Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200114
Name   oriT_ICEPmiCHN901 in_silico
Organism   Proteus mirabilis strain MD20140901 sequence
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   KX243408 (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_ICEPmiCHN901
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14266 GenBank   APO17132
Name   traI_-_ICEPmiCHN901 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: 79771.82 Da        Isoelectric Point: 5.0941

>APO17132.1 Conjugative transfer protein TraI, relaxase [Proteus mirabilis]
MFKNLFFQTKALPELSSQLDTEIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQVLGFNLRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTTNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWVRKSNQSTHLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKST
SNERYESLAPEVLIKDDKPIWLAMLHIVEADLLFSSNVPSGVTLFSKPDWEATQQTQAEPQSRSSEHLDL
PEASSSIELSNSAESPSTKSSEQDDELRHASDVNHLQATENVPGDGCEKPNDSNDATISNNVNQHDADAF
NLPESLAWLPEASSALIMAGEQILIRYPDAVRPWCAPRKLLAELSRLDWLELDPANPTRKARTVTTNDGV
QEQGLLLKVSISKGLIALIDLSKQDAESVEPIQNEEASQRPSRTETANAQAKEPATRAERKQKPIAPNAN
SSTDLKHAQRQQVVNFVKDLPILLTDGNYPDVDHSADGIRVTIQTLRQVANEHGIPAGQLLRGISASDQC
QFDEGETVLFTAHAKR

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(39-350)


  Protein structure



No available structure.




T4CP

ID   16518 GenBank   APO17133
Name   traD_-_ICEPmiCHN901 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: 67156.97 Da        Isoelectric Point: 6.5130

>APO17133.1 IncF plasmid conjugative transfer protein TraD [Proteus mirabilis]
MKENAYEMPWRTNYEAMAVAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQKG
LKGKPLAFMELSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FSARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
LMEEEGDMFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAA

  Protein domains


Predicted by InterproScan.

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

(451-578)

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

(152-285)

  Protein structure



No available structure.



ID   16519 GenBank   APO17146
Name   traC_-_ICEPmiCHN901 insolico UniProt ID   _
Length   715 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 715 a.a.        Molecular weight: 80785.30 Da        Isoelectric Point: 7.6634

>APO17146.1 IncF plasmid conjugative transfer pilus assembly protein TraC [Proteus mirabilis]
MMGLRHRPSDPLLRASIRKRADFLDGGTVQPIEESTQTQVRNFQLIVTCKLPLESPIPTDRELSRASALR
ASFSQALATVGFRVTEMTDRNWLAALSAQLNWGKDASWRNPSPIRSEADKPLREQVLDYDRAIKVDSQGL
MLGDYRVKTLSFKRLPERIWFGHAASFAGDMMTGSRGLRGSFLLNVTIHFPSAEAMRSRLETKRQWAVNQ
AYGPMLKFVPVLAAKKKGFDVLFEALQEGDRPIRANMTLTLFSPTEEASISSVSNARTYFKELGFELMED
KYFCLPIFLNALPFGADRQAMNDLFRFKTMATRHIIPLLPLFADWKGTGTPVINFVSRNGQIMSVSLYDS
GSNYNCCIAAQSGSGKSFLVNEIISSYLSEGGQCWVIDVGRSYEKLCEVYDGEFLQFGRDSGICLNPFEI
VEDYDEEADVLVGLLAAMAAPTQSLTDFQMANLKRQTRELWEKKGRAMLVDDVAEALKNHEDRRVQDVGE
QLYPFTTQGEYGRFFNGHNNIRFKNRFTVLELEELKGRKHLQQVVLLQLIYQIQQEMYLGERDRRKIVFI
DEAWDLLTQGDVGKFIETGYRRFRKYGGSAVTVTQSVNDLYDSPTGKAIAENSANMYLLGQKAETINALK
KEGRLPLGEGGYEYLKTVHTVTGVYSEIFFITEMGTGIGRLIVDPFHKLLYSSRAEDVNAIKQLTRKGLS
VADAISQLLKERGYE

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(2-157)

TraG P-loop domain (P-loop_TraG)

(482-710)

TraG P-loop domain (P-loop_TraG)

(352-437)

Family of unknown function (DUF5934) (DUF5934)

(169-336)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 41003..64824

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_34 36982..37836 + 855 APO17129 Mrr restriction system protein -
Locus_35 37930..38211 + 282 APO17130 hypothetical protein -
Locus_36 38211..38684 + 474 APO17131 hypothetical protein -
Locus_37 38804..40954 + 2151 APO17132 Conjugative transfer protein TraI, relaxase -
Locus_38 41003..42823 + 1821 APO17133 IncF plasmid conjugative transfer protein TraD virb4
Locus_39 42833..43393 + 561 APO17134 Conjugative transfer protein 234 -
Locus_40 43380..44015 + 636 APO17135 Conjugative transfer protein s043 tfc7
Locus_41 44042..44629 - 588 APO17136 hypothetical protein -
Locus_42 44918..45199 + 282 APO17137 IncF plasmid conjugative transfer pilus assembly protein TraL traL
Locus_43 45196..45822 + 627 APO17138 IncF plasmid conjugative transfer pilus assembly protein TraE traE
Locus_44 45806..46702 + 897 APO17139 IncF plasmid conjugative transfer pilus assembly protein TraK traK
Locus_45 46705..47994 + 1290 APO17140 IncF plasmid conjugative transfer pilus assembly protein TraB traB
Locus_46 48069..48641 + 573 APO17141 Conjugative transfer protein TraV traV
Locus_47 48638..49024 + 387 APO17142 Conjugative transfer protein TraA -
Locus_48 49203..50036 + 834 APO17143 Ynd -
Locus_49 50029..50967 + 939 APO17144 Ync -
Locus_50 51099..51791 + 693 APO17145 Thiol:disulfide involved in conjugative transfer trbB
Locus_51 52086..54233 + 2148 APO17146 IncF plasmid conjugative transfer pilus assembly protein TraC virb4
Locus_52 54226..54573 + 348 APO17147 Conjugative transfer protein 345 -
Locus_53 54557..55069 + 513 APO17148 Conjugative signal peptidase TrhF -
Locus_54 55080..56204 + 1125 APO17149 IncF plasmid conjugative transfer pilus assembly protein TraW traW
Locus_55 56236..57216 + 981 APO17150 IncF plasmid conjugative transfer pilus assembly protein TraU traU
Locus_56 57219..60911 + 3693 APO17151 IncF plasmid conjugative transfer protein TraN traN
Locus_57 61370..62788 + 1419 APO17152 hypothetical protein -
Locus_58 62785..64824 + 2040 APO17153 Bipolar DNA helicase HerA virb4
Locus_59 65070..65183 + 114 APO17154 hypothetical protein -
Locus_60 65233..65946 - 714 APO17155 Endonuclease I precursor -
Locus_61 65949..66401 - 453 APO17156 Il-IS_2, transposase -
Locus_62 66672..67274 - 603 APO17157 hypothetical protein -
Locus_63 67641..67967 + 327 APO17158 hypothetical protein -
Locus_64 67983..68402 + 420 APO17159 Single-stranded DNA-binding protein -
Locus_65 68482..69300 + 819 APO17160 Recombination protein BET -
Locus_66 69383..69526 + 144 APO17161 hypothetical protein -

Host bacterium

ID   116 Element type   ICE (Integrative and conjugative element)
Element name   ICEPmiCHN901 GenBank   KX243408
Element size   89493 bp Coordinate of oriT [Strand]   3509..3807 [+]
Host bacterium   Proteus mirabilis strain MD20140901 sequence Coordinate of element   1..89493

Cargo genes

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