Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200345
Name   oriT_ICEAmaMED64 in_silico
Organism   Alteromonas mediterranea MED64
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP004848 (2895..3193 [+], 299 nt)
oriT length   299 nt
IRs (inverted repeats)      45..50, 52..57  (CAAACG..CGTTTG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 299 nt

>oriT_ICEAmaMED64
GCTCTGTTTGGCGGCGGATGACCTAGTCAAAAAAATCGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTCGCCAAACGGTTTGTATCTTCATGACGATACGTCGTTTTAGGCGTTTTTAAGTGAAATCGGGCTGTATCCCTTGTCAGGTATGGGATTGCGCGAGTTGATTTATATCGAGACGCCAAACAGTGATTGTTACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTTGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14369 GenBank   AGP81089
Name   TraI_2_I533_05525_ICEAmaMED64 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: 79789.91 Da        Isoelectric Point: 5.2251

>AGP81089.1 conjugal transfer pilus assembly protein TraI [Alteromonas mediterranea MED64]
MFKNLFFQTKALPELSSQLDTEIPRYPPFLKGLPAASPEDLQSTQDELITKLRQVLGFNLRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTTNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNTIGVPVERYLLDAMRRL
LASSQWLVNQRDARVWIRKSNQSTNLYLVWKSAAKEIIELLAKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESLAPEVLIKDGKPIWLPMLHISEADLLFSSNVPSGVRLFSKSEWEATQQTQAEPQSRSSEQPGL
SEASSSIELNNSAESPSTKSSEQDDERRLASDVNHLQATENAPGDECEKPNNSYDGAISNNVNQHDAEAL
NLPESLAWLPEASSALVMVDEQILVRYPDAVRHWCAPRKLLAELSRLDWLEIDPANPTRKARTVTTKGGV
QEQGLLLKVSISKGLTALIDLPKQDAESAAAIQNEEASPRPSRTETTNARAKEPSKRAECKQKPIAPNAN
SSIDPKHAQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVANEHGIPAGQLLRGISASDQC
QFDEGETVLFTAHAER

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(39-349)


  Protein structure



No available structure.




T4CP

ID   16861 GenBank   AGP81090
Name   t4cp2_I533_05530_ICEAmaMED64 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: 67134.99 Da        Isoelectric Point: 6.4440

>AGP81090.1 conjugal transfer pilus assembly protein TraD [Alteromonas mediterranea MED64]
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQMG
LKGKPLAFMELSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPERSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
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   16862 GenBank   AGP81105
Name   t4cp2_I533_05615_ICEAmaMED64 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: 90098.71 Da        Isoelectric Point: 6.2880

>AGP81105.1 IncF plasmid conjugative transfer pilus assembly protein TraC [Alteromonas mediterranea MED64]
MKASLYSGQRASELLPVLAYSDDEQLFFMEDQSVGFGFLCDPLPGGDESVADRVNVLLNNDWPKDTLLQF
GLYASPDIQTDLQRMMGLRHRQSDPLLRASIRKRADFLDGGTVQPIEESTQTQVRNFQLIVTCKLPLESP
IPTERELSRASALRASFSQALATVGFRVTEMTDRNWLAAISAQLNWGKDASWRNPSPIRSEADKPLREQV
LDYDRAIKVDSQGLMLGDYRVKTLSFKRLPERIWFGHAASFAGDMMTGSRGLRGSFLLNVTIHFPSAEAM
RSRLETKRQWAVNQAYGPMLKFVPVLAAKKKGFDVLFEALQEGDRPIRANMTLTLFSPTGEASISSVSNA
RTYFKELGFELMEDKYFCLPIFLNALPFGADRQAMNDLFRFKTMATRHVIPLLPLFADWKGTGTPVINFV
SRNGQIMSVSLYDSGSNYNCCIAAQSGSGKSFLVNEIISSYLSEGGQCWVIDVGRSYEKLCEVYDGEFLQ
FGRNSGICLNPFEIVEDYDEEADVLVGLLAAMAAPTQSLTDFQMANLKRQTRELWEKKGRAMLVDDVAEA
LKNHEDRRVQDVGEQLYPFTTQGEYGRFFNGHNNIRFKNRFTVLELEELKGRKHLQQVVLLQLIYQIQQE
MYLGERDRRKIVFIDEAWDLLTQGDVGKFIETGYRRFRKYGGSAVTVTQSVNDLYDSPTGKAIAENSANM
YLLGQKAETINALKKEGRLPLGEGGYEYLKTVHTVTGVYSEIFFITEMGTGIGRLIVDPFHKLLYSSRAE
DVNAIKQLTRKGLSVADAISQLLKERGYE

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(253-420)

TraC protein (TraC_F_IV)

(11-241)

TraG P-loop domain (P-loop_TraG)

(566-794)

TraG P-loop domain (P-loop_TraG)

(436-521)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1222450..1246587

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
I533_05510 1218429..1219283 + 855 AGP81086 hypothetical protein -
I533_05515 1219377..1219658 + 282 AGP81087 hypothetical protein -
I533_05520 1219658..1220131 + 474 AGP81088 hypothetical protein -
I533_05525 1220251..1222401 + 2151 AGP81089 conjugal transfer pilus assembly protein TraI -
I533_05530 1222450..1224270 + 1821 AGP81090 conjugal transfer pilus assembly protein TraD virb4
I533_05535 1224280..1224840 + 561 AGP81091 Conjugative transfer protein 234 -
I533_05540 1224827..1225462 + 636 AGP81092 hypothetical protein tfc7
I533_05545 1225734..1227290 + 1557 AGP81093 integrase catalytic subunit -
I533_05550 1227658..1228929 + 1272 AGP81094 hypothetical protein -
I533_05555 1229005..1229700 + 696 AGP81095 IstB ATP binding domain-containing protein virB11
I533_05560 1229779..1230351 - 573 AGP81096 hypothetical protein -
I533_05565 1230640..1230921 + 282 AGP81097 IncF plasmid conjugative transfer pilus assembly protein TraL traL
I533_05570 1230918..1231544 + 627 AGP81098 IncF plasmid conjugative transfer pilus assembly protein TraE traE
I533_05575 1231528..1232424 + 897 AGP81099 IncF plasmid conjugative transfer pilus assembly protein TraK traK
I533_05580 1232427..1233716 + 1290 AGP81100 IncF plasmid conjugative transfer pilus assembly protein TraB traB
I533_05585 1233791..1234363 + 573 AGP81101 conjugative transfer protein TraV traV
I533_05590 1234360..1234746 + 387 AGP81102 Conjugative transfer protein TraA -
I533_05595 1234966..1235757 + 792 AGP81103 Ynd -
I533_05610 1236818..1237510 + 693 AGP81104 thiol:disulfide interchange protein DsbC trbB
I533_05615 1237510..1239909 + 2400 AGP81105 IncF plasmid conjugative transfer pilus assembly protein TraC virb4
I533_05620 1239902..1240249 + 348 AGP81106 hypothetical protein -
I533_05625 1240233..1240745 + 513 AGP81107 signal peptidase I -
I533_05630 1240756..1241880 + 1125 AGP81108 hypothetical protein traW
I533_05635 1241864..1242892 + 1029 AGP81109 IncF plasmid conjugative transfer pilus assembly protein TraU traU
I533_05640 1242895..1246587 + 3693 AGP81110 mating pair stabilization TraN traN
I533_05645 1246819..1247151 + 333 AGP81111 hypothetical protein -
I533_05650 1247182..1247844 + 663 AGP81112 hypothetical protein -
I533_05655 1247935..1248537 - 603 AGP81113 hypothetical protein -
I533_05660 1248905..1249231 + 327 AGP81114 hypothetical protein -
I533_05665 1249247..1249666 + 420 AGP81115 single-stranded DNA-binding protein -
I533_05670 1249746..1250564 + 819 AGP81116 phage recombination protein -
I533_05675 1250647..1250790 + 144 AGP81117 hypothetical protein -

Host bacterium

ID   303 Element type   ICE (Integrative and conjugative element)
Element name   ICEAmaMED64 GenBank   CP004848
Element size   4397537 bp Coordinate of oriT [Strand]   2895..3193 [+]
Host bacterium   Alteromonas mediterranea MED64 Coordinate of element   1194615..1274449

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -