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Protein

Pentatricopeptide repeat-containing protein At4g13650

Gene

PCMP-H42

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 - Molecular functioni

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 At4g13650
<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-H42
Ordered Locus Names:At4g13650
ORF Names:F18A5.40
<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
AT4G13650

The Arabidopsis Information Resource

More...
TAIRi
locus:2119440 AT4G13650

<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_00003634251 – 1064Pentatricopeptide repeat-containing protein At4g13650Add BLAST1064

Proteomic databases

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

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PaxDbi
Q9SVP7

PRoteomics IDEntifications database

More...
PRIDEi
Q9SVP7

<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
Q9SVP7 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q9SVP7 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.AT4G13650.1

<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

More...
ProteinModelPortali
Q9SVP7

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

More...
SMRi
Q9SVP7

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>Repeati83 – 118PPR 1Add BLAST36
Repeati119 – 149PPR 2Add BLAST31
Repeati150 – 184PPR 3Add BLAST35
Repeati185 – 220PPR 4Add BLAST36
Repeati221 – 251PPR 5Add BLAST31
Repeati252 – 286PPR 6Add BLAST35
Repeati287 – 321PPR 7Add BLAST35
Repeati322 – 352PPR 8Add BLAST31
Repeati353 – 387PPR 9Add BLAST35
Repeati388 – 422PPR 10Add BLAST35
Repeati423 – 453PPR 11Add BLAST31
Repeati454 – 488PPR 12Add BLAST35
Repeati489 – 523PPR 13Add BLAST35
Repeati524 – 554PPR 14Add BLAST31
Repeati555 – 589PPR 15Add BLAST35
Repeati590 – 624PPR 16Add BLAST35
Repeati625 – 655PPR 17Add BLAST31
Repeati656 – 690PPR 18Add BLAST35
Repeati691 – 725PPR 19Add BLAST35
Repeati726 – 756PPR 20Add BLAST31
Repeati757 – 791PPR 21Add BLAST35
Repeati792 – 827PPR 22Add BLAST36
Repeati828 – 858PPR 23Add 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>Regioni863 – 938Type E motifAdd BLAST76
Regioni939 – 969Type E(+) motifAdd BLAST31
Regioni970 – 1064Type DYW motifAdd BLAST95

<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-H 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

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eggNOGi
KOG4197 Eukaryota
ENOG410Z7Z7 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000237570

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q9SVP7

Identification of Orthologs from Complete Genome Data

More...
OMAi
ITLYLRC

Database of Orthologous Groups

More...
OrthoDBi
1344243at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q9SVP7

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.25.40.10, 7 hits

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR032867 DYW_dom
IPR002885 Pentatricopeptide_repeat
IPR011990 TPR-like_helical_dom_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF14432 DYW_deaminase, 1 hit
PF01535 PPR, 7 hits
PF13041 PPR_2, 3 hits
PF13812 PPR_3, 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, 21 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.

Q9SVP7-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MNKYIWLVRL WHSKEEPMFL RSVSSSFIFI HGVPRKLKTR TVFPTLCGTR
60 70 80 90 100
RASFAAISVY ISEDESFQEK RIDSVENRGI RPNHQTLKWL LEGCLKTNGS
110 120 130 140 150
LDEGRKLHSQ ILKLGLDSNG CLSEKLFDFY LFKGDLYGAF KVFDEMPERT
160 170 180 190 200
IFTWNKMIKE LASRNLIGEV FGLFVRMVSE NVTPNEGTFS GVLEACRGGS
210 220 230 240 250
VAFDVVEQIH ARILYQGLRD STVVCNPLID LYSRNGFVDL ARRVFDGLRL
260 270 280 290 300
KDHSSWVAMI SGLSKNECEA EAIRLFCDMY VLGIMPTPYA FSSVLSACKK
310 320 330 340 350
IESLEIGEQL HGLVLKLGFS SDTYVCNALV SLYFHLGNLI SAEHIFSNMS
360 370 380 390 400
QRDAVTYNTL INGLSQCGYG EKAMELFKRM HLDGLEPDSN TLASLVVACS
410 420 430 440 450
ADGTLFRGQQ LHAYTTKLGF ASNNKIEGAL LNLYAKCADI ETALDYFLET
460 470 480 490 500
EVENVVLWNV MLVAYGLLDD LRNSFRIFRQ MQIEEIVPNQ YTYPSILKTC
510 520 530 540 550
IRLGDLELGE QIHSQIIKTN FQLNAYVCSV LIDMYAKLGK LDTAWDILIR
560 570 580 590 600
FAGKDVVSWT TMIAGYTQYN FDDKALTTFR QMLDRGIRSD EVGLTNAVSA
610 620 630 640 650
CAGLQALKEG QQIHAQACVS GFSSDLPFQN ALVTLYSRCG KIEESYLAFE
660 670 680 690 700
QTEAGDNIAW NALVSGFQQS GNNEEALRVF VRMNREGIDN NNFTFGSAVK
710 720 730 740 750
AASETANMKQ GKQVHAVITK TGYDSETEVC NALISMYAKC GSISDAEKQF
760 770 780 790 800
LEVSTKNEVS WNAIINAYSK HGFGSEALDS FDQMIHSNVR PNHVTLVGVL
810 820 830 840 850
SACSHIGLVD KGIAYFESMN SEYGLSPKPE HYVCVVDMLT RAGLLSRAKE
860 870 880 890 900
FIQEMPIKPD ALVWRTLLSA CVVHKNMEIG EFAAHHLLEL EPEDSATYVL
910 920 930 940 950
LSNLYAVSKK WDARDLTRQK MKEKGVKKEP GQSWIEVKNS IHSFYVGDQN
960 970 980 990 1000
HPLADEIHEY FQDLTKRASE IGYVQDCFSL LNELQHEQKD PIIFIHSEKL
1010 1020 1030 1040 1050
AISFGLLSLP ATVPINVMKN LRVCNDCHAW IKFVSKVSNR EIIVRDAYRF
1060
HHFEGGACSC KDYW
Length:1,064
Mass (Da):119,740
Last modified:February 10, 2009 - v2
<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:i87E47DF4376C9243
GO

<p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence CAB36829 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence CAB78407 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti1015I → M (PubMed:14993207).Curated1
Sequence conflicti1025N → D (PubMed:14993207).Curated1

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
AL035528 Genomic DNA Translation: CAB36829.1 Sequence problems.
AL161537 Genomic DNA Translation: CAB78407.1 Sequence problems.
CP002687 Genomic DNA Translation: AEE83309.1
BX827423 mRNA No translation available.

Protein sequence database of the Protein Information Resource

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PIRi
T05234

NCBI Reference Sequences

More...
RefSeqi
NP_193101.2, NM_117439.3

UniGene gene-oriented nucleotide sequence clusters

More...
UniGenei
At.50335

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT4G13650.1; AT4G13650.1; AT4G13650

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
826999

Gramene; a comparative resource for plants

More...
Gramenei
AT4G13650.1; AT4G13650.1; AT4G13650

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ath:AT4G13650

<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
AL035528 Genomic DNA Translation: CAB36829.1 Sequence problems.
AL161537 Genomic DNA Translation: CAB78407.1 Sequence problems.
CP002687 Genomic DNA Translation: AEE83309.1
BX827423 mRNA No translation available.
PIRiT05234
RefSeqiNP_193101.2, NM_117439.3
UniGeneiAt.50335

3D structure databases

ProteinModelPortaliQ9SVP7
SMRiQ9SVP7
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT4G13650.1

Proteomic databases

PaxDbiQ9SVP7
PRIDEiQ9SVP7

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G13650.1; AT4G13650.1; AT4G13650
GeneIDi826999
GrameneiAT4G13650.1; AT4G13650.1; AT4G13650
KEGGiath:AT4G13650

Organism-specific databases

AraportiAT4G13650
TAIRilocus:2119440 AT4G13650

Phylogenomic databases

eggNOGiKOG4197 Eukaryota
ENOG410Z7Z7 LUCA
HOGENOMiHOG000237570
InParanoidiQ9SVP7
OMAiITLYLRC
OrthoDBi1344243at2759
PhylomeDBiQ9SVP7

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q9SVP7

Gene expression databases

ExpressionAtlasiQ9SVP7 baseline and differential
GenevisibleiQ9SVP7 AT

Family and domain databases

Gene3Di1.25.40.10, 7 hits
InterProiView protein in InterPro
IPR032867 DYW_dom
IPR002885 Pentatricopeptide_repeat
IPR011990 TPR-like_helical_dom_sf
PfamiView protein in Pfam
PF14432 DYW_deaminase, 1 hit
PF01535 PPR, 7 hits
PF13041 PPR_2, 3 hits
PF13812 PPR_3, 1 hit
TIGRFAMsiTIGR00756 PPR, 5 hits
PROSITEiView protein in PROSITE
PS51375 PPR, 21 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 nameiPP307_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: Q9SVP7
<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: February 10, 2009
Last modified: January 16, 2019
This is version 100 of the entry and version 2 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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