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Entry version 102 (08 May 2019)
Sequence version 1 (01 Oct 2000)
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Protein

Pentatricopeptide repeat-containing protein At3g13880

Gene

PCMP-E89

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score:

Annotation score:2 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at transcript leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Biological processi

  • mitochondrial RNA modification Source: TAIR
  • RNA modification Source: GO_Central

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Pentatricopeptide repeat-containing protein At3g13880
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:PCMP-E89
Ordered Locus Names:At3g13880
ORF Names:MCP4.10
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiArabidopsis thaliana (Mouse-ear cress)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri3702 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000006548 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 3

Organism-specific databases

Arabidopsis Information Portal

More...
Araporti
AT3G13880

The Arabidopsis Information Resource

More...
TAIRi
locus:2087969 AT3G13880

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00003560871 – 748Pentatricopeptide repeat-containing protein At3g13880Add BLAST748

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
Q9LRV9

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

ExpressionAtlas, Differential and Baseline Expression

More...
ExpressionAtlasi
Q9LRV9 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q9LRV9 AT

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
3702.AT3G13880.1

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
Q9LRV9

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section indicates the positions and types of repeated sequence motifs or repeated domains within the protein.<p><a href='/help/repeat' target='_top'>More...</a></p>Repeati46 – 80PPR 1Add BLAST35
Repeati81 – 111PPR 2Add BLAST31
Repeati112 – 146PPR 3Add BLAST35
Repeati147 – 181PPR 4Add BLAST35
Repeati182 – 212PPR 5Add BLAST31
Repeati213 – 247PPR 6Add BLAST35
Repeati248 – 285PPR 7Add BLAST38
Repeati286 – 316PPR 8Add BLAST31
Repeati317 – 356PPR 9Add BLAST40
Repeati357 – 391PPR 10Add BLAST35
Repeati392 – 422PPR 11Add BLAST31
Repeati423 – 457PPR 12Add BLAST35
Repeati458 – 492PPR 13Add BLAST35
Repeati493 – 523PPR 14Add BLAST31
Repeati524 – 558PPR 15Add BLAST35
Repeati559 – 589PPR 16Add BLAST31
Repeati595 – 629PPR 17Add BLAST35

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni630 – 705Type E motifAdd BLAST76
Regioni706 – 736Type E(+) motifAdd BLAST31

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the PPR family. PCMP-E subfamily.Curated

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywords - Domaini

Repeat

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG4197 Eukaryota
ENOG410Z7Z7 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000237570

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q9LRV9

Identification of Orthologs from Complete Genome Data

More...
OMAi
EAVHGCV

Database of Orthologous Groups

More...
OrthoDBi
1344243at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q9LRV9

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.25.40.10, 5 hits

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR002885 Pentatricopeptide_repeat
IPR011990 TPR-like_helical_dom_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01535 PPR, 1 hit
PF13041 PPR_2, 5 hits

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00756 PPR, 6 hits

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51375 PPR, 15 hits

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

Q9LRV9-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MLLQFRAKTF FNNIAQDSLV TLITKRVGLG YRFLSSLCQP KNTALDSEGY
60 70 80 90 100
KILFQTAAKS GSVVLGKLAH GHMIKSSLNP CLYLLNNLLN MYCKCRELGF
110 120 130 140 150
ARQLFDRMPE RNIISFNSLI SGYTQMGFYE QAMELFLEAR EANLKLDKFT
160 170 180 190 200
YAGALGFCGE RCDLDLGELL HGLVVVNGLS QQVFLINVLI DMYSKCGKLD
210 220 230 240 250
QAMSLFDRCD ERDQVSWNSL ISGYVRVGAA EEPLNLLAKM HRDGLNLTTY
260 270 280 290 300
ALGSVLKACC INLNEGFIEK GMAIHCYTAK LGMEFDIVVR TALLDMYAKN
310 320 330 340 350
GSLKEAIKLF SLMPSKNVVT YNAMISGFLQ MDEITDEASS EAFKLFMDMQ
360 370 380 390 400
RRGLEPSPST FSVVLKACSA AKTLEYGRQI HALICKNNFQ SDEFIGSALI
410 420 430 440 450
ELYALMGSTE DGMQCFASTS KQDIASWTSM IDCHVQNEQL ESAFDLFRQL
460 470 480 490 500
FSSHIRPEEY TVSLMMSACA DFAALSSGEQ IQGYAIKSGI DAFTSVKTSS
510 520 530 540 550
ISMYAKSGNM PLANQVFIEV QNPDVATYSA MISSLAQHGS ANEALNIFES
560 570 580 590 600
MKTHGIKPNQ QAFLGVLIAC CHGGLVTQGL KYFQCMKNDY RINPNEKHFT
610 620 630 640 650
CLVDLLGRTG RLSDAENLIL SSGFQDHPVT WRALLSSCRV YKDSVIGKRV
660 670 680 690 700
AERLMELEPE ASGSYVLLHN IYNDSGVNSS AEEVRELMRD RGVKKEPALS
710 720 730 740
WIVIGNQTHS FAVADLSHPS SQMIYTMLET MDNVDFVDYT LVHFCSVT
Length:748
Mass (Da):83,194
Last modified:October 1, 2000 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iF1C5D4F3E51E5109
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AB028610 Genomic DNA Translation: BAB02912.1
CP002686 Genomic DNA Translation: AEE75430.1
BX824350 mRNA No translation available.

NCBI Reference Sequences

More...
RefSeqi
NP_188004.1, NM_112242.3

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT3G13880.1; AT3G13880.1; AT3G13880

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
820601

Gramene; a comparative resource for plants

More...
Gramenei
AT3G13880.1; AT3G13880.1; AT3G13880

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ath:AT3G13880

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

<p>This subsection of the <a href="http://www.uniprot.org/manual/cross_references_section">Cross-references</a> section provides links to various web resources that are relevant for a specific protein.<p><a href='/help/web_resource' target='_top'>More...</a></p>Web resourcesi

Arabidopsis PPR Protein Database

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB028610 Genomic DNA Translation: BAB02912.1
CP002686 Genomic DNA Translation: AEE75430.1
BX824350 mRNA No translation available.
RefSeqiNP_188004.1, NM_112242.3

3D structure databases

SMRiQ9LRV9
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT3G13880.1

Proteomic databases

PaxDbiQ9LRV9

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G13880.1; AT3G13880.1; AT3G13880
GeneIDi820601
GrameneiAT3G13880.1; AT3G13880.1; AT3G13880
KEGGiath:AT3G13880

Organism-specific databases

AraportiAT3G13880
TAIRilocus:2087969 AT3G13880

Phylogenomic databases

eggNOGiKOG4197 Eukaryota
ENOG410Z7Z7 LUCA
HOGENOMiHOG000237570
InParanoidiQ9LRV9
OMAiEAVHGCV
OrthoDBi1344243at2759
PhylomeDBiQ9LRV9

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q9LRV9

Gene expression databases

ExpressionAtlasiQ9LRV9 baseline and differential
GenevisibleiQ9LRV9 AT

Family and domain databases

Gene3Di1.25.40.10, 5 hits
InterProiView protein in InterPro
IPR002885 Pentatricopeptide_repeat
IPR011990 TPR-like_helical_dom_sf
PfamiView protein in Pfam
PF01535 PPR, 1 hit
PF13041 PPR_2, 5 hits
TIGRFAMsiTIGR00756 PPR, 6 hits
PROSITEiView protein in PROSITE
PS51375 PPR, 15 hits

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPP228_ARATH
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q9LRV9
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 16, 2008
Last sequence update: October 1, 2000
Last modified: May 8, 2019
This is version 102 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
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