oriTDB

The information of the oriT region

oriTDB accession number	100054
Name	oriT_pLB1
Sequence Completeness	intact
oriT length	190 nt
oriT sequence	GTGGGGTAGGTATCTCCCAACCGTGAAGCGCGATCCGATGGGATTGAGCGTAACGGTTAA CATTAGCCGCCGCAAGGCTTATCCCGCCATACAGTAGATATTTACCCCACAAACAAAAAG CGGTGGCAACTGCCACCGCTCTAAATTCCACGTCGCCTCGATGCTGAGTGAACGTGGACG GTAAAAGCTA
IR (inverted repeat)	IR1: [19-38] [39-58] nt (AACCGTGAAGCGCGATCCGA..TGGGATTGAGCGTAACGGTT) IR2: [117-128] [131-142] nt (AAAGCGGTGGCA..TGCCACCGCTCT)
Location of nic site	[86-87] nt
Conserved sequence flanking the nic site	TATCCCG\|C
Note	The putativenic site (TATCCCGC), which showed significant similarity to the RP4-type site.
	L:19-38;R:39-58;L:117-128;R:131-142;D:86-87

Visualization of oriT structure

1...5....10....15....20....25....30....35....40....45....50....55....60

1

GTGGGGTAGGTATCTCCCAACCGTGAAGCGCGATCCGATGGGATTGAGCGTAACGGTTAA

61

CATTAGCCGCCGCAAGGCTTATCCCGCCATACAGTAGATATTTACCCCACAAACAAAAAG

121

CGGTGGCAACTGCCACCGCTCTAAATTCCACGTCGCCTCGATGCTGAGTGAACGTGGACG

181

GTAAAAGCTA

Reference

[1] Miyazaki R et al (2006) Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in gamma-hexachlorocyclohexane degradation. Appl Environ Microbiol. 72(11):6923-33. [PMID:16963556]

I. Information of Relaxase

ID	52
Name	VirD2_pLB1
GenBank accession number	BAF30460
Family	MOB_P
Length	355 aa
UniProt ID	Q0KKL1
PDB ID	_
Pfam
Note	relaxase
Protein sequence [Download]	MSDFDSSFEAGQLAALFKPKLTSDPNRRGTDMLLRSLSSRRAGQGGSTRARLARVVSRAP EVMVKVTGRPKGKNHAAAHLDYIGRKGDVPLETRDGDILTDKEDRAELARDWGDPVYWRD NSTVAAVSMVFSMPAGTDPDKVLSAVREVARSEIADEWDFVMALHTDTPRPHVHLTVAAR GDTGRRFNPRPQTLHHYRERFAEELRALGVTAEATPRAARGVGTREPTTALRRARDDFAR GKRPQRPHTSDRCRNAARDHFLGRASAPPFMAASREQWGQAQRIYLAAADRLARSKDHQD RMLAGQVREFVRAGRVPTLHEQLVSSLVREKERREGVSRAGPQKANEDRPRGPQR

Reference

[1] Miyazaki R et al (2006) Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in gamma-hexachlorocyclohexane degradation. Appl Environ Microbiol. 72(11):6923-33. [PMID:16963556]

II. Auxiliary DNA-binding protein(s) of the relaxosome

#	ID	Name	GenBank	Length	Note
1	83	MobC_pLB1	BAF30459	183 aa	relaxosome formation

Information of T4CP

ID	52
Name	VirD4_pLB1
SecReT4 accesion number	114883645
GenBank accession number	BAF30462
Family	VirD4/TraG
Length	638
UniProt ID	Q0KKK9
PDB ID	_
Pfam	T4SS-DNA_transf [PF02534.13], Evalue: 1.40E-106, Aligned region: 95..547 TraG-D_C [PF12696.6], Evalue: 4.50E-28, Aligned region: 385..506 TrwB_AAD_bind [PF10412.8], Evalue: 2.40E-25, Aligned region: 130..522
Note	VirD4 type IV secration protein
Protein sequence [Download]	MIQKTGSNRLALALVLLPITLLLIGLLTGTVAWFFLKMPAAAYDPLKLPGFFWYYRHDPV VTEALWRGAVIGVPLPVLLMAIVLRPKKNLHGEARFAREGEIRKAGLRAKKGIVLGRVRN GFFRNGFLMVGKMEHVLLEAPTGSGKGVGIVIPNLLQWPDSVVVLDIKRENYEITAGFRR KGGQKVVLFNPTDREGRTARYNPLSYINRADPIEVLVELQKIATMLFVPPEKGEAFWTES ARTAFVGIASWIAAKSERPFSFGEIYRTITMPGMKAFFAKEAGDSALSEGCRAALSDFTS SADNTFTGIIQTVTSKLNLWINPIVDRATAESDFSLTDLRRIPTSIYLGVSPDELDRVAP LYNLFFQQLIDLNTRQLPDESEKLSVLLILDEFARLGRAQVIANAFSYVRGYGLRLLPVI QSRSQLRNVYGEHGADEIVSNCGVEIAFTPKELRVAKELSERLGYLGQDAESRSLTIHGL LANRSKTISEQRRALMLPQELMQLPEDDILVIRGGIPVIRGKKIRYFKDSVFRSRLTTAP AVPALPKPVAPIVPVDDLSDEELAAFNDYSALADDQVQDIPEDVLALDRDMPNLTVKDGS MAFDEIDFDDIIGPDPTKEEWEGQRRDLVLSEGEEYGR

Reference

[1] Miyazaki R et al (2006) Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in gamma-hexachlorocyclohexane degradation. Appl Environ Microbiol. 72(11):6923-33. [PMID:16963556]

Information of plasmid

ID	52
Plasmid name	pLB1
GenBank accession number	AB244976.1
Genome size	65998 bp
Coordinate of oriT [Strand]	49254..49443 [-]
Drug resistance	_
Heavy-metal resistance	_
Virulence factor	_
Xenobiotic degradation	gamma-hexachlorocyclohexane degradation
Host bacterium [NCBI Taxonomy ID]	Uncultured bacterium [77133]

Reference

[1] Miyazaki R et al (2006) Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in gamma-hexachlorocyclohexane degradation. Appl Environ Microbiol. 72(11):6923-33. [PMID:16963556]