Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   119266
Name   oriT_pYR6 in_silico
Organism   Yersinia ruckeri strain NVI-6614
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP098698 (40554..40641 [+], 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
TACGGGACAGGATATGTTTTGTAGCACCGCCTGCACGCAGTCGGCCCTACAAAACGACCTGGTCAGGGCAGAGCCCCGACACCCGCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12185 GenBank   WP_267257522
Name   traI_ND449_RS17365_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: 73911.50 Da        Isoelectric Point: 7.3675

>WP_267257522.1 TraI/MobA(P) family conjugative relaxase [Yersinia ruckeri]
MIPIVPEKRRDGRSSFIQLVSYLTLRDEVKPDMPISPDNPYIRPSRSKAAIFDRLIDYLDRKASVEDQTV
LAMFDDGTQQIKSGNVVCETNCFSLETASAEMNAVAMQNTRCVDAVYHCILSWREEDTPTDEQIFDSARY
CLKQLGMADHQYVVAVHRDTDNVHCHIAANRVNPKSYRAANLYNDVDTLHKACRHLEMKHGFTPDNGAWK
VNGSHQVVRSENDFKSIPRKAKQLEYYADSESLFSYATGECRQRIGEIVAGDNPSWNAIHTELIRAGLEL
KPKGEGLAIYSREDESLPPIKASSLHPDLTLYCLEETLGKFEPSPEIVMLTDDNDNIIHSNYKREFIYEP
RLHARDNTARIDRRLARADAREDLKARYQAYKSAWIKPKLEGGTLKQRYQLVAKRFAWQKARARIAIGDP
LLRKLTYHIIEVERMKAIAALRIAVKAEIKVFNANPENRRLSYRAWVEQQALNHDQAAIAQLRGWSYRLK
RANKTPPLSENGIRCAAADDCRPFNLEGYDTQINRDGVIQYRHDGIVQVQDRGERIEIANPFISDGQHIA
GAMTIAEEKSGEVMVFEGSRTFVNQACGLVGWFNEGGEKPLPLSDPQQRILAGYEVDRQASYSGILQPKS
GADKLHELEQGHKPQGGYRPQ

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(55-320)


  Protein structure



No available structure.




T4CP

ID   14276 GenBank   WP_267257502
Name   trbC_ND449_RS17385_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: 81729.39 Da        Isoelectric Point: 6.6681

>WP_267257502.1 F-type conjugative transfer protein TrbC [Yersinia ruckeri]
MAQSVEIEARRVRRSLGYTFINDALLSPFGVQFFLLAGLVMGWIFPASLLISVPGLLLHVMLFSDRPFRM
PLRMPTDVGGIDLTTEREMPKYRNGLWGFFRYVVRTRKFFPAAGVMCLGFARGKALARELWLTLDDTLRH
MLLLATTGSGKTEALLSVFLNAICWGRGICYSDGKGQNSLAFAMWSLARRFGREDDFYVLNFMTGGMDKL
LLLLLNDKKRQPSNTINLFGTANTTFIIQLMESMLPPAGSGDAGWQDKAKSMNAALVYAVYYKCKKEKRT
ISQTVIQSYLPLRKLAELYLEAKRDGWHKEAYNPLENYFNTLAGFRIELISQPSTWEQGVYDQHGYLIQQ
FNRMLTMFNDLYGHIFSTDAGDINIEDILHNDRILCTTIPALELSKGEASNIGKLYISAIRMTMARDLGC
ELEGMLNDVLIVKKYSGKFPFAIAMDELGAYFGPGMDNLASQMRSLGYMLIVSAQDIQRFIAEHRGEYMT
VNANLLTKWFMALQDEKDTFELAKITGGKGYYAELGAVEQAGGIITPNYEDATNNYIREKDRLDLGDLKE
LNPGEGMISFKSALVPSSAIYIPDDDKMTSALPMRINRFIEVQTPTEAELLALNPTLLRKLPPSAQEIED
ILLRLDSPEDSTHQIGIMDPILKRIVDLTLDLDNRADISYNPTQRGILLFEAAREALHQNKRKWRHQPTP
PKTIRVSKEVATSLADADLQNTLSN

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 46549..74936

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ND449_RS17370 (ND449_17355) 43041..43358 - 318 WP_050289016 hypothetical protein -
ND449_RS17375 (ND449_17360) 43368..43826 - 459 WP_144417027 phospholipase D family protein -
ND449_RS17380 (ND449_17365) 43922..44227 - 306 WP_265317723 hypothetical protein -
ND449_RS17385 (ND449_17370) 44310..46487 - 2178 WP_267257502 F-type conjugative transfer protein TrbC -
ND449_RS17390 (ND449_17375) 46549..47550 - 1002 WP_267257503 hypothetical protein trbB
ND449_RS17395 (ND449_17380) 47573..48889 - 1317 WP_267257504 conjugal transfer protein TrbA trbA
ND449_RS17400 (ND449_17385) 49037..49609 - 573 WP_088130798 hypothetical protein -
ND449_RS17405 (ND449_17390) 49621..51741 - 2121 WP_234049654 DotA/TraY family protein traY
ND449_RS17410 (ND449_17395) 51870..52475 - 606 WP_050289008 conjugal transfer protein TraX -
ND449_RS17415 (ND449_17400) 52468..53697 - 1230 WP_267257505 conjugal transfer protein TraW traW
ND449_RS17420 (ND449_17405) 53888..56962 - 3075 WP_120806750 type IV secretory system conjugative DNA transfer family protein traU
ND449_RS17425 (ND449_17410) 56965..57570 - 606 WP_267257506 hypothetical protein traT
ND449_RS17430 (ND449_17415) 57661..58065 - 405 WP_108088340 DUF6750 family protein traR
ND449_RS17435 (ND449_17420) 58080..58610 - 531 WP_050074337 conjugal transfer protein TraQ traQ
ND449_RS17440 (ND449_17425) 58619..59356 - 738 WP_234049652 hypothetical protein traP
ND449_RS17445 (ND449_17430) 59356..60567 - 1212 WP_267257507 conjugal transfer protein TraO traO
ND449_RS17450 (ND449_17435) 60572..61582 - 1011 WP_050289002 DotH/IcmK family type IV secretion protein traN
ND449_RS17455 (ND449_17440) 61585..62259 - 675 WP_050074341 DotI/IcmL/TraM family protein traM
ND449_RS17460 (ND449_17445) 62344..62829 - 486 WP_267257508 hypothetical protein traL
ND449_RS17465 (ND449_17450) 62839..66021 - 3183 WP_267257509 LPD7 domain-containing protein -
ND449_RS17470 (ND449_17455) 66080..66346 - 267 WP_050074346 IcmT/TraK family protein traK
ND449_RS17475 (ND449_17460) 66346..67503 - 1158 WP_267257510 plasmid transfer ATPase TraJ virB11
ND449_RS17480 (ND449_17465) 67490..67783 - 294 WP_267257511 hypothetical protein -
ND449_RS17485 (ND449_17470) 67817..68605 - 789 WP_120806743 type IV secretory system conjugative DNA transfer family protein traI
ND449_RS17490 (ND449_17475) 68602..69057 - 456 WP_120806742 DotD/TraH family lipoprotein -
ND449_RS17495 (ND449_17480) 69102..70481 - 1380 WP_267257512 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
ND449_RS17500 (ND449_17485) 70471..71139 - 669 WP_120806741 prepilin peptidase -
ND449_RS17505 (ND449_17490) 71136..71606 - 471 WP_234049647 lytic transglycosylase domain-containing protein virB1
ND449_RS17510 (ND449_17495) 71616..72224 - 609 WP_120806739 type 4 pilus major pilin -
ND449_RS17515 (ND449_17500) 72246..73373 - 1128 WP_234049646 type II secretion system F family protein -
ND449_RS17520 (ND449_17505) 73434..74936 - 1503 WP_205582781 GspE/PulE family protein virB11
ND449_RS17525 (ND449_17510) 74938..75474 - 537 WP_234049644 type IV pilus biogenesis protein PilP -
ND449_RS17530 (ND449_17515) 75461..76726 - 1266 WP_120806788 type 4b pilus protein PilO2 -
ND449_RS17535 (ND449_17520) 76731..78371 - 1641 WP_120806787 PilN family type IVB pilus formation outer membrane protein -
ND449_RS17540 (ND449_17525) 78382..78807 - 426 WP_234049643 type IV pilus biogenesis protein PilM -
ND449_RS17545 (ND449_17530) 78804..79811 - 1008 WP_265317530 toxin co-regulated pilus biosynthesis Q family protein -

Host bacterium

ID   19696 GenBank   NZ_CP098698
Plasmid name   pYR6 Incompatibility group   -
Plasmid size   83000 bp Coordinate of oriT [Strand]   40554..40641 [+]
Host baterium   Yersinia ruckeri strain NVI-6614

Cargo genes

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