Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200309
Name   oriT_ICEVflH-08942 in_silico
Organism   Vibrio fluvialis strain H08942 ICEVflInd1 integrating
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   KM213605 (5645..5943 [+], 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_ICEVflH-08942
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14350 GenBank   AIP92402
Name   TraI_2_ICEVflInd1_044_ICEVflH-08942 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: 79773.80 Da        Isoelectric Point: 5.2870

>AIP92402.1 conjugative transfer protein TraI [Vibrio fluvialis]
MFKNLFFQAKALPELSSQLDAEIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQVLGFNQRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTTNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWLRKSNQSTHLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESLAPEVLIKDDKPIWLPMLHISEADLLFSSNVPSSVRLFSKSEWEATQQTQAEPQSRSSEHSDL
PEASSSIEHRKSTESPSTNSSEQDDELRLASDVNNPQATENAPGDGCEKPNNSYDGAISNNVNQHDAEVL
NLPESLAWLPEASSALVVVGEQILIRYPDAVRPWCAPRKLLAELSRLDWLELDPANPTRKARTITTKDGV
QEQGLLLKISISKGLTALIDLSKQDAEPATAIQNEEASPRPSRTKTTNAQAKEPATRAERKQKPIGPNAN
SSTDPKHAQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVANEHGIPAGQLLRGISASDQC
QFDEGETVLFTAHAER

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(39-349)


  Protein structure



No available structure.




T4CP

ID   16842 GenBank   AIP92403
Name   t4cp2_ICEVflInd1_045_ICEVflH-08942 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

>AIP92403.1 IncF plasmid conjugative transfer protein TraD [Vibrio fluvialis]
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   16843 GenBank   AIP92419
Name   t4cp2_ICEVflInd1_064_ICEVflH-08942 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

>AIP92419.1 IncF plasmid conjugative transfer pilus assembly protein TraC [Vibrio fluvialis]
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: 45327..69464

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ICEVflInd1_042 41107..42297 + 1191 AIP92400 hypothetical protein -
ICEVflInd1_043 42298..43011 + 714 AIP92401 hypothetical protein -
ICEVflInd1_044 43128..45278 + 2151 AIP92402 conjugative transfer protein TraI -
ICEVflInd1_045 45327..47147 + 1821 AIP92403 IncF plasmid conjugative transfer protein TraD virb4
ICEVflInd1_046 47157..47717 + 561 AIP92404 hypothetical protein -
ICEVflInd1_047 47704..48339 + 636 AIP92405 conjugative transfer protein traJ tfc7
ICEVflInd1_048 48632..50167 + 1536 AIP92406 integrase catalytic subunit -
ICEVflInd1_049 50327..50575 + 249 AIP92407 hypothetical protein -
ICEVflInd1_050 50535..51806 + 1272 AIP92408 hypothetical protein -
ICEVflInd1_051 51882..52577 + 696 AIP92409 mobile element protein virB11
ICEVflInd1_052 52656..53228 - 573 AIP92410 hypothetical protein -
ICEVflInd1_054 53517..53798 + 282 AIP92411 IncF plasmid conjugative transfer pilus assembly protein TraL traL
ICEVflInd1_055 53795..54421 + 627 AIP92412 IncF plasmid conjugative transfer pilus assembly protein TraE traE
ICEVflInd1_056 54405..55301 + 897 AIP92413 IncF plasmid conjugative transfer pilus assembly protein TraK traK
ICEVflInd1_057 55304..56593 + 1290 AIP92414 IncF plasmid conjugative transfer pilus assembly protein TraB traB
ICEVflInd1_058 56590..57240 + 651 AIP92415 conjugative transfer protein TraV traV
ICEVflInd1_059 57237..57623 + 387 AIP92416 conjugative transfer protein TraA putative pilin subunit -
ICEVflInd1_060 57801..58634 + 834 AIP92417 Ynd -
ICEVflInd1_063 59695..60387 + 693 AIP92418 thiol disulfide trbB
ICEVflInd1_064 60387..62786 + 2400 AIP92419 IncF plasmid conjugative transfer pilus assembly protein TraC virb4
ICEVflInd1_065 62779..63126 + 348 AIP92420 hypothetical protein -
ICEVflInd1_066 63110..63622 + 513 AIP92421 conjugative signal peptidase TrhF -
ICEVflInd1_067 63633..64757 + 1125 AIP92422 IncF plasmid conjugative transfer pilus assembly protein TraW traW
ICEVflInd1_068 64741..65769 + 1029 AIP92423 IncF plasmid conjugative transfer pilus assembly protein TraU traU
ICEVflInd1_069 65772..69464 + 3693 AIP92424 IncF plasmid conjugative transfer protein TraN traN
ICEVflInd1_070 69695..70027 + 333 AIP92425 hypothetical protein -
ICEVflInd1_071 70058..70720 + 663 AIP92426 hypothetical protein -
ICEVflInd1_072 70811..71413 - 603 AIP92427 hypothetical protein -
ICEVflInd1_073 71781..72107 + 327 AIP92428 hypothetical protein -
ICEVflInd1_074 72123..72542 + 420 AIP92429 single-stranded DNA-binding protein -
ICEVflInd1_075 72622..73440 + 819 AIP92430 recombination protein BET -
ICEVflInd1_076 73522..73665 + 144 AIP92431 hypothetical protein -

Host bacterium

ID   277 Element type   ICE (Integrative and conjugative element)
Element name   ICEVflH-08942 GenBank   KM213605
Element size   102878 bp Coordinate of oriT [Strand]   5645..5943 [+]
Host bacterium   Vibrio fluvialis strain H08942 ICEVflInd1 integrating Coordinate of element   1..102878

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   -