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CDS Information : RER_45220

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close this sectionGenomic map

Display Clone

Rhodococcus erythropolis PR4 (= NBRC 100887) chromosome

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Overview 
Genome
Clone

close this sectionLocation

Organism Rhodococcus erythropolis PR4 (= NBRC 100887)
Replicon chromosome
Start / Stop / Direction 4,961,376 / 4,959,100 / -
Location complement(4959100..4961376)
Type CDS
Length 2,277 bp (758 aa)

close this sectionAnnotation

Product ATP-dependent DNA ligase LigD
Gene name ligD
Functional category Genetic Information Processing
- Replication and Repair
EC number 6.5.1.1
Note Similar to the ATP-dependent DNA ligase LigD (Rv0938) of Mycobacterium tuberculosis (P71571).
KEGG pathway
Sequence feature
References Uniprot:Q9HHC4 Pubmed:11053387
Uniprot:P71571 Pubmed:14985346,15499016,16476729

close this sectionComputational search results

BLASTP
Database:UniProtKB:14.0
1E=0Q0S6K7_RHOSRDNA ligase
ATP
Alignment
2E=0A0QBM3_MYCA1DNA ligaseAlignment
3E=0Q742F5_MYCPAPutative uncharacterized proteinAlignment
4E=0B2HEF3_MYCMMATP dependent DNA ligaseAlignment
5E=0Q5Z219_NOCFAPutative ATP-dependent DNA ligaseAlignment
HAMAP No significant hit
InterPro
Database:interpro:18.0
IPR000209 Peptidase S8 and S53, subtilisin, kexin, sedolisin (Domain)
 [147-211]  0.016 SSF52743
SSF52743   Subtilisin-like
IPR000977 ATP-dependent DNA ligase (Family)
 [460-753]  6e-51 PTHR10459
PTHR10459   ATP-DEPENDENT DNA LIGASE FAMILY
 [479-487]  PS00697
PS00697   DNA_LIGASE_A1
IPR002755 DNA primase, small subunit (Family)
 [137-258]  1.1e-21 PF01896
PF01896   DNA_primase_S
IPR008994 Nucleic acid-binding, OB-fold (Domain)
 [607-697]  8.6e-06 SSF50249
SSF50249   Nucleic acid-binding proteins
IPR012309 ATP dependent DNA ligase, C-terminal (Domain)
 [654-728]  1.1e-12 PF04679
PF04679   DNA_ligase_A_C
IPR012310 ATP dependent DNA ligase, central (Domain)
 [460-635]  1.8e-42 PF01068
PF01068   DNA_ligase_A_M
 [553-664]  11.561 PS50160
PS50160   DNA_LIGASE_A3
IPR012340 Nucleic acid-binding, OB-fold (Domain)
 [638-758]  4.7e-17 G3DSA:2.40.50.140
G3DSA:2.40.50.140   no description
IPR014144 DNA ligase D, 3'-phosphoesterase domain (Domain)
 [300-446]  1.4e-82 TIGR02777
TIGR02777   LigD_PE_dom: DNA ligase D, 3'-phosphoestera
IPR014145 DNA polymerase LigD, polymerase domain (Domain)
 [16-263]  8e-110 TIGR02778
TIGR02778   ligD_pol: DNA polymerase LigD, polymerase d
IPR014146 DNA polymerase LigD, ligase region (Domain)
 [460-756]  4.6e-106 TIGR02779
TIGR02779   NHEJ_ligase_lig: DNA polymerase LigD, ligas
IPR016059 ATP-dependent DNA ligase, conserved site (Conserved_site)
 [479-487]  PS00697
PS00697   DNA_LIGASE_A1
SignalP No significant hit
TMHMM No significant hit
SOSUI No significant hit

close this sectionCalculated information (Amino acid sequence)

size of protein 758 amino acids
molecular mass 83,256.71 Da
pI 5.49
aa composition
AlaValLeuIlePheTrpProMetGlySer
9.4
(71aa)
8.2
(62aa)
9.8
(74aa)
3.2
(24aa)
2.6
(20aa)
2.6
(20aa)
5.3
(40aa)
1.5
(11aa)
10.2
(77aa)
5.4
(41aa)
ThrCysAsnGlnTyrLysHisArgAspGlu
6.6
(50aa)
0.1
(1aa)
2.4
(18aa)
2.8
(21aa)
2.6
(20aa)
3.7
(28aa)
2
(15aa)
7.9
(60aa)
7
(53aa)
6.9
(52aa)

open this sectionSequence

close this sectionCovered clones

NBRC No. clone name start stop length(bp)
G12-001-196 REGR1S7011E01 4,933,313 4,975,954 42,642

close this sectionDistribution of Our Microbial Genomic DNA clones

We have been distributing copies of the microbial genomic DNA clones constructed during the course of each of the genomic DNA sequencing projects.
You can find more detailed information at http://www.nbrc.nite.go.jp/e/mdna-e.html.