Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104348
Name   oriT_2020CK-00216|unnamed1 in_silico
Organism   Enterobacter kobei strain 2020CK-00216
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP118561 (82602..82704 [-], 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_2020CK-00216|unnamed1
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3181 GenBank   WP_023307204
Name   traI_PXH70_RS23065_2020CK-00216|unnamed1 insolico UniProt ID   A0A1Q1PS85
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189264.44 Da        Isoelectric Point: 6.1121

>WP_023307204.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMHT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
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)

(967-1150)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1430-1551)


  Protein structure



No available structure.




T4CP

ID   3096 GenBank   WP_022652256
Name   traD_PXH70_RS23070_2020CK-00216|unnamed1 insolico UniProt ID   _
Length   736 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 736 a.a.        Molecular weight: 82566.18 Da        Isoelectric Point: 5.1609

>WP_022652256.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENVGQPQQPQQPQQ
PQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGEVVDMAAWEAW
QAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  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.



ID   3097 GenBank   WP_008324134
Name   traC_PXH70_RS23145_2020CK-00216|unnamed1 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: 58118..83252

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PXH70_RS23070 (PXH70_23070) 58118..60328 - 2211 WP_022652256 type IV conjugative transfer system coupling protein TraD virb4
PXH70_RS23075 (PXH70_23075) 60462..61136 - 675 WP_008324909 tetratricopeptide repeat protein -
PXH70_RS23080 (PXH70_23080) 61211..61642 - 432 WP_008324118 entry exclusion protein -
PXH70_RS23085 (PXH70_23085) 61664..64486 - 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
PXH70_RS23090 (PXH70_23090) 64486..65856 - 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
PXH70_RS23095 (PXH70_23095) 65843..66271 - 429 WP_008324122 hypothetical protein -
PXH70_RS23100 (PXH70_23100) 66264..66818 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
PXH70_RS23105 (PXH70_23105) 66808..67056 - 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
PXH70_RS23110 (PXH70_23110) 67073..67822 - 750 WP_274850492 type-F conjugative transfer system pilin assembly protein TraF traF
PXH70_RS23115 (PXH70_23115) 67853..68041 - 189 WP_008324128 conjugal transfer protein TrbE -
PXH70_RS23120 (PXH70_23120) 68073..69926 - 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
PXH70_RS23125 (PXH70_23125) 69923..70552 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
PXH70_RS23130 (PXH70_23130) 70569..71555 - 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
PXH70_RS23135 (PXH70_23135) 71558..72205 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
PXH70_RS23140 (PXH70_23140) 72205..72552 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
PXH70_RS23145 (PXH70_23145) 72549..75179 - 2631 WP_008324134 type IV secretion system protein TraC virb4
PXH70_RS23150 (PXH70_23150) 75172..75738 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
PXH70_RS23155 (PXH70_23155) 75728..76129 - 402 WP_008324137 hypothetical protein -
PXH70_RS23160 (PXH70_23160) 76113..76298 - 186 WP_008324139 hypothetical protein -
PXH70_RS23165 (PXH70_23165) 76302..76526 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
PXH70_RS23170 (PXH70_23170) 76646..77185 - 540 WP_008324154 type IV conjugative transfer system lipoprotein TraV traV
PXH70_RS23175 (PXH70_23175) 77207..78601 - 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
PXH70_RS23180 (PXH70_23180) 78588..79331 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
PXH70_RS23185 (PXH70_23185) 79318..79884 - 567 WP_008324158 type IV conjugative transfer system protein TraE traE
PXH70_RS23190 (PXH70_23190) 79899..80204 - 306 WP_008324160 type IV conjugative transfer system protein TraL traL
PXH70_RS23195 (PXH70_23195) 80355..80705 - 351 WP_008324162 type IV conjugative transfer system pilin TraA -
PXH70_RS23200 (PXH70_23200) 80763..80987 - 225 WP_008324165 TraY domain-containing protein -
PXH70_RS23205 (PXH70_23205) 81074..81763 - 690 WP_008324166 hypothetical protein -
PXH70_RS23210 (PXH70_23210) 81952..82344 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
PXH70_RS23215 (PXH70_23215) 82776..83252 + 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
PXH70_RS23220 (PXH70_23220) 83299..83829 - 531 WP_008324170 antirestriction protein -
PXH70_RS23225 (PXH70_23225) 84456..85286 - 831 Protein_94 N-6 DNA methylase -
PXH70_RS23230 (PXH70_23230) 85329..85592 - 264 WP_008324174 hypothetical protein -
PXH70_RS23235 (PXH70_23235) 85678..86022 - 345 WP_008324177 hypothetical protein -
PXH70_RS23240 (PXH70_23240) 86069..86356 - 288 WP_008324178 hypothetical protein -
PXH70_RS23245 (PXH70_23245) 86410..86784 - 375 WP_008324180 hypothetical protein -
PXH70_RS23250 (PXH70_23250) 87411..87770 - 360 WP_008324181 hypothetical protein -
PXH70_RS23255 (PXH70_23255) 87832..88155 - 324 WP_008324183 hypothetical protein -

Host bacterium

ID   4787 GenBank   NZ_CP118561
Plasmid name   2020CK-00216|unnamed1 Incompatibility group   IncFIB
Plasmid size   111328 bp Coordinate of oriT [Strand]   82602..82704 [-]
Host baterium   Enterobacter kobei strain 2020CK-00216

Cargo genes

Drug resistance gene   aph(3')-Ia, qnrS1
Virulence gene   -
Metal resistance gene   merE, merD, merA, merC, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -