PaperBLAST

PaperBLAST Hits for SwissProt::O07021 Lactate utilization protein B (Bacillus subtilis (strain 168)) (479 a.a., MAMKIGTDAF...)

Show query sequence

>SwissProt::O07021 Lactate utilization protein B (Bacillus subtilis (strain 168))
MAMKIGTDAFKERVSQGIDNEFMRGAVSGAQERLRTRRLEAAEELGNWEEWRSLSEEIRQ
HVLENLDFYLGQLAENVAKRGGHVYFAKTAEEASSYIRDVIQKKNGKKIVKSKSMVTEEI
NLNEVLEKEGCEVVETDLGEYILQIDDHDPPSHIVAPALHKNKEQIRDVFKERLDYQHTE
KPEELVMHARAILRKKFLEADIGITGCNFAIADTGSVSLVTNEGNGRLVSTLPKTQITVM
GMERIVPSFSEFEVLVSMLTRSAVGQRLTSYITALTGPKLEGEVDGPEEFHLVIVDNGRS
NILGTEFQSVLQCIRCAACINVCPVYRHVGGHSYGSIYSGPIGAVLSPLLGGYDDYKELP
YASSLCAACSEACPVKIPLHELLLKHRQNIVEKEGRAPISEKLAMKAFGLGASSLSLYKM
GSKWAPAAMTPFTEDEKISKGPGPLKNWTQIRDFPAPHKSRFRDWFADRETSERTKEEQ

Running BLASTp...

Found 57 similar proteins in the literature:

lutB / O07021 component of an iron-sulfur oxidase linked to L-lactate utilization (EC 1.1.1.27) from Bacillus subtilis (strain 168) (see paper)
LUTB_BACSU / O07021 Lactate utilization protein B from Bacillus subtilis (strain 168) (see paper)
BSU34040 putative iron-sulfur oxidoreductase from Bacillus subtilis subsp. subtilis str. 168
100% identity, 100% coverage

• function: Is essential for L-lactate degradation and allows cells to grow with lactate as the sole carbon source. Has probably a role as an electron transporter during oxidation of L-lactate. May also allow cells to utilize an alternative carbon source during biofilm formation, since it contributes to the formation of architecturally complex communities when lactate is present.
  disruption phenotype: Cells lacking this gene are unable to grow on minimal medium with L-lactate as the sole carbon source. Cells lacking the lutABC operon exhibit little or no defect in biofilm formation on MSgg medium, but form small colonies that almost completely lacked surface architecture when glycerol is replaced with L-lactate in the MSgg medium.
• Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
  Pfeiffer, Genes 2021
  • “...] 15869466 9f HVO_1692 ludB self [ 21 ] 30707467 9f HVO_1692 (cont.) probably 35% BSU34040 O07021 [ 316 ] 19201793 matches up to HVO_1692 pos 490 of 733 9f HVO_1692 (cont.) probably 35% PST_3338 O4VPR6 [ 317 ] 25917905 matches up to HVO_1692 pos 400...”
• Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
  Pfeiffer, Genes 2021
  • “...15869466 9f HVO_1692 ludB self [ 21 ] 30707467 9f HVO_1692 (cont.) probably 35% BSU34040 O07021 [ 316 ] 19201793 matches up to HVO_1692 pos 490 of 733 9f HVO_1692 (cont.) probably 35% PST_3338 O4VPR6 [ 317 ] 25917905 matches up to HVO_1692 pos 400 of...”

LUTB_BACCR / Q81GA4 Lactate utilization protein B from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711) (see paper)
BC1304 iron-sulfur cluster-binding protein from Bacillus cereus ATCC 14579
72% identity, 98% coverage

• function: Is involved in L-lactate degradation and allows cells to grow with lactate as the sole carbon source. Has probably a role as an electron transporter during oxidation of L-lactate.
• Domain structure of phage P4 alpha protein deduced by mutational analysis
  Ziegelin, Journal of bacteriology 1995
  • “...in an extract of E. coli dnaB dnaC mutant strain BC1304 as described previously (28, 29). Viral fd DNA was used as the template for the primase and...”
• dnaC-dependent reconstitution of replication forks in Escherichia coli lysates
  Nüsslein-Crystalla, Journal of bacteriology 1982
  • “...K-12 derivatives. All strains except NY177, WM485, and BC1304 require low concentrations of thymine (2 Fig/ml). Preparation of crude protein extracts. Cells...”
  • “...thy dnaC2 WM485 Blr arg leu his met pro thy dnaC201 BC1304 arg endA polAI thy dnaB1304 dnaC201 SG1719 argG gal his) lac leu malA metB mtl rpsL thy ton xyl...”

APL_0445 putative electron transport protein from Actinobacillus pleuropneumoniae L20
59% identity, 98% coverage

• Comparative profiling of the transcriptional response to iron restriction in six serotypes of Actinobacillus pleuropneumoniae with different virulence potential
  Klitgaard, BMC genomics 2010
  • “...Putative NAD(P)H nitroreductase C -0.54 APL_0446 + ykgE Putative dehydrogenase subunit, Fe-S oxidoreductase C -2.63 APL_0445 + ykgF Iron-sulfur electron transport protein C -1.79 APL_0444 + engA Putative GTP binding protein S -1.10 APL_0416 - N-acetyl-D-glucosamine kinase KG -0.36 APL_0155 + nqrF Na+-translocating NADH-ubiquinone oxidoreductase subunit...”
• Transcriptional profiling of Actinobacillus pleuropneumoniae during the acute phase of a natural infection in pigs
  Deslandes, BMC genomics 2010
  • “...APL_0556 rcpC Flp operon protein C -1.815 O APL_0427 adhA NADP-specific glutamate dehydrogenase 1.081 O APL_0445 ykgF Putative electron transport protein -1.144 O APL_0560 rhlB ATP-dependent RNA helicase RhlB -2.063 O APL_0672 APL_0672 Hypothetical protein 0.927 O APL_1959 adhI Alcohol dehydrogenase 1 1.015 O APL_2001 APL_2001...”

HAPS_0679 iron-sulfur cluster binding reductase from Haemophilus parasuis SH0165
58% identity, 98% coverage

• Proteome Analysis of Outer Membrane Vesicles From a Highly Virulent Strain of Haemophilus parasuis
  Zhang, Frontiers in veterinary science 2021
  • “...27 ). The iron metabolism-related proteins yfeA (ACL32714.1), dsbC (ACL31879.1), hxuA (ACL33616.1), fbpA (ACL32742.1), and HAPS_0679 (ACL32327.1) were found in OMV proteome data. In addition, several virulence-associated proteins also were identified: they are vtaA9 (ADZ54070.1), tbpA (ACL33656.1), pgi (ACL32784.1), manB (ACL32480.1), ompP5 (ACL33726.1), TolC (ACL33604.1), and...”
  • “...Heme/hemopexin-binding protein A Iron metabolism ACL32742.1 37640.63669 fbpA Periplasmic iron-binding protein Iron metabolism ACL32327.1 51816.66395 HAPS_0679 Iron-sulfur cluster binding reductase Iron metabolism ACL32714.1 32632.15631 yfeA Chelated iron ABC transporter Iron metabolism; Potential virulence factor ACL33656.1 102313.5803 tbpA Transferrin-binding protein 1 precursor Potential virulence factor ACL32784.1 61260.10128...”

ECO26_0341 putative amino acid dehydrogenase from Escherichia coli O26:H11 str. 11368
56% identity, 99% coverage

• Evolution of enterohemorrhagic escherichia coli O26 based on single-nucleotide polymorphisms
  Bletz, Genome biology and evolution 2013
  • “...T G b Synonymous 78.33 ECO26_0094 murC (1) 102806 T G Nonsynonymous (Tyr Asp) 5.83 ECO26_0341 ykgF (1) 363280 T G c Synonymous 56.67 ECO26_0370 prpC (1) 398342 T C c Nonsynonymous (Tyr His) 56.67 ECO26_0554 ybcF (1) 598509 A G Nonsynonymous (Thr Ala) 5.83 ECO26_0653...”

YkgF / b0307 putative amino acid dehydrogenase with NAD(P)-binding domain and ferridoxin-like domain from Escherichia coli K-12 substr. MG1655 (see 4 papers)
b0307 predicted amino acid dehydrogenase with NAD(P)-binding domain and ferridoxin-like domain from Escherichia coli str. K-12 substr. MG1655
56% identity, 99% coverage

• DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
  Polen, Applied and environmental microbiology 2003
  • “...Putative lyase/synthase Putative dehydratase 0.25* 0.33* 0.85 b0306 b0307 b0308 ykgE ykgF ykgG 2 2 2 Putative dehydrogenase subunit ORF, hypothetical protein...”

BA_3775 fer4, 4Fe-4S binding domain from Bacillus anthracis str. A2012
BA3269 iron-sulfur cluster-binding protein from Bacillus anthracis str. Ames
55% identity, 95% coverage

• Genomic characterization of <i>Bacillus cereus</i> isolated from food poisoning cases revealed the mechanism of toxin production
  Zhou, Frontiers in microbiology 2023
  • “...identified key genes in gene co-expression networks. The findings indicate that BA_0477, BA_3774 , and BA_3775 , which were closely associated with prophage ( Supplementary Table 5 ), were the key genes within the contracted gene families of the LY01-LY09 strains ( Supplementary Figure 7A )....”
• Investigating the genome diversity of B. cereus and evolutionary aspects of B. anthracis emergence
  Papazisi, Genomics 2011
  • “...+ BA3131 alcohol dehydrogenase, zinc-containing + BA3189 manganese ABC transporter, substrate-binding protein/adhesin (+) a + BA3269 iron-sulfur cluster-binding protein + + BA3299 microbial collagenase, putative + BA3307 o L-serine dehydratase, iron-sulfur-dependent, alpha subunit + + BA3308 o L-serine dehydratase, iron-sulfur-dependent, beta subunit + + BA3435 o...”

llmg_1916 putative electron transport protein from Lactococcus lactis subsp. cremoris MG1363
50% identity, 95% coverage

• Manganese Modulates Metabolic Activity and Redox Homeostasis in Translationally Blocked Lactococcus cremoris, Impacting Metabolic Persistence, Cell Culturability, and Flavor Formation
  Nugroho, Microbiology spectrum 2022
  • “...6.190.11 0.27 2.77 Aldehyde-alcohol dehydrogenase adhE llmg_2432 8.10.05 7.720.13 0.41 2.53 Putative electron transport protein llmg_1916 6.90.1 6.580.04 0.48 2.64 Peptide methionine sulfoxide reductase MsrA (Protein-methionine-S-oxide reductase) (EC 1.8.4.11) pmsR msrA llmg_2281 6.250.06 5.970.07 0.52 2.71 Glycine betaine/proline ABC transporter (EC 3.6.3.32) busAA llmg_1048 8.170.04 7.920.02...”

WO5_01154 LutB/LldF family L-lactate oxidation iron-sulfur protein from Enterococcus faecalis EnGen0354
52% identity, 97% coverage

• Differences of protein expression in enterococcus faecalis biofilm during resistance to environmental pressures
  Jiang, Technology and health care : official journal of the European Society for Engineering and Medicine 2024
  • “...metabolic process; carbohydrate metabolic process - 0.63 1.02E-04 - 0.71 4.25E-05 - 1.33 1.35E-05 A0A0M2ARI4 WO5_01154 Iron-sulfur cluster-binding protein Lactate oxidation - 1.36 5.00E-05 - 0.65 1.20E-02 - 2.01 1.04E-07 1: Biological process annotation of Gene ontology from UNIPROTKB. 243 proteins was maximumly found in Translation,...”
• Variations in protein expression associated with oral cancer
  Jiang, Technology and health care : official journal of the European Society for Engineering and Medicine 2023
  • “...dehydratase-related proteins were greatly reduced in the B group. An iron-sulfur cluster-binding protein encoded by WO5_01154 was also significantly downregulated since L-serine dehydratases are iron-sulfur proteins[ 23 ]. This binding protein may participate in the catalysis of dehydratase. Lindenstrauss et al.[ 24 ] demonstrated that the...”

EF1109 iron-sulfur cluster binding protein from Enterococcus faecalis V583
52% identity, 97% coverage

• Mutations associated with reduced surotomycin susceptibility in Clostridium difficile and Enterococcus species
  Adams, Antimicrobial agents and chemotherapy 2015
  • “...(485/486) 449delA (565/608) M110I G170V L52P A29T N150fs EF2912c EF1109 EF0797 EF1027 MprF2 EF1797 DrmA 31-bp del NA EF1367 a Boldface indicates that the gene...”
• Transcriptional response of Enterococcus faecalis V583 to erythromycin
  Aakra, Antimicrobial agents and chemotherapy 2005
  • “...Protein synthesis EF0900 EF0939 EF0956 EF0957 EF1020 EF1068 EF1109 EF1211 EF1347 EF1348 EF1349 EF1526 EF1612 EF1613 EF1826 EF2589 EF2646 EF2863 EF2961 EF3157...”

N007_09410 LutB/LldF family L-lactate oxidation iron-sulfur protein from Alicyclobacillus acidoterrestris ATCC 49025
50% identity, 97% coverage

• Transcriptome-Based Selection and Validation of Reference Genes for Gene Expression Analysis of Alicyclobacillus acidoterrestris Under Acid Stress
  Zhao, Frontiers in microbiology 2021
  • “...F: AAGTGTTCTATGGGCAGATG 110 R: AAGAGACCTGACAAAACTCC N007_05875 DNA polymerase I polA F: GTCGGGTTCCCTTGTAGT 138 R: CAAATGCGGTGTATGGTT N007_09410 Lactate utilization protein lldF F: CCATGATTACCGGCCCAAAG 158 R: CGGGCAGACGTTTAGACAAG N007_05885 Isocitrate dehydrogenase icd F: TCACCTTGTCTAAATTCGCA 202 R: CAGCAAATTCTTACACGTCC N007_06870 4-Hydroxy-tetrahydrodipicolinate synthase dapA F: GGCTGACCAATCAACTCCA 286 R: TTACTCAAATCTCCCACATCG N007_09120 16S Ribosomal...”

CpC231_0828 LutB/LldF family L-lactate oxidation iron-sulfur protein from Corynebacterium pseudotuberculosis C231
D9Q9T3 Iron-sulfur cluster-binding protein from Corynebacterium pseudotuberculosis (strain C231)
41% identity, 91% coverage

• Changes in protein abundance are observed in bacterial isolates from a natural host
  Rees, Frontiers in cellular and infection microbiology 2015
  • “...modification D9Q9T2 CpC231_0827 CpC231_0827 Uncharacterized protein 0.334 1.982 * 2.146 * Function unknown D9Q9T3 lutB CpC231_0828 Lactate utilization protein B 0.234 1.888 * 2.065 * Energy production and conversion D9Q9T4 lutA CpC231_0829 Lactate utilization protein A 0.239 1.848 * 2.476 * Energy production and conversion D9Q9Y9...”
  • “...field isolates in contrast to the reference strain. CpC231_0829 is lactate utilization protein A (LutA), CpC231_0828 is lactate utilization protein B (LutB) while CpC231_0827 is an uncharacterized protein. BLAST and homolog search for CpC231_0827 show that this protein includes a 5-formyltetrahydrofolate cyclo-ligase domain found in enzymes...”
• Changes in protein abundance are observed in bacterial isolates from a natural host
  Rees, Frontiers in cellular and infection microbiology 2015
  • “...* Posttranslational modification D9Q9T2 CpC231_0827 CpC231_0827 Uncharacterized protein 0.334 1.982 * 2.146 * Function unknown D9Q9T3 lutB CpC231_0828 Lactate utilization protein B 0.234 1.888 * 2.065 * Energy production and conversion D9Q9T4 lutA CpC231_0829 Lactate utilization protein A 0.239 1.848 * 2.476 * Energy production and...”

Q4KII3 Iron-sulfur cluster-binding protein from Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)
39% identity, 94% coverage

• Differential protein expression during growth on model and commercial mixtures of naphthenic acids in Pseudomonas fluorescens Pf-5
  McKew, MicrobiologyOpen 2021
  • “...Q4K5Q1, (all p <0.004) and Q4K6Q0 ( p =0.01), along with an ironsulfur clusterbinding protein (Q4KII3, p =0.002), which are all involved in the electron transport chain also had significantly higher abundance with both NA treatments compared with controls. Several proteins relating to inorganic ion metabolism...”

HP15_4089 L-lactate dehydrogenase, LutB subunit from Marinobacter adhaerens HP15
40% identity, 95% coverage

• mutant phenotype: Specifically important for utilization of L-lactate or D,L-lactate. This is related to the LutABC system from Bacillus subtilis (PMC3347220, PMC2668416).

PST_3338 probable iron-sulphur protein from Pseudomonas stutzeri A1501
39% identity, 90% coverage

• Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
  Pfeiffer, Genes 2021
  • “...] 19201793 matches up to HVO_1692 pos 490 of 733 9f HVO_1692 (cont.) probably 35% PST_3338 O4VPR6 [ 317 ] 25917905 matches up to HVO_1692 pos 400 of 733 9f HVO_1693 ludC self [ 21 ] 30707467 9f HVO_1693 (cont.) probably 30% BSU34030 O32259 [ 316...”

H16_B0091 Iron-sulfur cluster-binding protein from Ralstonia eutropha H16
H16_B0091, H16_RS19180 LutB/LldF family L-lactate oxidation iron-sulfur protein from Cupriavidus necator H16
39% identity, 96% coverage

• (R/S)-lactate/2-hydroxybutyrate dehydrogenases in and biosynthesis of block copolyesters by Ralstonia eutropha
  Ishihara, Applied microbiology and biotechnology 2023
  • “...h16_A1681 and h16_A1682 along with the intergenic region. The genes h16_B0093 , h16_B0092 , and h16_B0091 , sharing 44.2%, 26.0%, and 40.1% identities to lutA , lutC , and lutB derived from Bacillus subtilis , respectively, are a homolog set of [Fe-S] cluster protein-dependent l -lactate...”
  • “...l -Lactate cytochrome reductase Cytochrome 381 H16_B1817 LldD l -Lactate cytochrome c reductase Cytochrome 391 H16_B0091 LldF Iron-sulfur cluster-binding protein ( l -Lactate dehydrogenase complex) Unknown 481 H16_B0092 LldG Conserved hypothetical protein ( l -Lactate dehydrogenase complex) Unknown 233 H16_B0093 LldE Fe-S oxidoreductase ( l -Lactate...”
• Identification and characterization of L- and D-lactate-inducible systems from Escherichia coli MG1655, Cupriavidus necator H16 and Pseudomonas species
  Augustiniene, Scientific reports 2022
  • “...is controlled by potential inducible system Cn GntR/P H16_RS19190 . Iron-sulfur cluster-binding protein (locus tag H16_RS19180 ) and (Fe-S)-binding protein (locus tag H16_RS19190 ) encoded by genes of this operon exhibit 40% and 40.5% sequence identity, respectively, with the proteins encoded by the gene cluster H16_RS06895-H16_RS06915...”

BMAA1430 iron-sulfur cluster binding protein from Burkholderia mallei ATCC 23344
41% identity, 95% coverage

• Inactivation of [Fe-S] metalloproteins mediates nitric oxide-dependent killing of Burkholderia mallei
  Jones-Carson, PloS one 2008
  • “...0.5 cysteine desulfurase [Fe-S] assembly BMA1709 iscR 6.9 2.9 [Fe-S] assembly transcription factor [Fe-S] assembly BMAA1430 2.0 0.5 [Fe-S] binding protein [Fe-S] assembly B. mallei is resistant to the oxidative burst of macrophages despite its marked susceptibility to ROS We investigated the possible mechanism for the...”

CV_3028 probable iron-sulphur protein from Chromobacterium violaceum ATCC 12472
43% identity, 86% coverage

• GeLC-MS-based proteomics of Chromobacterium violaceum: comparison of proteome changes elicited by hydrogen peroxide
  Lima, Scientific reports 2016
  • “...for CV_3029, whose function remains unknown. Expression of other members of this operon also varies. CV_3028 emerges only under control conditions. CV_3029 showed a statistically non-significant decrease and CV_3030 was not detected in this analysis. In bacteria, the hydrogen peroxide response is mediated by modifications in...”

RR42_RS21285 L-lactate dehydrogenase, LutB subunit from Cupriavidus basilensis FW507-4G11
44% identity, 79% coverage

• mutant phenotype: Specifically important for utilization of L-lactate or D,L-lactate. (Also important on various nitrogen sources with lactate as the carbon source.) This is related to the LutABC system from Bacillus subtilis (PMC3347220, PMC2668416).

ACBG90_00430 LutB/LldF family L-lactate oxidation iron-sulfur protein from Stutzerimonas kunmingensis
38% identity, 93% coverage

• Genomic Insights into <i>Stutzerimonas kunmingensis</i> TFRC-KFRI-1 Isolated from Manila Clam (<i>Ruditapes philippinarum</i>): Functional and Phylogenetic Analysis
  Lee, Microorganisms 2024
  • “...metabolism were also annotated, including L-lactate permease (ACBG90_00420 and ACBG90_07385) and L-lactate oxidation iron-sulfur protein (ACBG90_00430), which are involved in lactate transport and oxidation, respectively. The genome also harbors genes encoding components of the pyrroloquinoline quinone (PQQ) biosynthesis pathway, including pqqC (ACBG90_20540), pqqD (ACBG90_20545), and pqqE...”

Q5F883 L-lactate dehydrogenase (subunit 1/3) (EC 1.1.1.27) from Neisseria gonorrhoeae (see paper)
NGO0906 hypothetical protein from Neisseria gonorrhoeae FA 1090
39% identity, 95% coverage

• Proteomic analysis of Neisseria gonorrhoeae biofilms shows shift to anaerobic respiration and changes in nutrient transport and outermembrane proteins
  Phillips, PloS one 2012
  • “...F-type H+-transporting ATPase subunit b ATP-proton motive force interconversion 1.637 (2) 0.717 (2) 0.593 (3) NGO0906 hypothetical protein Electron transport 1.073 (1) 0.614 (1) NGO1373 cbb3-type cytochrome c oxidase subunit II Electron transport 1.479 (1) 1.930 (1) NGO0375 Pgm; phosphoglucomutase Sugars 1.368 (1) NGO0718 d RpiR...”

NMB1438 hypothetical protein from Neisseria meningitidis MC58
Q9JYT6 4Fe-4S ferredoxin-type domain-containing protein from Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)
39% identity, 95% coverage

• Interplay Between Virulence and Variability Factors as a Potential Driver of Invasive Meningococcal Disease
  Siena, Computational and structural biotechnology journal 2018
  • “...Stress response NEIS1371 NMB1436 Iron-sulphur protein Stress response NEIS1372 NMB1437 Iron-sulphur protein Stress response NEIS1373 NMB1438 Catalase Stress response katA NMB0216 Endonuclease Stress response nth NMB0533 Manganese transport system Stress response mntA NMB0588 Manganese transport system Stress response mntB NMB0587 Manganese transport system Stress response mntC...”
• Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence
  Ampattu, BMC genomics 2017
  • “...n.s. 2.81 2.18 NMB1437 - Hypothetical protein 0.87 n.s. n.s. n.s. n.s. n.s. n.s. n.s. NMB1438 - Hypothetical protein 1.26 n.s. n.s. n.s. 1.58 n.s. 1.87 n.s. NMB1622 norB Nitric oxide reductase n.s. n.s. n.s. n.s. 5.85 n.s. 5.40 n.s. NMB1623 aniA Copper-containing nitrite reductase n.s....”
• How the Knowledge of Interactions between Meningococcus and the Human Immune System Has Been Used to Prepare Effective Neisseria meningitidis Vaccines
  Gasparini, Journal of immunology research 2015
  • “...immunity, supplying energy to the pathogen [ 93 ] Uncharacterized proteins (NGO1686, NMB0741, NMB1436, NMB1437, NMB1438, and NMB1828) They protect from nonoxidative factors, but their mechanisms are still not understood; NMB1436, NMB1437, and NMB1438 are putatively involved in iron metabolism [ 122 , 195 ] Uncharacterized...”
• Fur-mediated global regulatory circuits in pathogenic Neisseria species
  Yu, Journal of bacteriology 2012
  • “...and gene loci such as sodB, kat, norB, aniA, and NMB1438 to -1436 and energy metabolism loci such as the nuo complex (NMB0242 to -0244) (Table 2) (22, 44)....”
• Transcriptional profiling of serogroup B Neisseria meningitidis growing in human blood: an approach to vaccine antigen discovery
  Hedman, PloS one 2012
  • “...clpX 0.782 0.627 0.823 NMB1436 0.866 1.017 1.259 0.642 NMB1437 1.324 1.309 1.626 1.025 0.896 NMB1438 1.254 1.344 1.487 1.118 Candidate vaccine antigen genes: identification of up-regulated genes encoding surface exposed proteins Differential gene expression lists were interrogated for genes encoding proteins identified as potential vaccine...”
• This is not your mother's repressor: the complex role of fur in pathogenesis
  Carpenter, Infection and immunity 2009
• Characterization of a novel Neisseria meningitidis Fur and iron-regulated operon required for protection from oxidative stress: utility of DNA microarray in the assignment of the biological role of hypothetical genes
  Grifantini, Molecular microbiology 2004 (PubMed)
  • “...by three genes, annotated as NMB1436, NMB1437 and NMB1438 and encoding proteins with so far unknown function. The operon was remarkably upregulated in the...”
  • “...constituted by three genes, annotated as NMB1436, NMB1437 and NMB1438 (Tettelin et al., 2000) and encoding so far unknown proteins with a molecular mass of...”
• Towards New Drug Targets? Function Prediction of Putative Proteins of Neisseria meningitidis MC58 and Their Virulence Characterization
  Shahbaaz, Omics : a journal of integrative biology 2015
  • “...40. 41. 42. Q9K194 Q7DDP7 Q9JZG0 P64161 Q9K1K7 Q9JZY3 43. Q9JYT6 44. P63702 45. 46. 47. 48. 49. 50. 51. 52. Q9K1D3 Q9K0W8 Q9JXB7 Q9JY28 Q9JY47 Q9JRY6 Q9JZ01...”

WP_039560866 LutB/LldF family L-lactate oxidation iron-sulfur protein from Pseudomonas flexibilis
37% identity, 95% coverage

• Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera
  Rudra, Frontiers in microbiology 2023
  • “...ZnuB WP_039607122 Supplementary Figure S76 1 aa Del 85120 LutB/LldF family L-lactate oxidation ironsulfur protein WP_039560866 Supplementary Figure S77 1 aa Del 433469 # Isolated exception present in some CSIs (#; see Supplementary Figures for details). CSIs specific for the Oryzihabitans clade (genus Chryseomonas ) Oryzihabitans...”

Q72B56 Iron-sulfur cluster-binding protein from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
DVU1782 iron-sulfur cluster-binding protein from Desulfovibrio vulgaris Hildenborough
39% identity, 100% coverage

• Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough.
  Marbehan, Frontiers in microbiology 2024
  • “...103 88 62 52 L-lactate dehydrogenase (LldG family) Q72B57 DVU_1781 23.9 L-lactate dehydrogenase (LldH family) Q72B56 DVU_1782 52.6 4 8 4 Lactate permeases, putative Q72B55 DVU_1783 27.4 3 14 2 Q72A87 DVU_2110 57.9 5 9 3 Q729R4 DVU_2285 53.0 5 13 5 Q725Z0 DVU_3284 57.7 Sulfate...”
• Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution
  Zhou, The ISME journal 2013
  • “...(fd II) DVU0384 DVU2451 DVU2683 DVU1780 DVU1781 DVU1782 DVU1783 DVU2286 DVU2287 DVU2288 DVU2289 DVU2290 DVU2291 DVU2292 DVU2293 Annotation Cytochrome c family...”
• Design and analysis of mismatch probes for long oligonucleotide microarrays
  Deng, BMC genomics 2008
  • “...DvH Putative cytochrome c nitrite reductase, catalytic subunit NfrA DVU1466 46451220 DvH Acetylglutamate kinase (argB) DVU1782 46451220 DvH Iron-sulfur cluster-binding protein DVU2526 46451220 DvH Periplasmic [NiFe] hydrogenase, large subunit, isozyme2(hynA-2) MMP0707 44921025 Mm Na+/H+ exchanger MMP0926 44921025 Mm Chemotaxis protein cheB MMP1559 45047480 Mm Formatedehydrogenase alpha...”

HP0138 conserved hypothetical iron-sulfur protein from Helicobacter pylori 26695
O24950 Conserved hypothetical iron-sulfur protein from Helicobacter pylori (strain ATCC 700392 / 26695)
40% identity, 93% coverage

• Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates
  Tuan, Microbial genomics 2021
  • “...HP0508 4.5 163266 HPF57_0158 [162843164288] (-) lldF L-lactate dehydrogenase to pyruvate anaerobic catabolism C 1023 HP0138 4.5 713996 HPF57_0678 [711939714599] (+) bamA outer membrane protein assembly factor; surface antigen D15 assembly of outer membrane -barrel proteins C 2058 HP0655 4.4 101839 HPF57_0101 [101587103584] (-) rpoD RNA...”
• A two-hybrid system reveals previously uncharacterized protein-protein interactions within the Helicobacter pylori NIF iron-sulfur maturation system
  Benoit, Scientific reports 2021
  • “...on the chromogenic screening media), for instance (i) between ApbC and three hypothetical proteins (HP0117, HP0138, HP0568), MiaB (HP0285), MoaA (HP0768) or QueA (HP0934), and (ii) between FdxA and the hydrogenase [4Fe4S] subunit HynA (HP0631), MqnE (HP0654), MqnC (HP0656), QueA(HP0934), AddB (HP1089), NuoB (HP1261) or RlmN...”
• Iron-sulfur protein maturation in Helicobacter pylori: identifying a Nfu-type cluster carrier protein and its iron-sulfur protein targets
  Benoit, Molecular microbiology 2018
  • “...NifU, Nfu) used as baits in the BACTH system ( Fig. 9 ). These are: HP0138 (hypothetical protein); HP0191 (fumarate reductase subunit); HP0269 (MiaB-like protein)l HP1109 (pyruvate ferredoxin oxidoreductase, subunit); HP1226 (HemN, O 2 -independent coproporphyrinogen-III oxidase); HP1261 (NuoB, NADH-Quinone oxidoreductase subunit B); and HP1508 (ferredoxin-like)....”
  • “...C 37 C 40 HP0132 SdaA L-serine dehydratase [4Fe-4S] C 341 C 383 C 394 HP0138 HP0138 Hypothetical, iron-sulfur cluster binding protein 2[4Fe-4S] (ferredoxin) C 314 C 318 C 321 C 325 ; C 364 C 368 C 371 C 375 HP0142 MutY A/G-specific adenine glycosylase...”
• Carbon Fixation Driven by Molecular Hydrogen Results in Chemolithoautotrophically Enhanced Growth of Helicobacter pylori
  Kuhns, Journal of bacteriology 2016
  • “...HP0370 HP1152 HP1460 HP1430 HP0163 HP1458 HP0466 HP0306 HP0138 HP0088 HP0742 HP1182 Heat shock protein (HslV) 50S ribosomal protein L23 (RplW) Biotin...”
• Identification of the genes that contribute to lactate utilization in Helicobacter pylori
  Iwatani, PloS one 2014
  • “...to amplify the complete plasmid excluding the first codon of hp0137 , whole region of hp0138 , and the last codon of hp0139 . The PCR fragment was ligated with the cat fragment to produce pSI06, which has the hp01370139 :: cat cassette to inactivate all...”
  • “...primer sets hp138-qF/hp138-qR, hp140-qF/hp140-qR, hp1222-qF/hp1222-qR, and Hp16S-F/Hp16S-R were used to amplify 100150 bp of each hp0138 , hp0140 , hp1222 , and 16S rRNA gene. Real-time quantitative PCRs were performed in 7300 Real-Time PCR System (Applied Biosystems) using Taqman-designed primers and probes (Life Technologies) and the...”
• Identification and characterization of Helicobacter pylori genes essential for gastric colonization
  Kavermann, The Journal of experimental medicine 2003
  • “...reproducible. Table I. Statistical Validation of the STM Approach Hp P149 mutant hp0072 hp0601 hp0094 hp0138 hp0407 hp0635 hp0755 hp0755 hp1225 23S-rrnB Mutants reisolated/gerbils 0/10 0/10 9/10 9/10 8/10 8/10 9/10 10/10 10/10 10/10 hp0755 was chosen twice with two different insertions within the gene. Screening...”
• Outer Membrane Vesicles Secreted by Helicobacter pylori Transmitting Gastric Pathogenic Virulence Factors
  Wei, ACS omega 2022
  • “...O26083 CeuE 279 O25213 HP_0466 280 O25253 hslV 281 O25006 HP_0218 282 P55992 gyrB 283 O24950 HP_0138 284 O25280 HP_0554 285 P56141 trpA 286 P56110 zwf 287 O25076 HP_0305 288 O25926 clpX 289 O25930 bamD 290 P56045 rplT 291 P56097 ftsZ 292 O25899 tonB 293 P56128...”
  • “...O25742 HP_1117 165 O25503 speE 166 O24881 HP_0040 167 P56458 serS 168 O25372 gatB 169 O24950 HP_0138 170 O25373 HP_0659 171 O25998 HP_1462 172 P56114 gatA 173 O25546 HP_0879 174 O25668 CbpA 175 P56067 cysM 176 O25469 HP_0780 177 O25249 pgbA 178 O25069 DppA 179 O25873...”

HPF57_0158 LutB/LldF family L-lactate oxidation iron-sulfur protein from Helicobacter pylori F57
40% identity, 93% coverage

• Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates
  Tuan, Microbial genomics 2021
  • “...4.6 549551 HPF57_0538 [549128550432] (+) pgbA plasminogen binding protein anti-immunity C 424 HP0508 4.5 163266 HPF57_0158 [162843164288] (-) lldF L-lactate dehydrogenase to pyruvate anaerobic catabolism C 1023 HP0138 4.5 713996 HPF57_0678 [711939714599] (+) bamA outer membrane protein assembly factor; surface antigen D15 assembly of outer membrane...”

PFCIRM129_10180 lactate utilization protein B from Propionibacterium freudenreichii subsp. freudenreichii
38% identity, 90% coverage

• Mutation of the Surface Layer Protein SlpB Has Pleiotropic Effects in the Probiotic Propionibacterium freudenreichii CIRM-BIA 129
  do, Frontiers in microbiology 2018
  • “...subunit) (MCB-beta) CYT I 69.5 16.2 9 4 0.4 59.4 26 9 1.2 b19 b19.a1 PFCIRM129_10180 Iron-sulfur protein CYT C 57.2 26.1 18 6 1.1 16.7 8 3 0.4 b20 b20.a1 PFCIRM129_08670 Cell-wall peptidases, NlpC/P60 family SEC protein SEC M 58.7 51.6 22 8 1.7 9.5...”

Dde_1843 Iron-sulfur cluster binding protein from Desulfovibrio desulfuricans G20
Dde_1843 LutB/LldF family L-lactate oxidation iron-sulfur protein from Oleidesulfovibrio alaskensis G20
37% identity, 100% coverage

• Transcriptome-wide marker gene expression analysis of stress-responsive sulfate-reducing bacteria
  Jawaharraj, Scientific reports 2023
  • “...cell materials 59 . In this study, the GO term related to lactate oxidation (Dde_3245, Dde_1843) was down-regulated in EC-2 (P-Cu) whereas the same was up-regulated in SLG-Cu (EC-3) with z-scores -0.04 and 0.04, respectively. This confirms that the lactate oxidation pathway was activated in EC-3...”

BCAL2485 putative iron-sulphur cluster binding electron transport protein from Burkholderia cenocepacia J2315
40% identity, 91% coverage

• Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment
  O'Grady, Frontiers in cellular and infection microbiology 2011
  • “...metal ion oxidation 1.6 BCAL0580 Putative chromate transport protein 1.6 BCAL1789 ExbB, iron-transport protein 1.7 BCAL2485 Putative ironsulfur cluster-binding electron 2.1 BCAL2486 Putative ironsulfur oxidoreductase 2.1 BCAM0447 Putative exported multicopper oxidase 13.0 BCAM1187 TonB-dependent siderophore receptor 1.7 BCAM1527 Putative cation efflux protein 1.8 BCAM2007 TonB-dependent siderophore...”
  • “...putative outer membrane porin (OmpC) and is in the same predicted operon as BCAL2486 and BCAL2485, which are ironsulfur oxidoreductase and ironsulfur electron transport proteins, respectively. All three genes are induced at least twofold in vivo (Table 4 ). Although ornibactin biosynthesis and uptake genes were...”

ZMO0021 hypothetical protein from Zymomonas mobilis subsp. mobilis ZM4
39% identity, 90% coverage

• Mechanism of Tolerance to the Lignin-Derived Inhibitor p-Benzoquinone and Metabolic Modification of Biorefinery Fermentation Strains
  Yan, Applied and environmental microbiology 2019
  • “...protein CCGATCTAGTAAGCCAATTCACC TTTCAAATCTGTTGGTTGGGTGT ZMO0021 Hypothetical protein CCACTTCATATCGCTTCTGTCG GCGTAATCGGTGATCCCAAA ZMO0074 Hypothetical...”
  • “...Oxidoreductases Reductases Dehydrogenases FAH ZMO1821 ZMO0074 ZMO0021 ZMO0020 ZMO1399 ZMO1696 ZMO1576 ZMO0778 ZMO0157 ZMO1949 ZMO1335 ZMO1254 ZMO1984 ZMO1303...”
• Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment
  Yi, Biotechnology for biofuels 2015
  • “...Genetic/environmental/cellular process/organismal systems ZMO1727 Aminotransferase 3.02 2.09 Unassigned ZMO0020 Hypothetical protein 3.08 2.14 2.36 Unassigned ZMO0021 Hypothetical protein 3.11 2.89 2.38 Unassigned ZMO0073 CBS domain-containing protein 5.98 4.13 Unassigned ZMO0157 d -isomer-specific 2-hydroxyacid dehydrogenase NAD-binding protein 2.28 2.22 Unassigned ZMO0268 Hypothetical protein 2.32 2.70 Unassigned ZMO0270...”
  • “...were also up-regulated over twofold change under at least two phenolic aldehyde inhibitors. ZMO0020 , ZMO0021 , ZMO0074 , ZMO0268 , ZMO0270 , ZMO0384 , ZMO0388 , ZMO0391 , ZMO0440 , ZMO0486 , ZMO1334 , ZMO1346 , ZMO1386 , ZMO1602 , ZMO1821 , ZMO1880 , ZZM4_0133...”
• Elucidation of Zymomonas mobilis physiology and stress responses by quantitative proteomics and transcriptomics
  Yang, Frontiers in microbiology 2014
  • “...chain 1.20 0.85 0.81 0.85 ZMO0020 Protein of unknown function DUF162 1.58 1.45 1.10 1.80 ZMO0021 Protein of unknown function DUF162 0.97 1.70 1.43 1.90 ZMO0027 IMP cyclohydrolase 1.52 1.05 1.02 1.05 ZMO0035 Ankyrin 0.72 1.25 0.96 1.60 ZMO0041 Shikimate 5dehydrogenase 0.71 0.90 0.84 0.95 ZMO0079...”
  • “...related to the EntnerDoudoroff (ED) pathway (ZMO1518 and pgi ), energy metabolism [e.g., electron transport (ZMO0021, ZMO1851, ZMO1885) and ATP synthesis gene atpC (ZMO0242)], cell wall formation (ZMO1724), regulator gene zrp (ZMO0372), and several transporter related genes such as signal peptidase I gene lepB (ZMO1710), Sec-independent...”

Cj0074c putative iron-sulfur protein from Campylobacter jejuni subsp. jejuni NCTC 11168
36% identity, 95% coverage

• Defining the metabolic requirements for the growth and colonization capacity of Campylobacter jejuni
  Hofreuter, Frontiers in cellular and infection microbiology 2014
  • “...by C. jejuni to pyruvate by the membrane-associated NAD-independent respiratory lactate dehydrogenase complex (L-iLDH; Cj0075c, Cj0074c; Cj0073c) though inactivation of these genes in C. jejuni NCTC 11168 did not abolish the growth of respective mutants with lactate (Thomas et al., 2011 ). However, a second L-iLDH,...”
• The CJIE1 prophage of Campylobacter jejuni affects protein expression in growth media with and without bile salts
  Clark, BMC microbiology 2014
  • “...3.150.78 Hypothetical protein CJJ81176_0110 gi|121613178 Cj0073c Unknown 0.830.21 0.870.99 1.270.67 Iron-sulfur cluster binding protein gi|121612415 Cj0074c Unknown 0.570.6 0.631.01 1.000.61 Anaerobic C4-dicarboxylate transporter gi|218561769 Cj0088 1.031.04 1.130.40 2.170.38 Hypothetical protein Cj0170 gi|218561850 Cj0170 Unknown 0.300.10 2.800.90 2.970.31 Hypothetical protein CJJ81176_0447 gi|121613189 Cj0427 Unknown 0.331.46 1.331.12 1.071.66...”
• Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing
  Cody, Journal of clinical microbiology 2013
  • “...of California, Berkeley CAMP0061 (Cj0069) CAMP0064 (Cj0074c) CAMP0157 (Cj0170)a CAMP0448 (Cj0486) CAMP0490 (icd) CAMP0610 (Cj0653c) CAMP0631 (cipA)a CAMP0741...”
• Cj1411c encodes for a cytochrome P450 involved in Campylobacter jejuni 81-176 pathogenicity
  Alvarez, PloS one 2013
  • “...partners. Interestingly one of the predicted redox partners for CYP1411c is an iron-sulfur protein ( Cj0074c ), known to be localized within the inner membrane fraction [ 23 ]. In C. jejuni 81-176, outer surface components are actively involved in mediating its pathogenicity. The unique localization...”
• Mutational and transcriptomic changes involved in the development of macrolide resistance in Campylobacter jejuni
  Hao, Antimicrobial agents and chemotherapy 2013
  • “...acnB, and frdABC), respiration (gpsA, Cj1357c, Cj1358c, Cj0074c, Cj0075c, Cj0265c, fdxA, and napAGH), central intermediary metabolism (ppa, gltB, aspA, and...”
• Insights into the mode of action of benzyl isothiocyanate on Campylobacter jejuni
  Dufour, Applied and environmental microbiology 2013
  • “...frdA frdB frdC Cj0414 Cj0415 Cj1476c Cj0265c Cj0037c Cj1153 Cj0074c Cj0075c Cj1514c Cj0264c Cj0559 oorA oorB acnB aspA dcuA glnA IlvD gapA fba atpE atpA atpD...”
• Nutrient acquisition and metabolism by Campylobacter jejuni
  Stahl, Frontiers in cellular and infection microbiology 2012
  • “...catabolized into pyruvate through one of several pathways. The first involves three genes, cj0073c , cj0074c , and cj0075c ( lldEFG/lutABC ). These three genes code for a non-flavin ironsulfur containing oxidoreductase complex that demonstrate NAD-independent, l -lactate dehydrogenase activity ( l -iLDH), thereby converting l...”
  • “...enzymes within the metabolic networks outlined in Figure 1 . These include SdaA, AcnB, Cj1585c, Cj0074c, FrdB, MfrB, GltD, OorD, and Cj1476c, plus many more not discussed in this review. It is important to note, that these proteins occupy key points within C. jejuni metabolism, and...”
• Regulation of oxidative stress response by CosR, an essential response regulator in Campylobacter jejuni
  Hwang, PloS one 2011
  • “...6.5 18.2 21 cj1227c putative two-component regulator CprR U:1.5 D:3.2 5.6 25.5 Electron transport 22 cj0074c iron-sulfur cluster binding protein Cj0074c D:1.9 U:2.2 6.5 54.9 23 cj0537 2-oxoglutarate-acceptor oxidoreductase subunit OorB OorB D:3.5 U:3.4 7.8 31.2 Unknown 24 cj0170 hypothetical protein Cj0170 D:1.5/2.2 U:3.4/3.2 7.6 28.7...”
• More

Dred_0690 protein of unknown function DUF162 from Desulfotomaculum reducens MI-1
37% identity, 64% coverage

• Comparative Proteomic Analysis of Desulfotomaculum reducens MI-1: Insights into the Metabolic Versatility of a Gram-Positive Sulfate- and Metal-Reducing Bacterium
  Otwell, Frontiers in microbiology 2016
  • “...(<0.01) 1.02 C LOCUS V: Dred_0689-90, SULFATE-INDUCED Dred_0689 Hypothetical protein 0.23 3.76 (<0.01) 2.74 C Dred_0690 hypothetical protein (HdrD) 0.01 2.35 (<0.01) 1.05 CM LOCUS VI: Dred_1325-30, SULFATE-INDUCED Dred_1325 Heterodisulfide reductase, C subunit (HdrC) 1.88 (<0.01) 6.02 (<0.01) 0.06 C Dred_1326 Hypothetical protein (hdrB) 1.25 (<0.01)...”
  • “...conditions but not relative to pyruvate conditions. Dred_0689 is annotated as a hypothetical protein and Dred_0690 is an HdrD-like protein (Figure 2 and Table 4 ). Both of these proteins have annotations that suggest involvement in lactate oxidation, described by IMG as L-lactate utilization proteins LutC...”
• The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1
  Junier, Environmental microbiology 2010
  • “...dred_1777 to dred_1786; locus VI is dred_0427 to dred_0433 and locus VII is dred_0689 to dred_0690. The asterisk * indicates a selenocysteine-containing protein. Fig. 6 Neighbour-joining phylogenetic tree of Fe-only hydrogenases based on aligments of the H cluster domain. Clades consisting entirely of the same genus...”

Q362_RS0100810, WP_028317114 L-lactate dehydrogenase (quinone) large subunit LdhH from Desulfobulbus elongatus DSM 2908
38% identity, 63% coverage

• Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle
  Detman, Biotechnology for biofuels 2018
  • “...Acetobacterium woodii DSM 1030 genome NC_016894; l -lactate utilization protein LutB containing FeS oxidoreductase WP_028317114 (Q362_RS0100810) from Desulfobulbus elongatus DSM 2908 assembly ASM62114v1; [FeFe]-hydrogenase large subunit Fe, Fe_hydrog_A WP_012939287 (ACFER_RS10010) from Acidaminococcus fermentans DSM 20731 genome NC_013740; Ni, Fe-hydrogenase III large subunit WP_075074147 (LARV_RS13630) from Longilinea...”
  • “...from Acetobacterium woodii DSM 1030 genome NC_016894; l -lactate utilization protein LutB containing FeS oxidoreductase WP_028317114 (Q362_RS0100810) from Desulfobulbus elongatus DSM 2908 assembly ASM62114v1; [FeFe]-hydrogenase large subunit Fe, Fe_hydrog_A WP_012939287 (ACFER_RS10010) from Acidaminococcus fermentans DSM 20731 genome NC_013740; Ni, Fe-hydrogenase III large subunit WP_075074147 (LARV_RS13630) from...”

HU689_06680 lactate utilization protein B from Shewanella algae
37% identity, 90% coverage

• Complete genome sequence of Shewanella algae strain 2NE11, a decolorizing bacterium isolated from industrial effluent in Peru
  Lizárraga, Biotechnology reports (Amsterdam, Netherlands) 2022
  • “...associated with an L-lactate permease activity ( HU689_06695 ) and a lactate utilization protein ( HU689_06680 ). Additionally, we found genes that could be related to the catabolic pathway of N-acetylglucosamine, involved in processes such as transport ( HU689_06290, HU689_06255 ), catalysis ( HU689_06275, HU689_06270 ),...”

THER_0617 L-lactate dehydrogenase (quinone) large subunit LdhH from Thermodesulfovibrio sp. N1
36% identity, 66% coverage

• Characterization and Genome Analysis of the First Facultatively Alkaliphilic Thermodesulfovibrio Isolated from the Deep Terrestrial Subsurface
  Frank, Frontiers in microbiology 2016
  • “...putative lactate dehydrogenases (LDH) belonging to the CCG family, encoded by the gene cluster THER_0621- THER_0617. The cluster comprises lactate permease, putative glycolate oxidase subunit GlcD, Fe-S oxidoreductase with a 4Fe-4S dicluster domain and two CCG domains, an L-lactate utilization protein LutC, and a LutB protein...”

DVU_3033 / Q726S3 quinone-dependent L-lactate dehydrogenase large subunit (EC 1.1.2.3) from Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough) (see 4 papers)
Q726S3 Iron-sulfur cluster-binding protein from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
DVU3033 iron-sulfur cluster-binding protein from Desulfovibrio vulgaris Hildenborough
37% identity, 64% coverage

• Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough.
  Marbehan, Frontiers in microbiology 2024
  • “...dehydrogenase subunit A LldG Q726S4 DVU_3032 22.6 21 63 11 L-lactate dehydrogenase subunit B LldH Q726S3 DVU_3033 79.6 106 63 43 Lactate dehydrogenase P62051 DVU_0600 32.2 2 13 2 D-lactate dehydrogenase subunit A (Dld-II family) Q72DV3 DVU_0826 47.4 2 4 2 D-lactate dehydrogenase subunit B (Dld-II...”
• Key Enzymes for Anaerobic Lactate Metabolism in Geobacter sulfurreducens
  Ueki, Applied and environmental microbiology 2021 (secret)
• Proteomic and Isotopic Response of Desulfovibrio vulgaris to DsrC Perturbation
  Leavitt, Frontiers in microbiology 2019
  • “...Ldh1a belongs to a gene cluster found in the organic acid oxidation region (DVU3025 to DVU3033), previously identified in the genomes of D. vulgaris and Desulfo vibrio alaskensis G20 ( Pereira et al., 2007 ; Wall et al., 2008 ), and recently named as the luo...”
• A stable genetic polymorphism underpinning microbial syntrophy
  Großkopf, The ISME journal 2016
  • “...to encode for a sigma-54 dependent response regulator that controls the downstream operon (DVU3025 - DVU3033), which includes the genes lactate permease and pyruvate decarboxylase. Notably, both enzymes are involved in the lactate oxidation pathway, with the first enzyme catalyzing the lactate uptake and the second...”
• Antimicrobial Effects of Free Nitrous Acid on Desulfovibrio vulgaris: Implications for Sulfide-Induced Corrosion of Concrete
  Gao, Applied and environmental microbiology 2016
  • “...Lactate oxidation DVU3030 DVU3027 DVU3031 DVU3032 DVU3028 DVU3033 DVU0600 DVU2110 DVU2285 DVU2451 DVU2683 DVU3026 DVU3029 DVU1569 DVU1570 DVU3025 DVU0577...”
• The primary pathway for lactate oxidation in Desulfovibrio vulgaris
  Vita, Frontiers in microbiology 2015
  • “...Table S1 ). The two 500 bp regions upstream and downstream of the DVU3032 and DVU3033 genes, respectively, were cloned into the pNOTCm, which produced pNOTCm32-33, and the mutagenic plasmid was transferred into Dv H by electrotransformation. Briefly, cells grown in 80 mL medium C (OD...”
  • “...histidine conserved in enzymes that bind lactate ( Griffin et al., 1992 ). DVU3032 and DVU3033 were annotated as a conserved hypothetical protein and iron sulfur cluster-binding protein, respectively. However, their amino-acid sequences shared 26% amino acid sequence identity with the three subunits of the non-flavin...”
• The electron transfer system of syntrophically grown Desulfovibrio vulgaris
  Walker, Journal of bacteriology 2009
  • “...transcription of genes in a predicted operon (DVU3024 to DVU3033) coding for lactate uptake and oxidation. The enzymes in this pathway are predicted to produce...”

BPHYT_RS26970 L-lactate dehydrogenase, LldF subunit from Burkholderia phytofirmans PsJN
37% identity, 95% coverage

• mutant phenotype: Specifically important for utilization of L-lactate and D,L-lactate as well as L-rhamnose and L-fucose, which are catabolized via L-lactate

lldG / Q8EGS5 L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (EC 1.1.2.3) from Shewanella oneidensis (strain MR-1) (see paper)
SO1519, SO_1519 iron-sulfur cluster-binding protein from Shewanella oneidensis MR-1
38% identity, 90% coverage

• A dynamic periplasmic electron transfer network enables respiratory flexibility beyond a thermodynamic regulatory regime
  Sturm, The ISME journal 2015
  • “...SO_number Gene name Fold change Dcrp DcyaC SO_1518 SO_1519 SO_1520 SO_2912 SO_2913 SO_2915 SO_2916 SO_0027 SO_3720 SO_0845 SO_0848 SO_1428 SO_1429 SO_1430 lldG...”
• Shewanella oneidensis MR-1 sensory box protein involved in aerobic and anoxic growth
  Sundararajan, Applied and environmental microbiology 2011
  • “...SO0399 (frdB) SO0583 (bfd) SO0768 SO1329 (cyaA) SO1427 SO1519 SO1520 SO1521 SO1522 SO1927 (sdhC) SO1928 (sdhA) SO1929 (sdhB) SO1930 (sucA) SO1931 (sucB) SO1932...”
• An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences
  Turse, PloS one 2010
  • “...lactate utilization pathway in S. oneidensis MR-1 [51] , and we observed protein components (LldF, SO1519 and Lld-II, SO1521) of this second pathway in all isolates. While orthologs featuring similar topology for this second lactate utilization pathway exist in S. putrefaciens CN32, we only observed these...”

GSU1620 iron-sulfur cluster binding protein, putative from Geobacter sulfurreducens PCA
35% identity, 66% coverage

• Key Enzymes for Anaerobic Lactate Metabolism in Geobacter sulfurreducens
  Ueki, Applied and environmental microbiology 2021
  • “...in growth on lactate. Genome analysis of Geobacter species identified candidate genes, GSU1623, GSU1624, and GSU1620, for lactate dehydrogenase. Deletion mutants of the identified genes for d-lactate dehydrogenase ( GSU1623 GSU1624 mutant) or l-lactate dehydrogenase ( GSU1620 mutant) could not grow on d-lactate or l-lactate but could grow...”
• Lactate oxidation coupled to iron or electrode reduction by Geobacter sulfurreducens PCA
  Call, Applied and environmental microbiology 2011
  • “...permeases (GSU1622 and GSU0226) and lactate dehydrogenases (GSU1620 and GSU1621), which are highly conserved among lactate-oxidizing bacteria, including those...”

D2S272 4Fe-4S ferredoxin-type domain-containing protein from Haloterrigena turkmenica (strain ATCC 51198 / DSM 5511 / JCM 9101 / NCIMB 13204 / VKM B-1734 / 4k)
37% identity, 58% coverage

• Genomic Markers for Essential Tremor.
  Jiménez-Jiménez, Pharmaceuticals (Basel, Switzerland) 2021
  • “...with 18 affected with ET; genetic anticipation over generations) This gene was mapped close to D2S272 at chromosome 2p25-p22 (maximum LOD score = 5.92). Affected relatives showed a CAG repeat expansion not clearly located in the ETM2 locus. [ 30 ] United States of America ETM2...”
• A novel autosomal recessive non-syndromic hearing impairment locus (DFNB47) maps to chromosome 2p25.1-p24.3.
  Hassan, Human genetics 2006
• Microsatellite diversity and the demographic history of modern humans.
  Jorde, Proceedings of the National Academy of Sciences of the United States of America 1997
• A gene (ETM) for essential tremor maps to chromosome 2p22-p25.
  Higgins, Movement disorders : official journal of the Movement Disorder Society 1997 (PubMed)

Dde_3245 Iron-sulfur cluster binding protein from Desulfovibrio desulfuricans G20
Dde_3245 L-lactate dehydrogenase (quinone) large subunit LdhH from Oleidesulfovibrio alaskensis G20
37% identity, 64% coverage

• Transcriptome-wide marker gene expression analysis of stress-responsive sulfate-reducing bacteria
  Jawaharraj, Scientific reports 2023
  • “...producing cell materials 59 . In this study, the GO term related to lactate oxidation (Dde_3245, Dde_1843) was down-regulated in EC-2 (P-Cu) whereas the same was up-regulated in SLG-Cu (EC-3) with z-scores -0.04 and 0.04, respectively. This confirms that the lactate oxidation pathway was activated in...”
• Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes
  Meyer, Journal of bacteriology 2013
  • “...redox pair) Gene locus tag(s) Dde_1207-Dde_1213 Dde_3523-Dde_3530 Dde_3245 Dde_0312 Dde_3540 M. maripaludis M. hungatei M. maripaludis M. hungatei Mutant growth...”
  • “...the lactate dehydrogenase (LdhB-1, Dde_3240, and LdhB-2, Dde_3245) showed no growth in coculture on lactate, confirming their essential function during...”
• Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth
  Meyer, Journal of bacteriology 2013
  • “...putative iron-sulfur subunits (LdhB-1/2, Dde_3240 and Dde_3245), two phosphate acetyltransferases (Pta, Dde_3241 and Dde_3243), an acetate kinase (Ack,...”
  • “...is significantly upregulated during syntrophy (Dde_3239-40 and Dde_3245). This cytoplasmic lactate dehydrogenase, LdhAB, is not homologous to the previously...”

HVO_1692 4Fe-S protein from Haloferax volcanii DS2
36% identity, 59% coverage

• Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
  Pfeiffer, Genes 2021
  • “...315 ] 15869466 9e OE_1665R (cont.) probably 25% SSO3197 Q97U28 [ 315 ] 15869466 9f HVO_1692 ludB self [ 21 ] 30707467 9f HVO_1692 (cont.) probably 35% BSU34040 O07021 [ 316 ] 19201793 matches up to HVO_1692 pos 490 of 733 9f HVO_1692 (cont.) probably 35%...”
  • “...Supplementary Text S1 Section S9 ). (f) Haloarchaea may contain an NAD-independent L-lactate dehydrogenase, LudBC (HVO_1692 and HVO_1693). The deletion of this gene pair impairs growth on rhamnose, which is catabolized to pyruvate and lactate [ 21 ]. There is a very distant relationship (for details,...”

DOS48_07580 LUD domain-containing protein from Halorubrum sp. PV6
37% identity, 60% coverage

• Unraveling Anaerobic Metabolisms in a Hypersaline Sediment
  Solchaga, Frontiers in microbiology 2022
  • “...this gene is clustered with one coding for a ferredoxin-like protein of unknown function (e.g.,: DOS48_07580 in Halorubrum sp. PV6) that, in addition to the LUD domain, contains multiple 4Fe-4S binding domains ( Table 4A ). Both catalytic enzymes seem to be soluble proteins that are...”

HMPREF1322_RS00725 lactate utilization protein B from Porphyromonas gingivalis W50
38% identity, 90% coverage

• Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis
  Costeira, mSystems 2023
  • “...245.42 3.57 0.27 1.53E-38 Helix-turn-helix domain-containing protein HMPREF1322_RS08255 1,559.13 2.94 0.23 2.65E-38 IS5/IS1182 family transposase HMPREF1322_RS00725 911.64 2.93 0.23 5.26E-38 Lactate utilization protein HMPREF1322_RS05425 530.83 3.76 0.29 1.83E-37 DUF2023 family protein HMPREF1322_RS00485 425.30 3.46 0.27 2.24E-37 DUF4906 domain-containing protein HMPREF1322_RS07380 45,140.22 3.08 0.24 3.93E-37 OmpH family...”
  • “...in a genomic region (NZ_AJZS01000011.1 1220 kb) containing the (Fe-S)-binding protein HMPREF1322_RS00720, lactate utilization protein HMPREF1322_RS00725, hypothetical protein HMPREF1322_RS00730, PaaI family thioesterase HMPREF1322_RS00735, and ABC transporter ATP-binding protein HMPREF1322_RS00740 ( Fig. 5 top panel, purple; Fig. 6 ). In annotating DMAs to genes, if genes up...”
• Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis
  Costeira, 2022

PG1172 iron-sulfur cluster binding protein, putative from Porphyromonas gingivalis W83
38% identity, 90% coverage

• Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis
  Costeira, mSystems 2023
  • “...protein HMPREF1322_RS00730 (W83: PG1173) in the lactate utilization cluster, the lactate utilization protein HMPREF1322_RS00725 (W83: PG1172), the 4-alpha-glucanotransferase HMPREF1322_RS03650 (W83: PG0767), and ABC transporter protein gene cluster HMPREF1322_RS00745 (W83: PG1176) and HMPREF1322_RS00740 (W83: PG1175) ( Table 6 ). Seven of the 15 genes had DMAs located...”
  • “...in excess hemin, and the hypothetical protein HMPREF1322_RS00730 (W83: PG1173), lactate utilization protein HMPREF1322_RS00725 (W83: PG1172), 4-alpha-glucanotransferase HMPREF1322_RS03650 (W83: PG0767), ABC transporter protein HMPREF1322_RS00745 (W83: PG1176), and HMPREF1322_RS00740 (W83: PG1175), which were under-expressed in excess hemin ( Table 9 ). We assessed whether genome-wide DEGs were...”
• Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis
  Costeira, 2022
• Nitric oxide stress resistance in Porphyromonas gingivalis is mediated by a putative hydroxylamine reductase
  Boutrin, Journal of bacteriology 2012
  • “...12 upregulated genes (PG1858, dps, PG0777, PG0776, PG1172, PG1171, PG1239, hcp, PG2034, PG0108, PG0616, and PG0195) that were differentially expressed following...”
• Gene expression profile analysis of Porphyromonas gingivalis during invasion of human coronary artery endothelial cells
  Rodrigues, Infection and immunity 2005
  • “...PG0092 PG0120 PG0186 PG0195 PG0280 PG0686 PG1116 PG1172 PG1286 PG1321 PG1492 PG1682 PG1683 PG1795 PG1864 PG1896 PG2064 Transporter, putative...”
  • “...metabolism Hypothetical protein 5.37 6.67 10.51 4.63 PG1172 PG1286 PG1321 PG1682 PG1683 PG1896 PG2064 a b Locus number, identification and functional...”

DR_RS09770 LUD domain-containing protein from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
39% identity, 64% coverage

• Comparative genomics of Deinococcus radiodurans: unveiling genetic discrepancies between ATCC 13939K and BAA-816 strains
  Jeong, Frontiers in microbiology 2024
  • “...aligns with lutB , its noted as a pseudogene, with only a partial LutB protein (DR_RS09770) present in the NCBI-annotated genome NC_001263.1 ( Supplementary Table S2 ). A previously identified frameshift in DR _ 1908 ( Hwang et al., 2013 ) has been corrected by a...”

Dred_0433 CoB--CoM heterodisulfide reductase from Desulfotomaculum reducens MI-1
34% identity, 53% coverage

• Comparative Proteomic Analysis of Desulfotomaculum reducens MI-1: Insights into the Metabolic Versatility of a Gram-Positive Sulfate- and Metal-Reducing Bacterium
  Otwell, Frontiers in microbiology 2016
  • “...U LOCUS III: Dred_0432-3, Fe(III)-CITRATE-INDUCED Dred_0432 Hypothetical protein (FeS) Fecit only (1 unique pep) C Dred_0433 CoBCoM heterodisulfide reductase (HdrD) 1.80 (<0.01) NI NI CM LOCUS VI: Dred_1778-84, Fe(III)-CITRATE-INDUCED Dred_1778 Electron transfer flavoprotein subunit beta (EtfB) 0.01 0.02 2.73 (<0.01) C Dred_1779 Electron transfer flavoprotein subunit...”
  • “...identified on pyruvate and Fe(III)-citrate and is increased ~3.5-fold on Fe(III)-citrate ( p < 0.01). Dred_0433 is completely unique to the Fe(III)-citrate condition. The identification of Dred_0432 on Fe(III)-citrate is based on a single unique peptide in 5/6 replicates. Dred_0433 is localized to the cytoplasmic membrane...”
• The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1
  Junier, Environmental microbiology 2010
  • “...is dred_1325 to dred_1330; locus V Is dred_1777 to dred_1786; locus VI is dred_0427 to dred_0433 and locus VII is dred_0689 to dred_0690. The asterisk * indicates a selenocysteine-containing protein. Fig. 6 Neighbour-joining phylogenetic tree of Fe-only hydrogenases based on aligments of the H cluster domain....”

Dred_0432 protein of unknown function DUF162 from Desulfotomaculum reducens MI-1
27% identity, 70% coverage

• Comparative Proteomic Analysis of Desulfotomaculum reducens MI-1: Insights into the Metabolic Versatility of a Gram-Positive Sulfate- and Metal-Reducing Bacterium
  Otwell, Frontiers in microbiology 2016
  • “...Dred_0145 Heterodisulfide reductase subunit (HdrD) 0.7 (0.03) 1.61 (<0.01) 0.43 U LOCUS III: Dred_0432-3, Fe(III)-CITRATE-INDUCED Dred_0432 Hypothetical protein (FeS) Fecit only (1 unique pep) C Dred_0433 CoBCoM heterodisulfide reductase (HdrD) 1.80 (<0.01) NI NI CM LOCUS VI: Dred_1778-84, Fe(III)-CITRATE-INDUCED Dred_1778 Electron transfer flavoprotein subunit beta (EtfB)...”
  • “...identified in our study. Dred_0432-3, however, is significant on the Fe(III)-citrate condition (Table 4 ). Dred_0432 was only identified on pyruvate and Fe(III)-citrate and is increased ~3.5-fold on Fe(III)-citrate ( p < 0.01). Dred_0433 is completely unique to the Fe(III)-citrate condition. The identification of Dred_0432 on...”

APPSER1_RS02040 anaerobic glycerol-3-phosphate dehydrogenase subunit GlpC from Actinobacillus pleuropneumoniae serovar 1 str. 4074
APL_0381 anaerobic glycerol-3-phosphate dehydrogenase subunit C from Actinobacillus pleuropneumoniae L20
26% identity, 38% coverage

• Effects of OxyR regulator on oxidative stress, Apx toxin secretion and virulence of Actinobacillus pleuropneumoniae
  Guo, Frontiers in cellular and infection microbiology 2023
  • “...molybdopterin-dependent oxidoreductase APPSER1_RS09175 1.667295 glycerol-3-phosphate dehydrogenase subunit GlpB APPSER1_RS02035 3.75196 anaerobic glycerol-3-phosphate dehydrogenase subunit C APPSER1_RS02040 3.980692 catalase APPSER1_RS05435* 4.049482 thiol peroxidase APPSER1_RS08140* -1.91597 glutathione peroxidase APPSER1_RS07695 -1.5886 superoxide dismutase family protein APPSER1_RS00020* -1.49949 DNA starvation/stationary phase protection protein APPSER1_RS08165* -1.4029 heme anaerobic degradation radical SAM...”
• Actinobacillus pleuropneumoniae genes expression in biofilms cultured under static conditions and in a drip-flow apparatus
  Tremblay, BMC genomics 2013
  • “...those, subunits for two key enzymes for anaerobic metabolism were identified: glycerol-3-phosphate dehydrogenase (APL_0379 and APL_0381) and formate dehydrogenase (APL_0894 and APL_0895). The largest group of up-regulated genes were transport-related genes followed by genes associated with regulatory functions (Figure 3 A). Among the transport-related genes, two...”
  • “...APL_0048 arcA APL_0049 APL_0189 dus APL_0234 APL_0236 APL_0330 APL_0331 hlp APL_0364 ssa1 /aasP APL_0379 glpA APL_0381 glpC APL_0382 ribD APL_0383 ribE APL_0384 ribA APL_0391 macA APL_0394 rpoE APL_0395 rseA APL_0443 APL_0449 APL_0626 macB APL_0627 cpxA APL_0629 cpxR APL_0840 tolC APL_0891 fdhD APL_0892 fdxG APL_0893 fdxG APL_0894...”
• Effects of growth conditions on biofilm formation by Actinobacillus pleuropneumoniae
  Labrie, Veterinary research 2010
  • “...2.156 APL_0892 fdxG Formate dehydrogenase, nitrate-inducible, major subunit 2.116 APL_1798 torA Trimethylamine-N-oxide reductase precursor 1.977 APL_0381 glpC Anaerobic glycerol-3-phosphate dehydrogenase subunit C 1.919 APL_0842 pntA NAD(P) transhydrogenase subunit alpha 1.903 APL_0895 fdnI Formate dehydrogenase, cytochrome b556 subunit 1.816 APL_1208 adhC Putative alcohol dehydrogenase class 3 1.801...”

BAS3035 conserved hypothetical protein from Bacillus anthracis str. Sterne
BA3268 conserved hypothetical protein from Bacillus anthracis str. Ames
27% identity, 22% coverage

• Identification of a protein subset of the anthrax spore immunome in humans immunized with the anthrax vaccine adsorbed preparation
  Kudva, Infection and immunity 2005
  • “...BAS3377 BA3641 BA3642 BAS4394 BA4734 BAS4648 BA5003 BAS4647 BAS3035 BAS3034 BAS2639 BA5002 BA3268 BA3267 BA2830 BAS1932 BAS5205 BA2079 BA5604 367 BAS5183 BA5578...”
• Identification of a protein subset of the anthrax spore immunome in humans immunized with the anthrax vaccine adsorbed preparation
  Kudva, Infection and immunity 2005
  • “...BA4734 BAS4648 BA5003 BAS4647 BAS3035 BAS3034 BAS2639 BA5002 BA3268 BA3267 BA2830 BAS1932 BAS5205 BA2079 BA5604 367 BAS5183 BA5578 380 BAS5217 BA5615 545 739...”

APL_0444 hypothetical protein from Actinobacillus pleuropneumoniae L20
21% identity, 39% coverage

• Comparative profiling of the transcriptional response to iron restriction in six serotypes of Actinobacillus pleuropneumoniae with different virulence potential
  Klitgaard, BMC genomics 2010
  • “...dehydrogenase subunit, Fe-S oxidoreductase C -2.63 APL_0445 + ykgF Iron-sulfur electron transport protein C -1.79 APL_0444 + engA Putative GTP binding protein S -1.10 APL_0416 - N-acetyl-D-glucosamine kinase KG -0.36 APL_0155 + nqrF Na+-translocating NADH-ubiquinone oxidoreductase subunit F C -0.37 APL_0154 + nqrE Na+-transporting NADH-ubiquinone oxidoreductase...”

BA1317 ykgG family protein from Bacillus anthracis str. Ames
28% identity, 26% coverage

• SpoVG is Necessary for Sporulation in Bacillus anthracis
  Chen, Microorganisms 2020
  • “...the comC gene (BA1318, NCBI Reference Sequence: NC_003997.3, region 1265988 to 1266710) is located between BA1317 and BA1319. The amino acid sequence of the ComC proteins of B. anthracis and B. subtilis share only 38.91% sequence identity (92% sequence coverage) ( Supplemental Table S4 ). These...”

APJL_0471 hypothetical protein from Actinobacillus pleuropneumoniae serovar 3 str. JL03
21% identity, 39% coverage

• A Transcriptome Map of Actinobacillus pleuropneumoniae at Single-Nucleotide Resolution Using Deep RNA-Seq
  Su, PloS one 2016
  • “...466478 90 - Y APJL_0425(-) APJL_0426(+) - A APP-S16 517137 517215 79 - Y APJL_0468(+) APJL_0471(-) - A APP-S17 598881 599063 182 - Y APJL_0553(+) APJL_0559(+) t44 B APP-S18 703124 703153 30 Y Y APJL_0644(-) APJL_0645(-) - C APP-S19 753851 754045 195 - Y APJL_0686(-) APJL_0687(-)...”

HD1219 conserved hypothetical protein from Haemophilus ducreyi 35000HP
24% identity, 33% coverage

• Comparative proteomic analysis of the Haemophilus ducreyi porin-deficient mutant 35000HP::P2AB
  Davie, Journal of bacteriology 2009
  • “...HD0646 RpsL SecB RpoD RpmF HD0776 PutP ArgH RecB HD1190 HD1219 RarA Kgd HD1377 MoaE HD1400 Pta ManB MukB Rnc AceF GroEL GroES RpmI RpoB NusG HD1887 OmpP2B LspA2...”

BA_3774 DUF162, Uncharacterized ACR, YkgG family COG1556 from Bacillus anthracis str. A2012
27% identity, 22% coverage

• Genomic characterization of <i>Bacillus cereus</i> isolated from food poisoning cases revealed the mechanism of toxin production
  Zhou, Frontiers in microbiology 2023
  • “...6 ), and identified key genes in gene co-expression networks. The findings indicate that BA_0477, BA_3774 , and BA_3775 , which were closely associated with prophage ( Supplementary Table 5 ), were the key genes within the contracted gene families of the LY01-LY09 strains ( Supplementary...”

PM1855 unknown from Pasteurella multocida subsp. multocida str. Pm70
25% identity, 21% coverage

• Phase variation in the glycosyltransferase genes of Pasteurella multocida associated with outbreaks of fowl cholera on free-range layer farms
  Omaleki, Microbial genomics 2022
  • “...2012 PM1582 70 1 274 htpE insertion position 126 B3 2014 PM1845 to PM1853 and PM1855 10 8 No stop codon or frame shift B2 2016 PM2248 62 1 20 gatG 14bp deletion PM842 , PM843, PM1855 B4 2016 PM2290 50 1 7 htpE del position...”
  • “..., PM843, PM1855 B2 2017 PM2356 50 1 20 gatG 14bp deletion PM842 , PM843, PM1855 B1-shed1 2016 PM2269 and PM2305 50 2 9 natC 7bp insertion PM842 , PM843, PM1855 B1-shed1 2017 PM2369 1 9 natC 7bp insertion PM842 , PM843, PM1855 B1-shed1 2017 DEC...”

GSU1621 conserved domain protein from Geobacter sulfurreducens PCA
27% identity, 22% coverage

• Key Enzymes for Anaerobic Lactate Metabolism in Geobacter sulfurreducens
  Ueki, Applied and environmental microbiology 2021 (secret)
• Lactate oxidation coupled to iron or electrode reduction by Geobacter sulfurreducens PCA
  Call, Applied and environmental microbiology 2011
  • “...and GSU0226) and lactate dehydrogenases (GSU1620 and GSU1621), which are highly conserved among lactate-oxidizing bacteria, including those of the Shewanella...”

New Search

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.