Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102860
Name   oriT_pKPGJ-1a in_silico
Organism   Klebsiella variicola strain GJ1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP017283 (92220..92276 [+], 57 nt)
oriT length   57 nt
IRs (inverted repeats)      13..20, 23..30  (GCAAAATT..AATTTTGC)
Location of nic site      39..40
Conserved sequence flanking the
  nic site    		  GGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 57 nt

>oriT_pKPGJ-1a
TAAAGTTAATCAGCAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2134 GenBank   WP_077138950
Name   traI_BBD63_RS01370_pKPGJ-1a insolico UniProt ID   _
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189412.54 Da        Isoelectric Point: 6.0094

>WP_077138950.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLFEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMTFTPGSTLIVDQGETLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGSREQAVLAGVVREALKAEKVLGEREVTIT
TLEPVWLDSRHQQVRDHYREGMVMERWSAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLKGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVGQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVQLYSAQDMQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQI
RSGALLSVPVSPGNGLQLLVSRQSYNAEKSILRHVLEGKEAVTPLMDKVPDAQLAGLTDGQQNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERPDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIERVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTSEAQAQTIVITALNADRRQVNAMIHDARQDAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVTLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGRAALRQAGLRPETTLAKFISPGRKYPQPHVALPAFDRNGRQAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAAFAGLQASRNGASLLARDMEEGVRLARENPQSGVVVRLEGEVRPWN
PGAITGGRVWADRLPDGTGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDRPAGGADVAV
RDVVRDMERIKETPASPPTLPDAPEERRRDEAVSQVVRENVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

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

(631-710)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1430-1551)

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

(573-625)

AAA domain (AAA_30)

(967-1151)


  Protein structure



No available structure.




T4CP

ID   1797 GenBank   WP_077138951
Name   traD_BBD63_RS01375_pKPGJ-1a insolico UniProt ID   _
Length   758 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 758 a.a.        Molecular weight: 85004.73 Da        Isoelectric Point: 5.1609

>WP_077138951.1 type IV conjugative transfer system coupling protein TraD [Klebsiella variicola]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQLAPAPRAADTASASASVAGAAGTGGVEPELKTKAEEA
EQLPPGISESGEVVDMAAWEAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  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.



ID   1798 GenBank   WP_077138961
Name   traC_BBD63_RS01445_pKPGJ-1a insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 98782.49 Da        Isoelectric Point: 6.0216

>WP_077138961.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNPLDSVTRTVNSLLTALKMPDASSEANDVLGQMRFPQFSRVLPYRDYDAETGLFMNEKTMGFMLEAQP
INGANETIVSSLENLMRTKLPREVPVAVHLVSSHLVGQDIEYGLRELSWTGEKADTFNAITRAYYLRAAE
EGFPLPDHLNLPLTLRNYRVYISCCVPRKRGSKASVMEMENQVKIIRASLQGAQIATRSVDADAFIRIAG
EMINHNPDALYPTERELDPLKDLNYQCVDDTFDLKVKADYMTLGLRGNGRNSTARIMNFQLTKNPELAFL
WNMADNYSNLLNPELSVSCPFILTLVLSVEDQVKAQNEANLKFMDLEKKSKTSYAKFFPGVAQEAKEWGD
LRQRLSSGQSSLVSYFLNVTLFCRDDQETALKVEQDVLNSFRKNGFELISPRFNHMRNFLVNLPFMAGGG
LFKQLRESGVLQRAESFNVANLMPVVADSPLATSGLLAPTYRNQLAFIDLFSRGMGNTNFNMAVCGTSGA
GKTGLIQPLIRSVIDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLKFNPFANVTDDTIDEMAERLRDQL
SVMASPNGNLDEVHEGLLLKAVKATWLTKKNQARIDDVVDYLMMARDSEEYSGSPTIRSRLDEMVVLLTQ
YTRNGVYGSYFNSDEPSLKDEARMVVLELGGLEDRPSLLVAVMFSLILYIENRMYRTPRSLKKLNVIDEG
WRLLDFKNNKVGAFIEKGYRTARRHTGSYITITQNIVDFDSETASSAARAAWGNSSYKIILKQSAKEFAK
YNQLYPDQYSQLQRDMIKGFGSAKDNWFSSFMLSVEHLTSWHRLFVDPLSRAMYSSDGPDFEFLQQRRRE
GLSIHEAVWELAWKKSGPEMAALERWLHAHEGKTIS

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(470-765)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 67713..92824

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BBD63_RS01375 (BBD63_26565) 67713..69989 - 2277 WP_077138951 type IV conjugative transfer system coupling protein TraD virb4
BBD63_RS01380 (BBD63_26570) 70123..70797 - 675 WP_077138952 tetratricopeptide repeat protein -
BBD63_RS01385 (BBD63_26575) 70872..71303 - 432 WP_077138953 entry exclusion protein -
BBD63_RS01390 (BBD63_26580) 71325..74147 - 2823 WP_077138954 conjugal transfer mating-pair stabilization protein TraG traG
BBD63_RS01395 (BBD63_26585) 74147..75481 - 1335 WP_230199841 conjugal transfer pilus assembly protein TraH traH
BBD63_RS01400 (BBD63_26590) 75520..76065 - 546 WP_077138955 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
BBD63_RS01405 (BBD63_26595) 76055..76303 - 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
BBD63_RS01410 (BBD63_26600) 76320..77057 - 738 WP_077138956 type-F conjugative transfer system pilin assembly protein TraF traF
BBD63_RS01415 (BBD63_26605) 77100..77288 - 189 WP_077138957 hypothetical protein -
BBD63_RS01420 (BBD63_26610) 77320..79200 - 1881 WP_077138958 type-F conjugative transfer system mating-pair stabilization protein TraN traN
BBD63_RS01425 (BBD63_26615) 79197..79826 - 630 WP_077138959 type-F conjugative transfer system pilin assembly protein TrbC trbC
BBD63_RS01430 (BBD63_26620) 79843..80829 - 987 WP_032637387 conjugal transfer pilus assembly protein TraU traU
BBD63_RS01435 (BBD63_26625) 80832..81479 - 648 WP_077138960 type-F conjugative transfer system protein TraW traW
BBD63_RS01440 (BBD63_26630) 81479..81826 - 348 WP_011201813 type-F conjugative transfer system protein TrbI -
BBD63_RS01445 (BBD63_26635) 81823..84453 - 2631 WP_077138961 type IV secretion system protein TraC virb4
BBD63_RS30960 84446..85114 - 669 WP_227516824 conjugal transfer protein TraP -
BBD63_RS30965 85104..85274 - 171 WP_227516825 Clp protease -
BBD63_RS01460 85492..85677 - 186 WP_016674194 hypothetical protein -
BBD63_RS01465 (BBD63_26650) 85681..85905 - 225 WP_016674195 TraR/DksA C4-type zinc finger protein -
BBD63_RS01470 (BBD63_26655) 86025..86564 - 540 WP_077138963 type IV conjugative transfer system lipoprotein TraV traV
BBD63_RS01475 (BBD63_26660) 86586..87980 - 1395 WP_060446827 F-type conjugal transfer pilus assembly protein TraB traB
BBD63_RS01480 (BBD63_26665) 87967..88710 - 744 WP_077138964 type-F conjugative transfer system secretin TraK traK
BBD63_RS01485 (BBD63_26670) 88697..89263 - 567 WP_077138965 type IV conjugative transfer system protein TraE traE
BBD63_RS01490 (BBD63_26675) 89278..89583 - 306 WP_071667439 type IV conjugative transfer system protein TraL traL
BBD63_RS01495 (BBD63_26680) 89734..90084 - 351 WP_077138966 type IV conjugative transfer system pilin TraA -
BBD63_RS30970 (BBD63_26685) 90150..90365 - 216 WP_321187714 TraY domain-containing protein -
BBD63_RS29565 91127..91336 - 210 WP_145952642 hypothetical protein -
BBD63_RS01505 (BBD63_26690) 91521..91916 - 396 WP_040218546 conjugal transfer relaxosome DNA-binding protein TraM -
BBD63_RS01510 (BBD63_26695) 92348..92824 + 477 WP_058673456 transglycosylase SLT domain-containing protein virB1
BBD63_RS01515 (BBD63_26700) 92870..93376 - 507 Protein_109 antirestriction protein -
BBD63_RS01520 (BBD63_26705) 93857..94687 - 831 WP_077138967 N-6 DNA methylase -
BBD63_RS01525 (BBD63_26710) 94730..94993 - 264 WP_008324174 hypothetical protein -
BBD63_RS01530 (BBD63_26715) 95079..95423 - 345 WP_077138968 hypothetical protein -
BBD63_RS01535 (BBD63_26720) 95470..95757 - 288 WP_077138969 hypothetical protein -
BBD63_RS01540 (BBD63_26725) 95818..96213 - 396 WP_077138970 ammonia monooxygenase -
BBD63_RS29570 96636..97118 - 483 WP_193791192 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   3303 GenBank   NZ_CP017283
Plasmid name   pKPGJ-1a Incompatibility group   IncFII
Plasmid size   108867 bp Coordinate of oriT [Strand]   92220..92276 [+]
Host baterium   Klebsiella variicola strain GJ1

Cargo genes

Drug resistance gene   blaNDM-9, sul1, qacE, aadA2, dfrA12, aph(3')-Ia
Virulence gene   -
Metal resistance gene   merP, merT, merE, merD
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -