Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200521
Name   oriT_ICEAmeAS2 in_silico
Organism   Alteromonas mediterranea UM4b
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_021714 (3068..3366 [+], 299 nt)
oriT length   299 nt
IRs (inverted repeats)      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_ICEAmeAS2
GCGCTGTTTGGCGGCGGATGACTGAGCCAAAAAAATCGATACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATTTTCATGGCAATACGTCTTTTTAGGCGTTTTTAAGTGAAATCGGCCTGTATCCCTTGTCAGGTATGGGATTGCGCGAGTTGATTTATATCGAGACGCCAAACAGCGATTGTTACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTTGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14579 GenBank   WP_015066554
Name   mobH_I636_RS05790_ICEAmeAS2 insolico UniProt ID   A0A126PXG1
Length   716 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 716 a.a.        Molecular weight: 79697.61 Da        Isoelectric Point: 5.0021

>WP_015066554.1 MULTISPECIES: MobH family relaxase [Alteromonas]
MFKKLFFQTKALPELSSQLDADIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQVLGFNQREFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTSNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWIRKSNQSTDLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESLAPEVLIKDGNPIWLPMLHISEADLLFSSNVPSSVRLFSKSEWESTQQTQAEPQSSSSEQPGL
PEASSSIELSNSDESPSSKSSDQDDELRHASDVNHLEENENVPGDGCEKPNNSYDGAISNNVNQYDADSL
NLPESLAWLPEASSALIMVGEQALIRYPDAVRPWCAPRKLLAELSRLDWLELDPANPTRKARTVTTKDGV
QEQGLLLKVSISKGLTALIDISKQDEESVAAIQNKEASQRPSRTETTSAQAKELATRAERKQTPIAPNAN
SSTDPKHAQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVAKEHGIPAGQLLRGISASDQC
QFDEGETVLFTAHAKR

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(39-349)


  Protein structure


Source ID Structure
AlphaFold DB A0A126PXG1


T4CP

ID   17198 GenBank   WP_011788469
Name   traD_I636_RS05795_ICEAmeAS2 insolico UniProt ID   _
Length   607 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 607 a.a.        Molecular weight: 67154.02 Da        Isoelectric Point: 6.6444

>WP_011788469.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MKENAYEMPWRTNYEAMAAAGWLVVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQK
GLKGKPLAFMALSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGHGKQMGSTWIHGV
EPKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGS
PERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPD
LKTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLE
GLLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLT
DAMVGSAIGSLLLSDLTAVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFA
DFAARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGE
RLMEEEGDMFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAA

  Protein domains


Predicted by InterproScan.

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

(452-579)

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

(153-286)

  Protein structure



No available structure.



ID   17199 GenBank   WP_015066568
Name   traC_I636_RS05970_ICEAmeAS2 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: 90260.85 Da        Isoelectric Point: 6.1321

>WP_015066568.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MKASLYSGQRASELLPVLAYSDDEQLFFMEDQSVGFGFLCDPLPGGDESVADRVNVLLNNDWPKDTLLQF
GLYASPDIQTDLQRMMGLRHRQSDPLLRASIRKRADFLDGGTVQSIEESTQTQVRNFQLIVTCKLPLESP
IPTERELSRASALRASFSQALATVGFRVTEMTDRNWLAAISAQLNWGKDASWRNPSPIRSEADKPLREQV
LDYDRAIKVDSQGLMLGDYRVKTLSFKRLPERIWFGHAASFAGDMMTGSRGLRGSFLLNVTIHFPSAEAM
RSRLETKRQWAVNQAYGPMLKFVPVLAAKKKRFDVLFEALQEGDRPIRANMTLTLFSPTEEASISSVSNA
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)

Family of unknown function (DUF5934) (DUF5934)

(253-420)

TraC protein (TraC_F_IV)

(11-241)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1294777..1306648

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
I636_RS05780 (I636_05885) 1290557..1291747 + 1191 WP_015066552 nucleotidyltransferase -
I636_RS05785 (I636_05890) 1291748..1292461 + 714 WP_015066553 hypothetical protein -
I636_RS05790 (I636_05895) 1292578..1294728 + 2151 WP_015066554 MobH family relaxase -
I636_RS05795 (I636_05900) 1294777..1296600 + 1824 WP_011788469 conjugative transfer system coupling protein TraD virb4
I636_RS05800 (I636_05905) 1296610..1297170 + 561 WP_011788470 hypothetical protein -
I636_RS05805 (I636_05910) 1297157..1297792 + 636 WP_011788471 DUF4400 domain-containing protein tfc7
I636_RS05810 (I636_05915) 1297819..1298406 - 588 WP_020744993 hypothetical protein -
I636_RS05815 (I636_05920) 1298568..1298975 - 408 WP_007148576 Cd(II)/Pb(II)-responsive transcriptional regulator -
I636_RS05820 (I636_05925) 1299071..1299967 + 897 WP_020744994 cation transporter -
I636_RS19825 1299971..1300057 + 87 Protein_1156 signal peptidase II -
I636_RS05825 (I636_05930) 1300133..1301296 + 1164 WP_043961024 DcaP family trimeric outer membrane transporter -
I636_RS05830 (I636_05935) 1301390..1301698 - 309 Protein_1158 Na/Pi cotransporter family protein -
I636_RS05835 (I636_05940) 1301756..1302082 + 327 WP_020744997 SEL1-like repeat protein -
I636_RS05840 (I636_05945) 1302136..1302468 - 333 WP_020744998 hypothetical protein -
I636_RS05850 (I636_05955) 1302925..1303206 + 282 WP_000433891 type IV conjugative transfer system protein TraL traL
I636_RS05855 (I636_05960) 1303203..1303829 + 627 WP_000667170 TraE/TraK family type IV conjugative transfer system protein traE
I636_RS05860 (I636_05965) 1303813..1304709 + 897 WP_020745000 type-F conjugative transfer system secretin TraK traK
I636_RS05865 (I636_05970) 1304712..1306001 + 1290 WP_020745001 TraB/VirB10 family protein traB
I636_RS05870 (I636_05975) 1306076..1306648 + 573 WP_015066557 TraV family lipoprotein traV
I636_RS05875 (I636_05980) 1306645..1307034 + 390 WP_011788478 TraA family conjugative transfer protein -
I636_RS05880 (I636_05985) 1307443..1309938 + 2496 WP_011788479 heavy metal translocating P-type ATPase -
I636_RS05885 (I636_05990) 1309964..1310428 + 465 WP_011788480 Cu(I)-responsive transcriptional regulator -
I636_RS05890 (I636_05995) 1310515..1310790 - 276 WP_015066559 MerR family DNA-binding protein -
I636_RS20040 (I636_06000) 1311244..1311405 + 162 WP_157669811 hypothetical protein -

Host bacterium

ID   463 Element type   ICE (Integrative and conjugative element)
Element name   ICEAmeAS2 GenBank   NC_021714
Element size   4438767 bp Coordinate of oriT [Strand]   3068..3366 [+]
Host bacterium   Alteromonas mediterranea UM4b Coordinate of element   1268049..1378509

Cargo genes

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