PaperBLAST
PaperBLAST Hits for Shew_2785 (85 a.a., MALLIDDSCI...)
Show query sequence
>Shew_2785
MALLIDDSCINCDMCEPECPNQAITMGEEIYEIDPNLCTECVGHYDKPTCVSVCPIDCID
PDPAHVESQDELLVKYHLITGKPID
Running BLASTp...
Found 70 similar proteins in the literature:
swp_3663 4Fe-4S ferredoxin, iron-sulfur binding from Shewanella piezotolerans WP3
82% identity, 99% coverage
- Condition-Specific Molecular Network Analysis Revealed That Flagellar Proteins Are Involved in Electron Transfer Processes of Shewanella piezotolerans WP3
Ding, Genetics research 2021 - “...Size Density P value KEGG pathways Members 1 9 0.58 3.49 E 04 Carbon metabolism swp_3663, swp_5025, swp_4312, swp_1239, swp_2139, swp_2142, swp_3875, swp_3458, swp_0182 2 9 0.50 9.74 E 04 Oxidative phosphorylation swp_4058, swp_0854, swp_4352, swp_3589, swp_4940, swp_1424, swp_1425, swp_0430, swp_0429 3 6 0.87 1.26 E...”
NP_249053 4Fe-4S ferredoxin from Pseudomonas aeruginosa PAO1
PA0362 ferredoxin (4Fe-4S) from Pseudomonas aeruginosa PAO1
71% identity, 96% coverage
- The structure of the 2[4Fe-4S] ferredoxin from Pseudomonas aeruginosa at 1.32-A resolution: comparison with other high-resolution structures of ferredoxins and contributing structural features to reduction potential values.
Giastas, Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry 2006 (PubMed)- GeneRIF: The significantly higher resolution of the PaFd (Pseudomonas aeruginosa 2[4Fe-4S] ferredoxin) structure makes possible a reliable comparison with available high-resolution structures of [4Fe-4S]-containing ferredoxins.
- The FinR-regulated essential gene fprA, encoding ferredoxin NADP+ reductase: Roles in superoxide-mediated stress protection and virulence of Pseudomonas aeruginosa
Boonma, PloS one 2017 - “...essentiality of fprA . PAO1 has several genes encoding Fdx of different families, e.g., fdx1 (PA0362), encoding two[4Fe-4S]-containing bacterial ferredoxin; fdx2 (PA3809) (a member of the isc operon that is involved in iron-sulfur cluster biogenesis), encoding a [2Fe-2S]-containing ferredoxin; rnfB (PA3490), encoding a ferredoxin-like protein; and...”
- “...fdx2 , pTS- fdxA , pTS- rnfB and pTS- fprB for trans expression of fdx1 (PA0362), fdx2 (PA3809), fdxA (PA3621), rnfB (PA3490) and fprB , respectively. The specific primer pairs for PCR amplification of full-length fdx1 , fdx2 , fdxA , rnfB , and fprB genes...”
- A bacteria-specific 2[4Fe-4S] ferredoxin is essential in Pseudomonas aeruginosa
Elsen, BMC microbiology 2010 - “...function relies on a given Fdx. One of P. aeruginosa Fdxs is encoded by the PA0362 locus ( fdx1 ) and it belongs to a separated family of proteins containing two [4Fe-4S] clusters [ 9 ]. The sequences of proteins of this family are characterized by...”
- “...do not anaerobically catabolize aromatics), the importance of the fdx1 gene of the P. aeruginosa PA0362 locus has been investigated in the present work. The possibility of endogenous in vivo functional substitution has been examined by removing the chromosomal copy of the gene. Also, the main...”
- Toxicogenomic response of Pseudomonas aeruginosa to ortho-phenylphenol
Nde, BMC genomics 2008 - “...Energy metabolism PA5553_atpC_at PA5553 2.175 0.00502 ATP synthase epsilon chain atp C Energy metabolism PA0362_fdx1_at PA0362 2.125 0.000346 ferredoxin [4Fe-4S] fdx 1 Energy metabolism PA3527_pyrC_at PA3527 2.218 0.0211 dihydroorotase pyr C Nucleotide biosynthesis and metabolism PA5331_pyrE_at PA5331 2.156 0.0166 orotate phosphoribosyltransferase pyr E Nucleotide biosynthesis and...”
- “...generation by oxidative phosphorylation and elements mediating electron transfer (glutaredoxin (PA5129), ferredoxin I (PA3621), ferredoxin (PA0362) and the Na + -translocating NADH: quinone oxidoreductase subunit Nqr5 (PA2995) were upregulated. Other components involved in the oxidative phosphorylation pathway: (PA5561 ( atp 1) and PA5556 (ATP synthase alpha...”
- In vitro analysis of tobramycin-treated Pseudomonas aeruginosa biofilms on cystic fibrosis-derived airway epithelial cells
Anderson, Infection and immunity 2008 - “...8.6 6.5 3.6 2.8 2.8 2.1 2.0 Iron PA3531 PA4764 PA0362 PA4131 PA3491 PA5217 16.5 4.2 2.1 2.0 2.0 2.3 PA5216 2.4 PA3812 PA3813 PA2399 PA3809 PA2386 PA2426 PA4231...”
- Isolation and characterization of an R' plasmid in Pseudomonas aeruginosa
Holloway, Journal of bacteriology 1978 - “...used in this studya Strain PA025 (R68.45) PA0222 PA0357 PA0362 PA0372 PA0373 PA0486 PA01032 PA02003 PA02033 4 4 this study this study 8 5 this study this...”
- “...by propagating F116L on PA02003(R'PA1) and transducing into PA0362 as recipient; arg+ transductants are found at about 50% of the normal frequency. Thus, F116L...”
FXO12_19935 YfhL family 4Fe-4S dicluster ferredoxin from Pseudomonas sp. J380
67% identity, 96% coverage
- A Novel Marine Pathogen Isolated from Wild Cunners (Tautogolabrus adspersus): Comparative Genomics and Transcriptome Profiling of Pseudomonas sp. Strain J380
Umasuthan, Microorganisms 2021 - “...cluster (ISC), including hscA (FXO12_24275) and fdx (FXO12_24280), two other putative fdx -like genes (FXO12_11905, FXO12_19935) and cyaY (FXO12_19255) decreased under iron-limited conditions ( Figure 8 C and Table 4 ). Interactive analysis of GO terms and genes involved in iron homeostasis identified three GO clusters...”
- “...the ISC biogenesis pathway [ 99 ]. Two other putative fdx -like genes (FXO12_11905 and FXO12_19935) and an iron-trafficking CyaY protein that supplies iron for ISC biogenesis were also less-expressed under iron-limitation. In contrast, a 2Fe-2S ISC binding domain-containing protein (FXO12_23050) was up-regulated. Not surprisingly, the...”
CH_091751 ferredoxin from Pseudomonas aeruginosa (see paper)
70% identity, 95% coverage
2fgoA / Q9I6D2 Structure of the 2[4fe-4s] ferredoxin from pseudomonas aeruginosa (see paper)
70% identity, 95% coverage
- Ligand: iron/sulfur cluster (2fgoA)
PSPTO_0416 ferredoxin from Pseudomonas syringae pv. tomato str. DC3000
66% identity, 96% coverage
FER_ALLVD / P00208 Ferredoxin; 2[4Fe-4S] ferredoxin from Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D) (Chromatium vinosum) (see 4 papers)
fdx / GI|1518927 ferredoxin (see 3 papers)
65% identity, 96% coverage
- function: Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.
cofactor: [4Fe-4S] cluster (Binds 2 [4Fe-4S] clusters.)
NGO1859 putative ferredoxin from Neisseria gonorrhoeae FA 1090
67% identity, 93% coverage
MU9_1665 YfhL family 4Fe-4S dicluster ferredoxin from Morganella morganii subsp. morganii KT
69% identity, 92% coverage
3eunA / P00208 Crystal structure of the 2[4fe-4s] c57a ferredoxin variant from allochromatium vinosum (see paper)
63% identity, 95% coverage
- Ligand: iron/sulfur cluster (3eunA)
HI0527 ferredoxin (fdx-2) from Haemophilus influenzae Rd KW20
64% identity, 92% coverage
- Genome-scale approaches to identify genes essential for Haemophilus influenzae pathogenesis
Wong, Frontiers in cellular and infection microbiology 2012 - “...biosynthesis d HI0406 accA Acetyl-CoA carboxylase carboxyltransferase subunit alpha d HI0432 nudC NADH pyrophosphatase d HI0527 fdx-2 Ferredoxin d HI0936 Cytochrome C-type biogenesis d TRANSCRIPTION/DNA PROCESSING HI0700 Hypothetical protein d HI0814 alaS Alanyl-tRNA synthetase d HI1056 Type III restriction-modification system methyltransferase-like protein d HI1459 RNA polymerase...”
YfhL / b2562 putative 4Fe-4S cluster-containing protein YfhL from Escherichia coli K-12 substr. MG1655 (see 3 papers)
YFHL_ECOLI / P52102 Ferredoxin YfhL; EcFd from Escherichia coli (strain K12) (see paper)
b2562 predicted 4Fe-4S cluster-containing protein from Escherichia coli str. K-12 substr. MG1655
64% identity, 92% coverage
2zvsA / P52102 Crystal structure of the 2[4fe-4s] ferredoxin from escherichia coli (see paper)
63% identity, 92% coverage
- Ligand: iron/sulfur cluster (2zvsA)
Mmc1_0249 4Fe-4S ferredoxin, iron-sulfur binding domain protein from Magnetococcus sp. MC-1
58% identity, 95% coverage
A1S_2297 putative 4Fe-4S ferredoxin from Acinetobacter baumannii ATCC 17978
64% identity, 75% coverage
jhp0262 Ferredoxin from Helicobacter pylori J99
53% identity, 96% coverage
FDX2_SORC5 / A9FH21 Ferredoxin Fdx2 from Sorangium cellulosum (strain So ce56) (Polyangium cellulosum (strain So ce56)) (see paper)
56% identity, 74% coverage
HP0277 ferredoxin from Helicobacter pylori 26695
HPG27_256 ferrodoxin from Helicobacter pylori G27
HPG27_RS01390 YfhL family 4Fe-4S dicluster ferredoxin from Helicobacter pylori G27
53% identity, 96% coverage
- A two-hybrid system reveals previously uncharacterized protein-protein interactions within the Helicobacter pylori NIF iron-sulfur maturation system
Benoit, Scientific reports 2021 - “...to coordinate FeS clusters, two proteins, HP0207 (a member of the Nbp35/ApbC ATPase family) and HP0277 (previously annotated as FdxA, a member of the YfhL ferredoxin-like family) were further studied, using a bacterial two-hybrid system approach to identify proteinprotein interactions. ApbC was found to interact with...”
- “...HP0207 ApbC/Mrp 24999 Member of Nbp35 ATPase (unknown; FeS carrier?) Yes 368 (40) Unknown e HP0277 FdxA 25054 Ferredoxin (unknown; FeS carrier?) Yes/no d 84 (9.5) Unknown e a HP number refers to strain 26695 26 . b Based on chromosomal mutagenesis attempts (as found in...”
- Iron-sulfur protein maturation in Helicobacter pylori: identifying a Nfu-type cluster carrier protein and its iron-sulfur protein targets
Benoit, Molecular microbiology 2018 - “...that interacted with Nfu were also found to interact with NifU, with the exception of HP0277 (ferredoxin), which was shown to make complexes with either NifS or Nfu, but not with NifU. Preliminary experiments with T18-AcnB (HP0779) suggested AcnB only interacts with (T25-)Nfu, but not with...”
- “...donor proteins (NifS, NifU, Nfu) ( Fig. 8 ). We also found that one protein (HP0277) appears to interact with NifS or Nfu, but not with NifU. HP0277 encodes for a ferredoxin-type protein. However, while most ferredoxin-like proteins harbor one or two conserved CX 2 CX...”
- Acid-regulated gene expression of Helicobacter pylori: Insight into acid protection and gastric colonization
Marcus, Helicobacter 2018 - “...1.42 0.03 0.00 1.68 0.04 0.00 2.20 0.21 0.02 phosphoenolpyruvate synthase ( ppsA ) HPG27_RS01390 HP0277 1.26 0.11 0.20 1.79 0.09 0.03 2.11 0.07 0.01 ferredoxin ( fdxB ) Entner-Doudoroff Pathway HPG27_RS05455 HP1101 1.77 0.18 0.05 1.47 0.15 0.10 1.90 0.09 0.00 glucose-6-phosphate 1-dehydrogenase ( zwf,...”
- Clarithromycin-Based Triple Therapy is Still Useful as an Initial Treatment for Helicobacter pylori Infection in the Dominican Republic
Miftahussurur, The American journal of tropical medicine and hygiene 2017 - “...37del, 179H None None E473G I322V recA (hp0153) fdxA (hp0277) fdxB (hp1508) None V64I, M65L, P245A, I304T, A428I, A439T None N32S, S79I N32S, S79I S122R, P123S,...”
- Colloidal bismuth subcitrate impedes proton entry into Helicobacter pylori and increases the efficacy of growth-dependent antibiotics
Marcus, Alimentary pharmacology & therapeutics 2015 - “...ATP synthase F0, subunit b HP1133 2.14 ATP synthase F1, subunit gamma ( atpF ) HP0277 2.40 ferredoxin ( atpG) HP0388 2.75 ubiquinone menaquinone biosynthesis methlytransferase * Accession number from H. pylori strain 26695...”
- Genes of Helicobacter pylori regulated by attachment to AGS cells
Kim, Infection and immunity 2004 - “...as the genes encoding thioredoxin (HP1458) and ferrodoxin (HP0277), the detoxification gene, the superoxide dismutase gene (sodB [HP0389]), the gene encoding a...”
- “...HP1122 HP1585 HP0601 HP0472 HP0359 Description HP1458 HP0277 HP0389 HP1510 Temporal regulator of flagellar apparatus biogenesis (flgM) Flagellar basal-body rod...”
- Growth phase-dependent response of Helicobacter pylori to iron starvation
Merrell, Infection and immunity 2003 - “...2.1 2.3 2.1 2.5 Energy metabolism *HP0026 HP0176 HP0277 *#HP0294 HP0691 HP0692 *HP0943 *HP1238 *HP1399 HP1538 HP1539 JHP0022 JHP0162 JHP0262 JHP0279 JHP0637...”
- Acid-adaptive genes of Helicobacter pylori
Wen, Infection and immunity 2003 - “...1.52 1.27 2.78 2.65 3.09 2.95 2.59 2.63 2.58 HP0194 HP0277 HP0357 HP0588 HP0589 HP0590 HP0591 0.96 0.85 0.90 1.11 1.06 1.01 1.23 1.05 2.22 1.55 3.52 1.64 6.74...”
- More
- Genetic requirements and transcriptomics of Helicobacter pylori biofilm formation on abiotic and biotic surfaces
Hathroubi, NPJ biofilms and microbiomes 2020 - “...These genes are all expressed to lower levels in the biofilm cells. Name Product Fold-change HPG27_256 Ferredoxin 4.39 HPG27_516 Hypothetical protein 3.01 HPG27_1015 Zinc-metalloprotease 2.86 HPG27_1271 Hypothetical protein 2.84 HPG27_1035 Pseudo uridylate synthase I 2.71 HPG27_1180 Hypothetical protein 2.62 HPG27_1008 SodB, iron-dependent superoxide dismutase 2.61 HPG27_591...”
- “...) (Table 3 and Supplementary Table 3 ). Genes related to energy metabolism, including ferredoxin (HPG27_256), thioredoxin ( trxA ), and the super dismutase sodB were among the most downregulated genes in our biofilm cells. Interestingly, these same genes were also downregulated in other studies, after...”
- Acid-regulated gene expression of Helicobacter pylori: Insight into acid protection and gastric colonization
Marcus, Helicobacter 2018 - “...HP0121 1.42 0.03 0.00 1.68 0.04 0.00 2.20 0.21 0.02 phosphoenolpyruvate synthase ( ppsA ) HPG27_RS01390 HP0277 1.26 0.11 0.20 1.79 0.09 0.03 2.11 0.07 0.01 ferredoxin ( fdxB ) Entner-Doudoroff Pathway HPG27_RS05455 HP1101 1.77 0.18 0.05 1.47 0.15 0.10 1.90 0.09 0.00 glucose-6-phosphate 1-dehydrogenase (...”
fdx / CAA12251.1 ferredoxin from Thauera aromatica (see paper)
53% identity, 95% coverage
1rgvA / O88151 Crystal structure of the ferredoxin from thauera aromatica (see paper)
52% identity, 94% coverage
- Ligand: iron/sulfur cluster (1rgvA)
RPA0662 ferredoxin from Rhodopseudomonas palustris CGA009
49% identity, 93% coverage
- Anaerobic Degradation of Syringic Acid by an Adapted Strain of Rhodopseudomonas palustris
Oshlag, Applied and environmental microbiology 2020 - “...5.70* 0.87 rpa0650 badK Cyclohex-1-ene-1-carboxyl-CoA hydratase 5.62* 0.69 rpa0667 hbaF Inner membrane translocator 5.50* 0.98 rpa0662 badB Ferredoxin 5.01* 0.55 rpa0661 badA Benzoate-CoA ligase 4.91* 0.77 rpa0668 hbaE ABC transporter subunit substrate-binding component 4.83* 0.95 rpa0665 hbaH ABC transporter ATP-binding protein 4.67* 0.50 rpa0673 hbaR Hydroxybenzoate...”
SMGWSS_137 ferredoxin (4Fe-4S) from Candidatus Sulcia muelleri GWSS
48% identity, 94% coverage
- One bacterial cell, one complete genome
Woyke, PloS one 2010 - “...SMGWSS_171 30S ribosomal subunit protein S18 75.34 DMIN_01600 SMGWSS_162 putative outer membrane protein 81.23 DMIN_01330 SMGWSS_137 chaperone protein DnaJ 87.14 DMIN_02500 SMGWSS_255 dihydrolipoamide acyltransferase E2 component 89.05 DMIN_00160 SMGWSS_017 putative ATP synthase F1, epsilon subunit 89.11 DMIN_01860 SMGWSS_191 hypothetical protein 89.71 DMIN_00320 SMGWSS_033 highly suspect ATP...”
Q8KCZ6 Ferredoxin-1 from Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)
56% identity, 69% coverage
- Cryo-EM structure of the whole photosynthetic reaction center apparatus from the green sulfur bacterium Chlorobaculum tepidum
Xie, Proceedings of the National Academy of Sciences of the United States of America 2023 - “...potential docking site for ferredoxin. A homology model of the ferredoxin from C. tepidum (Uniprot: Q8KCZ6) was built using Alphafold. Several positively charged residues are in the proximity of the potential docking site (enlarged view in the Right ). The primary charge separation event is followed...”
- Molecular asymmetry of a photosynthetic supercomplex from green sulfur bacteria
Puskar, Nature communications 2022 - “...of the potential ferredoxin docking site. White surface represents the ferredoxin enzyme (UniProt accession number: Q8KCZ6). The interactions between PscB and the two FMO trimers are also different. PscB has a larger contact area with FMO1 than FMO2 (Fig. 3 c). The N- and C-terminal loops...”
- “...force field 87 . The atomic coordinate of the ferredoxin from C. tepidum (accession number: Q8KCZ6) was predicted and calculated using AlphaFold2 (version 2.0) 88 . The figures for the cryo-EM density maps and atomic models were prepared using UCSF Chimera or ChimeraX (version 1.2.5) 89...”
FE46_RS08120 4Fe-4S dicluster domain-containing protein from Flavobacterium psychrophilum
36% identity, 68% coverage
DMIN_01330 4Fe-4S binding domain protein from Candidatus Sulcia muelleri DMIN
57% identity, 68% coverage
- One bacterial cell, one complete genome
Woyke, PloS one 2010 - “...DMIN_01680 SMGWSS_171 30S ribosomal subunit protein S18 75.34 DMIN_01600 SMGWSS_162 putative outer membrane protein 81.23 DMIN_01330 SMGWSS_137 chaperone protein DnaJ 87.14 DMIN_02500 SMGWSS_255 dihydrolipoamide acyltransferase E2 component 89.05 DMIN_00160 SMGWSS_017 putative ATP synthase F1, epsilon subunit 89.11 DMIN_01860 SMGWSS_191 hypothetical protein 89.71 DMIN_00320 SMGWSS_033 highly suspect...”
all2512 transcriptional regulator from Nostoc sp. PCC 7120
47% identity, 10% coverage
- Tradeoffs between phage resistance and nitrogen fixation drive the evolution of genes essential for cyanobacterial heterocyst functionality
Kolan, The ISME journal 2024 - “...( Table 1 ), suggesting this gene has a regulatory role. Among the regulatory genes, all2512 was identified as encoding PatB, which is an important regulator in heterocysts maturation [ 48 ]. The remaining mutant genes had other known (10) or unknown functions (4; Supplementary Table...”
- Rapid Transcriptional Reprogramming Triggered by Alteration of the Carbon/Nitrogen Balance Has an Impact on Energy Metabolism in Nostoc sp. PCC 7120
Gollan, Life (Basel, Switzerland) 2020 - “...operon 2.4 0.002 devH alr3952 CRP family transcriptional regulator Het glycolipid biosynthesis 2.2 0.006 patB/cnfR all2512 Heterocyst patterning Heterocyst development 2.4 0.001 nrrA all4312 OmpR family regulator 2.1 <0.001 1 Fold changes of genes upregulated or downregulated in low CO 2 , compared to high CO...”
- Overproduction of the Flv3B flavodiiron, enhances the photobiological hydrogen production by the nitrogen-fixing cyanobacterium Nostoc PCC 7120
Roumezi, Microbial cell factories 2020 - “...of plasmids and strains To construct the Flv3B overproducing strain, the promoter region of patB (all2512, 500bp upstream the start codon) was amplified by PCR from Nostoc sp. PCC 7120 genomic DNA using the ppatB forward and ppatB reverse primers (Table 2 ). The ppatB reverse...”
- The small Ca2+-binding protein CSE links Ca2+ signalling with nitrogen metabolism and filament integrity in Anabaena sp. PCC 7120
Walter, BMC microbiology 2020 - “...3.42E-04 all5341 all5359 hgl, hgd, het glycolipid biosynthesis: glycosyltransferases, hgdA-C, hglA-G/T, hetN/I 4.5 < 0.034 all2512 patB heterocyst-specific transcriptional regulator 4.7 0.026 all0177 flv1B heterocyst-specific flavodiiron protein 3.7 5.19E-09 all0178 flv3B heterocyst-specific flavodiiron protein 3.1 0.034 all1430 fdxH heterocyst ferredoxin 5.5 6.44E-07 alr2514 cox2B cytochrome c...”
- Functional Overlap of hetP and hetZ in Regulation of Heterocyst Differentiation in Anabaena sp. Strain PCC 7120
Zhang, Journal of bacteriology 2018 - “...all1440 all1454 all1455 all1456 all1457 all1516 all1517 all2512 all2868 all3793 all4460 all4617 all5341 all5342 all5347 all7607 all8046 alr0267 alr0611 alr0663...”
- Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes
Beck, PLoS genetics 2018 - “...these are asr1405 (hypothetical protein), all1432 (UBA/THIF-type binding protein, probable hesA), asl1434 (rop-like domain protein), all2512 (probable transcriptional regulator PatB), and asr2523 (TPR domain protein). The putative regulatory genes are located almost always in close genomic proximity to the other genes of module, suggesting a role...”
- The smallest known genomes of multicellular and toxic cyanobacteria: comparison, minimal gene sets for linked traits and the evolutionary implications
Stucken, PloS one 2010 - “...CRD_01538 CRC_01381 SynJA3, SynJA2, Cya7425 186680864 patB core set 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein all2512 no CRC_01763 186680869 hypothetical protein alr2517 * no CRC_03082 SynJA3, SynJA2, Cya8801 186680870 cupin 2 domain-containing protein alr2518 * no CRC_03081 SynJA3, SynJA2, Mcht 186680871 nitrogenase-associated protein alr2520 * no...”
BMF77_02997 transcriptional regulator from Dolichospermum sp. UHCC 0315A
40% identity, 12% coverage
- Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315
Teikari, Scientific reports 2019 - “...1,28 BMF77_00701 Phycobilisome rod-core linker polypeptide CpcG4 1,13 BMF77_00909 Cytochrome c oxidase subunit 2 1,05 BMF77_02997 Ferredoxin 1,89 BMF77_01997 Ferredoxin 1,38 BMF77_01935 Ferredoxin, heterocyst 1,57 BMF77_02996 Ferredoxin-3 1,79 BMF77_03623 Plastocyanin 1,25 Nitrogen cycle BMF77_04749 2-isopropylmalate synthase 1,21 BMF77_01994 Nitrogenase iron protein 2,00 BMF77_01967 Nitrogenase iron protein...”
Npun_R0334 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein from Nostoc punctiforme
46% identity, 9% coverage
RPA4631 ferredoxin 2[4Fe-4S], fdxN from Rhodopseudomonas palustris CGA009
54% identity, 64% coverage
Avin_10510 4Fe-4S ferredoxin, iron-sulfur binding domain protein from Azotobacter vinelandii AvOP
54% identity, 66% coverage
- Transcriptional Analysis of an Ammonium-Excreting Strain of Azotobacter vinelandii Deregulated for Nitrogen Fixation
Barney, Applied and environmental microbiology 2017 - “...material). The genes associated with the fix system (Avin_10510 to Avin_10550) showed an elevated level of transcription in AZBB163 [5-fold higher on average...”
- The Electron Bifurcating FixABCX Protein Complex from Azotobacter vinelandii: Generation of Low-Potential Reducing Equivalents for Nitrogenase Catalysis
Ledbetter, Biochemistry 2017 - “...Figure S2 ). The 4.3 kb fix operon, which includes six genes ( fixfd , Avin_10510; fixA , Avin_10520; fixB , Avin_10530; fixC , Avin_10540; fixX , Avin_10550; ORF6, Avin_10560) ( Figure S2 ), was PCR amplified using primers specified in Table S2 . The PCR...”
ZMO1818 4Fe-4S ferredoxin iron-sulfur binding domain protein from Zymomonas mobilis subsp. mobilis ZM4
47% identity, 62% coverage
- Functional analysis of the methylerythritol phosphate pathway terminal enzymes IspG and IspH from Zymomonas mobilis
Misra, Microbiology spectrum 2024 - “...From the genome annotation of Z. mobilis in KEGG , there are five predicted ferredoxins (ZMO1818, ZMO0220, ZMO2028, ZMO0860, and ZMO0456) and one predicted flavodoxin (ZMO1851) and a second possible flavodoxin (ZMO1949) that are possible candidates for these electron transfer reactions. A recent study suggests that...”
- Elucidation of Zymomonas mobilis physiology and stress responses by quantitative proteomics and transcriptomics
Yang, Frontiers in microbiology 2014 - “...such as the catalase gene (ZMO0918), glutaredoxin gene (ZMO0070), thioredoxin gene (ZMO1705), ferredoxin gene fdxN (ZMO1818), organic hydroperoxide resistance gene (ZMO0693), ATP-dependent Clp protease gene clpB (ZMO1424), RNA polymerase sigma-32 factor gene rpoH (ZMO0749), and integration host factor gene ihfB (ZMO1801) ( Additional Files 11 ,...”
- Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses
Yang, PloS one 2013 - “...a p-value Ratio p-value Sig Index b ZMO1373 TIR protein 3.4 9.50E-06 0.7 5.13E-08 1 ZMO1818 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein 3.2 8.40E-05 0.3 3.89E-03 1 ZMO0101 putative oxidoreductase 3.2 9.60E-05 1.5 1.66E-31 1 ZMO0405 ATP-dependent Clp protease, ATP-binding subunit ClpA 3.1 2.00E-04 0.7 5.37E-14...”
CRC_01763 helix-turn-helix domain-containing protein from Cylindrospermopsis raciborskii CS-505
43% identity, 10% coverage
WP_026790610 4Fe-4S binding protein from Pleomorphomonas oryzae DSM 16300
45% identity, 75% coverage
- Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes
Degli, Biology direct 2016 - “...AHM55439 WP_036840581 CCG40004 CCG09362 CDB40895 ? MH0143_GL0088070, CCZ21865 Yes, 5 Yes, 1 Short ferredoxin WP_025436274 WP_026790610. CCG39997 CCG06940 CDB40908 CDB53367 MH0030_GL0000056, CCZ22365 Yes, 2 Yes, 3 a updated Meta Genomic Species with current CCZ accession number of formerly CAG:977 ?not present in currently incomplete genome We...”
bsr1739 ferredoxin from Bradyrhizobium japonicum USDA 110
49% identity, 62% coverage
- Metabolomic Profiling of Bradyrhizobium diazoefficiens-Induced Root Nodules Reveals Both Host Plant-Specific and Developmental Signatures
Lardi, International journal of molecular sciences 2016 - “...cytochrome P450-family protein 4.9 blr3719 hypothetical protein 3.6 4.3 blr3722 dihydrolipoamide dehydrogenase lpd 2.8 4.9 bsr1739 Ferredoxin fdxN 5.1 bsr1760 ferredoxin-like protein frxA 5.9 bsr1775 probable ferredoxin fixX 6.3 Amino acid transport and metabolism blr1756 nitrogenase metalloclusters biosynthesis protein nifS 5.4 blr1971 putative peptidase 4.6 blr2071...”
- Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation
Čuklina, BMC genomics 2016 - “...of well-known RpoN-dependent genes [ 33 ]. Notably, the RpoN-promoter of the symbiotically important fdxN (bsr1739) gene, which was originally described as an unconventional but functional RpoN-dependent promoter [ 33 ], was correctly predicted by our algorithm. Its score of 2.9 belongs to the highest scores...”
- Soybean seed extracts preferentially express genomic loci of Bradyrhizobium japonicum in the initial interaction with soybean, Glycine max (L.) Merr
Wei, DNA research : an international journal for rapid publication of reports on genes and genomes 2008 - “...Rhizobium sp. NGR234 (blr1752 in LIS 3), 30 alanine dehydrogenase (blr1738 in LIS 3), ferredoxin (bsr1739, bsr1750 in LIS 3), putative bacA (blr1902 in LIS 5), two NoeE homologs (blr2073, blr2074 in LIS 8), and putative transketolase (blr2168, blr2169 in LIS 9) were also putatively induced....”
- Whole-genome transcriptional profiling of Bradyrhizobium japonicum during chemoautotrophic growth
Franck, Journal of bacteriology 2008 - “...carboxylase Nitrogen fixation and nitrogen metabolism fdxN (bsr1739) nifD (blr1743) nifK (blr1744) nifE (blr1745) nixN (blr1746) nifX (blr1747) fdxB (bsr1750)...”
cce_1898 transcriptional regulator from Cyanothece sp. ATCC 51142
38% identity, 12% coverage
bsr1760 ferredoxin-like protein from Bradyrhizobium japonicum USDA 110
44% identity, 64% coverage
msl8750 ferredoxin 2[4Fe-4S], fdxN from Mesorhizobium loti MAFF303099
47% identity, 67% coverage
- Identification of ferredoxin II as a major calcium binding protein in the nitrogen-fixing symbiotic bacterium Mesorhizobium loti
Moscatiello, BMC microbiology 2015 - “...to the RhizoBase at Kazusa Genome Resources, there are five ferredoxins (msl0793, mll5100, mlr5869, mlr5930, msl8750) plus a ferredoxin-like protein (msl5859) and a probable ferredoxin (msr9193) in Mesorhizobium loti with low sequence homology to the one identified by our analyses (mlr3855). Moreover, we retrieved sequences from...”
- Disclosure of the differences of Mesorhizobium loti under the free-living and symbiotic conditions by comparative proteome analysis without bacteroid isolation
Tatsukami, BMC microbiology 2013 - “...NifX, NifS, NifW) [ 28 ], electron donation (FixX, FixP), and symbiosis-unique ferredoxins (mlr5869, mlr5930, msl8750), were also found to be unique to the symbiotic condition. In addition, NifA and RpoN, which are known to cooperatively regulate nif and fix genes, were detected only under the...”
fdxN / AAC33373.1 FdxN from Rippkaea orientalis PCC 8801 (see paper)
36% identity, 63% coverage
Cj0333c ferredoxin from Campylobacter jejuni subsp. jejuni NCTC 11168
48% identity, 61% coverage
- Transcriptomic analysis of Campylobacter jejuni NCTC 11168 in response to epinephrine and norepinephrine
Xu, Frontiers in microbiology 2015 - “...The genes of a non-haem iron protein Rrc ( Cj0012c ) and ferredoxin FdxA ( Cj0333c ) were up-regulated by Epi or NE. The hemerythrin HerB ( Cj1224 ) involved in protecting the activity of oxidoreductases from oxygen damage (Kendall et al., 2014 ) was also...”
- Defining the metabolic requirements for the growth and colonization capacity of Campylobacter jejuni
Hofreuter, Frontiers in cellular and infection microbiology 2014 - “...the oxidation of 2-oxoglutarate to succinyl-CoA catalyzed by the OOR, whereas the putative ferredoxins FdxA (Cj0333c) and Cj0369c are no electron acceptors for OOR (Weerakoon and Olson, 2008 ). Several other electron donors besides FADH have been described to fuel the respiration chain of C. jejuni...”
- The CJIE1 prophage of Campylobacter jejuni affects protein expression in growth media with and without bile salts
Clark, BMC microbiology 2014 - “...membrane protein Cj0236c gi|153952171 0.530.75 0.970.76 Chemotaxis histidine kinase Cj0284c gi|218561946 0.830.61 0.530.42 Ferredoxin 4Fe-4S Cj0333c gi|121612302 1.100.89 0.530.15 Tryptophan synthase subunit alpha Cj0349 gi|121613100 0.670.47 0.800.56 Cytochrome c551 peroxidase Cj0358 gi|121612870 0.670.55 0.500.17 Putative integral membrane protein Cj0421c gi|218562079 1.000.71 0.730.12 Putative periplasmic protein Cj0425...”
- Comparison of PCR binary typing (P-BIT), a new approach to epidemiological subtyping of Campylobacter jejuni, with serotyping, pulsed-field gel electrophoresis, and multilocus sequence typing methods
Cornelius, Applied and environmental microbiology 2010 - “...Rev: GCAAGATTTTTGGTTCTCTTGC 299 46 fdxA (Cj0333c) For: TGCTTGTGGTTCTTGTATTGATG Rev: CTGGAGTGTCCCCACTTCTC 245 69 cmeB (Cj0366c) For: CAACCCGCACCAGGTTATAC...”
- The Campylobacter jejuni NADH:ubiquinone oxidoreductase (complex I) utilizes flavodoxin rather than NADH
Weerakoon, Journal of bacteriology 2008 - “...cat inserted within oorB (Cj0537) cat inserted within fdxA (Cj0333c) cat inserted within Cj0369c NCTCa This study This study This study This study This study...”
- “...into pCR2.1-TOPO cat inserted into SspI-digested pOorB fdxA (Cj0333c) cloned from WT into pCR2.1-TOPO cat inserted into BsaMI-digested pFdxA Cj0369c cloned from...”
HH0646 ferredoxin from Helicobacter hepaticus ATCC 51449
46% identity, 62% coverage
SWOL_RS10890 4Fe-4S binding protein from Syntrophomonas wolfei subsp. wolfei str. Goettingen G311
47% identity, 67% coverage
Mmc1_1207 4Fe-4S ferredoxin, iron-sulfur binding domain protein from Magnetococcus sp. MC-1
40% identity, 61% coverage
MSR1_18600 4Fe-4S dicluster domain-containing protein from Magnetospirillum gryphiswaldense MSR-1
50% identity, 67% coverage
- Towards a 'chassis' for bacterial magnetosome biosynthesis: genome streamlining of Magnetospirillum gryphiswaldense by multiple deletions
Zwiener, Microbial cell factories 2021 - “...16 genes, namely nifWABZTHDK , fixABC , draGT and three ferredoxin genes ( msr1_18560 ; msr1_18600 ; msr1_18640 ). The nif operon is likely linked to nitrogen fixation in M. gryphiswaldense [ 58 ] (Additional file 1 : Fig. S1) which is irrelevant under the denitrifying...”
- “...for nitrogen fixation (shown in red): nifWABZTHDK , fixABC , draGT and three ferredoxins (MSR1_18560; MSR1_18600; MSR1_18640). Black arrows represent other genes encoding a putative rubrerythrin protein (MSR1_18580), a SIR2-like domain containing protein (MSR1_18630), a GAF domain-containing protein (MSR1_18650), a biliverdin-producing heme oxygenase (MSR1_18660) and a...”
FER_GOTA9 / P00198 4Fe-4S ferredoxin FdxA; Ferredoxin from Gottschalkia acidurici (strain ATCC 7906 / DSM 604 / BCRC 14475 / CIP 104303 / KCTC 5404 / NCIMB 10678 / 9a) (Clostridium acidurici) (see 2 papers)
44% identity, 67% coverage
- function: Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.
cofactor: [4Fe-4S] cluster (Binds 2 [4Fe-4S] clusters.)
SMUL_0303 DUF362 domain-containing protein from Sulfurospirillum multivorans DSM 12446
43% identity, 61% coverage
- Hydrogen production by Sulfurospirillum species enables syntrophic interactions of Epsilonproteobacteria
Kruse, Nature communications 2018 - “...independent biological replicates. Hyf-like Hyf hydrogenase (SMUL_23832392; SCA02S_RS01920-RS01965), MBH membrane-bound hydrogenase (SMUL_14231425; SCA02S_RS01350-RS01360), Fd ferredoxin (SMUL_0303; SCA025_RS12260), PFOR pyruvate:ferredoxin oxidoreductase (SMUL_2630; SCA02S_RS04525), Pyr pyruvate, Fum fumarate A search for the hyf gene cluster in genomes of Epsilonproteobacteria shows that it is ubiquitous in, but not limited...”
- Proteomics of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates
Goris, Scientific reports 2015 - “...of them is the typical epsilonproteobacterial PFOR, which most likely reduces a ferredoxin encoded by SMUL_0303. This is opposed to the situation in the Epsilonproteobacterium Helicobacter pylori , where presumably flavodoxin is interacting with the PFOR 41 . An ortholog of this flavodoxin (SMUL_2785) was not...”
- “...involvement of a quinone-reducing pyruvate dehydrogenase and of a pyruvate:ferredoxin/flavodoxin oxidoreductase presumably reducing the ferredoxin SMUL_0303. An epsilonproteobacterial complex I mediates the electron transfer from ferredoxin to the quinone pool. All in all, these findings contribute to a deeper insight into organohalide respiration and might help...”
PDB|1FDN ferredoxin from Clostridium acidurici (see 5 papers)
43% identity, 66% coverage
1fcaA / P00198 Structure of the ferredoxin from clostridium acidurici: model at 1.8 angstroms resolution (see paper)
43% identity, 66% coverage
- Ligand: iron/sulfur cluster (1fcaA)
UCYN_05600 helix-turn-helix domain-containing protein from Candidatus Atelocyanobacterium thalassa isolate ALOHA
42% identity, 9% coverage
Aazo_1357 4Fe-4S binding protein from 'Nostoc azollae' 0708
35% identity, 73% coverage
- Surveying DNA Elements within Functional Genes of Heterocyst-Forming Cyanobacteria
Hilton, PloS one 2016 - “...subunit nifK Aazo_1352 8 2 uptake hydrogenase small subunit hupS Aazo_3866 4 2 ferredoxin fdxN Aazo_1357 3 1 nitrogenase cofactor biosynthesis protein nifB Aazo_1358 2 2 nitrogenase molybdenum-iron cofactor biosynthesis protein nifE Aazo_1350 2 1 pyruvate ferredoxin/flavodoxin oxidoreductase nifJ Cal7507_5433 2 1 flavin reductase domain-containing FMN-binding...”
X276_26075 DUF362 domain-containing protein from Clostridium beijerinckii NRRL B-598
Cbei_0118 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein from Clostridium beijerincki NCIMB 8052
41% identity, 66% coverage
- Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level
Patakova, Scientific reports 2019 - “...data, we hypothesise that during exponential growth phase, among putative ferredoxins, ferredoxin with locus tag X276_26075 plays the major role in electron flux from central metabolism. The analogous expression profile to this ferredoxin was identified for a cluster of genes for the assembly machinery of FeS...”
- Genome-wide dynamic transcriptional profiling in Clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq
Wang, BMC genomics 2012 - “...expressed genes also included those encoding proteins that mediate electron transfer, such as Cbei_1416 (rubrerythrin), Cbei_0118, Cbei_3348 (desulfoferrodoxin), Cbei_4318, Cbei_4319 (flavodoxin), and those genes related to cell motility (Cbei_4289), phosphotransferase system (PTS) for sugar uptake (Cbei_1219) and glycolytic activity (Cbei_1903, fba and Cbei_0597, gap ) (Figure...”
BT2414, BT_2414 ferredoxin from Bacteroides thetaiotaomicron VPI-5482
46% identity, 72% coverage
- Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...9.3-fold, respectively). PIOMA14_I_1049 (PIOMA14_RS05315) coding for the 4Fe-4S binding protein (ferredoxin, similar to PG1421 and BT2414) was also downregulated by 8.9-fold ( Fig.2E ; see Fig. S1 in the supplemental material). The major iron-dependent metabolic enzyme pyruvate:ferredoxin (flavodoxin) oxidoreductase, PIOMA14_I_0521, was downregulated by 4.3-fold. Finally, PIOMA14_II_0247...”
- “...memb. protein, DUF4361 domain-containing protein 2.8 0.046 BT_RS12130 BT2400 DNA-3-methyladenine glycosylase I 4.8 4E-05 BT_RS12205 BT2414 4Fe-4S binding protein (FdxA) 7.6 0.175 BT_RS12375 BT2442 OmpA family protein 2.5 0.57 BT_RS12505 BT2469 Tyrosine-type recombinase/integrase 2.5 0.056 BT_RS12805 BT2532 RagB/SusD family nutrient uptake outer memb. protein 5.4 3E-04...”
- “...(purple arrow). Comparison of genomic locus of P. gingivalis W83 (PG_RS10480, PG1421), B. thetaiotaomicron VPI-5482 (BT_2414), and P. intermedia 17 (PIN17_RS06895). The conclusion from the above-described regulated genes is that iron/hemin uptake and iron-independent metabolism mechanisms are drastically upregulated while the iron-dependent metabolism and oxidative stress...”
- Do reactive oxygen species or does oxygen itself confer obligate anaerobiosis? The case of Bacteroides thetaiotaomicron
Khademian, Molecular microbiology 2020 - “...this study BT_1747 Pyruvate:ferredoxin oxidoreductase PFOR BT_4738 Pyruvate:formate lyase PFL4738 BT_2955 Pyruvate:formate lyase homolog PFL2955 BT_2414 Putative ferredoxin Fdx BT_0616 to BT_0622 Putative NADH:ferredoxin oxidoreductase operon Rnf BT_1834 Putative Fe-Fe hydrogenase subunit Hyd1834 BT_3472 Hydrogenase subunit homolog Hyd3472 BT_2256 ( fum ) Fumarase Fumarase...”
SYN_03059 ferridoxin from Syntrophus aciditrophicus SB
43% identity, 72% coverage
- Enoyl-Coenzyme A Respiration via Formate Cycling in Syntrophic Bacteria
Agne, mBio 2021 - “...indicates a high purity and [4Fe-4S]-cluster occupation in comparison to the heterologously produced gene product SYN_03059 (390:280 ratio of 0.63) ( 12 ). The functional integrity of the purified Fd was demonstrated by its virtual complete reduction in the presence of 5mM pyruvate, 0.5mM CoA, and...”
- The Beta Subunit of Non-bifurcating NADH-Dependent [FeFe]-Hydrogenases Differs From Those of Multimeric Electron-Bifurcating [FeFe]-Hydrogenases
Losey, Frontiers in microbiology 2020 - “...genome using the Clostridium pasteurianum ferredoxin (GenBank Nucleotide ID: M11214) as the search query identified SYN_03059 as the most similar match. A DNA sequence encoding for SYN_03059 was also ordered from Integrated DNA Technologies for recombinant protein expression and the plasmid referred to as pIDTAmp-SbFd. Expression...”
- “...of this fraction showed a large number of matches and high sequence coverage to the SYN_03059 gene product ( Supplementary Table S6 ). SYN_03059 annotates as a ferredoxin with two [4Fe-4S] clusters, a predicted molecular mass of 6.01 kDa, and a pI of 3.63. In a...”
CLSPOx_00425 DUF362 domain-containing protein from Clostridium sporogenes
39% identity, 66% coverage
CLSA_c01660 DUF362 domain-containing protein from Clostridium saccharobutylicum DSM 13864
39% identity, 66% coverage
GI|144806 ferredoxin from Clostridium pasteurianum (see 4 papers)
P00195 Ferredoxin from Clostridium pasteurianum
41% identity, 66% coverage
BT_RS12205 DUF362 domain-containing protein from Bacteroides thetaiotaomicron VPI-5482
46% identity, 72% coverage
HM1_2505 DUF362 domain-containing protein from Heliomicrobium modesticaldum Ice1
HM1_2505 4fe-4S ferredoxin, iron-sulfur binding domain protein from Heliobacterium modesticaldum Ice1
39% identity, 73% coverage
- Identification and characterization of the low molecular mass ferredoxins involved in central metabolism in Heliomicrobium modesticaldum
Walters, Photosynthesis research 2024 (PubMed)- “...seven candidates: HM1_1462 (PshB1), HM1_1461 (PshB2), HM1_2505 (Fdx3), HM1_0869 (FdxB), HM1_1043, HM1_0357, and HM1_2767. Heterologous expression in Escherichia...”
- “...These genes are HM1_1462 (PshB1), HM1_1461 (PshB2), HM1_2505 (Fdx3), HM1_0869 (FdxB), HM1_1043, HM1_0357, and HM1_2767. (The names in parentheses are the...”
- Thermodynamics of the Electron Acceptors in Heliobacterium modesticaldum: An Exemplar of an Early Homodimeric Type I Photosynthetic Reaction Center
Ferlez, Biochemistry 2016 (PubMed)- “...for PshBII, and -452 5 mV/-533 8 mV for HM1_2505 as determined by EPR spectroscopy. FX is therefore suitably poised to reduce one [4Fe-4S]2+/1+ cluster in these...”
- “...dicluster ferredoxins in H. modesticaldum, PshBI, PshBII, and HM1_2505, by EPR spectroscopy. We use the measured midpoint potential of FX and a...”
CH_016396 ferredoxin from Clostridium butyricum (see 2 papers)
40% identity, 65% coverage
PIN17_RS06895, PIOMA14_I_1049, PIOMA14_RS05315 4Fe-4S binding protein from Prevotella intermedia
47% identity, 69% coverage
- Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...locus of P. gingivalis W83 (PG_RS10480, PG1421), B. thetaiotaomicron VPI-5482 (BT_2414), and P. intermedia 17 (PIN17_RS06895). The conclusion from the above-described regulated genes is that iron/hemin uptake and iron-independent metabolism mechanisms are drastically upregulated while the iron-dependent metabolism and oxidative stress defense mechanisms are downregulated under...”
- “...0.00040257 PIOMA14_RS04855 to 60 PIOMA14_I_0955 to 56 YitT family protein and porin 8.9 0.003 PIOMA14_RS05315 PIOMA14_I_1049 4Fe-4S binding protein 2.4 0.013 PIOMA14_RS05915 PIOMA14_I_1159 Acyltransferase family protein 3.2 0.095 PIOMA14_RS06410 PIOMA14_I_1256 Site-specific integrase 3.2 0.027 PIOMA14_RS06655 PIOMA14_I_1304 GntR family transcriptional regulator 9.3 to 8.6 2.933E-12 to 1.7193E-11...”
- “...operon PIOMA14_I_1410 to PIOMA14_I_1412 encoding the fumarate reductase/succinate dehydrogenase system (8.5-, 9.2-, and 9.3-fold, respectively). PIOMA14_I_1049 (PIOMA14_RS05315) coding for the 4Fe-4S binding protein (ferredoxin, similar to PG1421 and BT2414) was also downregulated by 8.9-fold ( Fig.2E ; see Fig. S1 in the supplemental material). The major...”
- “...2.0 0.00040257 PIOMA14_RS04855 to 60 PIOMA14_I_0955 to 56 YitT family protein and porin 8.9 0.003 PIOMA14_RS05315 PIOMA14_I_1049 4Fe-4S binding protein 2.4 0.013 PIOMA14_RS05915 PIOMA14_I_1159 Acyltransferase family protein 3.2 0.095 PIOMA14_RS06410 PIOMA14_I_1256 Site-specific integrase 3.2 0.027 PIOMA14_RS06655 PIOMA14_I_1304 GntR family transcriptional regulator 9.3 to 8.6 2.933E-12 to...”
- “...PIOMA14_I_1410 to PIOMA14_I_1412 encoding the fumarate reductase/succinate dehydrogenase system (8.5-, 9.2-, and 9.3-fold, respectively). PIOMA14_I_1049 (PIOMA14_RS05315) coding for the 4Fe-4S binding protein (ferredoxin, similar to PG1421 and BT2414) was also downregulated by 8.9-fold ( Fig.2E ; see Fig. S1 in the supplemental material). The major iron-dependent...”
PG1421 ferredoxin, 4Fe-4S from Porphyromonas gingivalis W83
HMPREF1322_RS09700, PG_RS10480 DUF362 domain-containing protein from Porphyromonas gingivalis W83
43% identity, 72% coverage
- Defining the role of Hmu and Hus systems in Porphyromonas gingivalis heme and iron homeostasis and virulence
Śmiga, Scientific reports 2024 - “...encoding thioredoxin (TrxA; PG0034), thioredoxin domain-containing protein (PG0275), rubrerythrin (Rbr; PG0195), and 4Fe-4S binding proteins (PG1421 and PG1813) were down-regulated. Partial starvation of the mutant strains due to the lack of the main components of the heme supply systems did not change the expression of FeoB...”
- Growth of Porphyromonas gingivalis on human serum albumin triggers programmed cell death
Ghods, Journal of oral microbiology 2023 - “...to regulation of gingipain expression and localization [ 43 , 44 ], as well as PG1421 (3.6 logFC), a predicted ferredoxin. Lastly, PG1780, encoding a serine palmitoyltransferase which is required for sphingolipid biosynthesis [ 45 ], was upregulated in strain W83 (2.3 logFC) along with PG0276...”
- “...asRNAs corresponding to the two iron-related gene products involved in oxidative stress discussed above [ferredoxin (PG1421) and rubrerythrin (PG0195)], along with PG1615 and PG1617 (putatively involved in succinate metabolism) and PG0537 (aminoacyl-histidine dipeptidase) were found to be highly expressed (up to 10.5-fold; q -value <0.01) during...”
- Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...(frd) locus in Bacteroidetes (purple arrow). Comparison of genomic locus of P. gingivalis W83 (PG_RS10480, PG1421), B. thetaiotaomicron VPI-5482 (BT_2414), and P. intermedia 17 (PIN17_RS06895). The conclusion from the above-described regulated genes is that iron/hemin uptake and iron-independent metabolism mechanisms are drastically upregulated while the iron-dependent...”
- “...9.2-, and 9.3-fold, respectively). PIOMA14_I_1049 (PIOMA14_RS05315) coding for the 4Fe-4S binding protein (ferredoxin, similar to PG1421 and BT2414) was also downregulated by 8.9-fold ( Fig.2E ; see Fig. S1 in the supplemental material). The major iron-dependent metabolic enzyme pyruvate:ferredoxin (flavodoxin) oxidoreductase, PIOMA14_I_0521, was downregulated by 4.3-fold....”
- The Porphyromonas gingivalis Hybrid Cluster Protein Hcp Is Required for Growth with Nitrite and Survival with Host Cells
Belvin, Infection and immunity 2019 - “...rplI PG2213 rpmA PG0662 PG1270 rpmG PG0505 PG0985 PG1421 rpmH Flda 1.98204 1.99588 2.00158 2.02056 2.03365 2.05698 2.07932 2.08023 2.1393 2.16475 2.17355...”
- Microarray analysis of the transcriptional responses of Porphyromonas gingivalis to polyphosphate
Moon, BMC microbiology 2014 - “...PG1556 HmuV d Hemin acquisition d 2.15 PG1729 thiol peroxidase Cellular processes : Detoxification 3.12 PG1421 Ferredoxin, 4Fe-4S Energy metabolism : Electron transport 28.54 PG0195 Rubrerythrin Energy metabolism : Electron transport 15.49 PG0034 Thioredoxin Energy metabolism : Electron transport 2.76 PG1286 Ferritin Transport and binding proteins:...”
- “...2.76 PG0195 Rubrerythrin 15.49 PG0548 Pyruvate ferredoxin/flavodoxin oxidoreductase family protein 2.58 PG0616 Thioredoxin, putative 1.52 PG1421 Ferredoxin, 4Fe-4S 28.54 PG1813 Ferredoxin, 4Fe-4S 1.65 Energy metabolism : Glycolysis/gluconeogenesis PG0130 Phosphoglyceromutase 1.68 Energy metabolism : Purines, pyrimidines, nucleosides, and nucleotides PG1996 Deoxyribose-phosphate aldolase 1.73 Energy metabolism : Pentose...”
- Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
Lewis, Microbiology spectrum 2023 - “...protein (frd) locus in Bacteroidetes (purple arrow). Comparison of genomic locus of P. gingivalis W83 (PG_RS10480, PG1421), B. thetaiotaomicron VPI-5482 (BT_2414), and P. intermedia 17 (PIN17_RS06895). The conclusion from the above-described regulated genes is that iron/hemin uptake and iron-independent metabolism mechanisms are drastically upregulated while the...”
- Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis
Costeira, mSystems 2023 - “...genes encoding homologous proteins of the rubrerythrin family (HMPREF1322_RS04040), iron-sulfur cluster domain-contain containing proteins (e.g., HMPREF1322_RS09700), a thiamine phosphate synthase (HMPREF1322_RS02110), electron transport complex subunits (e.g., HMPREF1322_RS04875, HMPREF1322_RS04865, and HMPREF1322_RS04880), SDR family/ferredoxin oxidoreductases (e.g., HMPREF1322_RS07305 and HMPREF1322_RS04445), and several dehydrogenases ( Table 1 ; Table S1...”
- “...lfcSE P -value Gene symbol Gene product HMPREF1322_RS04040 36,595.19 3.51 0.22 5.16E-55 Rubrerythrin family protein HMPREF1322_RS09700 10,401.67 5.11 0.38 7.99E-42 4Fe-4S dicluster domain-containing protein HMPREF1322_RS02110 21,476.06 5.74 0.48 4.96E-33 Thiamine phosphate synthase HMPREF1322_RS04875 4,568.08 3.08 0.29 1.10E-26 RnfABCDGE type electron transport complex subunit G HMPREF1322_RS09380 6,878.27...”
- Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis
Costeira, 2022
1clfA / P00195 Clostridium pasteurianum ferredoxin (see paper)
40% identity, 65% coverage
- Ligand: iron/sulfur cluster (1clfA)
BMF77_01997 DUF362 domain-containing protein from Dolichospermum sp. UHCC 0315A
34% identity, 72% coverage
- Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315
Teikari, Scientific reports 2019 - “...rod-core linker polypeptide CpcG4 1,13 BMF77_00909 Cytochrome c oxidase subunit 2 1,05 BMF77_02997 Ferredoxin 1,89 BMF77_01997 Ferredoxin 1,38 BMF77_01935 Ferredoxin, heterocyst 1,57 BMF77_02996 Ferredoxin-3 1,79 BMF77_03623 Plastocyanin 1,25 Nitrogen cycle BMF77_04749 2-isopropylmalate synthase 1,21 BMF77_01994 Nitrogenase iron protein 2,00 BMF77_01967 Nitrogenase iron protein 1 1,98 BMF77_01966...”
Cbs_1773, X276_18165 [FeFe] hydrogenase, group A from Clostridium beijerinckii ATCC 35702
Cbei_1773 hydrogenase, Fe-only from Clostridium beijerincki NCIMB 8052
42% identity, 9% coverage
- Improving sustainable hydrogen production from green waste: [FeFe]-hydrogenases quantitative gene expression RT-qPCR analysis in presence of autochthonous consortia
Arizzi, Biotechnology for biofuels 2021 - “...] Cbei_1773 was also observed in transcriptomic analysis [ 46 ] in the coding sequence X276_18165 from C. beijerinckii NRRL B-598, but the authors could not unambiguously assign to this gene the role of expressing the hydrogenase that mainly produces hydrogen in the exponential growth phase...”
- Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level
Patakova, Scientific reports 2019 - “...C . beijerinckii NRRL B-598 in exponential growth phase. A potential candidate might be hydrogenase X276_18165 (see Suppl. File 2a ), which shares 99% homology with that isolated from C . beijerinckii SM10 35 . This hydrogenase is one of the group of enzymes annotated as...”
- Evidence of mixotrophic carbon-capture by n-butanol-producer Clostridium beijerinckii
Sandoval-Espinola, Scientific reports 2017 - “...belongs to the WL pathway, a PFOR (Cbs_4318), a carbonic anhydrase (Cbs_4425), and a hydrogenase (Cbs_1773). Conversely, there was a repression of a putative CODH (Cbs_5054), a gene that belongs to the formate dehydrogenase complex (Cbs_3799), a flavodoxin (Cbs_3109), and several genes that putatively code for...”
- Improving sustainable hydrogen production from green waste: [FeFe]-hydrogenases quantitative gene expression RT-qPCR analysis in presence of autochthonous consortia
Arizzi, Biotechnology for biofuels 2021 - “...a previously reported classification [ 15 ]. The 6 hyd genes of C. beijerinckii are: Cbei_1773 (encoding for a protein with structure type M2c and cluster A5), Cbei_1901 (encoding for a protein with structure type M2a and cluster B2), Cbei_0327 (encoding for a protein with structure...”
- “...optimal hydrogen productions according to the literature [ 56 ]. At time 0 (inoculum addition) Cbei_1773 and Cbei_0327 genes were expressed, respectively, 1- and 1.5-fold more than the genes encoding for the monomeric Cbei_4000 , the membrane-bound Cbei_3796 and the catalytic subunit alpha Cbei_4110 of the...”
- Evidence of mixotrophic carbon-capture by n-butanol-producer Clostridium beijerinckii
Sandoval-Espinola, Scientific reports 2017 - “...its WL cluster. In addition to these genes, C . beijerinckii contains Fe-only and NiFe-hydrogenases (Cbei_1773, Cbei_3796, Cbei_4110 and Cbei_3013) with similarities to those of C . ljungdahlii . In this species, along with H 2 generation, these enzymes have hydrogen uptake capabilities, providing extra reducing...”
- “...the highest expression levels: the correlation between expression and hydrogen oscillation/evolution suggested that Cbei_3013 and Cbei_1773 are primarily used for H 2 uptake and H 2 evolution, respectively. Additionally, the genes encoding for putative carbonic anhydrases also showed expression (Cbei_4425/Cbei_1031). This enzyme allows for even more...”
- The iron-hydrogenase of Thermotoga maritima utilizes ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production
Schut, Journal of bacteriology 2009 - “...Pelotomaculum thermopropionicum Petrotoga mobilis a BT_1834 Cbei_1773 Cbei_3796 Cbei_4000 Cbei_0327 Cbei_1901 CBO3302 CBO3550 CLI_3472 CLI_3772 CD3314 CD0894...”
Csac_0737 4Fe-4S ferredoxin, iron-sulfur binding domain protein from Caldicellulosiruptor saccharolyticus DSM 8903
43% identity, 72% coverage
CAC0303 Ferredoxin from Clostridium acetobutylicum ATCC 824
CA_C0303 DUF362 domain-containing protein from Clostridium acetobutylicum ATCC 824
39% identity, 66% coverage
- A site-differentiated [4Fe-4S] cluster controls electron transfer reactivity of Clostridium acetobutylicum [FeFe]-hydrogenase I
Lubner, Chemical science 2022 - “...investigated for H 2 production and uptake activities using C. acetobutylicum ferredoxin (CaFd, gene ID CAC0303), the native electron donor/acceptor to CaI. 20 The H 2 uptake and evolution activities were measured at pH 6 and 8.3 in both dye-linked (methylene blue, MB and methyl viologen,...”
- Pyruvate:ferredoxin oxidoreductase is coupled to light-independent hydrogen production in Chlamydomonas reinhardtii
Noth, The Journal of biological chemistry 2013 - “...of C. acetobutylicum [Fe-Fe]-hydrogenase HYDA and ferredoxin CAC0303. C. reinhardtii strain CC124 (137c, mt nit1 nit2) was grown in Tris acetate-phosphate...”
- “...indicated by bold letters). The C. acetobutylicum ferredoxin CAC0303 encoding region was amplified from the E. coli expression vector pET21c0303 (55) using hot...”
- Rewiring hydrogenase-dependent redox circuits in cyanobacteria
Ducat, Proceedings of the National Academy of Sciences of the United States of America 2011 - “...that expression of ferredoxin from C. acetobutylicum (CAC0303) (41), our strongest pairing in our previously reported synthetic circuit (28), could increase...”
- “...from Clostricium acetobutylicum, Clostridium acetobutylicum ferredoxin CAC0303, ferredoxin I from Spinacia oleracea, and hydrogenase maturation factors (HydEF,...”
- Characterization of two 2[4Fe4S] ferredoxins from Clostridium acetobutylicum
Guerrini, Current microbiology 2008 (PubMed)- “...focused our biophysical and biochemical investigations on CAC0303 and CAC3527, which possess the sequence signature and length of classical 2[4Fe4S] clostridial...”
- “...followed by in vitro Fe-S incorporation and purification, CAC0303 was shown to have a regular electron paramagnetic resonance (EPR) signal for a classical...”
- Complete activity profile of Clostridium acetobutylicum [FeFe]-hydrogenase and kinetic parameters for endogenous redox partners
Demuez, FEMS microbiology letters 2007 (PubMed)- “...purified and identified as encoded by ORF CAC0303. Clostridium acetobutylicum recombinant holoflavodoxin CAC0587 was also purified. The kinetic parameters of C....”
- “...[FeFe]-hydrogenase for both physiological partners, ferredoxin CAC0303 and flavodoxin CAC0587, are reported for hydrogen uptake and hydrogen evolution...”
- DNA array-based transcriptional analysis of asporogenous, nonsolventogenic Clostridium acetobutylicum strains SKO1 and M5
Tomas, Journal of bacteriology 2003 - “...encoding flavodoxin (CAC0587), ferredoxin (CAC0303), thioredoxin(CAC1547),andthreeoxidoreductases (CAC2018, CAC2459, and CAP0135). Several sugar metabolism...”
- Molecular characterization of the missing electron pathways for butanol synthesis in Clostridium acetobutylicum
Foulquier, Nature communications 2022 - “...presented in Table 1 . Activities were measured at 340nm by NADP + reduction using CA_C0303 reduced ferredoxin as the electron donor. During the purification process, the purified enzyme lost 60% of its activity after 48h. Table 1 Purification of ferredoxin-NADP + reductases from C. acetobutylicum...”
- “...measuring the reduction of NAD + or NADP + using electrons from reduced ferredoxin ( CA_C0303 ) with H 2 as the reductant of ferredoxin ( CA_C0303 ) 32 in the presence of FeFe hydrogenase from Clostridium acetobutylicum ( CA_C0028 ) 33 . Ferredoxin ( CA_C0303...”
- Genome-Wide TSS Distribution in Three Related Clostridia with Normalized Capp-Switch Sequencing
Hocq, Microbiology spectrum 2022 - “...Predicted open reading frames are shown in yellow. (b) Opposing TSSs flank the ferredoxin gene CA_C0303. (c) Two alternative TSSs are located upstream of the pyruvate ferredoxin oxidoreductase gene CA_C2229. (d) Detection of a new coding sequence (orange) downstream from CA_P0016. A total of 1,250 TSSs...”
- “...mapping identified novel transcriptional features ( Fig.1b to d ). For example, expression of the CA_C0303 gene, encoding a ferredoxin, is flanked by inward-facing TSS ( Fig.1b ), suggesting that the antisense transcript could regulate CA_C0303 expression. As a second example, transcription of CA_C2229, encoding the...”
- Ferredoxin-linked flavoenzyme defines a family of pyridine nucleotide-independent thioredoxin reductases
Buey, Proceedings of the National Academy of Sciences of the United States of America 2018 - “...model for the homologous Fdx from C. acetobutylicum (CaFdx; CA_C0303) (Fig. 3B) and visually examined a possible structure of the FFTR- Fdx complex. Here, we...”
- Cap0037, a Novel Global Regulator of Clostridium acetobutylicum Metabolism
Nguyen, mBio 2016 - “...by the 500-fold-higher expression of CA_C0587 encoding the major flavodoxin and the 1.5-fold-lower expression of CA_C0303 encoding the major ferredoxin, as well as the possibility that reduced flavodoxin might be a better substrate than ferredoxin for the ferredoxin-NAD + reductase. In solventogenesis, the normalized electron fluxes...”
- “...electron carrier. However, in the CA_P0037 :: int mutant, the expression level of fdx ( CA_C0303 ), encoding the main ferredoxin, was not reduced. In iron deficiency or in a fur mutant or CA_P0037 inactivation, the levels of genes belonging to the ribGBAH operon, which is...”
- A Quantitative System-Scale Characterization of the Metabolism of Clostridium acetobutylicum
Yoo, mBio 2015 - “...Fig.S1A ) and crotonyl-CoA (see Fig.S1B ) were modulated using constant concentrations of purified ferredoxin (CA_C0303) and hydrogenase (CA_C0028). Based on the initial slope in Fig.S1B in the supplemental material, it was calculated that in the presence of excess crotonyl-CoA, 2.15mol of NADH was required for...”
- “...of hydA ; this is associated with a 2-fold decrease in the expression of fdx1 (CA_C0303), which encodes the primary ferredoxin, the key redox partner for the hydrogenase. As these results were confirmed by the proteomic analysis, they may explain the 1.3-fold decrease in H 2...”
B2M23_RS02975 DUF362 domain-containing protein from Eubacterium limosum
44% identity, 73% coverage
8zqdA / A0A1I9RYV3 Anaerobically isolated active [fefe]-hydrogenase cba5h
42% identity, 9% coverage
- Ligands: zinc ion; iron/sulfur cluster; dicarbonyl[bis(cyanide-kappac)]-mu-(iminodimethanethiolatato-1kappas:2kappas)-mu-(oxomethylidene)diiron(2+) (8zqdA)
D3S191 CoB--CoM heterodisulfide reductase iron-sulfur subunit A from Ferroglobus placidus (strain DSM 10642 / AEDII12DO)
36% identity, 8% coverage
1durA / P00193 Replacement for 1fdx 2(4fe4s) ferredoxin from (now) peptostreptococcus asaccharolyticus
43% identity, 72% coverage
- Ligand: iron/sulfur cluster (1durA)
swp_2142 4Fe-4S ferredoxin, iron-sulfur binding from Shewanella piezotolerans WP3
34% identity, 33% coverage
- Condition-Specific Molecular Network Analysis Revealed That Flagellar Proteins Are Involved in Electron Transfer Processes of Shewanella piezotolerans WP3
Ding, Genetics research 2021 - “...pathways Members 1 9 0.58 3.49 E 04 Carbon metabolism swp_3663, swp_5025, swp_4312, swp_1239, swp_2139, swp_2142, swp_3875, swp_3458, swp_0182 2 9 0.50 9.74 E 04 Oxidative phosphorylation swp_4058, swp_0854, swp_4352, swp_3589, swp_4940, swp_1424, swp_1425, swp_0430, swp_0429 3 6 0.87 1.26 E 03 Flagellar assembly swp_1531, swp_3616,...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory