Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200386
Name   oriT_ICEPvuChnBC22 in_silico
Organism   Proteus vulgaris strain SCpv22 sequence
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   MH160822 (3814..4112 [+], 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_ICEPvuChnBC22
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14413 GenBank   QBQ84507
Name   traI_-_ICEPvuChnBC22 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: 79760.84 Da        Isoelectric Point: 5.2184

>QBQ84507.1 TraI [Proteus vulgaris]
MFKNLFFQAKALPELSSQLDAEIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQVLGFNQRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTSNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWIRKSNQSTHLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESLAPEVLIKDDKPIWLAMLHIVEADLLFSSNVPSSVRLFSKSEWEATPQTQAEPQSRSSEQPGL
PDASSSIEHGNSSESPSTKSSDQDDELRLASDVNNPQANENAPGDGCENPNNSYDGAISNNVNQHDAEAF
NLPESLAWLPEASSALVMVDEQIMIRYPDAVRHWCAPRKLLAELSRLDWLELDPANPTRKARTVTTKDGV
QEQGLLLKVSISKGLTALIDLPKQDAEPAAAIQNEEALQRPSRTKTTNAQAKEPATRAERKQKPIGPNAN
SSTDPKHAQRQQMVNFVKDLPILLTDGDYPYVDHSADGIRVTIQTLRQVAKEHGIPAGQLLRGISASDEC
QFDEGETVLFTARAER

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(39-349)


  Protein structure



No available structure.




T4CP

ID   16934 GenBank   QBQ84508
Name   traD_-_ICEPvuChnBC22 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: 67102.94 Da        Isoelectric Point: 6.2511

>QBQ84508.1 TraD [Proteus vulgaris]
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYLLYKLQMG
LKGKPLAFMELSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKTNTLAKQAMAMLLFYYERIQPIAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVDNRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FAARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
LMEEEGDMFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAA

  Protein domains


Predicted by InterproScan.

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

(152-277)

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

(451-578)

  Protein structure



No available structure.



ID   16935 GenBank   QBQ84522
Name   traC_-_ICEPvuChnBC22 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: 90171.75 Da        Isoelectric Point: 5.9727

>QBQ84522.1 TraC [Proteus vulgaris]
MKASLYSGQRASELLPVLAYSDDEQLFFMEDQSVGFGFLCDPLPGGDESVADRVNVLLNNDWPKDTLLQF
GLYASPDIQTDLQRMMGLRHRQSDPLLRASIRKRADFLDGGTVQPIEESTQTQVRNFQLIVTCKLPLESP
IPTDRELSRASALRASFSQALATVGFRVTEMTDRNWLAALSAQLNWGKDASWRNPSPIRSEADKPLREQV
LDYDRAIKVDSQGLMLGDYRVKTLSFKRLPERIWFGHAASFAGDMMTGSRGLRGSFLLNVTIHFPSAEAM
RSRLETKRQWAVNQAYGPMLKFVPVLAAKKKGFDVLFEALQEGDRPIRANMTLTLFSPTEEASISSVSNA
RTYFKELGFELMEDKYFCLPIFLNALPFGADRQAMNDLFRFKTMATRHIIPLLPLFADWKGTGTPVINFV
SRNGQIMSVSLYDSGSNYNCCIAAQSGSGKSFLVNEIISSYLSEGGQCWVIDVGRSYEKLCEVYDGEFLQ
FGRDSGICLNPFEIVEDYDEEADVLVGLLAAMAAPTQSLTDFQMANLKRQTRELWEKKGRAMLVDDVAEA
LKNHEDRRVQDVGEQLYPFTTQGEYGRFFNGHNNIRFKNRFTVLELEELKGRKHLQQVVLLQLIYQIQQE
MYLGERDRRKIVFIDEAWDLLTQGDVGKFIETGYRRFRKYGGSAVTVTQSVNDLYDSPTGKAIAENSANM
YLLGQKAETINALKKEGRLPLGEGGYEYLKTVHTVTGVYSEIFFITEMGTGIGRLIVDPFHKLLYSSRAE
DVNAIKQLTRKGLSVADAISQLLKERGYE

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(436-521)

TraG P-loop domain (P-loop_TraG)

(566-794)

Family of unknown function (DUF5934) (DUF5934)

(253-420)

TraC protein (TraC_F_IV)

(11-241)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 94967..119788

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_112 90163..90960 + 798 QBQ84504 TnpII transposase -
Locus_113 91026..91358 + 333 QBQ84505 hypothetical protein -
Locus_114 91430..92611 + 1182 QBQ84506 putative inner membrane protein -
Locus_115 92768..94918 + 2151 QBQ84507 TraI -
Locus_116 94967..96787 + 1821 QBQ84508 TraD virb4
Locus_117 96797..97357 + 561 QBQ84509 Conjugative transfer protein -
Locus_118 97344..97979 + 636 QBQ84510 Conjugative transfer protein s043 tfc7
Locus_119 98420..98689 + 270 QBQ84511 hypothetical protein -
Locus_120 98682..99788 + 1107 QBQ84512 Transcriptional regulator -
Locus_121 99925..100206 + 282 QBQ84513 TraL traL
Locus_122 100203..100829 + 627 QBQ84514 TraE traE
Locus_123 100813..101709 + 897 QBQ84515 TraK traK
Locus_124 101712..103001 + 1290 QBQ84516 TraB traB
Locus_125 102998..103648 + 651 QBQ84517 TraV traV
Locus_126 103645..104031 + 387 QBQ84518 TraA -
Locus_127 104210..105043 + 834 QBQ84519 Ynd -
Locus_128 105036..105974 + 939 QBQ84520 Ync -
Locus_129 106106..106798 + 693 QBQ84521 Thiol:disulfide involved in conjugative transfer trbB
Locus_130 106798..109197 + 2400 QBQ84522 TraC virb4
Locus_131 109190..109537 + 348 QBQ84523 Conjugative transfer protein -
Locus_132 109521..110033 + 513 QBQ84524 TrhF -
Locus_133 110044..111168 + 1125 QBQ84525 TraW traW
Locus_134 111152..112180 + 1029 QBQ84526 TraU traU
Locus_135 112183..115875 + 3693 QBQ84527 TraN traN
Locus_136 116334..117752 + 1419 QBQ84528 hypothetical protein -
Locus_137 117749..119788 + 2040 QBQ84529 HerA virb4
Locus_138 120197..120910 - 714 QBQ84530 Endonuclease I precursor -
Locus_139 120913..121479 - 567 QBQ84531 Il-IS_2 transposase -
Locus_140 122222..122734 - 513 QBQ84532 putative lipoprotein signal peptidase LspA -
Locus_141 122738..123634 - 897 QBQ84533 Cobalt-zinc-cadmium resistance protein CzcD -
Locus_142 123730..124137 + 408 QBQ84534 d(II)/Pb(II)-responsive transcriptional regulator -

Host bacterium

ID   343 Element type   ICE (Integrative and conjugative element)
Element name   ICEPvuChnBC22 GenBank   MH160822
Element size   148751 bp Coordinate of oriT [Strand]   3814..4112 [+]
Host bacterium   Proteus vulgaris strain SCpv22 sequence Coordinate of element   1..148751

Cargo genes

Drug resistance gene   aph(4)-Ia, aac(3)-IVa, sul1, blaDHA-1, qacE, ARR-3, aac(6')-Ib-cr, catB3, blaOXA-1, aph(3')-Ia, cfr, dfrA32, ere(A), aadA2, tet(C), blaNDM-1, floR, aph(6)-Id, aph(3'')-Ib, sul2
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -