Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   122130
Name   oriT_pIncFII(Yp) in_silico
Organism   Enterobacter hormaechei subsp. xiangfangensis strain APCR 84
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JARQZG010000021 (39904..40006 [-], 103 nt)
oriT length   103 nt
IRs (inverted repeats)      89..94, 96..101  (AAATAA..TTATTT)
 28..33, 40..45  (GCAAAA..TTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 103 nt

>oriT_pIncFII(Yp)
CTCACCACCAAAAGTTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13949 GenBank   WP_016479978
Name   traI_P5A20_RS22190_pIncFII(Yp) insolico UniProt ID   A0A0G3B767
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189285.41 Da        Isoelectric Point: 6.0099

>WP_016479978.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGDDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
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)

DNA helicase TraI (TraI_C)

(1430-1551)

AAA domain (AAA_30)

(967-1150)


  Protein structure



No available structure.




T4CP

ID   16360 GenBank   WP_016479979
Name   traD_P5A20_RS22195_pIncFII(Yp) 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.



ID   16361 GenBank   WP_008324134
Name   traC_P5A20_RS22270_pIncFII(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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 15384..40554

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
P5A20_RS22195 (P5A20_22180) 15384..17630 - 2247 WP_016479979 type IV conjugative transfer system coupling protein TraD virb4
P5A20_RS22200 (P5A20_22185) 17764..18438 - 675 WP_008324909 tetratricopeptide repeat protein -
P5A20_RS22205 (P5A20_22190) 18513..18944 - 432 WP_008324118 entry exclusion protein -
P5A20_RS22210 (P5A20_22195) 18966..21788 - 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
P5A20_RS22215 (P5A20_22200) 21788..23158 - 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
P5A20_RS22220 (P5A20_22205) 23145..23573 - 429 WP_008324122 hypothetical protein -
P5A20_RS22225 (P5A20_22210) 23566..24120 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
P5A20_RS22230 (P5A20_22215) 24110..24358 - 249 WP_016479982 type-F conjugative transfer system pilin chaperone TraQ -
P5A20_RS22235 (P5A20_22220) 24375..25124 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
P5A20_RS22240 (P5A20_22225) 25155..25343 - 189 WP_008324128 conjugal transfer protein TrbE -
P5A20_RS22245 (P5A20_22230) 25375..27228 - 1854 WP_016479983 type-F conjugative transfer system mating-pair stabilization protein TraN traN
P5A20_RS22250 (P5A20_22235) 27225..27854 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
P5A20_RS22255 (P5A20_22240) 27871..28857 - 987 WP_042934586 conjugal transfer pilus assembly protein TraU traU
P5A20_RS22260 (P5A20_22245) 28860..29507 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
P5A20_RS22265 (P5A20_22250) 29507..29854 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
P5A20_RS22270 (P5A20_22255) 29851..32481 - 2631 WP_008324134 type IV secretion system protein TraC virb4
P5A20_RS22275 (P5A20_22260) 32474..33040 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
P5A20_RS22280 (P5A20_22265) 33030..33431 - 402 WP_016479985 hypothetical protein -
P5A20_RS22285 (P5A20_22270) 33415..33600 - 186 WP_008324139 hypothetical protein -
P5A20_RS22290 (P5A20_22275) 33604..33828 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
P5A20_RS22295 (P5A20_22280) 33948..34487 - 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
P5A20_RS22300 (P5A20_22285) 34509..35903 - 1395 WP_016479986 F-type conjugal transfer pilus assembly protein TraB traB
P5A20_RS22305 (P5A20_22290) 35890..36633 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
P5A20_RS22310 (P5A20_22295) 36620..37186 - 567 WP_016247535 type IV conjugative transfer system protein TraE traE
P5A20_RS22315 (P5A20_22300) 37201..37506 - 306 WP_008324160 type IV conjugative transfer system protein TraL traL
P5A20_RS22320 (P5A20_22305) 37657..38007 - 351 WP_016247536 type IV conjugative transfer system pilin TraA -
P5A20_RS22325 (P5A20_22310) 38065..38289 - 225 WP_008324165 TraY domain-containing protein -
P5A20_RS22330 (P5A20_22315) 38376..39065 - 690 WP_008324166 hypothetical protein -
P5A20_RS22335 (P5A20_22320) 39254..39646 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
P5A20_RS22340 (P5A20_22325) 40078..40554 + 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
P5A20_RS22345 (P5A20_22330) 40601..41131 - 531 WP_008324170 antirestriction protein -
P5A20_RS22350 (P5A20_22335) 41758..42588 - 831 WP_008324171 N-6 DNA methylase -
P5A20_RS22355 (P5A20_22340) 42631..42894 - 264 WP_008324174 hypothetical protein -
P5A20_RS22360 (P5A20_22345) 42980..43324 - 345 WP_008324177 hypothetical protein -
P5A20_RS22365 (P5A20_22350) 43371..43658 - 288 WP_008324178 hypothetical protein -
P5A20_RS22370 (P5A20_22355) 43712..44086 - 375 WP_008324180 hypothetical protein -
P5A20_RS22375 (P5A20_22360) 44713..45072 - 360 WP_015493069 hypothetical protein -
P5A20_RS22380 (P5A20_22365) 45134..45457 - 324 WP_008324183 hypothetical protein -

Host bacterium

ID   22557 GenBank   NZ_JARQZG010000021
Plasmid name   pIncFII(Yp) Incompatibility group   IncFII
Plasmid size   55007 bp Coordinate of oriT [Strand]   39904..40006 [-]
Host baterium   Enterobacter hormaechei subsp. xiangfangensis strain APCR 84

Cargo genes

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