Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118496
Name   oriT_pNDM_6TM in_silico
Organism   Klebsiella variicola strain 6TM
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CM008891 (25548..25596 [-], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..11, 18..23  (GCAAAA..TTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  GGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pNDM_6TM
AATCAGCAAAACTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11742 GenBank   WP_016479978
Name   traI_CS911_RS01555_pNDM_6TM 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   13753 GenBank   WP_101429066
Name   traD_CS911_RS01550_pNDM_6TM insolico UniProt ID   _
Length   745 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 745 a.a.        Molecular weight: 83598.26 Da        Isoelectric Point: 5.1609

>WP_101429066.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGEV
VDMAAWEAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  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: 28047..50150

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CS911_RS01400 (CS911_01595) 24416..24958 + 543 WP_020804853 antirestriction protein -
CS911_RS01405 (CS911_01600) 24981..25403 - 423 WP_020315406 transglycosylase SLT domain-containing protein -
CS911_RS01410 (CS911_01605) 25907..26299 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
CS911_RS01415 (CS911_01610) 26488..27177 + 690 WP_008324166 hypothetical protein -
CS911_RS01420 (CS911_01615) 27264..27488 + 225 WP_008324165 TraY domain-containing protein -
CS911_RS01425 (CS911_01620) 27546..27896 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
CS911_RS01430 (CS911_01625) 28047..28352 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
CS911_RS01435 (CS911_01630) 28367..28933 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
CS911_RS01440 (CS911_01635) 28920..29663 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
CS911_RS01445 (CS911_01640) 29650..31042 + 1393 Protein_44 F-type conjugal transfer pilus assembly protein TraB -
CS911_RS01450 (CS911_01645) 31064..31602 + 539 Protein_45 type IV conjugative transfer system lipoprotein TraV -
CS911_RS01455 (CS911_01650) 31722..31946 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
CS911_RS01460 (CS911_01655) 31950..32135 + 186 WP_008324139 hypothetical protein -
CS911_RS01470 (CS911_01665) 32351..33073 + 723 WP_228158566 conjugal transfer pilus-stabilizing protein TraP -
CS911_RS01475 (CS911_01670) 33066..35694 + 2629 Protein_49 type IV secretion system protein TraC -
CS911_RS01480 (CS911_01675) 35691..36059 + 369 WP_101473096 type-F conjugative transfer system protein TrbI -
CS911_RS01485 (CS911_01680) 36077..36682 + 606 WP_322869388 type-F conjugative transfer system protein TraW traW
CS911_RS01490 (CS911_01685) 36685..37671 + 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
CS911_RS01495 (CS911_01690) 37688..38317 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
CS911_RS01500 (CS911_01695) 38314..40167 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CS911_RS01505 (CS911_01700) 40199..40387 + 189 WP_008324128 conjugal transfer protein TrbE -
CS911_RS01510 (CS911_01705) 40418..41167 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
CS911_RS01515 (CS911_01710) 41184..41432 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
CS911_RS01520 (CS911_01715) 41422..41976 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CS911_RS01525 (CS911_01720) 41969..42397 + 429 WP_008324122 hypothetical protein -
CS911_RS01530 (CS911_01725) 42384..43754 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
CS911_RS01535 (CS911_01730) 43754..46576 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
CS911_RS01540 (CS911_01735) 46598..47029 + 432 WP_008324118 entry exclusion protein -
CS911_RS31025 47104..47442 + 339 WP_032072912 tetratricopeptide repeat protein -
CS911_RS31030 47450..47779 + 330 WP_227649319 tetratricopeptide repeat protein -
CS911_RS01550 (CS911_01745) 47913..50150 + 2238 WP_101429066 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   18929 GenBank   NZ_CM008891
Plasmid name   pNDM_6TM Incompatibility group   IncFII
Plasmid size   120078 bp Coordinate of oriT [Strand]   25548..25596 [-]
Host baterium   Klebsiella variicola strain 6TM

Cargo genes

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