Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   122116
Name   oriT_IncFII(Yp) in_silico
Organism   Enterobacter hormaechei subsp. xiangfangensis strain CNCI 199
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQGED010000022 (34590..34692 [+], 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_IncFII(Yp)
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTTCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13943 GenBank   WP_022652257
Name   traI_O7046_RS20785_IncFII(Yp) insolico UniProt ID   A0A3S5I3M3
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189292.49 Da        Isoelectric Point: 6.1121

>WP_022652257.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMHT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVVPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTSEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVMLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
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)

AAA domain (AAA_30)

(967-1148)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1430-1551)


  Protein structure



No available structure.




T4CP

ID   16350 GenBank   WP_008324134
Name   traC_O7046_RS20700_IncFII(Yp) 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   16351 GenBank   WP_023307203
Name   traD_O7046_RS20780_IncFII(Yp) 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: 34042..59168

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
O7046_RS20590 (O7046_20595) 29138..29461 + 324 WP_008324183 hypothetical protein -
O7046_RS20595 (O7046_20600) 29523..29789 + 267 WP_022652251 hypothetical protein -
O7046_RS20600 (O7046_20605) 30510..30884 + 375 WP_008324180 hypothetical protein -
O7046_RS20605 (O7046_20610) 30938..31225 + 288 WP_008324178 hypothetical protein -
O7046_RS20610 (O7046_20615) 31272..31616 + 345 WP_022652252 hypothetical protein -
O7046_RS20615 (O7046_20620) 31702..31965 + 264 WP_008324174 hypothetical protein -
O7046_RS20620 (O7046_20625) 32008..32838 + 831 WP_022652253 N-6 DNA methylase -
O7046_RS20625 (O7046_20630) 33465..33995 + 531 WP_008324170 antirestriction protein -
O7046_RS20630 (O7046_20635) 34042..34518 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
O7046_RS20635 (O7046_20640) 34950..35342 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
O7046_RS20640 (O7046_20645) 35531..36220 + 690 WP_008324166 hypothetical protein -
O7046_RS20645 (O7046_20650) 36307..36531 + 225 WP_008324165 TraY domain-containing protein -
O7046_RS20650 (O7046_20655) 36589..36939 + 351 WP_008324162 type IV conjugative transfer system pilin TraA -
O7046_RS20655 (O7046_20660) 37090..37395 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
O7046_RS20660 (O7046_20665) 37410..37976 + 567 WP_008324158 type IV conjugative transfer system protein TraE traE
O7046_RS20665 (O7046_20670) 37963..38706 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
O7046_RS20670 (O7046_20675) 38693..40087 + 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
O7046_RS20675 (O7046_20680) 40109..40648 + 540 WP_008324154 type IV conjugative transfer system lipoprotein TraV traV
O7046_RS20680 (O7046_20685) 40768..40992 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
O7046_RS20685 (O7046_20690) 40996..41181 + 186 WP_022652254 hypothetical protein -
O7046_RS20690 (O7046_20695) 41165..41566 + 402 WP_008324137 hypothetical protein -
O7046_RS20695 (O7046_20700) 41556..42122 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
O7046_RS20700 (O7046_20705) 42115..44745 + 2631 WP_008324134 type IV secretion system protein TraC virb4
O7046_RS20705 (O7046_20710) 44742..45089 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
O7046_RS20710 (O7046_20715) 45089..45736 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
O7046_RS20715 (O7046_20720) 45739..46725 + 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
O7046_RS20720 (O7046_20725) 46742..47371 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
O7046_RS20725 (O7046_20730) 47368..49221 + 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
O7046_RS20730 (O7046_20735) 49253..49441 + 189 WP_008324128 conjugal transfer protein TrbE -
O7046_RS20735 (O7046_20740) 49472..50221 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
O7046_RS20740 (O7046_20745) 50238..50486 + 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
O7046_RS20745 (O7046_20750) 50476..51030 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
O7046_RS20750 (O7046_20755) 51023..51451 + 429 WP_008324122 hypothetical protein -
O7046_RS20755 (O7046_20760) 51438..52808 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
O7046_RS20760 (O7046_20765) 52808..55630 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
O7046_RS20765 (O7046_20770) 55652..56083 + 432 WP_008324118 entry exclusion protein -
O7046_RS20770 (O7046_20775) 56158..56496 + 339 WP_032072912 tetratricopeptide repeat protein -
O7046_RS20775 (O7046_20780) 56504..56833 + 330 WP_223856629 tetratricopeptide repeat protein -
O7046_RS20780 (O7046_20785) 56967..59168 + 2202 WP_023307203 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   22543 GenBank   NZ_JAQGED010000022
Plasmid name   IncFII(Yp) Incompatibility group   IncFII
Plasmid size   70218 bp Coordinate of oriT [Strand]   34590..34692 [+]
Host baterium   Enterobacter hormaechei subsp. xiangfangensis strain CNCI 199

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -