PaperBLAST
PaperBLAST Hits for tr|Q9I3A6|Q9I3A6_PSEAE Phosphohistidine phosphatase SixA OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA1616 PE=4 SV=1 (154 a.a., MKLWLLRHGE...)
Show query sequence
>tr|Q9I3A6|Q9I3A6_PSEAE Phosphohistidine phosphatase SixA OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA1616 PE=4 SV=1
MKLWLLRHGEAESHASRDSERRLTAHGRKEVLQSAARLAGLPLDGILASPYVRAQQTAEL
VREALGLVEPVGTAPWLTPDDDPREVLGFLDERSERNLLLVSHQPLVGALGGLLVHGNRR
DPLPMSTASLAELEGDFAAAGLMTLVSLYHPRHG
Running BLASTp...
Found 21 similar proteins in the literature:
PA1616 hypothetical protein from Pseudomonas aeruginosa PAO1
Q9I3A6 Phosphohistidine phosphatase SixA from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
100% identity, 100% coverage
- Molecular Mechanism of the β-Lactamase Mediated β-Lactam Antibiotic Resistance of Pseudomonas aeruginosa Isolated From a Chinese Teaching Hospital
Lin, Frontiers in microbiology 2022 - “...- sul1 ) were encoded on a plasmid (pPA1609-475), while the bla CARB-3 gene of PA1616 also related to a class 1 integron was located on the chromosome. The results suggest that -lactam antibiotic resistance and clonal dissemination exist in this hospital population. It indicates the...”
- “...have been deposited in GenBank under accession numbers CP090649 (PA1609), CP090650 (pPA1609-475), CP090651 (pPA1609-47), CP090648 (PA1616), and CP090647 (PA1681). Results Antimicrobial Susceptibility In this study, the MIC levels of the 12 antibiotics (including oxacillin, piperacillintazobactam, cefuroxime, ceftazidime, cefepime, aztreonam, imipenem, meropenem, gentamicin, amikacin, levofloxacin, and polymyxin...”
- Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
Vemula, Heliyon 2025 - “...2343 Q9HT47 3425 Q9HYN5 4507 Q9I3A5 180 P06200 1262 Q9HTX6 2344 Q9HT48 3426 Q9HYN6 4508 Q9I3A6 181 P09786 1263 Q9HTY2 2345 Q9HT51 3427 Q9HYN7 4509 Q9I3A7 182 P0DPB9 1264 Q9HTY3 2346 Q9HT52 3428 Q9HYN8 4510 Q9I3B0 183 P11436 1265 Q9HTY5 2347 Q9HT53 3429 Q9HYP0 4511 Q9I3B3...”
P44164 Phosphohistidine phosphatase SixA homolog from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
HI1338 conserved hypothetical protein from Haemophilus influenzae Rd KW20
34% identity, 83% coverage
RSc1539 PROBABLE HYDROLASE PROTEIN from Ralstonia solanacearum GMI1000
43% identity, 77% coverage
BJD94_00805 phosphohistidine phosphatase SixA from Vibrio vulnificus Env1
35% identity, 87% coverage
YPTB2635 putative phosphohistidine phosphatase from Yersinia pseudotuberculosis IP 32953
YPO2748 putative phosphohistidine phosphatase from Yersinia pestis CO92
35% identity, 83% coverage
SENTW_2511 phosphohistidine phosphatase SixA from Salmonella enterica subsp. enterica serovar Weltevreden str.
34% identity, 88% coverage
STM2387 phosphohistidine phosphatase from Salmonella typhimurium LT2
34% identity, 88% coverage
1ujcA / P76502 Structure of the protein histidine phosphatase sixa complexed with tungstate (see paper)
34% identity, 90% coverage
- Ligand: tungstate(vi)ion (1ujcA)
YfcW / b2340 phosphohistidine phosphatase SixA from Escherichia coli K-12 substr. MG1655 (see 10 papers)
P76502 phosphohistidine phosphatase (EC 3.9.1.3) from Escherichia coli (see 2 papers)
NP_416842 phosphohistidine phosphatase SixA from Escherichia coli str. K-12 substr. MG1655
b2340 phosphohistidine phosphatase from Escherichia coli str. K-12 substr. MG1655
34% identity, 88% coverage
UTI89_C2624 phosphohistidine phosphatase SixA from Escherichia coli UTI89
34% identity, 88% coverage
MCR_0837 SixA phosphatase family protein from Moraxella catarrhalis BBH18
31% identity, 94% coverage
- Characterization of the molecular interplay between Moraxella catarrhalis and human respiratory tract epithelial cells
de, PloS one 2013 - “...catarrhalis , we generated directed gene deletion mutants for a selection of eight genes (MCR_0609, MCR_0837, aroA , ecnAB , lgt1 , MCR_1483, and MCR_1742) that have not previously been linked to adhesion ( Table 1 ). Importantly, deletion of these genes did not affect growth...”
- “...compared to wild-type, confirming the Tn-seq results (Figure 2AB). Mutants of trmB , MCR_0609, and MCR_0837, however, displayed wild-type adherence levels, while deletion of MCR_1742, encoding an uncharacterized outer membrane protein, even appeared to result in enhanced adhesion to both cell lines (Figure 2AB). This apparent...”
sll0400 phosphohistidine phosphatase SixA from Synechocystis sp. PCC 6803
Q55129 Uncharacterized protein sll0400 from Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)
NP_442193 hypothetical protein from Synechocystis sp. PCC 6803
35% identity, 81% coverage
C4X49_12010 SixA phosphatase family protein from Acinetobacter baumannii
31% identity, 98% coverage
SSO1195 Phosphohistidine phosphatase (sixA) from Sulfolobus solfataricus P2
35% identity, 68% coverage
AF1002 conserved hypothetical protein from Archaeoglobus fulgidus DSM 4304
36% identity, 77% coverage
NE0848 Phosphoglycerate mutase family from Nitrosomonas europaea ATCC 19718
36% identity, 77% coverage
LIMLP_16015 phosphohistidine phosphatase SixA from Leptospira interrogans serovar Manilae
31% identity, 69% coverage
Q82ZR6 Phosphoglycerate mutase family protein from Enterococcus faecalis (strain ATCC 700802 / V583)
EF2982 phosphoglycerate mutase family protein from Enterococcus faecalis V583
OG1RF_12264 histidine phosphatase family protein from Enterococcus faecalis OG1RF
33% identity, 55% coverage
- Identification and comparison of protein composition of biofilms in response to EGCG from Enterococcus faecalis and Staphylococcus lugdunensis, which showed opposite patterns in biofilm-forming abilities
Cho, Biofilm 2024 - “...specific 2-hydroxyacid dehydrogenase family protein 24.12 28.49 1.18 Q839C2 EF_0253 Aldehyde dehydrogenase 20.04 16.65 0.83 Q82ZR6 EF_2433 Phosphoglycerate mutase family protein 20.12 16.62 0.83 Q834K0 topA DNA topoisomerase 1 23.88 19.67 0.82 Q831P0 EF_2461 Inositol monophosphatase protein family 22.21 17.94 0.81 Q833B0 EF_2057 Heptaprenyl diphosphate synthase,...”
- The transcriptome of the nosocomial pathogen Enterococcus faecalis V583 reveals adaptive responses to growth in blood
Vebø, PloS one 2009 - “...of intracellular glucose catabolic intermediates. Simultaneously, glycolysis genes gap-1 (EF1526), glycerate kinase (EF2646) and pgm (EF2982) were up-regulated, indicating increased carbon flux from sources other than hexose sugars. Interestingly, the glycerol catabolic pathway (EF1929-27), was highly up-regulated in response to growth in blood, and was also...”
- Detailed Soluble Proteome Analyses of a Dairy-Isolated Enterococcus faecalis: A Possible Approach to Assess Food Safety and Potential Probiotic Value
Cirrincione, Frontiers in nutrition 2019 - “...them the aldehyde-alcohol dehydrogenase (9.47 fold change - OG1RF_10627), phosphoglycerate mutase (5.50 fold change - OG1RF_12264), formate acetyltransferase (5.30 fold change - OG1RF_11329), 2-dehydropantoate 2-reductase (5.20 fold change - OG1RF_11367), uracil phosphoribosyltransferase (5.14 fold change - OG1RF_11432) show the highest fold change values. For what concern...”
J2N86_RS13365 histidine phosphatase family protein from Legionella lytica
34% identity, 34% coverage
SCO1809 hypothetical protein from Streptomyces coelicolor A3(2)
30% identity, 66% coverage
YtjC / b4395 putative phosphatase from Escherichia coli K-12 substr. MG1655 (see 7 papers)
gpmB / RF|NP_418812 PGAM from Escherichia coli K12 (see paper)
P0A7A2 Probable phosphoglycerate mutase GpmB from Escherichia coli (strain K12)
b4395 phosphoglycerate mutase from Escherichia coli str. K-12 substr. MG1655
DR76_2507 2,3-diphosphoglycerate-dependent phosphoglycerate mutase GpmB from Escherichia coli ATCC 25922
34% identity, 31% coverage
- Functional Prediction of Biological Profile During Eutrophication in Marine Environment
Sbaoui, Bioinformatics and biology insights 2022 - “...with Zn-dependent exopeptidase domain GlpX P0A9C9 Fructose-1,6-bisphosphatase 1 class 2 GltA P0ABH7 Citrate synthase GpmB P0A7A2 Putative phosphoglyceromutase 2 GuaC P60560 GMP reductase HcaF Q47140 Putative 3-phenylpropionate/cinnamate dioxygenase subunit Hcp P75825 Hydroxylamine oxidoreductase-like protein HemH P23871 Ferrochelatase HemW P52062 Heme chaperone Hha P0ACE3 Hemolysin expression-modulating protein...”
- The Protein Interactome of Glycolysis in Escherichia coli
Chowdhury, Proteomes 2021 - “...(3-PG) 13 1 7 GpmI P37689 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 3-phosphoglycerate (3-PG) 1 2 7 GpmB P0A7A2 Probable phosphoglycerate mutase 3-phosphoglycerate (3-PG) 1 0 8 Eno P0A6P9 Enolase 2-phosphoglycerate (2-PG) 85 5 9 PykA P21599 Pyruvate kinase II Phosphoenolpyruvate (PEP) 20 2 9 PykF P0AD61 Pyruvate kinase...”
- Systems Biology Approach to Bioremediation of Nitroaromatics: Constraint-Based Analysis of 2,4,6-Trinitrotoluene Biotransformation by Escherichia coli
Iman, Molecules (Basel, Switzerland) 2017 - “...<=> h[c] + no2[c] (b3367 or b1223) PGM Phosphoglycerate mutase 2pg[c] <=> 3pg[c] (b3612 or b4395 or b0755) PTAr Phosphotransacetylase accoa[c] + pi[c] <=> actp[c] + coa[c] (b2297 or b2458) PPS Phosphoenolpyruvate synthase atp[c] + h2o[c] + pyr[c] -> amp[c] + 2 h[c] + pep[c] +...”
- Sparse Regulatory Networks
James, The annals of applied statistics 2010 - “...to be regulated by trpR. Correspondingly, they all have moderate to large estimated activation strengths. b4395 again has an overlapping regulatory region to b4393. The results suggest this is not regulated by trpR. 4.4. Relaxing zero coefficients The results from Section 4.3 use the same relatively...”
- luxS-dependent gene regulation in Escherichia coli K-12 revealed by genomic expression profiling
Wang, Journal of bacteriology 2005 - “...b3829 b1517 b1511 b1520 b2236 b1519 b4308 b1512 b1514 b4395 b3796 b3852 b4017 b2087 b0974 b1127 b1019 b1550 b4196 b0630 b1022 b1437 b4186 b2406 b3939 b3945...”
- Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli
Gingras, Microbial genomics 2018 - “...2 TMP 1 406354 DR76_2556 DR76_2564 2722303..2729487 DR76_2559 folA Dihydrofolate reductase 16 16 2 187 DR76_2507 DR76_2508 2666704..2668901 DR76_2506 rob Right origin-binding protein 1 2 The full list of enriched plasmids can be found in Table S2. This fold increase in MIC is meeting the EUCAST...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 798,070 different protein sequences to 1,261,478 scientific articles. Searches against EuropePMC were last performed on May 12 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