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Protein

Pentatricopeptide repeat-containing protein At5g39710

Gene

EMB2745

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 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 At5g39710
Alternative name(s):
Protein EMBRYO DEFECTIVE 2745
<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:EMB2745
Ordered Locus Names:At5g39710
ORF Names:MIJ24.190
<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

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Araporti
AT5G39710

The Arabidopsis Information Resource

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TAIRi
locus:2164910 AT5G39710

<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; Source: COMPARTMENTS

<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_00003635441 – 747Pentatricopeptide repeat-containing protein At5g39710Add BLAST747

Proteomic databases

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

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PaxDbi
Q9FIX3

<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
Q9FIX3 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

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Genevisiblei
Q9FIX3 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

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STRINGi
3702.AT5G39710.1

<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
Q9FIX3

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

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SMRi
Q9FIX3

Database of comparative protein structure models

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ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

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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>Repeati133 – 167PPR 1Add BLAST35
Repeati168 – 203PPR 2Add BLAST36
Repeati204 – 238PPR 3Add BLAST35
Repeati239 – 273PPR 4Add BLAST35
Repeati274 – 308PPR 5Add BLAST35
Repeati309 – 343PPR 6Add BLAST35
Repeati344 – 378PPR 7Add BLAST35
Repeati379 – 413PPR 8Add BLAST35
Repeati414 – 448PPR 9Add BLAST35
Repeati449 – 483PPR 10Add BLAST35
Repeati484 – 518PPR 11Add BLAST35
Repeati519 – 553PPR 12Add BLAST35
Repeati554 – 588PPR 13Add BLAST35
Repeati604 – 638PPR 14Add BLAST35
Repeati639 – 673PPR 15Add 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

<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
HOG000084219

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
Q9FIX3

Identification of Orthologs from Complete Genome Data

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OMAi
AKFNGFM

Database of Orthologous Groups

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OrthoDBi
1344243at2759

Database for complete collections of gene phylogenies

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PhylomeDBi
Q9FIX3

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
1.25.40.10, 5 hits

Integrated resource of protein families, domains and functional sites

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InterProi
View protein in InterPro
IPR002885 Pentatricopeptide_repeat
IPR011990 TPR-like_helical_dom_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF12854 PPR_1, 3 hits
PF13041 PPR_2, 5 hits

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00756 PPR, 12 hits

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51375 PPR, 16 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.

Q9FIX3-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MFLTKTLIRR SLSTFASSPS DSLLADKALT FLKRHPYQLH HLSANFTPEA
60 70 80 90 100
ASNLLLKSQN DQALILKFLN WANPHQFFTL RCKCITLHIL TKFKLYKTAQ
110 120 130 140 150
ILAEDVAAKT LDDEYASLVF KSLQETYDLC YSTSSVFDLV VKSYSRLSLI
160 170 180 190 200
DKALSIVHLA QAHGFMPGVL SYNAVLDATI RSKRNISFAE NVFKEMLESQ
210 220 230 240 250
VSPNVFTYNI LIRGFCFAGN IDVALTLFDK METKGCLPNV VTYNTLIDGY
260 270 280 290 300
CKLRKIDDGF KLLRSMALKG LEPNLISYNV VINGLCREGR MKEVSFVLTE
310 320 330 340 350
MNRRGYSLDE VTYNTLIKGY CKEGNFHQAL VMHAEMLRHG LTPSVITYTS
360 370 380 390 400
LIHSMCKAGN MNRAMEFLDQ MRVRGLCPNE RTYTTLVDGF SQKGYMNEAY
410 420 430 440 450
RVLREMNDNG FSPSVVTYNA LINGHCVTGK MEDAIAVLED MKEKGLSPDV
460 470 480 490 500
VSYSTVLSGF CRSYDVDEAL RVKREMVEKG IKPDTITYSS LIQGFCEQRR
510 520 530 540 550
TKEACDLYEE MLRVGLPPDE FTYTALINAY CMEGDLEKAL QLHNEMVEKG
560 570 580 590 600
VLPDVVTYSV LINGLNKQSR TREAKRLLLK LFYEESVPSD VTYHTLIENC
610 620 630 640 650
SNIEFKSVVS LIKGFCMKGM MTEADQVFES MLGKNHKPDG TAYNIMIHGH
660 670 680 690 700
CRAGDIRKAY TLYKEMVKSG FLLHTVTVIA LVKALHKEGK VNELNSVIVH
710 720 730 740
VLRSCELSEA EQAKVLVEIN HREGNMDVVL DVLAEMAKDG FLPNGIS
Length:747
Mass (Da):84,274
Last modified:March 1, 2001 - 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:i1DAC020F52DD1E90
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
AB016876, AB012243 Genomic DNA Translation: BAB11377.1
CP002688 Genomic DNA Translation: AED94466.1

NCBI Reference Sequences

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RefSeqi
NP_198787.1, NM_123333.2

UniGene gene-oriented nucleotide sequence clusters

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UniGenei
At.55259

Genome annotation databases

Ensembl plant genome annotation project

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EnsemblPlantsi
AT5G39710.1; AT5G39710.1; AT5G39710

Database of genes from NCBI RefSeq genomes

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GeneIDi
833967

Gramene; a comparative resource for plants

More...
Gramenei
AT5G39710.1; AT5G39710.1; AT5G39710

KEGG: Kyoto Encyclopedia of Genes and Genomes

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KEGGi
ath:AT5G39710

<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
AB016876, AB012243 Genomic DNA Translation: BAB11377.1
CP002688 Genomic DNA Translation: AED94466.1
RefSeqiNP_198787.1, NM_123333.2
UniGeneiAt.55259

3D structure databases

ProteinModelPortaliQ9FIX3
SMRiQ9FIX3
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT5G39710.1

Proteomic databases

PaxDbiQ9FIX3

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G39710.1; AT5G39710.1; AT5G39710
GeneIDi833967
GrameneiAT5G39710.1; AT5G39710.1; AT5G39710
KEGGiath:AT5G39710

Organism-specific databases

AraportiAT5G39710
TAIRilocus:2164910 AT5G39710

Phylogenomic databases

eggNOGiKOG4197 Eukaryota
ENOG410Z7Z7 LUCA
HOGENOMiHOG000084219
InParanoidiQ9FIX3
OMAiAKFNGFM
OrthoDBi1344243at2759
PhylomeDBiQ9FIX3

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q9FIX3

Gene expression databases

ExpressionAtlasiQ9FIX3 baseline and differential
GenevisibleiQ9FIX3 AT

Family and domain databases

Gene3Di1.25.40.10, 5 hits
InterProiView protein in InterPro
IPR002885 Pentatricopeptide_repeat
IPR011990 TPR-like_helical_dom_sf
PfamiView protein in Pfam
PF12854 PPR_1, 3 hits
PF13041 PPR_2, 5 hits
TIGRFAMsiTIGR00756 PPR, 12 hits
PROSITEiView protein in PROSITE
PS51375 PPR, 16 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 nameiPP407_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: Q9FIX3
<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: March 1, 2001
Last modified: January 16, 2019
This is version 97 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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