oriTDB
The information of the oriT region
oriTDB accession number 200006
Name oriT_ICEBs1  experimental
Sequence Completeness core
oriT length 24 nt
oriT sequence ACCCCCCCACGCTAACAGGGGGGT
IR (inverted repeat)[1-7] [18-24] nt  (ACCCCCC..GGGGGGT)
Location of nic site [13-14] nt
Conserved sequence flanking the
  nic site 		_
Note The oriT overlapped the 3'end of conQ and the 5' end of nicK.
L:1-7;R:18-24;D:13-14
Visualization of oriT structure (The oriT was characterized experimentally)
Reference
[1] Lee CA et al (2012) The Bacillus subtilis conjugative transposon ICEBs1 mobilizes plasmids lacking dedicated mobilization functions. J Bacteriol. 194(12):3165-72. [PMID:22505685]
[2] Lee CA et al (2007) Identification of the origin of transfer (oriT) and DNA relaxase required for conjugation of the integrative and conjugative element ICEBs1 of Bacillus subtilis. J Bacteriol. 189(20):7254-61. [PMID:17693500]
[3] Lee CA et al (2010) Autonomous plasmid-like replication of a conjugative transposon. Mol Microbiol. 75(2):268-79. [PMID:19943900]
I. Information of Relaxase
ID 220
Name YdcR (NicK)_ICEBs1 insolico
GenBank accession number CAB12294
Family MOBT
Length 352 aa
UniProt ID P96635
PDB ID _
Pfam Rep_trans [PF02486.18], Evalue: 1.60E-66, Aligned region: 126..327
Note The ICEBs1 ydcR (nicK) gene product is homologous to the pT181 family of plasmid DNA relaxases.
Protein sequence [Download] MDELKQPPHANRGVVIVKEKNEAVESPLVSMVDYIRVSFKTHDVDRIIEEVLHLSKDFMT
EKQSGFYGYVGTYELDYIKVFYSAPDDNRGVLIEMSGQGCRQFESFLECRKKTWYDFFQD
CMQQGGSFTRFDLAIDDKKTYFSIPELLKKAQKGECISRFRKSDFNGSFDLSDGITGGTT
IYFGSKKSEAYLCFYEKNYEQAEKYNIPLEELGDWNRYELRLKNERAQVAIDALLKTKDL
TLIAMQIINNYVRFVDADENITREHWKTSLFWSDFIGDVGRLPLYVKPQKDFYQKSRNWL
RNSCAPTMKMVLEADEHLGKTDLSDMIAEAELADKHKKMLDVYMADVADMVV
Reference
[1] Lee CA et al (2012) The Bacillus subtilis conjugative transposon ICEBs1 mobilizes plasmids lacking dedicated mobilization functions. J Bacteriol. 194(12):3165-72. [PMID:22505685]
[2] Lee CA et al (2007) Identification of the origin of transfer (oriT) and DNA relaxase required for conjugation of the integrative and conjugative element ICEBs1 of Bacillus subtilis. J Bacteriol. 189(20):7254-61. [PMID:17693500]
[3] Lee CA et al (2010) Autonomous plasmid-like replication of a conjugative transposon. Mol Microbiol. 75(2):268-79. [PMID:19943900]


II. Auxiliary DNA-binding protein(s) of the relaxosome
# ID Name GenBank Length Note
1 308 _ insolico
Information of T4CP
ID 220
Name YdcQ_ICEBs1 insolico
SecReT4 accesion number _
GenBank accession number CAB12293
Family TrwB/TraD
Length 480
UniProt ID P96634
PDB ID _
Pfam
Note putative coupling protein
Protein sequence [Download]

Reference
[1] Lee CA et al (2007) Autonomous plasmid-like replication of a conjugative transposon. J Bacteriol. 189(20):7254-61. [PMID:17693500]
Information of mobile element
ID 11
Element type ICE (Conjugative transposon)
ICE description ICEBs1
ICEberg accesion number 59
GenBank accession number AL009126.3
Family ICEBs1
Genome size 20510 bp
Coordinate of oriT  [+/-] 534790..534813 [+]
Drug resistance _
Heavy-metal resistance _
Virulence factor _
Xenobiotic degradation _
Host bacterium [NCBI Taxonomy ID] Bacillus subtilis subsp. subtilis str. 168 [224308]
Reference
[1] Lee CA et al (2012) The Bacillus subtilis conjugative transposon ICEBs1 mobilizes plasmids lacking dedicated mobilization functions. J Bacteriol. 194(12):3165-72. [PMID:22505685]

Microbial Bioinformatics Group in MML, SJTU