Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200397
Name   oriT_ICESupCHN110003 in_silico
Organism   Shewanella algae strain 110003 sequence
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   MG014393 (5646..5944 [+], 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_ICESupCHN110003
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14424 GenBank   AVR65399
Name   traI_ICESupCHN110003_033_ICESupCHN110003 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: 79801.99 Da        Isoelectric Point: 5.3707

>AVR65399.1 conjugative transfer protein TraI, relaxase [Shewanella algae]
MFKNLFFQAKALPELSSQLDAEIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQVLSFNQRDFQRLIQPC
IDHLASYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTTNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWIRKSNQSTNLYLVWKSAAKEIIELLTKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESFAPEVLIKDGKPIWLPMLHISEADLLFSSNVPSGVTLFNKSEWEATQQTQAEPQSRSSEHPDL
PEASSSIELSNSTKSPSTKPSEKDDELRHASDVSTPQATENAPGDECEKPNNSYDGAISNNVNQQDAEAL
NLPESLAWFPEASSALIMVGEQLLIRYPDAVRPWCAPRKLLAELSRLDWLELDPANPTRKARTVTTNDGV
QEQGLLLKVSISKGLTALIDLSKQDAESVTAIQNKEASQRPSRINITNAQAKEPATRAERKQKPIAANAN
SSTDPKHAQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVAKEHGIPAGQLLRGISASDEC
QFDEGETVLFTAHAKR

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(39-349)


  Protein structure



No available structure.




T4CP

ID   16945 GenBank   AVR65400
Name   traD_ICESupCHN110003_034_ICESupCHN110003 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: 67163.00 Da        Isoelectric Point: 6.6444

>AVR65400.1 IncF plasmid conjugative transfer protein TraD [Shewanella algae]
MKENAYEMPWRTNYEAMATAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQKG
LKGKPLAFMALSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDTMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDMDDSRLITDSGRIINNAQVAYIGLDSLTD
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   16946 GenBank   AVR65412
Name   traC_ICESupCHN110003_046_ICESupCHN110003 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

>AVR65412.1 IncF plasmid conjugative transfer pilus assembly protein TraC [Shewanella algae]
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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 39417..58187

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ICESupCHN110003_032 36269..37123 + 855 AVR65398 mrr restriction system protein -
ICESupCHN110003_033 37218..39368 + 2151 AVR65399 conjugative transfer protein TraI, relaxase -
ICESupCHN110003_034 39417..41237 + 1821 AVR65400 IncF plasmid conjugative transfer protein TraD virb4
ICESupCHN110003_035 41247..41807 + 561 AVR65401 conjugative transfer protein 234 -
ICESupCHN110003_036 41794..42429 + 636 AVR65402 conjugative transfer protein s043 tfc7
ICESupCHN110003_037 42456..43043 - 588 AVR65403 hypothetical protein -
ICESupCHN110003_038 43332..43613 + 282 AVR65404 IncF plasmid conjugative transfer pilus assembly protein TraL traL
ICESupCHN110003_039 43610..44236 + 627 AVR65405 IncF plasmid conjugative transfer pilus assembly protein TraE traE
ICESupCHN110003_040 44220..45116 + 897 AVR65406 IncF plasmid conjugative transfer pilus assembly protein TraK traK
ICESupCHN110003_041 45119..46408 + 1290 AVR65407 IncF plasmid conjugative transfer pilus assembly protein TraB traB
ICESupCHN110003_042 46405..47055 + 651 AVR65408 conjugative transfer protein TraV traV
ICESupCHN110003_043 47052..47426 + 375 AVR65409 conjugative transfer protein TraA -
ICESupCHN110003_044 47502..48230 + 729 AVR65410 hypothetical protein -
ICESupCHN110003_045 48418..49110 + 693 AVR65411 thiol:disulfide involved in conjugative transfer trbB
ICESupCHN110003_046 49110..51509 + 2400 AVR65412 IncF plasmid conjugative transfer pilus assembly protein TraC virb4
ICESupCHN110003_047 51502..51849 + 348 AVR65413 conjugative transfer protein 345 -
ICESupCHN110003_048 51833..52345 + 513 AVR65414 conjugative signal peptidase TrhF -
ICESupCHN110003_049 52356..53480 + 1125 AVR65415 IncF plasmid conjugative transfer pilus assembly protein TraW traW
ICESupCHN110003_050 53512..54492 + 981 AVR65416 IncF plasmid conjugative transfer pilus assembly protein TraU traU
ICESupCHN110003_051 54495..58187 + 3693 AVR65417 IncF plasmid conjugative transfer protein TraN traN
ICESupCHN110003_052 58610..60310 + 1701 AVR65418 putative ATP-dependent endonuclease of the OLD family -
ICESupCHN110003_053 60312..61946 + 1635 AVR65419 ATP-dependent DNA helicase UvrD/PcrA -
ICESupCHN110003_054 62141..62824 - 684 AVR65420 endonuclease I precursor -

Host bacterium

ID   353 Element type   ICE (Integrative and conjugative element)
Element name   ICESupCHN110003 GenBank   MG014393
Element size   91669 bp Coordinate of oriT [Strand]   5646..5944 [+]
Host bacterium   Shewanella algae strain 110003 sequence Coordinate of element   1..91669

Cargo genes

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