Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200382
Name   oriT_ICEPmiFra1 in_silico
Organism   Proteus mirabilis sequence
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   MF490434 (4390..4688 [+], 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_ICEPmiFra1
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14408 GenBank   AVR61311
Name   traI_-_ICEPmiFra1 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

>AVR61311.1 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   16925 GenBank   AVR61312
Name   traD_-_ICEPmiFra1 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

>AVR61312.1 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   16926 GenBank   AVR61326
Name   traC_-_ICEPmiFra1 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

>AVR61326.1 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 39218..64039

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_27 35681..36862 + 1182 AVR61310 membrane protein -
Locus_28 37019..39169 + 2151 AVR61311 conjugative transfer protein TraI, phosphohydrolase -
Locus_29 39218..41038 + 1821 AVR61312 IncF plasmid conjugative transfer protein TraD virb4
Locus_30 41048..41608 + 561 AVR61313 conjugative transfer protein -
Locus_31 41595..42230 + 636 AVR61314 conjugal transfer protein tfc7
Locus_32 42302..42940 + 639 AVR61315 hypothetical protein -
Locus_33 42933..44039 + 1107 AVR61316 zinc peptidase -
Locus_34 44176..44457 + 282 AVR61317 conjugal transfer protein TraL traL
Locus_35 44454..45080 + 627 AVR61318 conjugal transfer pilus assembly protein TraE traE
Locus_36 45061..45960 + 900 AVR61319 conjugal transfer pilus assembly protein TraK traK
Locus_37 45963..47252 + 1290 AVR61320 conjugal transfer pilus assembly protein TraB traB
Locus_38 47327..47899 + 573 AVR61321 conjugal transfer pilus assembly protein TraV traV
Locus_39 47896..48282 + 387 AVR61322 conjugative transfer protein TraA -
Locus_40 48461..49294 + 834 AVR61323 transcriptional regulator with AbiEi antitoxin N-terminal domain -
Locus_41 49287..50225 + 939 AVR61324 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
Locus_42 50357..51049 + 693 AVR61325 disulfide isomerase trbB
Locus_43 51049..53448 + 2400 AVR61326 type-IV secretion system protein TraC virb4
Locus_44 53441..53788 + 348 AVR61327 hypothetical protein -
Locus_45 53772..54284 + 513 AVR61328 conjugative signal peptidase TrhF -
Locus_46 54292..55419 + 1128 AVR61329 IncF plasmid conjugative transfer pilus assembly protein TraW traW
Locus_47 55403..56431 + 1029 AVR61330 conjugal transfer protein TraU traU
Locus_48 56434..60126 + 3693 AVR61331 conjugal transfer protein TraN traN
Locus_49 60585..62003 + 1419 AVR61332 hypothetical protein -
Locus_50 62000..64039 + 2040 AVR61333 ATPase virb4
Locus_51 65164..65730 - 567 AVR61334 ISL3 family transposase -
Locus_52 66473..66985 - 513 AVR61335 lipoprotein signal peptidase -
Locus_53 66989..67885 - 897 AVR61336 cation transporter -
Locus_54 67981..68388 + 408 AVR61337 MerR family transcriptional regulator -
Locus_55 68625..68846 - 222 AVR61338 hypothetical protein -

Host bacterium

ID   339 Element type   ICE (Integrative and conjugative element)
Element name   ICEPmiFra1 GenBank   MF490434
Element size   107395 bp Coordinate of oriT [Strand]   4390..4688 [+]
Host bacterium   Proteus mirabilis sequence Coordinate of element   1..107395

Cargo genes

Drug resistance gene   floR, aph(6)-Id, aph(3'')-Ib, sul2, tet(C), aph(3')-Ia, dfrA32, ere(A), aadA2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -