Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200398
Name   oriT_ICETET in_silico
Organism   Vibrio cholerae strain IDH_1986 sequence
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   MK165649 (4841..5139 [+], 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_ICETET
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14425 GenBank   QAY18233
Name   traI_-_ICETET 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

>QAY18233.1 conjugal transfer pilus assembly protein TraI [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   16947 GenBank   QAY18234
Name   traD_-_ICETET 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

>QAY18234.1 conjugal transfer pilus assembly protein TraD [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   16948 GenBank   QAY18251
Name   traC_-_ICETET 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

>QAY18251.1 conjugal transfer ATP-binding 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: 38546..62683

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_32 34525..35379 + 855 QAY18230 Mrr restriction system protein -
Locus_33 35473..35754 + 282 QAY18231 hypothetical protein -
Locus_34 35754..36227 + 474 QAY18232 hypothetical protein -
Locus_35 36347..38497 + 2151 QAY18233 conjugal transfer pilus assembly protein TraI -
Locus_36 38546..40366 + 1821 QAY18234 conjugal transfer pilus assembly protein TraD virb4
Locus_37 40376..40936 + 561 QAY18235 conjugative transfer protein 234 -
Locus_38 40914..41558 + 645 QAY18236 conjugative transfer protein tfc7
Locus_39 41830..43386 + 1557 QAY18237 transposase/integrase -
Locus_40 43546..43794 + 249 QAY18238 hypothetical protein -
Locus_41 43754..45025 + 1272 QAY18239 Transposase -
Locus_42 45101..45796 + 696 QAY18240 ISPsy4 transposition helper protein virB11
Locus_43 45875..46447 - 573 QAY18241 DNA helicase family protein -
Locus_44 46736..47017 + 282 QAY18242 conjugative transfer pilus assembly protein TraL traL
Locus_45 47014..47640 + 627 QAY18243 conjugative transfer pilus assembly protein TraE traE
Locus_46 47621..48520 + 900 QAY18244 conjugal transfer pilus assembly protein TraK traK
Locus_47 48523..49812 + 1290 QAY18245 conjugal transfer pilus assembly protein TraB traB
Locus_48 49809..50459 + 651 QAY18246 Conjugative transfer protein TraV traV
Locus_49 50456..50842 + 387 QAY18247 conjugal transfer pilus assembly protein TraA -
Locus_50 51020..51853 + 834 QAY18248 Ynd -
Locus_51 51846..52535 + 690 QAY18249 Ync' -
Locus_52 52914..53606 + 693 QAY18250 disulfide isomerase DsbC trbB
Locus_53 53606..56005 + 2400 QAY18251 conjugal transfer ATP-binding protein TraC virb4
Locus_54 55998..56345 + 348 QAY18252 hypothetical protein -
Locus_55 56329..56841 + 513 QAY18253 conjugative signal peptidase TrhF -
Locus_56 56792..57976 + 1185 QAY18254 conjugal transfer pilus assembly protein TraW traW
Locus_57 57960..58988 + 1029 QAY18255 conjugal transfer pilus assembly protein TraU traU
Locus_58 58991..62683 + 3693 QAY18256 conjugal transfer mating pair stabilization protein TraN traN
Locus_59 62915..63247 + 333 QAY18257 hypothetical protein -
Locus_60 63278..63940 + 663 QAY18258 Putative glycosylase -
Locus_61 64031..64633 - 603 QAY18259 hypothetical protein -
Locus_62 65001..65327 + 327 QAY18260 hypothetical protein -
Locus_63 65343..65762 + 420 QAY18261 single-stranded DNA-binding protein -
Locus_64 65842..66660 + 819 QAY18263 recombination protein BET -

Host bacterium

ID   354 Element type   ICE (Integrative and conjugative element)
Element name   ICETET GenBank   MK165649
Element size   91463 bp Coordinate of oriT [Strand]   4841..5139 [+]
Host bacterium   Vibrio cholerae strain IDH_1986 sequence Coordinate of element   1..91463

Cargo genes

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