Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108488
Name   oriT_p13840_1 in_silico
Organism   Enterobacter roggenkampii strain 13840-yvys
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP083820 (71288..71390 [-], 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_p13840_1
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5676 GenBank   WP_023307204
Name   traI_LCD41_RS23135_p13840_1 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   6057 GenBank   WP_106105154
Name   traD_LCD41_RS23140_p13840_1 insolico UniProt ID   _
Length   742 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 742 a.a.        Molecular weight: 83272.93 Da        Isoelectric Point: 5.1609

>WP_106105154.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENVGQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGEVVDM
AAWEAWQAEQDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  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   6058 GenBank   WP_008324134
Name   traC_LCD41_RS23215_p13840_1 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: 46786..71938

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LCD41_RS23140 (LCD41_23195) 46786..49014 - 2229 WP_106105154 type IV conjugative transfer system coupling protein TraD virb4
LCD41_RS23145 (LCD41_23200) 49148..49822 - 675 WP_008324909 tetratricopeptide repeat protein -
LCD41_RS23150 (LCD41_23205) 49897..50328 - 432 WP_008324118 entry exclusion protein -
LCD41_RS23155 (LCD41_23210) 50350..53172 - 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
LCD41_RS23160 (LCD41_23215) 53172..54542 - 1371 WP_008324121 conjugal transfer pilus assembly protein TraH traH
LCD41_RS23165 (LCD41_23220) 54529..54957 - 429 WP_008324122 hypothetical protein -
LCD41_RS23170 (LCD41_23225) 54950..55504 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
LCD41_RS23175 (LCD41_23230) 55494..55742 - 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
LCD41_RS23180 (LCD41_23235) 55759..56508 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
LCD41_RS23185 (LCD41_23240) 56539..56727 - 189 WP_008324128 conjugal transfer protein TrbE -
LCD41_RS23190 (LCD41_23245) 56759..58612 - 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
LCD41_RS23195 (LCD41_23250) 58609..59238 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
LCD41_RS23200 (LCD41_23255) 59255..60241 - 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
LCD41_RS23205 (LCD41_23260) 60244..60891 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
LCD41_RS23210 (LCD41_23265) 60891..61238 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
LCD41_RS23215 (LCD41_23270) 61235..63865 - 2631 WP_008324134 type IV secretion system protein TraC virb4
LCD41_RS23220 (LCD41_23275) 63858..64424 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
LCD41_RS23225 (LCD41_23280) 64414..64815 - 402 WP_008324137 hypothetical protein -
LCD41_RS23230 (LCD41_23285) 64799..64984 - 186 WP_008324139 hypothetical protein -
LCD41_RS23235 (LCD41_23290) 64988..65212 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
LCD41_RS23240 (LCD41_23295) 65332..65871 - 540 WP_008324154 type IV conjugative transfer system lipoprotein TraV traV
LCD41_RS23245 (LCD41_23300) 65893..67287 - 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
LCD41_RS23250 (LCD41_23305) 67274..68017 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
LCD41_RS23255 (LCD41_23310) 68004..68570 - 567 WP_008324158 type IV conjugative transfer system protein TraE traE
LCD41_RS23260 (LCD41_23315) 68585..68890 - 306 WP_008324160 type IV conjugative transfer system protein TraL traL
LCD41_RS23265 (LCD41_23320) 69041..69391 - 351 WP_008324162 type IV conjugative transfer system pilin TraA -
LCD41_RS23270 (LCD41_23325) 69449..69673 - 225 WP_008324165 TraY domain-containing protein -
LCD41_RS23275 (LCD41_23330) 69760..70449 - 690 WP_008324166 hypothetical protein -
LCD41_RS23280 (LCD41_23335) 70638..71030 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
LCD41_RS23285 (LCD41_23340) 71462..71938 + 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
LCD41_RS23290 (LCD41_23345) 71985..72515 - 531 WP_008324170 antirestriction protein -
LCD41_RS23295 (LCD41_23350) 73142..73972 - 831 WP_008324171 N-6 DNA methylase -
LCD41_RS23300 (LCD41_23355) 74015..74278 - 264 WP_008324174 hypothetical protein -
LCD41_RS23305 (LCD41_23360) 74364..74708 - 345 WP_008324177 hypothetical protein -
LCD41_RS23310 (LCD41_23365) 74755..75042 - 288 WP_008324178 hypothetical protein -
LCD41_RS23315 (LCD41_23370) 75096..75470 - 375 WP_008324180 hypothetical protein -
LCD41_RS23320 (LCD41_23375) 76097..76456 - 360 WP_047353151 hypothetical protein -
LCD41_RS23325 (LCD41_23380) 76518..76841 - 324 WP_047353152 hypothetical protein -

Host bacterium

ID   8923 GenBank   NZ_CP083820
Plasmid name   p13840_1 Incompatibility group   IncFIB
Plasmid size   94721 bp Coordinate of oriT [Strand]   71288..71390 [-]
Host baterium   Enterobacter roggenkampii strain 13840-yvys

Cargo genes

Drug resistance gene   mcr-10
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -