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Protein

Pentatricopeptide repeat-containing protein At4g02750

Gene

PCMP-H24

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 - 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 At4g02750
<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-H24
Ordered Locus Names:At4g02750
ORF Names:T5J8.5
<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
AT4G02750

The Arabidopsis Information Resource

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TAIRi
locus:2140235 AT4G02750

<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_00003634191 – 781Pentatricopeptide repeat-containing protein At4g02750Add BLAST781

Proteomic databases

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

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PaxDbi
Q9SY02

PRoteomics IDEntifications database

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PRIDEi
Q9SY02

<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
Q9SY02 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q9SY02 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.AT4G02750.1

<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
Q9SY02

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

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SMRi
Q9SY02

Database of comparative protein structure models

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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>Repeati63 – 93PPR 1Add BLAST31
Repeati94 – 128PPR 2Add BLAST35
Repeati129 – 155PPR 3Add BLAST27
Repeati156 – 190PPR 4Add BLAST35
Repeati191 – 217PPR 5Add BLAST27
Repeati218 – 248PPR 6Add BLAST31
Repeati249 – 279PPR 7Add BLAST31
Repeati280 – 314PPR 8Add BLAST35
Repeati315 – 341PPR 9Add BLAST27
Repeati342 – 376PPR 10Add BLAST35
Repeati377 – 407PPR 11Add BLAST31
Repeati408 – 442PPR 12Add BLAST35
Repeati443 – 473PPR 13Add BLAST31
Repeati474 – 508PPR 14Add BLAST35
Repeati509 – 544PPR 15Add BLAST36
Repeati545 – 575PPR 16Add 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>Regioni580 – 655Type E motifAdd BLAST76
Regioni656 – 686Type E(+) motifAdd BLAST31
Regioni687 – 781Type DYW motifAdd BLAST95

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 biasi702 – 707Poly-Glu6

<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

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
Q9SY02

Identification of Orthologs from Complete Genome Data

More...
OMAi
EDLDMRM

Database of Orthologous Groups

More...
OrthoDBi
EOG093602I2

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q9SY02

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, 11 hits
PF12854 PPR_1, 1 hit
PF13041 PPR_2, 1 hit

Superfamily database of structural and functional annotation

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SUPFAMi
SSF48452 SSF48452, 2 hits

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00756 PPR, 13 hits

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51375 PPR, 17 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.

Q9SY02-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MEINKFRALS RRAQQLHYTS LNGLKRRCNN AHGAANFHSL KRATQTQIQK
60 70 80 90 100
SQTKPLLKCG DSDIKEWNVA ISSYMRTGRC NEALRVFKRM PRWSSVSYNG
110 120 130 140 150
MISGYLRNGE FELARKLFDE MPERDLVSWN VMIKGYVRNR NLGKARELFE
160 170 180 190 200
IMPERDVCSW NTMLSGYAQN GCVDDARSVF DRMPEKNDVS WNALLSAYVQ
210 220 230 240 250
NSKMEEACML FKSRENWALV SWNCLLGGFV KKKKIVEARQ FFDSMNVRDV
260 270 280 290 300
VSWNTIITGY AQSGKIDEAR QLFDESPVQD VFTWTAMVSG YIQNRMVEEA
310 320 330 340 350
RELFDKMPER NEVSWNAMLA GYVQGERMEM AKELFDVMPC RNVSTWNTMI
360 370 380 390 400
TGYAQCGKIS EAKNLFDKMP KRDPVSWAAM IAGYSQSGHS FEALRLFVQM
410 420 430 440 450
EREGGRLNRS SFSSALSTCA DVVALELGKQ LHGRLVKGGY ETGCFVGNAL
460 470 480 490 500
LLMYCKCGSI EEANDLFKEM AGKDIVSWNT MIAGYSRHGF GEVALRFFES
510 520 530 540 550
MKREGLKPDD ATMVAVLSAC SHTGLVDKGR QYFYTMTQDY GVMPNSQHYA
560 570 580 590 600
CMVDLLGRAG LLEDAHNLMK NMPFEPDAAI WGTLLGASRV HGNTELAETA
610 620 630 640 650
ADKIFAMEPE NSGMYVLLSN LYASSGRWGD VGKLRVRMRD KGVKKVPGYS
660 670 680 690 700
WIEIQNKTHT FSVGDEFHPE KDEIFAFLEE LDLRMKKAGY VSKTSVVLHD
710 720 730 740 750
VEEEEKERMV RYHSERLAVA YGIMRVSSGR PIRVIKNLRV CEDCHNAIKY
760 770 780
MARITGRLII LRDNNRFHHF KDGSCSCGDY W
Length:781
Mass (Da):89,037
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:i6E8DE8B6C425E20A
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

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DDBJi
Links Updated
AC004044 Genomic DNA Translation: AAD15348.1
AL161495 Genomic DNA Translation: CAB77760.1
CP002687 Genomic DNA Translation: AEE82224.1

Protein sequence database of the Protein Information Resource

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PIRi
A85035

NCBI Reference Sequences

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RefSeqi
NP_192184.1, NM_116509.2

UniGene gene-oriented nucleotide sequence clusters

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UniGenei
At.50610

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT4G02750.1; AT4G02750.1; AT4G02750

Database of genes from NCBI RefSeq genomes

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GeneIDi
828187

Gramene; a comparative resource for plants

More...
Gramenei
AT4G02750.1; AT4G02750.1; AT4G02750

KEGG: Kyoto Encyclopedia of Genes and Genomes

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KEGGi
ath:AT4G02750

<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
AC004044 Genomic DNA Translation: AAD15348.1
AL161495 Genomic DNA Translation: CAB77760.1
CP002687 Genomic DNA Translation: AEE82224.1
PIRiA85035
RefSeqiNP_192184.1, NM_116509.2
UniGeneiAt.50610

3D structure databases

ProteinModelPortaliQ9SY02
SMRiQ9SY02
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT4G02750.1

Proteomic databases

PaxDbiQ9SY02
PRIDEiQ9SY02

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G02750.1; AT4G02750.1; AT4G02750
GeneIDi828187
GrameneiAT4G02750.1; AT4G02750.1; AT4G02750
KEGGiath:AT4G02750

Organism-specific databases

AraportiAT4G02750
TAIRilocus:2140235 AT4G02750

Phylogenomic databases

eggNOGiKOG4197 Eukaryota
ENOG410Z7Z7 LUCA
HOGENOMiHOG000237570
InParanoidiQ9SY02
OMAiEDLDMRM
OrthoDBiEOG093602I2
PhylomeDBiQ9SY02

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q9SY02

Gene expression databases

ExpressionAtlasiQ9SY02 baseline and differential
GenevisibleiQ9SY02 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, 11 hits
PF12854 PPR_1, 1 hit
PF13041 PPR_2, 1 hit
SUPFAMiSSF48452 SSF48452, 2 hits
TIGRFAMsiTIGR00756 PPR, 13 hits
PROSITEiView protein in PROSITE
PS51375 PPR, 17 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 nameiPP301_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: Q9SY02
<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: December 5, 2018
This is version 104 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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