PaperBLAST
PaperBLAST Hits for XP_001391544.1 uncharacterized protein (Aspergillus niger) (244 a.a., MRSFSDSISR...)
Show query sequence
>XP_001391544.1 uncharacterized protein (Aspergillus niger)
MRSFSDSISRWTAALTLLWLGLVNAHTVITYPGYRGNNLHTNGTVEETNGLGVAWKNGSY
VYPYGMQWIYPCGGMATSRNRTKWPVTGGAVAVQPGWFRGHETAFVYINIGWGTIPPNMS
NPMLSVFEIEGPTNNPYPGTICMPQVPLPANMSVSPGDNATIQVVLAAKHGAALYDCVDI
TFAEPEDVEEVTKDNCFNSTDIAFKYVFASKSLTTSGALARLSSPGLTAAVPVLVMVVFG
LFMM
Running BLASTp...
Found 21 similar proteins in the literature:
An07g04620 uncharacterized protein from Aspergillus niger
100% identity, 100% coverage
AFUA_5G08800, Afu5g08800 conserved hypothetical protein from Aspergillus fumigatus Af293
65% identity, 98% coverage
- A possible role for fumagillin in cellular damage during host infection by Aspergillus fumigatus
Guruceaga, Virulence 2018 - “...NosA Afu4g09710 rosA 3.87 6.59 C6 transcription factor Afu5g00950 3.71 1.26 4.09 0.72 Hypothetical protein Afu5g08800 3.99 4.82 Pectin lyase Afu5g10170 3.79 4.50 Pectin lyase Afu5g10380 3.57 3.31 C6 transcription factor Afu5g14290 4.36 1.16 Aldehyde dehydrogenase Afu7g01000 4.11 7.86 Indoleamine 2.3-dioxygenase Afu7g02010 4.19 5.94 5.72 8.21...”
- Investigation of Aspergillus fumigatus biofilm formation by various "omics" approaches
Muszkieta, Frontiers in microbiology 2013 - “...5.6 2.49 238.51 7.90 AFUA_8G00900 Cell surface antigen spherulin 4, putative 7.31 2.87 212.52 7.73 AFUA_5G08800 Hypothetical protein 8.32 3.06 155.28 7.28 AFUA_3G01500 Hypothetical protein 4.89 2.29 117.44 6.88 AFUA_5G13250 DUF614 domain protein 9.8 3.29 98.50 6.62 AFUA_1G14560 Alpha-mannosidase 3.99 2.00 84.72 6.40 AFUA_1G00990 Short chain...”
- Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model
Do, BMC genomics 2009 - “...corresponding grey and green nodes (hub nodes) : 1062 (AFU3G14590), 1172 (AFU4G08340), 1553 (AFU5G08750), 1554 (AFU5G08800), 1806 (AFU6G06430), 1289 (AFU4G12010), 1931 (AFU6G10610), 1933 (AFU6G10650), 1934 (AFU6G10660), 2038 (AFU7G00170), 2036 (AFU7G00120), 2039 (AFU7G00200), 2050 (AFU7G01000), 2077 (AFU7G01920), 2078 (AFU7G01930), 2311 (AFU8G06340), 2312 (AFU8G06350). (A) network of 37C,...”
X325_EMENI / Q5B428 Lytic polysaccharide monooxygenase-like protein ANIA_04702; LPMO-like protein ANIA_04702; X325 family protein ANIA_04702 from Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (Aspergillus nidulans) (see paper)
63% identity, 98% coverage
- function: Lytic polysaccharide monooxygenase-like protein that has diverged to biological functions other than polysaccharide degradation since it does not perform oxidative cleavage of polysaccharides (PubMed:37452022). Acts as a cell surface-bound protein that functions in the copper-accumulation pathway (By similarity). May also act as the major cell wall sensor that regulates MAP kinase-dependent hyphal anastomosis, the fusion of hyphal cells (By similarity).
cofactor: Cu(2+) (Binds 1 copper ion per subunit.)
PADG_07354 uncharacterized protein from Paracoccidioides brasiliensis Pb18
52% identity, 95% coverage
- Identification and immunogenic potential of glycosylphosphatidylinositol-anchored proteins in Paracoccidioides brasiliensis
Gonçales, Frontiers in fungal biology 2023 - “...a group of GPI-proteins of unknown function, including PADG_03914, PADG_02867, PADG_04289, PADG_05482, PADG_07620, PADG_04649, PADG_08385, PADG_07354, PADG_06677, PADG_02955, PADG_06557, and PADG_00497, showed elevated expression in mycelia, indicating their potential roles in regulating the mycelial phase of P. brasiliensis ( Figure1 ). Figure1 Quantitative transcriptional expression of...”
FVEG_13122 hypothetical protein from Fusarium verticillioides 7600
51% identity, 95% coverage
- Careful with That Axe, Gene, Genome Perturbation after a PEG-Mediated Protoplast Transformation in Fusarium verticillioides
Scala, Toxins 2017 - “...the genes affected by genomic variations, we analyzed the relative expression of FVEG_03821, FVEG_03822, FVEG_13121, FVEG_13122, FVEG_13123, FVEG_07317 and FVEG_07318 ( Figure 5 ). Results indicated a profound alteration of gene expression in Fv_ lds1 D and Fv_ lds1 T strains at two and seven days...”
- “...lds1 D, DIP4 negatively affected the expression of FVEG_13121 with respect to the WT, whereas FVEG_13122 and FVEG_13123 are more expressed with respect to the WT. In Fv_ lds1 T, FVEG_13121 is down-modulated in comparison to the WT strain; the expression of the FVEG_13122 is similar...”
- A Natural Mutation Involving both Pathogenicity and Perithecium Formation in the Fusarium graminearum Species Complex
Suga, G3 (Bethesda, Md.) 2016 - “...F. avenaceum FAVG1_10471, F. oxysporum FOXB_02761, F. oxysporum f. sp. cubense race4 FOC4_g10001017, F. verticillioides FVEG_13122, F. fujikuroi FFUJ_05566, and Nectria hematococca mpVI NECHADRAFT_92223 (E value: 2e 165 to 2e 116 ), although the function of these proteins has not been determined. FGSG_02810 also has homology...”
FFUJ_05566 uncharacterized protein from Fusarium fujikuroi IMI 58289
53% identity, 93% coverage
FGSG_02810 hypothetical protein from Fusarium graminearum PH-1
55% identity, 91% coverage
- A Natural Mutation Involving both Pathogenicity and Perithecium Formation in the Fusarium graminearum Species Complex
Suga, G3 (Bethesda, Md.) 2016 - “...was detected in the mapped region of the mutant strain. The wild-type strain contains the FGSG_02810 gene, encoding a putative glycosylphosphatidylinositol anchor protein, in this region. The contribution of FGSG_02810 to pathogenicity and perithecium formation was confirmed by complementation in the mutant strain using gene transfer,...”
- “...and Fa0444002 (HQ599309) have been deposited in GenBank. Construction of the transformation vector The FGSG_02809, FGSG_02810, and FGSG_02811 genes, including regions upstream and downstream of the open reading frame, were amplified from Fg0407011 by PCR using the HS458/HS459, HS450/HS451, and HS442/HS443 primer pairs, respectively ( Table...”
FPSE_05581 hypothetical protein from Fusarium pseudograminearum CS3096
55% identity, 91% coverage
XP_008598424 GPI anchored protein, putative from Beauveria bassiana ARSEF 2860
55% identity, 80% coverage
ISF_08023 hypothetical protein from Cordyceps fumosorosea ARSEF 2679
49% identity, 78% coverage
NECHADRAFT_92223 uncharacterized protein from Fusarium vanettenii 77-13-4
55% identity, 82% coverage
X325_NEUCR / V5IRP6 Lytic polysaccharide monooxygenase-like protein ham-7; LPMO-like protein ham-7; Hyphal anastamosis protein 7; X325 family protein ham-7 from Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (see 3 papers)
57% identity, 73% coverage
- function: Lytic polysaccharide monooxygenase-like protein that has diverged to biological functions other than polysaccharide degradation since it does not perform oxidative cleavage of polysaccharides (Probable). Acts as the major cell wall sensor that regulates MAK-1- dependent hyphal anastomosis, the fusion of hyphal cells (PubMed:21666072, PubMed:22879952, PubMed:25279949). May also act as a cell surface-bound protein that functions in the copper-accumulation pathway (By similarity).
cofactor: Cu(2+) (Binds 1 copper ion per subunit.)
disruption phenotype: Leads to alteration in cell fusion between conidial anastomosis tubes (PubMed:21666072). Displays reduced basal MAK-1 activity (PubMed:22879952, PubMed:25279949).
PADG_04289 uncharacterized protein from Paracoccidioides brasiliensis Pb18
32% identity, 79% coverage
- Identification and immunogenic potential of glycosylphosphatidylinositol-anchored proteins in Paracoccidioides brasiliensis
Gonçales, Frontiers in fungal biology 2023 - “...(H/L34) ( Figure1 ). Additionally, a group of GPI-proteins of unknown function, including PADG_03914, PADG_02867, PADG_04289, PADG_05482, PADG_07620, PADG_04649, PADG_08385, PADG_07354, PADG_06677, PADG_02955, PADG_06557, and PADG_00497, showed elevated expression in mycelia, indicating their potential roles in regulating the mycelial phase of P. brasiliensis ( Figure1 )....”
CIMG_07738 uncharacterized protein from Coccidioides immitis RS
31% identity, 89% coverage
C3VER8 Copper acquisition factor BIM1-like domain-containing protein from Hyaloscypha finlandica
33% identity, 67% coverage
- The haustorial transcriptome of the cucurbit pathogen Podosphaera xanthii reveals new insights into the biotrophy and pathogenesis of powdery mildew fungi.
Polonio, BMC genomics 2019 - “...40.277 Pxanthii_hau_25818 257 Q08656 ATP synthase protein. Neurospora crassa 1.00E-18 72.92% 13 37.807 Pxanthii_hau_27,213 1001 C3VER8 Putative uncharacterized protein. Cadophora finlandica. 9.00E-61 59.49% 14 32.385 Pxanthii_hau_15585 1295 A0A0B1P6R5 Uncharacterized protein. Uncinula necator . 0.044 90% 15 30.763 Pxanthii_hau_10927 1975 L8B996 Uncharacterized protein. Phlebia radiata . 0.001...”
- “...DH14 0.0 53.81% Pxanthii_hau_15,694 602 Q12737 Bilirubin oxidase. Myrothecium verrucaria. 4.0e-145 47.51% Pxanthii_hau_27,213 PHEC27213 209 C3VER8 Putative uncharacterized protein. Cadophora finlandica. 6.00e-71 53% Pxanthii_hau_0000217529 PHEC217529 86 A0A0A2WL92 Uncharacterized protein. Beauveria bassiana D15 1.00E-51 99% a Number of amino acids in the unprocessed form (with signal peptide)...”
VC83_07867 uncharacterized protein from Pseudogymnoascus destructans
32% identity, 82% coverage
- Pseudogymnoascus destructans transcriptome changes during white-nose syndrome infections
Reeder, Virulence 2017 - “...4.25E-07 522.8 88.4 1.23E-09 Cell Wall Remodeling VC83_03500 Spherulin-1A SR1A_PHYPO 22.2 9.41E-05 31.4 758.3 6.99E-06 VC83_07867 Uncharacterized protein AFUA_6G02800 YA280_ASPFU 21.2 8.97E-08 169.0 3783.0 5.93E-11 VC83_00788 Endochitinase 1 CHI1_APHAL 11.6 2.07E-04 106.9 1327.3 1.93E-05 VC83_07327 Probable glucan endo-1,3--glucosidase eglC EGLC_NEOFI 6.5 1.93E-03 221.5 1489.4 4.95E-04 VC83_04729...”
FPRO_01717 uncharacterized protein from Fusarium proliferatum ET1
29% identity, 66% coverage
An12g07750 uncharacterized protein from Aspergillus niger
29% identity, 77% coverage
Afu6g02800 GPI anchored protein, putative from Aspergillus fumigatus Af293
B0YDG5 GPI anchored protein, putative from Aspergillus fumigatus (strain CBS 144.89 / FGSC A1163 / CEA10)
27% identity, 80% coverage
- Genes differentially expressed in conidia and hyphae of Aspergillus fumigatus upon exposure to human neutrophils
Sugui, PloS one 2008 - “...the genes encoding a copper transporter (Afu6g02810), a metalloreductase (Afu6g602820) and a putative GPI-anchored protein (Afu6g02800) Since these three genes are located adjacent to each other on chromosome 6, a deletion vector was constructed to delete all three genes at once. The vector was constructed by...”
- “...a 950-bp fragment and a 520-bp fragment flanking the coding regions of the first gene Afu6g02800 and the third gene Afu6g02820, respectively. The deletion constructs were then cloned into the pDHt/SK2 vector [22] and integrated into the B-5233 genome via Agrobacterium tumefaciens -mediated transformation [22] ....”
- Characterization of Extracellular Vesicles Produced by Aspergillus fumigatus Protoplasts
Rizzo, mSphere 2020 - “...putative B0Y688 AFUB_066060 GPI-anchored cell wall organization protein Ecm33 B0Y5M3 AFUB_063890 Ecm33 GPI-anchored protein, putative B0YDG5 AFUB_095500 Cell wall integrity signaling protein Lsp1, putative B0Y7E0 AFUB_073480 Pil1 Cell wall serine-threonine-rich galactomannoprotein Mp1 B0YEP2 AFUB_099880 Mp1 1,3-Beta-glucanosyltransferase Gel1 B0XT72 AFUB_018250 Gel1 1,3-Beta-glucanosyltransferase Gel4 B0XVI5 AFUB_022370 Gel4 Mannan...”
CIMG_10032 expression library immunization antigen 1 from Coccidioides immitis RS
29% identity, 58% coverage
PADG_04649 uncharacterized protein from Paracoccidioides brasiliensis Pb18
27% identity, 55% coverage
- Identification and immunogenic potential of glycosylphosphatidylinositol-anchored proteins in Paracoccidioides brasiliensis
Gonçales, Frontiers in fungal biology 2023 - “...). Additionally, a group of GPI-proteins of unknown function, including PADG_03914, PADG_02867, PADG_04289, PADG_05482, PADG_07620, PADG_04649, PADG_08385, PADG_07354, PADG_06677, PADG_02955, PADG_06557, and PADG_00497, showed elevated expression in mycelia, indicating their potential roles in regulating the mycelial phase of P. brasiliensis ( Figure1 ). Figure1 Quantitative transcriptional...”
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