Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200124
Name   oriT_ICEValHN437 in_silico
Organism   Vibrio alginolyticus strain HN437 sequence
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   KT072771 (3488..3786 [+], 299 nt)
oriT length   299 nt
IRs (inverted repeats)      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_ICEValHN437
GCTCTGTTTGGCGGCGGATGAATGAGCCAAAAAAATCGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTCGCCAAACGGTTTGTATCTTCATGACGATACGTCTTTTTAGGCGTTTTTAAGTGAAATCGGGCTGTATCCCTTGTCAGATATGGGATTGCGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGCTACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTTGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14277 GenBank   ALF35094
Name   traI_ICEValHN437_020_ICEValHN437 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: 79655.68 Da        Isoelectric Point: 5.0979

>ALF35094.1 Conjugative transfer protein, TraI [Vibrio alginolyticus]
MFKNLFFQTKALPELSSQLDAEIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQVIGFNQRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTTNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWIRKSNQSTHLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESLAPEVLIKDDTPIWLPMLHIVEADLLFSSNVPSSVALFSKSEWEATQQTQAEPQCRSSEHSDL
PEASSSIELSNSAESPSSKSSDQDDELRLASDVNHLQATENAPGDECEKPNNSYDGAISNNVNQQDAEAL
NLPESLAWLPEASSALIMVGEQLLIRYPDAVRPWCAPRKLLAELSRLDWLELDPANPTRKARTITTKDGV
QEQGLLLKVSISKGLTALIDISKHDTESAAAIQNKEASQRPSRTETTNAQAKESATRAERKQKPIAANAN
SSTDPKHAQRQQMVSFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVANEHGIPAGQLLRGISASDEC
QFDEGETVLFTAHAKR

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(39-349)


  Protein structure



No available structure.




T4CP

ID   16540 GenBank   ALF35152
Name   traD_ICEValHN437_021_ICEValHN437 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: 67068.90 Da        Isoelectric Point: 6.6974

>ALF35152.1 Conjugative transfer protein, TraD [Vibrio alginolyticus]
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEILTELPPEPFWWMTGISSGMALYRLPEAYRLHKLQKG
LKGKPLAFMELSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKKTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FAARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
LMEEEGDMFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAA

  Protein domains


Predicted by InterproScan.

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

(451-578)

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

(152-285)

  Protein structure



No available structure.



ID   16541 GenBank   ALF35093
Name   traC_ICEValHN437_037_ICEValHN437 insolico UniProt ID   _
Length   800 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 800 a.a.        Molecular weight: 90283.82 Da        Isoelectric Point: 5.8195

>ALF35093.1 Conjugative transfer pilus assembly protein, TraC [Vibrio alginolyticus]
MKASLYSGQRASELLPVLAYSDDEQLFFMEDQSVGFGFLCDPLLGGDESVADRVNVLLNNDWPKDTLLQF
GLYASPDIQTDLQRMMGLRHRQSDPLLRASIRKRADFLDGGTVQPIEESTQTQVRNFQLIVTCKLPLESP
IPTERELSRASALRASFSQALATVGFRVTEMTDRNWLAALSAQLNWGKDASWRNPSPIRSEADKPLREQV
LDYDRAIKVDSQGLMLGDYRVKTLSFKRLPERIWFGHAASFAGDMMTGSRGLRGSFLLNVTIHFPSAESI
RSRLETKRQWAVNQAYGPMLKFVPVLAAKKKGFDVLFEALQEGDRPIRANMNLTLFSPTEEASISSVSNA
RTYFKELGFELMEDKYFCLPIFLNALPFGADRQAMNDLFRFKTMATRHVIPLLPLFADWKGTGTPVINFV
SRNGQIMSVSLYDSGSNYNCCIAAQSGSGKSFLVNEIISSYLSEGGQCWVIDVGRSYEKLCEVYDGEFLQ
FGRDSGICLNPFEIVEDYDEEADVLVGLLAAMAAPTQSLTDFQMANLKRQTRELWEKKGRAMLVDDVAEA
LKNHDDRRVQDVGEQLYPFTTQGEYGRFFNGHNNIRFKNRFTVLELEELKGRKHLQQVVLLQLIYQIQQE
MYLGERDRRKIVFIDEAWDLLTQGDVGKFIETGYRRFRKYGGSAVTVTQSVNDLYDSPTGKAIAENSANM
YLLGQKAETINALKKEGRLPLGEGGYEYLKTVHTVTGVYSEIFFITEMGTGIGRLIVDPFHKLLYSSRAE
DVNAIKQLTRKGLSVADAISQLLKERGFDE

  Protein domains


Predicted by InterproScan.

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)

Family of unknown function (DUF5934) (DUF5934)

(253-420)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 22133..42213

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ICEValHN437_019 18985..19839 + 855 ALF35181 Mrr restriction system protein -
ICEValHN437_020 19934..22084 + 2151 ALF35094 Conjugative transfer protein, TraI -
ICEValHN437_021 22133..23953 + 1821 ALF35152 Conjugative transfer protein, TraD virb4
ICEValHN437_022 23963..24523 + 561 ALF35170 Conjugative transfer protein, S091 -
ICEValHN437_023 24510..25145 + 636 ALF35088 Conjugative transfer protein, traJ tfc7
ICEValHN437_024 25119..25238 - 120 ALF35137 Hypothetical protein -
ICEValHN437_025 25283..26389 + 1107 ALF35110 Fic family protein -
ICEValHN437_026 26445..26579 - 135 ALF35175 Hypothetical protein -
ICEValHN437_027 26591..26881 - 291 ALF35171 HigA protein -
ICEValHN437_028 27114..27395 + 282 ALF35174 Conjugative transfer pilus assembly protein, TraL traL
ICEValHN437_029 27392..28018 + 627 ALF35091 Conjugative transfer pilus assembly protein, TraE traE
ICEValHN437_030 28002..28898 + 897 ALF35101 Conjugative transfer pilus assembly protein, TraK traK
ICEValHN437_031 28901..30190 + 1290 ALF35120 Conjugative transfer pilus assembly protein, TraB traB
ICEValHN437_032 30187..30837 + 651 ALF35147 Conjugative transfer protein, TraV traV
ICEValHN437_033 30834..31220 + 387 ALF35115 Conjugative transfer protein, TraA -
ICEValHN437_034 31261..31767 - 507 ALF35113 Acetyltransferase -
ICEValHN437_035 31758..32024 - 267 ALF35143 Hypothetical protein -
ICEValHN437_036 32440..33132 + 693 ALF35178 Thiol:disulfide involved in conjugative transfer, DsbC trbB
ICEValHN437_037 33133..35535 + 2403 ALF35093 Conjugative transfer pilus assembly protein, TraC virb4
ICEValHN437_038 35528..35875 + 348 ALF35159 Conjugative transfer protein 345 -
ICEValHN437_039 35859..36371 + 513 ALF35119 Conjugative signal peptidase, TrhF -
ICEValHN437_040 36382..37506 + 1125 ALF35158 Conjugative transfer pilus assembly protein, TraW traW
ICEValHN437_041 37766..38518 + 753 ALF35141 Conjugative transfer pilus assembly protein, TraU traU
ICEValHN437_042 38521..42213 + 3693 ALF35155 Conjugative transfer protein, TraN traN
ICEValHN437_043 42445..42777 + 333 ALF35162 Hypothetical protein -
ICEValHN437_044 42808..43470 + 663 ALF35106 Hypothetical protein -
ICEValHN437_045 43561..44163 - 603 ALF35123 Hypothetical protein, S063 -
ICEValHN437_046 44531..44857 + 327 ALF35134 Hypothetical protein, S089 -
ICEValHN437_047 44873..45292 + 420 ALF35105 Single-stranded DNA-binding protein, Ssb -
ICEValHN437_048 45371..46189 + 819 ALF35161 Recombination protein, Bet -
ICEValHN437_049 46272..46415 + 144 ALF35098 Hypothetical protein, OrfZ -

Host bacterium

ID   126 Element type   ICE (Integrative and conjugative element)
Element name   ICEValHN437 GenBank   KT072771
Element size   94290 bp Coordinate of oriT [Strand]   3488..3786 [+]
Host bacterium   Vibrio alginolyticus strain HN437 sequence Coordinate of element   1..94290

Cargo genes

Drug resistance gene   -
Virulence gene   ugd
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -