PaperBLAST – Find papers about a protein or its homologs

 

PaperBLAST

PaperBLAST Hits for sp|A1WVR8|GATC_HALHL Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C OS=Halorhodospira halophila (strain DSM 244 / SL1) OX=349124 GN=gatC PE=3 SV=1 (95 a.a., MAIDADEVQQ...)

Other sequence analysis tools:

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Found 30 similar proteins in the literature:

PA4482 aspartyl/glutamyl-tRNA amidotransferase subunit C from Pseudomonas aeruginosa PAO1
55% identity, 99% coverage

ACIAD0824 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C from Acinetobacter sp. ADP1
53% identity, 90% coverage

ZMO0784 glutamyl-tRNA(Gln) amidotransferase, C subunit from Zymomonas mobilis subsp. mobilis ZM4
43% identity, 97% coverage

AZOBR_RS20640 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC from Azospirillum baldaniorum
44% identity, 100% coverage

RL2075 putative glutamyl-tRNA(Gln) amidotransferase subunit C from Rhizobium leguminosarum bv. viciae 3841
38% identity, 100% coverage

BAB2_0645 Glu-tRNAGln amidotransferase, C subunit:Glutamyl-tRNA(Gln) amidotransferase C subunit from Brucella melitensis biovar Abortus 2308
38% identity, 100% coverage

DVU0809 glutamyl-tRNA(Gln) amidotransferase, C subunit from Desulfovibrio vulgaris Hildenborough
36% identity, 99% coverage

D9S200 Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C from Thermosediminibacter oceani (strain ATCC BAA-1034 / DSM 16646 / JW/IW-1228P)
34% identity, 99% coverage

GSU3383 glutamyl-tRNA(Gln) amidotransferase, C subunit from Geobacter sulfurreducens PCA
35% identity, 100% coverage

gatC / O06492 glutamyl-tRNAGln amidotransferase subunit C (EC 6.3.5.7) from Bacillus subtilis (strain 168) (see paper)
O06492 Glutamyl-tRNA(Gln) amidotransferase subunit C from Bacillus subtilis (strain 168)
BSU06670 aspartyl/glutamyl-tRNA amidotransferase subunit C from Bacillus subtilis subsp. subtilis str. 168
33% identity, 97% coverage

AH68_09115 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC from Bifidobacterium catenulatum PV20-2
35% identity, 91% coverage

Q92J74 Glutamyl-tRNA(Gln) amidotransferase subunit C from Rickettsia conorii (strain ATCC VR-613 / Malish 7)
28% identity, 93% coverage

H375_4740 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC from Rickettsia prowazekii str. Breinl
27% identity, 93% coverage

RT0142 glutaminyl-tRNA synthase (glutamine-hydrolyzing) subunit C from Rickettsia typhi str. wilmington
27% identity, 93% coverage

MAB_3342c Glutamyl-tRNA(Gln) amidotransferase subunit C (GatC) from Mycobacterium abscessus ATCC 19977
36% identity, 91% coverage

SERP1439 glutamyl-tRNA(Gln) amidotransferase, C subunit from Staphylococcus epidermidis RP62A
36% identity, 89% coverage

CLP_3829 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC from Clostridium butyricum E4 str. BoNT E BL5262
31% identity, 99% coverage

HMPREF0389_00480 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC from Filifactor alocis ATCC 35896
29% identity, 91% coverage

Bd0058 glutamyl-tRNA(Gln) amidotransferase (subunit C) from Bdellovibrio bacteriovorus HD100
34% identity, 97% coverage

SAOUHSC_02118 glutamyl-tRNA(Gln) amidotransferase, C subunit from Staphylococcus aureus subsp. aureus NCTC 8325
Q2FFJ4 Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C from Staphylococcus aureus (strain USA300)
SA1717 glutamyl-tRNAGln amidotransferase subunit C from Staphylococcus aureus subsp. aureus N315
SAUSA300_1882 aspartyl/glutamyl-tRNA amidotransferase subunit C from Staphylococcus aureus subsp. aureus USA300_FPR3757
MW1842 glutamyl-tRNAGln amidotransferase subunit C from Staphylococcus aureus subsp. aureus MW2
36% identity, 89% coverage

slr0033 unknown protein from Synechocystis sp. PCC 6803
32% identity, 88% coverage

cce_0284 glutamyl-tRNA (Gln) amidotransferase subunit C from Cyanothece sp. ATCC 51142
32% identity, 94% coverage

CBO3267 aspartyl/glutamyl-tRNA amidotransferase subunit C from Clostridium botulinum A str. ATCC 3502
26% identity, 100% coverage

Gmet_0076 Glu-tRNAGln amidotransferase, C subunit from Geobacter metallireducens GS-15
32% identity, 100% coverage

FN0755 Glutamyl-tRNA(Gln) amidotransferase subunit C from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
27% identity, 98% coverage

gatC / Q9RUV6 glutamyl-tRNAGln amidotransferase subunit C (EC 6.3.5.7; EC 6.3.5.6) from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1) (see paper)
DR1275 Glu-tRNA(Gln) amidotransferase, subunit C from Deinococcus radiodurans R1
32% identity, 97% coverage

Rv3012c aspartyl/glutamyl-tRNA amidotransferase subunit C from Mycobacterium tuberculosis H37Rv
32% identity, 93% coverage

TM0252 glutamyl tRNA-Gln amidotransferase, subunit C from Thermotoga maritima MSB8
29% identity, 95% coverage

FORC47_RS01875 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC from Bacillus cereus
32% identity, 97% coverage

3al0C / Q9WY94,Q9X2I8 Crystal structure of the glutamine transamidosome from thermotoga maritima in the glutamylation state. (see paper)
29% identity, 16% coverage

New Search

For advice on how to use these tools together, see Interactive tools for functional annotation of bacterial genomes.

Statistics

The PaperBLAST database links 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 2025.

How It Works

PaperBLAST builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot, BRENDA, CAZy (as made available by dbCAN), BioLiP, CharProtDB, MetaCyc, EcoCyc, TCDB, REBASE, the Fitness Browser, and a subset of the European Nucleotide Archive with the /experiment tag. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E < 0.001.

To build the database, we query EuropePMC with locus tags, with RefSeq protein identifiers, and with UniProt accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use queries of the form "locus_tag AND genus_name" to try to ensure that the paper is actually discussing that gene. Because EuropePMC indexes most recent biomedical papers, even if they are not open access, some of the links may be to papers that you cannot read or that our computers cannot read. We query each of these identifiers that appears in the open access part of EuropePMC, as well as every locus tag that appears in the 500 most-referenced genomes, so that a gene may appear in the PaperBLAST results even though none of the papers that mention it are open access. We also incorporate text-mined links from EuropePMC that link open access articles to UniProt or RefSeq identifiers. (This yields some additional links because EuropePMC uses different heuristics for their text mining than we do.)

For every article that mentions a locus tag, a RefSeq protein identifier, or a UniProt accession, we try to select one or two snippets of text that refer to the protein. If we cannot get access to the full text, we try to select a snippet from the abstract, but unfortunately, unique identifiers such as locus tags are rarely provided in abstracts.

PaperBLAST also incorporates manually-curated protein functions:

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:

Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.

Secrets

PaperBLAST cannot provide snippets for many of the papers that are published in non-open-access journals. This limitation applies even if the paper is marked as "free" on the publisher's web site and is available in PubmedCentral or EuropePMC. If a journal that you publish in is marked as "secret," please consider publishing elsewhere.

Omissions from the PaperBLAST Database

Many important articles are missing from PaperBLAST, either because the article's full text is not in EuropePMC (as for many older articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an article that characterizes a protein's function but is missing from PaperBLAST, please notify the curators at UniProt or add an entry to GeneRIF. Entries in either of these databases will eventually be incorporated into PaperBLAST. Note that to add an entry to UniProt, you will need to find the UniProt identifier for the protein. If the protein is not already in UniProt, you can ask them to create an entry. To add an entry to GeneRIF, you will need an NCBI Gene identifier, but unfortunately many prokaryotic proteins in RefSeq do not have corresponding Gene identifers.

References

PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.

Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.

Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.

UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.

BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.

The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.

CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.

The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.

The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.

REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.

Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.

by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory