Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200117
Name   oriT_ICEPmiCHN904 in_silico
Organism   Proteus mirabilis strain MD20140904 sequence
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   KX243411 (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_ICEPmiCHN904
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14269 GenBank   APO17393
Name   traI_-_ICEPmiCHN904 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

>APO17393.1 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   16524 GenBank   APO17394
Name   traD_-_ICEPmiCHN904 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

>APO17394.1 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   16525 GenBank   APO17407
Name   traC_-_ICEPmiCHN904 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

>APO17407.1 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: 39966..63744

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_37 35945..36799 + 855 APO17390 Mrr restriction system protein -
Locus_38 36893..37174 + 282 APO17391 hypothetical protein -
Locus_39 37174..37647 + 474 APO17392 hypothetical protein -
Locus_40 37767..39917 + 2151 APO17393 Conjugative transfer protein TraI, relaxase -
Locus_41 39966..41786 + 1821 APO17394 IncF plasmid conjugative transfer protein TraD virb4
Locus_42 41796..42356 + 561 APO17395 Conjugative transfer protein 234 -
Locus_43 42343..42978 + 636 APO17396 Conjugative transfer protein s043 tfc7
Locus_44 43005..43592 - 588 APO17397 hypothetical protein -
Locus_45 43881..44162 + 282 APO17398 IncF plasmid conjugative transfer pilus assembly protein TraL traL
Locus_46 44159..44785 + 627 APO17399 IncF plasmid conjugative transfer pilus assembly protein TraE traE
Locus_47 44769..45665 + 897 APO17400 IncF plasmid conjugative transfer pilus assembly protein TraK traK
Locus_48 45668..46957 + 1290 APO17401 IncF plasmid conjugative transfer pilus assembly protein TraB traB
Locus_49 47032..47604 + 573 APO17402 Conjugative transfer protein TraV traV
Locus_50 47601..47987 + 387 APO17403 Conjugative transfer protein TraA -
Locus_51 48166..48999 + 834 APO17404 Ynd -
Locus_52 48992..49930 + 939 APO17405 Ync -
Locus_53 50062..50754 + 693 APO17406 Thiol:disulfide involved in conjugative transfer trbB
Locus_54 50754..53153 + 2400 APO17407 IncF plasmid conjugative transfer pilus assembly protein TraC virb4
Locus_55 53146..53493 + 348 APO17408 Conjugative transfer protein 345 -
Locus_56 53477..53989 + 513 APO17409 Conjugative signal peptidase TrhF -
Locus_57 54000..55124 + 1125 APO17410 IncF plasmid conjugative transfer pilus assembly protein TraW traW
Locus_58 55156..56136 + 981 APO17411 IncF plasmid conjugative transfer pilus assembly protein TraU traU
Locus_59 56139..59831 + 3693 APO17412 IncF plasmid conjugative transfer protein TraN traN
Locus_60 60290..61708 + 1419 APO17413 hypothetical protein -
Locus_61 61705..63744 + 2040 APO17414 Bipolar DNA helicase HerA virb4
Locus_62 64153..64866 - 714 APO17415 Endonuclease I precursor -
Locus_63 64869..65321 - 453 APO17416 Il-IS_2, transposase -
Locus_64 66063..66575 - 513 APO17417 Lipoprotein signal peptidase -
Locus_65 66579..67334 - 756 APO17418 Cobalt-zinc-cadmium resistance protein CzcD -
Locus_66 67571..67978 + 408 APO17419 Cd(II)/Pb(II)-responsive transcriptional regulator -
Locus_67 68121..68243 + 123 APO17420 hypothetical protein -
Locus_68 68255..68476 - 222 APO17421 hypothetical protein -

Host bacterium

ID   119 Element type   ICE (Integrative and conjugative element)
Element name   ICEPmiCHN904 GenBank   KX243411
Element size   94942 bp Coordinate of oriT [Strand]   3509..3807 [+]
Host bacterium   Proteus mirabilis strain MD20140904 sequence Coordinate of element   1..94942

Cargo genes

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