Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120628
Name   oriT_pCFR-e790 in_silico
Organism   Citrobacter freundii complex sp. CFNIH9
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP026241 (34772..34874 [-], 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_pCFR-e790
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTTCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12996 GenBank   WP_022652257
Name   traI_C2U43_RS26020_pCFR-e790 insolico UniProt ID   A0A3S5I3M3
Length   1746 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1746 a.a.        Molecular weight: 189292.49 Da        Isoelectric Point: 6.1121

>WP_022652257.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMHT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEERSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVVPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
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)

(967-1148)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1430-1551)


  Protein structure



No available structure.




T4CP

ID   15259 GenBank   WP_023307203
Name   traD_C2U43_RS26025_pCFR-e790 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   15260 GenBank   WP_008324134
Name   traC_C2U43_RS26100_pCFR-e790 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: 10298..35422

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C2U43_RS26025 (C2U43_26025) 10298..12499 - 2202 WP_023307203 type IV conjugative transfer system coupling protein TraD virb4
C2U43_RS26030 (C2U43_26030) 12803..13306 - 504 WP_227522316 tetratricopeptide repeat protein -
C2U43_RS26035 (C2U43_26035) 13381..13812 - 432 WP_008324118 entry exclusion protein -
C2U43_RS26040 (C2U43_26040) 13834..16656 - 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
C2U43_RS26045 (C2U43_26045) 16656..18026 - 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
C2U43_RS26050 (C2U43_26050) 18013..18441 - 429 WP_008324122 hypothetical protein -
C2U43_RS26055 (C2U43_26055) 18434..18988 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
C2U43_RS26060 (C2U43_26060) 18978..19226 - 249 WP_008324126 type-F conjugative transfer system pilin chaperone TraQ -
C2U43_RS26065 (C2U43_26065) 19243..19992 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
C2U43_RS26070 (C2U43_26070) 20023..20211 - 189 WP_008324128 conjugal transfer protein TrbE -
C2U43_RS26075 (C2U43_26075) 20243..22096 - 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
C2U43_RS26080 (C2U43_26080) 22093..22722 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
C2U43_RS26085 (C2U43_26085) 22739..23725 - 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
C2U43_RS26090 (C2U43_26090) 23728..24375 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
C2U43_RS26095 (C2U43_26095) 24375..24722 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
C2U43_RS26100 (C2U43_26100) 24719..27349 - 2631 WP_008324134 type IV secretion system protein TraC virb4
C2U43_RS26105 (C2U43_26105) 27342..27908 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
C2U43_RS26110 (C2U43_26110) 27898..28299 - 402 WP_008324137 hypothetical protein -
C2U43_RS26115 (C2U43_26115) 28283..28468 - 186 WP_022652254 hypothetical protein -
C2U43_RS26120 (C2U43_26120) 28472..28696 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
C2U43_RS26125 (C2U43_26125) 28816..29355 - 540 WP_008324154 type IV conjugative transfer system lipoprotein TraV traV
C2U43_RS26130 (C2U43_26130) 29377..30771 - 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
C2U43_RS26135 (C2U43_26135) 30758..31501 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
C2U43_RS26140 (C2U43_26140) 31488..32054 - 567 WP_008324158 type IV conjugative transfer system protein TraE traE
C2U43_RS26145 (C2U43_26145) 32069..32374 - 306 WP_008324160 type IV conjugative transfer system protein TraL traL
C2U43_RS26150 (C2U43_26150) 32525..32875 - 351 WP_008324162 type IV conjugative transfer system pilin TraA -
C2U43_RS26155 (C2U43_26155) 32933..33157 - 225 WP_008324165 TraY domain-containing protein -
C2U43_RS26160 (C2U43_26160) 33244..33933 - 690 WP_008324166 hypothetical protein -
C2U43_RS26165 (C2U43_26165) 34122..34514 - 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
C2U43_RS26170 (C2U43_26170) 34946..35422 + 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
C2U43_RS26175 (C2U43_26175) 35469..35999 - 531 WP_008324170 antirestriction protein -
C2U43_RS26180 (C2U43_26180) 36626..37456 - 831 WP_022652253 N-6 DNA methylase -
C2U43_RS26185 (C2U43_26185) 37499..37762 - 264 WP_008324174 hypothetical protein -
C2U43_RS26190 (C2U43_26190) 37848..38192 - 345 WP_022652252 hypothetical protein -
C2U43_RS26195 (C2U43_26195) 38239..38526 - 288 WP_008324178 hypothetical protein -
C2U43_RS26200 (C2U43_26200) 38580..38954 - 375 WP_008324180 hypothetical protein -
C2U43_RS26205 (C2U43_26205) 39675..39941 - 267 WP_022652251 hypothetical protein -
C2U43_RS26210 (C2U43_26210) 40003..40326 - 324 WP_008324183 hypothetical protein -

Host bacterium

ID   21057 GenBank   NZ_CP026241
Plasmid name   pCFR-e790 Incompatibility group   IncFII
Plasmid size   200651 bp Coordinate of oriT [Strand]   34772..34874 [-]
Host baterium   Citrobacter freundii complex sp. CFNIH9

Cargo genes

Drug resistance gene   mph(A), aac(3)-IId, blaTEM-1B, tet(D), catA2, sul2
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -