PaperBLAST
PaperBLAST Hits for NP_116583.2 Mil1p (Saccharomyces cerevisiae S288C) (1073 a.a., MSDSEEDLGV...)
Show query sequence
>NP_116583.2 Mil1p (Saccharomyces cerevisiae S288C)
MSDSEEDLGVQLKGLKIARHLKESGEHTDEESNSSPEHDCGLSNQDDLTVMHTQAKEEVF
KRREEDGTRTEDALHEGEAGKEGTGFPSSQSVCSPNEADSGIDRADKPILLDPFKSVHDT
DPVPGTKSRSNSDSDSDSDDGGWQEMPAVSSFNIYNHRGELELTSKVRNSEQASETSPTV
PPGKNCKSVNDSRFDYTKMAAEQQAQRSYRTNKKTDFLFDHKVLKKKINSSQTSVNLTSS
PSTTSLNNEKNNDDDDDDSYDEYEDDVEPVNDLNRDSQLNITKNLLSDMEKFAYVGAINI
LANQMCTNLATLCLCIDIKSHKKLAHRLQFTQKDMAAWKTVVLSRLYDHLGISQEEIVMI
EKLSLHKIQLEDLCKCLKTTQSIDNPWENDRDHEEDGIEETTERMSPNEQNGSVQASTPD
PEQSATPETPKAKQSPLSSDVPGKVLDPENVKSQDKLNIDVAWTIICDLFLICLQSSTYD
SRSRTLLINFAKVLNMTSLEICEFERRVTDSLDMEQSTEDQVWDEQDHMRNRRRSKRRKK
MAYVALAMVGGSLVLGLSGGLLAPVIGGGIAAGLSTIGITGATSFLTGVGGTTVVAVSST
AIGANIGARGMSKRMGSVRTFEFRPLHNNRRVNLILTVSGWMVGNEDDVRLPFSTVDPVE
GDLYSLYWEPEMLKSIGQTVSIVATEIFTTSLQQILGATVLTALISSIQWPMALSKLGYI
LDNPWNVSLDRAWSAGKILADTLIARNLGARPITLVGFSIGARVIFSCLIELCKKKALGL
IENVYLFGTPAVMKKEQLVMARSVVSGRFVNGYSDKDWFLAYLFRAAAGGFSAVMGISTI
ENVEGIENINCTEFVDGHLNYRKSMPKLLKRIGIAVLSEEFVEIEEMMNPEEVKRKRKLI
NDVDAAQKKLSERKKHNSWVPKWLKPKKSKWKVMVEEAVEEGRDMQDLPENDVNNNENEN
PDEHEGIARQKRRDAALVDHGALMHELQLIKQAMHEDEIKNKACLPGEDKEVESSNDFLG
ESHYKPPSTPKINPPQSPNNFQLLSAGRTILPEDDDFDPRGKKKVEFSFPDDI
Running BLASTp...
Found 12 similar proteins in the literature:
MIL1_YEAST / P43564 Probable lipase MIL1; Medium adaptin-interacting ligand 1; EC 3.1.1.- from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 3 papers)
NP_116583 Mil1p from Saccharomyces cerevisiae S288C
100% identity, 100% coverage
YFL034W Putative integral membrane protein that interacts with Rpp0p, which is a component of the ribosomal stalk from Saccharomyces cerevisiae
100% identity, 100% coverage
- The alternate AP-1 adaptor subunit Apm2 interacts with the Mil1 regulatory protein and confers differential cargo sorting
Whitfield, Molecular biology of the cell 2016 (no snippet) - Chemogenetic E-MAP in Saccharomyces cerevisiae for Identification of Membrane Transporters Operating Lipid Flip Flop
Vazquez, PLoS genetics 2016 - “...high correlations of a deletion in the acyltransferase paralog YDR018c or in the lipase paralog YFL034w with deletions in amino acid permeases suggest that these ORFs may disturb amino acid transport or signaling mediated through such transporters, possibly by disturbing the lipid composition of membranes. Furthermore,...”
- Genome-Wide Screens in Saccharomyces cerevisiae Highlight a Role for Cardiolipin in Biogenesis of Mitochondrial Outer Membrane Multispan Proteins
Sauerwald, Molecular and cellular biology 2015 - “...fmp33 strain hit1 strain jlp2 strain ngr1 strain yfl034w strain ypl067c strain SGA crd1 GFP-OM14 strain SGA fmp32 GFP-OM14 strain SGA fmp33 GFP-OM14 strain...”
- “...SGA jlp2 GFP-OM14 strain SGA ngr1 GFP-OM14 strain SGA yfl034w GFP-OM14 strain SGA ypl067c GFP-OM14 strain MATa MATa MATa MATa MATa MATa MATa MATa MATa MATa...”
- RNA polymerase II contributes to preventing transcription-mediated replication fork stalls
Felipe-Abrio, The EMBO journal 2015 - “...gene. This reduction in the speed was also observed at YFL034W, located near a late replication origin (Fig 5A). We could detect The EMBO Journal Vol 34 | No...”
- “...500 500 0 0 0 20 30 40 0 0 20 30 40 Time after G1 (min) YFL034W ARS603 IP-BrdU (AU) - HU 15 15 15 10 10 10 5 5 5 0 0 0 20 30 0 0 40 20 30 40 Time after G1 (min)...”
- Different nucleosomal architectures at early and late replicating origins in Saccharomyces cerevisiae
Soriano, BMC genomics 2014 - “...along S phase. (A) , ARS603 is represented by a red rectangle and flanking genes, YFL034W and YFL033C, by blue ones. Vertical bars indicate sites for digestion with restriction enzymes PvuII and HindIII. Green rectangle represents the end-terminal probe. The nucleosomal profile from the G1 sample...”
- Mutation rates across budding yeast chromosome VI are correlated with replication timing
Lang, Genome biology and evolution 2011 - “...GL35 b YFR019W FAB1 184490 GL11 b YFL036W RPO41 58781 GL36 YFR021W ATG18 194800 GL12 YFL034W Uncharacterized 65475 GL37 YFR023W PES4 199862 GL13 YFL032W Hypothetical 74870 GL38 YFR026C Hypothetical 205736 GL14 YFL027C GYP8 80417 GL39 YFR030W MET10 213300 GL15 YFL025C BST1 84143 GL40 YFR032C Hypothetical 222078...”
- Role of PUG1 in inducible porphyrin and heme transport in Saccharomyces cerevisiae
Protchenko, Eukaryotic cell 2008 - “...YMR052C-A YOR092W YOR292C YOR291W YDR107C YOL075C YBR235W YFL034W YPR114W YLR241W YLR426W YDL222C YBR241C YDR387C YDL133W YGR045C YDL199C YNL115C YKR106W Q0010...”
- Integrative investigation of metabolic and transcriptomic data
Pir, BMC bioinformatics 2006 - “...3.4E-02 LV4+ MSC2, PRX1, AMS1, PHM8, YMR034C, HXT1, MTH1, YPL099C, TRS23, CYC7, ZRG17, YLR431C, GPG1, YFL034W, PKH1, HXT3, YER028C monosaccharide transport 1.2E-05 hexose transport 1.2E-05 carbohydrate transport 5.5E-05 transport 6.5E-04 establishment of localization 7.4E-04 LV4- CNM67, MRK1, MKC7, YDL157C, YDR119W, QCR8, QCR9, INH1, COX8, COX4, HAP4,...”
- More
YELD_SCHPO / O14244 Uncharacterized membrane protein C6F6.13c from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
SPAC6F6.13c DUF726 family protein from Schizosaccharomyces pombe
42% identity, 63% coverage
- The Natural Product Resveratrol Inhibits Yeast Cell Separation by Extensively Modulating the Transcriptional Landscape and Reprogramming the Intracellular Metabolome
Wang, PloS one 2016 - “...right): wild-type, SPAC24B11.12c, rho4, hht3,pof3, isp6, pmc1, SPBC21B10.13c, mfm2, SPBC19G7.04, ste7, spd1, SPBC3B8.06, SPBC1773.02c, SPBC800.11, SPAC6F6.13c, dak2, plr1, SPBC119.03, cdm1, chs2, SPBC25B2.08, SPBC27.05, gpx1, klp6, SPBC839.02, pho1, gal1, SPBPB2B2.18, SPCPB1C11.02, SPCC1183.11, SPAC9E9.04, bgs4, SPAPB24D3.07c, SPBC2A9.13, SPBC31F10.17c, cys11, SPCC757.12, SPAC24H6.13, SPCC965.06, SPBC28F2.11, ctr4, ace2, top1, rnc1, ski3,...”
NCU02065 DUF726 domain-containing protein from Neurospora crassa OR74A
32% identity, 39% coverage
- Experimental Evolution of Multidrug Resistance in Neurospora crassa under Antifungal Azole Stress
Zhou, Journal of fungi (Basel, Switzerland) 2022 - “...RIP defective protein ( NCU02034 ), 3-hydroxyacyl-CoA dehydrogenase ( NCU16336 ), DUF726 domain-containing protein ( NCU02065 ), mitochondrial intermediate peptidase ( NCU02063 ), zinc metallopeptidase ( NCU02060 ), uridine nucleosidase Urh1 ( NCU02055 ), transcription initiation factor ( NCU02052 ), GTP-binding protein ( NCU02044 ), sterol-4alpha-carboxylate...”
- “...). To be noted, 30thK2 and 30thK1 shared 10 commonly mutated genes. These genes include NCU02065 , NCU02063 , NCU02051 , NCU02026 , NCU02024 , NCU02012, and NCU01993 , whose mutants were tested above, and three hypothetical protein encoding genes without available mutants ( NCU16667 ,...”
TGME49_203300 hypothetical protein from Toxoplasma gondii ME49
34% identity, 29% coverage
A0A6J8D250 Uncharacterized membrane protein F35D11.3,Transmembrane and coiled-coil domain-containing protein 4 from Mytilus coruscus
32% identity, 38% coverage
CBG13461 Protein CBG13461 from Caenorhabditis briggsae
32% identity, 40% coverage
YK68_SCHPO / Q9US10 Uncharacterized membrane protein C6F6.13c from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
31% identity, 39% coverage
AT4G36210 hypothetical protein from Arabidopsis thaliana
30% identity, 37% coverage
DDB_G0275413 DUF726 family protein from Dictyostelium discoideum AX4
33% identity, 25% coverage
- The amoebal MAP kinase response to Legionella pneumophila is regulated by DupA
Li, Cell host & microbe 2009 - “...3.00 4.57 2.27 DDB_G0288203 HEAT repeat 2.84 4.20 1.21 DDB_G0267440 LimpC, CD36 2.19 2.70 1.21 DDB_G0275413 Vacuolar sorting protein 9 (VPS9) 3.64 4.08 0.79 DDB_G0289485 Vacuolin A1 2.51 5.45 1.52 Lipid metabolism Reduced Expression DDB_G0275125 B-like phospholipase (2 genes) 0.160.19 0.340.36 1.121.52 DDB_G0286651 Saposin-like type B...”
AT2G18100 hypothetical protein from Arabidopsis thaliana
30% identity, 37% coverage
- DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
Dubin, eLife 2015 - “...THIOREDOXIN REDUCTASE 2 (NTR2) 9.96E-04 2_7666059 AT2G17430 MILDEW RESISTANCE LOCUS O 7 (MLO7) 7.56E-04 2_7915712 AT2G18100 Protein of unknown function (DUF726) 1.73E-06 2_7915712 AT2G17980 ATSLY member of SLY1 Gene Family 1.33E-05 2_7915712 AT2G18400 Ribosomal protein L6 family protein 1.26E-04 2_7915712 AT2G18150 Haem peroxidase 8.05E-04 2_7915712 AT2G18050...”
XP_567060 hypothetical protein from Cryptococcus neoformans var. neoformans JEC21
29% identity, 20% coverage
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