Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200520
Name   oriT_ICEAmeAS1 in_silico
Organism   Alteromonas mediterranea DE1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_019393 (8388..8686 [+], 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_ICEAmeAS1
GCGCTGTTTGGCGGCGGATGACTGAGCCAAAAAAATCGATACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATTTTCATGGCAATACGTCTTTTTAGGCGTTTTTAAGTGAAATCGGCCTGTATCCCTTGTCAGGTATGGGATTGCGCGAGTTGATTTATATCGAGACGCCAAACAGCGATTGTTACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTTGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14578 GenBank   WP_015066554
Name   mobH_AMAD1_RS05815_ICEAmeAS1 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   17196 GenBank   WP_011788469
Name   traD_AMAD1_RS05820_ICEAmeAS1 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   17197 GenBank   WP_015066568
Name   traC_AMAD1_RS05970_ICEAmeAS1 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: 1303675..1311317

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AMAD1_RS05805 (amad1_05870) 1299455..1300645 + 1191 WP_015066552 nucleotidyltransferase -
AMAD1_RS05810 (amad1_05875) 1300646..1301359 + 714 WP_015066553 hypothetical protein -
AMAD1_RS05815 (amad1_05880) 1301476..1303626 + 2151 WP_015066554 MobH family relaxase -
AMAD1_RS05820 (amad1_05885) 1303675..1305498 + 1824 WP_011788469 conjugative transfer system coupling protein TraD virb4
AMAD1_RS05825 (amad1_05890) 1305508..1306068 + 561 WP_011788470 hypothetical protein -
AMAD1_RS05830 (amad1_05895) 1306055..1306690 + 636 WP_011788471 DUF4400 domain-containing protein tfc7
AMAD1_RS05835 (amad1_05900) 1306717..1307304 - 588 WP_011788472 hypothetical protein -
AMAD1_RS05845 (amad1_05910) 1307593..1307874 + 282 WP_011788474 type IV conjugative transfer system protein TraL traL
AMAD1_RS05850 (amad1_05915) 1307871..1308498 + 628 Protein_1156 TraE/TraK family type IV conjugative transfer system protein -
AMAD1_RS05855 (amad1_05920) 1308482..1309378 + 897 WP_015066556 type-F conjugative transfer system secretin TraK traK
AMAD1_RS05860 (amad1_05925) 1309381..1310670 + 1290 WP_011788476 TraB/VirB10 family protein traB
AMAD1_RS05865 (amad1_05930) 1310745..1311317 + 573 WP_015066557 TraV family lipoprotein traV
AMAD1_RS05870 (amad1_05935) 1311314..1311703 + 390 WP_011788478 TraA family conjugative transfer protein -
AMAD1_RS05875 (amad1_05940) 1312112..1314607 + 2496 WP_011788479 heavy metal translocating P-type ATPase -
AMAD1_RS05880 (amad1_05945) 1314633..1315097 + 465 WP_015066558 Cu(I)-responsive transcriptional regulator -
AMAD1_RS05885 (amad1_05950) 1315184..1315459 - 276 WP_015066559 MerR family DNA-binding protein -
AMAD1_RS05890 (amad1_05955) 1315913..1316074 + 162 WP_157669811 hypothetical protein -

Host bacterium

ID   462 Element type   ICE (Integrative and conjugative element)
Element name   ICEAmeAS1 GenBank   NC_019393
Element size   4643844 bp Coordinate of oriT [Strand]   8388..8686 [+]
Host bacterium   Alteromonas mediterranea DE1 Coordinate of element   1271627..1383296

Cargo genes

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