PaperBLAST
PaperBLAST Hits for IAI46_04040 (86 a.a., MNLLSTEIKQ...)
Show query sequence
>IAI46_04040
MNLLSTEIKQLIIDTLNLEGMTPEEIDAEAPLFGDGLGLDSIDALELGLALKNRYGVVLS
AESQDMRQHFYSVETLAKFVSAQRSQ
Running BLASTp...
Found 13 similar proteins in the literature:
Z4853 putative acyl carrier protein from Escherichia coli O157:H7 EDL933
ECs4328 putative acyl carrier protein from Escherichia coli O157:H7 str. Sakai
72% identity, 99% coverage
- The phosphopantetheinyl transferases: catalysis of a post-translational modification crucial for life
Beld, Natural product reports 2014 - “...O-island 138 gene cluster which contains fatty acid biosynthesis-like genes, including two putative carrier proteins Z4853 and Z4854. When these ACPs were expressed in E. coli K12 (which lacks the O-island 138 gene cluster), 4-phosphopantetheinylation was independent of the presence of AcpS but dependent on the...”
- “...a set of interesting FAS-related enzymes ( Fig. 4 ). Sequence alignment of the ACPs Z4853 (or Ecs4328) and Z4854 (or Ecs4329) reveals the conserved serine for PPant modification, but with a motif that contains DSI instead of the typical AcpP DSL motif. This motif is...”
- Enterohemorrhagic Escherichia coli O157:H7 gene expression profiling in response to growth in the presence of host epithelia
Jandu, PloS one 2009 - “...Z4919 putative ATP-binding protein of ABC transport system 3.6493 1763215_s_at bioD dethiobiotin synthetase 3.0056 1767427_s_at Z4853 putative acyl carrier protein 2.5431 1764491_s_at escT escT 2.4659 1765592_s_at urge putative urease accessory protein G 2.4320 1759270_s_at gltD glutamate synthase, small subunit 2.4262 1769074_s_at fepC ATP-binding component of ferric...”
- Use of a recombinant Coccidioides immitis complement fixation antigen-chitinase in conventional serological assays
Johnson, Journal of clinical microbiology 1996 - “...Serum b 1:2 1:4 1:8 1:16 1:32 1:64 1:128 1:256 1:512 control 4 4 3 3 0 0 Z4853 AP rCF CF pool 4 4 4 4 4 4 4 4 2 3 0 0 Z4765 AP rCF CF pool 2 4 3 4 3 4 4 4 4 4 3...”
- A hemolytic-uremic syndrome-associated strain O113:H21 Shiga toxin-producing Escherichia coli specifically expresses a transcriptional module containing dicA and is related to gene network dysregulation in Caco-2 cells
Bando, PloS one 2017 - “...differentially expressed transcripts ( Fig 2 ) showed that only two transcripts ( ECs1070 and ECs4328 , both functionally uncharacterized) are common between EH41 and Ec472/01 strains. Noteworthy, none of these transcripts is a known or putative virulence factor. On the other hand, it is well...”
- The phosphopantetheinyl transferases: catalysis of a post-translational modification crucial for life
Beld, Natural product reports 2014 - “...of interesting FAS-related enzymes ( Fig. 4 ). Sequence alignment of the ACPs Z4853 (or Ecs4328) and Z4854 (or Ecs4329) reveals the conserved serine for PPant modification, but with a motif that contains DSI instead of the typical AcpP DSL motif. This motif is also found...”
- Examination of the genome-wide transcriptional response of Escherichia coli O157:H7 to cinnamaldehyde exposure
Visvalingam, Applied and environmental microbiology 2013 - “...marAc marRc marBc mdtEFb Membrane/membrane transport ECs2113 ECs2112 ECs4328 yhiD yedE ynjD ynjE yhjX gfcB efeU tolCb Anaerobiosis ansB speF Type 1 fimbrial...”
- Genome evolution in major Escherichia coli O157:H7 lineages
Zhang, BMC genomics 2007 - “...which contains genes for a fatty acid biosynthesis system, only the putative acyl carrier gene ECs4328 showed variation, and this variation was not lineage-related. All other ORFs in S-loop#225/OI#138 were conserved across all E. coli O157:H7 strains examined. In the LEE-containing S-loop#244/OI#148 [ 5 , 31...”
c1200 Putative acyl carrier protein from Escherichia coli CFT073
72% identity, 99% coverage
- CpxA Phosphatase Inhibitor Activates CpxRA and Is a Potential Treatment for Uropathogenic Escherichia coli in a Murine Model of Infection
Fortney, Microbiology spectrum 2022 - “...the transport of peptides (DppF) and sugars (ExuT and AgaB), increased lipid biosynthesis and localization (c1200, c2468, and LptG), alterations in transcription (CspI, c3307, and c5025), a decrease in genome replication in nutrient stress (CspD), the use of formate as an electron donor (FdoH) and nitrate...”
- Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation
Johnston, NPJ biofilms and microbiomes 2021 - “...c1204 lipoprotein B c1203 SAM-dependent methyltransferase C c1202 3-ketoacyl-ACP synthase D c1201 lysophospholipid acyltransferase E c1200 acyl carrier protein F c1199 acyl carrier protein G c1198 COG4648 - pyrophosphatase H c1197 acyl-ACP synthetase I c1196 3-hydroxyacyl-ACP dehydratase J c1194 glycosyltransferase / acyltransferase K c1193 thioesterase L...”
- Exact determination of UV-induced crosslinks in 16S ribosomal RNA in 30S ribosomal subunits
Wilms, RNA (New York, N.Y.) 1997 (secret)
HPJ52_RS03890 phosphopantetheine-binding protein from Acinetobacter baumannii
61% identity, 98% coverage
- Transcriptomic investigations of polymyxins and colistin/sulbactam combination against carbapenem-resistant Acinetobacter baumannii
Bian, Computational and structural biotechnology journal 2024 - “...DEGs shared by all three polymyxins, fatty acid synthesis genes fabG, fabF, acpP2 , HPJ52_RS03825, HPJ52_RS03890, as well as fatty acid catabolism genes fadI, mmgC, acdA, paaG, paaJ , and HPJ52_RS04880, were all up-regulated 2- to 32-fold; paaG and paaJ are also associated with phenylacetic acid...”
Gmet_1689 Phosphopantetheine-binding protein from Geobacter metallireducens GS-15
56% identity, 95% coverage
RSp0370 phosphopantetheine-binding protein from Ralstonia pseudosolanacearum GMI1000
51% identity, 98% coverage
- Of its five acyl carrier proteins, only AcpP1 functions in Ralstonia solanacearum fatty acid synthesis
Yin, Frontiers in microbiology 2022 - “...acpP2 ), also located on the chromosome. AcpP3, AcpP4, and AcpP5 are encoded by RSp1659, RSp0370, and RSp0369, respectively (now named acpP3 , acpP4 , and acpP5 , respectively), and these genes are encoded on the megaplasmid. However, the function of none of these ACPs has...”
- “...clarified. Discussion The R. solanacearum GMI1000 genome contains five open reading frames, RSc1053, RSc0434, RSp1659, RSp0370, and RSp0369, that encode putative ACPs, AcpP1, AcpP2, AcpP3, AcpP4, and AcpP5, respectively. We confirmed that these ACPs are successfully phosphopantetheinylated and identified the active site at which the Ppant...”
Fjoh_1089 hypothetical protein from Flavobacterium johnsoniae UW101
50% identity, 100% coverage
LF41_3126 phosphopantetheine-binding protein from Lysobacter dokdonensis DS-58
45% identity, 89% coverage
- Genome sequence of Lysobacter dokdonensis DS-58(T), a gliding bacterium isolated from soil in Dokdo, Korea
Kwak, Standards in genomic sciences 2015 - “...20, fatty acyl-CoA synthetase (LF41_3122); 21, acyltransferase (LF41_3123); 22, dehydratase (LF41_3124); 23, acyl carrier protein (LF41_3126); 24, monooxygenase (LF41_3127); 25, pteridine-dependent deoxygenase (LF41_3128). Strains are: Lysobacter dokdonensis DS-58, Lysobacter arseniciresistens ZS79, Arenimonas composti DSM 18010, Lysobacter daejeonensis GH1-9, Xanthomonas albilineans GPE PC73, Pseudoxanthomonas suwonensis 111, Xanthomonas...”
BCAL0845 acyl carrier protein from Burkholderia cenocepacia J2315
42% identity, 99% coverage
RSc0434 HYPOTHETICAL PROTEIN from Ralstonia solanacearum GMI1000
39% identity, 76% coverage
- Of its five acyl carrier proteins, only AcpP1 functions in Ralstonia solanacearum fatty acid synthesis
Yin, Frontiers in microbiology 2022 - “...occurs in the fatty acid biosynthesis gene ( fab ) cluster. AcpP2 is encoded by RSc0434 (now named acpP2 ), also located on the chromosome. AcpP3, AcpP4, and AcpP5 are encoded by RSp1659, RSp0370, and RSp0369, respectively (now named acpP3 , acpP4 , and acpP5 ,...”
- “...to be clarified. Discussion The R. solanacearum GMI1000 genome contains five open reading frames, RSc1053, RSc0434, RSp1659, RSp0370, and RSp0369, that encode putative ACPs, AcpP1, AcpP2, AcpP3, AcpP4, and AcpP5, respectively. We confirmed that these ACPs are successfully phosphopantetheinylated and identified the active site at which...”
MXAN_6392 putative acyl carrier protein from Myxococcus xanthus DK 1622
38% identity, 79% coverage
SAG0665 acyl carrier protein AcpC from Streptococcus agalactiae 2603V/R
gbs0647 Unknown from Streptococcus agalactiae NEM316
WP_000611493 phosphopantetheine-binding protein from Streptococcus agalactiae
43% identity, 73% coverage
C5O77_01055 phosphopantetheine-binding protein from Limosilactobacillus reuteri
32% identity, 81% coverage
DS891_00405 phosphopantetheine-binding protein from Pseudoalteromonas sp. JC28
39% identity, 78% coverage
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