Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   122120
Name   oriT_IncFII(Yp) in_silico
Organism   Enterobacter hormaechei subsp. xiangfangensis strain RGCR 38
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQHXY010000020 (30497..30599 [+], 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   13945 GenBank   WP_022652257
Name   traI_PF038_RS20835_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   16356 GenBank   WP_008324134
Name   traC_PF038_RS20755_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   16357 GenBank   WP_023307203
Name   traD_PF038_RS20830_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: 29949..55074

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PF038_RS20645 (PF038_20625) 25045..25368 + 324 WP_008324183 hypothetical protein -
PF038_RS20650 (PF038_20630) 25430..25696 + 267 WP_022652251 hypothetical protein -
PF038_RS20655 (PF038_20635) 26417..26791 + 375 WP_008324180 hypothetical protein -
PF038_RS20660 (PF038_20640) 26845..27132 + 288 WP_008324178 hypothetical protein -
PF038_RS20665 (PF038_20645) 27179..27523 + 345 WP_022652252 hypothetical protein -
PF038_RS20670 (PF038_20650) 27609..27872 + 264 WP_008324174 hypothetical protein -
PF038_RS20675 (PF038_20655) 27915..28745 + 831 WP_022652253 N-6 DNA methylase -
PF038_RS20680 (PF038_20660) 29372..29902 + 531 WP_008324170 antirestriction protein -
PF038_RS20685 (PF038_20665) 29949..30425 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
PF038_RS20690 (PF038_20670) 30857..31249 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
PF038_RS20695 (PF038_20675) 31438..32127 + 690 WP_008324166 hypothetical protein -
PF038_RS20700 (PF038_20680) 32214..32438 + 225 WP_008324165 TraY domain-containing protein -
PF038_RS20705 (PF038_20685) 32496..32846 + 351 WP_008324162 type IV conjugative transfer system pilin TraA -
PF038_RS20710 (PF038_20690) 32997..33302 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
PF038_RS20715 (PF038_20695) 33317..33883 + 567 WP_008324158 type IV conjugative transfer system protein TraE traE
PF038_RS20720 (PF038_20700) 33870..34613 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
PF038_RS20725 (PF038_20705) 34600..35994 + 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
PF038_RS20730 (PF038_20710) 36016..36555 + 540 WP_008324154 type IV conjugative transfer system lipoprotein TraV traV
PF038_RS20735 (PF038_20715) 36675..36899 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
PF038_RS20740 (PF038_20720) 36903..37088 + 186 WP_022652254 hypothetical protein -
PF038_RS20745 (PF038_20725) 37072..37473 + 402 WP_008324137 hypothetical protein -
PF038_RS20750 (PF038_20730) 37463..38029 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
PF038_RS20755 (PF038_20735) 38022..40652 + 2631 WP_008324134 type IV secretion system protein TraC virb4
PF038_RS20760 (PF038_20740) 40649..40996 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
PF038_RS20765 (PF038_20745) 40996..41643 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
PF038_RS20770 (PF038_20750) 41646..42632 + 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
PF038_RS20775 (PF038_20755) 42649..43278 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
PF038_RS20780 (PF038_20760) 43275..45128 + 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
PF038_RS20785 (PF038_20765) 45160..45348 + 189 WP_008324128 conjugal transfer protein TrbE -
PF038_RS20790 (PF038_20770) 45379..46128 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
PF038_RS20795 (PF038_20775) 46145..46393 + 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
PF038_RS20800 (PF038_20780) 46383..46937 + 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
PF038_RS20805 (PF038_20785) 46930..47358 + 429 WP_008324122 hypothetical protein -
PF038_RS20810 (PF038_20790) 47345..48715 + 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
PF038_RS20815 (PF038_20795) 48715..51537 + 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
PF038_RS20820 (PF038_20800) 51559..51990 + 432 WP_008324118 entry exclusion protein -
PF038_RS20825 (PF038_20805) 52065..52739 + 675 WP_008324909 tetratricopeptide repeat protein -
PF038_RS20830 (PF038_20810) 52873..55074 + 2202 WP_023307203 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   22547 GenBank   NZ_JAQHXY010000020
Plasmid name   IncFII(Yp) Incompatibility group   IncFII
Plasmid size   69253 bp Coordinate of oriT [Strand]   30497..30599 [+]
Host baterium   Enterobacter hormaechei subsp. xiangfangensis strain RGCR 38

Cargo genes

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