PaperBLAST
PaperBLAST Hits for Psyr_4741 (66 a.a., MHIQLNGEPF...)
Show query sequence
>Psyr_4741
MHIQLNGEPFELPDGETVAALLTRLDLAGRRVAVELNLDIVPRSQHVATVLSEGDQVEVV
HAIGGG
Running BLASTp...
Found 18 similar proteins in the literature:
PSPTO_0433 thiamine biosynthesis protein ThiS from Pseudomonas syringae pv. tomato str. DC3000
92% identity, 100% coverage
- Thiamine Is Required for Virulence and Survival of Pseudomonas syringae pv. tomato DC3000 on Tomatoes
Liu, Frontiers in microbiology 2022 - “...(ORFs) of ThiD ( thiD, pspto_4798 ), ThiE ( thiE, pspto_4799 ), ThiS ( thiS, pspto_0433 ), ThiG ( thiG, pspto_0434 ), and ApbE ( apbE, pspto_2105 ) in the genome of Pst DC3000 (gene bank accession #: AE016853.1 ) were identified by performing BLAST with...”
BP3690 conserved hypothetical protein from Bordetella pertussis Tohama I
56% identity, 100% coverage
- A curated genome-scale metabolic model of Bordetella pertussis metabolism
Fyson, PLoS computational biology 2017 - “...ThiS, ThiF and ThiG for which there are obvious homologs in B. pertussis (encoded by BP3690, BP0610 and BP3597 respectively) along with thiazole tautomerase, TenI (BP3809) and ThiE (BP0316). The model was curated to include this biosynthetic pathway. LPS biosynthesis The SEED metabolic models include LPS...”
ZMO0738 bifunctional sulfur carrier protein/thiazole synthase protein from Zymomonas mobilis subsp. mobilis ZM4
50% identity, 20% coverage
- Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4
Ong, PLoS computational biology 2020 - “...-0.140 7 AMPMS2_f, DM_4CRSOL_f , ICYSDS_f, PMPK_f , THZPSN3_f , TMPPP_f , TYRL_f 3 ZMO0172, ZMO0738, ZMO1834 Thiamine biosynthesis a Module number shows relative position of module based on sorted average cofitness values. b Suffix "_f" represents forward component and "_r" represents reverse component of the...”
- Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and Promoters
Vera, mSystems 2020 - “...TSS_3396 1531155 + 0 ZMO1504 DUF1321 domain-containing protein 2,902 2,551 3,093 TSS_1713 740401 + 27 ZMO0738 thiG Thiazole biosynthesis protein 3,806 4,307 3,870 TSS_3522 1588943 + 0 ZMO1556 gshA Glutamate-cysteine ligase 3,646 4,394 4,837 TSS_2374 1067836 + 81 ZMO1052 purC Phosphoribosylaminoimidazole- succinocarboxamide synthase 4,868 5,365 5,980...”
BA0731 conserved hypothetical protein from Bacillus anthracis str. Ames
BAS0697 conserved hypothetical protein from Bacillus anthracis str. Sterne
45% identity, 99% coverage
SENTW_4269 sulfur carrier protein ThiS from Salmonella enterica subsp. enterica serovar Weltevreden str.
42% identity, 100% coverage
STM4161 putative involved in thiamine biosynthesis from Salmonella typhimurium LT2
41% identity, 100% coverage
Fisuc_2908 thiamine biosynthesis protein ThiS from Fibrobacter succinogenes subsp. succinogenes S85
44% identity, 94% coverage
- Generation and Characterization of Acid Tolerant Fibrobacter succinogenes S85
Wu, Scientific reports 2017 - “...ferredoxin iron-sulfur binding domain protein Fisuc_2558 1.9 2.99E-15 Chorismate mutase Fisuc_2559 2.0 1.03E-16 Prephenate dehydrogenase Fisuc_2908 2.1 0.000191 (Sulfur transfer protein involved in) thiamine biosynthesis protein ThiS Acid survival for E . coli knockout mutants To date, genetic manipulation tools are not available to construct targeted...”
BMA2729 thiamine biosynthesis protein ThiS, putative from Burkholderia mallei ATCC 23344
44% identity, 100% coverage
BCAL0298 thiamine biosynthesis protein ThiS from Burkholderia cenocepacia J2315
WQ49_RS12045 sulfur carrier protein ThiS from Burkholderia cenocepacia
46% identity, 100% coverage
CD1702A putative thiamine biosynthesis protein from Clostridium difficile 630
39% identity, 97% coverage
- Comparative transcriptional analysis of clinically relevant heat stress response in Clostridium difficile strain 630
Ternan, PloS one 2012 - “...acetyl CoA, were upregulated as were genes encoding components of de novo thiamine biosynthesis (CD1702, CD1702A, [ thiC , thiS ] and CD1599, CD1600, CD1601 [ thiD , thiK , thiE1 ]), suggesting an increased requirement for biosynthesis of various vitamins, including thiamine and folates, under...”
Saro_3290 thiamine biosynthesis protein ThiS from Novosphingobium aromaticivorans DSM 12444
41% identity, 20% coverage
W5S_RS01145 sulfur carrier protein ThiS from Pectobacterium parmentieri
36% identity, 100% coverage
- Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic Bacteria
Zoledowska, Microorganisms 2019 - “...the thiamine and sulfur metabolism pathway: W5S_RS00965 (cystathionine gamma-synthase, WP_014698476.1), W5S_RS01140 (thiazole synthase ThiG, WP_012822036.1), W5S_RS01145 (sulfur carrier protein ThiS, WP_014698484.1), W5S_RS01150 (adenylyltransferase ThiF, WP_014698485.1), W5S_RS01155 (thiamine phosphate synthase ThiE, WP_014698486.1), W5S_RS01160 (phosphomethylpyrimidine synthase ThiC, WP_014698487.1), W5S_RS05940 (hydroxymethylpyrimidine/phosphomethylpyrimidine kinase ThiD, WP_014698998.1), while the last one, W5S_RS18250...”
CAC2924 Uncharacterized protein, possibly involved in thiamine biosynthesis from Clostridium acetobutylicum ATCC 824
34% identity, 94% coverage
H16_A0237 thiamine biosynthesis sulfur transfer protein from Ralstonia eutropha H16
36% identity, 100% coverage
Pcar_0338 thiamine biosynthesis protein ThiS from Pelobacter carbinolicus str. DSM 2380
37% identity, 97% coverage
thiS / O32583 sulfur carrier protein ThiS from Escherichia coli (strain K12) (see 14 papers)
THIS_ECOLI / O32583 Sulfur carrier protein ThiS; Thiamine biosynthesis protein ThiS from Escherichia coli (strain K12) (see 2 papers)
YP_026279 sulfur carrier protein ThiS from Escherichia coli str. K-12 substr. MG1655
b4407 sulfur carrier protein ThiS from Escherichia coli str. K-12 substr. MG1655
35% identity, 100% coverage
- function: Is the sulfur donor in the synthesis of the thiazole phosphate moiety of thiamine phosphate.
- Heat shock transcription factor δ³² is targeted for degradation via an ubiquitin-like protein ThiS in Escherichia coli.
Xu, Biochemical and biophysical research communications 2015 (PubMed)- GeneRIF: ThiS, an ubiquitin-like protein, is covalently attached to delta(32) and at least 27 other proteins, leading to their subsequent degradation by proteases, in a similar manner to the ubiquitin-proteasome system (UPS) in eukaryotes.
- Functional redundancy of ubiquitin-like sulfur-carrier proteins facilitates flexible, efficient sulfur utilization in the primordial archaeon Thermococcus kodakarensis
Hidese, mBio 2024 - “...; TK2118 (UblB), Q5JEX1 ; Escherichia coli MoaD (EcMoaD), P30748 ; E. coli ThiS (EcThiS), O32583 ; SAMP1 from Haloferax volcanii (HvSAMP1), D4GUF6 ; SAMP2 from H. volcanii (HvSAMP2), D4GZE7 ; SAMP3 from H. volcanii (HvSAMP3), D4GVB0 ; TtuB from Thermus thermophilus HB27, Q72LF4 ; MOCS2A...”
- Ubiquitin-like small archaeal modifier proteins (SAMPs) in Haloferax volcanii.
Humbard, Nature 2010 - “.... The following protein sequences were also described: ScUb (P61864); ScUrm1 (P40554); EcMoaD (CAA49864); EcThiS (O32583); ScUba4p (P38820); HsMOCS3 (O95396); EcMoeB (P12282); ScYor285W (Q12305); ScYor251c (Q08686); EcSseA (P31142); EcMoaE; (P30749); HsMOCS2B (O96007); BsMobB (O31704) (GenBank or Swiss-Prot accession numbers in parenthesis; Sc, Saccharomyces cerevisiae ; Ec,...”
- Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets
Hartleb, PLoS computational biology 2016 - “...TYRL Thiamine diphosphate b3992 THZPSN3 Thiamine diphosphate b3993 TMPPP Thiamine diphosphate b3994 AMPMS2 Thiamine diphosphate b4407 THZPSN3 Thiamine diphosphate G lobal F it further indicated the removal of calcium and copper from the biomass, which was also suggested by the BioMog algorithm based on E ....”
- Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
Xu, BMC bioinformatics 2009 - “...b3368, b3634, b3639 b3804, b3805, b3850 b3974, b3990, b3991 b3992, b3993, b3994 b3997, b4039, b4040 b4407, s0001 SS MM APM GM MLM PPB genes b0159 b0159 b0175 b0185 b0522, b0523 b2687 b0386 b2585 b1092 b0945, b1062 b2942 b2818 b3018 b1094 b1131, b1281 b3939 b3172 b4041 b2316...”
- A functional update of the Escherichia coli K-12 genome
Serres, Genome biology 2001 - “...identified and assigned to Bnums. These include the protein-coding b4406 ( yaeP, SWISS-PROT P52099) and b4407 ( thiS, SWISS-PROT 032583) and the RNA encoding b4408. The current number of E. coli genes is 4,401, with 4,285 encoding proteins and 116 encoding RNAs. MAGPIE identified 5,527 candidate...”
Vpar_0455 thiamine biosynthesis protein ThiS from Veillonella parvula DSM 2008
33% identity, 100% coverage
F452_RS0109400 sulfur carrier protein ThiS from Porphyromonas gulae DSM 15663
PG2111 thiS protein from Porphyromonas gingivalis W83
33% identity, 100% coverage
- Antibacterial effects of sodium tripolyphosphate against Porphyromonas species associated with periodontitis of companion animals
Lee, Journal of veterinary science 2019 - “...ThiF 9.67E-32 4.86 F452_RS0109380 Thiamine biosynthesis protein ThiH 1.69E-26 9.45 F452_RS0108175 Thiamine pyrophosphokinase 4.16E-34 11.28 F452_RS0109400 Thiamine biosynthesis protein ThiS 1.28E-52 +6.63 F452_RS0108990 Cysteine desulfurase 2.97E-34 5.02 F452_RS0104455 Thiazole biosynthesis protein ThiJ 1.93E-44 8.26 F452_RS0104440 Thiamine-monophosphate kinase 6.26E-87 15.48 F452_RS0100070 Thiamine biosynthesis protein ApbE 1.65E-18 2.93...”
- Role of extracytoplasmic function sigma factor PG1660 (RpoE) in the oxidative stress resistance regulatory network of Porphyromonas gingivalis
Dou, Molecular oral microbiology 2018 - “...observed in these genes. 3.8 PG1660 regulates expression of PG0844 , PG00374 , PG1511 , PG2111 ( thiS ) and PG1459 PG0844 , PG1459 , PG0374 , PG1511 and PG2111 ( thiS ) were highly downregulated in FLL354 under both anaerobic and hydrogen peroxide stress conditions...”
- “...could bind to the promoter of PG0844 (A), PG1459 (B), PG0374 (C), PG1511 (D), and PG2111 (E). For A anad B: 1, reaction without rPG1660 as control; 2, reaction with addition of rPG1660; 3, reaction with addition of non-labeled promoter as competitor. For C, D and...”
- Comprehensive transcriptome analysis of the periodontopathogenic bacterium Porphyromonas gingivalis W83
Høvik, Journal of bacteriology 2012 - “...genes are organized in an operon (PG2107 to PG2111) with an LANL-predicted TPP (thiamine pyrophosphate) riboswitch located in the 5= UTR. This TPP riboswitch...”
- Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83
Nelson, Journal of bacteriology 2003 - “...(68); and a thiamine biosynthesis operon (PG2107 to PG2111, which is most similar to the thiamine biosynthesis operon of Escherichia coli). These atypical...”
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