Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119232
Name   oriT_pYR6 in_silico
Organism   Yersinia ruckeri strain NVI-4570
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP098708 (40913..41000 [-], 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_pYR6
TACGGGACAGGATATGTTTTGTAGCACCGCCTGCACGCAGCCGGCCCTACAAAACGACCTGGTCAGGGCAGAGCCCCGACACCCGCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12171 GenBank   WP_234049660
Name   traI_ND447_RS17750_pYR6 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   14253 GenBank   WP_240442712
Name   trbC_ND447_RS17730_pYR6 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: 81714.44 Da        Isoelectric Point: 6.8288

>WP_240442712.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Yersinia]
MAQSVEIEARRVRRSLGYTFINDALLSPFGVQFFLLAGLVMGWIFPASLLISVPGLLLHVMLFSDRPFRM
PLRMPTDVGGIDLTTEREMPKYRNGLWGFFRYVVRTRKFFPAAGVMCLGFARGKALARELWLTLDDALRH
MLLLATTGSGKTEALLSVFLNAICWGRGICYSDGKGQNSLAFAMWSLARRFGREDDFYVLNFMTGGMDKL
LLLLLNDKKRQPSNTINLFGTANTTFIIQLMESMLPPAGSGDAGWQDKAKSMNAALVYAVYYKCKKEKRT
ISQTVIQSYLPLRKLAELYLEAKRDGWHKEAYNPLENYFNTLAGFRIELISQPSTWEQGVYDQHGYLIQQ
FNRMLTMFNDLYGHIFSTDAGDINIEDILHNDRILCTTIPALELSKGEASNIGKLYISAIRMTMARDLGC
ELEGMLNDVLIVKKYSGKFPFAIAMDELGAYFGPGMDNLASQMRSLGYMLIVSAQDIQRFIAEHRGEYMT
VNANLLTKWFMALQDEKDTFELAKITGGKGYYAELGAVEQAGGIITPNYEDAKNNYIREKDRLDLGDLKE
LNPGEGMISFKSALVPSSAIYIPDDDKMTSALPMRINRFIEVQTPTEAELLALNPTLLRKLPPSAQEIED
ILLRLDGPEDSTHQIGIMDPILKRIVDLTLDLDNRADISYNPTQRGILMFEAAREALHQNKRKWRHQPTP
PKTIRVSKEVATSLADADLQNTISN

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 6852..35005

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ND447_RS17575 (ND447_17565) 1977..2984 + 1008 WP_265317530 toxin co-regulated pilus biosynthesis Q family protein -
ND447_RS17580 (ND447_17570) 2981..3406 + 426 WP_234049643 type IV pilus biogenesis protein PilM -
ND447_RS17585 (ND447_17575) 3417..5057 + 1641 WP_267262820 PilN family type IVB pilus formation outer membrane protein -
ND447_RS17590 (ND447_17580) 5062..6327 + 1266 WP_120806788 type 4b pilus protein PilO2 -
ND447_RS17595 (ND447_17585) 6314..6850 + 537 WP_234049644 type IV pilus biogenesis protein PilP -
ND447_RS17600 (ND447_17590) 6852..8354 + 1503 WP_205582781 GspE/PulE family protein virB11
ND447_RS17605 (ND447_17595) 8415..9542 + 1128 WP_234049646 type II secretion system F family protein -
ND447_RS17610 (ND447_17600) 9564..10172 + 609 WP_120806739 type 4 pilus major pilin -
ND447_RS17615 (ND447_17605) 10182..10652 + 471 WP_234049647 lytic transglycosylase domain-containing protein virB1
ND447_RS17620 (ND447_17610) 10649..11317 + 669 WP_120806741 prepilin peptidase -
ND447_RS17625 (ND447_17615) 11307..12686 + 1380 WP_234049648 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
ND447_RS17630 (ND447_17620) 12731..13186 + 456 WP_120806742 DotD/TraH family lipoprotein -
ND447_RS17635 (ND447_17625) 13183..13971 + 789 WP_050074349 type IV secretory system conjugative DNA transfer family protein traI
ND447_RS17640 (ND447_17630) 13991..15166 + 1176 WP_145559185 plasmid transfer ATPase TraJ virB11
ND447_RS17645 (ND447_17635) 15166..15432 + 267 WP_050074346 IcmT/TraK family protein traK
ND447_RS17650 (ND447_17640) 15491..18715 + 3225 WP_267262821 LPD7 domain-containing protein -
ND447_RS17655 (ND447_17645) 18725..19210 + 486 WP_234049650 hypothetical protein traL
ND447_RS17660 (ND447_17650) 19295..19969 + 675 WP_050074341 DotI/IcmL/TraM family protein traM
ND447_RS17665 (ND447_17655) 19972..20982 + 1011 WP_267262822 DotH/IcmK family type IV secretion protein traN
ND447_RS17670 (ND447_17660) 20987..22198 + 1212 WP_265317532 conjugal transfer protein TraO traO
ND447_RS17675 (ND447_17665) 22198..22935 + 738 WP_234049652 hypothetical protein traP
ND447_RS17680 (ND447_17670) 22944..23474 + 531 WP_050074337 conjugal transfer protein TraQ traQ
ND447_RS17685 (ND447_17675) 23489..23893 + 405 WP_108088340 DUF6750 family protein traR
ND447_RS17690 (ND447_17680) 23984..24589 + 606 WP_050074479 hypothetical protein traT
ND447_RS17695 (ND447_17685) 24592..27666 + 3075 WP_234049653 type IV secretory system conjugative DNA transfer family protein traU
ND447_RS17700 (ND447_17690) 27857..29086 + 1230 WP_120806751 conjugal transfer protein TraW traW
ND447_RS17705 (ND447_17695) 29079..29684 + 606 WP_050289008 conjugal transfer protein TraX -
ND447_RS17710 (ND447_17700) 29813..31933 + 2121 WP_234049654 DotA/TraY family protein traY
ND447_RS17715 (ND447_17705) 31945..32517 + 573 WP_088130798 hypothetical protein -
ND447_RS17720 (ND447_17710) 32665..33981 + 1317 WP_234049655 conjugal transfer protein TrbA trbA
ND447_RS17725 (ND447_17715) 34004..35005 + 1002 WP_265317513 hypothetical protein trbB
ND447_RS17730 (ND447_17720) 35067..37244 + 2178 WP_240442712 F-type conjugative transfer protein TrbC -
ND447_RS17735 (ND447_17725) 37327..37632 + 306 WP_267262812 hypothetical protein -
ND447_RS17740 (ND447_17730) 37650..38186 + 537 WP_234049659 phospholipase D family protein -
ND447_RS17745 (ND447_17735) 38196..38513 + 318 WP_050289016 hypothetical protein -

Host bacterium

ID   19662 GenBank   NZ_CP098708
Plasmid name   pYR6 Incompatibility group   -
Plasmid size   71441 bp Coordinate of oriT [Strand]   40913..41000 [-]
Host baterium   Yersinia ruckeri strain NVI-4570

Cargo genes

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