PaperBLAST
PaperBLAST Hits for TX73_004910 (83 a.a., MAEAATTDVK...)
Show query sequence
>TX73_004910
MAEAATTDVKKLSFERALEELETIVKRLEDGKVPLEESVTIYERGEALKRRCEDLLRQAE
ARVDKITTDAQGAPTGTEPLDVQ
Running BLASTp...
Found 30 similar proteins in the literature:
SMc00970 PUTATIVE EXODEOXYRIBONUCLEASE PROTEIN from Sinorhizobium meliloti 1021
57% identity, 100% coverage
CC2070 exodeoxyribonuclease small subunit from Caulobacter crescentus CB15
48% identity, 94% coverage
YPO3175 exodeoxyribonuclease VII small subunit from Yersinia pestis CO92
YPTB0941 exonuclease VII, small subunit from Yersinia pseudotuberculosis IP 32953
46% identity, 85% coverage
Q8Y7C3 Exodeoxyribonuclease 7 small subunit from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
lmo1362 similar to exodeoxyribonuclease small subunit from Listeria monocytogenes EGD-e
49% identity, 73% coverage
B5Y0W9 Exodeoxyribonuclease 7 small subunit from Klebsiella pneumoniae (strain 342)
49% identity, 76% coverage
Cp258_0745 exodeoxyribonuclease VII small subunit from Corynebacterium pseudotuberculosis 258
48% identity, 65% coverage
YajE / b0422 exodeoxyribonuclease VII subunit XseB (EC 3.1.11.6) from Escherichia coli K-12 substr. MG1655 (see 2 papers)
xseB / P0A8G9 exodeoxyribonuclease VII subunit XseB (EC 3.1.11.6) from Escherichia coli (strain K12) (see paper)
EX7S_ECOLI / P0A8G9 Exodeoxyribonuclease 7 small subunit; Exodeoxyribonuclease VII small subunit; ExoVII small subunit; Exonuclease VII small subunit; EC 3.1.11.6 from Escherichia coli (strain K12) (see 4 papers)
P0A8G9 exodeoxyribonuclease VII (subunit 1/2) (EC 3.1.11.6) from Escherichia coli (see 2 papers)
b0422 exodeoxyribonuclease VII small subunit from Escherichia coli str. K-12 substr. MG1655
51% identity, 73% coverage
- function: Bidirectionally degrades single-stranded DNA into large acid- insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides. It can degrade 3' or 5' ss regions extending from the termini of duplex DNA molecules and displaced ss regions. It can also excise thymine dimers in vitro (Probable) (PubMed:22718974, PubMed:4602029, PubMed:4602030). Required for production of the mature 5'-end of retron Ec78 or Ec83 msDNA. When in excess of the large subunit, counteracts the large subunit's toxicity (PubMed:26626352).
catalytic activity: Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'- direction to yield nucleoside 5'-phosphates.
cofactor: (Does not require a metal cofactor.)
subunit: Heterooligomer composed of two different subunits with an approximate ratio of 4:1 for small to large subunit (Probable). Also estimated to have a 6:1 ration for small to large subunits (Probable).
disruption phenotype: No longer processes msDNA correctly (when retron Ec78 or Ec83 are expressed in the strain). - Identification and mapping of self-assembling protein domains encoded by the Escherichia coli K-12 genome by use of lambda repressor fusions
Mariño-Ramírez, Journal of bacteriology 2004 - “...b2879 b1372 b0727 b2744 b0368 b3991 b1323 b4196 b4324 b0422 b0208 b0268 b0357 b0407 b0413 b0447 b0492 b0559 b0597 b0577 b0660 b0736 b0742 COG1519 COG2186...”
- Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
Sabina, Journal of bacteriology 2003 - “...b0355 b3767 b1433 b0922 b2567 b0284 b0002 b3867 b1326 b1762 b2115 b0422 b0353 b1513 7.6 6.2 6.1 5.9 4.5 4.3 4.3 3.8 3.6 3.4 3.4 3.1 3.0 2.9 2.9 2.8 2.8 2.8...”
- Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
Smulski, Journal of bacteriology 2001 - “...b0738 b0998 b3519 b1421 b1610 b3453 b1183 b3495 b1521 b0422 b4031 b2605 b3073 b3103 b3877 b0058 b0105 b0119 b0163 b0233 b0286 b0288 Fold induction 2.1 4.7 4.3...”
- Past, Present, and Future of Genome Modification in Escherichia coli
Mori, Microorganisms 2022 - “...2,629,510 EG11072 P04994 exodeoxyribonuclease VII subunit XseA nuclease ECK0416 xseB yajE 437,106 437,348 C EG11098 P0A8G9 exodeoxyribonuclease VII subunit XseB nuclease ECK1747 xthA xth 1,827,234 1,828,040 EG11073 P09030 exodeoxyribonuclease III nuclease ECK0535 ybcK 564,907 566,433 G6300 P77698 Predicted recombinase YbcK recombinase DLP12 prophage ECK2639 yfjX 2,769,827...”
- Knowns and Unknowns of Vitamin B6 Metabolism in Escherichia coli
Tramonti, EcoSal Plus 2021 (secret)
BH2782 exodeoxyribonuclease VII (small subunit) from Bacillus halodurans C-125
44% identity, 66% coverage
Q836W5 Exodeoxyribonuclease 7 small subunit from Enterococcus faecalis (strain ATCC 700802 / V583)
45% identity, 72% coverage
RT0339 exodeoxyribonuclease VII small subunit from Rickettsia typhi str. wilmington
48% identity, 67% coverage
C289_1857, F510_2204 exodeoxyribonuclease VII small subunit from Anoxybacillus gonensis
40% identity, 87% coverage
- Analysis of anoxybacillus genomes from the aspects of lifestyle adaptations, prophage diversity, and carbohydrate metabolism
Goh, PloS one 2014 - “...repair proteins MutS and MutL (C289_11321133, F510_26602661), DNA helicases (C289_1757, C289_1228, F510_0226, F510_1755), exonuclease VII (C289_1857, F510_2204), ssDNA-specific exonuclease (C289_0349, F510_1276), ssDNA DNA-binding protein (C289_0909, F510_0599), DNA polymerase III holoenzyme (C289_0194, C289_0649, C289_0926, C289_2575, C289_1717, C289_2686, F510_1083, F510_0179, F510_0616, F510_0200, F510_2324, F510_0296), and NAD-dependent DNA ligase...”
- “...proteins MutS and MutL (C289_11321133, F510_26602661), DNA helicases (C289_1757, C289_1228, F510_0226, F510_1755), exonuclease VII (C289_1857, F510_2204), ssDNA-specific exonuclease (C289_0349, F510_1276), ssDNA DNA-binding protein (C289_0909, F510_0599), DNA polymerase III holoenzyme (C289_0194, C289_0649, C289_0926, C289_2575, C289_1717, C289_2686, F510_1083, F510_0179, F510_0616, F510_0200, F510_2324, F510_0296), and NAD-dependent DNA ligase LigA...”
H375_2600 exodeoxyribonuclease VII small subunit from Rickettsia prowazekii str. Breinl
48% identity, 67% coverage
LIMLP_07750 exodeoxyribonuclease VII small subunit from Leptospira interrogans serovar Manilae
47% identity, 62% coverage
PA4042 exodeoxyribonuclease VII small subunit from Pseudomonas aeruginosa PAO1
50% identity, 65% coverage
- Pseudomonas aeruginosa heteroresistance to levofloxacin caused by upregulated expression of essential genes for DNA replication and repair
Li, Frontiers in microbiology 2022 - “...(qRT-PCR) verification, including 7 DEGs in the PAS71 strain [ recA (PA3617), uvrD (PA5443), xseB (PA4042), ssb (PA4232), mutM (PA0357), crc (PA5332), and rhlA (PA3479)] and 7 DEGs in the PAS81 strain [ recA (PA3617), gspD (PA0685), vgrG1 (PA0091), hcpC (PA0263), clpV1 (PA0090), ppkA (PA0074), and...”
- “...DNA primase DnaG ( dnaG , PA0577), exonucleases ExoVII ( xseA , PA3777; xseB , PA4042) and single-stranded-DNA-specific exonuclease RecJ ( recJ , PA3725), bifunctional glycosylase Fpg ( mutM , PA0357), monofunctional glycosylase MPG (PA4010), and AP-endonuclease Xth ( crc , PA5332) of the PAS71 strain...”
- The methylation-independent mismatch repair machinery in Pseudomonas aeruginosa
On, Microbiology (Reading, England) 2021 - “...and XseB, PA does not possess the larger XseA subunit, and its smaller XseB subunit (PA4042) is only 50% identical to the E. coli orthologue. Furthermore, in PA, the xseB gene is operonic with a geranyltransferase encoded by ispA , and does not likely function as...”
- The Small RNAs PA2952.1 and PrrH as Regulators of Virulence, Motility, and Iron Metabolism in Pseudomonas aeruginosa
Coleman, Applied and environmental microbiology 2021 (secret) - A switch in the poly(dC)/RmlB complex regulates bacterial persister formation
Chen, Nature communications 2019 - “...which has been annotated as a putative exonuclease VII small subunit XseB (8.8kDa; locus tag, PA4042) (Supplementary Table 4 ). In the following tests, His-tagged XseB failed to degrade Cy5-labeled double-stranded DNA, but did exhibit single strand-specific 53 cleavage activity, which resulted in the rapid disappearance...”
PP0529 exodeoxyribonuclease VII, small subunit from Pseudomonas putida KT2440
48% identity, 63% coverage
BPUM_2161 exodeoxyribonuclease VII small subunit from Bacillus pumilus SAFR-032
33% identity, 94% coverage
SAOUHSC_01619 exodeoxyribonuclease VII, small subunit from Staphylococcus aureus subsp. aureus NCTC 8325
43% identity, 65% coverage
TM1769 exodeoxyribonuclease, small subunit from Thermotoga maritima MSB8
39% identity, 67% coverage
- Delineation of structural domains and identification of functionally important residues in DNA repair enzyme exonuclease VII
Poleszak, Nucleic acids research 2012 - “.... ( 19 ) characterized experimentally the XseA/B homologs from Thermatoga maritima , TM1768 and TM1769. They predicted that the large subunit of ExoVII is composed of two domains: the N-terminal OB-fold domain and a C-terminal domain termed ExoVII_Large. Here, we present a structural model for...”
- Identification of two conserved aspartic acid residues required for DNA digestion by a novel thermophilic Exonuclease VII in Thermotoga maritima
Larrea, Nucleic acids research 2008 - “...have characterized an ExoVII homolog from Thermotoga maritima . Thermotoga maritima XseA/B homologs TM1768 and TM1769 were co-expressed and purified, and show robust nuclease activity at 80C. This activity is magnesium dependent and is inhibited by phosphate ions, which distinguish it from E. coli ExoVII. Nevertheless,...”
- “...Briefly, our results show that T. maritima ExoVII is composed of two subunits (TM1768 and TM1769), is a linear ssDNA-specific nuclease releasing oligonucleotide products, and is processive just like its E. coli counterpart. Surprisingly, the T. maritima ExoVII requires Mg 2+ and is strongly inhibited in...”
IV454_13465 exodeoxyribonuclease VII small subunit from Massilia antarctica
42% identity, 66% coverage
BC4178 Exodeoxyribonuclease VII small subunit from Bacillus cereus ATCC 14579
39% identity, 65% coverage
Bd0198 exodeoxyribonuclease VII, small subunit from Bdellovibrio bacteriovorus HD100
38% identity, 81% coverage
Krad_1121 exodeoxyribonuclease VII small subunit from Kineococcus radiotolerans SRS30216 = ATCC BAA-149
51% identity, 54% coverage
Rv1107c exodeoxyribonuclease VII small subunit from Mycobacterium tuberculosis H37Rv
40% identity, 73% coverage
Bmul_4822 exodeoxyribonuclease VII small subunit from Burkholderia multivorans ATCC 17616
45% identity, 55% coverage
EX7S_HAEIN / P43914 Exodeoxyribonuclease 7 small subunit; Exodeoxyribonuclease VII small subunit; Exonuclease VII small subunit; EC 3.1.11.6 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (see paper)
39% identity, 73% coverage
- function: Bidirectionally degrades single-stranded DNA into large acid- insoluble oligonucleotides, which are then degraded further into small acid-soluble oligonucleotides.
catalytic activity: Exonucleolytic cleavage in either 5'- to 3'- or 3'- to 5'- direction to yield nucleoside 5'-phosphates.
subunit: Heterooligomer composed of large and small subunits.
disruption phenotype: Essential, neither gene for this protein can be deleted (PubMed:18242643).
spr1088 Exodeoxyribonuclease small subunit from Streptococcus pneumoniae R6
39% identity, 69% coverage
P58001 Exodeoxyribonuclease 7 small subunit from Chlamydia trachomatis serovar D (strain ATCC VR-885 / DSM 19411 / UW-3/Cx)
35% identity, 72% coverage
LHK_02322 Ex7S from Laribacter hongkongensis HLHK9
35% identity, 83% coverage
SAK_0598 exodeoxyribonuclease VII, small subunit from Streptococcus agalactiae A909
39% identity, 67% coverage
NMB0262 exodeoxyribonuclease, small subunit from Neisseria meningitidis MC58
36% identity, 70% 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