105 3.155004501 John Wiley & Sons, Ltd Table A9 The protein mass spectrometry result for the determination...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Remaining flexible in old alliances: functional plasticity in constrained mutualisms
  Wernegreen, DNA and cell biology 2009
  • “...of SoxR-reducing complex; posttranscriptional regulation ydgN (rsxC) b1629 - - - BU115 - Bbp110 Member of SoxR-reducing complex; posttranscriptional regulation...”
• Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
  Lee, Applied and environmental microbiology 2009
  • “...b1423 b1440 b1441 b1442 b1443 b1444 b1470 b1487 b1536 b1629 b1690 b1729 b1784 b1955 b1967 b2014 b2080 b2112 b2135 b2165 b2660 b2654 b2655 b2658 b2672 b2809...”
• Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
  Sabina, Journal of bacteriology 2003
  • “...3.4 3.1 3.0 2.9 2.9 2.8 2.8 2.8 2.6 2.5 KAS yjfI b1629 b1644 b4181 b1629 b1644 a 52 25 21 Inhibitor and gene b no. Expression ratio ycjX glvG mviM yceO yjcB...”
• DNA microarray-based identification of genes controlled by autoinducer 2-stimulated quorum sensing in Escherichia coli
  DeLisa, Journal of bacteriology 2001
  • “...tap pstC yehA rfaY rfaD uhpT cheW b1629 evgS fliP nlpC flgN Hemolysin expression-modulating protein Probable protein-tyrosine-phosphatase Outer membrane porin...”

c2021 Electron transport complex protein rnfC from Escherichia coli CFT073
31% identity, 18% coverage

• Rhipicephalus microplus and Its Impact on Anaplasma marginale Multistrain Infections in Contrasting Epidemiological Contexts
  Pérez, Pathogens (Basel, Switzerland) 2025 (no snippet)
• Bacterial resistance to leucyl-tRNA synthetase inhibitor GSK2251052 develops during treatment of complicated urinary tract infections
  O'Dwyer, Antimicrobial agents and chemotherapy 2015
  • “...3 blood leuS atpF c1471 c1472 c1527 c1590 c2021 c2295 c2473 c4898 Leucyl-tRNA synthetase ATP synthase FoF1 subunit B Hypothetical protein Hypothetical protein...”

SEEHRA37_02971 electron transport complex subunit RsxC from Salmonella enterica subsp. enterica serovar Heidelberg str. SARA37
25% identity, 58% coverage

• Comparative genomic analysis and virulence differences in closely related salmonella enterica serotype heidelberg isolates from humans, retail meats, and animals
  Hoffmann, Genome biology and evolution 2014
  • “...dehydrogenase PutA CA G 975 SEEHRA37_04036 2 Electron transport complex protein RnfC TC I 276 SEEHRA37_02971 2 Protein involved in chromosome partitioning MukB GC GA 1514 SEEHRA37_14706 2 N -ethylmaleimide reductase AT G 351 SEEHRA37_02866 2 Hypothetical protein CT L 1039 SEEHRA37_16509 2 Multidrug efflux system...”

RnfC2 / H6LBX7 ion-translocating oxidoreductase complex subunit C (EC 1.5.1.54) from Acetobacterium woodii (strain ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1) (see 6 papers)
H6LBX7 ferredoxin-NAD+ oxidoreductase (Na+-transporting) (EC 7.2.1.2) from Acetobacterium woodii (see paper)
Awo_c09290 electron transport complex subunit RsxC from Acetobacterium woodii DSM 1030
23% identity, 43% coverage

• A new metabolic trait in an acetogen: Mixed acid fermentation of fructose in a methylene-tetrahydrofolate reductase mutant of Acetobacterium woodii
  Moon, Environmental microbiology reports 2023
  • “...the three subunits RnfC2, MetV and MetF (Bertsch et al., 2015 ), encoded by rnfC2 (Awo_c09290), metV (Awo_c09300) and metF (Awo_c09310) that are clustered with other genes encoding the enzymes of the methyl branch of the WLP, such as fhs1 (Awo_c09260; formylTHF synthetase), fchA (Awo_c09270; methenylTHF...”
  • “...methyl branch 29,762 5362 2.46 Awo_c09280 Methylenetetrahydrofolate dehydrogenase FolD WLP methyl branch 48,052 11,292 2.08 Awo_c09290 Electron transport complex Rnf, C subunit RnfC2 MTHFR 171,346 29,713 2.52 Awo_c10670 CODH Ni 2+ insertion accessory protein CooC1 ACS/CODH 1000 1997 0.99 Awo_c10680 Corrinoid activation/regeneration protein 4126 7952 0.94...”
• Heterotrimeric NADH-oxidizing methylenetetrahydrofolate reductase from the acetogenic bacterium Acetobacterium woodii
  Bertsch, Journal of bacteriology 2015
  • “...MTHFR is postulated to have three subunits, encoded by Awo_c09290 to Awo_c09310, that are part of the cluster of the genes that encode the enzymes catalyzing...”
• An ancient pathway combining carbon dioxide fixation with the generation and utilization of a sodium ion gradient for ATP synthesis
  Poehlein, PloS one 2012
  • “..., the gene encoding the methylene-THF reductase is preceded in A. woodii by two genes (Awo_c09290, Awo_c09300) of unknown function. Homologues of Awo_c09300 are also found together with metF in many acetogens such as M. thermoacetica and C. ljungdahlii , but also in other bacteria and...”
  • “...the small and large subunit of the methylene-THF reductase are cotranscribed with the preceding gene, Awo_c09290, indicating that it is also involved in the reduction of methylene-THF. Awo_c09290 encodes a protein with similarity (61%) to the RnfC-subunit of the Rnf complex, and the residues for binding...”

Pstu14405_15960 electron transport complex subunit RsxC from Stutzerimonas stutzeri
25% identity, 25% coverage

• Detection of Known and Novel Small Proteins in Pseudomonas stutzeri Using a Combination of Bottom-Up and Digest-Free Proteomics and Proteogenomics
  Meier-Credo, Analytical chemistry 2023
  • “...Pstu14405_09665) that differ in 6 out of their 203 aa, electron transport complex subunit RsxC (Pstu14405_15960), glycerol kinase GlpK (Pstu14405_08555) as well as several transposases, that would have been missed entirely. Differential Protein Expression in Aerobic and Oxygen-Limiting Growth We then studied how P. stutzeri remodels...”

STM1457 putative respiratory-chain NADH dehydrogenase from Salmonella typhimurium LT2
25% identity, 58% coverage

• Multi-locus variable-number tandem repeat analysis for outbreak studies of Salmonella enterica serotype Enteritidis
  Malorny, BMC microbiology 2008
  • “...(SE-10) 45 7.8 7.8 tolA SENTR2 c 39 9.3 9.3 ftsK SENTR3 93 4.4 4.4 STM1457 homologue SENTR4 (SE-1) 7 4.9 4.9 Putative bacteriophage tail protein, STY631a homologue SENTR5 (SE-5) 6 10.0 10.0 yohM SENTR6 (SE-2) 7 5.1 5.1 non-coding SENTR7 (SE-9) 9 3.1 3.1 ushA...”

CSPO_9c00170 proline reductase-associated electron transfer protein PrdC from Clostridium sporogenes
29% identity, 59% coverage

• Genome sequence of Clostridium sporogenes DSM 795(T), an amino acid-degrading, nontoxic surrogate of neurotoxin-producing Clostridium botulinum
  Poehlein, Standards in genomic sciences 2015
  • “...a transposase (CSPO_9c00150), a second copy of PrdH2 (CSPO_9c00160) and a non-selenocysteine-containing version of PrdC (CSPO_9c00170). Furthermore, we identified gene clusters for the degradation of glycine, another one for its derivative betaine (N,N,N-trimethylglycine), and a cluster involved in selenocysteine incorporation into proteins (Figure 5 ). Figure...”

SEN2051 propanediol utilization ferredoxin from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
29% identity, 53% coverage

• Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates
  Betancor, BMC microbiology 2009
  • “...47/03 (only SEN4286) SEN4286-SEN4291 SGAL ROD40, Type I Restriction Modification System Methyltransferase SING 1 32/00 SEN2051 CT18, TY2, LT2, DT104, SL1344, SPA, SGAL pduS (ferredoxin) SING 2 32/02 SEN2293 CT18, TY2, LT2, SL1344, SBG, SPA, SGAL Hypothetical Protein SING 3 32/00 SEN2494 CT18, LT2, SL1344, DT104,...”

RNFC_VIBC3 / A0A0H3AJC2 Ion-translocating oxidoreductase complex subunit C; Rnf electron transport complex subunit C; EC 7.-.-.- from Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (see paper)
31% identity, 14% coverage

• function: Part of a membrane-bound complex that couples electron transfer with translocation of ions across the membrane.
  cofactor: [4Fe-4S] cluster (Binds 2 [4Fe-4S] clusters per subunit.)
  subunit: The complex is composed of six subunits: RnfA, RnfB, RnfC, RnfD, RnfE and RnfG.

Cthe_2430 electron transport complex, RnfABCDGE type, C subunit from Clostridium thermocellum ATCC 27405
26% identity, 52% coverage

• Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production
  Roberts, BMC systems biology 2010
  • “...Results are shown in Figure 3 . There were nine single gene deletions (Cthe_1028, Cthe_1029, Cthe_2430, Cthe_2431, Cthe_2432, Cthe_2433, Cthe_2434, Cthe_2435, and Cthe_3003), associated with seven distinct model reactions, that were predicted to increase the upper bound on ethanol secretion relative to the wild-type ethanol secretion...”

Q9KT88 Ion-translocating oxidoreductase complex subunit C from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
31% identity, 14% coverage

• Comparative genome analysis of non-toxigenic non-O1 versus toxigenic O1 Vibrio cholerae.
  Mukherjee, Genomics discovery 2014
  • “...potassium transport system protein kup kup Q9KM59 kup L1QTS9 Electron transport complex protein RnfC rnfC Q9KT88 rnfC L1QUE4 Probable oxaloacetate decarboxylase gamma chain 2 oadG2 Q9KTU4 oadG L1R348 Thiamine import ATP-binding protein ThiQ thiQ Q9KP42 OSU_1092 L1QYX4 Vitamin B12 import ATP-binding protein BtuD btuD Q9KSL1 btuD...”

YP_001511593 respiratory-chain NADH dehydrogenase domain-containing protein from Clostridium sp. OhILAs
27% identity, 58% coverage

• Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence
  Fonknechten, BMC genomics 2010
  • “...Kim et al. have identified RnfC as a selenoprotein in Alkaliphilus oremlandii OhILAs (accession no. YP_001511593). However, the genomic context and the alignment of this sequence with the PrdC of several clostridial species (Figure 2 ) show that this selenoprotein (RnfC) is actually PrdC. This alignment...”
• The selenoproteome of Clostridium sp. OhILAs: characterization of anaerobic bacterial selenoprotein methionine sulfoxide reductase A
  Kim, Proteins 2009
  • “...YP_001512574 YP_001512575 pfam09719 (low homology) 2 83 (223) 81 (221) Predicted NADH:ubiquinone oxidoreductase, subunit RnfC YP_001511593 (partial sequence) COG4656 1 389 (424) * annotated as selenoproteins in the current genome annotation Table 2 Specific activity and kinetic constants of Clostridium MsrA forms MsrA forms Specific activity...”

B5XWP9 Ion-translocating oxidoreductase complex subunit C from Klebsiella pneumoniae (strain 342)
30% identity, 17% coverage

• Disruption of KPC-producing Klebsiella pneumoniae membrane via induction of oxidative stress by cinnamon bark (Cinnamomum verum J. Presl) essential oil
  Yang, PloS one 2019
  • “...initiator-associating protein DiaA diaA A6TEG8 DNA processing Control 78 Electron transport complex subunit C rnfC B5XWP9 Energy synthesis Control 79 Elongation factor P(R)-beta-lysine ligase epmA A6TH74 Protein biosynthesis Control 80 Endonuclease V nfi A6TGQ5 Stress response Control 81 Exodeoxyribonuclease 7 small subunit xseB B5Y0W9 DNA processing...”
  • “...biosynthesis protein CobD Upregulated * A6TAW4 D-amino acid dehydrogenase Lost A6T739 Dihydroorotate dehydrogenase (quinone) Lost B5XWP9 Electron transport complex subunit C Lost B5XWS2 Glucans biosynthesis protein D Lost A6TGV0 Glycerol-3-phosphate acyltransferase Lost A6TDR6 Glycine cleavage system H protein Lost B5XNC0 Large-conductance mechanosensitive channel Lost A6TFK0 L-lactate...”

DR88_4075 electron transport complex subunit RsxC from Klebsiella pneumoniae
29% identity, 20% coverage

• Chemogenomic Screen for Imipenem Resistance in Gram-Negative Bacteria
  El, mSystems 2019
  • “...c K. pneumoniae b C COG4656 Na + -translocating ferredoxin:NAD + oxidoreductase Rnf DR76_3209 (2) DR88_4075 (2) rnfC G COG2814 Predicted arabinose efflux permease DR76_1590 (2) nanT DR76_1762 (2) DR76_4561 (2) araJ DR88_690 (3) J COG0445 tRNA U34 5-carboxymethylaminomethy modifying enzyme MnmG/GidA DR76_727 (4) DR88_3339 (2)...”

VK055_0512 electron transport complex subunit RsxC from Klebsiella pneumoniae subsp. pneumoniae
30% identity, 18% coverage

• The Capsule Regulatory Network of Klebsiella pneumoniae Defined by density-TraDISort
  Dorman, mBio 2018
  • “...transport complex protein RnfA 0.98 KP1_3036 VK055_0514 rnfC_2 Electron transport complex protein RnfC 0.38 KP1_3038 VK055_0512 nqrB_1 ( rnfD ) Electron transport complex protein RnfD 0.99 KP1_3039 VK055_0511 rnfE Electron transport complex protein RnfE 0.78 KP1_3041 VK055_0509 slyA_1 Transcriptional regulator SlyA 1.00 KP1_3054 VK055_0496 lpp Major...”

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Statistics

How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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.