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Entry version 105 (08 May 2019)
Sequence version 1 (01 Oct 2000)
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Protein

Pentatricopeptide repeat-containing protein At5g13270, chloroplastic

Gene

PCMP-H90

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: TAIR

<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 At5g13270, chloroplastic
<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-H90
Ordered Locus Names:At5g13270
ORF Names:T31B5_90
<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 5

Organism-specific databases

Arabidopsis Information Portal

More...
Araporti
AT5G13270

The Arabidopsis Information Resource

More...
TAIRi
locus:2183886 AT5G13270

<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>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 - Cellular componenti

Chloroplast, Plastid

<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 transit peptide.<p><a href='/help/transit' target='_top'>More...</a></p>Transit peptidei1 – 80ChloroplastSequence analysisAdd BLAST80
<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_000036351581 – 752Pentatricopeptide repeat-containing protein At5g13270, chloroplasticAdd BLAST672

Proteomic databases

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

More...
PaxDbi
Q9LYU9

PRoteomics IDEntifications database

More...
PRIDEi
Q9LYU9

<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
Q9LYU9 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q9LYU9 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

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
16446, 1 interactor

STRING: functional protein association networks

More...
STRINGi
3702.AT5G13270.1

<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>Repeati47 – 81PPR 1Add BLAST35
Repeati82 – 116PPR 2Add BLAST35
Repeati117 – 147PPR 3Add BLAST31
Repeati148 – 182PPR 4Add BLAST35
Repeati183 – 217PPR 5Add BLAST35
Repeati218 – 248PPR 6Add BLAST31
Repeati249 – 283PPR 7Add BLAST35
Repeati284 – 318PPR 8Add BLAST35
Repeati319 – 349PPR 9Add BLAST31
Repeati350 – 384PPR 10Add BLAST35
Repeati386 – 420PPR 11Add BLAST35
Repeati421 – 451PPR 12Add BLAST31
Repeati452 – 486PPR 13Add BLAST35
Repeati487 – 522PPR 14Add BLAST36
Repeati523 – 553PPR 15Add 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>Regioni558 – 633Type E motifAdd BLAST76
Regioni634 – 664Type E(+) motifAdd BLAST31
Regioni665 – 752Type DYW motifAdd BLAST88

<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

Keywords - Domaini

Repeat, Transit peptide

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
Q9LYU9

Identification of Orthologs from Complete Genome Data

More...
OMAi
FDQMAVK

Database of Orthologous Groups

More...
OrthoDBi
1344243at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q9LYU9

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.25.40.10, 4 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, 2 hits

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, 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.

<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 in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

Q9LYU9-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTILTVQSSF SSSRVPVIKN ANFDQIPSWV SLKSSTSSPS VKISHKQGQV
60 70 80 90 100
ENLHLVSLSK HRKLNEAFEF LQEMDKAGVS VSSYSYQCLF EACRELRSLS
110 120 130 140 150
HGRLLHDRMR MGIENPSVLL QNCVLQMYCE CRSLEDADKL FDEMSELNAV
160 170 180 190 200
SRTTMISAYA EQGILDKAVG LFSGMLASGD KPPSSMYTTL LKSLVNPRAL
210 220 230 240 250
DFGRQIHAHV IRAGLCSNTS IETGIVNMYV KCGWLVGAKR VFDQMAVKKP
260 270 280 290 300
VACTGLMVGY TQAGRARDAL KLFVDLVTEG VEWDSFVFSV VLKACASLEE
310 320 330 340 350
LNLGKQIHAC VAKLGLESEV SVGTPLVDFY IKCSSFESAC RAFQEIREPN
360 370 380 390 400
DVSWSAIISG YCQMSQFEEA VKTFKSLRSK NASILNSFTY TSIFQACSVL
410 420 430 440 450
ADCNIGGQVH ADAIKRSLIG SQYGESALIT MYSKCGCLDD ANEVFESMDN
460 470 480 490 500
PDIVAWTAFI SGHAYYGNAS EALRLFEKMV SCGMKPNSVT FIAVLTACSH
510 520 530 540 550
AGLVEQGKHC LDTMLRKYNV APTIDHYDCM IDIYARSGLL DEALKFMKNM
560 570 580 590 600
PFEPDAMSWK CFLSGCWTHK NLELGEIAGE ELRQLDPEDT AGYVLPFNLY
610 620 630 640 650
TWAGKWEEAA EMMKLMNERM LKKELSCSWI QEKGKIHRFI VGDKHHPQTQ
660 670 680 690 700
EIYEKLKEFD GFMEGDMFQC NMTERREQLL DHSERLAIAF GLISVHGNAP
710 720 730 740 750
APIKVFKNLR ACPDCHEFAK HVSLVTGHEI VIRDSRRFHH FKEGKCSCND

YW
Length:752
Mass (Da):84,263
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:i5405C8BC13F1E09C
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
AL163491 Genomic DNA Translation: CAB86634.1
CP002688 Genomic DNA Translation: AED91873.1

Protein sequence database of the Protein Information Resource

More...
PIRi
T48574

NCBI Reference Sequences

More...
RefSeqi
NP_196831.1, NM_121330.2

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT5G13270.1; AT5G13270.1; AT5G13270

Database of genes from NCBI RefSeq genomes

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GeneIDi
831168

Gramene; a comparative resource for plants

More...
Gramenei
AT5G13270.1; AT5G13270.1; AT5G13270

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ath:AT5G13270

<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
AL163491 Genomic DNA Translation: CAB86634.1
CP002688 Genomic DNA Translation: AED91873.1
PIRiT48574
RefSeqiNP_196831.1, NM_121330.2

3D structure databases

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

SWISS-MODEL Interactive Workspace

More...
SWISS-MODEL-Workspacei
Submit a new modelling project...

Protein-protein interaction databases

BioGridi16446, 1 interactor
STRINGi3702.AT5G13270.1

Proteomic databases

PaxDbiQ9LYU9
PRIDEiQ9LYU9

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G13270.1; AT5G13270.1; AT5G13270
GeneIDi831168
GrameneiAT5G13270.1; AT5G13270.1; AT5G13270
KEGGiath:AT5G13270

Organism-specific databases

AraportiAT5G13270
TAIRilocus:2183886 AT5G13270

Phylogenomic databases

eggNOGiKOG4197 Eukaryota
ENOG410Z7Z7 LUCA
HOGENOMiHOG000237570
InParanoidiQ9LYU9
OMAiFDQMAVK
OrthoDBi1344243at2759
PhylomeDBiQ9LYU9

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q9LYU9

Gene expression databases

ExpressionAtlasiQ9LYU9 baseline and differential
GenevisibleiQ9LYU9 AT

Family and domain databases

Gene3Di1.25.40.10, 4 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, 2 hits
TIGRFAMsiTIGR00756 PPR, 5 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 nameiPP378_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: Q9LYU9
<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: October 1, 2000
Last modified: May 8, 2019
This is version 105 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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