PaperBLAST
PaperBLAST Hits for TCDB::Q97UF5 AraS, component of Arabinose, fructose, xylose porter (Sulfolobus solfataricus) (620 a.a., MSRRRLYKAI...)
Show query sequence
>TCDB::Q97UF5 AraS, component of Arabinose, fructose, xylose porter (Sulfolobus solfataricus)
MSRRRLYKAISRTAIIIIVVVIIIAAIAGGLAAYYSSSKPPATSTSLTSTSSSLSVTTSS
TTSTLSSITTTTSTASSYVVDFINPWGAEDPVGLKWIGGNFSIYYPGYSVQFTSLPGASG
VEERYVVINDIEAGKLQGIFWAHGGPEVLSYVELLPSPHDLYNMTPLLAQEGLFQKGVTE
ALMAISYNGTIFGSPTNVHRAEELYFNPQILKKYNLPIPTNLSLLIYDTQQLEAHGINPW
AMSGAEGGYEQLHLWFAIFLSVAAQYYGAAGAAKLSNELMYGVLNLNNVTVQKIINETDN
VFLQFVGQSSVIPSWQSQSIWSALALVIKGQTVFEAGGNWLAEYAAIWYNTTTYPATQPY
LNWSNITLMAMPFPGTQGIYVIDMDSVAIPTVNNPQEQAAINFAKFWASYEGQKIWTYYK
GVSIWANSTDYYSTPMQWYDYQSLLNTPAQNFTWAFADGTLFDDVFYFLIAQELNLQEQG
SSYIPTFNAALFKAENMTFHEWQIAAKDGFGFVGQRGNPFGNYLPPWVNPSTYTYNSSYT
PSFLLTPPHYLLPYLKKLGQQQYANKVNSVNYYAINGVNLLPFPLLIVLMIYLDQTRYKY
VIKTFLNKINFFQIYFYLNF
Running BLASTp...
Found 17 similar proteins in the literature:
TC 3.A.1.1.14 / Q97UF5 AraS, component of Arabinose, fructose, xylose porter from Sulfolobus solfataricus (see paper)
SSO3066 Arabinose ABC transporter, arabinose binding protein from Sulfolobus solfataricus P2
100% identity, 100% coverage
- substrates: Arabinose, Xylose, fructose
- "Hot standards" for the thermoacidophilic archaeon Sulfolobus solfataricus
Zaparty, Extremophiles : life under extreme conditions 2010 - “...SSO3047 ABC transporter, permease 1.37 (0.55) SSO3053 Maltose ABC transporter, maltose binding protein 2.29 (0.85) SSO3066 Arabinose ABC transporter, arabinose binding protein 1.51 (0.61) SSO3120 Metabolite transport protein, putative 1.69 (0.94) SSO3198 Muconate cycloisomerase related protein 1.28 (0.49) SSO6391 SSU ribosomal protein S14AB (rps14AB) 1.44 (0.53)...”
- Something old, something new, something borrowed; how the thermoacidophilic archaeon Sulfolobus solfataricus responds to oxidative stress
Maaty, PloS one 2009 - “...COG0277 Y Conserved hypothetical protein SSO1005 1.71E-03 2.34 Y Arabinose ABC transporter, arabinose binding protein SSO3066 3.57E-05 2.37 COG1653 N Isocitrate lyase (aceA/icl) SSO1333 9.01E-04 2.37 COG2224 Y The mRNAs coding for DPSL (SSO2079), and the two flanking genes (SSO2078 and 2080) showed the largest changes...”
- Response of the hyperthermophilic archaeon Sulfolobus solfataricus to UV damage
Fröls, Journal of bacteriology 2007 - “...SSO3207 SSO0451 5491N SR R SSO2200 0433R R R SSO0911 R SR SSO3066 R R R R SR SR SR SR ssh7A ssh7A ssh7A SSO9180 SSO10610 SSO9535 SSO0271 8 (2/2) 8 (1/2) 7 (2/3)...”
- “...SSO5826), kinases (SSO2751 and SSO3207), transporters (SSO2288 and SSO3066), and diverse ATPases (SSO0909, SSO2750, and SSO2200). Among the last group is the...”
- Dynamic metabolic adjustments and genome plasticity are implicated in the heat shock response of the extremely thermoacidophilic archaeon Sulfolobus solfataricus
Tachdjian, Journal of bacteriology 2006 - “...oppD SSO1277 oppF SSO1281 SSO1282 oppD SSO1283 SSO3066 SSO3067 SSO3069 SSO2848 SSO2849 SSO2850 SSO1000 SSO1170 SSO3053 SSO2035 SSO2135 SSO2137 SSO2228 SSO2704...”
- Production of recombinant and tagged proteins in the hyperthermophilic archaeon Sulfolobus solfataricus
Albers, Applied and environmental microbiology 2006 - “...region 241 bp upstream of the araS gene (SSO3066) was amplified from S. solfataricus genomic DNA with the primer pair araSF (CCC CCCCTAGGGCACCATATGTTTAGAGATG)...”
- Archaeal homolog of bacterial type IV prepilin signal peptidases with broad substrate specificity
Albers, Journal of bacteriology 2003 - “...SSO2681 SSO2847 SSO0037 SSO2684 SSO0489 SSO0117 SSO1171 SSO2846 SSO3066 SSO2712 SSO3140 Signal sequence 3924 ALBERS ET AL. PibD seems to be functionally more...”
- Archaeal signal peptides--a comparative survey at the genome level
Bardy, Protein science : a publication of the Protein Society 2003 - “...three S. solfataricus sugarbinding proteins (SSO0999, SSO2847, SSO3066) shown to be processed at the preflagellin-like cleavage site (Albers and Driessen 2002)....”
- “...secreted proteins. Indeed, the sugar-binding proteins SSO2847 and SSO3066 shown in S. solfataricus as secreted and processed by the FlaK equivalent are not...”
GLCS_SACS2 / Q97UZ1 Glucose-binding protein GlcS; GBP from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (Sulfolobus solfataricus) (see 2 papers)
TC 3.A.1.1.13 / Q97UZ1 GlcS, component of Glucose, mannose, galactose porter from Sulfolobus solfataricus (see paper)
SSO2847 Sugar-binding periplasmic protein from Sulfolobus solfataricus P2
45% identity, 69% coverage
- function: Part of the ABC transporter complex GlcSTUV involved in glucose uptake (Probable). Binds glucose. Can also bind galactose and mannose (PubMed:10400586, PubMed:11260467).
subunit: The complex is composed of two ATP-binding proteins (GlcV), two transmembrane proteins (GlcT and GlcU) and a solute-binding protein (GlcS). - substrates: Galactose, Mannose, glucose
- Hydroxyurea-Mediated Cytotoxicity Without Inhibition of Ribonucleotide Reductase
Liew, Cell reports 2016 - “...the Orc1-3 and WhiP proteins to the three replication origins (AC) and distal control locus SSO2847 (D) in cells treated with 0 or 10mM HU for 7hr. ChIP reactions were performed in triplicate, and data are expressed as fractional recovery of the total input material. (EH)...”
- Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation
Bräsen, Microbiology and molecular biology reviews : MMBR 2014 - “...(501). The previously identified glucose transporter (binding protein SSO2847) was not required for glucose transport in this strain, as demonstrated by the...”
- Carbohydrate hydrolysis and transport in the extreme thermoacidophile Sulfolobus solfataricus
Lalithambika, Applied and environmental microbiology 2012 - “...inserted at an SphI site. PBL2106, a strain lacking Sso2847 and its flanking genes, was produced by deletion of the region including ORFs Sso2833 through...”
- “...Forward Sso1354 internal Reverse Sso2847 internal Forward Sso2847 internal Reverse TAGATAGTGCATGCGAATTATCCAGTCCTCTATTTCTCTTACG...”
- Versatile Genetic Tool Box for the Crenarchaeote Sulfolobus acidocaldarius
Wagner, Frontiers in microbiology 2012 - “...the maltose binding protein ( saci 1165) was amplified employing primers 2258 and 986. glcS (sso2847) without signal sequence was amplified using the primers 987 and 988. glcT (sso2848), glcU (sso2849), and glcV (sso2850) were amplified in a single PCR with the primers 989 and 2259....”
- Absence of diauxie during simultaneous utilization of glucose and Xylose by Sulfolobus acidocaldarius
Joshua, Journal of bacteriology 2011 - “...to 38% homology with the amino acid sequence of Sso2847 to -2850 (GlcSTUV), the glucose ABC transporter in S. solfataricus (see Fig. S6 in the supplemental...”
- Archaeal homolog of bacterial type IV prepilin signal peptidases with broad substrate specificity
Albers, Journal of bacteriology 2003 - “...Berkeley SSO0118 SSO0999 SSO2146 SSO2152 SSO2323 SSO2681 SSO2847 SSO0037 SSO2684 SSO0489 SSO0117 SSO1171 SSO2846 SSO3066 SSO2712 SSO3140 Signal sequence 3924...”
- Archaeal signal peptides--a comparative survey at the genome level
Bardy, Protein science : a publication of the Protein Society 2003 - “...the three S. solfataricus sugarbinding proteins (SSO0999, SSO2847, SSO3066) shown to be processed at the preflagellin-like cleavage site (Albers and Driessen...”
- “...subset of secreted proteins. Indeed, the sugar-binding proteins SSO2847 and SSO3066 shown in S. solfataricus as secreted and processed by the FlaK equivalent...”
TC 3.A.1.1.24 / Q72KX2 Glucose-binding protein aka TT_C0328, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) from Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (see paper)
TTC0328 No description from Thermus thermophilus HB27
27% identity, 51% coverage
SY28_RS04315 ABC transporter substrate-binding protein from Meiothermus taiwanensis
26% identity, 57% coverage
2b3bA / Q72KX2 Thermus thermophilus glucose/galactose binding protein with bound glucose (see paper)
27% identity, 51% coverage
- Ligand: alpha-d-glucopyranose (2b3bA)
CTN_0660 Extracellular solute-binding protein, family 1 precursor from Thermotoga neapolitana DSM 4359
25% identity, 60% coverage
PH1214 cytoplasmic protein from Pyrococcus horikoshii OT3
23% identity, 51% coverage
BCAL3041 maltose-binding protein from Burkholderia cenocepacia J2315
27% identity, 33% coverage
- Identification of small RNAs abundant in Burkholderia cenocepacia biofilms reveal putative regulators with a potential role in carbon and iron metabolism
Sass, Scientific reports 2017 - “...aromatic compounds, e.g. gluconate permease (BCAL3365), galactonate transporter (BCAL0184, BCAM2500), glycerol kinase (BCAL0925), glycerol-phosphate transporter (BCAL3041), 6-phosphogluconolactonase (BCAL3043) and salicylate hydroxylase(BCAM1274). Predicted targets of ncS16 include a higher percentage of outer membrane and cell envelope components, as well as genes for transport of inorganic compounds. The...”
- The AHL- and BDSF-dependent quorum sensing systems control specific and overlapping sets of genes in Burkholderia cenocepacia H111
Schmid, PloS one 2012 - “...transaminase protein 2.8 1.6 0.5 0.8 CCE50475 BCAL2352 Carbonic anhydrase 4.3 1.0 7.0 1.1 CCE49840 BCAL3041 Protein involved in carbohydrate transport 4.5 2.0 0.5 1.6 CCE51244 BCAL3285 Nitric oxide dioxygenase; flavohemoprotein 6.7 0.6 na 0.8 CCE46722 BCAM0184 Fucose-Binding lectin protein bclB 183.0 0.5 na 0.8 CCE46720...”
- Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment
O'Grady, Frontiers in cellular and infection microbiology 2011 - “...ABC transporter 1.6 BCAL3039 ABC transporter, membrane permease 1.5 BCAL3040 ABC transporter, membrane permease 1.7 BCAL3041 MalE, maltose-binding protein 2.1 BCAL3364 Putative gluconokinase 1.7 BCAM0094 Xylulose kinase 1.7 BCAM1330 Cellulose polysaccharide export protein 1.7 BCAM1333 Cellulose exopolysaccharide acyltransferase 1.6 BCAM1390 Putative aldolase 3.0 BCAM2260 Major facilitator...”
- “...ATP-binding component 1.61 BCAL3039 ABC transporter, membrane permease 1.54 BCAL3040 ABC transporter, membrane permease 1.71 BCAL3041 Maltose-binding protein 2.09 BCAL3163 Putative nucleotidyltransferase 1.68 BCAL3203 Putative periplasmic TolB protein 1.64 BCAL3204 Putative OmpA family lipoprotein 1.68 BCAL3205 Putative exported protein 1.62 BCAL3289 Putative glycolate oxidase subunit GlcE...”
BTH_I1553 maltose ABC transporter, periplasmic maltose-binding protein from Burkholderia thailandensis E264
27% identity, 33% coverage
BPSL2611 maltose-binding protein from Burkholderia pseudomallei K96243
27% identity, 33% coverage
RL4252 putative solute-binding component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
24% identity, 49% coverage
RLV_4312 ABC transporter substrate-binding protein from Rhizobium leguminosarum bv. viciae
24% identity, 49% coverage
NGR_c33060 predicted bacterial extracellular solute-binding protein from Rhizobium sp. NGR234
24% identity, 49% coverage
NGR_c33060 ABC transporter substrate-binding protein from Sinorhizobium fredii NGR234
24% identity, 49% coverage
RL1824 putative solute-binding component of ABC transporter from Rhizobium leguminosarum bv. viciae 3841
24% identity, 49% coverage
SMc04396 PUTATIVE PERIPLASMIC BINDING PROTEIN from Sinorhizobium meliloti 1021
25% identity, 49% coverage
- Loss of malic enzymes leads to metabolic imbalance and altered levels of trehalose and putrescine in the bacterium Sinorhizobium meliloti
Zhang, BMC microbiology 2016 - “...the up-regulation of 14 solute transport genes annotated as putative sugars transporters, and among these, smc04396 and smb20036 are induced by dextrin and the cyclic polyol quinic acid, respectively [ 28 ]. The succinate-grown dme mutant cells also showed increased transcription of the TCA cycle genes...”
- Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome
Mauchline, Proceedings of the National Academy of Sciences of the United States of America 2006 - “...SMc03061 Maltotriose, turanose, sucrose, maltose SMc04396 Dextrin Oligosaccharide: -glucosides (1) SMc04259 Gentiobiose, salicin, cellobiose Oligosaccharide:...”
4g68A / J9PBT4 Biochemical and structural insights into xylan utilization by the thermophilic bacteriumcaldanaerobius polysaccharolyticus (see paper)
26% identity, 17% coverage
- Ligands: alpha-d-xylopyranose; beta-d-xylopyranose (4g68A)
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