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Protein
Submitted name:

ATP-dependent DNA ligase LigD

Gene

ligD

Organism
Rubrivivax gelatinosus (strain NBRC 100245 / IL144)
Status
Unreviewed-Annotation score: Annotation score: 1 out of 5-Protein predictedi

Functioni

GO - Molecular functioni

  1. ATP binding Source: InterPro
  2. DNA ligase (ATP) activity Source: UniProtKB-EC
  3. DNA primase activity Source: InterPro

GO - Biological processi

  1. DNA recombination Source: InterPro
  2. DNA repair Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

LigaseImported

Enzyme and pathway databases

BioCyciRGEL983917:GLJR-2668-MONOMER.

Names & Taxonomyi

Protein namesi
Submitted name:
ATP-dependent DNA ligase LigDImported (EC:6.5.1.1Imported)
Gene namesi
Name:ligDImported
Ordered Locus Names:RGE_26430Imported
OrganismiRubrivivax gelatinosus (strain NBRC 100245 / IL144)Imported
Taxonomic identifieri983917 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesRubrivivax
ProteomesiUP000007883: Chromosome

Family & Domainsi

Phylogenomic databases

KOiK01971.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
InterProiIPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR014146. DNA_pol_LigD_ligase_dom.
IPR002755. DNA_primase_S.
IPR014144. LigD_PE_domain.
IPR014145. LigD_pol.
IPR012340. NA-bd_OB-fold.
IPR014143. NHEJ_ligase_prk.
[Graphical view]
PfamiPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF01896. DNA_primase_S. 1 hit.
PF13298. LigD_N. 1 hit.
[Graphical view]
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.
PROSITEiPS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

I0HSJ5-1 [UniParc]FASTAAdd to Basket

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        10         20         30         40         50
MPRTAAPARD PLQHYRERRD FRATPEPGAD AVQPGADTGR FVIQKHDATR
60 70 80 90 100
LHYDFRLELD GVLLSWAVPK GPSLDPADRR MAVRTEDHPL AYADFEGRIP
110 120 130 140 150
AGHYGAGQVI VWDRGSWTPL AEPRAALAAG KLPFELDGEK LHGAWELVRM
160 170 180 190 200
KPKPGERGEN WLLFKKRDAQ ARPRAEFDVV AEQPDSVAAT AADKPRRRQS
210 220 230 240 250
RAALALDSVA PKAPQPETLA PQLATLASAA PSSGSWLYET KFDGYRLLAR
260 270 280 290 300
IRRGVPRLFT RNGHDWTDKL PALAAALKGL GLQSAWIDGE LVALGSRGAA
310 320 330 340 350
DFNALQNAFD GRDTARLLYY VFDLPYVQGR DLRELALDTR RALLQSLLDE
360 370 380 390 400
HPLDGVRFSE ELPAGGAGPL ATACERQLEG VIAKRRDAPY RSLRSEAWLK
410 420 430 440 450
LKCRRRQEFV VAGYTERTNA SGEIGSLILA VHDADGRLVH AGKVGTGWDT
460 470 480 490 500
RAARDLFTRL QPLAREAVPF AAGTPSPGRW SRRAPGLERW VRPEFVVEVE
510 520 530 540 550
FAEWTPGGSV RHAVFVGVRE DKPAAQVLRE RAVVPDTAPS AAPTASSSGR
560 570 580 590 600
IARVRITHGE RIVDKASGLS KLDLLRWYDG VAERMLPHLK ARPVALLRAP
610 620 630 640 650
QGVGRPVFFQ KHAERTEIPG LVLLDPALWP GHEPLMEIRS AEALLSAAQM
660 670 680 690 700
NTIEFHTWNA TTRTIAKPDR LVFDLDPGEG VDFAAVREGA LLVRTLLDEL
710 720 730 740 750
GLASWLKTSG GKGLHVVVPV APRVAVDVVK PFSRAVVAHL AEQVPERFVV
760 770 780 790 800
RSGPANRVGR IFVDWLRNGE GATTVAAFSA RARPGLGVSI PVSWDALPEL
810 820 830 840 850
RGGDQWTLAN AREHLSFERE DPWAAFWTTR QALAPAMRRL GFDPRAGGDG

R
Length:851
Mass (Da):93,495
Last modified:June 13, 2012 - v1
Checksum:iA26F3B1F4D460DAA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP012320 Genomic DNA. Translation: BAL95982.1.
RefSeqiWP_014428844.1. NC_017075.1.
YP_005437481.1. NC_017075.1.

Genome annotation databases

EnsemblBacteriaiBAL95982; BAL95982; RGE_26430.
GeneIDi12026758.
KEGGirge:RGE_26430.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP012320 Genomic DNA. Translation: BAL95982.1.
RefSeqiWP_014428844.1. NC_017075.1.
YP_005437481.1. NC_017075.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAL95982; BAL95982; RGE_26430.
GeneIDi12026758.
KEGGirge:RGE_26430.

Phylogenomic databases

KOiK01971.

Enzyme and pathway databases

BioCyciRGEL983917:GLJR-2668-MONOMER.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
InterProiIPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR014146. DNA_pol_LigD_ligase_dom.
IPR002755. DNA_primase_S.
IPR014144. LigD_PE_domain.
IPR014145. LigD_pol.
IPR012340. NA-bd_OB-fold.
IPR014143. NHEJ_ligase_prk.
[Graphical view]
PfamiPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF01896. DNA_primase_S. 1 hit.
PF13298. LigD_N. 1 hit.
[Graphical view]
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.
PROSITEiPS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Complete genome sequence of phototrophic betaproteobacterium Rubrivivax gelatinosus IL144."
    Nagashima S., Sekine M., Takami A., Shimizu T., Nakamura S., Aono E., Sakamoto K., Nakazawa H., Yamazaki S., Fujita N., Shimada K., Hanada S., Nagashima K.
    Submitted (FEB-2012) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: NBRC 100245 / IL144Imported.

Entry informationi

Entry nameiI0HSJ5_RUBGI
AccessioniPrimary (citable) accession number: I0HSJ5
Entry historyi
Integrated into UniProtKB/TrEMBL: June 13, 2012
Last sequence update: June 13, 2012
Last modified: February 4, 2015
This is version 14 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.