PaperBLAST
PaperBLAST Hits for Rv0755A (61 a.a., MKELSVAEQR...)
Show query sequence
>Rv0755A
MKELSVAEQRYQAVLAVISDGLSISQVAEKVGVSRQTLHTWLARYEAEGLDGLRIGTGTA
L
Running BLASTp...
Found 5 similar proteins in the literature:
Q8VKE6 Transposase from Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
100% identity, 86% coverage
Rv0755A PUTATIVE TRANSPOSASE (FRAGMENT) from Mycobacterium tuberculosis H37Rv
100% identity, 100% coverage
- Structure of a Wbl protein and implications for NO sensing by M. tuberculosis
Kudhair, Nature communications 2017 - “...mftF , and Rv1393c ) have functions in intermediary metabolism and respiration, and 1 ( Rv0755A ) code for a transposase. The presence of both up- (22 operons) and downregulated (3 operons) genes suggests that WhiB1 can act (directly or indirectly) as both a repressor and...”
- “...Rv3612c 4.5 Hypothetical protein espA-E ppsE Rv2935 4.4 Phthiocerol synthesis polyketide synthase type I ppsE Rv0755A Rv0755A 4.2 Transposase Rv0755A Rv2159c Rv2159c 4.1 Hypothetical protein Rv2159c Rv1638A Rv1638A 4.1 Hypothetical protein Rv1639c-Rv1638A lipX Rv1169c 4.1 Lipase lipX Rv1986 Rv1986 4.1 Amino acid transporter Rv1986 Rv3572 Rv3572...”
- Targeting Mycobacterium tuberculosis Tumor Necrosis Factor Alpha-Downregulating Genes for the Development of Antituberculous Vaccines
Olsen, mBio 2016 - “...that could mediate TNF-downregulating activity in infected C10 cultures ( Fig.3 ). Subclone 40-5 encompasses rv0755A (a fragment of a putative transposase), thrV (anticodon tRNA-Thr), and rv0756c (hypothetical protein). Subclone 164-2, which contains three genes from the acid-responsive mymA operon ( 38 , 39 ), rv3087...”
- “...the fact that, while the validity of the functional annotation of xylB , rv0730 , rv0755A , thrV , and rv0756c has not been tested, results obtained from biochemical analysis of the products of the two genes encoding triacylglycerol synthases ( rv3087 and rv3088 ) and...”
- Global study of IS6110 in a successful Mycobacterium tuberculosis strain: clues for deciphering its behavior and for its rapid detection
Millán-Lou, Journal of clinical microbiology 2013 - “...al. (27) This work This work mgtC ogt ung Rv0755A, thrV Rv0794c, Rv0797 Rv1668c, Rv1869 Rv2286c, yjcE Rv2349c (plcC) Rv2813, Rv2814 (DR region) Rv2823c Rv3229c...”
- “...18, and 594 bp upstream of the RV0794c, Rv1668c, Rv0755A, MT3429 (RvD5 region), and Rv2813 genes, respectively (Table 2). The 12th IS6110 site was located...”
- Genetic features shared by Mycobacterium tuberculosis strains involved in microevolution events
Pérez-Lago, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2013 (PubMed)- “...an IS6110 copy located upstream of a transposase (Rv0755A). These markers could be involved in mechanisms leading to genotypic variation. Both features were...”
- “...IS 6110 copy located upstream of a transposase (Rv0755A). These markers could be involved in mechanisms leading to genotypic variation. Both features were...”
EC390_RS07930, EC391_RS14810, EGM60_RS19600, EGM63_RS09950, EGM64_RS22700, MAPS_RS00050, MAPS_RS15850 IS481-like element ISMav5 family transposase from Mycobacterium avium subsp. paratuberculosis
MAP0428 hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
MAP0589c hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
MAP0850c hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
91% identity, 13% coverage
- Characterisation of IS1311 in Mycobacterium avium subspecies paratuberculosis genomes: Typing, continental clustering, microbial evolution and host adaptation
Mizzi, PloS one 2024 - “...HTH-type transcriptional regulator (MCIPBHBI_00012) 1 12533 13849 IS 481 -like element IS Mav5 family transposase (MAPS_RS00050) TetR/AcrR family transcriptional regulator (MAPS_RS00060) - - - - - 2 35405 36721 hypothetical protein (MCIPBHBI_00033) hypothetical protein (MCIPBHBI_00035) 2 35330 36646 hypothetical protein (MAPS_RS23020) hypothetical protein (MAPS_RS00170) 1 *...”
- “...(MCIPBHBI_02837) hypothetical protein (MCIPBHBI_02839) 8 3399740 3401056 IS 481 -like element IS Mav5 family transposase (MAPS_RS15850) hypothetical protein (MAPS_RS15860) 3 871380 872696 hypothetical protein (JOCMOIII_00893) IS 481 family transposase ISMav5 (JOCMOIII_00895) 5 1458042 1459358 *putative Toll/interleukin-1 receptor domain-containing protein (MCIPBHBI_01447) putative PPE family protein PPE32 (MCIPBHBI_01449)...”
- Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes
Lim, Veterinary research 2021 - “...gene (MAP_RS00045) and generated two additional transposases, IS 481 -like element IS Mav5 family transposase (EC390_RS07930, EC391_RS14810, EGM63_RS09950, EGM64_RS22700, and EGM60_RS19600) and IS 256 family transposase (EC390_RS11115, EC391_RS11625, EGM63_RS06755, EGM64_RS02850, and EGM60_RS22795). A notable feature of this gap was that its inserted location was the end...”
- “...(MAP_RS00045) and generated two additional transposases, IS 481 -like element IS Mav5 family transposase (EC390_RS07930, EC391_RS14810, EGM63_RS09950, EGM64_RS22700, and EGM60_RS19600) and IS 256 family transposase (EC390_RS11115, EC391_RS11625, EGM63_RS06755, EGM64_RS02850, and EGM60_RS22795). A notable feature of this gap was that its inserted location was the end of...”
- “...additional transposases, IS 481 -like element IS Mav5 family transposase (EC390_RS07930, EC391_RS14810, EGM63_RS09950, EGM64_RS22700, and EGM60_RS19600) and IS 256 family transposase (EC390_RS11115, EC391_RS11625, EGM63_RS06755, EGM64_RS02850, and EGM60_RS22795). A notable feature of this gap was that its inserted location was the end of the genome inverted region...”
- “...and generated two additional transposases, IS 481 -like element IS Mav5 family transposase (EC390_RS07930, EC391_RS14810, EGM63_RS09950, EGM64_RS22700, and EGM60_RS19600) and IS 256 family transposase (EC390_RS11115, EC391_RS11625, EGM63_RS06755, EGM64_RS02850, and EGM60_RS22795). A notable feature of this gap was that its inserted location was the end of the...”
- “...generated two additional transposases, IS 481 -like element IS Mav5 family transposase (EC390_RS07930, EC391_RS14810, EGM63_RS09950, EGM64_RS22700, and EGM60_RS19600) and IS 256 family transposase (EC390_RS11115, EC391_RS11625, EGM63_RS06755, EGM64_RS02850, and EGM60_RS22795). A notable feature of this gap was that its inserted location was the end of the genome...”
- Comparative genomic hybridizations reveal genetic regions within the Mycobacterium avium complex that are divergent from Mycobacterium avium subsp. paratuberculosis isolates
Paustian, Journal of bacteriology 2005 - “...MAP0106c MAP0159c MAP0253 MAP0284c MAP0338c MAP0388 MAP0428 MAP0589c MAP0664c MAP0832c MAP0850c MAP0851 MAP0856c MAP0859c MAP0866 MAP1048c MAP1287 MAP1432...”
- Comparative genomic hybridizations reveal genetic regions within the Mycobacterium avium complex that are divergent from Mycobacterium avium subsp. paratuberculosis isolates
Paustian, Journal of bacteriology 2005 - “...MAP0159c MAP0253 MAP0284c MAP0338c MAP0388 MAP0428 MAP0589c MAP0664c MAP0832c MAP0850c MAP0851 MAP0856c MAP0859c MAP0866 MAP1048c MAP1287 MAP1432 MAP1723...”
- Optical mapping of the Mycobacterium avium subspecies paratuberculosis genome
Wu, BMC genomics 2009 - “...new copies of the coding sequences > 99.8% were identified, identical to the MAP0849c and MAP0850c genes located immediately downstream of the MAP3758c gene. Conclusion The optical map of M. ap ATCC 19698 clearly indicated the miss-assembly of the sequenced genome of M. ap K-10. Moreover,...”
- Discovery of stable and variable differences in the Mycobacterium avium subsp. paratuberculosis type I, II, and III genomes by pan-genome microarray analysis
Castellanos, Applied and environmental microbiology 2009 - “...MAP0282c to MAP0284c MAP0387 to MAP0389 MAP4, or LSPp4 MAP0850c to MAP0866 MAP5, or LSPp5 MAP0956 to MAP0967 MAP1231 to MAP1237c MAP1344 to MAP1349c MAP1631c to...”
- Comparative genomic analysis of Mycobacterium avium subspecies obtained from multiple host species
Paustian, BMC genomics 2008 - “...MAP-2 3 MAP0387 MAP0389 HOM, AV-SI LSPP3 MAP-3 4 MAP0746 MAP0766c AV-SI (6007, 6049) 5 MAP0850c MAP0866 HOM, AV-SI RDA I130 MAP_RD2 LSPP4 MAP-4 6 MAP0956 MAP0967 HOM LSPP5 MAP-5 7 MAP1230 MAP1237c HOM GS LSPP6 MAP-6 8 MAP1344 MAP1349c HOM, AV-SI LSPP7 MAP-7 9 MAP1376c...”
- Comparative genomic hybridizations reveal genetic regions within the Mycobacterium avium complex that are divergent from Mycobacterium avium subsp. paratuberculosis isolates
Paustian, Journal of bacteriology 2005 - “...MAP0338c MAP0388 MAP0428 MAP0589c MAP0664c MAP0832c MAP0850c MAP0851 MAP0856c MAP0859c MAP0866 MAP1048c MAP1287 MAP1432 MAP1723 MAP1822c MAP1824c MAP1946...”
- “...MAP_RD1 MAP_RD1 MAP0092 MAP0096c MAP0106c MAP0107 MAP0845 MAP0850c MAP0866 MAP0867c MAP2146c MAP2158 MAP2164 MAP2189 MAP2198 MAP2749c MAP2756c MAP2765c MAP2770...”
- The complete genome sequence of Mycobacterium avium subspecies paratuberculosis
Li, Proceedings of the National Academy of Sciences of the United States of America 2005 - “...regions. For example, MAP0028c and MAP0029c, MAP0849c and MAP0850c, and MAP2155, MAP2156, and MAP2157 are clustered within 5 kb of each other in noncoding...”
MAP0253 hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
83% identity, 13% coverage
MAP0664c hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
MAP2302 hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
83% identity, 13% 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