Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 200056 |
| Name | oriT_SXT(MO10)  |
| Organism | Vibrio cholerae STX transposon-like element and pilus assembly region |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | AY055428 (3516..3814 [+], 299 nt) |
| oriT length | 299 nt |
| IRs (inverted repeats) | 178..192, 216..230 (ATCGAGACGCCAAAC..GTTTGGCGTTTCGAT) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | The relaxase TraI_SXT(MO10) and the oriT_SXT(MO10) are key factors for SXT(MO10) replication and stability. After deletion the relaxase TraI_SXT(MO10) or the oriT_SXT(MO10), there are ~5-fold reduction of SXT(MO10) copy numbers [PMID:26061412]. |
oriT sequence
Download Length: 299 nt
GCTCTGTTTGGCGGCGGATGACCTAGTCAAAAAAATCGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTCGCCAAACGGTTTGTATCTTCATGACGATACGTCGTTTTAGGCGTTTTTAAGTGAAATCGGGCTGTATCCCTTGTCAGGTATGGGATTGCGCGAGTTGATTTATATCGAGACGCCAAACAGTGATTGTTACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTTGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA
Visualization of oriT structure (The oriT was characterized experimentally)
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] Daccord A et al. (2010) Integrating conjugative elements of the SXT/R391 family trigger the excision and drive the mobilization of a new class of Vibrio genomic islands. Mol Microbiol. 78(3):576-88. [PMID:20807202]
[2] Wozniak RA et al. (2009) Comparative ICE genomics: insights into the evolution of the SXT/R391 family of ICEs. PLoS Genet. 5(12):e1000786. [PMID:20041216]
[3] Peters SE et al. (1991) Novel mercury resistance determinants carried by IncJ plasmids pMERPH and R391. Mol Gen Genet. 228(1-2):294-9. [PMID:1886614]
Relaxase
| ID | 270 | GenBank | AAL59675 |
| Name | TraI_SXT(MO10)  |
UniProt ID | Q8KQY3 |
| Length | 716 a.a. | PDB ID | |
| Note | The relaxase TraI_SXT(MO10) and the oriT_SXT(MO10) are key factors for SXT(MO10) replication and stability. After deletion the relaxase TraI_SXT(MO10) or the oriT_SXT(MO10), there are ~5-fold reduction of SXT(MO10) copy numbers [PMID:26061412]. | ||
Relaxase protein sequence
Download Length: 716 a.a. Molecular weight: 79841.81 Da Isoelectric Point: 5.3504
MFKNLFFQAKALPDLSSQLDAEIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQVLGFNLRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTTNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWLRKSNQSTHLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESLAPEVLIKDDKPIWLPMLHISEADLLFSSNVPSSVRLFSKSEWEATQKTQEEPQSHSSEHSDL
PEASSSIEHRKSDESPSTNSSEQENELRHASDVSNPQATENAPGDECEKPNDSSDADIANNANQHHAEAL
NLPESLAWLPEASSALVMVGEQVLIRYPDAVRHWCAPRKLLAELSRLDWLELDPANLTRKARTVTTNDGV
QEQGLLLKVSISKGLTALIDLPKQDAEPAAAIQNEEALQRPSRTETTNAQAKEPATRAERKQKPIAANTN
SSTDPKHAQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVANAHGIPAGQLLRGISASDQC
QFDEGETVLFTAHAKR
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q8KQY3 |
Reference
[1] Ceccarelli D et al. (2008) Identification of the origin of transfer (oriT) and a new gene required for mobilization of the SXT/R391 family of integrating conjugative elements. J Bacteriol. 190(15):5328-38. [PMID:18539733]
T4CP
| ID | 270 | GenBank | AAL59680 |
| Name | TraD_SXT(MO10) |
UniProt ID | Q8KQY2 |
| Length | 599 a.a. | PDB ID | _ |
| Note | _ | ||
T4CP protein sequence
Download Length: 599 a.a. Molecular weight: 66264.05 Da Isoelectric Point: 6.6439
MPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQMGLKGKPLA
FMALSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKKTLLNQGHGKQMGSTWIHGVEPKEEDVY
QPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSPERFVYFH
PGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDLKTLRRFL
EGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEGLLSMFEH
DRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLTDAMVGSAI
GSLLLSDLTDVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFADFAARTGS
EAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGERLMEEEGD
MFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAV
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q8KQY2 |
Reference
[1] Ceccarelli D et al. (2008) Identification of the origin of transfer (oriT) and a new gene required for mobilization of the SXT/R391 family of integrating conjugative elements. J Bacteriol. 190(15):5328-38. [PMID:18539733]
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 47396..67147
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| Locus_40 | 45176..47326 | + | 2151 | AAL59675 | conjugative relaxase | - |
| Locus_41 | 47396..49195 | + | 1800 | AAL59680 | conjugative coupling factor | virb4 |
| Locus_42 | 49753..50388 | + | 636 | AAL59721 | putative conjugation coupling factor | tfc7 |
| Locus_43 | 50414..50692 | - | 279 | AAL59720 | unknown | - |
| Locus_44 | 50689..51012 | - | 324 | AAL59719 | unknown | - |
| Locus_45 | 51187..51474 | + | 288 | AAL59674 | sex pilus assembly | traL |
| Locus_46 | 51471..52097 | + | 627 | AAL59679 | sex pilus assembly | traE |
| Locus_47 | 52078..52977 | + | 900 | AAL59718 | unknown | traK |
| Locus_48 | 52980..54269 | + | 1290 | AAL59682 | sex pilus assembly | traB |
| Locus_49 | 54266..54916 | + | 651 | AAL59672 | sex pilus assembly | traV |
| Locus_50 | 54913..55299 | + | 387 | AAL59683 | putative pilin subunit | - |
| Locus_51 | 55664..56311 | + | 648 | AAL59717 | unknown | - |
| Locus_52 | 56292..57242 | + | 951 | AAL59716 | unknown | - |
| Locus_53 | 57374..58066 | + | 693 | AAL59715 | putative disulfide bond isomerase | trbB |
| Locus_54 | 58066..60465 | + | 2400 | AAL59681 | sex pilus assembly | virb4 |
| Locus_55 | 60789..61301 | + | 513 | AAL59670 | conjugation signal peptidase | - |
| Locus_56 | 61216..62436 | + | 1221 | AAL59671 | sex pilus assembly | traW |
| Locus_57 | 62420..63448 | + | 1029 | AAL59673 | sex pilus assembly | traU |
| Locus_58 | 63683..67147 | + | 3465 | AAL59755 | mating pair stabilization | traN |
| Locus_59 | 67924..69006 | - | 1083 | AAL59714 | unknown | - |
| Locus_60 | 69006..70070 | - | 1065 | AAL59713 | unknown | - |
| Locus_61 | 70183..70899 | - | 717 | AAL59712 | unknown | - |
| Locus_62 | 71008..71610 | - | 603 | AAL59711 | unknown | - |
Host bacterium
| ID | 64 | Element type | |
| Element name | SXT(MO10) | GenBank | AY055428 |
| Element size | 99483 bp | Coordinate of oriT [Strand] | 3516..3814 [+] |
| Host bacterium | Vibrio cholerae STX transposon-like element and pilus assembly region |
Cargo genes
| Drug resistance gene | dfrA18, floR, aph(6)-Id, aph(3'')-Ib, sul2 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |