Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200415
Name   oriT_Tn6861 in_silico
Organism   Providencia rettgeri strain PROV002
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP059345 (5646..5944 [+], 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_Tn6861
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14443 GenBank   QLQ94386
Name   TraI_2_H0907_03580_Tn6861 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: 79771.82 Da        Isoelectric Point: 5.0941

>QLQ94386.1 TraI domain-containing protein [Providencia rettgeri]
MFKNLFFQTKALPELSSQLDTEIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQVLGFNLRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTTNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWVRKSNQSTHLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKST
SNERYESLAPEVLIKDDKPIWLAMLHIVEADLLFSSNVPSGVTLFSKPDWEATQQTQAEPQSRSSEHLDL
PEASSSIELSNSAESPSTKSSEQDDELRHASDVNHLQATENVPGDGCEKPNDSNDATISNNVNQHDADAF
NLPESLAWLPEASSALIMAGEQILIRYPDAVRPWCAPRKLLAELSRLDWLELDPANPTRKARTVTTNDGV
QEQGLLLKVSISKGLIALIDLSKQDAESVEPIQNEEASQRPSRTETANAQAKEPATRAERKQKPIAPNAN
SSTDLKHAQRQQVVNFVKDLPILLTDGNYPDVDHSADGIRVTIQTLRQVANEHGIPAGQLLRGISASDQC
QFDEGETVLFTAHAKR

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(39-350)


  Protein structure



No available structure.




T4CP

ID   16979 GenBank   QLQ94387
Name   traD_H0907_03585_Tn6861 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: 67156.97 Da        Isoelectric Point: 6.5130

>QLQ94387.1 conjugative transfer system coupling protein TraD [Providencia rettgeri]
MKENAYEMPWRTNYEAMAVAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQKG
LKGKPLAFMELSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FSARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
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   16980 GenBank   QLQ94399
Name   traC_H0907_03650_Tn6861 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: 90174.75 Da        Isoelectric Point: 5.8177

>QLQ94399.1 type IV secretion system protein TraC [Providencia rettgeri]
MKASLYSGQRASELLPVLAYSDDEQLFFMEDQSVGFGFLCDPLPGGDESVADRVNVLLNNDWPKDTLLQF
GLYASPDIQTDLQLMMGLRHRQSDPLLRASIRKRADFLDGGTVQPIEESTQTQVRNFQLIVTCKLPLESP
IPTERELSRTSALRASFSQALTTVGFRVTEMTDRNWLAALSAQLNWGKDASWRNPSPIRSEADKPLREQV
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: 814760..838538

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H0907_03565 810739..811593 + 855 QLQ94383 restriction endonuclease -
H0907_03570 811687..811968 + 282 QLQ94384 hypothetical protein -
H0907_03575 811968..812441 + 474 QLQ94385 hypothetical protein -
H0907_03580 812561..814711 + 2151 QLQ94386 TraI domain-containing protein -
H0907_03585 814760..816580 + 1821 QLQ94387 conjugative transfer system coupling protein TraD virb4
H0907_03590 816590..817150 + 561 QLQ94388 conjugative transfer protein -
H0907_03595 817137..817772 + 636 QLQ94389 DUF4400 domain-containing protein tfc7
H0907_03600 817799..818386 - 588 QLQ94390 plasmid-related protein -
H0907_03605 818675..818956 + 282 QLQ94391 type IV conjugative transfer system protein TraL traL
H0907_03610 818953..819579 + 627 QLQ94392 pilus assembly protein traE
H0907_03615 819563..820459 + 897 QLQ95689 type-F conjugative transfer system secretin TraK traK
H0907_03620 820462..821751 + 1290 QLQ94393 conjugal transfer protein TraB traB
H0907_03625 821826..822398 + 573 QLQ94394 type IV conjugative transfer system lipoprotein TraV traV
H0907_03630 822395..822781 + 387 QLQ94395 hypothetical protein -
H0907_03635 823002..823793 + 792 QLQ94396 type IV toxin-antitoxin system AbiEi family antitoxin -
H0907_03640 823786..824724 + 939 QLQ94397 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
H0907_03645 824856..825548 + 693 QLQ94398 DsbC family protein trbB
H0907_03650 825548..827947 + 2400 QLQ94399 type IV secretion system protein TraC virb4
H0907_03655 827940..828287 + 348 QLQ94400 plasmid-related protein -
H0907_03660 828271..828783 + 513 QLQ94401 S26 family signal peptidase -
H0907_03665 828794..829918 + 1125 QLQ94402 pilus assembly protein traW
H0907_03670 829902..830930 + 1029 QLQ94403 TraU family protein traU
H0907_03675 830933..834625 + 3693 QLQ94404 conjugal transfer protein TraN traN
H0907_03680 835084..836502 + 1419 QLQ94405 SIR2 family protein -
H0907_03685 836499..838538 + 2040 QLQ94406 ATP-binding protein virb4
H0907_03690 838947..839621 - 675 QLQ95690 endonuclease -
H0907_03695 839663..840952 - 1290 QLQ94407 ISL3 family transposase -
H0907_03700 840974..841480 - 507 QLQ94408 signal peptidase II -
H0907_03705 841490..842386 - 897 QLQ94409 cation transporter -
H0907_03710 842482..842889 + 408 QLQ94410 Cd(II)/Pb(II)-responsive transcriptional regulator -

Host bacterium

ID   370 Element type   ICE (Integrative and conjugative element)
Element name   Tn6861 GenBank   CP059345
Element size   4674814 bp Coordinate of oriT [Strand]   5646..5944 [+]
Host bacterium   Providencia rettgeri strain PROV002 Coordinate of element   727272..869956

Cargo genes

Drug resistance gene   ARR-3, dfrA27, aadA16, qacE, sul1, blaPER-1, aph(3')-VIb, tet(C), aadA6, mph(A)
Virulence gene   -
Metal resistance gene   merE, merD, merB, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -