Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200380
Name   oriT_ICEPmiChnSTP3 in_silico
Organism   Proteus mirabilis strain STP3 sequence
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   MT449450 (114477..114775 [-], 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_ICEPmiChnSTP3
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14406 GenBank   QVW29910
Name   traI_-_ICEPmiChnSTP3 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

>QVW29910.1 conjugative transfer protein TraI, phosphohydrolase [Proteus mirabilis]
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   16921 GenBank   QVW29895
Name   traC_-_ICEPmiChnSTP3 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

>QVW29895.1 type-IV secretion system protein TraC [Proteus mirabilis]
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.



ID   16922 GenBank   QVW29909
Name   traD_-_ICEPmiChnSTP3 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

>QVW29909.1 IncF plasmid conjugative transfer protein TraD [Proteus mirabilis]
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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 56889..81710

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_61 52082..52303 + 222 QVW29883 hypothetical protein -
Locus_62 52540..52947 - 408 QVW29884 MerR family transcriptional regulator -
Locus_63 53043..53939 + 897 QVW29885 cation transporter -
Locus_64 53943..54455 + 513 QVW29886 lipoprotein signal peptidase -
Locus_65 55198..55764 + 567 QVW29887 ISL3 family transposase -
Locus_66 56889..58928 - 2040 QVW29888 ATPase virb4
Locus_67 58925..60343 - 1419 QVW29889 hypothetical protein -
Locus_68 60802..64494 - 3693 QVW29890 conjugal transfer protein TraN traN
Locus_69 64497..65525 - 1029 QVW29891 conjugal transfer protein TraU traU
Locus_70 65509..66636 - 1128 QVW29892 IncF plasmid conjugative transfer pilus assembly protein TraW traW
Locus_71 66644..67156 - 513 QVW29893 conjugative signal peptidase TrhF -
Locus_72 67140..67487 - 348 QVW29894 hypothetical protein -
Locus_73 67480..69879 - 2400 QVW29895 type-IV secretion system protein TraC virb4
Locus_74 69879..70571 - 693 QVW29896 disulfide isomerase trbB
Locus_75 70703..71641 - 939 QVW29897 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
Locus_76 71634..72467 - 834 QVW29898 transcriptional regulator with AbiEi antitoxin N-terminal domain -
Locus_77 72646..73032 - 387 QVW29899 conjugative transfer protein TraA -
Locus_78 73029..73601 - 573 QVW29900 conjugal transfer pilus assembly protein TraV traV
Locus_79 73676..74965 - 1290 QVW29901 conjugal transfer pilus assembly protein TraB traB
Locus_80 74968..75867 - 900 QVW29902 conjugal transfer pilus assembly protein TraK traK
Locus_81 75848..76240 - 393 QVW29903 conjugal transfer pilus assembly protein TraE traE
Locus_82 76471..76752 - 282 QVW29904 conjugal transfer protein TraL traL
Locus_83 76889..77995 - 1107 QVW29905 zinc peptidase -
Locus_84 77988..78626 - 639 QVW29906 hypothetical protein -
Locus_85 78698..79333 - 636 QVW29907 conjugal transfer protein tfc7
Locus_86 79320..79880 - 561 QVW29908 conjugative transfer protein -
Locus_87 79890..81710 - 1821 QVW29909 IncF plasmid conjugative transfer protein TraD virb4
Locus_88 81759..83909 - 2151 QVW29910 conjugative transfer protein TraI, phosphohydrolase -
Locus_89 84066..85247 - 1182 QVW29911 membrane protein -

Host bacterium

ID   337 Element type   ICE (Integrative and conjugative element)
Element name   ICEPmiChnSTP3 GenBank   MT449450
Element size   118916 bp Coordinate of oriT [Strand]   114477..114775 [-]
Host bacterium   Proteus mirabilis strain STP3 sequence Coordinate of element   1..118916

Cargo genes

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