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Protein

Pentatricopeptide repeat-containing protein At4g39530

Gene

PCMP-E52

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>
-Protein inferred from homologyi <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

  • 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 At4g39530
<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-E52
Ordered Locus Names:At4g39530
ORF Names:F23K16.160
<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 4

Organism-specific databases

Arabidopsis Information Portal

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Araporti
AT4G39530

The Arabidopsis Information Resource

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TAIRi
locus:2122551 AT4G39530

<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_00003634741 – 834Pentatricopeptide repeat-containing protein At4g39530Add BLAST834

Proteomic databases

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

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PaxDbi
Q9SVA5

PRoteomics IDEntifications database

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PRIDEi
Q9SVA5

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
Q9SVA5

<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

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ExpressionAtlasi
Q9SVA5 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q9SVA5 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.AT4G39530.1

<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

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

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ProteinModelPortali
Q9SVA5

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

More...
SMRi
Q9SVA5

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>Repeati78 – 112PPR 1Add BLAST35
Repeati113 – 144PPR 2Add BLAST32
Repeati145 – 181PPR 3Add BLAST37
Repeati182 – 212PPR 4Add BLAST31
Repeati213 – 247PPR 5Add BLAST35
Repeati248 – 282PPR 6Add BLAST35
Repeati283 – 313PPR 7Add BLAST31
Repeati314 – 348PPR 8Add BLAST35
Repeati349 – 383PPR 9Add BLAST35
Repeati384 – 414PPR 10Add BLAST31
Repeati415 – 452PPR 11Add BLAST38
Repeati453 – 487PPR 12Add BLAST35
Repeati488 – 518PPR 13Add BLAST31
Repeati519 – 553PPR 14Add BLAST35
Repeati554 – 588PPR 15Add BLAST35
Repeati589 – 619PPR 16Add BLAST31
Repeati620 – 654PPR 17Add BLAST35
Repeati655 – 689PPR 18Add BLAST35
Repeati690 – 720PPR 19Add BLAST31

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>Regioni725 – 800Type E motifAdd BLAST76
Regioni801 – 831Type E(+) motifAdd BLAST31

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi18 – 26Poly-Ser9

<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
Q9SVA5

Identification of Orthologs from Complete Genome Data

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OMAi
SMFHGQQ

Database of Orthologous Groups

More...
OrthoDBi
EOG093602MF

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q9SVA5

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
1.25.40.10, 6 hits

Integrated resource of protein families, domains and functional sites

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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, 9 hits
PF13041 PPR_2, 3 hits

Superfamily database of structural and functional annotation

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SUPFAMi
SSF48452 SSF48452, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00756 PPR, 5 hits

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51375 PPR, 18 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>.<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.

Q9SVA5-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MRSYRCWRKV QETIRLYSSS SSSASSLLEF VNADFPSTIG IRGRREFARL
60 70 80 90 100
LQLRASDDLL HYQNVVHGQI IVWGLELDTY LSNILINLYS RAGGMVYARK
110 120 130 140 150
VFEKMPERNL VSWSTMVSAC NHHGIYEESL VVFLEFWRTR KDSPNEYILS
160 170 180 190 200
SFIQACSGLD GRGRWMVFQL QSFLVKSGFD RDVYVGTLLI DFYLKDGNID
210 220 230 240 250
YARLVFDALP EKSTVTWTTM ISGCVKMGRS YVSLQLFYQL MEDNVVPDGY
260 270 280 290 300
ILSTVLSACS ILPFLEGGKQ IHAHILRYGL EMDASLMNVL IDSYVKCGRV
310 320 330 340 350
IAAHKLFNGM PNKNIISWTT LLSGYKQNAL HKEAMELFTS MSKFGLKPDM
360 370 380 390 400
YACSSILTSC ASLHALGFGT QVHAYTIKAN LGNDSYVTNS LIDMYAKCDC
410 420 430 440 450
LTDARKVFDI FAAADVVLFN AMIEGYSRLG TQWELHEALN IFRDMRFRLI
460 470 480 490 500
RPSLLTFVSL LRASASLTSL GLSKQIHGLM FKYGLNLDIF AGSALIDVYS
510 520 530 540 550
NCYCLKDSRL VFDEMKVKDL VIWNSMFAGY VQQSENEEAL NLFLELQLSR
560 570 580 590 600
ERPDEFTFAN MVTAAGNLAS VQLGQEFHCQ LLKRGLECNP YITNALLDMY
610 620 630 640 650
AKCGSPEDAH KAFDSAASRD VVCWNSVISS YANHGEGKKA LQMLEKMMSE
660 670 680 690 700
GIEPNYITFV GVLSACSHAG LVEDGLKQFE LMLRFGIEPE TEHYVCMVSL
710 720 730 740 750
LGRAGRLNKA RELIEKMPTK PAAIVWRSLL SGCAKAGNVE LAEHAAEMAI
760 770 780 790 800
LSDPKDSGSF TMLSNIYASK GMWTEAKKVR ERMKVEGVVK EPGRSWIGIN
810 820 830
KEVHIFLSKD KSHCKANQIY EVLDDLLVQI RGVS
Length:834
Mass (Da):93,794
Last modified:May 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:i277C14CC6148E457
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
AL078620 Genomic DNA Translation: CAB44688.1
AL161595 Genomic DNA Translation: CAB80616.1
CP002687 Genomic DNA Translation: AEE87082.1

Protein sequence database of the Protein Information Resource

More...
PIRi
T09369

NCBI Reference Sequences

More...
RefSeqi
NP_195663.1, NM_120113.2

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT4G39530.1; AT4G39530.1; AT4G39530

Database of genes from NCBI RefSeq genomes

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GeneIDi
830107

Gramene; a comparative resource for plants

More...
Gramenei
AT4G39530.1; AT4G39530.1; AT4G39530

KEGG: Kyoto Encyclopedia of Genes and Genomes

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KEGGi
ath:AT4G39530

<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
AL078620 Genomic DNA Translation: CAB44688.1
AL161595 Genomic DNA Translation: CAB80616.1
CP002687 Genomic DNA Translation: AEE87082.1
PIRiT09369
RefSeqiNP_195663.1, NM_120113.2

3D structure databases

ProteinModelPortaliQ9SVA5
SMRiQ9SVA5
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT4G39530.1

PTM databases

iPTMnetiQ9SVA5

Proteomic databases

PaxDbiQ9SVA5
PRIDEiQ9SVA5

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G39530.1; AT4G39530.1; AT4G39530
GeneIDi830107
GrameneiAT4G39530.1; AT4G39530.1; AT4G39530
KEGGiath:AT4G39530

Organism-specific databases

AraportiAT4G39530
TAIRilocus:2122551 AT4G39530

Phylogenomic databases

eggNOGiKOG4197 Eukaryota
ENOG410Z7Z7 LUCA
HOGENOMiHOG000237570
InParanoidiQ9SVA5
OMAiSMFHGQQ
OrthoDBiEOG093602MF
PhylomeDBiQ9SVA5

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q9SVA5

Gene expression databases

ExpressionAtlasiQ9SVA5 baseline and differential
GenevisibleiQ9SVA5 AT

Family and domain databases

Gene3Di1.25.40.10, 6 hits
InterProiView protein in InterPro
IPR002885 Pentatricopeptide_repeat
IPR011990 TPR-like_helical_dom_sf
PfamiView protein in Pfam
PF01535 PPR, 9 hits
PF13041 PPR_2, 3 hits
SUPFAMiSSF48452 SSF48452, 1 hit
TIGRFAMsiTIGR00756 PPR, 5 hits
PROSITEiView protein in PROSITE
PS51375 PPR, 18 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 nameiPP357_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: Q9SVA5
<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: February 10, 2009
Last sequence update: May 1, 2000
Last modified: November 7, 2018
This is version 99 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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