Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200112
Name   oriT_ICEPmiCHN3335 in_silico
Organism   Proteus mirabilis strain TJ3335 sequence
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   KX243416 (3509..3807 [+], 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_ICEPmiCHN3335
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14264 GenBank   APO17822
Name   traI_-_ICEPmiCHN3335 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

>APO17822.1 Conjugative transfer protein TraI, relaxase [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   16514 GenBank   APO17823
Name   traD_-_ICEPmiCHN3335 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

>APO17823.1 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.



ID   16515 GenBank   APO17837
Name   traC_-_ICEPmiCHN3335 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

>APO17837.1 IncF plasmid conjugative transfer pilus assembly 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 40516..65337

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_32 36979..38160 + 1182 APO17821 putative inner membrane protein -
Locus_33 38317..40467 + 2151 APO17822 Conjugative transfer protein TraI, relaxase -
Locus_34 40516..42336 + 1821 APO17823 IncF plasmid conjugative transfer protein TraD virb4
Locus_35 42346..42906 + 561 APO17824 Conjugative transfer protein 234 -
Locus_36 42893..43528 + 636 APO17825 Conjugative transfer protein s043 tfc7
Locus_37 43600..44238 + 639 APO17826 hypothetical protein -
Locus_38 44231..45337 + 1107 APO17827 Transcriptional regulator -
Locus_39 45474..45755 + 282 APO17828 IncF plasmid conjugative transfer pilus assembly protein TraL traL
Locus_40 45752..46378 + 627 APO17829 IncF plasmid conjugative transfer pilus assembly protein TraE traE
Locus_41 46362..47258 + 897 APO17830 IncF plasmid conjugative transfer pilus assembly protein TraK traK
Locus_42 47261..48550 + 1290 APO17831 IncF plasmid conjugative transfer pilus assembly protein TraB traB
Locus_43 48625..49197 + 573 APO17832 Conjugative transfer protein TraV traV
Locus_44 49194..49580 + 387 APO17833 Conjugative transfer protein TraA -
Locus_45 49759..50592 + 834 APO17834 Ynd -
Locus_46 50585..51523 + 939 APO17835 Ync -
Locus_47 51655..52347 + 693 APO17836 Thiol:disulfide involved in conjugative transfer trbB
Locus_48 52347..54746 + 2400 APO17837 IncF plasmid conjugative transfer pilus assembly protein TraC virb4
Locus_49 54739..55086 + 348 APO17838 Conjugative transfer protein 345 -
Locus_50 55070..55582 + 513 APO17839 Conjugative signal peptidase TrhF -
Locus_51 55590..56717 + 1128 APO17840 IncF plasmid conjugative transfer pilus assembly protein TraW traW
Locus_52 56749..57729 + 981 APO17841 IncF plasmid conjugative transfer pilus assembly protein TraU traU
Locus_53 57732..61424 + 3693 APO17842 IncF plasmid conjugative transfer protein TraN traN
Locus_54 61883..63301 + 1419 APO17843 hypothetical protein -
Locus_55 63298..65337 + 2040 APO17844 Bipolar DNA helicase HerA virb4
Locus_56 65583..65696 + 114 APO17845 hypothetical protein -
Locus_57 65746..66459 - 714 APO17846 Endonuclease I precursor -
Locus_58 66462..66914 - 453 APO17847 Il-IS_2, transposase -
Locus_59 67175..67777 - 603 APO17848 hypothetical protein -
Locus_60 68144..68470 + 327 APO17849 hypothetical protein -
Locus_61 68486..68905 + 420 APO17850 Single-stranded DNA-binding protein -
Locus_62 68985..69803 + 819 APO17851 Recombination protein BET -
Locus_63 69886..70029 + 144 APO17852 hypothetical protein -

Host bacterium

ID   114 Element type   ICE (Integrative and conjugative element)
Element name   ICEPmiCHN3335 GenBank   KX243416
Element size   89996 bp Coordinate of oriT [Strand]   3509..3807 [+]
Host bacterium   Proteus mirabilis strain TJ3335 sequence Coordinate of element   1..89996

Cargo genes

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