Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105343
Name   oriT_p17Y0412.1 in_silico
Organism   Yersinia ruckeri strain 17Y0412
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP084638 (39143..39230 [-], 88 nt)
oriT length   88 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 88 nt

>oriT_p17Y0412.1
TACGGGACAGGATATGTTTTGTAGCACCGCCTGCACGCAGCCGGCCCTACAAAACGACCTGGTCAGGGCAGAGCCCCGACACCCGCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3646 GenBank   WP_234049660
Name   Relaxase_LGL85_RS17825_p17Y0412.1 insolico UniProt ID   _
Length   651 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 651 a.a.        Molecular weight: 73907.47 Da        Isoelectric Point: 7.3837

>WP_234049660.1 TraI/MobA(P) family conjugative relaxase [Yersinia ruckeri]
MIPIVPEKRRDGRSSFIQLVSYLTLRDEVKPDMPISPDNPYIRPSLSKAAIFDRLIDYLDRKASVEDQTV
LAMFDDGTQQIKSGNVVCETNCFSLETASAEMNAVAMQNTRCVDAVYHCILSWREEDTPTDEQIFDSARY
CLKQLGMADHQYVVAVHRDTDNVHCHIAANRVNPKSYRAANLYNDVDTLHKACRHLEMKHGFTPDNGAWK
VNGSHQVVRSENDFKSIPRKAKQLEYYADSESLFSYATGECRQRIGEIVAGDNPSWNAIHTELIRAGLEL
KPKGEGLAIYSREDESLPPIKASSLHPDLTLYCLEETLGKFEPSPEIVMLTDDNDNIIHSNYKREFIYEP
RLHARDNTARIDRRLARADAREDLKARYQAYKSAWIKPKLEGGTLKQRYQHVAKRFAWQKARARIAIGDP
LLRKLTYHIIEVERMKAIAALRIAVKAEKKVFNANPENRRLSYRAWVEQQALNHDQAAIAQLRGWSYRLK
RANKTPPLSENGIRCAAADDCRPFNLEGYDTQINRDGVIQYRHDGIVQVQDRGERIEIANPFISDGQHIA
GAMTIAEEKSGEVMVFEGSRTFVNQACGLVGWFNEGGEKPLPLSDPQQRILAGYEVDRQASYSGILQPKS
GADKLHELEQGHKPQGGYRPQ

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(55-320)


  Protein structure



No available structure.




T4CP

ID   3617 GenBank   WP_234049657
Name   trbC_LGL85_RS17805_p17Y0412.1 insolico UniProt ID   _
Length   725 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 725 a.a.        Molecular weight: 81748.46 Da        Isoelectric Point: 6.8288

>WP_234049657.1 F-type conjugative transfer protein TrbC [Yersinia ruckeri]
MAQSVEIEARRVRRSLGYTFINDALLSPFGVQFFLLAGLVMGWIFPASLLISVPGLLLHVMLFSDRPFRM
PLRMPTDVGGIDLTTEREMPKYRNGLWGFFRYVVRTRKFFPAAGVMCLGFARGKALARELWLTLDDALRH
MLLLATTGSGKTEALLSVFLNAICWGRGICYSDGKGQNSLAFAMWSLARRFGREDDFYVLNFMTGGMDKL
LLLLLNDKKRQPSNTINLFGTANTTFIIQLMESMLPPAGSGDAGWQDKAKSMNAALVYAVYYKCKKEKRT
ISQTVIQSYLPLRKLAELYLEAKRDGWHKEAYNPLENYFNTLAGFRIELISQPSTWEQGVYDQHGYLIQQ
FNRMLTMFNDLYGHIFSTDAGDINIEDILHNDRILCTTIPALELSKGEASNIGKLYISAIRMTMARDLGC
ELEGMLNDVLIVKKYSGKFPFAIAMDELGAYFGPGMDNLASQMRSLGYMLIVSAQDIQRFIAEHRGEYMT
VNANLLTKWFMALQDEKDTFELAKITGGKGYYAELGAVEQAGGIITPNYEDAKNNYIREKDRLDLGDLKE
LNPGEGMISFKSALVPSSAIYIPDDDKMTSALPMRINRFIEVQTPTEAELLALNPTLFRKLPPSAQEIED
ILLRLDGPEDSTHQIGIMDPILKRIVDLTLDLDNRADISYNPTQRGILMFEAAREALHQNKRKWRHQPTP
PKTIRVSKEVATSLADADLQNTISN

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 5100..33235

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LGL85_RS17650 (LGL85_17700) 225..1232 + 1008 WP_234049642 TcpQ domain-containing protein -
LGL85_RS17655 (LGL85_17705) 1229..1654 + 426 WP_234049643 type IV pilus biogenesis protein PilM -
LGL85_RS17660 (LGL85_17710) 1665..3305 + 1641 WP_120806787 PilN family type IVB pilus formation outer membrane protein -
LGL85_RS17665 (LGL85_17715) 3310..4575 + 1266 WP_120806788 type 4b pilus protein PilO2 -
LGL85_RS17670 (LGL85_17720) 4562..5098 + 537 WP_234049644 type IV pilus biogenesis protein PilP -
LGL85_RS17675 (LGL85_17725) 5100..6602 + 1503 WP_234049645 ATPase, T2SS/T4P/T4SS family virB11
LGL85_RS17680 (LGL85_17730) 6663..7790 + 1128 WP_234049646 type II secretion system F family protein -
LGL85_RS17685 (LGL85_17735) 7812..8420 + 609 WP_120806739 type 4 pilus major pilin -
LGL85_RS17690 (LGL85_17740) 8430..8900 + 471 WP_234049647 lytic transglycosylase domain-containing protein virB1
LGL85_RS17695 (LGL85_17745) 8897..9565 + 669 WP_120806741 prepilin peptidase -
LGL85_RS17700 (LGL85_17750) 9555..10934 + 1380 WP_234049648 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
LGL85_RS17705 (LGL85_17755) 10979..11434 + 456 WP_120806742 DotD/TraH family lipoprotein -
LGL85_RS17710 (LGL85_17760) 11431..12219 + 789 WP_050074349 type IV secretory system conjugative DNA transfer family protein traI
LGL85_RS17715 (LGL85_17765) 12239..13414 + 1176 WP_145559185 plasmid transfer ATPase TraJ virB11
LGL85_RS17720 (LGL85_17770) 13414..13680 + 267 WP_050074346 IcmT/TraK family protein traK
LGL85_RS17725 (LGL85_17775) 13739..16945 + 3207 WP_234049649 LPD7 domain-containing protein -
LGL85_RS17730 (LGL85_17780) 16955..17440 + 486 WP_234049650 hypothetical protein traL
LGL85_RS17735 (LGL85_17785) 17525..18199 + 675 WP_050074341 DotI/IcmL/TraM family protein traM
LGL85_RS17740 (LGL85_17790) 18202..19212 + 1011 WP_050289002 DotH/IcmK family type IV secretion protein traN
LGL85_RS17745 (LGL85_17795) 19217..20428 + 1212 WP_234049651 conjugal transfer protein TraO traO
LGL85_RS17750 (LGL85_17800) 20428..21165 + 738 WP_234049652 hypothetical protein traP
LGL85_RS17755 (LGL85_17805) 21174..21704 + 531 WP_050074337 conjugal transfer protein TraQ traQ
LGL85_RS17760 (LGL85_17810) 21719..22123 + 405 WP_108088340 DUF6750 family protein traR
LGL85_RS17765 (LGL85_17815) 22214..22819 + 606 WP_050074479 hypothetical protein traT
LGL85_RS17770 (LGL85_17820) 22822..25896 + 3075 WP_234049653 type IV secretory system conjugative DNA transfer family protein traU
LGL85_RS17775 (LGL85_17825) 26087..27316 + 1230 WP_120806751 conjugal transfer protein TraW traW
LGL85_RS17780 (LGL85_17830) 27309..27914 + 606 WP_050289008 conjugal transfer protein TraX -
LGL85_RS17785 (LGL85_17835) 28043..30163 + 2121 WP_234049654 DotA/TraY family protein traY
LGL85_RS17790 (LGL85_17840) 30175..30747 + 573 WP_088130798 hypothetical protein -
LGL85_RS17795 (LGL85_17845) 30895..32211 + 1317 WP_234049655 conjugal transfer protein TrbA trbA
LGL85_RS17800 (LGL85_17850) 32234..33235 + 1002 WP_234049656 hypothetical protein trbB
LGL85_RS17805 (LGL85_17855) 33297..35474 + 2178 WP_234049657 F-type conjugative transfer protein TrbC -
LGL85_RS17810 (LGL85_17860) 35557..35862 + 306 WP_234049658 hypothetical protein -
LGL85_RS17815 (LGL85_17865) 35880..36416 + 537 WP_234049659 phospholipase D family protein -
LGL85_RS17820 (LGL85_17870) 36426..36743 + 318 WP_050289016 hypothetical protein -

Host bacterium

ID   5781 GenBank   NZ_CP084638
Plasmid name   p17Y0412.1 Incompatibility group   -
Plasmid size   83706 bp Coordinate of oriT [Strand]   39143..39230 [-]
Host baterium   Yersinia ruckeri strain 17Y0412

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   arsH, arsR, arsB, arsC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -