Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121012
Name   oriT_pSTN0717-36-2 in_silico
Organism   Citrobacter portucalensis strain STN0717-36
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP022496 (73623..73679 [-], 57 nt)
oriT length   57 nt
IRs (inverted repeats)      13..20, 23..30  (GCAAAATT..AATTTTGC)
Location of nic site      39..40
Conserved sequence flanking the
  nic site    		  GGTGTGGAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 57 nt

>oriT_pSTN0717-36-2
TAAAGTTAATCAGCAAAATTTTAATTTTGCGTGGGGTGTGGAGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13260 GenBank   WP_200923499
Name   traI_JLF47_RS25505_pSTN0717-36-2 insolico UniProt ID   _
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189158.49 Da        Isoelectric Point: 6.1681

>WP_200923499.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRIQ
DGANKHRLGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVDTAIKQIEAMASTRVMTGGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMQT
LKATGFDIKAYREAADLRVEQGNIPVTAPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARPG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNILVLDELSVSAMTRDLQRTGQADIFPDKSVPHSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEARSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGMLHVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPVGDSPFTAAKVGQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMNKVPDAQLAGLTDGQQNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERPDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLINRDIGSALTTIERVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTPEAQAQTIVITALNADRRQVNAMIHDARQDAGEVGEKDVTLPVL
TPANIRDGELRRMTTWEASRDSLVLLDSTYYSIEALDGEAHLVTLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKFISPGRKYPQPHVALPAFDRNGRQAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAVFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLAGEARPWN
PGAITGGRVWADGLPDGTGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDRPAGGADVAV
RDVVRDMDRIKETPASPLTLPDAPEERRRDEAVSQVVRESVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(967-1152)

TrwC relaxase (TrwC)

(10-283)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(573-625)

DNA helicase TraI (TraI_C)

(1430-1551)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(631-710)


  Protein structure



No available structure.




T4CP

ID   15543 GenBank   WP_008324134
Name   traC_JLF47_RS25430_pSTN0717-36-2 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   15544 GenBank   WP_200923498
Name   traD_JLF47_RS25500_pSTN0717-36-2 insolico UniProt ID   _
Length   741 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 741 a.a.        Molecular weight: 83056.66 Da        Isoelectric Point: 5.0372

>WP_200923498.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVIAPEGGAENAGQPQQPQQPQQ
PQQPQQPQQPQQPQQLQQPAPCAADTASASASVAGAAGTGGVEPELKTKAEEAEQLPPGISESGEVVDMA
AWEAWQAEQDELSPQERQRREEVNINVYRAPEKDLEPGGYI

  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: 73075..98357

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JLF47_RS25315 68138..68461 + 324 WP_200923491 theronine dehydrogenase -
JLF47_RS25320 (STN0717CIT36_P20720) 68523..68897 + 375 WP_200923492 hypothetical protein -
JLF47_RS25325 (STN0717CIT36_P20730) 69543..69917 + 375 WP_032637252 hypothetical protein -
JLF47_RS25330 (STN0717CIT36_P20740) 69971..70258 + 288 WP_200923493 hypothetical protein -
JLF47_RS25335 (STN0717CIT36_P20750) 70305..70649 + 345 WP_047359689 hypothetical protein -
JLF47_RS25340 (STN0717CIT36_P20760) 70735..70998 + 264 WP_008324174 hypothetical protein -
JLF47_RS25345 (STN0717CIT36_P20770) 71041..71871 + 831 WP_200923494 N-6 DNA methylase -
JLF47_RS25350 72078..72248 - 171 WP_236115583 hypothetical protein -
JLF47_RS25355 (STN0717CIT36_P20780) 72498..73028 + 531 WP_200923495 antirestriction protein -
JLF47_RS25360 (STN0717CIT36_P20790) 73075..73551 - 477 WP_200923496 transglycosylase SLT domain-containing protein virB1
JLF47_RS25365 (STN0717CIT36_P20800) 73983..74378 + 396 WP_040218546 conjugal transfer relaxosome DNA-binding protein TraM -
JLF47_RS25370 (STN0717CIT36_P20810) 74563..75267 + 705 WP_071667437 hypothetical protein -
JLF47_RS25375 (STN0717CIT36_P20820) 75376..75750 + 375 WP_040218544 TraY domain-containing protein -
JLF47_RS25380 (STN0717CIT36_P20830) 75816..76166 + 351 WP_071667438 type IV conjugative transfer system pilin TraA -
JLF47_RS25385 (STN0717CIT36_P20840) 76317..76622 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
JLF47_RS25390 (STN0717CIT36_P20850) 76637..77203 + 567 WP_008324158 type IV conjugative transfer system protein TraE traE
JLF47_RS25395 (STN0717CIT36_P20860) 77190..77933 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
JLF47_RS25400 (STN0717CIT36_P20870) 77920..79314 + 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
JLF47_RS25405 (STN0717CIT36_P20880) 79336..79875 + 540 WP_008324154 type IV conjugative transfer system lipoprotein TraV traV
JLF47_RS25410 (STN0717CIT36_P20890) 79995..80219 + 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
JLF47_RS25415 (STN0717CIT36_P20900) 80223..80408 + 186 WP_008324139 hypothetical protein -
JLF47_RS25420 (STN0717CIT36_P20910) 80392..80793 + 402 WP_008324137 hypothetical protein -
JLF47_RS25425 (STN0717CIT36_P20920) 80783..81349 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
JLF47_RS25430 (STN0717CIT36_P20930) 81342..83972 + 2631 WP_008324134 type IV secretion system protein TraC virb4
JLF47_RS25435 (STN0717CIT36_P20940) 83969..84316 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
JLF47_RS25440 (STN0717CIT36_P20950) 84316..84963 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
JLF47_RS25445 (STN0717CIT36_P20960) 84966..85952 + 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
JLF47_RS25450 (STN0717CIT36_P20970) 85969..86598 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
JLF47_RS25455 (STN0717CIT36_P20980) 86595..88448 + 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
JLF47_RS25460 (STN0717CIT36_P20990) 88480..88668 + 189 WP_008324128 conjugal transfer protein TrbE -
JLF47_RS25465 (STN0717CIT36_P21000) 88705..89448 + 744 WP_060446849 type-F conjugative transfer system pilin assembly protein TraF traF
JLF47_RS25470 (STN0717CIT36_P21010) 89465..89713 + 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
JLF47_RS25475 (STN0717CIT36_P21020) 89703..90248 + 546 WP_060446834 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
JLF47_RS25480 (STN0717CIT36_P21030) 90287..91621 + 1335 WP_230199841 conjugal transfer pilus assembly protein TraH traH
JLF47_RS25485 (STN0717CIT36_P21040) 91621..94443 + 2823 WP_200923497 conjugal transfer mating-pair stabilization protein TraG traG
JLF47_RS25490 (STN0717CIT36_P21050) 94462..94959 + 498 WP_063132060 hypothetical protein -
JLF47_RS25495 (STN0717CIT36_P21060) 95035..95760 + 726 WP_140157827 conjugal transfer complement resistance protein TraT -
JLF47_RS25500 (STN0717CIT36_P21070) 96132..98357 + 2226 WP_200923498 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   21441 GenBank   NZ_AP022496
Plasmid name   pSTN0717-36-2 Incompatibility group   Col440I
Plasmid size   118786 bp Coordinate of oriT [Strand]   73623..73679 [-]
Host baterium   Citrobacter portucalensis strain STN0717-36

Cargo genes

Drug resistance gene   -
Virulence gene   wbtL
Metal resistance gene   arsR, arsD, arsA, arsB, arsC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -