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Entry version 65 (12 Aug 2020)
Sequence version 1 (25 Nov 2008)
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Protein

Peptide deformylase

Gene

def

Organism
Thermodesulfovibrio yellowstonii (strain ATCC 51303 / DSM 11347 / YP87)
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>
-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

Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.UniRule annotation

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Fe2+UniRule annotationNote: Binds 1 Fe2+ ion.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi93IronUniRule annotation1
Metal bindingi135IronUniRule annotation1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei136UniRule annotation1
Metal bindingi139IronUniRule annotation1

<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

<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>Keywordsi

Molecular functionHydrolase
Biological processProtein biosynthesis
LigandIron, Metal-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
TYEL289376:G1GCQ-329-MONOMER

<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%5Fand%5Ftaxonomy%5Fsection">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:
Peptide deformylaseUniRule annotation (EC:3.5.1.88UniRule annotation)
Short name:
PDFUniRule annotation
Alternative name(s):
Polypeptide deformylaseUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:defUniRule annotation
Ordered Locus Names:THEYE_A0329
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiThermodesulfovibrio yellowstonii (strain ATCC 51303 / DSM 11347 / YP87)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri289376 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiBacteriaNitrospiraeNitrospiralesNitrospiraceaeThermodesulfovibrio
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000000718 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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

<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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_10000973561 – 165Peptide deformylaseAdd BLAST165

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
B5YIL7

<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
289376.THEYE_A0329

<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

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SMRi
B5YIL7

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

<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 polypeptide deformylase family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG0242, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_061901_2_1_0

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
B5YIL7

KEGG Orthology (KO)

More...
KOi
K01462

Identification of Orthologs from Complete Genome Data

More...
OMAi
VCIQHEI

Database of Orthologous Groups

More...
OrthoDBi
1649129at2

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00487, Pep_deformylase, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.90.45.10, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_00163, Pep_deformylase, 1 hit

Integrated resource of protein families, domains and functional sites

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InterProi
View protein in InterPro
IPR023635, Peptide_deformylase
IPR036821, Peptide_deformylase_sf

The PANTHER Classification System

More...
PANTHERi
PTHR10458, PTHR10458, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01327, Pep_deformylase, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF004749, Pep_def, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR01576, PDEFORMYLASE

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF56420, SSF56420, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00079, pept_deformyl, 1 hit

<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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

B5YIL7-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAILEIKKYP DEVLKKKAET ISEINGDLQK LIDNMIETMY NANGIGLAAP
60 70 80 90 100
QVGVLKRLIV VDTSPREQNQ SLIVLINPEI TDSEGEILSE EGCLSLPGFT
110 120 130 140 150
TRLKRKERVI VKGLDRNGKE IEIEATGLLA RALQHEIDHL DGILLIDKIS
160
PLKRELFRKK FKTKK
Length:165
Mass (Da):18,570
Last modified:November 25, 2008 - 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:i396EA10220E4A59B
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

More...
DDBJi
Links Updated
CP001147 Genomic DNA Translation: ACI20745.1

NCBI Reference Sequences

More...
RefSeqi
WP_012545479.1, NC_011296.1
YP_002248176.1, NC_011296.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
ACI20745; ACI20745; THEYE_A0329

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
tye:THEYE_A0329

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|289376.4.peg.322

<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

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001147 Genomic DNA Translation: ACI20745.1
RefSeqiWP_012545479.1, NC_011296.1
YP_002248176.1, NC_011296.1

3D structure databases

SMRiB5YIL7
ModBaseiSearch...

Protein-protein interaction databases

STRINGi289376.THEYE_A0329

Proteomic databases

PRIDEiB5YIL7

Genome annotation databases

EnsemblBacteriaiACI20745; ACI20745; THEYE_A0329
KEGGitye:THEYE_A0329
PATRICifig|289376.4.peg.322

Phylogenomic databases

eggNOGiCOG0242, Bacteria
HOGENOMiCLU_061901_2_1_0
InParanoidiB5YIL7
KOiK01462
OMAiVCIQHEI
OrthoDBi1649129at2

Enzyme and pathway databases

BioCyciTYEL289376:G1GCQ-329-MONOMER

Family and domain databases

CDDicd00487, Pep_deformylase, 1 hit
Gene3Di3.90.45.10, 1 hit
HAMAPiMF_00163, Pep_deformylase, 1 hit
InterProiView protein in InterPro
IPR023635, Peptide_deformylase
IPR036821, Peptide_deformylase_sf
PANTHERiPTHR10458, PTHR10458, 1 hit
PfamiView protein in Pfam
PF01327, Pep_deformylase, 1 hit
PIRSFiPIRSF004749, Pep_def, 1 hit
PRINTSiPR01576, PDEFORMYLASE
SUPFAMiSSF56420, SSF56420, 1 hit
TIGRFAMsiTIGR00079, pept_deformyl, 1 hit

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 nameiDEF_THEYD
<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: B5YIL7
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: November 25, 2008
Last modified: August 12, 2020
This is version 65 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 programProkaryotic 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

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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