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Entry version 85 (08 May 2019)
Sequence version 2 (10 Feb 2009)
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Protein

Pentatricopeptide repeat-containing protein At4g39952, mitochondrial

Gene

PCMP-E98

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

  • 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 At4g39952, mitochondrial
<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-E98
Ordered Locus Names:At4g39952
ORF Names:T5J17.13
<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

More...
Araporti
AT4G39952

The Arabidopsis Information Resource

More...
TAIRi
locus:504955244 AT4G39952

<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

Mitochondrion

<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 – 17MitochondrionSequence analysisAdd BLAST17
<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_000036347618 – 775Pentatricopeptide repeat-containing protein At4g39952, mitochondrialAdd BLAST758

Proteomic databases

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

More...
PaxDbi
Q3E9N1

PRoteomics IDEntifications database

More...
PRIDEi
Q3E9N1

<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
Q3E9N1 baseline and differential

<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
Q3E9N1

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>Repeati58 – 88PPR 1Add BLAST31
Repeati89 – 123PPR 2Add BLAST35
Repeati124 – 158PPR 3Add BLAST35
Repeati160 – 190PPR 4Add BLAST31
Repeati191 – 225PPR 5Add BLAST35
Repeati229 – 263PPR 6Add BLAST35
Repeati264 – 294PPR 7Add BLAST31
Repeati295 – 329PPR 8Add BLAST35
Repeati330 – 364PPR 9Add BLAST35
Repeati365 – 395PPR 10Add BLAST31
Repeati397 – 431PPR 11Add BLAST35
Repeati432 – 466PPR 12Add BLAST35
Repeati467 – 493PPR 13Add BLAST27
Repeati497 – 531PPR 14Add BLAST35
Repeati532 – 566PPR 15Add BLAST35
Repeati567 – 597PPR 16Add BLAST31
Repeati598 – 632PPR 17Add BLAST35
Repeati633 – 667PPR 18Add BLAST35
Repeati668 – 698PPR 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>Regioni703 – 775Type E motif; degenerateAdd BLAST73

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 – 23Poly-Ser6

<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

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
HOG000083857

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q3E9N1

Identification of Orthologs from Complete Genome Data

More...
OMAi
HCYSIKH

Database of Orthologous Groups

More...
OrthoDBi
1344243at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q3E9N1

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.25.40.10, 6 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, 9 hits
PF13041 PPR_2, 3 hits

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF48452 SSF48452, 1 hit

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, 19 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.

<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.

Q3E9N1-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MLRRLLKPNL VVTLRKLSSS SASYVDRHIS VILCDQSLSL ESLRKHNALI
60 70 80 90 100
ITGGLSENIF VASKLISSYA SYGKPNLSSR VFHLVTRRDI FLWNSIIKAH
110 120 130 140 150
FSNGDYARSL CFFFSMLLSG QSPDHFTAPM VVSACAELLW FHVGTFVHGL
160 170 180 190 200
VLKHGGFDRN TAVGASFVYF YSKCGFLQDA CLVFDEMPDR DVVAWTAIIS
210 220 230 240 250
GHVQNGESEG GLGYLCKMHS AGSDVDKPNP RTLECGFQAC SNLGALKEGR
260 270 280 290 300
CLHGFAVKNG LASSKFVQSS MFSFYSKSGN PSEAYLSFRE LGDEDMFSWT
310 320 330 340 350
SIIASLARSG DMEESFDMFW EMQNKGMHPD GVVISCLINE LGKMMLVPQG
360 370 380 390 400
KAFHGFVIRH CFSLDSTVCN SLLSMYCKFE LLSVAEKLFC RISEEGNKEA
410 420 430 440 450
WNTMLKGYGK MKCHVKCIEL FRKIQNLGIE IDSASATSVI SSCSHIGAVL
460 470 480 490 500
LGKSLHCYVV KTSLDLTISV VNSLIDLYGK MGDLTVAWRM FCEADTNVIT
510 520 530 540 550
WNAMIASYVH CEQSEKAIAL FDRMVSENFK PSSITLVTLL MACVNTGSLE
560 570 580 590 600
RGQMIHRYIT ETEHEMNLSL SAALIDMYAK CGHLEKSREL FDAGNQKDAV
610 620 630 640 650
CWNVMISGYG MHGDVESAIA LFDQMEESDV KPTGPTFLAL LSACTHAGLV
660 670 680 690 700
EQGKKLFLKM HQYDVKPNLK HYSCLVDLLS RSGNLEEAES TVMSMPFSPD
710 720 730 740 750
GVIWGTLLSS CMTHGEFEMG IRMAERAVAS DPQNDGYYIM LANMYSAAGK
760 770
WEEAERAREM MRESGVGKRA GHSVV
Length:775
Mass (Da):85,828
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:iE0DAC5534CE4B9FE
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AL035708 Genomic DNA No translation available.
AL161596 Genomic DNA No translation available.
CP002687 Genomic DNA Translation: AEE87144.1

NCBI Reference Sequences

More...
RefSeqi
NP_680777.2, NM_148411.3

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT4G39952.1; AT4G39952.1; AT4G39952

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
830155

Gramene; a comparative resource for plants

More...
Gramenei
AT4G39952.1; AT4G39952.1; AT4G39952

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ath:AT4G39952

<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
AL035708 Genomic DNA No translation available.
AL161596 Genomic DNA No translation available.
CP002687 Genomic DNA Translation: AEE87144.1
RefSeqiNP_680777.2, NM_148411.3

3D structure databases

SMRiQ3E9N1
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PaxDbiQ3E9N1
PRIDEiQ3E9N1

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G39952.1; AT4G39952.1; AT4G39952
GeneIDi830155
GrameneiAT4G39952.1; AT4G39952.1; AT4G39952
KEGGiath:AT4G39952

Organism-specific databases

AraportiAT4G39952
TAIRilocus:504955244 AT4G39952

Phylogenomic databases

eggNOGiKOG4197 Eukaryota
ENOG410Z7Z7 LUCA
HOGENOMiHOG000083857
InParanoidiQ3E9N1
OMAiHCYSIKH
OrthoDBi1344243at2759
PhylomeDBiQ3E9N1

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q3E9N1

Gene expression databases

ExpressionAtlasiQ3E9N1 baseline and differential

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, 6 hits
PROSITEiView protein in PROSITE
PS51375 PPR, 19 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 nameiPP359_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: Q3E9N1
<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: May 8, 2019
This is version 85 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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