PaperBLAST
PaperBLAST Hits for sp|P29364|KHSE_PSEAE Homoserine kinase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=thrB PE=3 SV=2 (316 a.a., MSVFTPLERS...)
Show query sequence
>sp|P29364|KHSE_PSEAE Homoserine kinase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=thrB PE=3 SV=2
MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD
LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV
GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAALDAER
PALPRANLHADLFRDNVLFDGPHLAGLIDFYNACSGWMLYDLAITLNDWCSNTDGSLDPA
RARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQDVLIHDPAEFEI
RLAQRQNVEIHLPFAL
Running BLASTp...
Found 19 similar proteins in the literature:
KHSE_PSEAE / P29364 Homoserine kinase; HK; HSK; EC 2.7.1.39 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
PA5495 homoserine kinase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
Q02DL4 Homoserine kinase from Pseudomonas aeruginosa (strain UCBPP-PA14)
99% identity, 100% coverage
CPH89_RS10590 homoserine kinase from Pseudomonas fluorescens
74% identity, 100% coverage
- Transcriptome Reveals Regulation of Quorum Sensing of <i>Hafnia alvei</i> H4 on the Coculture System of <i>Hafnia alvei</i> H4 and <i>Pseudomonas fluorescens</i> ATCC13525
Wang, Foods (Basel, Switzerland) 2024 - “...katB involved in the tryptophan metabolism of P. fluorescens ACTT13525 were upregulated, while the gene CPH89_RS10590 (related to amino acid metabolism) was downregulated, which suggests that QS of H. alvei induces metabolic disorders in P. fluorescens . Moreover, the results of the study indicate that the...”
- “...system tip protein VgrG amino acid metabolism CPH89_RS22860 1.373666561 methionine gamma-lyase CPH89_RS03900 1.088510925 L-serine ammonia-lyase CPH89_RS10590 0.592860749 homoserine kinase mmsB 1.524151588 3-hydroxyisobutyrate dehydrogenase CPH89_RS06815 0.574998597 catalase katB 1.644147633 catalase KatB CPH89_RS08005 2.317725314 D-amino acid dehydrogenase CPH89_RS00185 0.475801482 aspartate/tyrosine/aromatic aminotransferase CPH89_RS21450 1.152619749 aspartate aminotransferase family protein CPH89_RS16850...”
PP0121 homoserine kinase from Pseudomonas putida KT2440
71% identity, 100% coverage
thrB / AAF21132.1 homoserine kinase from Methylobacillus flagellatus (see paper)
43% identity, 94% coverage
BCAM0899 putative homoserine kinase from Burkholderia cenocepacia J2315
43% identity, 92% coverage
NGO2075 ThrB from Neisseria gonorrhoeae FA 1090
40% identity, 94% coverage
NGK_2537 homoserine kinase from Neisseria gonorrhoeae NCCP11945
40% identity, 94% coverage
A9HS91 Homoserine kinase from Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / CCUG 37298 / CIP 103539 / LMG 7603 / PAl5)
41% identity, 94% coverage
- Differential protein profiling of soil diazotroph Rhodococcus qingshengii S10107 towards low-temperature and nitrogen deficiency.
Suyal, Scientific reports 2019 - “...LeuD1, ArgF, ArgC (N-acetyl-gamma-glutamyl-phosphate reductase, B7JY20), HisF, Putative glutamatecysteine ligase (AZC2303,A8I5N7), ProB, ThrB (Homoserine kinase, A9HS91), DapD (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase,B2JID7), Alr (Alanine racemase,W8HAH8) and AroB (3-dehydroquinate synthase, Q0S0N0) were involved in biosynthesis of different amino acids under BM, while , DapA1 (4-hydroxy-tetrahydrodipicolinate synthase, A0A1H4N6J7), TyrS (Tyrosine tRNA...”
CC3364 homoserine kinase from Caulobacter crescentus CB15
CCNA_03475 homoserine kinase from Caulobacter crescentus NA1000
40% identity, 96% coverage
BAB1_0502 Aminoglycoside phosphotransferase:Homoserine kinase ThrB from Brucella melitensis biovar Abortus 2308
37% identity, 97% coverage
BMEI1458 HOMOSERINE KINASE from Brucella melitensis 16M
37% identity, 97% coverage
RPA4270 homoserine kinase from Rhodopseudomonas palustris CGA009
38% identity, 94% coverage
Ga0059261_3253 homoserine kinase (EC 2.7.1.39) from Sphingomonas koreensis DSMZ 15582
38% identity, 87% coverage
- mutant phenotype: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00938.
Rru_A3053 Homoserine kinase ThrB from Rhodospirillum rubrum ATCC 11170
38% identity, 96% coverage
ZMO1600 homoserine kinase from Zymomonas mobilis subsp. mobilis ZM4
37% identity, 87% coverage
ABO_0042 phosphotransferase family protein from Alcanivorax borkumensis SK2
36% identity, 97% coverage
A1S_3244 homoserine kinase from Acinetobacter baumannii ATCC 17978
33% identity, 87% coverage
HMPREF0421_20507, WP_009993807 phosphotransferase enzyme family protein from Gardnerella vaginalis ATCC 14019
31% identity, 31% coverage
- Mechanisms of S. agalactiae promoting G. vaginalis biofilm formation leading to recurrence of BV
Li, NPJ biofilms and microbiomes 2024 - “...ATP-binding protein/permease WP_029600583 NS NS ABC transporter ATP-binding protein/permease WP_004118354 NS NS C1 family peptidase WP_009993807 None NS Phosphotransferase WP_009994439 None NS VTT domain-containing protein IMMUNE EVASION WP_004115062 ahpC None NS Alkyl hydroperoxide reductase subunit C WP_048653136 NS NS Rib/alpha-like domain-containing protein IRON ACQUISITION WP_004573592 None...”
- Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential
Yeoman, PloS one 2010 - “...HMPREF0424_1123 HMPREF0421_20427 191 Multidrug resistance ABC transporter 94/100/94 HMPREF0424_0217 HMPREF0421_20340 283 Bleomycin hydrolase 91/100/91 n/a HMPREF0421_20507 1079 Aminoglycoside phosphotransferase -/100/- HMPREF0424_0210 HMPREF0421_20333 276 DedA-family protein 92/100/92 Iron acquisition HMPREF0424_0013 HMPREF0421_20160 1120 Ferritin 92/100/87 HMPREF0424_0160 HMPREF0421_21358 168 FTR1-family iron permease 80/100/79 HMPREF0424_0161 HMPREF0421_21357 169 TPD-family pathogen-specific lactoferrin...”
- “...strains 317 and 594 were isolated [42] . These strains each encode an aminoglycoside phosphotransferase (HMPREF0421_20507 and ORF 1079), related to that of the more modern nosocomial pathogen Stenotrophomonas maltophilia (e-value 210 27 ) [43] . The aminoglycoside phosphotransferase of S. maltophilia , and a number...”
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