Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200367
Name   oriT_ICEPflCDM8 in_silico
Organism   Pseudoalteromonas sp. M8
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP047240 (3518..3816 [+], 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_ICEPflCDM8
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14393 GenBank   QUI69953
Name   TraI_2_GSF13_09210_ICEPflCDM8 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: 79584.47 Da        Isoelectric Point: 5.2770

>QUI69953.1 phosphohydrolase [Pseudoalteromonas sp. M8]
MFKNLFFQTKALPELSSQLDAEIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQVLGFNQREFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTTNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LAGSQWLVNQRDARVWLRKSNQSTHLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESLAPEVLLKDGKPIWLPMLHISEADLLFSSNVPSGVTLFNKSDWEATQKTQEEPQSRSSEHSDL
PEGSSSIEHGNSSESPSTNSSEQDDELRHASDVNNPQANENAPGDGCEKPNNSYDGAISNNVNQHDAEAL
NLPESLAWLPEASSALVMVGEQILIRYPDAVRPWCAPRKLLAELSQLDWLELDPANPTRKARTITTNDGV
QEQGLLLKVSISKGLTALIDLPKQDAESAAAIQNEEASQRPSRTKITNAQAKEPATRAERNQKPIAPNAQ
SSTDPKHAQRQKMVNFVKDLPILLTDGNYPDVDHSADGIRVTIQTLRQVANEHGIPAGQLLRGISASDQC
QFDEGETVLFTAHAKR

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(39-349)


  Protein structure



No available structure.




T4CP

ID   16899 GenBank   QUI69954
Name   traD_GSF13_09215_ICEPflCDM8 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: 67028.85 Da        Isoelectric Point: 6.6970

>QUI69954.1 conjugative transfer system coupling protein TraD [Pseudoalteromonas sp. M8]
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPAPFWWMTGISSGMALYRLPEAYRLHKLQKG
LKGKPLAFMELSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
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)

(152-285)

  Protein structure



No available structure.



ID   16900 GenBank   QUI69966
Name   traC_GSF13_09285_ICEPflCDM8 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: 90157.73 Da        Isoelectric Point: 5.9727

>QUI69966.1 type IV secretion system protein TraC [Pseudoalteromonas sp. M8]
MKASLYSGQRASELLPVLAYSDDEQLFFMEDQSVGFGFLCDPLPGGDESVADRVNVLLNNDWPKDTLLQF
GLYASPDIQTDLQRMMGLRHRQSDPLLRASIRKRADFLDGGTVQPIEESTQTQVRNFQLIVTCKLPLESP
IPTERELSRASALRASFSQALATVGFRVTEMTDRNWLAAISAQLNWGKDASWRNPSPIRSEADKPLREQV
LDYDRAIKVDSQGLMLGDYRVKTLSFKRLPERIWFGHAASFAGDMMTGSRGLRGSFLLNVTIHFPSAEAM
RSRLETKRQWAVNQAYGPMLKFVPVLAAKKKGFDVLFEALQEGDRPIRANMTLTLFSPTEEASISSVSNA
RTYFKELGFELMEDKYFCLPIFLNALPFGADRQAMNDLFRFKTMATRHVIPLLPLFADWKGTGTPVINFV
SRNGQIMSVSLYDSGSNYNCCIAAQSGSGKSFLVNEIISSYLSEGGQCWVIDVGRSYEKLCEVYDGEFLQ
FGRDSGICLNPFEIVEDYDEEADVLVGLLAAMAAPTQSLTDFQMANLKRQTRELWEKKGRAMLVDDVAEA
LKNHDDRRVQDVGEQLYPFTTQGEYGRFFNGHNNIRFKNRFTVLELEELKGRKHLQQVVLLQLIYQIQQE
MYLGERDRRKIVFIDEAWDLLTQGDVGKFIETGYRRFRKYGGSAVTVTQSVNDLYDSPTGKAIAENSANM
YLLGQKAETINALKKEGRLPLGEGGYEYLKTVHTVTGVYSEIFFITEMGTGIGRLIVDPFHKLLYSSRAE
DVNAIKQLTRKGLSVADAISQLLKERGYE

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(11-241)

Family of unknown function (DUF5934) (DUF5934)

(253-420)

TraG P-loop domain (P-loop_TraG)

(436-521)

TraG P-loop domain (P-loop_TraG)

(568-794)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 995180..1018956

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GSF13_09200 991369..991932 + 564 QUI69951 hypothetical protein -
GSF13_09205 991932..992843 + 912 QUI69952 DUF4868 domain-containing protein -
GSF13_09210 992982..995132 + 2151 QUI69953 phosphohydrolase -
GSF13_09215 995180..997000 + 1821 QUI69954 conjugative transfer system coupling protein TraD virb4
GSF13_09220 997010..997570 + 561 QUI69955 conjugative transfer protein -
GSF13_09225 997557..998192 + 636 QUI69956 DUF4400 domain-containing protein tfc7
GSF13_09230 998219..998806 - 588 QUI69957 plasmid-related protein -
GSF13_09235 998820..999058 - 239 Protein_776 hypothetical protein -
GSF13_09240 999094..999375 + 282 QUI69958 type IV conjugative transfer system protein TraL traL
GSF13_09245 999372..999998 + 627 QUI69959 pilus assembly protein traE
GSF13_09250 999982..1000878 + 897 QUI72726 hypothetical protein traK
GSF13_09255 1000881..1002170 + 1290 QUI69960 conjugal transfer protein TraB traB
GSF13_09260 1002245..1002817 + 573 QUI69961 type IV conjugative transfer system lipoprotein TraV traV
GSF13_09265 1002814..1003200 + 387 QUI69962 hypothetical protein -
GSF13_09270 1003420..1004211 + 792 QUI69963 hypothetical protein -
GSF13_09275 1004204..1005142 + 939 QUI69964 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
GSF13_09280 1005274..1005966 + 693 QUI69965 thioredoxin fold domain-containing protein trbB
GSF13_09285 1005966..1008365 + 2400 QUI69966 type IV secretion system protein TraC virb4
GSF13_09290 1008358..1008705 + 348 QUI69967 plasmid-related protein -
GSF13_09295 1008782..1009201 + 420 QUI72727 S26 family signal peptidase -
GSF13_09300 1009212..1010336 + 1125 QUI72728 pilus assembly protein traW
GSF13_09305 1010320..1011348 + 1029 QUI69968 conjugal transfer protein TraU traU
GSF13_09310 1011351..1015043 + 3693 QUI69969 conjugal transfer protein TraN traN
GSF13_09315 1015502..1016920 + 1419 QUI69970 hypothetical protein -
GSF13_09320 1016917..1018956 + 2040 QUI69971 DUF87 domain-containing protein virb4
GSF13_09325 1019365..1020039 - 675 QUI72729 deoxyribonuclease I -
GSF13_09330 1020081..1021368 - 1288 Protein_795 ISL3 family transposase -
GSF13_09335 1021390..1021902 - 513 QUI69972 signal peptidase II -
GSF13_09340 1021906..1022802 - 897 QUI69973 cation diffusion facilitator family transporter -
GSF13_09345 1022898..1023305 + 408 QUI69974 Cd(II)/Pb(II)-responsive transcriptional regulator -

Host bacterium

ID   324 Element type   ICE (Integrative and conjugative element)
Element name   ICEPflCDM8 GenBank   CP047240
Element size   4390426 bp Coordinate of oriT [Strand]   3518..3816 [+]
Host bacterium   Pseudoalteromonas sp. M8 Coordinate of element   950152..1060244

Cargo genes

Drug resistance gene   tet(59), floR, aph(6)-Id, aph(3'')-Ib, sul2, tet(C), aac(3)-IVa, aph(3')-Ia, dfrA32, ere(A), aadA2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -