Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200406
Name   oriT_ICEVpaChn0574 in_silico
Organism   Vibrio parahaemolyticus strain Vb0574 ICEVb0574 mobile element
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   MN199028 (3361..3658 [+], 298 nt)
oriT length   298 nt
IRs (inverted repeats)      44..49, 51..56  (CAAACG..CGTTTG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 298 nt

>oriT_ICEVpaChn0574
GCTCTGTTTGGCGGCGGATGACCTAGTCAAAAAATCGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTCGCCAAACGGTTTGTATCTTCATGACGATACGTCGTTTTAGGCGTTTTTAAGTGAAATCGGGCTGTATCCCTTGTCAGGTATGGGATTGCGCGAGTTGATTTATATCGAGACGCCAAACAGCGATTGTTACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTTGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14434 GenBank   QIB99820
Name   TraI_2_-_ICEVpaChn0574 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: 79734.70 Da        Isoelectric Point: 5.1503

>QIB99820.1 hypothetical protein [Vibrio parahaemolyticus]
MFKNLFFQAKALPELSSQLDAEIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQVLGFNQRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDENGLYQWNPFLETLSQWTTNSSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWVRKSNQSTHLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESLAPEVLIKDDKPIWLPMLHISEADLLFRSNVPSSVRLFSKSEWEATQQTQAEPQSRSSEHSDL
PEASSSIEHGNSAESSSTNSSEQDDELRLASDVNNPQANENALGDGCEKPNNSYDGAISNNVNQHDAEAL
NLPESLAWLPEASSALVMVDEQILIRYPDAVRHWCAPRKLLAELSRLDWLELDPANPTRKARTVTTNDGV
QEQGLLLKVSISKGLSALIDLPKQDAESAAAIQNEEASQRPSRTKITNAQAKEPATRAERNQKPIALNAN
SITDPKHAQRQKMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVANEHGIPAGQLLRGISASDQC
QFDEGETVLFTAHAER

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(39-349)


  Protein structure



No available structure.




T4CP

ID   16966 GenBank   QIB99821
Name   t4cp2_-_ICEVpaChn0574 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: 67068.91 Da        Isoelectric Point: 6.6444

>QIB99821.1 hypothetical protein [Vibrio parahaemolyticus]
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQKG
LKGKPLAFMALTHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKNAMAMLIFYYERIQPIAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FAARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
LMEEEGDMFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAA

  Protein domains


Predicted by InterproScan.

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

(152-285)

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

(451-578)

  Protein structure



No available structure.



ID   16966 GenBank   QIB99821
Name   t4cp2_-_ICEVpaChn0574 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: 67068.91 Da        Isoelectric Point: 6.6444

>QIB99821.1 hypothetical protein [Vibrio parahaemolyticus]
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQKG
LKGKPLAFMALTHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKNAMAMLIFYYERIQPIAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FAARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
LMEEEGDMFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAA

  Protein domains


Predicted by InterproScan.

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

(152-285)

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

(451-578)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 23708..50785

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_14 20172..21353 + 1182 QIB99819 Endonuclease NucS -
Locus_15 21510..23660 + 2151 QIB99820 hypothetical protein -
Locus_16 23708..25528 + 1821 QIB99821 hypothetical protein virb4
Locus_17 25538..26098 + 561 QIB99822 hypothetical protein -
Locus_18 26085..26720 + 636 QIB99823 hypothetical protein tfc7
Locus_19 27141..28403 + 1263 QIB99824 hypothetical protein -
Locus_20 28653..29528 + 876 QIB99825 Beta-lactamase CTX-M-14 -
Locus_21 29869..30399 - 531 QIB99826 hypothetical protein -
Locus_22 30688..30969 + 282 QIB99827 hypothetical protein traL
Locus_23 30966..31592 + 627 QIB99828 hypothetical protein traE
Locus_24 31573..32472 + 900 QIB99829 hypothetical protein traK
Locus_25 32475..33764 + 1290 QIB99830 hypothetical protein traB
Locus_26 33839..34411 + 573 QIB99831 hypothetical protein traV
Locus_27 34408..34794 + 387 QIB99832 hypothetical protein -
Locus_28 34973..35806 + 834 QIB99833 hypothetical protein -
Locus_29 35799..36527 + 729 QIB99834 hypothetical protein -
Locus_30 36648..37259 + 612 QIB99835 hypothetical protein -
Locus_31 37565..37783 + 219 QIB99836 hypothetical protein -
Locus_32 37921..39138 - 1218 QIB99837 Tetracycline resistance protein -
Locus_33 39219..39851 + 633 QIB99838 Tetracycline repressor protein -
Locus_34 40336..40884 + 549 QIB99839 hypothetical protein -
Locus_35 41016..41708 + 693 QIB99840 Thiol:disulfide interchange protein trbB
Locus_36 41708..44107 + 2400 QIB99841 hypothetical protein virb4
Locus_37 44100..44447 + 348 QIB99842 hypothetical protein -
Locus_38 44431..44943 + 513 QIB99843 hypothetical protein -
Locus_39 44954..46078 + 1125 QIB99844 hypothetical protein traW
Locus_40 46062..47090 + 1029 QIB99845 hypothetical protein traU
Locus_41 47093..50785 + 3693 QIB99846 hypothetical protein traN
Locus_42 51016..51348 + 333 QIB99847 hypothetical protein -
Locus_43 51379..52041 + 663 QIB99848 hypothetical protein -
Locus_44 52132..52734 - 603 QIB99849 hypothetical protein -
Locus_45 53104..53430 + 327 QIB99850 hypothetical protein -
Locus_46 53446..53865 + 420 QIB99851 Single-stranded DNA-binding protein -
Locus_47 53945..54763 + 819 QIB99852 hypothetical protein -
Locus_48 54845..54988 + 144 QIB99853 hypothetical protein -

Host bacterium

ID   361 Element type   ICE (Integrative and conjugative element)
Element name   ICEVpaChn0574 GenBank   MN199028
Element size   76762 bp Coordinate of oriT [Strand]   3361..3658 [+]
Host bacterium   Vibrio parahaemolyticus strain Vb0574 ICEVb0574 mobile element Coordinate of element   1..76762

Cargo genes

Drug resistance gene   blaCTX-M-14, tet(E)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -