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UniProtKB - P0ADT5 (YGIC_ECOLI)

Entry version 100 (10 Feb 2021)
Sequence version 1 (06 Dec 2005)
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Protein

Putative acid--amine ligase YgiC

Gene

ygiC

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

May be a ligase forming an amide bond. Shows ATPase activity. Despite its similarity to the C-terminal synthetase domain of Gss, is not a glutathionylspermidine (Gsp) synthetase. Cannot synthesize Gsp, glutathione (GSH), or GSH intermediates, from GSH and spermidine, cysteine and glutamate, gamma-glutamylcysteine and spermidine, and gamma-glutamylcysteine and glycine. Does not bind to Gsp.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei100Transition state stabilizerBy similarity1
<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 bindingi102Magnesium 1By similarity1
Metal bindingi115Magnesium 1By similarity1
Metal bindingi115Magnesium 2By similarity1
Metal bindingi117Magnesium 2By similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 sitei267ATPBy similarity1
Binding sitei302ATPBy similarity1
Binding sitei309ATP; via amide nitrogenBy similarity1
Binding sitei336ATPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi100 – 102ATPBy similarity3
Nucleotide bindingi371 – 373ATPBy similarity3

<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

Complete GO annotation on QuickGO ...

<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 functionLigase
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:EG11165-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:
Putative acid--amine ligase YgiC (EC:6.3.1.-)
<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:ygiC
Ordered Locus Names:b3038, JW3006
<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>OrganismiEscherichia coli (strain K12)
<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 identifieri83333 [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 lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<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
  • UP000000318 <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
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Deletion of this gene does not affect the ability to synthesize glutathionylspermidine. There is no visible differences between wild-type and mutant strain growth in LB media.1 Publication

<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_00001694011 – 386Putative acid--amine ligase YgiCAdd BLAST386

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P0ADT5

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

More...PaxDbi		P0ADT5

PRoteomics IDEntifications database

More...PRIDEi		P0ADT5

<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		4262389, 16 interactors

Database of interacting proteins

More...DIPi		DIP-48176N

Protein interaction database and analysis system

More...IntActi		P0ADT5, 14 interactors

STRING: functional protein association networks

More...STRINGi		511145.b3038

<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		P0ADT5

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 glutathionylspermidine synthase preATP-grasp family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG0754, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_059175_0_0_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P0ADT5

Database for complete collections of gene phylogenies

More...PhylomeDBi		P0ADT5

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR005494, GSPS_pre-ATP-grasp-like_dom
IPR016185, PreATP-grasp_dom_sf

Pfam protein domain database

More...Pfami		View protein in Pfam
PF03738, GSP_synth, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF52440, SSF52440, 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.

P0ADT5-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MERVSITERP DWREKAHEYG FNFHTMYGEP YWCEDAYYKL TLAQVEKLEE 
        60         70         80         90        100
VTAELHQMCL KVVEKVIASD ELMTKFRIPK HTWSFVRQSW LTHQPSLYSR 
       110        120        130        140        150
LDLAWDGTGE PKLLENNADT PTSLYEAAFF QWIWLEDQLN AGNLPEGSDQ 
       160        170        180        190        200
FNSLQEKLID RFVELREQYG FQLLHLTCCR DTVEDRGTIQ YLQDCATEAE 
       210        220        230        240        250
IATEFLYIDD IGLGEKGQFT DLQDQVISNL FKLYPWEFML REMFSTKLED 
       260        270        280        290        300
AGVRWLEPAW KSIISNKALL PLLWEMFPNH PNLLPAYFAE DDHPQMEKYV 
       310        320        330        340        350
VKPIFSREGA NVSIIENGKT IEAAEGPYGE EGMIVQQFHP LPKFGDSYML 
       360        370        380 
IGSWLVNDQP AGIGIREDRA LITQDMSRFY PHIFVE
Length:386
Mass (Da):45,026
Last modified:December 6, 2005 - 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:i5DB19CE4F3FE4783
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
M77129 Genomic DNA Translation: AAA71876.1
U28377 Genomic DNA Translation: AAA69206.1
U00096 Genomic DNA Translation: AAC76074.1
AP009048 Genomic DNA Translation: BAE77094.1

Protein sequence database of the Protein Information Resource

More...PIRi		S22361

NCBI Reference Sequences

More...RefSeqi		NP_417510.1, NC_000913.3
WP_000442860.1, NZ_STEB01000001.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC76074; AAC76074; b3038
BAE77094; BAE77094; BAE77094

Database of genes from NCBI RefSeq genomes

More...GeneIDi		57729141
947249

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW3006
eco:b3038

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.3694

<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
M77129 Genomic DNA Translation: AAA71876.1
U28377 Genomic DNA Translation: AAA69206.1
U00096 Genomic DNA Translation: AAC76074.1
AP009048 Genomic DNA Translation: BAE77094.1
PIRiS22361
RefSeqiNP_417510.1, NC_000913.3
WP_000442860.1, NZ_STEB01000001.1

3D structure databases

SMRiP0ADT5
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4262389, 16 interactors
DIPiDIP-48176N
IntActiP0ADT5, 14 interactors
STRINGi511145.b3038

Proteomic databases

jPOSTiP0ADT5
PaxDbiP0ADT5
PRIDEiP0ADT5

Genome annotation databases

EnsemblBacteriaiAAC76074; AAC76074; b3038
BAE77094; BAE77094; BAE77094
GeneIDi57729141
947249
KEGGiecj:JW3006
eco:b3038
PATRICifig|1411691.4.peg.3694

Organism-specific databases

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

More...EchoBASEi		EB1153

Phylogenomic databases

eggNOGiCOG0754, Bacteria
HOGENOMiCLU_059175_0_0_6
InParanoidiP0ADT5
PhylomeDBiP0ADT5

Enzyme and pathway databases

BioCyciEcoCyc:EG11165-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P0ADT5

Family and domain databases

InterProiView protein in InterPro
IPR005494, GSPS_pre-ATP-grasp-like_dom
IPR016185, PreATP-grasp_dom_sf
PfamiView protein in Pfam
PF03738, GSP_synth, 1 hit
SUPFAMiSSF52440, SSF52440, 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 nameiYGIC_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: P0ADT5
Secondary accession number(s): P24196, Q2M9G2
<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: December 6, 2005
Last sequence update: December 6, 2005
Last modified: February 10, 2021
This is version 100 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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