PaperBLAST
PaperBLAST Hits for tr|Q9I0N4|Q9I0N4_PSEAE Probable thiosulfate sulfurtransferase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA2603 PE=1 SV=1 (527 a.a., MSQIAVRTFH...)
Show query sequence
>tr|Q9I0N4|Q9I0N4_PSEAE Probable thiosulfate sulfurtransferase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA2603 PE=1 SV=1
MSQIAVRTFHDIRAALLARRELALLDVREEDPFAQAHPLFAANLPLSRLELEIHARVPRR
DTPITVYDDGEGLAPVAAQRLLDLGYSDVALLDGGLSGWRNAGGELFRDVNVPSKAFGEL
VEAERHTPSLAAEEVQALLDARAEAVILDARRFDEYQTMSIPGGISVPGAELVLRVAELA
PDPRTRVIVNCAGRTRSIIGTQSLLNAGIPNPVAALRNGTIGWTLAGQQLEHGQTRRFGA
ISQDTRKAAAQRARAVADRAGVERLDLAGLAQWQDEHDRTTYLLDVRTPEEYEAGHLPGS
RSTPGGQLVQETDHVASVRGARLVLVDDDGVRANMSASWLAQMGWQVAVLDGLSEADFSE
RGAWSAPLPRQPRADTIDPTTLADWLGEPGTRVLDFTASANYAKRHIPGAAWVLRSQLKQ
ALERLGTAERYVLTCGSSLLARFAVAEVQALSGKPVFLLDGGTSAWVAAGLPTEDGESLL
ASPRIDRYRRPYEGTDNPREAMQGYLDWEFGLVEQLGRDGTHGFFVI
Running BLASTp...
Found 26 similar proteins in the literature:
PA2603 probable thiosulfate sulfurtransferase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
- Systems-Wide Dissection of Organic Acid Assimilation in Pseudomonas aeruginosa Reveals a Novel Path To Underground Metabolism
Dolan, mBio 2022 - “...decreased (blue) in abundance are indicated. Notable ORFs are labeled (PA3619, prpB , metE , PA2603, prpR , prpF , acnD , and PA3391). (F) Western blot showing PrpB (32.1 kDa) protein expression levels in PAO1, the prpC mutant, and the acsA mutant after exposure to...”
- Combinatorial approach for screening and assessment of multiple therapeutic enzymes from marine isolate Pseudomonas aeruginosa AR01
Jagadeesan, RSC advances 2019 - “...Ela-R R-TTACAACGCGCTCGGGCAGGTCAC Uricase PA2366 882284 26154612616945 Uri-F F-ATGCCCAAGTCATCCGCCGCCGAA 1485 Uri-R R-TCACGCCGCTACCGGCGGCGGCAG Rhodanese or thiosulfate sulfurtransferase PA2603 882309 55615995562414 Rho-F F-ATGTCCGTTTTCTCCGACCTGCCA 816 Rho-R R-TCAAACCTCTACAGGGGTATCGGG 2.11. Colony PCR A single colony of P. aeruginosa AR01 was scraped from a marine agar plate and washed once with 100 L...”
1yt8A / Q9I0N4 Crystal structure of thiosulfate sulfurtransferase from pseudomonas aeruginosa
100% identity, 99% coverage
- Ligand: sulfite ion (1yt8A)
Bphy_5232 rhodanese-related sulfurtransferase from Paraburkholderia phymatum STM815
Bphy_5232 rhodanese domain-containing protein from Burkholderia phymatum STM815
63% identity, 99% coverage
BCAM1395 putative sulfurtransferase from Burkholderia cenocepacia J2315
67% identity, 97% coverage
Pnuc_1350 rhodanese domain-containing protein from Polynucleobacter sp. QLW-P1DMWA-1
60% identity, 99% coverage
bll7966 bll7966 from Bradyrhizobium japonicum USDA 110
61% identity, 66% coverage
Atu6089 hypothetical protein from Agrobacterium tumefaciens str. C58 (Cereon)
63% identity, 58% coverage
- Novel Agrobacterium fabrum str. 1D1416 for Citrus Transformation
Alabed, Microorganisms 2024 - “...block comprised 15 genes (Atu6014 to Atu6030), while the second included 40 genes (Atu6047 to Atu6089). Atu6015, also known as nos or NAD/NADP-dependent octopine/nopaline dehydrogenase , is located just inside the right border of the T-DNA and is included in the first block of genes. Other...”
BB0537 putative sulfurtransferase from Bordetella bronchiseptica RB50
44% identity, 96% coverage
- Differentially expressed genes in Bordetella pertussis strains belonging to a lineage which recently spread globally
de, PloS one 2014 - “...ptxP3/ptxP1 ) ORF Gene Product Predicted localization ptxP3 ptxP1 0 mM 5 mM 50 mM BB0537 sulfurtransferase Un BP0380 Sodium:sulfate symportert Cm 1.0 1.5 1.0 1.3 1.6 BP0958 cysM cysteine synthase B C 1.0 1.1 1.0 1.0 1.2 BP0966 sbp sulfate-binding protein precursor P 7.3 *...”
- Genetic verification of Bordetella pertussis seed strains used for production of Japanese acellular pertussis vaccines
Kamachi, Biologicals : journal of the International Association of Biological Standardization 2010 (PubMed)- “...blot analyses revealed the absence of four orthologous genes (BB0537, BB0920, BB1149 and BB4885), which are specifically absent in the strain Tohama, and in the...”
- “...cultures for Japanese aP vaccine production with probes BB0537 (in RD11), BB0920 (RD12), BB1149 (RD13) and BB4885 (RD14). Lanes; 1, B. parapertussis ATCC...”
- Is the Sequenced Bordetella pertussis strain Tohama I representative of the species?
Caro, Journal of clinical microbiology 2008 - “...CDS Product RD-11 (BB0534-BB0541) BB0534 BB0535 BB0536 BB0537 BB0538 BB0539 BB0540 BB0541 Putative exported protein Hypothetical protein Conserved hypothetical...”
PSPTO2632 rhodanese domain protein/cystathionine beta-lyase from Pseudomonas syringae pv. tomato str. DC3000
PSPTO_2632 cystathionine beta-lyase from Pseudomonas syringae pv. tomato str. DC3000
42% identity, 54% coverage
- Protein domains and architectural innovation in plant-associated Proteobacteria
Studholme, BMC genomics 2005 - “...novel gene, most strikingly for glf , PSPTO2441, PSPTO4696, hopPtoS (1,2 &3), PSPTO4699, PSPTO1070 & PSPTO2632, which were each associated with low GC regions containing few ORFs with orthologues in other Pseudomonas genomes. One other feature frequently associated with horizontally transferred genes is the presence of...”
- Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches
Sahu, BMC bioinformatics 2014 - “...with the highest number of edges (hubs) are PSPTO_0135, PSPTO_0400, PSPTO_0540, PSPTO_0808, PSPTO_1510, PSPTO_2303, PSPTO_2529, PSPTO_2632, PSPTO_3161, PSPTO_3583, PSPTO_3890, PSPTO_3912 and PSPTO_4001 with more than 400 PPIs in the Arabidopsis-Pseudomonas interactome. There are also several effectors with more than 40 predicted PPIs. These are PSPTO_4497, PSPTO_1482,...”
MIM_c37440 rhodanese-like domain-containing protein from Advenella mimigardefordensis DPN7
37% identity, 96% coverage
BB4882 conserved hypothetical protein from Bordetella bronchiseptica RB50
38% identity, 92% coverage
FTS_0824 rhodanese-like domain-containing protein from Francisella tularensis subsp. holarctica FSC200
FTL_0834 Rhodanese-like family protein from Francisella tularensis subsp. holarctica
23% identity, 38% coverage
FTT_1127 rhodanese-like family protein from Francisella tularensis subsp. tularensis SCHU S4
23% identity, 38% coverage
6mxvB / Q5NFU2 The crystal structure of a rhodanese-like family protein from francisella tularensis subsp. Tularensis schu s4
23% identity, 38% coverage
- Ligand: magnesium ion (6mxvB)
Dde_0679 Rhodanese-related sulfurtransferase from Desulfovibrio desulfuricans G20
23% identity, 55% coverage
cg0074 sulfurtransferase from Corynebacterium glutamicum ATCC 13032
35% identity, 17% coverage
- Transcriptome profiles of high-lysine adaptation reveal insights into osmotic stress response in Corynebacterium glutamicum
Wang, Frontiers in bioengineering and biotechnology 2022 - “...stock pECXK-99E C. glutamicum - E. coli shuttle expression vector, Kan r Lab stock pXMJ19- cg0074 pXMJ19 derivative, containing the cg0074 gene from C. glutamicum This study pXMJ19- cg1152 pXMJ19 derivative, containing the cg1152 gene from C. glutamicum This study pXMJ19- cg0767 pXMJ19 derivative, containing the...”
- “...4A ). In addition, the 10 top upregulated DEGs from the long-term RNA-seq data ( cg0074 , ssiF , cg0767 , idhA3 , lysE , cg0470 , cg0785 , cg0362 , cg2919 , and ssuC ) were also included for the selection of promising gene targets...”
AZL_022680 molybdopterin biosynthesis protein from Azospirillum sp. B510
31% identity, 23% coverage
BC4210 Rhodanese-related sulfurtransferases from Bacillus cereus ATCC 14579
38% identity, 15% coverage
- Response of Bacillus cereus ATCC 14579 to challenges with sublethal concentrations of enterocin AS-48
Grande, BMC microbiology 2009 - “...(in grey), PadR homologues (in black), conserved proteins with putative function: BC4203, BC4205, BC4209 and BC4210 encoding for putative hydrolase, spore lyase, lypoate-protA ligase and rhodase, respectively (dashed lined), putative conserved regulators: BC4204, BC4211 and BC4212 for putative iron dependent repressor, LacI type regulator and TetR...”
NMA0994 putative periplasmic protein from Neisseria meningitidis Z2491
34% identity, 15% coverage
Eab7_0861 rhodanese-like domain-containing protein from Exiguobacterium antarcticum B7
34% identity, 15% coverage
3tp9A / C8WS08 Crystal structure of alicyclobacillus acidocaldarius protein with beta-lactamase and rhodanese domains
41% identity, 18% coverage
MM2931 hydrolase from Methanosarcina mazei Goe1
33% identity, 17% coverage
CMN_00157 rhodanese-like domain-containing protein from Clavibacter nebraskensis NCPPB 2581
37% identity, 18% coverage
SGO_0667 rhodanese family protein from Streptococcus gordonii str. Challis substr. CH1
34% identity, 15% coverage
- Streptococcus gordonii Type I Lipoteichoic Acid Contributes to Surface Protein Biogenesis
Lima, mSphere 2019 - “...family transporter ArcT SGO_1589 Putative transaminase/peptidase LytR SGO_0535 Putative transcriptional regulator Pyk SGO_1339 Pyruvate kinase SGO_0667 Rhodanese family protein SGO_1338 Signal peptidase I SrtB SGO_2104 Sortase B SGO_1110 Surface antigen SCP-like domain SGO_0482 ThiJ/PfpI family protein InfA SGO_1963 Translation initiation factor IF-1 TpiA SGO_0762 Triosephosphate isomerase...”
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