Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200136
Name   oriT_ICEVchChnAHV1003 in_silico
Organism   Vibrio cholerae SXT element
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   KT151663 (95944..96242 [-], 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_ICEVchChnAHV1003
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14289 GenBank   ALP45190
Name   traI_-_ICEVchChnAHV1003 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

>ALP45190.1 conjugative transfer protein relaxase [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   16564 GenBank   ALP45172
Name   traC_-_ICEVchChnAHV1003 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

>ALP45172.1 plasmid conjugative transfer pilus assembly 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.



ID   16565 GenBank   ALP45189
Name   traD_-_ICEVchChnAHV1003 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

>ALP45189.1 plasmid conjugative 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 29105..53242

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_29 24903..25046 - 144 ALP45160 hypothetical protein -
Locus_30 25128..25946 - 819 ALP45161 recombination protein BET -
Locus_31 26026..26445 - 420 ALP45162 single-stranded DNA-binding protein -
Locus_32 26461..26787 - 327 ALP45163 hypothetical protein -
Locus_33 27155..27757 + 603 ALP45164 hypothetical protein -
Locus_34 27848..28510 - 663 ALP45165 hypothetical protein -
Locus_35 28541..28873 - 333 ALP45166 hypothetical protein -
Locus_36 29105..32797 - 3693 ALP45167 plasmid conjugative transfer protein traN
Locus_37 32800..33828 - 1029 ALP45168 plasmid conjugative transfer pilus assembly protein trau traU
Locus_38 33812..34936 - 1125 ALP45169 plasmid conjugative transfer pilus assembly protein traw traW
Locus_39 34947..35459 - 513 ALP45170 conjugative signal peptidase -
Locus_40 35443..35790 - 348 ALP45171 hypothetical protein -
Locus_41 35783..38182 - 2400 ALP45172 plasmid conjugative transfer pilus assembly protein trac virb4
Locus_42 38182..38874 - 693 ALP45173 thiol:disulfide protein trbB
Locus_43 39253..39942 - 690 ALP45174 ync -
Locus_44 39935..40768 - 834 ALP45175 ynd -
Locus_45 40946..41332 - 387 ALP45176 conjugative transfer protein -
Locus_46 41329..41979 - 651 ALP45177 conjugative transfer protein traV
Locus_47 41976..43265 - 1290 ALP45178 plasmid conjugative transfer pilus assembly protein trab traB
Locus_48 43268..44164 - 897 ALP45179 plasmid conjugative transfer pilus assembly protein trak traK
Locus_49 44148..44774 - 627 ALP45180 plasmid conjugative transfer pilus assembly protein trae traE
Locus_50 44771..45052 - 282 ALP45181 plasmid conjugative transfer pilus assembly protein tral traL
Locus_51 45341..45913 + 573 ALP45182 hypothetical protein -
Locus_52 45992..46687 - 696 ALP45183 ISPsy4 transposition helper protein virB11
Locus_53 46763..48034 - 1272 ALP45184 hypothetical protein -
Locus_54 47994..48242 - 249 ALP45185 hypothetical protein -
Locus_55 48402..49958 - 1557 ALP45186 transposase -
Locus_56 50230..50865 - 636 ALP45187 conjugative transfer protein tfc7
Locus_57 50852..51412 - 561 ALP45188 conjugative transfer protein -
Locus_58 51422..53242 - 1821 ALP45189 plasmid conjugative transfer protein virb4
Locus_59 53291..55441 - 2151 ALP45190 conjugative transfer protein relaxase -
Locus_60 55561..56034 - 474 ALP45191 hypothetical protein -
Locus_61 56034..56315 - 282 ALP45192 hypothetical protein -
Locus_62 56409..57263 - 855 ALP45193 mrr restriction system protein -

Host bacterium

ID   138 Element type   ICE (Integrative and conjugative element)
Element name   ICEVchChnAHV1003 GenBank   KT151663
Element size   101887 bp Coordinate of oriT [Strand]   95944..96242 [-]
Host bacterium   Vibrio cholerae SXT element Coordinate of element   1..101856

Cargo genes

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