Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

UniProtKB - U4KD10 (U4KD10_9VIBR)

Entry version 47 (02 Dec 2020)
Sequence version 1 (11 Dec 2013)
Previous versions | rss
Add a publicationFeedback
Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Vibrio nigripulchritudo
Status
Unreviewed-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

Cell wall formation.UniRule annotationARBA 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

Protein has several cofactor binding sites:

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.UniRule annotationARBA annotation
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

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 bindingi281Magnesium or manganese 1UniRule annotation1
Metal bindingi294Magnesium or manganese 1UniRule annotation1
Metal bindingi294Magnesium or manganese 2UniRule annotation1
Metal bindingi296Magnesium or manganese 2UniRule 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

Complete GO annotation on QuickGO ...

GO - Biological processi

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 functionLigaseUniRule annotationImportedARBA annotation
Biological processCell shape, Cell wall biogenesis/degradationUniRule annotationARBA annotation, Peptidoglycan synthesisUniRule annotationARBA annotation
LigandATP-bindingPROSITE-ProRule annotationARBA annotation, MagnesiumUniRule annotation, ManganeseUniRule annotation, Metal-bindingUniRule annotation, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		VNIG28173:VIBNI_RS23905-MONOMER

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...UniPathwayi		UPA00219

<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:
D-alanine--D-alanine ligaseUniRule annotationARBA annotation (EC:6.3.2.4UniRule annotationARBA annotation)
Alternative name(s):
D-Ala-D-Ala ligaseUniRule annotation
D-alanylalanine synthetaseUniRule 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:ddlUniRule annotation
ORF Names:VIBNI_B1133Imported
<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>OrganismiVibrio nigripulchritudoImported
<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 identifieri28173 [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 › Vibrionales › Vibrionaceae › Vibrio
<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
  • UP000016895 <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 2

<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

Complete GO annotation on QuickGO ...

Keywords - Cellular componenti

CytoplasmUniRule annotation

<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		1238450.VIBNISOn1_1560005

<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 <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini121 – 327ATP-graspInterPro annotationAdd BLAST207

<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 D-alanine--D-alanine ligase family.UniRule annotationARBA annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG1181, Bacteria

Database of Orthologous Groups

More...OrthoDBi		764798at2

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.30.1490.20, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_00047, Dala_Dala_lig, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR011761, ATP-grasp
IPR013815, ATP_grasp_subdomain_1
IPR000291, D-Ala_lig_Van_CS
IPR005905, D_ala_D_ala
IPR011095, Dala_Dala_lig_C
IPR011127, Dala_Dala_lig_N
IPR016185, PreATP-grasp_dom_sf

Pfam protein domain database

More...Pfami		View protein in Pfam
PF07478, Dala_Dala_lig_C, 1 hit
PF01820, Dala_Dala_lig_N, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF039102, Ddl/VanB, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF52440, SSF52440, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR01205, D_ala_D_alaTIGR, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS50975, ATP_GRASP, 1 hit
PS00843, DALA_DALA_LIGASE_1, 1 hit
PS00844, DALA_DALA_LIGASE_2, 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.

U4KD10-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTRKNILLLC GGGSNEHEVS LVSANYVQQQ LQLDPSFNVI RVEMTKDEWR 
        60         70         80         90        100
LSSGEKTELD ISHSNLKGES HEIHIDYIVP CLHGFPGETG DVQSIFELAK 
       110        120        130        140        150
IPYLGCGPEA SISSFNKITS KLWYDALGIP NTPYVFLSSN NEDAHEKART 
       160        170        180        190        200
AFEEWGVLFV KAARQGSSVG CYKVTESKEI SEAVNKAFTF SDQVLIEKAV 
       210        220        230        240        250
KPRELEVAAF EHNGELIISK PGEVIAPENG YYTYEEKYGA DSHSLTVVEA 
       260        270        280        290        300
EGLTDAQIEE IQSHSRKVFL QMGLKDLSRI DFFLTEDNEI YLNEVNTFPG 
       310        320        330 
MTPISMFPKM VEHHGVSFKD FLSNAINNAL SNPTA
Length:335
Mass (Da):37,337
Last modified:December 11, 2013 - 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:i9A1BC6C42AB527A5
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
FO203527 Genomic DNA Translation: CCO60901.1

NCBI Reference Sequences

More...RefSeqi		WP_022561435.1, NC_022543.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		CCO60901; CCO60901; VIBNI_B1133

Database of genes from NCBI RefSeq genomes

More...GeneIDi		29465477

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		vni:VIBNI_B1133

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1260221.3.peg.4749

<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
FO203527 Genomic DNA Translation: CCO60901.1
RefSeqiWP_022561435.1, NC_022543.1

3D structure databases

Database of comparative protein structure models

More...ModBasei		Search...

SWISS-MODEL Interactive Workspace

More...SWISS-MODEL-Workspacei		Submit a new modelling project...

Protein-protein interaction databases

STRINGi1238450.VIBNISOn1_1560005

Genome annotation databases

EnsemblBacteriaiCCO60901; CCO60901; VIBNI_B1133
GeneIDi29465477
KEGGivni:VIBNI_B1133
PATRICifig|1260221.3.peg.4749

Phylogenomic databases

eggNOGiCOG1181, Bacteria
OrthoDBi764798at2

Enzyme and pathway databases

UniPathwayiUPA00219
BioCyciVNIG28173:VIBNI_RS23905-MONOMER

Family and domain databases

Gene3Di3.30.1490.20, 1 hit
HAMAPiMF_00047, Dala_Dala_lig, 1 hit
InterProiView protein in InterPro
IPR011761, ATP-grasp
IPR013815, ATP_grasp_subdomain_1
IPR000291, D-Ala_lig_Van_CS
IPR005905, D_ala_D_ala
IPR011095, Dala_Dala_lig_C
IPR011127, Dala_Dala_lig_N
IPR016185, PreATP-grasp_dom_sf
PfamiView protein in Pfam
PF07478, Dala_Dala_lig_C, 1 hit
PF01820, Dala_Dala_lig_N, 1 hit
PIRSFiPIRSF039102, Ddl/VanB, 1 hit
SUPFAMiSSF52440, SSF52440, 1 hit
TIGRFAMsiTIGR01205, D_ala_D_alaTIGR, 1 hit
PROSITEiView protein in PROSITE
PS50975, ATP_GRASP, 1 hit
PS00843, DALA_DALA_LIGASE_1, 1 hit
PS00844, DALA_DALA_LIGASE_2, 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 nameiU4KD10_9VIBR
<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: U4KD10
<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/TrEMBL: December 11, 2013
Last sequence update: December 11, 2013
Last modified: December 2, 2020
This is version 47 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 statusiUnreviewed (UniProtKB/TrEMBL)

<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 proteomeImported
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.

Do not show this banner again