PaperBLAST
Full List of Papers Linked to Q9SL67
PRS4B_ARATH / Q9SL67 26S proteasome regulatory subunit 4 homolog B; 26S proteasome AAA-ATPase subunit RPT2b; 26S proteasome subunit 4 homolog B; Regulatory particle triple-A ATPase subunit 2b from Arabidopsis thaliana (Mouse-ear cress) (see 5 papers)
NP_179604 AAA-type ATPase family protein from Arabidopsis thaliana
AT2G20140 26S protease regulatory complex subunit 4, putative from Arabidopsis thaliana
- function: The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex (PubMed:22158466). Acts redundantly with RPT2A in the regulation of gametogenesis (PubMed:21784786, PubMed:22158466). With RPT2A plays a critical role in 26S proteasome assembly (PubMed:22158466).
subunit: Component of the 19S regulatory particle (RP/PA700) base subcomplex of the 26S proteasome. The 26S proteasome is composed of a core protease (CP), known as the 20S proteasome, capped at one or both ends by the 19S regulatory particle (RP/PA700). The RP/PA700 complex is composed of at least 17 different subunits in two subcomplexes, the base and the lid, which form the portions proximal and distal to the 20S proteolytic core, respectively.
disruption phenotype: No visible phenotype under normal growth conditions (PubMed:22158466). The double mutants rpt2a and rpt2b are blocked in both male and female gametogenesis (PubMed:21784786, PubMed:22158466). - Membrane Proteomics of Arabidopsis Glucosinolate Mutants cyp79B2/B3 and myb28/29
Mostafa, Frontiers in plant science 2017 - “...LPA1 1.368 0.016 Member of photosystem D, H, S, T, M Peng et al., 2006 Q9SL67 At2g20140 26S proteasome regulatory subunit 4 homolog B RPT2B 1.361 0.007 Hydrolysis of ATP and generation of gametes D, T Tair Q9FXA1 At1g49750 At1g49750 protein AT1G49750 1.340 0.034 D, H,...”
- Involvement of a universal amino acid synthesis impediment in cytoplasmic male sterility in pepper
Fang, Scientific reports 2016 - “...3 354 7.04 35.62 * Q9FF53 Probable aquaporin PIP2-4 226.80 2 291 8.22 30.95 * Q9SL67 26S proteasome regulatory subunit 4 homolog B 114.79 2 443 5.85 49.22 * P49209 60S ribosomal protein L9-1 99.11 2 194 9.48 22.02 * Q6Q4D0 Protein TONSOKU (Protein BRUSHY 1)...”
- Arabidopsis RPT2a encoding the 26S proteasome subunit is required for various aspects of root meristem maintenance, and regulates gametogenesis redundantly with its homolog, RPT2b.
Ueda, Plant & cell physiology 2011 (PubMed)- GeneRIF: RPT2a and RPT2b proteins seem to be functionally equivalent in the root apical meristem, but RPT2b is dispensable for meristem function. [RPT2b]
- The RPT2 subunit of the 26S proteasome directs complex assembly, histone dynamics, and gametophyte and sporophyte development in Arabidopsis.
Lee, The Plant cell 2011 - GeneRIF: RPT2 is essential for assembly of the plant 26S proteasome and RPT2a and b isoforms are functionally equivalent. [RPT2b]
- The Structural Role of RPN10 in the 26S Proteasome and an RPN2-Binding Residue on RPN13 Are Functionally Important in Arabidopsis
Lin, International journal of molecular sciences 2024 - “...(NA) PAB1 At1g16470 32.7/43.4 (75.3 80.1) RPT2a At4g29040 ND/ND (NA) PAB2 At1g79210 17.3/ND (NA) RPT2b At2g20140 93.3/98.7 (94.5 19.0) PAC1 At3g22110 102.9/101.3 (101.5 27.4) RPT3 At5g58290 139.4/118.4 (117.7 16.2) PAC2 At4g15160 ND/ND (NA) RPT4a At5g43010 17.5/16.8 (104.2 180.6) PAD1 At3g51260 124.0/107.3 (115.6 3.7) RPT4b At1g45000 111.8/120.1...”
- Rho GTPase ROP1 Interactome Analysis Reveals Novel ROP1-Associated Pathways for Pollen Tube Polar Growth in Arabidopsis
Li, International journal of molecular sciences 2020 - “...and growth. The five candidates encoded the KINKY POLLEN (KIP) protein (AT5G49680), exostosin family protein (AT2G20140), cation/hydrogen exchanger CHX28 (AT3G52080), AAA-type ATPase protein (AT2G02480), and QUASIMODO2 LIKE 2 (AT2G03480). The kip mutant had a short pollen tube phenotype consistent with a previous report [ 33 ]...”
- Combined Proteomic and Metabolomic Profiling of the Arabidopsis thaliana vps29 Mutant Reveals Pleiotropic Functions of the Retromer in Seed Development
Durand, International journal of molecular sciences 2019 - “...in abundance of several H + -ATPases (At2g18960, 23.5; At4g27500, 15; At1g78920, 9; At4g39080, 6.5; At2g20140, 6.5; and At1g07670, specific to vps29 seeds). The increase of the energy metabolism appears to be essential for vps29 seeds to ensure protein turnover. Indeed, mRNA translational (GO: 0006412) and...”
- Membrane Proteomics of Arabidopsis Glucosinolate Mutants cyp79B2/B3 and myb28/29
Mostafa, Frontiers in plant science 2017 - “...1.368 0.016 Member of photosystem D, H, S, T, M Peng et al., 2006 Q9SL67 At2g20140 26S proteasome regulatory subunit 4 homolog B RPT2B 1.361 0.007 Hydrolysis of ATP and generation of gametes D, T Tair Q9FXA1 At1g49750 At1g49750 protein AT1G49750 1.340 0.034 D, H, S,...”
- Transcriptomic and proteomic approach to identify differentially expressed genes and proteins in Arabidopsis thaliana mutants lacking chloroplastic 1 and cytosolic FBPases reveals several levels of metabolic regulation
Soto-Suárez, BMC plant biology 2016 - “...belonged to the most representatives functional categories, such as protein synthesis, degradation, and post-translational modification (At2g20140), RNA regulation, processing and binding (At3g61850), glycolysis and gluconeogenesis (At4g15210, At5g20830 and At1g50460), photosynthesis and Calvin-cycle-related genes (At1g79530 and At2g39730), transport (At1g07340 and At3g19930), development (At5g24780), redox regulation (At1g76760 and...”
- “...+-0.1 1.6 0.01 0.6 +-0.01 0.0 +-0.1 0.2 +-0.1 2.7 0.2 -0.2 +-0.1 0.0 0.1 At2g20140 26S protease regulatory complex subunit 4 5'TGAGCCAGGCACTGGGAA 3'CGCTTGGTGCCAACAGCA 0.7 0.1 0.0 0.02 0.0 0.03 2.2 0.08 1.2 0.1 -0.2 0.1 -0.8 0.2 2.7 0.2 At3g61850 DAG1 (DOF affecting germination 1)...”
- Proteomic analysis of endoplasmic reticulum stress responses in rice seeds
Qian, Scientific reports 2015 - “...T-complex protein LOC_Os06g36700 Protein degradation gi|115444877 2.723 AT1G45000 26S protease regulatory subunit LOC_Os02g10640 gi|115474241 2.457 AT2G20140 26S protease regulatory subunit 4 LOC_Os07g49150 gi|556560 4.396 26S protease regulatory subunit 6A LOC_Os02g56000 gi|115445841 3.909 AT5G58290 26S protease regulatory subunit 6B LOC_Os02g21970 gi|115444937 6.237 AT5G19990 26S proteasome regulatory particle...”
- Suppression of the auxin response pathway enhances susceptibility to Phytophthora cinnamomi while phosphite-mediated resistance stimulates the auxin signalling pathway
Eshraghi, BMC plant biology 2014 - “...AT4G29040 T-DNA-insertion Defective in 26S proteasome subunit [ 65 , 68 , 91 ] rpt2b AT2G20140 T-DNA-insertion Defective in 26S Proteasome Subunit [ 65 , 91 ] rpt5a AT3G05530 T-DNA-insertion Defective in 26S Proteasome Subunits [ 68 ] rpn10 AT4G38630 T-DNA-insertion Defective in ubiquitin/26S proteasome-mediated proteolysis...”
- Comparative large scale characterization of plant versus mammal proteins reveals similar and idiosyncratic N-α-acetylation features
Bienvenut, Molecular & cellular proteomics : MCP 2012 - “...S proteasome regulatory subunit 4 for both the Arabidopsis (At2g20140 and RPT2b) and the human samples (P62191 and RPT2). Of note, several of these proteins...”
- Differential regulation of the PanA and PanB proteasome-activating nucleotidase and 20S proteasomal proteins of the haloarchaeon Haloferax volcanii
Reuter, Journal of bacteriology 2004 - “...AtRpt1b (At1g53780), AtRpt2a (At4g29040), AtRpt2b (At2g20140), AtRpt3 (At5g58290), AtRpt4a (At1g45000), AtRpt4b (At5g43010), AtRpt5a (At3g05530), AtRpt5b...”
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