Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200116
Name   oriT_ICEPmiCHN903 in_silico
Organism   Proteus mirabilis strain MD20140903 sequence
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   KX243410 (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_ICEPmiCHN903
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14268 GenBank   APO17303
Name   traI_-_ICEPmiCHN903 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

>APO17303.1 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   16522 GenBank   APO17304
Name   traD_-_ICEPmiCHN903 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

>APO17304.1 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   16523 GenBank   APO17317
Name   traC_-_ICEPmiCHN903 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

>APO17317.1 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: 40972..64750

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_32 36951..37805 + 855 APO17300 Mrr restriction system protein -
Locus_33 37899..38180 + 282 APO17301 hypothetical protein -
Locus_34 38180..38653 + 474 APO17302 hypothetical protein -
Locus_35 38773..40923 + 2151 APO17303 Conjugative transfer protein TraI, relaxase -
Locus_36 40972..42792 + 1821 APO17304 IncF plasmid conjugative transfer protein TraD virb4
Locus_37 42802..43362 + 561 APO17305 Conjugative transfer protein 234 -
Locus_38 43349..43984 + 636 APO17306 Conjugative transfer protein s043 tfc7
Locus_39 44011..44598 - 588 APO17307 hypothetical protein -
Locus_40 44887..45168 + 282 APO17308 IncF plasmid conjugative transfer pilus assembly protein TraL traL
Locus_41 45165..45791 + 627 APO17309 IncF plasmid conjugative transfer pilus assembly protein TraE traE
Locus_42 45775..46671 + 897 APO17310 IncF plasmid conjugative transfer pilus assembly protein TraK traK
Locus_43 46674..47963 + 1290 APO17311 IncF plasmid conjugative transfer pilus assembly protein TraB traB
Locus_44 47960..48610 + 651 APO17312 Conjugative transfer protein TraV traV
Locus_45 48607..48993 + 387 APO17313 Conjugative transfer protein TraA -
Locus_46 49172..50005 + 834 APO17314 Ynd -
Locus_47 49998..50936 + 939 APO17315 Ync -
Locus_48 51068..51760 + 693 APO17316 Thiol:disulfide involved in conjugative transfer trbB
Locus_49 51760..54159 + 2400 APO17317 IncF plasmid conjugative transfer pilus assembly protein TraC virb4
Locus_50 54152..54499 + 348 APO17318 Conjugative transfer protein 345 -
Locus_51 54483..54995 + 513 APO17319 Conjugative signal peptidase TrhF -
Locus_52 55006..56130 + 1125 APO17320 IncF plasmid conjugative transfer pilus assembly protein TraW traW
Locus_53 56162..57142 + 981 APO17321 IncF plasmid conjugative transfer pilus assembly protein TraU traU
Locus_54 57145..60837 + 3693 APO17322 IncF plasmid conjugative transfer protein TraN traN
Locus_55 61296..62714 + 1419 APO17323 hypothetical protein -
Locus_56 62711..64750 + 2040 APO17324 Bipolar DNA helicase HerA virb4
Locus_57 64996..65109 + 114 APO17325 hypothetical protein -
Locus_58 65159..65872 - 714 APO17326 Endonuclease I precursor -
Locus_59 65875..66327 - 453 APO17327 Il-IS_2, transposase -
Locus_60 66598..67200 - 603 APO17328 hypothetical protein -
Locus_61 67567..67893 + 327 APO17329 hypothetical protein -
Locus_62 67909..68328 + 420 APO17330 Single-stranded DNA-binding protein -
Locus_63 68408..69226 + 819 APO17331 Recombination protein BET -
Locus_64 69309..69452 + 144 APO17332 hypothetical protein -

Host bacterium

ID   118 Element type   ICE (Integrative and conjugative element)
Element name   ICEPmiCHN903 GenBank   KX243410
Element size   89644 bp Coordinate of oriT [Strand]   3509..3807 [+]
Host bacterium   Proteus mirabilis strain MD20140903 sequence Coordinate of element   1..89644

Cargo genes

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