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Entry version 58 (11 Dec 2019)
Sequence version 1 (01 Sep 2009)
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Protein
Submitted name:

DNA ligase D

Gene

Rpic12D_0488

Organism
Ralstonia pickettii (strain 12D)
Status
Unreviewed-Annotation score:

Annotation score:1 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 predictedi <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

<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 functionLigaseImported

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
RPIC428406:GH9Y-485-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
Submitted name:
DNA ligase DImported
<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
Ordered Locus Names:Rpic12D_0488Imported
<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>OrganismiRalstonia pickettii (strain 12D)Imported
<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 identifieri428406 [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 lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeRalstonia
<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
  • UP000008208 <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 1

<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_and_domains_section">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>Domaini323 – 419DNA_LIGASE_A3InterPro annotationAdd BLAST97

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 31DisorderedSequence analysisAdd BLAST31
Regioni187 – 228DisorderedSequence analysisAdd BLAST42

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi196 – 210PolyampholyteSequence analysisAdd BLAST15

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000222509

KEGG Orthology (KO)

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KOi
K01971

Identification of Orthologs from Complete Genome Data

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OMAi
YMANLGC

Family and domain databases

Conserved Domains Database

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CDDi
cd04862 PaeLigD_Pol_like, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR012309 DNA_ligase_ATP-dep_C
IPR012310 DNA_ligase_ATP-dep_cent
IPR014146 LigD_ligase_dom
IPR014144 LigD_PE_domain
IPR014145 LigD_pol_dom
IPR012340 NA-bd_OB-fold
IPR014143 NHEJ_ligase_prk
IPR033651 PaeLigD_Pol-like

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF04679 DNA_ligase_A_C, 1 hit
PF01068 DNA_ligase_A_M, 1 hit
PF13298 LigD_N, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF50249 SSF50249, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR02777 LigD_PE_dom, 1 hit
TIGR02778 ligD_pol, 1 hit
TIGR02779 NHEJ_ligase_lig, 1 hit
TIGR02776 NHEJ_ligase_prk, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50160 DNA_LIGASE_A3, 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.

C6BCT3-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MPRHLADYRR KRDFTQTQEP AGARRKADEQ RDHGALHFVI QKHDATRLHY
60 70 80 90 100
DFRLELDGTL KSWAVPKGPS LDPADKRLAV HVEDHPLDYA DFEGHIPEGQ
110 120 130 140 150
YGGGDVIVWD RGTWRPHGDP RKAYRDGKLK FDLHGEKLHG AWALVRTHLH
160 170 180 190 200
GTGRHPKEQW LLIKERDDQV RASSDYDVTE ALPASVITGE NIGSKPRGKA
210 220 230 240 250
KAKSSDGKTG RSEPEQVQPP AGAVPAPLPR TLEPQLATLV DGPPAQGEWD
260 270 280 290 300
YEVKFDGYRI LARIDGDTVR LFSRNGRDWT GKLPRQARTL QALGLREAWL
310 320 330 340 350
DGEVVVMGER GVPDFQALQN AFETAHAEHI AYYLFDIPFC NGMDLRGVPL
360 370 380 390 400
RERRALLERI LNAAPGDLDR EAVLFSGTFH AAPEDLLSSA CSMSLEGVIG
410 420 430 440 450
KRADAAYRAG RSPAWIKLKC GQRQEFVIGG YSAPKGSRSG FGALLLGVYD
460 470 480 490 500
DAGKLRYAGR VGTGFNETSL HALHHELTGL TVDTPPFANP PTGSDARDVQ
510 520 530 540 550
WVKPERVAEI AFAEWTREGI VRQAVFQGLR DDKPARNIVR EQAKPPSAAA
560 570 580 590 600
RKETRAVHAT ERKVRPGAER IADVDVTHPD RVIEKASGTT KADLARYYAG
610 620 630 640 650
VAEWMLPHLH NRPTSLVRAP DGIDGERFFQ KHSAALKLQG ITQLDPSLDP
660 670 680 690 700
GHPSLLAINS AEALVGAVQM GTVEFHTWNA LADRIEQPDR IVFDIDPDPA
710 720 730 740 750
LPFARVIEAT QLMLAMLDEL GLKAFLKTSG GHGMHVVVPL TRREASGWDT
760 770 780 790 800
LKAFAQAVVQ HMAATFPDRF VAKMGPQNRV GKIFIDYLRN NRGASTVAAY
810 820 830 840 850
SVRARTGLPV SVPIRHDELE GLQSSAQWTL RTLPDRLAKL KGDPWADYAG
860
TRQSVTADMR KRVGAND
Length:867
Mass (Da):95,853
Last modified:September 1, 2009 - 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:i0C1DAAD75C2EC432
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
CP001644 Genomic DNA Translation: ACS61794.1

NCBI Reference Sequences

More...
RefSeqi
WP_012761269.1, NC_012856.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
ACS61794; ACS61794; Rpic12D_0488

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
rpf:Rpic12D_0488

<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
CP001644 Genomic DNA Translation: ACS61794.1
RefSeqiWP_012761269.1, NC_012856.1

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...

Genome annotation databases

EnsemblBacteriaiACS61794; ACS61794; Rpic12D_0488
KEGGirpf:Rpic12D_0488

Phylogenomic databases

HOGENOMiHOG000222509
KOiK01971
OMAiYMANLGC

Enzyme and pathway databases

BioCyciRPIC428406:GH9Y-485-MONOMER

Family and domain databases

CDDicd04862 PaeLigD_Pol_like, 1 hit
InterProiView protein in InterPro
IPR012309 DNA_ligase_ATP-dep_C
IPR012310 DNA_ligase_ATP-dep_cent
IPR014146 LigD_ligase_dom
IPR014144 LigD_PE_domain
IPR014145 LigD_pol_dom
IPR012340 NA-bd_OB-fold
IPR014143 NHEJ_ligase_prk
IPR033651 PaeLigD_Pol-like
PfamiView protein in Pfam
PF04679 DNA_ligase_A_C, 1 hit
PF01068 DNA_ligase_A_M, 1 hit
PF13298 LigD_N, 1 hit
SUPFAMiSSF50249 SSF50249, 1 hit
TIGRFAMsiTIGR02777 LigD_PE_dom, 1 hit
TIGR02778 ligD_pol, 1 hit
TIGR02779 NHEJ_ligase_lig, 1 hit
TIGR02776 NHEJ_ligase_prk, 1 hit
PROSITEiView protein in PROSITE
PS50160 DNA_LIGASE_A3, 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 nameiC6BCT3_RALP1
<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: C6BCT3
<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/TrEMBL: September 1, 2009
Last sequence update: September 1, 2009
Last modified: December 11, 2019
This is version 58 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)
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