Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200365
Name   oriT_ICEPciChn180 in_silico
Organism   Proteus terrae subsp. cibarius strain SDQ8C180-2T
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP073356 (120336..120634 [-], 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_ICEPciChn180
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14391 GenBank   UAX01280
Name   TraI_2_KDN45_14915_ICEPciChn180 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: 79644.48 Da        Isoelectric Point: 5.3431

>UAX01280.1 TraI domain-containing protein [Proteus terrae subsp. cibarius]
MFKNLFFQAKAIPELSSQLDADIPRYPPFLKGLPAASPKDLQSTQDELIAKLRQVLGFNQRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTTNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWIRKSNQSTHLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESLAPEVLIKDDKPIWLPMLHISEADLLFSSNVPSSVRLFSKSEWEATQQTQAESQSRSSEHSDL
PEASSSIEHGNSSESPSTNSSEQDDELSHASDVNHLQATENAPGDGCEKPNNSYDGAISNNVNQHDAEAL
NLTESLVWLPEASSALVMVGEQILIRYPDAVRPWCAPRKLLAELSRLDWLELDPANPTRKARTVTTNDGV
HEQGLLLKVSISKGLTALIDFSKQDAESVTAIQNEEASQRPSRTETANAQAKELATRAERKQKPIAPNAN
SSTDPKHAQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVANAHGIPAGQLLRGISASDEC
QFDEGETVLFTAHAKR

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(40-349)


  Protein structure



No available structure.




T4CP

ID   16895 GenBank   UAX01267
Name   traC_KDN45_14845_ICEPciChn180 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: 5.9735

>UAX01267.1 type IV secretion system protein TraC [Proteus terrae subsp. cibarius]
MKASLYSGQRASELLPVLAYSDDEQLFFMEDQSVGFGFLCDPLPGGDESVADRVNVLLNNDWPKDTLLQF
GLYASPDIQTDLQRMMGLRHRQSDPLLRASIRKRADFLDGGTVQPIEESTQTQVRNFQLIVTCKLPLESP
IPTERELSRASALRASFSQALATVGFRVTEMTDRNWLAALSAQLNWGKDASWRNPSPIRSEADKPLREQV
LDYDRAIKVDSQGLMLGDYRVKTLSFKRLPERIWFGHAASFAGDMMTGSRGLRGSFLLNVTIHFPSAEAM
RSRLETKRQWAVNQAYGPMLKFVPVLAAKKKGFDVLFEALQEGDRPIRANMTLTLFSPTEEASISSVSNA
RTYFKELGFELMEDKYFCLPIFLNALPFGADRQAMNDLFRFKTMATRHVIPLLPLFADWKGTGTPVINFV
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)

TraC protein (TraC_F_IV)

(11-241)

Family of unknown function (DUF5934) (DUF5934)

(253-420)

  Protein structure



No available structure.



ID   16896 GenBank   UAX01279
Name   traD_KDN45_14910_ICEPciChn180 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: 67059.86 Da        Isoelectric Point: 6.5728

>UAX01279.1 conjugative transfer system coupling protein TraD [Proteus terrae subsp. cibarius]
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLHKLQKG
LKGKPLAFMELSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPSFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FAARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
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)

(152-286)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 3238187..3258052

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KDN45_14810 3233762..3235666 - 1905 UAX01260 ATP-dependent helicase -
KDN45_14815 3235675..3237627 - 1953 UAX01261 AAA family ATPase -
KDN45_14820 3238187..3241879 - 3693 UAX01262 conjugal transfer protein TraN traN
KDN45_14825 3241882..3242910 - 1029 UAX01263 TraU family protein traU
KDN45_14830 3242894..3244018 - 1125 UAX01264 pilus assembly protein traW
KDN45_14835 3244029..3244541 - 513 UAX01265 S26 family signal peptidase -
KDN45_14840 3244525..3244872 - 348 UAX01266 plasmid-related protein -
KDN45_14845 3244865..3247264 - 2400 UAX01267 type IV secretion system protein TraC virb4
KDN45_14850 3247264..3247956 - 693 UAX01268 DsbC family protein trbB
KDN45_14855 3248088..3249026 - 939 UAX01269 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
KDN45_14860 3249019..3249810 - 792 UAX01270 type IV toxin-antitoxin system AbiEi family antitoxin -
KDN45_14865 3250031..3250417 - 387 UAX01271 hypothetical protein -
KDN45_14870 3250414..3250986 - 573 UAX01272 type IV conjugative transfer system lipoprotein TraV traV
KDN45_14875 3251061..3252350 - 1290 UAX01273 TraB/VirB10 family protein traB
KDN45_14880 3252353..3253249 - 897 UAX03602 type-F conjugative transfer system secretin TraK traK
KDN45_14885 3253233..3253859 - 627 UAX01274 pilus assembly protein traE
KDN45_14890 3253856..3254137 - 282 UAX01275 type IV conjugative transfer system protein TraL traL
KDN45_14895 3254426..3255013 + 588 UAX01276 plasmid-related protein -
KDN45_14900 3255040..3255675 - 636 UAX01277 DUF4400 domain-containing protein tfc7
KDN45_14905 3255662..3256222 - 561 UAX01278 conjugative transfer protein -
KDN45_14910 3256232..3258052 - 1821 UAX01279 conjugative transfer system coupling protein TraD virb4
KDN45_14915 3258100..3260250 - 2151 UAX01280 TraI domain-containing protein -
KDN45_14920 3260368..3261081 - 714 UAX01281 hypothetical protein -
KDN45_14925 3261082..3262272 - 1191 UAX01282 nucleotidyltransferase -

Host bacterium

ID   322 Element type   ICE (Integrative and conjugative element)
Element name   ICEPciChn180 GenBank   CP073356
Element size   3959345 bp Coordinate of oriT [Strand]   120336..120634 [-]
Host bacterium   Proteus terrae subsp. cibarius strain SDQ8C180-2T Coordinate of element   3209019..3335275

Cargo genes

Drug resistance gene   sul2, tet(X6), aph(4)-Ia, aac(3)-IVa, aph(3')-Ia, aph(3'')-Ib, aph(6)-Id
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIA