Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108361
Name   oriT_pCF5125-3 in_silico
Organism   Citrobacter freundii strain CF5125
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP125313 (17175..17277 [+], 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_pCF5125-3
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5592 GenBank   WP_057064462
Name   traI_QKW62_RS27500_pCF5125-3 insolico UniProt ID   A0AA40NJB4
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 188948.08 Da        Isoelectric Point: 6.0680

>WP_057064462.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKIFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQCMAEWMQT
LKATGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLASTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTRVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGAVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVGQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQVIEKEADRQI
RSGALLSVPVSPGNGLQLLVSRQSYNAEKSILRHVLEGKEAVTPLMDKVPDAQLAGLTDGQQNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERPDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTPEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVTLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
DRGVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKFISPGRKYPQPHVALPAFDRNGRQAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLAGEARPWN
PGAITGGRVWADSLPDSTGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDGPAGGADVAV
RDVVRDMERIKETPASPLTLPDAPEERRRDEAVSQVVRENVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1430-1551)

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

(573-625)

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

(631-710)

AAA domain (AAA_30)

(967-1150)


  Protein structure



No available structure.




T4CP

ID   5971 GenBank   WP_058654351
Name   traC_QKW62_RS27425_pCF5125-3 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: 98855.54 Da        Isoelectric Point: 5.7676

>WP_058654351.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNPLDTVTRTVNSLLTALKMPDASSEANDVLGQMRFPQFSRVLPYRDYDAETGLFMNEKTMGFMLEAQP
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   5972 GenBank   WP_057064463
Name   traD_QKW62_RS27495_pCF5125-3 insolico UniProt ID   _
Length   722 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 722 a.a.        Molecular weight: 80873.32 Da        Isoelectric Point: 5.1609

>WP_057064463.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGVIVALTLSIKLTWQTFVNGMVWYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVIAPEASAENTGQPQQPQQLTP
APRAADAPSASASAAGAAGTGGVEPELKTKAEEAEQLPPGISESGEVVDMAAWEAWQAEQDELSPQERQR
REEVNINVHRAPEKDLEPGGYI

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 16627..41417

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QKW62_RS27310 (QKW62_27305) 11725..11964 + 240 WP_016589766 hypothetical protein -
QKW62_RS27315 (QKW62_27310) 11964..12461 + 498 WP_058655938 MucR family transcriptional regulator -
QKW62_RS27320 (QKW62_27315) 12532..12666 + 135 WP_255358724 hypothetical protein -
QKW62_RS27325 (QKW62_27320) 13089..13463 + 375 WP_032637252 hypothetical protein -
QKW62_RS27330 (QKW62_27325) 13517..13810 + 294 WP_175282692 hypothetical protein -
QKW62_RS27335 (QKW62_27330) 13857..14201 + 345 WP_008324177 hypothetical protein -
QKW62_RS27340 (QKW62_27335) 14287..14550 + 264 WP_008324174 hypothetical protein -
QKW62_RS27345 (QKW62_27340) 14593..15423 + 831 WP_008324171 N-6 DNA methylase -
QKW62_RS27350 (QKW62_27345) 16050..16580 + 531 WP_008324170 antirestriction protein -
QKW62_RS27355 (QKW62_27350) 16627..17103 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
QKW62_RS27360 (QKW62_27355) 17535..17927 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
QKW62_RS27365 (QKW62_27360) 18116..18805 + 690 WP_008324166 hypothetical protein -
QKW62_RS27370 (QKW62_27365) 18892..19116 + 225 WP_008324165 TraY domain-containing protein -
QKW62_RS27375 (QKW62_27370) 19174..19524 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
QKW62_RS27380 (QKW62_27375) 19675..19980 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
QKW62_RS27385 (QKW62_27380) 19995..20561 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
QKW62_RS27390 (QKW62_27385) 20548..21291 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
QKW62_RS27395 (QKW62_27390) 21278..22672 + 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
QKW62_RS27400 (QKW62_27395) 22694..23233 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
QKW62_RS27405 (QKW62_27400) 23353..23577 + 225 WP_016247532 TraR/DksA C4-type zinc finger protein -
QKW62_RS27410 (QKW62_27405) 23581..23766 + 186 WP_016674194 hypothetical protein -
QKW62_RS27415 (QKW62_27410) 23750..24154 + 405 WP_058670650 hypothetical protein -
QKW62_RS27420 (QKW62_27415) 24144..24710 + 567 WP_058670651 conjugal transfer pilus-stabilizing protein TraP -
QKW62_RS27425 (QKW62_27420) 24703..27333 + 2631 WP_058654351 type IV secretion system protein TraC virb4
QKW62_RS27430 (QKW62_27425) 27330..27677 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
QKW62_RS27435 (QKW62_27430) 27677..28324 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
QKW62_RS27440 (QKW62_27435) 28327..29313 + 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
QKW62_RS27445 (QKW62_27440) 29330..29959 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
QKW62_RS27450 (QKW62_27445) 29956..31809 + 1854 WP_016247529 type-F conjugative transfer system mating-pair stabilization protein TraN traN
QKW62_RS27455 (QKW62_27450) 31841..32029 + 189 WP_008324128 conjugal transfer protein TrbE -
QKW62_RS27460 (QKW62_27455) 32060..32809 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
QKW62_RS27465 (QKW62_27460) 32826..33074 + 249 WP_094354130 type-F conjugative transfer system pilin chaperone TraQ -
QKW62_RS27470 (QKW62_27465) 33064..33609 + 546 WP_045379409 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
QKW62_RS27475 (QKW62_27470) 33648..34982 + 1335 WP_230199841 conjugal transfer pilus assembly protein TraH traH
QKW62_RS27480 (QKW62_27475) 34982..37804 + 2823 WP_045379403 conjugal transfer mating-pair stabilization protein TraG traG
QKW62_RS27485 (QKW62_27480) 37818..38294 + 477 WP_071886900 hypothetical protein -
QKW62_RS27490 (QKW62_27485) 38331..38891 + 561 WP_283146526 hypothetical protein -
QKW62_RS27495 (QKW62_27490) 39249..41417 + 2169 WP_057064463 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   8796 GenBank   NZ_CP125313
Plasmid name   pCF5125-3 Incompatibility group   IncFII
Plasmid size   76037 bp Coordinate of oriT [Strand]   17175..17277 [+]
Host baterium   Citrobacter freundii strain CF5125

Cargo genes

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