Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 100054
• Name: oriT_pLB1
• Organism: Uncultured bacterium
• Sequence Completeness: intact
• NCBI accession of oriT (coordinates [strand]): AB244976 (49254..49443 [-], 190 nt)
• oriT length: 190 nt
• IRs (inverted repeats): IR1: 19..38, 39..58 (AACCGTGAAGCGCGATCCGA..TGGGATTGAGCGTAACGGTT) IR2: 117..128, 131..142 (AAAGCGGTGGCA..TGCCACCGCTCT)
• Location of nic site: 86..87
• Conserved sequence flanking the nic site: TATCCCG|C
• Note: The putativenic site (TATCCCGC), which showed significant similarity to the RP4-type site.

oriT sequence

• Length: 190 nt

>oriT_pLB1
GTGGGGTAGGTATCTCCCAACCGTGAAGCGCGATCCGATGGGATTGAGCGTAACGGTTAACATTAGCCGCCGCAAGGCTTATCCCGCCATACAGTAGATATTTACCCCACAAACAAAAAGCGGTGGCAACTGCCACCGCTCTAAATTCCACGTCGCCTCGATGCTGAGTGAACGTGGACGGTAAAAGCTA

oriT secondary structure

Predicted by RNAfold.

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]

Relaxase

VirD2_pLB1

• ID: 52
• GenBank: BAF30460
• Name: VirD2_pLB1
• UniProt ID: Q0KKL1
• Length: 355 a.a.
• Note: relaxase

Relaxase protein sequence

• Length: 355 a.a.
• Molecular weight: 39696.63 Da
• Isoelectric Point: 11.2981

>BAF30460.1 relaxase (plasmid) [uncultured bacterium]
MSDFDSSFEAGQLAALFKPKLTSDPNRRGTDMLLRSLSSRRAGQGGSTRARLARVVSRAPEVMVKVTGRP
KGKNHAAAHLDYIGRKGDVPLETRDGDILTDKEDRAELARDWGDPVYWRDNSTVAAVSMVFSMPAGTDPD
KVLSAVREVARSEIADEWDFVMALHTDTPRPHVHLTVAARGDTGRRFNPRPQTLHHYRERFAEELRALGV
TAEATPRAARGVGTREPTTALRRARDDFARGKRPQRPHTSDRCRNAARDHFLGRASAPPFMAASREQWGQ
AQRIYLAAADRLARSKDHQDRMLAGQVREFVRAGRVPTLHEQLVSSLVREKERREGVSRAGPQKANEDRP
RGPQR

Protein domains

No domain identified.

Protein structure

• AlphaFold DB: Q0KKL1

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]

Auxiliary protein

MobC_pLB1

• ID: 83
• GenBank: BAF30459
• Name: MobC_pLB1
• UniProt ID: Q0KKL2
• Length: 183 a.a.
• PDB ID: _
• Note: relaxosome formation

Auxiliary protein sequence

• Length: 183 a.a.
• Molecular weight: 20036.20 Da
• Isoelectric Point: 10.4452

>BAF30459.1 MobC-like protein (plasmid) [uncultured bacterium]
MEKTLGFKIEAAKLAKIDALAQTRGGRGPFMRQLVDAVLRQSGAAMEAAPIAEREAAGEHRLYLRPTETE
LAVIRHRAKERRMTPATWAMALVRRHIGIAAPVDRELREELLNCRQALQRIGRNVNQIARAANKMALADN
AAEIAGELQKVNDLRAAIGAAVEGIGAATKADLVYWEVPGERL

Protein domains

Predicted by InterproScan.

• Bacterial mobilisation protein (MobC) (MobC) (118-153)

Protein structure

• AlphaFold DB: Q0KKL2

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]

T4CP

VirD4_pLB1

• ID: 52
• GenBank: BAF30462
• Name: VirD4_pLB1
• UniProt ID: Q0KKK9
• Length: 638 a.a.
• PDB ID: _
• Note: VirD4 type IV secration protein

T4CP protein sequence

• Length: 638 a.a.
• Molecular weight: 71046.96 Da
• Isoelectric Point: 5.9062

>BAF30462.1 VirD4 type IV secration protein (plasmid) [uncultured bacterium]
MIQKTGSNRLALALVLLPITLLLIGLLTGTVAWFFLKMPAAAYDPLKLPGFFWYYRHDPVVTEALWRGAV
IGVPLPVLLMAIVLRPKKNLHGEARFAREGEIRKAGLRAKKGIVLGRVRNGFFRNGFLMVGKMEHVLLEA
PTGSGKGVGIVIPNLLQWPDSVVVLDIKRENYEITAGFRRKGGQKVVLFNPTDREGRTARYNPLSYINRA
DPIEVLVELQKIATMLFVPPEKGEAFWTESARTAFVGIASWIAAKSERPFSFGEIYRTITMPGMKAFFAK
EAGDSALSEGCRAALSDFTSSADNTFTGIIQTVTSKLNLWINPIVDRATAESDFSLTDLRRIPTSIYLGV
SPDELDRVAPLYNLFFQQLIDLNTRQLPDESEKLSVLLILDEFARLGRAQVIANAFSYVRGYGLRLLPVI
QSRSQLRNVYGEHGADEIVSNCGVEIAFTPKELRVAKELSERLGYLGQDAESRSLTIHGLLANRSKTISE
QRRALMLPQELMQLPEDDILVIRGGIPVIRGKKIRYFKDSVFRSRLTTAPAVPALPKPVAPIVPVDDLSD
EELAAFNDYSALADDQVQDIPEDVLALDRDMPNLTVKDGSMAFDEIDFDDIIGPDPTKEEWEGQRRDLVL
SEGEEYGR

Protein domains

Predicted by InterproScan.

• Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf) (96-539)

Protein structure

• AlphaFold DB: Q0KKK9

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]

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 54618..64582

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
Locus_34	49982..51049	+	1068	BAF30460	relaxase	-
Locus_35	51526..52734	-	1209	BAF30461	putative DNA primase	-
Locus_36	52724..54640	-	1917	BAF30462	VirD4 type IV secration protein	-
Locus_37	54618..55610	-	993	BAF30463	VirB11 type IV secretion protein	virB11
Locus_38	55607..56782	-	1176	BAF30464	VirB10 type IV secretion protein	virB10
Locus_39	56877..57719	-	843	BAF30465	VirB9 type IV secretion protein	virB9
Locus_40	57716..58399	-	684	BAF30466	VirB8 type IV secretion protein	virB8
Locus_41	58447..58620	-	174	BAF30467	hypothetical protein	-
Locus_42	58740..59756	-	1017	BAF30468	VirB6 type IV secretion protein	virB6
Locus_43	59797..60102	-	306	BAF30469	hypothetical protein	-
Locus_44	60105..60818	-	714	BAF30470	VirB5 type IV secretion protein	virB5
Locus_45	60832..63216	-	2385	BAF30471	VirB4 type IV secretion protein	virb4
Locus_46	63203..63547	-	345	BAF30472	VirB3 type IV secretion protein	virB3
Locus_47	63554..63895	-	342	BAF30473	VirB2 type IV secretion protein	virB2
Locus_48	63917..64582	-	666	BAF30474	VirB1 type IV secretion protein	virB1
Locus_49	64597..64920	-	324	BAF30475	hypothetical protein	-

Host bacterium

• ID: 52
• GenBank: AB244976
• Plasmid name: pLB1
• Incompatibility group: _
• Plasmid size: 65998 bp
• Coordinate of oriT [Strand]: 49254..49443 [-]
• Host baterium: Uncultured bacterium

Cargo genes

• Drug resistance gene: -
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: gamma-hexachlorocyclohexane degradation
• Symbiosis gene: -
• Anti-CRISPR: -