Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200405
Name   oriT_ICEVchThd1 in_silico
Organism   Vibrio cholerae strain TSY216
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP007653 (5166..5464 [+], 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_ICEVchThd1
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14433 GenBank   AKO74217
Name   TraI_2_EN12_02990_ICEVchThd1 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: 79789.91 Da        Isoelectric Point: 5.2251

>AKO74217.1 phosphohydrolase [Vibrio cholerae]
MFKNLFFQTKALPELSSQLDTEIPRYPPFLKGLPAASPEDLQSTQDELITKLRQVLGFNLRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTTNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNTIGVPVERYLLDAMRRL
LASSQWLVNQRDARVWIRKSNQSTNLYLVWKSAAKEIIELLAKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESLAPEVLIKDGKPIWLPMLHISEADLLFSSNVPSGVRLFSKSEWEATQQTQAEPQSRSSEQPGL
SEASSSIELNNSAESPSTKSSEQDDERRLASDVNHLQATENAPGDECEKPNNSYDGAISNNVNQHDAEAL
NLPESLAWLPEASSALVMVDEQILVRYPDAVRHWCAPRKLLAELSRLDWLEIDPANPTRKARTVTTKGGV
QEQGLLLKVSISKGLTALIDLPKQDAESAAAIQNEEASPRPSRTETTNARAKEPSKRAECKQKPIAPNAN
SSIDPKHAQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVANEHGIPAGQLLRGISASDQC
QFDEGETVLFTAHAER

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(39-349)


  Protein structure



No available structure.




T4CP

ID   16964 GenBank   AKO74218
Name   t4cp2_EN12_02995_ICEVchThd1 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: 67134.99 Da        Isoelectric Point: 6.4440

>AKO74218.1 conjugal transfer protein [Vibrio cholerae]
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQMG
LKGKPLAFMELSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPERSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
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.



ID   16965 GenBank   AKO74234
Name   t4cp2_EN12_03085_ICEVchThd1 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: 90098.71 Da        Isoelectric Point: 6.2880

>AKO74234.1 conjugal transfer protein TraC [Vibrio cholerae]
MKASLYSGQRASELLPVLAYSDDEQLFFMEDQSVGFGFLCDPLPGGDESVADRVNVLLNNDWPKDTLLQF
GLYASPDIQTDLQRMMGLRHRQSDPLLRASIRKRADFLDGGTVQPIEESTQTQVRNFQLIVTCKLPLESP
IPTERELSRASALRASFSQALATVGFRVTEMTDRNWLAAISAQLNWGKDASWRNPSPIRSEADKPLREQV
LDYDRAIKVDSQGLMLGDYRVKTLSFKRLPERIWFGHAASFAGDMMTGSRGLRGSFLLNVTIHFPSAEAM
RSRLETKRQWAVNQAYGPMLKFVPVLAAKKKGFDVLFEALQEGDRPIRANMTLTLFSPTGEASISSVSNA
RTYFKELGFELMEDKYFCLPIFLNALPFGADRQAMNDLFRFKTMATRHVIPLLPLFADWKGTGTPVINFV
SRNGQIMSVSLYDSGSNYNCCIAAQSGSGKSFLVNEIISSYLSEGGQCWVIDVGRSYEKLCEVYDGEFLQ
FGRNSGICLNPFEIVEDYDEEADVLVGLLAAMAAPTQSLTDFQMANLKRQTRELWEKKGRAMLVDDVAEA
LKNHEDRRVQDVGEQLYPFTTQGEYGRFFNGHNNIRFKNRFTVLELEELKGRKHLQQVVLLQLIYQIQQE
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)

(566-794)

TraG P-loop domain (P-loop_TraG)

(436-521)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 627884..652021

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EN12_02975 623863..624717 + 855 AKO74214 restriction endonuclease -
EN12_02980 624811..625092 + 282 AKO74215 hypothetical protein -
EN12_02985 625092..625565 + 474 AKO74216 hypothetical protein -
EN12_02990 625685..627835 + 2151 AKO74217 phosphohydrolase -
EN12_02995 627884..629704 + 1821 AKO74218 conjugal transfer protein virb4
EN12_03000 629714..630274 + 561 AKO74219 hypothetical protein -
EN12_03005 630261..630896 + 636 AKO74220 conjugal transfer protein tfc7
EN12_03010 631168..632724 + 1557 AKO74221 transposase -
EN12_03020 632884..633132 + 249 AKO74222 hypothetical protein -
EN12_03025 633092..634363 + 1272 AKO74223 transposase -
EN12_03030 634439..635134 + 696 AKO74224 ATPase AAA virB11
EN12_03035 635213..635785 - 573 AKO74225 hypothetical protein -
EN12_03040 636074..636355 + 282 AKO74226 conjugal transfer protein TraL traL
EN12_03045 636352..636978 + 627 AKO74227 pilus assembly protein traE
EN12_03050 637052..637858 + 807 AKO74228 hypothetical protein traK
EN12_03055 637861..639150 + 1290 AKO74229 conjugal transfer protein TraB traB
EN12_03060 639147..639797 + 651 AKO74230 conjugal transfer protein TraV traV
EN12_03065 639794..640180 + 387 AKO74231 membrane protein -
EN12_03070 640400..641191 + 792 AKO74232 hypothetical protein -
EN12_03080 642252..642944 + 693 AKO74233 disulfide isomerase trbB
EN12_03085 642944..645343 + 2400 AKO74234 conjugal transfer protein TraC virb4
EN12_03090 645336..645683 + 348 AKO74235 hypothetical protein -
EN12_03095 645667..646179 + 513 AKO74236 peptidase -
EN12_03100 646190..647314 + 1125 AKO74237 pilus assembly protein traW
EN12_03105 647298..648326 + 1029 AKO74238 conjugal transfer protein TraU traU
EN12_03110 648329..652021 + 3693 AKO74239 conjugal transfer protein TraN traN
EN12_03115 652253..652585 + 333 AKO74240 hypothetical protein -
EN12_03120 652616..653278 + 663 AKO74241 hypothetical protein -
EN12_03125 653369..653971 - 603 AKO74242 hypothetical protein -
EN12_03130 654339..654665 + 327 AKO74243 hypothetical protein -
EN12_03135 654681..655100 + 420 AKO74244 single-stranded DNA-binding protein -
EN12_03140 655180..655998 + 819 AKO74245 recombinase -

Host bacterium

ID   360 Element type   ICE (Integrative and conjugative element)
Element name   ICEVchThd1 GenBank   CP007653
Element size   3053204 bp Coordinate of oriT [Strand]   5166..5464 [+]
Host bacterium   Vibrio cholerae strain TSY216 Coordinate of element   579719..680801

Cargo genes

Drug resistance gene   mph(A), tet(59), aph(6)-Id, aph(3'')-Ib, sul2, dfrA1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -