oriTDB
The information of the oriT region
oriTDB accession number 100054
Name oriT_pLB1  insolico
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
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 insolico
GenBank accession number BAF30460
Family MOBP
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 insolico BAF30459 183 aa relaxosome formation
Information of T4CP
ID 52
Name VirD4_pLB1 insolico
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 insolico 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]

Microbial Bioinformatics Group in MML, SJTU