PaperBLAST
PaperBLAST Hits for XP_001559809.2 hypothetical protein (Botrytis cinerea B05.10) (859 a.a., MASLTLDILR...)
Show query sequence
>XP_001559809.2 hypothetical protein (Botrytis cinerea B05.10)
MASLTLDILREPQTQIFTTVVVLFFFIALIFFARNASLYPKNSAQDEENPSAFKSFLRFF
YASFLKPHNGDGTENGQQDALESFYKAQAGVYDATRERLLRGRKDMLALVAAQLVNKASR
ERTHDTKRIWVDIGGGTGWNIEAMSEYVSVPEFFSSVYLVDFSPSLCEVARKRFSRLGWK
NIKVVCQDARTFRLEDHEDIDIGAVNLSRSPTSNYFSNPDAVGGADLITLSYSLSMIPDF
YSVIDSLANLLAPSGTIGVVDFYVQSIVDLSCRNYTGGVINRHVNWLGRLFWRAWFDVDR
VNLEAGRRDYLEYRFGTVLSADSRNSLLGFIPYYMWLGCQKKPASTIAAPNYPHEMVERL
DAAVTESPYLSPINHTKTLSRTVDGSTLPEIRSKAFEAAIVNLSANLPLPSFFYQNHHWR
IHYDDQLKKHTQFGQEYIYAFTWEDTRVDERLLNITRDDVILAITSAGDNILSYALKSPR
RIHAIDLNPNQNHLLELKVASFATLPYSDFWKLFGLGKHPHFRELLLTRLSPHMSSRAFQ
YWLTHAHVFTTSSRGLYETGGSRHAIRIIRLLSQTLGFSSEIKNLLASKTLNEQREVWQT
KIRPIIMSRIFSYLVVSQETFLWKALGVPKNQLHMLEADYIASESVARNSSPLEHSEIDL
KKSKGSAVWEYMIQTLDPVIENSLIGEDNPYYLVCLQGSYTQRCHPDYLRPKSHQKLSRH
DAFDGLRIHTDEIDEVIQRITPGTLTIAVVMDSMDWFDPGAEAAEKQIKKLNRALKMGGR
VLLRSAALTPWYISTFERLGFVGKRVGARIGGACIDRVNMYASCYLLTKVEDLEPLTPTA
SPSRISGRQGSMELEKLEI
Running BLASTp...
Found 15 similar proteins in the literature:
BCIN_05g04180 hypothetical protein from Botrytis cinerea B05.10
100% identity, 100% coverage
FGSG_00742 hypothetical protein from Fusarium graminearum PH-1
65% identity, 95% coverage
Pc22g21330 uncharacterized protein from Penicillium rubens
58% identity, 95% coverage
An02g02840 uncharacterized protein from Aspergillus niger
58% identity, 98% coverage
CHLREDRAFT_77062 uncharacterized protein from Chlamydomonas reinhardtii
Q6DN05 Betaine lipid synthase from Chlamydomonas reinhardtii
29% identity, 47% coverage
- Diacylglyceryl-N,N,N-trimethylhomoserine-dependent lipid remodeling in a green alga, Chlorella kessleri
Oishi, Communications biology 2022 - “...analysis, the amino acid sequences of BTA1 homologs were searched in available databases with CrBTA1 (CHLREDRAFT_77062) and BtaA (RSP_0856) and BtaB (RSP_0857) of Rhodobacter sphaeroides 2.4.1 as queries. The homolog sequences of CrBTA1 obtained are summarized in Supplementary Table 2 . The sequences were aligned after...”
- Quantitative proteomic comparison of salt stress in Chlamydomonas reinhardtii and the snow alga Chlamydomonas nivalis reveals mechanisms for salt-triggered fatty acid accumulation via reallocation of carbon resources
Hounslow, Biotechnology for biofuels 2021 - “...[ 63 ] 1.162 1.181 1.209 1.250 1.375 A8J2S0 Citrate synthase Tricarboxylic acid cycle -2.725 Q6DN05 Betaine lipid synthase Betaine lipid synthesis, including DGTS synthesis -1.093 A8HXT4 Pyruvate carboxylase Pyruvate metabolism, gluconeogenesis, links carbohydrate and lipid metabolism -1.047 -1.100 A8JGF4 Biotin carboxylase, acetyl-CoA carboxylase component Malonyl-CoA...”
BtaA / Q93TQ1 S-adenosylmethionine:diacylglycerol 3-amino-3-carboxypropyl transferase from Cereibacter sphaeroides (see paper)
RSP_0856 S-adenosylmethionine-diacylglycerol 3-amino-3-carboxypropyl transferase from Rhodobacter sphaeroides 2.4.1
29% identity, 24% coverage
mlr1574 hypothetical protein from Mesorhizobium loti MAFF303099
23% identity, 42% coverage
- Accumulation of novel glycolipids and ornithine lipids in Mesorhizobium loti under phosphate deprivation
Diercks, Journal of bacteriology 2015 - “...the enzymes BtaA and BtaB (41), with homologs (mlr1574 and mlr1575, respectively) also found in Mesorhizobium. The mesorhizobial BtaA and BtaB homologs are not...”
- A processive glycosyltransferase involved in glycolipid synthesis during phosphate deprivation in Mesorhizobium loti
Devers, Journal of bacteriology 2011 - “...compiled by Yuan et al. (36). Interestingly, the mlr1574 gene of Mesorhizobium, which presumably is involved in DGTS synthesis under phosphate deprivation, was...”
- “...out of 18). Therefore, in contrast to the DGTS gene mlr1574, the pgt gene presumably does not contain a Pho box. These results indicate that Pgt activity might...”
- Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria
Yuan, Nucleic acids research 2006 - “...( btaA -like) 2 Atu2119 CTGTCATCAAACTGTAGC 44 0.58 A.tumefaciens Hypothetical protein ( btaA -like) 3 mlr1574 CTGTCACCGGCCTGTCAT +1 0.55 M.loti Hypothetical protein ( btaA -like) H Exopolysaccharide 1 SMb21317 CTGTCATGCACCTGCATC 385 0.39 S.meliloti expG , activator of exopolysaccharide II synthesis 2 SMc02851 CTTTCAAAGAGCCGCCAC 158 0.37 S.meliloti...”
- “...predicted 64 nt from the smc01848 start codon and orthologs of smc01848 in M.loti ( mlr1574 ) and Agrobacterium tumefaciens ( atu211 9) also have predicted Pho boxes in the corresponding promoter regions ( Table 5 ). These data strongly suggest that DGTS synthesis induced upon...”
MED193_17364 S-adenosylmethionine-diacylglycerol 3-amino-3-carboxypropyltransferase from Roseobacter sp. MED193
A3X3R1 S-adenosylmethionine-diacylglycerol 3-amino-3-carboxypropyltransferase from Roseobacter sp. MED193
24% identity, 41% coverage
- Bacterial catabolism of membrane phospholipids links marine biogeochemical cycles
Westermann, Science advances 2023 - “...4.38 0.00 MED193_17359 A3X3R3 PlcP Phosphodiesterase involved in lipid remodeling ++ 4.40 0.01 N/D N/D MED193_17364 A3X3R1 BtaA S-adenosylmethionine-diacylglycerol 3-amino-3-carboxypropyltransferase ++ 5.67 0.02 N/D N/D MED193_17614 A3X3L3 PhnI C-P lyase, ribosylation, core complex ++ 4.68 0.02 N/D N/D MED193_17624 A3X3L1 PhnJ C-P lyase, CP bond cleavage,...”
- Bacterial catabolism of membrane phospholipids links marine biogeochemical cycles
Westermann, Science advances 2023 - “...0.00 MED193_17359 A3X3R3 PlcP Phosphodiesterase involved in lipid remodeling ++ 4.40 0.01 N/D N/D MED193_17364 A3X3R1 BtaA S-adenosylmethionine-diacylglycerol 3-amino-3-carboxypropyltransferase ++ 5.67 0.02 N/D N/D MED193_17614 A3X3L3 PhnI C-P lyase, ribosylation, core complex ++ 4.68 0.02 N/D N/D MED193_17624 A3X3L1 PhnJ C-P lyase, CP bond cleavage, core...”
Atu2119 hypothetical protein from Agrobacterium tumefaciens str. C58 (Cereon)
22% identity, 41% coverage
NGR_c21260 putative S-adenosylmethionine:diacylglycerol 3-amino-3-carboxypropyl transferase from Rhizobium sp. NGR234
23% identity, 41% coverage
NGR_c21260 DUF3419 family protein from Sinorhizobium fredii NGR234
23% identity, 41% coverage
SMc01848 CONSERVED HYPOTHETICAL PROTEIN from Sinorhizobium meliloti 1021
23% identity, 42% coverage
- Transcriptomic Insight in the Control of Legume Root Secondary Infection by the Sinorhizobium meliloti Transcriptional Regulator Clr
Zou, Frontiers in microbiology 2017 - “...-1,3779 smc03806 GlnK nitrogen regulatory protein PII -1,3264 -1,3172 smc03072 Conserved hypothetical protein -1,5406 -1,2392 smc01848 Conserved hypothetical protein -1,4597 -1,2183 smc03052 FlgD basal body rod modification protein -1,1339 -1,2173 smb20263 Putative ABC transporter periplasmic protein -1,177 -1,1958 smc03046 Putative transcription regulator protein -1,0913 -1,149 smc02588...”
- Sinorhizobium meliloti phospholipase C required for lipid remodeling during phosphorus limitation
Zavaleta-Pastor, Proceedings of the National Academy of Sciences of the United States of America 2010 - “...S-adenosylmethionine: DAG 3-amino-3-carboxypropyl transferase (SMc01848); BtaB, diacylglyceryl homoserine N-methyltransferase (SMc01849); CgmB, cyclic...”
- “...biosynthesis (Fig. 4), SqdB (SMc03961) and BtaA (SMc01848), respectively, are preceded by a Pho box that mediates PhoB-controlled expression under phosphorus...”
- Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria
Yuan, Nucleic acids research 2006 - “...0.4 Hypothetical protein 33 SMc04280 Microarray c CTTTTGTAAAGATTTCAT 81 0.37 Hypothetical signal peptide protein 34 SMc01848 Microarray c TCGTCATCAAAGTGTAGC 47 0.41 Hypothetical protein ( btaA -like) * 2 a Pho-box sequences detected in this study and also by Krol and Becker (31). b Pho-box sequences detected...”
- “..., alkaline phosphatase 15 PA2635 CTGTCATCGTCCCGTCGC 53 0.39 P.aeruginosa Hypothetical protein G Membrane lipids 1 SMc01848 TCGTCATCAAAGTGTAGC 47 0.41 S.meliloti Hypothetical protein ( btaA -like) 2 Atu2119 CTGTCATCAAACTGTAGC 44 0.58 A.tumefaciens Hypothetical protein ( btaA -like) 3 mlr1574 CTGTCACCGGCCTGTCAT +1 0.55 M.loti Hypothetical protein ( btaA...”
Atu2120 O-methyltransferase from Agrobacterium tumefaciens str. C58 (Cereon)
27% identity, 22% coverage
NGR_c21270 O-methyltransferase from Rhizobium sp. NGR234
NGR_c21270 class I SAM-dependent methyltransferase from Sinorhizobium fredii NGR234
24% identity, 25% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 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