Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200133
Name   oriT_ICEVchCHN4210 in_silico
Organism   Vibrio cholerae strain ICDC-4210 sequence
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   KT151662 (104455..104753 [-], 299 nt)
oriT length   299 nt
IRs (inverted repeats)      234..242, 254..262  (AAAGCCAAA..TTTGGCTTT)
 45..50, 52..57  (CAAACG..CGTTTG)
 7..12, 26..31  (TTTGGC..GCCAAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 299 nt

>oriT_ICEVchCHN4210
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14286 GenBank   ALP45084
Name   traI_-_ICEVchCHN4210 insolico UniProt ID   _
Length   716 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 716 a.a.        Molecular weight: 79739.87 Da        Isoelectric Point: 5.3647

>ALP45084.1 conjugative transfer protein relaxase [Vibrio cholerae]
MFKNLFFQAKALPELSSQLDAEIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQILGFNQRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLQTLSQWATNNRIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWVRKSNQSTNLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKSG
SNERYESLAPEVLIKDDKPIWLPMLHISETDLLFSSNVPSGVTLFSKPEWEATQQTQAEPQSRSSEHPGL
SEASSSIEHSSSAQSPSTNSSEQDDELRHASDVNNPQATENAPGDECEKPNNSYDGAIADNVNQQNEAAL
NLPESLAWLPEASSALVVVGEQVLIRYPDAVRPWCAPRKLLAELSRLDWLELDPANPTRKARTVTTNDGV
QEQGLLLKVSISKRLIALIDISKQDTEPATAIQNEEALQRPSRTKTTNAQAKEPATRAERKQKPIAPNAK
SSTDPKYVQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVANAHGIPAGQLLRGISASDEC
QFDEGETVLFTAHAKR

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(39-349)


  Protein structure



No available structure.




T4CP

ID   16558 GenBank   ALP45070
Name   traC_-_ICEVchCHN4210 insolico UniProt ID   _
Length   799 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 799 a.a.        Molecular weight: 90157.73 Da        Isoelectric Point: 5.9727

>ALP45070.1 plasmid conjugative transfer pilus assembly protein trac [Vibrio cholerae]
MKASLYSGQRASELLPVLAYSDDEQLFFMEDQSVGFGFLCDPLPGGDESVADRVNVLLNNDWPKDTLLQF
GLYASPDIQTDLQRMMGLRHRQSDPLLRASIRKRADFLDGGTVQPIEESTQTQVRNFQLIVTCKLPLESP
IPTERELSRASALRASFSQALATVGFRVTEMTDRNWLAALSAQLNWGKDASWRNPSPIRSEADKPLREQV
LDYDRAIKVDSQGLMLGDYRVKTLSFKRLPERIWFGHAASFAGDMMTGSRGLRGSFLLNVTIHFPSAEAM
RSRLETKRQWAVNQAYGPMLKFVPVLAAKKKGFDVLFEALQEGDRPIRANMTLTLFSPTEEASISSVSNA
RTYFKELGFELMEDKYFCLPIFLNALPFGADRQAMNDLFRFKTMATRHVIPLLPLFADWKGTGTPVINFV
SRNGQIMSVSLYDSGSNYNCCIAAQSGSGKSFLVNEIISSYLSEGGQCWVIDVGRSYEKLCEVYDGEFLQ
FGRDSGICLNPFEIVEDYDEEADVLVGLLAAMAAPTQSLTDFQMANLKRQTRELWEKKGRAMLVDDVAEA
LKNHDDRRVQDVGEQLYPFTTQGEYGRFFNGHNNIRFKNRFTVLELEELKGRKHLQQVVLLQLIYQIQQE
MYLGERDRRKIVFIDEAWDLLTQGDVGKFIETGYRRFRKYGGSAVTVTQSVNDLYDSPTGKAIAENSANM
YLLGQKAETINALKKEGRLPLGEGGYEYLKTVHTVTGVYSEIFFITEMGTGIGRLIVDPFHKLLYSSRAE
DVNAIKQLTRKGLSVADAISQLLKERGYE

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(253-420)

TraC protein (TraC_F_IV)

(11-241)

TraG P-loop domain (P-loop_TraG)

(436-521)

TraG P-loop domain (P-loop_TraG)

(568-794)

  Protein structure



No available structure.



ID   16559 GenBank   ALP45083
Name   traD_-_ICEVchCHN4210 insolico UniProt ID   _
Length   606 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 606 a.a.        Molecular weight: 67039.87 Da        Isoelectric Point: 6.7825

>ALP45083.1 plasmid conjugative transfer protein [Vibrio cholerae]
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQKG
LKGKPLAFMALSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVNDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVDNRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FAARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
LMEEEGDMFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAA

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(152-285)

TraM recognition site of TraD and TraG (TraG-D_C)

(451-578)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 31545..51409

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_29 26784..27386 + 603 ALP45061 hypothetical protein -
Locus_30 27495..28169 + 675 ALP45062 extracellular deoxyribonuclease dns -
Locus_31 28234..28752 - 519 ALP45063 plasmid-related regulatory protein -
Locus_32 28772..31045 - 2274 ALP45064 plasmid-related membrane protein -
Locus_33 31545..35237 - 3693 ALP45065 plasmid conjugative transfer protein traN
Locus_34 35240..36268 - 1029 ALP45066 plasmid conjugative transfer pilus assembly protein trau traU
Locus_35 36252..37376 - 1125 ALP45067 plasmid conjugative transfer pilus assembly protein traw traW
Locus_36 37387..37899 - 513 ALP45068 conjugative signal peptidase -
Locus_37 37883..38230 - 348 ALP45069 hypothetical protein -
Locus_38 38223..40622 - 2400 ALP45070 plasmid conjugative transfer pilus assembly protein trac virb4
Locus_39 40622..41314 - 693 ALP45071 thiol:disulfide protein trbB
Locus_40 41446..42384 - 939 ALP45072 ync -
Locus_41 42377..43210 - 834 ALP45073 ynd -
Locus_42 43388..43774 - 387 ALP45074 conjugative transfer protein -
Locus_43 43771..44421 - 651 ALP45075 conjugative transfer protein traV
Locus_44 44418..45707 - 1290 ALP45076 plasmid conjugative transfer pilus assembly protein trab traB
Locus_45 45710..46606 - 897 ALP45077 plasmid conjugative transfer pilus assembly protein trak traK
Locus_46 46590..47216 - 627 ALP45078 plasmid conjugative transfer pilus assembly protein trae traE
Locus_47 47213..47494 - 282 ALP45079 plasmid conjugative transfer pilus assembly protein tral traL
Locus_48 47783..48370 + 588 ALP45080 hypothetical protein -
Locus_49 48397..49032 - 636 ALP45081 conjugative transfer protein tfc7
Locus_50 49019..49579 - 561 ALP45082 conjugative transfer protein -
Locus_51 49589..51409 - 1821 ALP45083 plasmid conjugative transfer protein virb4
Locus_52 51458..53608 - 2151 ALP45084 conjugative transfer protein relaxase -
Locus_53 53730..53894 + 165 ALP45085 hypothetical protein -
Locus_54 53857..55992 - 2136 ALP45086 putative DNA helicase -

Host bacterium

ID   135 Element type   ICE (Integrative and conjugative element)
Element name   ICEVchCHN4210 GenBank   KT151662
Element size   110349 bp Coordinate of oriT [Strand]   104455..104753 [-]
Host bacterium   Vibrio cholerae strain ICDC-4210 sequence Coordinate of element   1..110349

Cargo genes

Drug resistance gene   sul2, aph(3'')-Ib, aph(6)-Id, tet(A), floR
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -