Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116537
Name   oriT_pF2119-IMP in_silico
Organism   Citrobacter freundii strain F2119
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP137118 (122960..123062 [-], 103 nt)
oriT length   103 nt
IRs (inverted repeats)      89..94, 96..101  (AAATAA..TTATTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 103 nt

>oriT_pF2119-IMP
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTTCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10559 GenBank   WP_284243371
Name   traI_R2X26_RS25685_pF2119-IMP 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: 189266.38 Da        Isoelectric Point: 6.1115

>WP_284243371.1 conjugative transfer relaxase/helicase TraI [Citrobacter freundii]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMHT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLINRDIGSALTTIERVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLLPGGQPATLLETIVKDYTGRTPEAQAQTIVITALNADRRQVNAMIHDARQDAGEVGEKEVTLPVL
TPANIRDGELRRMTTWEASRDSLVLLDSTYYSIEALDGEAHLVTLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKFISPGRKYPQPHVALPAFDRNGRQAGVWLS
ALTSGDGQLKGLGGEGRLMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLAGEARPWN
PGAITGGRVWADGLPDSTGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDGPAGGADVAV
RDVVRDMARIKETPASPLTLPDAPEERRRDEAVSQVVRENVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1430-1551)

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

(573-625)

AAA domain (AAA_30)

(967-1152)

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

(631-710)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




T4CP

ID   12342 GenBank   WP_023307203
Name   traD_R2X26_RS25690_pF2119-IMP insolico UniProt ID   _
Length   733 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 733 a.a.        Molecular weight: 82212.80 Da        Isoelectric Point: 5.1609

>WP_023307203.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENVGQPQQPQQPQQ
PQQPQQPQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGEVVDMAAWEAWQAE
QDELSPQERQRREEVNINVHRAPEKDLEPGGYI

  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   12343 GenBank   WP_008324134
Name   traC_R2X26_RS25770_pF2119-IMP 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: 97260..123610

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
R2X26_RS25690 (R2X26_25690) 97260..99461 - 2202 WP_023307203 type IV conjugative transfer system coupling protein TraD virb4
R2X26_RS25695 (R2X26_25695) 99595..100269 - 675 WP_008324909 tetratricopeptide repeat protein -
R2X26_RS25700 (R2X26_25700) 100344..100775 - 432 WP_008324118 entry exclusion protein -
R2X26_RS25710 (R2X26_25710) 102187..104844 - 2658 Protein_119 conjugal transfer mating-pair stabilization protein TraG -
R2X26_RS25715 (R2X26_25715) 104844..106214 - 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
R2X26_RS25720 (R2X26_25720) 106201..106629 - 429 WP_008324122 hypothetical protein -
R2X26_RS25725 (R2X26_25725) 106622..107176 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
R2X26_RS25730 (R2X26_25730) 107166..107414 - 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
R2X26_RS25735 (R2X26_25735) 107431..108180 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
R2X26_RS25740 (R2X26_25740) 108211..108399 - 189 WP_008324128 conjugal transfer protein TrbE -
R2X26_RS25745 (R2X26_25745) 108431..110284 - 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
R2X26_RS25750 (R2X26_25750) 110281..110910 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
R2X26_RS25755 (R2X26_25755) 110927..111913 - 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
R2X26_RS25760 (R2X26_25760) 111916..112563 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
R2X26_RS25765 (R2X26_25765) 112563..112910 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
R2X26_RS25770 (R2X26_25770) 112907..115537 - 2631 WP_008324134 type IV secretion system protein TraC virb4
R2X26_RS25775 (R2X26_25775) 115530..116096 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
R2X26_RS25780 (R2X26_25780) 116086..116487 - 402 WP_008324137 hypothetical protein -
R2X26_RS25785 (R2X26_25785) 116471..116656 - 186 WP_022652254 hypothetical protein -
R2X26_RS25790 (R2X26_25790) 116660..116884 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
R2X26_RS25795 (R2X26_25795) 117004..117543 - 540 WP_008324154 type IV conjugative transfer system lipoprotein TraV traV
R2X26_RS25800 (R2X26_25800) 117565..118959 - 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
R2X26_RS25805 (R2X26_25805) 118946..119689 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
R2X26_RS25810 (R2X26_25810) 119676..120242 - 567 WP_008324158 type IV conjugative transfer system protein TraE traE
R2X26_RS25815 (R2X26_25815) 120257..120562 - 306 WP_008324160 type IV conjugative transfer system protein TraL traL
R2X26_RS25820 (R2X26_25820) 120713..121063 - 351 WP_008324162 type IV conjugative transfer system pilin TraA -
R2X26_RS25825 (R2X26_25825) 121121..121345 - 225 WP_008324165 TraY domain-containing protein -
R2X26_RS25830 (R2X26_25830) 121432..122121 - 690 WP_008324166 hypothetical protein -
R2X26_RS25835 (R2X26_25835) 122310..122702 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
R2X26_RS25840 (R2X26_25840) 123134..123610 + 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
R2X26_RS25845 (R2X26_25845) 123657..124187 - 531 WP_008324170 antirestriction protein -
R2X26_RS25850 (R2X26_25850) 124814..125644 - 831 WP_022652253 N-6 DNA methylase -
R2X26_RS25855 (R2X26_25855) 125687..125950 - 264 WP_008324174 hypothetical protein -
R2X26_RS25860 (R2X26_25860) 126036..126380 - 345 WP_022652252 hypothetical protein -
R2X26_RS25865 (R2X26_25865) 126427..126714 - 288 WP_008324178 hypothetical protein -
R2X26_RS25870 (R2X26_25870) 126768..127142 - 375 WP_008324180 hypothetical protein -
R2X26_RS25875 (R2X26_25875) 127863..128129 - 267 WP_022652251 hypothetical protein -
R2X26_RS25880 (R2X26_25880) 128191..128514 - 324 WP_008324183 hypothetical protein -

Host bacterium

ID   16970 GenBank   NZ_CP137118
Plasmid name   pF2119-IMP Incompatibility group   IncFIB
Plasmid size   160841 bp Coordinate of oriT [Strand]   122960..123062 [-]
Host baterium   Citrobacter freundii strain F2119

Cargo genes

Drug resistance gene   blaCTX-M-14, tet(A), blaIMP-1, aac(6')-Il, blaTEM-1B
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -