PaperBLAST
PaperBLAST Hits for WP_005916853.1 YdiY family protein (Xanthomonas citri pv. aurantifolii str. ICPB 11122) (266 a.a., MSRRVPLPAL...)
Show query sequence
>WP_005916853.1 YdiY family protein (Xanthomonas citri pv. aurantifolii str. ICPB 11122)
MSRRVPLPALLPLLLITPSVWAQAVAPAPADPAAVVLPSPWSGSSGELGYAAAHGNSTTD
SLNGRVRLRYTDGDWIHSLDATALRSSSEYTNTNDDGSTTRERQTTAERYTGSVGSALQL
GEHRQLTATGRYEHDDFATYDRLATFGIGYGTRLIDADRFYLDAQVGPGVRRAHNSDEDR
NETGLIGRGLFDLKYTVTDNTDLINTLLVESGEYNTYAQNDFGVQVSMNSHFALKAAWQM
RHNSDVSDGDKKTDTLTTVNLVYTFK
Running BLASTp...
Found 11 similar proteins in the literature:
XAUB_17400 YdiY family protein from Xanthomonas citri pv. aurantifolii str. ICPB 11122
XAC0623 conserved hypothetical protein from Xanthomonas axonopodis pv. citri str. 306
100% identity, 100% coverage
- Periplasm-enriched fractions from Xanthomonas citri subsp. citri type A and X. fuscans subsp. aurantifolii type B present distinct proteomic profiles under in vitro pathogenicity induction
Zandonadi, PloS one 2020 - “...50S ribosomal protein L25 (6) 23.3 5.2 25.7 5.3 500 12 41 III (XAC0951) C XAUB_17400 Conserved hypothetical protein (11) 29.1 5.2 25 2 5 VIII (XAC0623) OM+ 18 XauB 2,67E-01 Unique 0,0126284 XAUB_17400 Conserved hypothetical protein (11) 29.1 5.2 30.1 4.7 505 23 42 VIII...”
- Periplasm-enriched fractions from Xanthomonas citri subsp. citri type A and X. fuscans subsp. aurantifolii type B present distinct proteomic profiles under in vitro pathogenicity induction
Zandonadi, PloS one 2020 - “...41 III (XAC0951) C XAUB_17400 Conserved hypothetical protein (11) 29.1 5.2 25 2 5 VIII (XAC0623) OM+ 18 XauB 2,67E-01 Unique 0,0126284 XAUB_17400 Conserved hypothetical protein (11) 29.1 5.2 30.1 4.7 505 23 42 VIII (XAC0623) OM+ 19 XauB 1,43E-01 Unique 0,0212073 XAUB_08010 ATP synthase subunit...”
- Proteomics-based identification of differentially abundant proteins reveals adaptation mechanisms of Xanthomonas citri subsp. citri during Citrus sinensis infection
Moreira, BMC microbiology 2017 - “...8.09 A/B/LPS 40 XAC3966 Outer membrane lipoprotein SlyB slyB Up 2.45 3.17 4.10 A/B/LPS 42 XAC0623 Putative salt-induced outer membrane protein YdiY ydiY Up 6.83 8.70 1.38 A/B/LPS 43 XAC0190 Uncharacterized lipoprotein ---- Up 2.21 1.30 4.24 A/B/LPS 44 XAC0834 Two-component system regulatory protein colR Up...”
- “...up-regulated during the infectious process. XAC3966 and XAC0190 encode membrane lipoproteins with similar expression profiles. XAC0623 is a salt-induced putative outer membrane protein (YdiY) with expression peak at 1DAI (6,83) while XAC4219 corresponds to a protein with a lipid-binding SYLF domain. The last and most interesting...”
XCC3510 conserved hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913
XC_0650 hypothetical protein from Xanthomonas campestris pv. campestris str. 8004
94% identity, 100% coverage
- A MLVA genotyping scheme for global surveillance of the citrus pathogen Xanthomonas citri pv. citri suggests a worldwide geographical expansion of a single genetic lineage
Pruvost, PloS one 2014 - “...+ hypothetical protein 5 VIC-TGATCGAAGCACCGAGCAGT 3 5 GCAACCGGGCAGACCGTTGT 3 66.0 0.2 8 23 2 (0.116) Xcc3510 24 + aminopeptidase N 5 NED-ACCGCTCTACCGAATACGTCA 3 5 ATCGGCATTGTCCATCAACGTC 3 66.0 0.2 8 13 3 (0.031) Xcc3522 10 NA 5 NED-CCCAGCCACCGAACAGATCCG 3 5 AAATCCCTATCGCGCCCAGGT 3 64.0 0.2 1 25 3...”
- “...from 0.015 to 0.843 ( Table 1 ). Nine TR loci (Xcc1014, Xcc1662, Xcc2229, Xcc3088, Xcc3510, Xcc4071, Xcc4279, Xcc4927 and Xcc4946) had very low levels of polymorphism and differentiated a single isolate or haplotype ( Table 1 ). Strains sharing an identical MLVA-31 allelic profile always...”
- Identification of c-di-GMP Signaling Components in Xanthomonas oryzae and Their Orthologs in Xanthomonads Involved in Regulation of Bacterial Virulence Expression
Yang, Frontiers in microbiology 2019 - “...DNA replication. Among them, the elongation factor P (XC_2359) and a putative outer membrane protein (XC_0650), both widely conserved in bacteria, were characterized as the novel virulence factors regulated by the RpfC/RpfG/RpfF system at post-transcriptional but not transcriptional level (O'Connell et al., 2013 ). RpfG was...”
XF1628 hypothetical protein from Xylella fastidiosa 9a5c
65% identity, 94% coverage
VF_0300 putative salt-induced outer membrane protein from Vibrio fischeri ES114
VF_0300 YdiY family protein from Aliivibrio fischeri ES114
24% identity, 68% coverage
VIBR0546_03992 DUF481 domain-containing protein from Vibrio brasiliensis LMG 20546
25% identity, 87% coverage
- Effects of NaCl Concentration on the Behavior of Vibrio brasiliensis and Transcriptome Analysis
Hu, Foods (Basel, Switzerland) 2022 - “...1.527 2.87 10 5 up ompR osmolarity response regulator 2.471 1.305 9.71 10 5 up VIBR0546_03992 putative salt-induced outer membrane protein 2.567 1.360 4.52 10 4 up VIBR0546_17778 OmpR family two-component response regulator 2.039 1.028 9.87 10 3 up VIBR0546_02830 choline/carnitine/betaine transporter 0.079 3.660 3.18 10...”
- “...7 up VIBR0546_21600 putative sodium-type flagellar protein MotY precursor 6.971 2.801 5.54 10 6 up VIBR0546_03992 putative salt-induced outer membrane protein 2.468 1.304 3.57 10 5 up VIBR0546_06697 sodium/glutamate symporter 2.705 1.435 1.36 10 4 up VIBR0546_12742 sodium/alanine symporter 2.326 1.218 2.10 10 4 up VIBR0546_12482...”
t1207 putative outer membrane protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
25% identity, 97% coverage
- Prevalence and Diversity of Staphylococcus aureus and Staphylococcal Enterotoxins in Raw Milk From Northern Portugal
Oliveira, Frontiers in microbiology 2022 - “...CI: 0.07.6%) distinct isolates, while t002, t108, t117, t127, t189, t208, t267, t843, t899, t1200, t1207, t1334, t2383, t3585, t9216, and t19272, were associated to one (1.6%, 95% CI: 0.04.7%) S. aureus isolate ( Figure 2 ). FIGURE 2 Minimum spanning tree of the spa typing...”
- “...t011 and one t2383. S. aureus t1403, t2802, t571, t108, t189. t208, t267, t843, t1200, t1207, t1334, and t19272 were exclusively associated with strains that did not contain any of the virulence/resistance genes evaluated. In total, S. aureus t1403-none (16.1%, 95% CI: 7.025.3%) is the predominant...”
c2120 YdiY family protein from Escherichia coli CFT073
25% identity, 88% coverage
STM1327 putative salt-induced outer membrane protein from Salmonella typhimurium LT2
24% identity, 97% coverage
YdiY / b1722 acid-inducible putative outer membrane protein YdiY from Escherichia coli K-12 substr. MG1655 (see 4 papers)
TC 1.B.75.1.3 / P76206 YdiY OMP of 252 aas from Escherichia coli (strain K12)
b1722 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
25% identity, 88% coverage
- substrates: small molecules
tcdb comment: Acid induces its synthesis (Stancik et al. 2002) - Whole-Transcriptome Analysis of Verocytotoxigenic Escherichia coli O157:H7 (Sakai) Suggests Plant-Species-Specific Metabolic Responses on Exposure to Spinach and Lettuce Extracts
Crozier, Frontiers in microbiology 2016 - “...for high levels of differential expression: e.g., in spinach leaf lysates two hypothetical genes (b3238, b1722) were ranked as #2 and 3 for level of induction, at 50-fold. Probes corresponding to Z5022 and ECs4474 were induced 270- to 300-fold in spinach root exudates, but repressed in...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Gene expression analysis indicates extensive genotype-specific crosstalk between the conjugative F-plasmid and the E. coli chromosome
Harr, BMC microbiology 2006 - “...(MG1655)* F vs nonF (DH5)* MG1655 vs. DH5 # P (F-effect) P (strain-effect) Function Process b1722 3.03 2.36 -2.03 0.005 0.012 Conserved-Hypothetical-ORF flhD 2.34 2.61 -5.22 0.002 0.0002 regulator of flagellar biosynthesis, transcriptional initiation factor Motility, chemotaxis, energytaxis (i.e. aerotaxis, redoxtaxis) leuQ 2.78 2.19 3.50 0.050...”
- DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
Polen, Applied and environmental microbiology 2003 - “...or block biosynthesis 0.38* 0.53* 0.57* 0.66* 0.82* 0.60 b1722 b1722 1 ORF, hypothetical protein 2.32* 2.21 0.89 b1729 b1729 2 Part of a kinase 0.96 2.28*...”
- Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli
Reitzer, Microbiology and molecular biology reviews : MMBR 2001 - “...caiF, xseB-ispA-dxs, hcaA1, xdhABC (b2866-2868), ndh, pgpB, b1722, tolC, galETKM, ymcC, degQ, yheB, b0540, aer, glyQS, cadCBA, b2374, arsR, mviN, yieP,...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...P76177 P0AC69 P77552 P0ACX3 P0A8A4 P77748 P76206 P0ACY1 P39173 P76256 5.38/59,928.8 5.07/54,689 9.1/31,910.83 4.75/12,878.76 4.96/9,928 (4.5-5.5) 4.42/42,876.01...”
Z2751 orf, hypothetical protein from Escherichia coli O157:H7 EDL933
25% identity, 88% coverage
ZMO1563 hypothetical protein from Zymomonas mobilis subsp. mobilis ZM4
24% identity, 69% coverage
- Systems-Level Analysis of Oxygen Exposure in Zymomonas mobilis: Implications for Isoprenoid Production
Martien, mSystems 2019 - “...location in the genome, many are still completely uncharacterized. In particular, ZMO0122, ZMO0286, ZMO0994, ZMO1007, ZMO1563, ZMO1603, and ZMO1750 displayed trends in mRNA and protein levels that strongly suggest that they are involved in the response to oxygen, and yet they have no functional annotation (...”
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