PaperBLAST
PaperBLAST Hits for A4249_RS16280 (73 a.a., MDSQPTRPSG...)
Show query sequence
>A4249_RS16280
MDSQPTRPSGVSKRGFASMDPERQREIARKGGASVPSEKRSFSQDRSLAAQAGRKGGEAS
HGTKKDADAADGQ
Running BLASTp...
Found 11 similar proteins in the literature:
CC1178, CC_1178 conserved hypothetical protein from Caulobacter crescentus CB15
70% identity, 83% coverage
J7QHI8 Stress-induced protein from Methylocystis sp. (strain SC2)
BN69_2205 general stress protein from Methylocystis sp. SC2
70% identity, 59% coverage
alr1718 hypothetical protein from Nostoc sp. PCC 7120
46% identity, 44% coverage
- Cell surface-associated proteins in the filamentous cyanobacterium Anabaena sp. strain PCC 7120
Yoshimura, Microbes and environments 2012 - “...two positions between Met-23 and Thr-24 or between Thr-24 and Asn-25. Asr1134-, Asr4653-, Asr4319-, Asr3935-, Alr1718-, All0615-, All4201-, All4377- and All4782-derived proteins without signal peptides could be secreted by nonspecific and/or currently unknown translocation pathways ( 1 ). Earlier studies have shown that both Sec and...”
- “...gene expressions of asr1134 , asr4653 , alr0198 , alr0600 , alr0896 , all0459 , alr1718 , all4782 and alr0806 are upregulated under drought stress ( 12 ). The gene expression of all0459 , as part of the gene cluster from all0457 to all0459 , is...”
XCC2823 conserved hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913
47% identity, 71% coverage
P10713 Conidiation-specific protein 10 from Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
NCU07325 conidiation-specific protein con-10 from Neurospora crassa OR74A
57% identity, 63% coverage
- Data on occurrence of miRNA precursors in the Cucurbita maxima phloem sap.
Tolstyko, Data in brief 2020 - “...116 5.E24 364 26.74 236 64.84 cme-MIR390b P38121 135 3.E21 362 18.86 132 36.46 cme-MIR393a P10713 113 8.E28 1292 102.9 2777 214.94 cme-MIR396b P29987 149 5.E32 513 22.81 235 45.81 cme-MIR530b P55325 109 4.E24 223 1.64 6 2.69 cme-MIR854 P7676 106 6.E32 1528 108.11 3640 238.22...”
- Identification of miRNA precursors in the phloem of Cucurbita maxima.
Tolstyko, PeerJ 2019 - “...highly covered by reads in three phloem contigs with highest AC values (P21134, P19669 and P10713) and one such leaf contig (L16156) ( Fig. 2 ), whereas in leaf contigs L5508 and L11031 peaks of reading depth were located away from pre-miRNA regions, which had a...”
- “...135 3E21 No match P38121 362 18.9 49 miR393a 113 9E28 L11031 1,718 80.8 5 P10713 1,292 102.9 1,042 miR396b1 149 5E32 L19994 1,055 16.8 50 P29987 513 22.8 61 miR396b2 150 2E18 L21853 939 14.7 66 No match Note: AC, average coverage; LC, local coverage....”
- RNAseq and targeted metabolomics implicate RIC8 in regulation of energy homeostasis, amino acid compartmentation, and asexual development in <i>Neurospora crassa</i>
Quinn, mBio 2024 - “...1.9 1.9 NCU03043 flb-3 1.3 3.7 2.7 Conidiation-regulated genes NCU08769 con-6 NE b 1584.4 7585.2 NCU07325 con-10 NE 347.2 1912.6 NCU07324 con-13 76.7 7344.5 3258.8 a Positive numbers indicate increased expression in the mutant, while negative numbers indicate decreased expression. Boldface font indicates fold change regulation...”
- Adaptation to glucose starvation is associated with molecular reorganization of the circadian clock in Neurospora crassa
Szőke, eLife 2023 - “...choline dehydrogenase (NCU01853); fl : conidial development protein fluffy (NCU08726); con-10 : conidiation-specific protein 10 (NCU07325); ccg-2 : hydrophobin (NCU08457)) (n=4, SEM, Factorial ANOVA, significant treatment effect ( gdh-1 , ccg2 ), significant strain effect ( pect ) significant strain*treatment interaction ( aga-1 , gln-1 ,...”
- “...specific protein NCU05924 gh10-1 96 15 n.s . xylanase NCU00943 tre-1 77 102 n.s. trehalase NCU07325 con-10 70 13 n.s . conidiation specific protein NCU08189 gh10-2 67 13 n.s . xylanase NCU10055 nop-1 66 58 n.s . o psin NCU06905 thnr 65 n.s . 0.01 tetrahydroxynaphthalene...”
- A global search for novel transcription factors impacting the Neurospora crassa circadian clock
Muñoz-Guzmán, G3 (Bethesda, Md.) 2021 - “...different reporter in the selected TF KOs. For this, we utilized the output gene con-10 (NCU07325), which exhibits robust circadian expression ( Lauter and Yanofsky 1993 ; Hurley et al. 2014 ). con-10 is a vastly studied gene, expressed in late stages of conidial differentiation (...”
- The Zn(II)2Cys6-Type Transcription Factor ADA-6 Regulates Conidiation, Sexual Development, and Oxidative Stress Response in Neurospora crassa
Sun, Frontiers in microbiology 2019 - “...167.5816 19.71859 Genes preferentially expressed during conidiation NCU07324 Con-13 0.300536 2.568501 2.56481 0.480817 7.380787 57.28341 NCU07325 Con-10 10.91534 72.60819 263.9326 7.64009 77.11508 984.083 NCU08457 Eas 18.87683 270.4869 1248.747 82.90488 10027.32 17750.16 NCU08769 Con-6 3.702609 38.78643 69.66419 1.057798 72.8696 2500.538 NCU09235 Con-8 12.17338 203.7125 271.1714 26.04317 922.9603...”
- Light-regulated promoters for tunable, temporal, and affordable control of fungal gene expression
Fuller, Applied microbiology and biotechnology 2018 - “...- - - - NCU02190 oxysterol binding 157.6 X - - - AN2877 - AN3807 NCU07325 con-10 137.2 X - - - AN5015 - NCU07267 bli-3 111.4 X - - Ta_33514 - - NCU03967 vvd 97 X BC1G_04348 TR_81609 Ta_150699 - - BC1G_15404 NCU00582 Cryptochrome, cry...”
- Identification and characterization of the glucose dual-affinity transport system in Neurospora crassa: pleiotropic roles in nutrient transport, signaling, and carbon catabolite repression
Wang, Biotechnology for biofuels 2017 - “...the rodlet layer protein eas (NCU08457) [ 53 ], the conidiation-specific gene con - 10 (NCU07325) [ 54 ], the all development-altered regulator ada - 6 (NCU04866) [ 55 ], the Aspergillus flbC homolog NCU03184 [ 56 ], and the Aspergillus flbD ortholog rca - 1...”
- Identification and functional analysis of endogenous nitric oxide in a filamentous fungus
Pengkit, Scientific reports 2016 - “...Quantitative PCR analysis Expression of putative conidiation related genes (NCU08769, con-6 ; NCU09235, con-8 ; NCU07325, con-10 ; NCU07324, con-13 ; NCU08726, fluffy ; NCU08457, ccg-2 ; NCU09873, con-3 ; NCU00478, acon-2 ; NCU07617, acon-3 ) was analyzed during formation of aerial hypha and conidia. Fungal...”
- “...NCU08769 (con-6) reverse GP11F GGGCTTGATGGATCAAAA NCU09235 (con-8) forward GP11R ATCCCACATCTTGGCAAT NCU09235 (con-8) reverse GP12F AGGAAGAGGTTCAGGCCATC NCU07325 (con-10) forward GP12R GGCTCAAAGCTGCCGCTGGA NCU07325 (con-10) reverse GP13F AAGACTGGAAGGATACCGTT NCU07324 (con-13) forward GP13R GATTGACCATACAGCCGACA NCU07324 (con-13) reverse GP14F TCCAGCATCTCGTTGTCATC NCU08726 (fluffy) forward GP14R GGTGAAAAACGGGAGGAAAT NCU08726 (fluffy) reverse GP15F TTACTGCTGCCAGTCTATGT NCU08457...”
- Genome-wide characterization of light-regulated genes in Neurospora crassa
Wu, G3 (Bethesda, Md.) 2014 - “...that basal levels of WC-1 are sufficient to maintain photoresponses. The conidiation (con)-related genes con-10 (NCU07325) and con-6 (NCU08769) ( Berlin and Yanofsky 1985 ), originally identified by their induction during conidiation and previously shown to be light-responsive ( Corrochano et al. 1995 ; Lauter and...”
- “...2.4 NCU08626 phr photoreactivation-deficient 5.3 4.0 1.9 1.2 NCU00585 al-2 albino-2 5.2 5.3 3.9 2.5 NCU07325 con-10 conidiation-10 4.8 7.1 4.3 1.5 NCU11424 cao-2 carotenoid oxygenase-2 4.8 4.1 2.8 2.1 NCU07434 short-chain dehydrogenase/reductase SDR 4.6 3.8 1.5 1.7 NCU07267 bli-3 blue light-induced-3 4.6 6.8 4.6 2.4...”
- More
Npun_F4819 hypothetical protein from Nostoc punctiforme
43% identity, 56% coverage
- Transcriptomic analysis of cyanobacterial alkane overproduction reveals stress-related genes and inhibitors of lipid droplet formation
Arias, Microbial genomics 2020 - “...0.00134573 Npun_F3789 Protein of unknown function 8.11 5.00E05 0.00134573 Npun_F4818 Putative transporter 4.11 5.00E05 0.00134573 Npun_F4819 General stress response domain-containing protein 18.62 5.00E05 0.00134573 Npun_F5451 YcnF-like stress response PRC barrel domain-containing protein 9.48 5.00E05 0.00134573 Npun_F5452 YcnF-like stress response PRC barrel domain-containing protein 6.65 5.00E05 0.00134573...”
- “...to measure both Gene RT-qPCR RNA-seq Npun_F1653 3.430.61 6.87 Npun_F3794 8.230.71 16.93 Npun_F3795 9.040.80 12.81 Npun_F4819 7.991.02 18.62 Npun_R1332 21.443.24 63.53 Npun_F1545 1.760.38 2.34 Npun_F2189 6.861.37 10.56 Npun_F2191 6.911.29 6.54 Npun_F2818 2.420.50 2.24 Npun_F2819 2.420.50 2.65 Npun_R0971 6.591.28 5.80 Identification of regulated genes Upregulated genes in...”
ABZJ_01589 KGG domain-containing protein from Acinetobacter baumannii MDR-ZJ06
83% identity, 6% coverage
- Colistin Resistance in Acinetobacter baumannii MDR-ZJ06 Revealed by a Multiomics Approach
Hua, Frontiers in cellular and infection microbiology 2017 - “...9.13E-08 489 384143515 ABZJ_02269 (3R)-hydroxymyristoyl-ACP dehydratase 39 7 50.93 17988.69 6.3 0.97767 4.53E-08 459 384142835 ABZJ_01589 hypothetical protein 18 8 13.33 43721.35 4.96 0.97866 4.39E-08 833 384143336 ABZJ_02090 hypothetical protein 7 4 37.91 17951.03 4.82 1.00115 2.16E-08 586 384143810 ABZJ_02564 hypothetical protein 16 6 79.22 8718.62...”
ABUW_2433 KGG domain-containing protein from Acinetobacter baumannii
83% identity, 6% coverage
ACX60_11190, ACX60_RS20025, KZA74_11470 KGG domain-containing protein from Acinetobacter baumannii
83% identity, 6% coverage
HTZ92_1883 KGG domain-containing protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
83% identity, 6% coverage
- The VBNC state: a fundamental survival strategy of Acinetobacter baumannii
König, mBio 2023 - “...processes and cell protection. Among the stress resistance-related genes, a recently recognized intrinsically disordered protein (HTZ92_1883) stood out. This protein was described to be essential for desiccation resistance in A. baumannii AB5075 and named DtpA for its desiccation tolerance-promoting property ( 19 , 20 ). The...”
- “...various efflux pumps, DNA damage repair, and protection genes that were highly upregulated, but also HTZ92_1883 which is annotated as stress-induced protein. This gene was recently identified to be an intrinsically disordered protein (IDP) ( 19 , 20 ) and characterized to be essential for desiccation...”
ACICU_01429 hypothetical protein from Acinetobacter baumannii ACICU
83% identity, 7% coverage
- Transition of colistin dependence into colistin resistance in Acinetobacter baumannii
Lee, Scientific reports 2017 - “...c 7499.909 348.235 19525.670 625.399 21.537 31.221 ACICU_01427 Dehydrogenase 1272.509 25.529 3654.288 42.142 49.845 86.714 ACICU_01429 Hypothetical protein 1522.708 58.514 23480.619 66.453 26.023 353.342 ACICU_02269 Hypothetical protein 304.781 21.541 642.656 37.335 14.149 17.213 ACICU_02276 Hypothetical protein 210.887 8.398 689.267 7.406 25.112 93.063 ACICU_02382 Hypothetical protein 335.294...”
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