Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118495
Name   oriT_pNDM_1TM in_silico
Organism   Klebsiella variicola strain 1TM
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CM008917 (26417..26465 [-], 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_1TM
AATCAGCAAAACTTTAATTTTGCGTGGGGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11741 GenBank   WP_101415845
Name   traI_CS912_RS01550_pNDM_1TM 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: 189299.44 Da        Isoelectric Point: 6.0099

>WP_101415845.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGDDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGAGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
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)

AAA domain (AAA_30)

(967-1150)

DNA helicase TraI (TraI_C)

(1430-1551)


  Protein structure



No available structure.




T4CP

ID   13752 GenBank   WP_016479979
Name   traD_CS912_RS01545_pNDM_1TM 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: 29228..51013

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CS912_RS01400 (CS912_01395) 25284..25827 + 544 Protein_36 antirestriction protein -
CS912_RS01405 (CS912_01400) 25850..26272 - 423 WP_020315406 transglycosylase SLT domain-containing protein -
CS912_RS01410 (CS912_01405) 26776..27169 + 394 Protein_38 conjugal transfer relaxosome DNA-binding protein TraM -
CS912_RS01415 (CS912_01410) 27358..28047 + 690 WP_008324166 hypothetical protein -
CS912_RS01420 (CS912_01415) 28134..28355 + 222 WP_101415843 TraY domain-containing protein -
CS912_RS01425 (CS912_01420) 28413..28759 + 347 Protein_41 type IV conjugative transfer system pilin TraA -
CS912_RS01430 (CS912_01425) 28910..29213 + 304 Protein_42 type IV conjugative transfer system protein TraL -
CS912_RS01435 (CS912_01430) 29228..29794 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
CS912_RS01440 (CS912_01435) 29781..30520 + 740 Protein_44 type-F conjugative transfer system secretin TraK -
CS912_RS01445 (CS912_01440) 30507..31901 + 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
CS912_RS01450 (CS912_01445) 31923..32462 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
CS912_RS01455 (CS912_01450) 32582..32806 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
CS912_RS01460 (CS912_01455) 32810..32995 + 186 WP_008324139 hypothetical protein -
CS912_RS01465 (CS912_01460) 32979..33257 + 279 WP_101415844 hypothetical protein -
CS912_RS01470 (CS912_01465) 33367..33933 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
CS912_RS01475 (CS912_01470) 33926..36536 + 2611 Protein_51 type IV secretion system protein TraC -
CS912_RS31180 36567..36893 + 327 WP_265736173 type-F conjugative transfer system protein TrbI -
CS912_RS01480 (CS912_01475) 36893..37540 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
CS912_RS01485 (CS912_01480) 37589..38525 + 937 Protein_54 conjugal transfer pilus assembly protein TraU -
CS912_RS01490 (CS912_01485) 38542..39171 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
CS912_RS01495 (CS912_01490) 39168..41021 + 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CS912_RS01500 (CS912_01495) 41053..41241 + 189 WP_008324128 conjugal transfer protein TrbE -
CS912_RS01505 (CS912_01500) 41272..42021 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
CS912_RS01510 (CS912_01505) 42038..42286 + 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
CS912_RS01515 (CS912_01510) 42276..42830 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CS912_RS01520 (CS912_01515) 42823..43251 + 429 WP_008324122 hypothetical protein -
CS912_RS01525 (CS912_01520) 43238..44608 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
CS912_RS01530 (CS912_01525) 44608..47430 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
CS912_RS01535 (CS912_01530) 47452..47883 + 432 WP_008324118 entry exclusion protein -
CS912_RS30890 47958..48296 + 339 WP_032072912 tetratricopeptide repeat protein -
CS912_RS30895 48304..48633 + 330 WP_227649319 tetratricopeptide repeat protein -
CS912_RS01545 (CS912_01540) 48767..51013 + 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   18928 GenBank   NZ_CM008917
Plasmid name   pNDM_1TM Incompatibility group   IncFII
Plasmid size   120406 bp Coordinate of oriT [Strand]   26417..26465 [-]
Host baterium   Klebsiella variicola strain 1TM

Cargo genes

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