Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101109
Name   oriT_IncFII(Yp) in_silico
Organism   Enterobacter hormaechei subsp. xiangfangensis strain PLCR15
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAGQAU010000019 (18976..19078 [+], 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   1128 GenBank   WP_022652257
Name   traI_KBU53_RS20495_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   688 GenBank   WP_008324134
Name   traC_KBU53_RS20415_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   689 GenBank   WP_023307203
Name   traD_KBU53_RS20490_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: 18428..43553

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KBU53_RS20305 (KBU53_20270) 13524..13847 + 324 WP_008324183 hypothetical protein -
KBU53_RS20310 (KBU53_20275) 13909..14175 + 267 WP_022652251 hypothetical protein -
KBU53_RS20315 (KBU53_20280) 14896..15270 + 375 WP_008324180 hypothetical protein -
KBU53_RS20320 (KBU53_20285) 15324..15611 + 288 WP_008324178 hypothetical protein -
KBU53_RS20325 (KBU53_20290) 15658..16002 + 345 WP_022652252 hypothetical protein -
KBU53_RS20330 (KBU53_20295) 16088..16351 + 264 WP_008324174 hypothetical protein -
KBU53_RS20335 (KBU53_20300) 16394..17224 + 831 WP_022652253 N-6 DNA methylase -
KBU53_RS20340 (KBU53_20305) 17851..18381 + 531 WP_008324170 antirestriction protein -
KBU53_RS20345 (KBU53_20310) 18428..18904 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
KBU53_RS20350 (KBU53_20315) 19336..19728 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
KBU53_RS20355 (KBU53_20320) 19917..20606 + 690 WP_008324166 hypothetical protein -
KBU53_RS20360 (KBU53_20325) 20693..20917 + 225 WP_008324165 TraY domain-containing protein -
KBU53_RS20365 (KBU53_20330) 20975..21325 + 351 WP_008324162 type IV conjugative transfer system pilin TraA -
KBU53_RS20370 (KBU53_20335) 21476..21781 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
KBU53_RS20375 (KBU53_20340) 21796..22362 + 567 WP_008324158 type IV conjugative transfer system protein TraE traE
KBU53_RS20380 (KBU53_20345) 22349..23092 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
KBU53_RS20385 (KBU53_20350) 23079..24473 + 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
KBU53_RS20390 (KBU53_20355) 24495..25034 + 540 WP_008324154 type IV conjugative transfer system lipoprotein TraV traV
KBU53_RS20395 (KBU53_20360) 25154..25378 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
KBU53_RS20400 (KBU53_20365) 25382..25567 + 186 WP_022652254 hypothetical protein -
KBU53_RS20405 (KBU53_20370) 25551..25952 + 402 WP_008324137 hypothetical protein -
KBU53_RS20410 (KBU53_20375) 25942..26508 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
KBU53_RS20415 (KBU53_20380) 26501..29131 + 2631 WP_008324134 type IV secretion system protein TraC virb4
KBU53_RS20420 (KBU53_20385) 29128..29475 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
KBU53_RS20425 (KBU53_20390) 29475..30122 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
KBU53_RS20430 (KBU53_20395) 30125..31111 + 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
KBU53_RS20435 (KBU53_20400) 31128..31757 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
KBU53_RS20440 (KBU53_20405) 31754..33607 + 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
KBU53_RS20445 (KBU53_20410) 33639..33827 + 189 WP_008324128 conjugal transfer protein TrbE -
KBU53_RS20450 (KBU53_20415) 33858..34607 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
KBU53_RS20455 (KBU53_20420) 34624..34872 + 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
KBU53_RS20460 (KBU53_20425) 34862..35416 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
KBU53_RS20465 (KBU53_20430) 35409..35837 + 429 WP_008324122 hypothetical protein -
KBU53_RS20470 (KBU53_20435) 35824..37194 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
KBU53_RS20475 (KBU53_20440) 37194..40016 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
KBU53_RS20480 (KBU53_20445) 40038..40469 + 432 WP_008324118 entry exclusion protein -
KBU53_RS20485 (KBU53_20450) 40544..41218 + 675 WP_008324909 tetratricopeptide repeat protein -
KBU53_RS20490 (KBU53_20455) 41352..43553 + 2202 WP_023307203 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1553 GenBank   NZ_JAGQAU010000019
Plasmid name   IncFII(Yp) Incompatibility group   IncFII
Plasmid size   71017 bp Coordinate of oriT [Strand]   18976..19078 [+]
Host baterium   Enterobacter hormaechei subsp. xiangfangensis strain PLCR15

Cargo genes

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