PaperBLAST
PaperBLAST Hits for sp|Q9HV00|FDHE_PSEAE Protein FdhE homolog OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=fdhE PE=1 SV=1 (309 a.a., MSRTILQPGQ...)
Show query sequence
>sp|Q9HV00|FDHE_PSEAE Protein FdhE homolog OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=fdhE PE=1 SV=1
MSRTILQPGQIEAAANIPPHLHQPSRDLFARRGERLLQLAEGHPMGDYLRLVAGLCRLQQ
ALLDNPPALAPLDPERLRKSREHGMPPLAYDLLVREGAWLPWLDALLAGYPAPANAAVGA
ALEQLREAEEGQRKAWAIALLSGQFDLLPAALVPFLGAALQVAWSHWLLGLEEGAVVETE
SRTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHYVRIKCSHCEESKHLAYLSLE
HDGQPAEKAVLRAETCPSCQGYLKQFYLEFDRHADALADDLASLALDMRLAEDGYLRRSP
NLLLAPGGE
Running BLASTp...
Found 20 similar proteins in the literature:
PA4809 FdhE protein from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
2fiyA / Q9HV00 The crystal structure of the fdhe protein from pseudomonas aeruginosa
98% identity, 94% coverage
- Ligand: fe (iii) ion (2fiyA)
PP0492 formate dehydrogenase accessory protein FdhE, putative from Pseudomonas putida KT2440
60% identity, 96% coverage
t3586 FdhE protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
40% identity, 95% coverage
- Staphylococcus aureus Isolated from Ruminants with Mastitis in Northern Greece Dairy Herds: Genetic Relatedness and Phenotypic and Genotypic Characterization
Kotzamanidis, Toxins 2021 - “...belonged to 10 and 12 different spa types, respectively. The most prevalent spa types were t3586 (n = 48; 30.0%), t4038 (n = 28; 17.3%), and t1773 (n = 13; 8.0%), each of them consisting of isolates from all host species, comprising the majority (53 ovine,...”
- “...typing, which also revealed a remarkable genetic diversity among isolates. We found three spa types (t3586, t4038, and t1773) that contain isolates from all host species, comprising the majority of all isolates. We also found specific spa types that are exclusively associated with CM (t1166, t2678,...”
FdhE / b3891 formate dehydrogenase formation protein from Escherichia coli K-12 substr. MG1655 (see 7 papers)
NP_418327 formate dehydrogenase formation protein from Escherichia coli str. K-12 substr. MG1655
b3891 formate dehydrogenase accessory protein FdhE from Escherichia coli str. K-12 substr. MG1655
40% identity, 95% coverage
c4841 Protein fdhE from Escherichia coli CFT073
40% identity, 95% coverage
Q83PE8 Protein FdhE homolog from Shigella flexneri
40% identity, 95% coverage
LT85_RS04605 formate dehydrogenase accessory protein FdhE from Collimonas arenae
39% identity, 97% coverage
YPO4055 putative formate dehydrogenase formation protein from Yersinia pestis CO92
YPTB3930 putative formate dehydrogenase formation protein from Yersinia pseudotuberculosis IP 32953
39% identity, 95% coverage
ETAE_3341 formate dehydrogenase accessory protein from Edwardsiella tarda EIB202
41% identity, 99% coverage
HI0009 fdhE protein (fdhE) from Haemophilus influenzae Rd KW20
34% identity, 100% coverage
- Comparison of transcription of the Haemophilus influenzae iron/heme modulon genes in vitro and in vivo in the chinchilla middle ear
Whitby, BMC genomics 2013 - “...+1.21 +1.73 HI0008 Formate dehydrogenase-N, cytochrome B556 gamma subunit, FdnI +7.47 +5.23 +3.20 ns +1.76 HI0009 Formate dehydrogenase-N, accessory protein FdnE +3.35 +3.43 +1.88 ns +1.75 HI0185 Formaldehyde dehydrogenase, glutathione-dependent AdhC +5.86 +4.01 +8.04 +12.18 +2.85 HI0343 Twin-arginine signal-peptide-binding chaperone NapD +3.19 ns +1.66 +1.78 +1.60...”
- The iron/heme regulated genes of Haemophilus influenzae: comparative transcriptional profiling as a tool to define the species core modulon
Whitby, BMC genomics 2009 - “...beta subunit fdxH 7.49 6.00 3.40 HI0008 Formate dehydrogenase gamma subunit fdxI 7.47 5.23 3.20 HI0009 FdhE 3.35 3.43 1.88 HI0018 Uracil DNA glycosylase ung ns ns ns HI0026 Lipoate biosynthesis protein A lipA 3.19 2.00 ns HI0174 tRNA methyltransferase 2.36 2.08 1.93 HI0608 Conserved hypothetical...”
- The ArcA regulon and oxidative stress resistance in Haemophilus influenzae
Wong, Molecular microbiology 2007 - “...) 44 1.20E-08 26.8 1.69E-08 HI0747 NADH dehydrogenase ( ndh ) 11 4.06E-11 9.6 5.86E-11 HI0009 FdhE protein ( fdhE ) 9.7 8.39E-10 9.4 1.53E-09 HI0008 Formate dehydrogenase, gamma subunit ( fdxI ) 9.7 5.42E-09 12 3.81E-09 HI0007 Formate dehydrogenase, beta subunit ( fdxH ) 7.8...”
- “...( HI0007 ) (5-ATGGCTGGAACTGCTCAAGGCG and 5-GAAACACGATCTACACAAAGAG), fdxI ( HI0008 ) (5-ATGAGTAAAATTGAAATTAGCAAC and 5-AGATACCAGTGAATAACATAAAAG), fdhE ( HI0009 ) (5-ATGAGTATCAAAATCTTATC and 5-TGCTTCTTCTGCAGGAAAAATAAATG), lldP ( HI1218 ) (5-ATGCTGTCTTTTATTCTAAG and 5-TAGATTATAAAATAAAGGTAC), sucB ( HI1661 ) (5-ATGGCAATCGAAATTCTTG and 5-GATTTCTAATAACAATCTTG), HI0592 (5-ATGCTATTTCGTACATATATAC and 5-GAGAGCCCTGTTGGATG), potE ( HI0590 ) (5-ATGAGTGCTAAAAGCAATAAAATTG and 5-TTTTTTAAGATCAAATTTGTAAG) and...”
- Transcriptional profile of Haemophilus influenzae: effects of iron and heme
Whitby, Journal of bacteriology 2006 - “...of the predicted genes on the array. HI0007 to HI0009 were shown, by microarray, to be upregulated upon the addition of FeHm. The genes represented by these...”
NTHI0012 formate dehydrogenase accessory protein FdhE from Haemophilus influenzae 86-028NP
34% identity, 100% coverage
APL_0896 formate dehydrogenase accessory protein from Actinobacillus pleuropneumoniae L20
35% identity, 98% coverage
- Actinobacillus pleuropneumoniae genes expression in biofilms cultured under static conditions and in a drip-flow apparatus
Tremblay, BMC genomics 2013 - “...cpxA APL_0629 cpxR APL_0840 tolC APL_0891 fdhD APL_0892 fdxG APL_0893 fdxG APL_0894 fdxH APL_0895 fdnI APL_0896 fdhE APL_0936 APL_0959 APL_1045 APL_1110 APL_1159 APL_1387 APL_1494 ftpA APL_1550 wecD APL_1552 wecB APL_1553 APL_1554 wecA APL_1674 dmsA APL_1675 dmsB APL_1676 dmsC APL_1875 APL_1921 pgaA APL_1922 pgaB APL_1923 pgaC APL_1924...”
- “...subunits of the formate dehydrogenase were down-regulated in the biofilm (APL_0892, APL_0893, APL_0894, APL_0895 and APL_0896). Additionally, another key component of anaerobic metabolism, which is the anaerobic dimethyl sulfoxide reductase chain (APL_1674, APL_1675, APL_1676), was down-regulated in biofilm cells. A homologue for the transport of a...”
- Host-pathogen interactions of Actinobacillus pleuropneumoniae with porcine lung and tracheal epithelial cells
Auger, Infection and immunity 2009 - “...APL_1191 APL_1331 APL_1685 APL_1689 APL_1684 APL_1333 APL_1019 APL_0896 lldD rpe namA hyaA fucK fucO fucI hybB kdgK fdhE L-Lactate dehydrogenase...”
SO0104 fdhE protein from Shewanella oneidensis MR-1
31% identity, 90% coverage
SMa0009 probable FdhE formate formation from Sinorhizobium meliloti 1021
32% identity, 87% coverage
Dde_0706 formate dehydrogenase formation protein FdhE, putative from Desulfovibrio desulfuricans G20
37% identity, 37% coverage
- Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria
Saxena, Frontiers in microbiology 2023 - “...hdrA/qmoA, hdrB/qmoB , we enriched a total of 15 genes and other 10 genes include- dde_0706, dde_0718, dde_0812, dde_0813, dde_1207, dde_1210, dde_1211, dde_3513, dde_3514, dde_3515 (shown in Figure 4E ). As discussed in sulfur metabolism pathway, we know APS reductase is crucial in the conversion of...”
- “...4 12 Energy metabolism dde_3513, dde_0812, dde_1208, dde_3514, dde_1207, dde_0718, dde_0652, and dde_1209 dde_0813, dde_0717, dde_0706, dde_1211, dde_1210, and dde_0680 dde_3515 8 6 1 15 Two-component system dde_3756, dde_3237, dde_3755, dde_2138, dde_0364, and dde_2139, dde_2137 dde_2135, dde_2136, and dde_2134 NA 7 3 0 10 81 25...”
- New model for electron flow for sulfate reduction in Desulfovibrio alaskensis G20
Keller, Applied and environmental microbiology 2014 - “...An additional protein for formation of formate dehydrogenases (Dde_0706) was also increased. These enzymes could be involved in the production of the small...”
DVU0577 formate dehydrogenase formation protein FdhE, putative from Desulfovibrio vulgaris Hildenborough
37% identity, 37% coverage
Tph_c15370 formate dehydrogenase accessory protein FdhE from Thermacetogenium phaeum DSM 12270
34% identity, 37% coverage
- Energy-Conserving Enzyme Systems Active During Syntrophic Acetate Oxidation in the Thermophilic Bacterium Thermacetogenium phaeum
Keller, Frontiers in microbiology 2019 - “...Dehydrogenase Gene Cluster During growth with acetate, the genes coding for a membrane-bound formate dehydrogenase (Tph_c15370- c15410) were expressed. Genes coding for this enzyme system were found to be located next to quinone synthesis genes (Tph_c15430- c15460), to two genes of subunits of a heterodisulfide reductase...”
- “...gamma, Tph_c15390) and one large periplasmic subunit. The protein of the gene annotated as fdhE (Tph_c15370) is responsible for maturation of the formate dehydrogenase complex. Analysis of the gene neighborhood of the quinone-dependent formate dehydrogenase (Tph_c15390) with the same COG hit in IMG showed similarity with...”
DET0185 formate dehydrogenase accessory protein FdhE, putative from Dehalococcoides ethenogenes 195
31% identity, 37% coverage
- Meta-analyses of Dehalococcoides mccartyi strain 195 transcriptomic profiles identify a respiration rate-related gene expression transition point and interoperon recruitment of a key oxidoreductase subunit
Mansfeldt, Applied and environmental microbiology 2014 - “...either RDase catalytic subunits (Fig. 3b), Hym, Hup, and DET0185 to -0187 (Fig. 3c), or ATPase subunits (Fig. 3d). The loading matrix for all experiments and...”
- “...for the other respiration-linked enzymes (Hym, Hup, and DET0185 to -0187) also clustered into the bottom left quadrant, which contained the fast-respiration...”
- Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation
Lee, Applied and environmental microbiology 2012 - “...ND ND Downregulated DET0017 DET0022 DET0146 DET0178 DET0185 DET0341 DET0343 DET0345 DET0374 DET0381 DET0421 DET0528 DET0545 DET0614 DET0624 DET0636 DET0638...”
- “...electron acceptors. The formate dehydrogenase (Fdh)-homologous genes (DET0185 to DET0187) were previously observed to be highly expressed in both the...”
- Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains
West, Applied and environmental microbiology 2008 - “...Presence/absence in ANAS by PCRb DET0079 DET0119 DET0185 DET0186 DET0318 DET0343 DET0551 DET0666 DET0667 DET0668 DET0669 DET0670 DET0671 DET1158 DET1481 DET1483...”
- Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195
Nonaka, Journal of bacteriology 2006 - “...function Membrane Periplasm DET0128 DET0688 DET0936 DET0296 DET0185 DET0187 Experimentally observed (49). these bacteria encode five putative catalases, two...”
Swol_0796 Uncharacterized protein involved in formate dehydrogenase formation-like protein from Syntrophomonas wolfei subsp. wolfei str. Goettingen
30% identity, 37% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory