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Entry version 88 (16 Oct 2019)
Sequence version 2 (10 Feb 2009)
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Protein

Pentatricopeptide repeat-containing protein At4g01400, mitochondrial

Gene

At4g01400

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score:

Annotation score:3 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

<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 At4g01400, 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
Ordered Locus Names:At4g01400
ORF Names:F3D13.1
<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 lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliopsidaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
<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
AT4G01400

The Arabidopsis Information Resource

More...
TAIRi
locus:2125152 AT4G01400

<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 – 34MitochondrionSequence analysisAdd BLAST34
<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_000036341635 – 466Pentatricopeptide repeat-containing protein At4g01400, mitochondrialAdd BLAST432

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
Q8LDU5

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
Q8LDU5

<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
Q8LDU5 baseline and differential

<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
13234, 1 interactor

<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
Q8LDU5

Database of comparative protein structure models

More...
ModBasei
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>Repeati118 – 152PPR 1Add BLAST35
Repeati153 – 188PPR 2Add BLAST36
Repeati189 – 223PPR 3Add BLAST35
Repeati224 – 258PPR 4Add BLAST35
Repeati259 – 293PPR 5Add BLAST35
Repeati294 – 328PPR 6Add BLAST35
Repeati329 – 363PPR 7Add BLAST35
Repeati364 – 398PPR 8Add BLAST35

<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. P subfamily.Curated

Keywords - Domaini

Repeat, Transit peptide

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG0412 Eukaryota
KOG4197 Eukaryota
ENOG410XS60 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000244282

KEGG Orthology (KO)

More...
KOi
K20291

Identification of Orthologs from Complete Genome Data

More...
OMAi
FNQMFKR

Database of Orthologous Groups

More...
OrthoDBi
1344243at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q8LDU5

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.25.40.10, 2 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, 2 hits
PF12854 PPR_1, 1 hit
PF13041 PPR_2, 2 hits

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, 8 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.

Q8LDU5-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MIRRPIYDFA AVFRHLTSPL STSSRFLFYS SSEHEARKPI VSNPKSPIGS
60 70 80 90 100
PTRVQKLIAS QSDPLLAKEI FDYASQQPNF RHSRSSHLIL ILKLGRGRYF
110 120 130 140 150
NLIDDVLAKH RSSGYPLTGE IFTYLIKVYA EAKLPEKVLS TFYKMLEFNF
160 170 180 190 200
TPQPKHLNRI LDVLVSHRGY LQKAFELFKS SRLHGVMPNT RSYNLLMQAF
210 220 230 240 250
CLNDDLSIAY QLFGKMLERD VVPDVDSYKI LIQGFCRKGQ VNGAMELLDD
260 270 280 290 300
MLNKGFVPDR LSYTTLLNSL CRKTQLREAY KLLCRMKLKG CNPDLVHYNT
310 320 330 340 350
MILGFCREDR AMDARKVLDD MLSNGCSPNS VSYRTLIGGL CDQGMFDEGK
360 370 380 390 400
KYLEEMISKG FSPHFSVSNC LVKGFCSFGK VEEACDVVEV VMKNGETLHS
410 420 430 440 450
DTWEMVIPLI CNEDESEKIK LFLEDAVKEE ITGDTRIVDV GIGLGSYLSS
460
KLQMKRKNAR ERRRHL
Length:466
Mass (Da):53,250
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:i2F37FE0541BA4086
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 AAC19289 differs from that shown. Reason: Erroneous gene model prediction. The predicted gene has been split into 2 genes: At4g01395 and At4g01400.Curated
The sequence AAM63012 differs from that shown. Reason: Erroneous termination. Truncated C-terminus.Curated
The sequence CAB80949 differs from that shown. Reason: Erroneous gene model prediction. The predicted gene has been split into 2 genes: At4g01395 and At4g01400.Curated

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
AF069300 Genomic DNA Translation: AAC19289.1 Sequence problems.
AL161491 Genomic DNA Translation: CAB80949.1 Sequence problems.
CP002687 Genomic DNA Translation: AEE82019.2
AY085796 mRNA Translation: AAM63012.1 Sequence problems.

Protein sequence database of the Protein Information Resource

More...
PIRi
C85018
T01377

NCBI Reference Sequences

More...
RefSeqi
NP_001154199.1, NM_001160727.2

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT4G01400.1; AT4G01400.1; AT4G01400

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
28719435

Gramene; a comparative resource for plants

More...
Gramenei
AT4G01400.1; AT4G01400.1; AT4G01400

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ath:AT4G01400

<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

Pentatricopeptide repeat proteins

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF069300 Genomic DNA Translation: AAC19289.1 Sequence problems.
AL161491 Genomic DNA Translation: CAB80949.1 Sequence problems.
CP002687 Genomic DNA Translation: AEE82019.2
AY085796 mRNA Translation: AAM63012.1 Sequence problems.
PIRiC85018
T01377
RefSeqiNP_001154199.1, NM_001160727.2

3D structure databases

SMRiQ8LDU5
ModBaseiSearch...

Protein-protein interaction databases

BioGridi13234, 1 interactor

PTM databases

iPTMnetiQ8LDU5

Proteomic databases

PRIDEiQ8LDU5

Genome annotation databases

EnsemblPlantsiAT4G01400.1; AT4G01400.1; AT4G01400
GeneIDi28719435
GrameneiAT4G01400.1; AT4G01400.1; AT4G01400
KEGGiath:AT4G01400

Organism-specific databases

AraportiAT4G01400
TAIRilocus:2125152 AT4G01400

Phylogenomic databases

eggNOGiKOG0412 Eukaryota
KOG4197 Eukaryota
ENOG410XS60 LUCA
HOGENOMiHOG000244282
KOiK20291
OMAiFNQMFKR
OrthoDBi1344243at2759
PhylomeDBiQ8LDU5

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q8LDU5

Gene expression databases

ExpressionAtlasiQ8LDU5 baseline and differential

Family and domain databases

Gene3Di1.25.40.10, 2 hits
InterProiView protein in InterPro
IPR002885 Pentatricopeptide_repeat
IPR011990 TPR-like_helical_dom_sf
PfamiView protein in Pfam
PF01535 PPR, 2 hits
PF12854 PPR_1, 1 hit
PF13041 PPR_2, 2 hits
TIGRFAMsiTIGR00756 PPR, 6 hits
PROSITEiView protein in PROSITE
PS51375 PPR, 8 hits

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
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 nameiPP298_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: Q8LDU5
Secondary accession number(s): F4JI19, O81330, Q9M133
<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: October 16, 2019
This is version 88 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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