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Entry version 112 (13 Nov 2019)
Sequence version 2 (23 Jan 2007)
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Protein

tRNA-modifying protein YgfZ

Gene

ygfZ

Organism
Escherichia coli (strain K12)
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 protein 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

Folate-binding protein involved in regulating the level of ATP-DnaA and in the modification of some tRNAs. It is probably a key factor in regulatory networks that act via tRNA modification, such as initiation of chromosomal replication.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei27FolateSequence analysis1
Binding sitei189FolateSequence analysis1

<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

Biological processtRNA processing
LigandFolate-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:G7511-MONOMER
ECOL316407:JW2866-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_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:
tRNA-modifying protein YgfZ
<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:ygfZ
Synonyms:yzzW
Ordered Locus Names:b2898, JW2866
<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>OrganismiEscherichia coli (strain K12)
<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 identifieri83333 [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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<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
  • UP000000318 <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
  • UP000000625 Componenti: Chromosome

<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

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

<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 <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved1 Publication
<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_00001698342 – 326tRNA-modifying protein YgfZAdd BLAST325

Proteomic databases

Encyclopedia of Proteome Dynamics

More...
EPDi
P0ADE8

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P0ADE8

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

More...
PaxDbi
P0ADE8

PRoteomics IDEntifications database

More...
PRIDEi
P0ADE8

2D gel databases

Two-dimensional polyacrylamide gel electrophoresis database from the Geneva University Hospital

More...
SWISS-2DPAGEi
P0ADE8

<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
4261457, 786 interactors

Database of interacting proteins

More...
DIPi
DIP-48117N

Protein interaction database and analysis system

More...
IntActi
P0ADE8, 6 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b2898

<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

Secondary structure

1326
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

More...
SMRi
P0ADE8

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P0ADE8

<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 tRNA-modifying YgfZ family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4106XY2 Bacteria
COG0354 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000261300

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P0ADE8

KEGG Orthology (KO)

More...
KOi
K06980

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P0ADE8

Family and domain databases

HAMAP database of protein families

More...
HAMAPi
MF_01175 tRNA_modifying_YgfZ, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR028896 GCST/YgfZ/DmdA
IPR006222 GCV_T_N
IPR029043 GcvT/YgfZ_C
IPR023758 tRNA-modifying_YgfZ
IPR017703 YgfZ/GcvT_CS

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01571 GCV_T, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF006487 GcvT, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF101790 SSF101790, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR03317 ygfZ_signature, 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_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.

P0ADE8-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAFTPFPPRQ PTASARLPLT LMTLDDWALA TITGADSEKY MQGQVTADVS
60 70 80 90 100
QMAEDQHLLA AHCDAKGKMW SNLRLFRDGD GFAWIERRSV REPQLTELKK
110 120 130 140 150
YAVFSKVTIA PDDERVLLGV AGFQARAALA NLFSELPSKE KQVVKEGATT
160 170 180 190 200
LLWFEHPAER FLIVTDEATA NMLTDKLRGE AELNNSQQWL ALNIEAGFPV
210 220 230 240 250
IDAANSGQFI PQATNLQALG GISFKKGCYT GQEMVARAKF RGANKRALWL
260 270 280 290 300
LAGSASRLPE AGEDLELKMG ENWRRTGTVL AAVKLEDGQV VVQVVMNNDM
310 320
EPDSIFRVRD DANTLHIEPL PYSLEE
Length:326
Mass (Da):36,094
Last modified:January 23, 2007 - 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:i08E050CE26B56B77
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti8P → D AA sequence (PubMed:9298646).Curated1

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
U28375 Genomic DNA Translation: AAA83079.1
U00096 Genomic DNA Translation: AAC75936.1
AP009048 Genomic DNA Translation: BAE76963.1

Protein sequence database of the Protein Information Resource

More...
PIRi
B65074

NCBI Reference Sequences

More...
RefSeqi
NP_417374.1, NC_000913.3
WP_000886062.1, NZ_STEB01000001.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC75936; AAC75936; b2898
BAE76963; BAE76963; BAE76963

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
947384

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW2866
eco:b2898

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.3834

<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
U28375 Genomic DNA Translation: AAA83079.1
U00096 Genomic DNA Translation: AAC75936.1
AP009048 Genomic DNA Translation: BAE76963.1
PIRiB65074
RefSeqiNP_417374.1, NC_000913.3
WP_000886062.1, NZ_STEB01000001.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NRKX-ray2.80A1-325[»]
1VLYX-ray1.30A1-326[»]
SMRiP0ADE8
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi4261457, 786 interactors
DIPiDIP-48117N
IntActiP0ADE8, 6 interactors
STRINGi511145.b2898

2D gel databases

SWISS-2DPAGEiP0ADE8

Proteomic databases

EPDiP0ADE8
jPOSTiP0ADE8
PaxDbiP0ADE8
PRIDEiP0ADE8

Genome annotation databases

EnsemblBacteriaiAAC75936; AAC75936; b2898
BAE76963; BAE76963; BAE76963
GeneIDi947384
KEGGiecj:JW2866
eco:b2898
PATRICifig|1411691.4.peg.3834

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB2549

Phylogenomic databases

eggNOGiENOG4106XY2 Bacteria
COG0354 LUCA
HOGENOMiHOG000261300
InParanoidiP0ADE8
KOiK06980
PhylomeDBiP0ADE8

Enzyme and pathway databases

BioCyciEcoCyc:G7511-MONOMER
ECOL316407:JW2866-MONOMER

Miscellaneous databases

EvolutionaryTraceiP0ADE8

Protein Ontology

More...
PROi
PR:P0ADE8

Family and domain databases

HAMAPiMF_01175 tRNA_modifying_YgfZ, 1 hit
InterProiView protein in InterPro
IPR028896 GCST/YgfZ/DmdA
IPR006222 GCV_T_N
IPR029043 GcvT/YgfZ_C
IPR023758 tRNA-modifying_YgfZ
IPR017703 YgfZ/GcvT_CS
PfamiView protein in Pfam
PF01571 GCV_T, 1 hit
PIRSFiPIRSF006487 GcvT, 1 hit
SUPFAMiSSF101790 SSF101790, 1 hit
TIGRFAMsiTIGR03317 ygfZ_signature, 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 nameiYGFZ_ECOLI
<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: P0ADE8
Secondary accession number(s): P39179, Q2M9U3, Q46826
<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: December 6, 2005
Last sequence update: January 23, 2007
Last modified: November 13, 2019
This is version 112 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 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

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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