Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200366
Name   oriT_ICEPciChn2 in_silico
Organism   Proteus terrae subsp. cibarius strain SH19PTE4 sequence
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   MW423608 (4239..4537 [+], 299 nt)
oriT length   299 nt
IRs (inverted repeats)      45..50, 52..57  (CAAACG..CGTTTG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 299 nt

>oriT_ICEPciChn2
GCTCTGTTTGGCGGCGGATGACCTAGTCAAAAAAATCGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTCGCCAAACGGTTTGTATCTTCATGACGATACGTCGTTTTAGGCGTTTTTAAGTGAAATCGGGCTGTATCCCTTGTCAGGTATGGGATTGCGCGAGTTGATTTATATCGAGACGCCAAACAGTGATTGTTACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTTGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14392 GenBank   QZD36683
Name   traI_-_ICEPciChn2 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: 79887.83 Da        Isoelectric Point: 5.2132

>QZD36683.1 conjugative relaxase TraI [Proteus terrae subsp. cibarius]
MFKNLFFQTKALPELSSQLDADIPRYPPFLKGLPAASPEDLQSTQEELIVKLRQVLGFNQRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTSNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWIRKSNQTTHLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESLAPEVLIKDDKPIWLVMLHIVEADLLFSSNVPSSVTLFSKSEWEATQQTQEEPQSHSSEHSDL
PEASSSIEHRKSDESPSTNSSEQENELRHASDVSNPQATENAPGDECEKPNDSSDADIANNANQHHAEAL
NLPESLAWLPEASSALVMVGEQVLIRYPDAVRHWCAPRKLLAELSRLDWLELDPANLTRKARTVTTNDGV
QEQGLLLKVSISKGLTALIDLPKQDAEPAAAIQNEEALQRPSRTETTNAQAKEPATRAERKQKPIAANTN
SSTDPKHAQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVANAHGIPAGQLLRGISASDQC
QFDEGETVLFTAHAKR

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(39-349)


  Protein structure



No available structure.




T4CP

ID   16897 GenBank   QZD36684
Name   traD_-_ICEPciChn2 insolico UniProt ID   _
Length   599 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 599 a.a.        Molecular weight: 66220.04 Da        Isoelectric Point: 6.7822

>QZD36684.1 conjugative coupling factor TraD [Proteus terrae subsp. cibarius]
MPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQMGLKGKPLA
FMALSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKKTLLNQGHGKQMGSTWIHGVEPKEEDVY
QPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSPERFVYFH
PGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDLKTLRRFL
EGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEGLLSMFEH
DRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLTDAMVGSAI
GSLLLSDLTAVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFADFAARTGS
EAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGERLMEEEGD
MFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAV

  Protein domains


Predicted by InterproScan.

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

(444-571)

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

(145-278)

  Protein structure



No available structure.



ID   16898 GenBank   QZD36700
Name   traC_-_ICEPciChn2 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

>QZD36700.1 conjugal transfer protein TraC [Proteus terrae subsp. cibarius]
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: 60378..87414

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_36 58158..60308 + 2151 QZD36683 conjugative relaxase TraI -
Locus_37 60378..62177 + 1800 QZD36684 conjugative coupling factor TraD virb4
Locus_38 62734..63369 + 636 QZD36685 putative conjugation coupling factor tfc7
Locus_39 63395..63673 - 279 QZD36686 helix-turn-helix XRE family protein -
Locus_40 63670..63993 - 324 QZD36687 type II toxin-antitoxin system ParE family toxin -
Locus_41 64174..64455 + 282 QZD36688 conjugal transfer protein TraL traL
Locus_42 64452..65078 + 627 QZD36689 conjugal transfer pilus assembly protein TraE traE
Locus_43 65059..65958 + 900 QZD36690 conjugal transfer pilus assembly protein TraK traK
Locus_44 65961..67250 + 1290 QZD36691 conjugal transfer pilus assembly protein TraB traB
Locus_45 67247..67897 + 651 QZD36692 conjugal transfer pilus assembly protein TraV traV
Locus_46 67894..68280 + 387 QZD36693 conjugal transfer protein TraA -
Locus_47 68458..69291 + 834 QZD36694 transcriptional regulator with AbiEi antitoxin N-terminal domain Ynd -
Locus_48 70050..70457 - 408 QZD36695 PnbR-like regulatory protein -
Locus_49 70553..71449 + 897 QZD36696 putative membrane/transport protein -
Locus_50 71453..71965 + 513 QZD36697 putative lipoprotein signal peptide-like protein -
Locus_51 72062..73276 + 1215 QZD36698 ISPpu12 family transposase -
Locus_52 73732..74424 + 693 QZD36699 thiol:disulfide interchange protein DsbC trbB
Locus_53 74424..76823 + 2400 QZD36700 conjugal transfer protein TraC virb4
Locus_54 77147..77659 + 513 QZD36701 conjugative transfer signal peptidase TrhF -
Locus_55 77610..78794 + 1185 QZD36702 conjugal transfer pilus assembly protein TraW traW
Locus_56 78778..79806 + 1029 QZD36703 conjugal transfer protein TraU traU
Locus_57 79809..83501 + 3693 QZD36704 conjugal transfer protein TraN traN
Locus_58 83960..85378 + 1419 QZD36705 hypothetical protein -
Locus_59 85375..87414 + 2040 QZD36706 ATPase virb4
Locus_60 88539..89753 - 1215 QZD36707 ISPpu12 family transposase -
Locus_61 89850..90362 - 513 QZD36708 putative lipoprotein signal peptide-like protein -
Locus_62 90366..91262 - 897 QZD36709 putative membrane/transport protein -
Locus_63 91358..91765 + 408 QZD36710 PnbR-like regulatory protein -

Host bacterium

ID   323 Element type   ICE (Integrative and conjugative element)
Element name   ICEPciChn2 GenBank   MW423608
Element size   140916 bp Coordinate of oriT [Strand]   4239..4537 [+]
Host bacterium   Proteus terrae subsp. cibarius strain SH19PTE4 sequence Coordinate of element   1..140916

Cargo genes

Drug resistance gene   tet(X6), floR, aph(6)-Id, aph(3'')-Ib, sul2, tet(C), aph(3')-Ia, dfrA32, ere(A), aadA2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -