Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200519
Name   oriT_ICEAmaAnS1 in_silico
Organism   Alteromonas macleodii strain D7
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP014323 (3375..3673 [+], 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_ICEAmaAnS1
GCGCTGTTTGGCGGCGGATGACTGAGCCAAAAAAATCGATACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATTTTCATGGCAATACGTCTTTTTAGGCGTTTTTAAGTGAAATCGGCCTGTATCCCTTGTCAGGTATGGGATTGCGCGAGTTGATTTATATCGAGACGCCAAACAGCGATTGTTACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTTGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14577 GenBank   WP_015066554
Name   mobH_AVL55_RS05785_ICEAmaAnS1 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   17194 GenBank   WP_011788469
Name   traD_AVL55_RS05790_ICEAmaAnS1 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   17195 GenBank   WP_015066568
Name   traC_AVL55_RS05955_ICEAmaAnS1 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: 1300452..1311221

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AVL55_RS05775 (AVL55_05775) 1296232..1297422 + 1191 WP_015066552 nucleotidyltransferase -
AVL55_RS05780 (AVL55_05780) 1297423..1298136 + 714 WP_015066553 hypothetical protein -
AVL55_RS05785 (AVL55_05785) 1298253..1300403 + 2151 WP_015066554 MobH family relaxase -
AVL55_RS05790 (AVL55_05790) 1300452..1302275 + 1824 WP_011788469 conjugative transfer system coupling protein TraD virb4
AVL55_RS05795 (AVL55_05795) 1302285..1302845 + 561 WP_061094530 hypothetical protein -
AVL55_RS05800 (AVL55_05800) 1302832..1303467 + 636 WP_000033753 DUF4400 domain-containing protein tfc7
AVL55_RS05805 (AVL55_05805) 1303494..1304081 - 588 WP_061094531 hypothetical protein -
AVL55_RS05810 (AVL55_05810) 1304700..1305122 + 423 WP_035234747 hypothetical protein -
AVL55_RS05815 (AVL55_05815) 1305176..1305502 - 327 WP_020744997 SEL1-like repeat protein -
AVL55_RS05820 (AVL55_05820) 1305560..1305868 + 309 Protein_1156 Na/Pi cotransporter family protein -
AVL55_RS05825 (AVL55_05825) 1305962..1307125 - 1164 WP_043961024 DcaP family trimeric outer membrane transporter -
AVL55_RS05835 (AVL55_05835) 1307498..1307779 + 282 WP_000433891 type IV conjugative transfer system protein TraL traL
AVL55_RS05840 (AVL55_05840) 1307776..1308402 + 627 WP_000667170 TraE/TraK family type IV conjugative transfer system protein traE
AVL55_RS05845 (AVL55_05845) 1308386..1309282 + 897 WP_061096346 type-F conjugative transfer system secretin TraK traK
AVL55_RS05850 (AVL55_05850) 1309285..1310574 + 1290 WP_011788476 TraB/VirB10 family protein traB
AVL55_RS05855 (AVL55_05855) 1310649..1311221 + 573 WP_015066557 TraV family lipoprotein traV
AVL55_RS05860 (AVL55_05860) 1311218..1311607 + 390 WP_011788478 TraA family conjugative transfer protein -
AVL55_RS05865 (AVL55_05865) 1312016..1314511 + 2496 WP_011788479 heavy metal translocating P-type ATPase -
AVL55_RS05870 (AVL55_05870) 1314537..1315001 + 465 WP_011788480 Cu(I)-responsive transcriptional regulator -
AVL55_RS05875 (AVL55_05875) 1315088..1315603 - 516 Protein_1166 Cd(II)/Pb(II)-responsive transcriptional regulator -

Host bacterium

ID   461 Element type   ICE (Integrative and conjugative element)
Element name   ICEAmaAnS1 GenBank   NZ_CP014323
Element size   4575623 bp Coordinate of oriT [Strand]   3375..3673 [+]
Host bacterium   Alteromonas macleodii strain D7 Coordinate of element   1261260..1375632

Cargo genes

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