PaperBLAST
PaperBLAST Hits for CharProtDB::CH_013101 glycine reductase complex component C, alpha subunit; EC 1.21.4.2; EC 1.21.4.3; EC 1.21.4.4 (Eubacterium acidaminophilum) (385 a.a., MSDIKQMIGK...)
Show query sequence
>CharProtDB::CH_013101 glycine reductase complex component C, alpha subunit; EC 1.21.4.2; EC 1.21.4.3; EC 1.21.4.4 (Eubacterium acidaminophilum)
MSDIKQMIGKTFMEIADAIETGSFAGKVKVGITTLGSEHGVENLVKGAELAAKDAAGFDI
VLIGPKVETSLEVVEVATEEEAHKKMEELLDSGYIHSCVTVHYNFPIGVSTVGRVVTPGM
GKEMFIATTTGTSAAQRVEAMVRNALYGIITAKSMGIENPTVGILNLDGARAVERALKEL
AGNGYPITFAESLRADGGSVMRGNDLLGGAADVMVTDSLTGNIMMKVFSSYTTGGSYEGL
GYGYGPGIGDGYNRTILILSRASGVPVAANAIKYAAKLAQNNVKAIAAAEFKAAKAAGLE
SILAGLSKDTKKASTEEEVKMPPKEVVTGTISGVDVMDLEDAQKVLWKAGIYAESGMGCT
GPIVMVNEAKVEEAAKILKDAGIVA
Running BLASTp...
Found 12 similar proteins in the literature:
grdD / GI|2708734 glycine reductase complex component C, alpha subunit; EC 1.21.4.2; EC 1.21.4.3; EC 1.21.4.4 from Eubacterium acidaminophilum (see 3 papers)
100% identity, 100% coverage
CD630_23480, CDIF630erm_02587 glycine/sarcosine/betaine reductase complex component C subunit alpha from Clostridioides difficile
CD2348 glycine/sarcosine/betaine reductase complex component C alpha subunit from Clostridium difficile 630
66% identity, 99% coverage
- Iron Regulation in Clostridioides difficile
Berges, Frontiers in microbiology 2018 - “...-3.77 CD630_23430 CDIF630erm_02582 cat1 Succinyl-CoA:coenzyme A transferase -3.35 -3.58 CD630_23440 CDIF630erm_02583 Membrane protein -4.79 -5.28 CD630_23480 CDIF630erm_02587 grdD Glycine reductase complex component D OFF OFF CD630_23490 CDIF630erm_02588 grdC Glycine reductase complex component C -3.70 -3.70 CD630_23510 CDIF630erm_02589 grdB Glycine reductase complex component B OFF OFF CD630_23520...”
- “...CD630_23430 CDIF630erm_02582 cat1 Succinyl-CoA:coenzyme A transferase -3.35 -3.58 CD630_23440 CDIF630erm_02583 Membrane protein -4.79 -5.28 CD630_23480 CDIF630erm_02587 grdD Glycine reductase complex component D OFF OFF CD630_23490 CDIF630erm_02588 grdC Glycine reductase complex component C -3.70 -3.70 CD630_23510 CDIF630erm_02589 grdB Glycine reductase complex component B OFF OFF CD630_23520 CDIF630erm_02592...”
- “...phenylalanine, leucine ( hadAIBCB , etfBA , CDIF630erm_00523 00529), glycine degradation (g rdDCBAE , trxBA (CDIF630erm_02587 02597) and butyrate fermentation (CDIF630erm_01194 01199) with the formation of 3-phenylpropionate, isocaproate, butyrate, 5-methylcaproate, valerate and acetate (CDIF630erm_01194 01199, CDIF630erm_02577 02583) were significantly reduced, while the proline reductase ( prdFEDBARC...”
- Glycine fermentation by C. difficile promotes virulence and spore formation, and is induced by host cathelicidin
Rizvi, Infection and immunity 2023 (secret) - Diverse Energy-Conserving Pathways in Clostridium difficile: Growth in the Absence of Amino Acid Stickland Acceptors and the Role of the Wood-Ljungdahl Pathway
Gencic, Journal of bacteriology 2020 (secret) - Adaptive strategies and pathogenesis of Clostridium difficile from in vivo transcriptomics
Janoir, Infection and immunity 2013 - “...whereas those encoding subunits of the glycine reductase (CD2348 to CD2358) were downregulated (see Fig. S3 and Table S3). Thus, it appears that leucine-proline...”
- Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile
Antunes, Nucleic acids research 2012 - “...reductase complex component B subunit; grdC (CD2349), glycine reductase complex component C subunit ; grdD (CD2348), glycine reductase complex component C subunit ; ldhA (CD0394), 2-hydroxyisocaproate dehydrogenase; hadA (CD0395), 2-hydroxyisocaproate CoA transferase; hadI (CD0396), activator of dehydratase; acdB (CD0399), acyl-CoA dehydrogenase; gcvTPA (CD1657), bi-functional glycine dehydrogenase/aminomethyl...”
B9W14_09410 glycine/sarcosine/betaine reductase complex component C subunit alpha from Clostridium drakei
60% identity, 98% coverage
TDE0239 glycine reductase complex protein GrdD from Treponema denticola ATCC 35405
54% identity, 99% coverage
B2904_orf673, BP951000_1858 glycine/sarcosine/betaine reductase complex component C subunit alpha from Brachyspira pilosicoli 95/1000
55% identity, 99% coverage
- Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity
Mappley, BMC genomics 2012 - “...and B. murdochii 56-150 T (Bmur_2720 Bmur_2728) [ 28 ] was identified in B2904 (B2904_orf665 B2904_orf673) and WesB (wesB_0746 wesB_0754), but with an additional ATP-binding cassette (ABC)-type glycine betaine transport component in a separate locus (B2904_orf1065; wesB_1632). Moreover, a cluster for a transposase unique to B2904...”
- The complete genome sequence of the pathogenic intestinal spirochete Brachyspira pilosicoli and comparison with other Brachyspira genomes
Wanchanthuek, PloS one 2010 - “...copies for the glycine/sarcosine/betaine reductase complex, component C, alpha subunit ( grdC , BP951000_1857 and BP951000_1858), and two copies for a sodiumalanine symporter family protein (BP951000_1859 and BP951000_1860). In B.murdochii , the locus consisted of genes encoding putative glycine reductase complex component ( grdX , 4083292.C42.orf00552)...”
Bmur_2728 glycine/sarcosine/betaine reductase complex component C subunit alpha from Brachyspira murdochii DSM 12563
55% identity, 98% coverage
Tmari_0147 phosphate acyltransferase PlsX from Thermotoga maritima MSB8
29% identity, 52% coverage
SA1072 fatty acid/phospholipid synthesis protein from Staphylococcus aureus subsp. aureus N315
P65739 Phosphate acyltransferase from Staphylococcus aureus (strain N315)
24% identity, 52% coverage
SACOL1243 fatty acid/phospholipid synthesis protein PlsX from Staphylococcus aureus subsp. aureus COL
SAOUHSC_01197 fatty acid/phospholipid synthesis protein PlsX from Staphylococcus aureus subsp. aureus NCTC 8325
NWMN_1139 fatty acid/phospholipid synthesis protein from Staphylococcus aureus subsp. aureus str. Newman
B7H15_06400, CH51_RS06590 phosphate acyltransferase PlsX from Staphylococcus aureus F86379
24% identity, 52% coverage
- The Staphylococcus aureus LytSR two-component regulatory system affects biofilm formation
Sharma-Kuinkel, Journal of bacteriology 2009 - “...protein, putative 3.3 3.1 Lipid metabolism (4) SACOL1243 SACOL0637 SACOL0636 SACOL0638 plsX mvaD mvk Fatty acid/phospholipid synthesis protein PlsX Mevalonate...”
- Complete and SOS-mediated response of Staphylococcus aureus to the antibiotic ciprofloxacin
Cirz, Journal of bacteriology 2007 - “...biosynthesis Down-regulated ORFs SACOL0987 SACOL0988 SACOL1243 SACOL1244 SACOL1245 SACOL1571 SACOL1572 SACOL2079 Toxin production/resistance and pathogenesis...”
- Proteomic and Metabolomic Analyses of a Tea-Tree Oil-Selected Staphylococcus aureus Small Colony Variant
Torres, Antibiotics (Basel, Switzerland) 2019 - “...in SH1000-TTORS-1 SAOUHSC_00574 pta Phosphate acetyltransferase 2.7 SAOUHSC_01196 fapR Fatty acid biosynthesis transcriptional regulator 6.3 SAOUHSC_01197 plsX Glycerol-3-phosphate acyltransferase 2.3 SAOUHSC_01201 acpP Acyl carrier protein 2.0 SAOUHSC_01820 ackA Acetate kinase 3.2 SAOUHSC_02336 fabZ 3-Hydroxyacyl-(acyl carrier protein) dehydratase 9.1 antibiotics-08-00248-t003_Table 3 Table 3 Metabolites increased ( p...”
- (p)ppGpp/GTP and Malonyl-CoA Modulate Staphylococcus aureus Adaptation to FASII Antibiotics and Provide a Basis for Synergistic Bi-Therapy
Pathania, mBio 2021 - “...which alleviates FapR repression ( Fig.3 ). The S. aureus FapR regulon reportedly includes plsX (NWMN_1139, part of the fapR operon) and plsC (NWMN_1620); however, the S. aureus FapR binding site in the plsC promoter region is highly degenerate ( 13 ) (see Fig.5A ), and...”
- Staphylococcus aureus Stress Response to Bicarbonate Depletion
Liberini, International journal of molecular sciences 2024 - “...reductase 1.5 1.7 B7H15_11660 FabZ, 3-hydroxyacyl-ACP dehydratase 2.2 1.6 B7H15_07130 PlsY, glycerol3-phosphate acyltransferase 1.2 1.5 B7H15_06400 PlsX, phosphate acyltransferase 1.5 1 B7H15_06385 FakA, fatty acid kinase 1.1 1 B7H15_04195 FakB1, fatty acid binding protein 1 1.2 1 B7H15_07520 FakB2, fatty acid binding protein 2 1 1...”
- Staphylococcus aureus PhoU Homologs Regulate Persister Formation and Virulence
Shang, Frontiers in microbiology 2020 - “...3.86 ND CH51_RS01090 Long-chain fatty acid-CoA ligase 4.2 ND fapR Transcription factor FapR 2.51 ND CH51_RS06590 Phosphate acyltransferase 2.73 ND CH51_RS06595 Malonyl CoA-ACP transacylase 2.3 ND CH51_RS06600 3-Oxoacyl 2.4 ND CH51_RS04990 3-Oxoacyl-ACP synthase III 2.44 ND CH51_RS03140 Long-chain-fatty-acid-CoA ligase 3.85 ND CH51_RS05715 Glycerophosphodiester phosphodiesterase 2.04 ND...”
B7IUL2 Phosphate acyltransferase from Bacillus cereus (strain G9842)
27% identity, 52% coverage
SXYL_01656 phosphate acyltransferase PlsX from Staphylococcus xylosus
26% identity, 52% coverage
Q65JQ9 Phosphate acyltransferase from Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)
24% identity, 52% 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