Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115605
Name   oriT_pK92-NDM in_silico
Organism   Klebsiella michiganensis strain K92
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OL828744 (77791..77893 [+], 103 nt)
oriT length   103 nt
IRs (inverted repeats)      89..94, 96..101  (AAATAA..TTATTT)
 28..33, 40..45  (GCAAAA..TTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 103 nt

>oriT_pK92-NDM
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9991 GenBank   WP_016479978
Name   traI_N1J51_RS00620_pK92-NDM insolico UniProt ID   A0A0G3B767
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189285.41 Da        Isoelectric Point: 6.0099

>WP_016479978.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGDDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTSEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVMLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWAAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKYISPGRKYPQPHVALPAFDRNGRKAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLEGEARPWN
PGAITGGRVWADGLPDATGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDRPAGGADVAV
RDVVRDMDRIKETPASPLTLPDAPEERRRDEAVSQVVRESVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

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

(631-710)

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

(573-625)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1430-1551)

AAA domain (AAA_30)

(967-1150)


  Protein structure



No available structure.




T4CP

ID   11660 GenBank   WP_008324134
Name   traC_N1J51_RS00535_pK92-NDM 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: 98841.51 Da        Isoelectric Point: 5.7676

>WP_008324134.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacterales]
MSNPLDSVTRTVNSLLTALKMPDASSEANDVLGQMRFPQFSRVLPYRDYDAETGLFMNEKTMGFMLEAQP
INGANETIVSSLENLMRTKLPREVPVAVHLVSSHLVGQDIEYGLRELSWTGEKADTFNAITRAYYLRAAE
EGFPLPDHLNLPLTLRNYRVYISCCVPRKRGSKASVMEMENQVKIIRASLQGAQIATRSVDADAFIRIAG
EMINHNPDALYPTERELDPLKDLNYQCVDDTFDLKVKADYMTLGLRGNGRNSTARIMNFQLTKNPELAFL
WNMADNYSNLLNPELSVSCPFILTLVLSVEDQVKAQNEANLKFMDLEKKSKTSYAKFFPGVAQEAKEWGD
LRQRLSSGQSSLVSYFLNVTLFCRDDQETALKVEQDVLNSFRKNGFELISPRFNHMRNFLVNLPFMAGGG
LFKQLRESGVLQRAESFNVANLMPVVADSPLATSGLLAPTYRNQLAFIDLFSRGMGNTNFNMAVCGTSGA
GKTGLIQPLIRSVIDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLKFNPFANVTDDTIDEMAERLRDQL
SVMASPNGNLDEVHEGLLLKAVKATWLTKKNQARIDDVVDYLMMARDSEEYSGSPTIRSRLDEMVVLLTQ
YTRDGVYGSYFNSDEPSLKDEARMVVLELGGLEDRPSLLVAVMFSLILYIENRMYRTPRSLKKLNVIDEG
WRLLDFKNNKVGAFIEKGYRTARRHTGSYITITQNIVDFDSETASSAARAAWGNSSYKIILKQSAKEFAK
YNQLYPDQYSQLQRDMIKGFGSAKDNWFSSFMLSVEHLTSWHRLFVDPLSRAMYSSDGPDFEFLQQRRRE
GLSIHEAVWELAWKKSGPEMAALERWLHEHEGKTIS

  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.



ID   11661 GenBank   WP_016479979
Name   traD_N1J51_RS00615_pK92-NDM insolico UniProt ID   _
Length   748 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 748 a.a.        Molecular weight: 83951.64 Da        Isoelectric Point: 5.1609

>WP_016479979.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISES
GEVVDMAAWEAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  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: 77243..102414

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
N1J51_RS00425 72340..72663 + 324 WP_008324183 hypothetical protein -
N1J51_RS00430 72725..73084 + 360 WP_015493069 hypothetical protein -
N1J51_RS00435 73711..74085 + 375 WP_008324180 hypothetical protein -
N1J51_RS00440 74139..74426 + 288 WP_008324178 hypothetical protein -
N1J51_RS00445 74473..74817 + 345 WP_008324177 hypothetical protein -
N1J51_RS00450 74903..75166 + 264 WP_008324174 hypothetical protein -
N1J51_RS00455 75209..76039 + 831 WP_008324171 N-6 DNA methylase -
N1J51_RS00460 76666..77196 + 531 WP_008324170 antirestriction protein -
N1J51_RS00465 77243..77719 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
N1J51_RS00470 78151..78543 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
N1J51_RS00475 78732..79421 + 690 WP_008324166 hypothetical protein -
N1J51_RS00480 79508..79732 + 225 WP_008324165 TraY domain-containing protein -
N1J51_RS00485 79790..80140 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
N1J51_RS00490 80291..80596 + 306 WP_016479987 type IV conjugative transfer system protein TraL traL
N1J51_RS00495 80611..81177 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
N1J51_RS00500 81164..81907 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
N1J51_RS00505 81894..83288 + 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
N1J51_RS00510 83310..83849 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
N1J51_RS00515 83969..84193 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
N1J51_RS00520 84197..84382 + 186 WP_008324139 hypothetical protein -
N1J51_RS00525 84366..84767 + 402 WP_016479985 hypothetical protein -
N1J51_RS00530 84757..85323 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
N1J51_RS00535 85316..87946 + 2631 WP_008324134 type IV secretion system protein TraC virb4
N1J51_RS00540 87943..88290 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
N1J51_RS00545 88290..88937 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
N1J51_RS00550 88940..89926 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
N1J51_RS00555 89943..90572 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
N1J51_RS00560 90569..92422 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
N1J51_RS00565 92454..92642 + 189 WP_008324128 conjugal transfer protein TrbE -
N1J51_RS00570 92673..93422 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
N1J51_RS00575 93439..93687 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
N1J51_RS00580 93677..94231 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
N1J51_RS00585 94224..94652 + 429 WP_008324122 hypothetical protein -
N1J51_RS00590 94639..96009 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
N1J51_RS00595 96009..98831 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
N1J51_RS00600 98853..99284 + 432 WP_008324118 entry exclusion protein -
N1J51_RS00605 99377..99697 + 321 WP_227543090 tetratricopeptide repeat protein -
N1J51_RS00610 99705..100034 + 330 WP_223856629 tetratricopeptide repeat protein -
N1J51_RS00615 100168..102414 + 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   16038 GenBank   NZ_OL828744
Plasmid name   pK92-NDM Incompatibility group   IncFII
Plasmid size   110786 bp Coordinate of oriT [Strand]   77791..77893 [+]
Host baterium   Klebsiella michiganensis strain K92

Cargo genes

Drug resistance gene   sul1, rmtC, blaNDM-1
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -