Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200119
Name   oriT_ICEPvuCHN2213 in_silico
Organism   Proteus vulgaris strain 08MAS2213 sequence
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   KX243403 (5640..5938 [+], 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_ICEPvuCHN2213
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14271 GenBank   APO16688
Name   traI_-_ICEPvuCHN2213 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: 79730.84 Da        Isoelectric Point: 5.1606

>APO16688.1 Conjugative transfer protein TraI, relaxase [Proteus vulgaris]
MFKNLFFQTKALPELSSQLDTEIPRYPPFLKGLPAASPEDLQSTQDELITKLRQVLGFNLRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTTNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNTIGVPVERYLLDAMRRL
LASSQWLVNQRDARVWIRKSNQSTNLYLVWKSAAKEIIELLAKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESLAPEVLIKDGKPIWLPMLHISEADLLFSSNVPSGVRLFSKSEWEATQQTQAEPQSRSSEQPGL
SEASSSIELNNSAESPSTKSSEQDDERPLASDVNHLQATENAPGDECEKPNNSYDGAISNNVNQHDAEAL
NLPESLAWLPEASSALVMVDEQILVRYPDAVRHWCAPRKLLAELSRLDWLEIDPANPTRKARTVTTKGGV
QEQGLLLKVSISKGLTALIDLPKQDAESAAAIQNEEASPRPSRTETTNARAKEPSKRAECKQKPIAPNAN
SSIDPKHAQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVANEHGIPAGQLLRGISASDQC
QFDEGETVLFTAHAER

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(39-349)


  Protein structure



No available structure.




T4CP

ID   16528 GenBank   APO16689
Name   traD_-_ICEPvuCHN2213 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

>APO16689.1 IncF plasmid conjugative transfer protein TraD [Proteus vulgaris]
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   16529 GenBank   APO16706
Name   traC_-_ICEPvuCHN2213 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

>APO16706.1 IncF plasmid conjugative transfer pilus assembly protein TraC [Proteus vulgaris]
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: 42011..66155

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_34 37990..38844 + 855 APO16685 Mrr restriction system protein -
Locus_35 38938..39219 + 282 APO16686 hypothetical protein -
Locus_36 39219..39692 + 474 APO16687 hypothetical protein -
Locus_37 39812..41962 + 2151 APO16688 Conjugative transfer protein TraI, relaxase -
Locus_38 42011..43831 + 1821 APO16689 IncF plasmid conjugative transfer protein TraD virb4
Locus_39 43841..44401 + 561 APO16690 Conjugative transfer protein 234 -
Locus_40 44388..45023 + 636 APO16691 Conjugative transfer protein s043 tfc7
Locus_41 45295..46851 + 1557 APO16692 Mobile element protein -
Locus_42 47016..47264 + 249 APO16693 hypothetical protein -
Locus_43 47224..48495 + 1272 APO16694 hypothetical protein -
Locus_44 48571..49266 + 696 APO16695 Mobile element protein virB11
Locus_45 49345..49917 - 573 APO16696 hypothetical protein -
Locus_46 50206..50487 + 282 APO16697 IncF plasmid conjugative transfer pilus assembly protein TraL traL
Locus_47 50484..51110 + 627 APO16698 IncF plasmid conjugative transfer pilus assembly protein TraE traE
Locus_48 51094..51990 + 897 APO16699 IncF plasmid conjugative transfer pilus assembly protein TraK traK
Locus_49 51993..53282 + 1290 APO16700 IncF plasmid conjugative transfer pilus assembly protein TraB traB
Locus_50 53279..53929 + 651 APO16701 Conjugative transfer protein TraV traV
Locus_51 53926..54312 + 387 APO16702 Conjugative transfer protein TraA -
Locus_52 54490..55323 + 834 APO16703 Ynd -
Locus_53 55316..56254 + 939 APO16704 Ync -
Locus_54 56386..57078 + 693 APO16705 Thiol:disulfide involved in conjugative transfer trbB
Locus_55 57078..59477 + 2400 APO16706 IncF plasmid conjugative transfer pilus assembly protein TraC virb4
Locus_56 59470..59817 + 348 APO16707 Conjugative transfer protein 345 -
Locus_57 59801..60313 + 513 APO16708 Conjugative signal peptidase TrhF -
Locus_58 60324..61448 + 1125 APO16709 IncF plasmid conjugative transfer pilus assembly protein TraW traW
Locus_59 61432..62460 + 1029 APO16710 IncF plasmid conjugative transfer pilus assembly protein TraU traU
Locus_60 62463..66155 + 3693 APO16711 IncF plasmid conjugative transfer protein TraN traN
Locus_61 66387..66719 + 333 APO16712 hypothetical protein -
Locus_62 66750..67412 + 663 APO16713 hypothetical protein -
Locus_63 67503..68105 - 603 APO16714 hypothetical protein -
Locus_64 68473..68799 + 327 APO16715 hypothetical protein -
Locus_65 68815..69234 + 420 APO16716 Single-stranded DNA-binding protein -
Locus_66 69314..70132 + 819 APO16717 Recombination protein BET -
Locus_67 70214..70357 + 144 APO16718 hypothetical protein -

Host bacterium

ID   121 Element type   ICE (Integrative and conjugative element)
Element name   ICEPvuCHN2213 GenBank   KX243403
Element size   94342 bp Coordinate of oriT [Strand]   5640..5938 [+]
Host bacterium   Proteus vulgaris strain 08MAS2213 sequence Coordinate of element   1..94340

Cargo genes

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