Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121561
Name   oriT_pKPN692_1 in_silico
Organism   Klebsiella variicola subsp. variicola strain KPN692
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP089386 (266278..266327 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pKPN692_1
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13595 GenBank   WP_015065542
Name   traI_LUX40_RS27600_pKPN692_1 insolico UniProt ID   K7R3U7
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190318.03 Da        Isoelectric Point: 6.2890

>WP_015065542.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMSREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALAVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAAGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDTAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGGGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(576-628)

DNA helicase TraI (TraI_C)

(1432-1554)

TrwC relaxase (TrwC)

(11-283)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(634-713)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




T4CP

ID   15886 GenBank   WP_232393320
Name   t4cp2_LUX40_RS27335_pKPN692_1 insolico UniProt ID   _
Length   635 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 635 a.a.        Molecular weight: 70262.66 Da        Isoelectric Point: 6.1601

>WP_232393320.1 type IV secretory system conjugative DNA transfer family protein [Klebsiella variicola]
MIFDKLNHLLSPIANAVLAFIAFLQAHQLALALLSGVMLPFIFSAKQGGQEKPTFLQRILILLSMICFVF
GSIAPVAVWFLQRIYGREDIASPPLLTWTMALLFTVAGFILHVVLRRLISPEFDKVKRGMVKKTSMERDR
RTDVRRVKEILPVTTEYDPMDYIDLNKGIFIGLSREGEPQYIPLKEWQTQHADIIGTTGAGKGVVTGILL
YQSILADEGVFVLDPKNDEWAPHLYKKACADAGKPFVLIDLNKQEYQMNLIDGITADHLEELFVAGFSLA
EKGEAADFYRIDDRKAARTAAQFVKDNPGATIRDIYNGDYVQGIGETIKAFHGKTEELAMLNSINAPGGF
ALKEIFDKGGCCYIIGSMRNSKIITAQRMILVRLFQLAELRDRVAGNIRPIAIFKDEVKYHLSKPALEGL
GAARDKGVHILMAHQSIADLRDCPADLNGDAVVGAVVENCKFKLVYKLQDPDTAEWIARMSGTILVDDES
RKVTTTAVLTEKVDNERMLRQAESYYIDSNMLQNLPKFVSYIFSQNALAFPSLISPLKVKKAPLELFTLP
PVAVATVAEVKPVLDLDFDTTAPAVPAPGIIPVSATTTKKPSATPIPTPPVQPDEEWLMASQPAPNDEIH
SLLDL

  Protein domains


Predicted by InterproScan.

TraM recognition site of TraD and TraG (TraG-D_C)

(402-496)

  Protein structure



No available structure.



ID   15887 GenBank   WP_232393334
Name   t4cp2_LUX40_RS27410_pKPN692_1 insolico UniProt ID   _
Length   916 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 916 a.a.        Molecular weight: 105043.40 Da        Isoelectric Point: 7.3924

>WP_232393334.1 VirB3 family type IV secretion system protein [Klebsiella variicola]
MTILNKALTRPAALWGVPLVPLLFTLCIITLAAVWSRFYWLLLLLIPAFIELRRLAKEDIHFFDLKLLAF
KTRGNRAATRHFGTKALVANQYDAIDVTEFIKHMRLNESIPLSRYLPWSSHLHEQVVKNKKGDFVSTWEI
GGTIFECEDEHYLATLDMQLNNVIRSFEGLPVTFYTHLVSDEFTDTLECESGIPFSDEIARLFYASRDGK
PFYQRRLFFTVCFNPHTGIERATMKQKSLGERKTLLDNALQVMQEHRQAIGSALSRYAARPLGTYEENGH
VFSSQLAFYNFLITGRWQKVRVTRTPFYDVLGGTDIFPSTDIGQVSHTDGQSYFRGLEIKDYSTETITGL
YDSLLYARCRYVFTQSYTCMGKDEARGCIRTIEKRLKSAEDDAISQQEDLKVARDMLQSGIISFGKYHQT
LIVSAPTSEQVIRDTNTLADTLKDLGFIMTLSRESLSAAYLAQLPGVYHLRPRLVPVSSLNYAEMVSFHN
FHPHKRDGNAWGEAIAVVPTPSGGCQYVNLHNSQADVDEFSEKPPGNTMLLGSTGTGKSTLLMMFQHLMQ
KYRRPESFAPGATKKRFTSVVFDKDRSAEMSIRLQGGSYFRFRSGEKTGLNPFALAPTKRNRNFLKKLMR
MICTRDGKPLDPRDEERLSEAVDTIMLDYPPELRRNGITRMLEVLHEAPTKDARMNGLRIRLQQWAQGGE
FGWVFDNDVDTFDIDNIDNFGIDGTEFLDDKDVRSPLTFYLLYRVTSLLDGRRLVIFMDEFWKWLQDPEF
SKFALDMLKVIRKLNGIFFPATQSPEEMCKHEISAAIIEQCSTRIFMANQQAKEYDYVDMLRVPKAVYDI
VTTLDPYARQMVIMKSPLRRGDVRPYIAQITLDLSGLGRYTKLLSASADNLKIFDELWQEGMQPEDWKDE
MLRRAV

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(537-821)

Type IV secretory pathway, VirB3-like protein (VirB3)

(4-81)

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(272-473)

  Protein structure



No available structure.



ID   15888 GenBank   WP_015065541
Name   traD_LUX40_RS27605_pKPN692_1 insolico UniProt ID   _
Length   770 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 770 a.a.        Molecular weight: 86025.00 Da        Isoelectric Point: 5.0577

>WP_015065541.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTIKRPAAEPSVRTTEPSVLRVTTVPLIKPKAAAAAAAASTASSSGAPATAAGGTQ
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 184847..201307

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LUX40_RS27300 (LUX40_27300) 180584..180964 - 381 WP_232393314 S24 family peptidase -
LUX40_RS27305 (LUX40_27305) 180966..181205 - 240 WP_232393315 DNA polymerase V -
LUX40_RS27310 (LUX40_27310) 181652..182623 + 972 WP_232393316 ArdC family protein -
LUX40_RS27315 (LUX40_27315) 182756..182971 + 216 WP_232393317 hypothetical protein -
LUX40_RS27320 (LUX40_27320) 183103..183216 + 114 Protein_196 hypothetical protein -
LUX40_RS27325 (LUX40_27325) 183566..184093 - 528 WP_232393318 phospholipase D family protein -
LUX40_RS27330 (LUX40_27330) 184086..184832 - 747 WP_232393319 MobC family replication-relaxation protein -
LUX40_RS27335 (LUX40_27335) 184847..186754 - 1908 WP_232393320 type IV secretory system conjugative DNA transfer family protein virb4
LUX40_RS27340 (LUX40_27340) 187462..187854 - 393 WP_232393321 H-NS family nucleoid-associated regulatory protein -
LUX40_RS27345 (LUX40_27345) 187851..190052 - 2202 WP_232393322 type IA DNA topoisomerase -
LUX40_RS27350 (LUX40_27350) 190049..190357 - 309 WP_232393323 hypothetical protein -
LUX40_RS27355 (LUX40_27355) 190333..190668 - 336 WP_232393324 hypothetical protein -
LUX40_RS27360 (LUX40_27360) 190695..191012 - 318 WP_232393325 TrbM/KikA/MpfK family conjugal transfer protein -
LUX40_RS27365 (LUX40_27365) 191103..191504 - 402 WP_232393326 cag pathogenicity island Cag12 family protein -
LUX40_RS27370 (LUX40_27370) 191491..192540 - 1050 WP_232393327 P-type DNA transfer ATPase VirB11 virB11
LUX40_RS27375 (LUX40_27375) 192544..193740 - 1197 WP_232393328 VirB10/TraB/TrbI family type IV secretion system protein -
LUX40_RS27380 (LUX40_27380) 193737..194630 - 894 WP_232393329 P-type conjugative transfer protein VirB9 virB9
LUX40_RS27385 (LUX40_27385) 194623..195309 - 687 WP_232393330 virB8 family protein virB8
LUX40_RS27390 (LUX40_27390) 195302..195442 - 141 WP_000873539 hypothetical protein -
LUX40_RS27395 (LUX40_27395) 195519..196526 - 1008 WP_232393331 type IV secretion system protein virB6
LUX40_RS27400 (LUX40_27400) 196544..196828 - 285 WP_232393332 EexN family lipoprotein -
LUX40_RS27405 (LUX40_27405) 196840..197556 - 717 WP_232393333 type IV secretion system protein -
LUX40_RS27410 (LUX40_27410) 197575..200325 - 2751 WP_232393334 VirB3 family type IV secretion system protein virb4
LUX40_RS27415 (LUX40_27415) 200335..200634 - 300 WP_232393335 TrbC/VirB2 family protein virB2
LUX40_RS27420 (LUX40_27420) 200645..201307 - 663 WP_232393336 lytic transglycosylase domain-containing protein virB1
LUX40_RS27425 (LUX40_27425) 201310..201525 - 216 WP_232393337 hypothetical protein -
LUX40_RS27430 (LUX40_27430) 201518..201826 - 309 WP_232393338 hypothetical protein -
LUX40_RS27435 (LUX40_27435) 202135..203049 + 915 WP_332461567 helix-turn-helix domain-containing protein -
LUX40_RS27440 (LUX40_27440) 203053..204036 + 984 WP_232393340 glycosyltransferase family 9 protein -
LUX40_RS27445 (LUX40_27445) 204029..204517 + 489 WP_232393341 molybdopterin-dependent oxidoreductase -
LUX40_RS27450 (LUX40_27450) 204514..206232 + 1719 WP_232393342 hybrid sensor histidine kinase/response regulator -

Region 2: 236871..266885

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LUX40_RS27605 (LUX40_27605) 236871..239183 - 2313 WP_015065541 type IV conjugative transfer system coupling protein TraD virb4
LUX40_RS27610 (LUX40_27610) 239312..240001 - 690 WP_015065540 hypothetical protein -
LUX40_RS27615 (LUX40_27615) 240193..240924 - 732 WP_032329926 conjugal transfer complement resistance protein TraT -
LUX40_RS27620 (LUX40_27620) 241233..241757 - 525 WP_015065538 hypothetical protein -
LUX40_RS27625 (LUX40_27625) 241768..244611 - 2844 WP_023157999 conjugal transfer mating-pair stabilization protein TraG traG
LUX40_RS27630 (LUX40_27630) 244611..245990 - 1380 WP_023158000 conjugal transfer pilus assembly protein TraH traH
LUX40_RS27635 (LUX40_27635) 245968..246411 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
LUX40_RS27640 (LUX40_27640) 246457..247014 - 558 WP_023158002 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LUX40_RS27645 (LUX40_27645) 246986..247225 - 240 WP_023158003 type-F conjugative transfer system pilin chaperone TraQ -
LUX40_RS27650 (LUX40_27650) 247236..247988 - 753 WP_015065535 type-F conjugative transfer system pilin assembly protein TraF traF
LUX40_RS27655 (LUX40_27655) 248009..248335 - 327 WP_015065534 hypothetical protein -
LUX40_RS27660 (LUX40_27660) 248348..248596 - 249 WP_004152675 hypothetical protein -
LUX40_RS27665 (LUX40_27665) 248574..248828 - 255 WP_015065558 conjugal transfer protein TrbE -
LUX40_RS27670 (LUX40_27670) 248860..250815 - 1956 WP_015065533 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LUX40_RS27675 (LUX40_27675) 250874..251521 - 648 WP_015632510 type-F conjugative transfer system pilin assembly protein TrbC trbC
LUX40_RS27680 (LUX40_27680) 251600..251776 - 177 WP_162866177 hypothetical protein -
LUX40_RS27685 (LUX40_27685) 251797..252786 - 990 WP_015632509 conjugal transfer pilus assembly protein TraU traU
LUX40_RS27690 (LUX40_27690) 252783..253184 - 402 WP_023158005 hypothetical protein -
LUX40_RS27695 (LUX40_27695) 253219..253854 - 636 WP_023158006 type-F conjugative transfer system protein TraW traW
LUX40_RS27700 (LUX40_27700) 253854..254243 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
LUX40_RS27705 (LUX40_27705) 254243..256882 - 2640 WP_023158007 type IV secretion system protein TraC virb4
LUX40_RS27710 (LUX40_27710) 256954..257352 - 399 WP_023158008 hypothetical protein -
LUX40_RS27715 (LUX40_27715) 257360..257749 - 390 WP_023158009 hypothetical protein -
LUX40_RS27720 (LUX40_27720) 257792..258196 - 405 WP_016831042 hypothetical protein -
LUX40_RS27725 (LUX40_27725) 258263..258574 - 312 WP_014386200 hypothetical protein -
LUX40_RS27730 (LUX40_27730) 258575..258793 - 219 WP_014386199 hypothetical protein -
LUX40_RS27735 (LUX40_27735) 258817..259106 - 290 Protein_281 hypothetical protein -
LUX40_RS27740 (LUX40_27740) 259111..259521 - 411 WP_016831039 hypothetical protein -
LUX40_RS27745 (LUX40_27745) 259653..260237 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
LUX40_RS27750 (LUX40_27750) 260260..260856 - 597 Protein_284 conjugal transfer pilus-stabilizing protein TraP -
LUX40_RS27755 (LUX40_27755) 260849..262273 - 1425 WP_023158013 F-type conjugal transfer pilus assembly protein TraB traB
LUX40_RS27760 (LUX40_27760) 262273..263013 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
LUX40_RS27765 (LUX40_27765) 263000..263566 - 567 WP_016831035 type IV conjugative transfer system protein TraE traE
LUX40_RS27770 (LUX40_27770) 263586..263891 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
LUX40_RS27775 (LUX40_27775) 263905..264273 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
LUX40_RS27780 (LUX40_27780) 264335..264541 - 207 WP_171773970 TraY domain-containing protein -
LUX40_RS27785 (LUX40_27785) 264674..265393 - 720 WP_016831034 conjugal transfer protein TrbJ -
LUX40_RS27790 (LUX40_27790) 265593..266009 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
LUX40_RS27795 (LUX40_27795) 266400..266885 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
LUX40_RS27800 (LUX40_27800) 266918..267247 - 330 WP_011977736 DUF5983 family protein -
LUX40_RS27805 (LUX40_27805) 267280..268101 - 822 WP_004182076 DUF932 domain-containing protein -
LUX40_RS27810 (LUX40_27810) 268929..269492 - 564 WP_004182054 methyltransferase -
LUX40_RS27815 (LUX40_27815) 269540..270895 - 1356 WP_004182052 DUF3560 domain-containing protein -
LUX40_RS27820 (LUX40_27820) 270947..271177 - 231 WP_001568051 hypothetical protein -
LUX40_RS27825 (LUX40_27825) 271269..271496 - 228 WP_004182050 hypothetical protein -

Host bacterium

ID   21988 GenBank   NZ_CP089386
Plasmid name   pKPN692_1 Incompatibility group   IncFIB
Plasmid size   289376 bp Coordinate of oriT [Strand]   266278..266327 [+]
Host baterium   Klebsiella variicola subsp. variicola strain KPN692

Cargo genes

Drug resistance gene   sul2, aph(3'')-Ib, aph(6)-Id, blaTEM-1B, blaCTX-M-15, dfrA14, qnrB1, tet(A), aac(6')-Ib-cr
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, arsH, arsC, arsB, arsA, arsD, arsR, fecD, fecE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -