Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105363
Name   oriT_p5512.56-3-VIM1 in_silico
Organism   Klebsiella grimontii strain 5512.56
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP067384 (53788..53890 [+], 103 nt)
oriT length   103 nt
IRs (inverted repeats)      89..94, 96..101  (AAATAA..TTATTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 103 nt

>oriT_p5512.56-3-VIM1
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTTCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3661 GenBank   WP_209573204
Name   traI_JJJ11_RS00500_p5512.56-3-VIM1 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: 188934.05 Da        Isoelectric Point: 6.0680

>WP_209573204.1 conjugative transfer relaxase/helicase TraI [Klebsiella grimontii]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQCMAEWMQT
LKATGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLASTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTRVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGAVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVGQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQVIEKEADRQI
RSGALLSVPVSPGNGLQLLVSRQSYNAEKSILRHVLEGKEAVTPLMDKVPDAQLAGLTDGQQNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERPDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTPEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVTLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
DRGVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKFISPGRKYPQPHVALPAFDRNGRQAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLAGEARPWN
PGAITGGRVWADSLPDSTGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDGPAGGADVAV
RDVVRDMERIKETPASPLTLPDAPEERRRDEAVSQVVRENVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1430-1551)

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

(631-710)

TrwC relaxase (TrwC)

(10-283)

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

(573-625)

AAA domain (AAA_30)

(967-1150)


  Protein structure



No available structure.




T4CP

ID   3633 GenBank   WP_008324134
Name   traC_JJJ11_RS00420_p5512.56-3-VIM1 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   3634 GenBank   WP_023307203
Name   traD_JJJ11_RS00495_p5512.56-3-VIM1 insolico UniProt ID   _
Length   733 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 733 a.a.        Molecular weight: 82212.80 Da        Isoelectric Point: 5.1609

>WP_023307203.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENVGQPQQPQQPQQ
PQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGEVVDMAAWEAWQAE
QDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  Protein domains


Predicted by InterproScan.

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

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 53240..78365

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JJJ11_RS00310 (JJJ11_00310) 48337..48660 + 324 WP_008324183 hypothetical protein -
JJJ11_RS00315 (JJJ11_00315) 48722..49081 + 360 WP_008324181 hypothetical protein -
JJJ11_RS00320 (JJJ11_00320) 49708..50082 + 375 WP_008324180 hypothetical protein -
JJJ11_RS00325 (JJJ11_00325) 50136..50423 + 288 WP_008324178 hypothetical protein -
JJJ11_RS00330 (JJJ11_00330) 50470..50814 + 345 WP_008324177 hypothetical protein -
JJJ11_RS00335 (JJJ11_00335) 50900..51163 + 264 WP_008324174 hypothetical protein -
JJJ11_RS00340 (JJJ11_00340) 51206..52036 + 831 WP_008324171 N-6 DNA methylase -
JJJ11_RS00345 (JJJ11_00345) 52663..53193 + 531 WP_008324170 antirestriction protein -
JJJ11_RS00350 (JJJ11_00350) 53240..53716 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
JJJ11_RS00355 (JJJ11_00355) 54148..54540 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
JJJ11_RS00360 (JJJ11_00360) 54729..55418 + 690 WP_008324166 hypothetical protein -
JJJ11_RS00365 (JJJ11_00365) 55505..55729 + 225 WP_008324165 TraY domain-containing protein -
JJJ11_RS00370 (JJJ11_00370) 55787..56137 + 351 WP_008324162 type IV conjugative transfer system pilin TraA -
JJJ11_RS00375 (JJJ11_00375) 56288..56593 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
JJJ11_RS00380 (JJJ11_00380) 56608..57174 + 567 WP_008324158 type IV conjugative transfer system protein TraE traE
JJJ11_RS00385 (JJJ11_00385) 57161..57904 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
JJJ11_RS00390 (JJJ11_00390) 57891..59285 + 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
JJJ11_RS00395 (JJJ11_00395) 59307..59846 + 540 WP_008324154 type IV conjugative transfer system lipoprotein TraV traV
JJJ11_RS00400 (JJJ11_00400) 59966..60190 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
JJJ11_RS00405 (JJJ11_00405) 60194..60379 + 186 WP_022652254 hypothetical protein -
JJJ11_RS29500 60597..60764 + 168 WP_223274120 Clp protease -
JJJ11_RS00415 (JJJ11_00415) 60754..61320 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
JJJ11_RS00420 (JJJ11_00420) 61313..63943 + 2631 WP_008324134 type IV secretion system protein TraC virb4
JJJ11_RS00425 (JJJ11_00425) 63940..64287 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
JJJ11_RS00430 (JJJ11_00430) 64287..64934 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
JJJ11_RS00435 (JJJ11_00435) 64937..65923 + 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
JJJ11_RS00440 (JJJ11_00440) 65940..66569 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
JJJ11_RS00445 (JJJ11_00445) 66566..68419 + 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
JJJ11_RS00450 (JJJ11_00450) 68451..68639 + 189 WP_008324128 conjugal transfer protein TrbE -
JJJ11_RS00455 (JJJ11_00455) 68670..69419 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
JJJ11_RS00460 (JJJ11_00460) 69436..69684 + 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
JJJ11_RS00465 (JJJ11_00465) 69674..70228 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
JJJ11_RS00470 (JJJ11_00470) 70221..70649 + 429 WP_008324122 hypothetical protein -
JJJ11_RS00475 (JJJ11_00475) 70636..72006 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
JJJ11_RS00480 (JJJ11_00480) 72006..74828 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
JJJ11_RS00485 (JJJ11_00485) 74850..75281 + 432 WP_008324118 entry exclusion protein -
JJJ11_RS00490 (JJJ11_00490) 75356..76030 + 675 WP_008324909 tetratricopeptide repeat protein -
JJJ11_RS00495 (JJJ11_00495) 76164..78365 + 2202 WP_023307203 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   5801 GenBank   NZ_CP067384
Plasmid name   p5512.56-3-VIM1 Incompatibility group   IncFII
Plasmid size   90605 bp Coordinate of oriT [Strand]   53788..53890 [+]
Host baterium   Klebsiella grimontii strain 5512.56

Cargo genes

Drug resistance gene   blaVIM-1, aac(6')-Ib, cmlA1, blaOXA-9, qacE, sul1
Virulence gene   -
Metal resistance gene   merE, merD, merA, merC, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -