Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105959
Name   oriT_pYR10 in_silico
Organism   Yersinia ruckeri strain NVI-5089
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP098702 (36693..36780 [+], 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_pYR10
TACGGGACAGGATATGTTTTGTAGCACCGCCTGCACGCAGTCGGCCCTACAAAACGACCTGGTCAGGGCAGAGCCCCGACACCCGCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4015 GenBank   WP_265317721
Name   Relaxase_ND440_RS17400_pYR10 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: 73984.60 Da        Isoelectric Point: 7.5121

>WP_265317721.1 TraI/MobA(P) family conjugative relaxase [Yersinia ruckeri]
MIPIVPEKRRDGRSSFIQLVSYLTLRDEVKPDMPISPDNPYIRPSRSKAAIFDRLIDYLDRKASVEDQTV
LAMFDDGTQQIKSGNVVCETNCFSLETASAEMNAVAMQNTRCVDAVYHCILSWREEDTPTDEKIFDSARY
CLKQLGMADHQYVVAVHRDTDNVHCHIAANRVNPKSYRAANLYNDVDTLHKACRHLEMKHGFTPDNGAWK
VNGSHQVVRSENDFKSIPRKAKQLEYYADSESLFSYATGECRQRIGEIVAGDNPSWNAIHTELIRAGLEL
KPKGEGLAIYSREDESLPPIKASSLHPDLTLYCLEETLGKFEPSPEIVMLTDDNDNIIHSNYKREFIYEP
RLHARDNTARIDRRLARADAREDLKARYQAYKSAWIKPKLEGGTLKQRYQLVAKRFAWQKARARIAIGDP
LLRKLTYHIIEVERMKAIAALRIAVKAEKKVFNANPENRRLSYRAWVEQQALNHDQAAIAQLRGWSYRLK
RANKTPPLSENGIRCAAADDCRPFNLEGYDTQINRDGVIQYRHDGIVQVQDRGERIEIANPFISDGQHIA
GAMTIAEEKSGEVMVFEGSRTFVNQACGLVGWFNEGGEKPLPLSDPQQRILAGYEVDRQASYSGILQPKS
GADKLHELEQDHKPQGGYRPQ

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(55-320)


  Protein structure



No available structure.




T4CP

ID   4023 GenBank   WP_265317724
Name   trbC_ND440_RS17415_pYR10 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: 81699.37 Da        Isoelectric Point: 6.6681

>WP_265317724.1 F-type conjugative transfer protein TrbC [Yersinia ruckeri]
MAQSVEIEARRVRRSLGYTFINDALLSPFGVQFFLLAGLVMGWIFPASLLISVPGLLLHVMLFSDRPFRM
PLRMPTDVGGIDLTTEREMPKYRNGLWGFFRYVVRTRKFFPAAGVMCLGFARGKALARELWLTLDDTLRH
MLLLATTGSGKTEALLSVFLNAICWGRGICYSDGKGQNSLAFAMWSLARRFGREDDFYVLNFMTGGMDKL
LLLLLNDKKRQPSNTINLFGTANTTFIIQLMESMLPPAGSGDAGWQDKAKSMNAALVYAVYYKCKKEKRT
ISQTVIQSYLPLRKLAELYLEAKRDGWHKEAYNPLENYFNTLAGFRIELISQPSTWEQGVYDQHGYLIQQ
FNRMLTMFNDLYGHIFSTDAGDINIEDILHNDRILCTTIPALELSKGEASNIGKLYISAIRMTMARDLGC
ELEGMLNDVLIVKKYSGKFPFAIAMDELGAYFGPGMDNLASQMRSLGYMLIVSAQDIQRFIAEHRGEYMT
VNANLLTKWFMALQDEKDTFELAKITGGKGYYAELGAVEQAGGIITPNYEDATNNYIREKDRLDLGDLKE
LNPGEGMISFKSALVPSSAIYIPDDDKMTSALPMRINRFIEVQTPTEAELLALNPTLLRKLPPSAQEIED
ILLRLDGPEDSTHQIGIMDPILKRIVDLTLDLDNRADISYNPTQRGILLFEAAREALHQNKRKWRHQPTP
PKTIRVSKEVATSLADADLQNTLSN

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 42688..71055

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ND440_RS17405 (ND440_17400) 39180..39497 - 318 WP_050289016 hypothetical protein -
ND440_RS17410 (ND440_17405) 39507..39965 - 459 WP_315861869 phospholipase D family protein -
ND440_RS17415 (ND440_17410) 40449..42626 - 2178 WP_265317724 F-type conjugative transfer protein TrbC -
ND440_RS17420 (ND440_17415) 42688..43689 - 1002 WP_265317725 hypothetical protein trbB
ND440_RS17425 (ND440_17420) 43712..45040 - 1329 WP_265317726 conjugal transfer protein TrbA trbA
ND440_RS17430 (ND440_17425) 45196..45723 - 528 WP_050289011 hypothetical protein -
ND440_RS17435 (ND440_17430) 45743..47854 - 2112 WP_265317727 DotA/TraY family protein traY
ND440_RS17440 (ND440_17435) 47983..48588 - 606 WP_226723032 conjugal transfer protein TraX -
ND440_RS17445 (ND440_17440) 48581..49810 - 1230 WP_120806751 conjugal transfer protein TraW traW
ND440_RS17450 (ND440_17445) 50001..53075 - 3075 WP_120806750 type IV secretory system conjugative DNA transfer family protein traU
ND440_RS17455 (ND440_17450) 53078..53683 - 606 WP_050074479 hypothetical protein traT
ND440_RS17460 (ND440_17455) 53774..54178 - 405 WP_108088340 DUF6750 family protein traR
ND440_RS17465 (ND440_17460) 54193..54723 - 531 WP_050074337 conjugal transfer protein TraQ traQ
ND440_RS17470 (ND440_17465) 54732..55469 - 738 WP_234049652 hypothetical protein traP
ND440_RS17475 (ND440_17470) 55469..56680 - 1212 WP_265317532 conjugal transfer protein TraO traO
ND440_RS17480 (ND440_17475) 56685..57695 - 1011 WP_050289002 DotH/IcmK family type IV secretion protein traN
ND440_RS17485 (ND440_17480) 57698..58372 - 675 WP_050074341 DotI/IcmL/TraM family protein traM
ND440_RS17490 (ND440_17485) 58457..58942 - 486 WP_234049650 hypothetical protein traL
ND440_RS17495 (ND440_17490) 58952..62140 - 3189 WP_265317728 LPD7 domain-containing protein -
ND440_RS17500 (ND440_17495) 62199..62465 - 267 WP_050074346 IcmT/TraK family protein traK
ND440_RS17505 (ND440_17500) 62465..63622 - 1158 WP_265317729 plasmid transfer ATPase TraJ virB11
ND440_RS17510 (ND440_17505) 63609..63902 - 294 WP_265317730 hypothetical protein -
ND440_RS17515 (ND440_17510) 63936..64724 - 789 WP_120806743 type IV secretory system conjugative DNA transfer family protein traI
ND440_RS17520 (ND440_17515) 64721..65176 - 456 WP_120806742 DotD/TraH family lipoprotein -
ND440_RS17525 (ND440_17520) 65221..66600 - 1380 WP_265317731 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
ND440_RS17530 (ND440_17525) 66590..67258 - 669 WP_120806741 prepilin peptidase -
ND440_RS17535 (ND440_17530) 67255..67725 - 471 WP_234049647 lytic transglycosylase domain-containing protein virB1
ND440_RS17540 (ND440_17535) 67735..68343 - 609 WP_120806739 type 4 pilus major pilin -
ND440_RS17545 (ND440_17540) 68365..69492 - 1128 WP_234049646 type II secretion system F family protein -
ND440_RS17550 (ND440_17545) 69553..71055 - 1503 WP_205582781 ATPase, T2SS/T4P/T4SS family virB11
ND440_RS17555 (ND440_17550) 71057..71593 - 537 WP_234049644 type IV pilus biogenesis protein PilP -
ND440_RS17560 (ND440_17555) 71580..72845 - 1266 WP_120806788 type 4b pilus protein PilO2 -
ND440_RS17565 (ND440_17560) 72850..74490 - 1641 WP_120806787 PilN family type IVB pilus formation outer membrane protein -
ND440_RS17570 (ND440_17565) 74501..74926 - 426 WP_265317732 type IV pilus biogenesis protein PilM -
ND440_RS17575 (ND440_17570) 74923..75930 - 1008 WP_120806785 TcpQ domain-containing protein -

Host bacterium

ID   6396 GenBank   NZ_CP098702
Plasmid name   pYR10 Incompatibility group   -
Plasmid size   89273 bp Coordinate of oriT [Strand]   36693..36780 [+]
Host baterium   Yersinia ruckeri strain NVI-5089

Cargo genes

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