Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120577
Name   oriT_pOZ172 in_silico
Organism   Citrobacter freundii strain B38
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP016763 (45508..45610 [-], 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_pOZ172
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12960 GenBank   WP_065945169
Name   traI_CfB38_RS24990_pOZ172 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: 189250.41 Da        Isoelectric Point: 6.1119

>WP_065945169.1 conjugative transfer relaxase/helicase TraI [Citrobacter freundii]
MMSIGSVKSAGSAGNYYTDKDNYYVIGSMGERWAGKGAEALGLSGGVDQKVFTKVLEGRLPDGSDLSRTQ
DGANKHRPGYDFTFSAPKSVSVMAMLGGDKRLIEAHNRAVETAIKQIEAMASTRVMTEGRSETQLTGNLV
MALFNHDTSRDQEPQLHTHAVVANATQHGDEWRTLSSDKVGKTGFIENIYANQIAFGRLYRAALKDDVAA
MGYETETVGKHGMWELKGVPTEPYSSRSRTISEAVGDDASLKSRDVAALDTRQSKQKVDPEQRMAEWMHT
LKETGFDIKAYREAADLRVVQGNIPATTPEAIDINSSVGQAIAMLSDRRARFTYSELLATTLGQLPARSG
MVEMARDGIDAAIKNEQLIPLDKEKGLFTSNIHVLDELSVSAMTRDLQRTGQADIFPDKSVPRSRSYSDA
VSVLAQDRPPVAIISGQGGAAGQRERVAELTMMAREQGRDVQIIAADRRSRSALMQDERLSGEHITDRRG
LTEGMAFTPGSTLIVDQGEKLTLKETLTLLDGALRHNVQLLIADSGQRTGTGSALTVMKEAGVSTLAWQG
GEKTQVSVISEPDRRQRYDRLAADFARSVRAGEHSVAQVTGPREQAVLAGVVREALKAEKVLGEREVSIT
TLEPVWLDSRHQQVRDHYREGMVMERWNAEDRSRERFVIDRVTGRNNSLTLRNAQGETRVTRLSELNSSW
SLYRTGTLQVAEGDRLAVLGQAQGTRLRGGDTVTVKALGEAGLVVSLPGRKADVVLPAGDSPFTAAKVVQ
GWVESPGRSVSDSATVFASLSQRELDNTTLNKLALSGRAVRLYSAQTAQKTTEKLSRQSAWSVVSEQIKD
AAGHDRLDDALAHQKAGLHTPEQQAIHLAIPVLEGNGLAFTKPQLMAAAKEFEQDSLSLQAIEKEADRQV
RSGDLLSVPVSPGNGLQLLVSRQSYNAEKSIIRHVLEGKEAVTPLMDKVPDAQLAGLTDGQRNATRMILE
SPDRFTLVQGYAGVGKTTQFRAVMSAIGTLPEREQPRVIGVAPTHRAVSEMRDAGVPETQTLAAFIHDTQ
QQLRGGERTDFSNVLFLVDESSMVGNADMAKAYSLIAGGGGRAVSSGDTDQLQSIAPGQPFRLLQKRSAI
DVAVMQEIVRQTPELKPAVYSLISRDIGSALTTIESVAPAQVPRRADAWQPDSSVMEFSREREEAIAKAV
AAGDLMPGGQPATLLEAIVKDYTGRTSEAQAQTIVITALNADRRQVNAMIHDARQGAGEVGEKEVTLPVL
TPANIRDGELRRMATWEASRDSLVLLDSTYYSIEALDGEAHLVMLKDAQGNTRSLSPAQAATEGVTLYRQ
DTITVSEGDRMRFSKSDNERGFVANSVWSVSEIKGDSVTLSDGKQTRTLTPSAEQAEQHIDLAYAVTVEG
SQGASEPFSISLQGTDGGRKRMVSFESAYVALSRMKQHAQVYTDNRDKWVAAMEKSQAKSTAHDILEPRG
DRAVANAARLTATAKALGEVPAGRAALRQAGLQPEGSMAKYISPGRKYPQPHVALPAFDRNGRKAGVWLS
ALTSGDGQLKGLAGEGRVMGSGDAAFAGLQASRNGESLLARDMEEGVRLARENPQSGVVVRLEGEARPWN
PGAITGGRVWADGLPDATGTQPAETVPPEVLAQQAREAEVQRELDKRAEEAVREMARSGDRPAGGADVAV
RDVVRDMDRIKETPASPLTLPDAPEERRRDEAVSQVVRESVQRDRLQQMERETVRDLEREKTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

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

(631-710)

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

(573-625)

DNA helicase TraI (TraI_C)

(1430-1551)

AAA domain (AAA_30)

(967-1150)


  Protein structure



No available structure.




T4CP

ID   15218 GenBank   WP_065945170
Name   traD_CfB38_RS24995_pOZ172 insolico UniProt ID   _
Length   730 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 730 a.a.        Molecular weight: 81862.38 Da        Isoelectric Point: 5.1609

>WP_065945170.1 type IV conjugative transfer system coupling protein TraD [Citrobacter freundii]
MSFNAKDMTQGGQIASMRIRMFSQIANIIVYCLVILFGIIVAITLSVKLTWQTFVNGMVYYWCQTLAPMR
DIFKSQPVYTIRYYGHELKYNAQQILQDKYIQWCADQVWTAFILAAIIAAVVCVITFFVTTWILGHQGKQ
QSEDEITGGRQLTDDPKAVAKMLRRDGLASDIKIGELPLIKDSEIQNFCLHGTVGAGKSEVIRRLMNYAR
QRGDMVIVYDRSCEFVKSYYDPATDKILNPLDARCAAWDLWRECLTQPDFDNVSNTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDKDRSYSKLVDTLLSIKIEKLRSYLKNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIENNGESFTIRDWMRGVREDGKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVIGIQSYAQLEDIYGQKPAETLFDVLNTRAFFRSPSRNIA
EFAAGEIGEKEILKASEQYSYGVDPVRDGTSVGKDMERVTLVSYSDVQTLPDLSCYVTLPGPYPAVKMAL
KYQQRPKVAPEFIPRTIDGKAEERLNAALAAREHESRSIAMLFEPDADVVAPEGGAENAGQPQQPQQPQQ
PQQQQQPQQLTPAPRAADAASVAGAAGAGGVEPELKTKAEEAEQLPPGISESGEVVDMAAWEAWQAEQDE
LSPQERQRREEVNINVHRAPEKDLEPGGYI

  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   15219 GenBank   WP_008324134
Name   traC_CfB38_RS25070_pOZ172 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: 21042..46158

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CfB38_RS24995 (CfB38_5014) 21042..23234 - 2193 WP_065945170 type IV conjugative transfer system coupling protein TraD virb4
CfB38_RS25000 (CfB38_5015) 23368..24042 - 675 WP_065945171 tetratricopeptide repeat protein -
CfB38_RS25005 (CfB38_5016) 24117..24548 - 432 WP_008324118 entry exclusion protein -
CfB38_RS25010 (CfB38_5017) 24570..27392 - 2823 WP_008324119 conjugal transfer mating-pair stabilization protein TraG traG
CfB38_RS25015 (CfB38_5018) 27392..28762 - 1371 WP_016247527 conjugal transfer pilus assembly protein TraH traH
CfB38_RS25020 (CfB38_5019) 28749..29177 - 429 WP_008324122 hypothetical protein -
CfB38_RS25025 (CfB38_5020) 29170..29724 - 555 WP_008324125 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CfB38_RS25030 (CfB38_5021) 29714..29962 - 249 WP_065945172 type-F conjugative transfer system pilin chaperone TraQ -
CfB38_RS25035 (CfB38_5022) 29979..30728 - 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
CfB38_RS25040 (CfB38_5023) 30759..30947 - 189 WP_008324128 conjugal transfer protein TrbE -
CfB38_RS25045 (CfB38_5024) 30979..32832 - 1854 WP_022652255 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CfB38_RS25050 (CfB38_5025) 32829..33458 - 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
CfB38_RS25055 (CfB38_5026) 33475..34461 - 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
CfB38_RS25060 (CfB38_5027) 34464..35111 - 648 WP_008324132 type-F conjugative transfer system protein TraW traW
CfB38_RS25065 (CfB38_5028) 35111..35458 - 348 WP_008324133 type-F conjugative transfer system protein TrbI -
CfB38_RS25070 (CfB38_5029) 35455..38085 - 2631 WP_008324134 type IV secretion system protein TraC virb4
CfB38_RS25075 (CfB38_5030) 38078..38644 - 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
CfB38_RS25080 (CfB38_5031) 38634..39035 - 402 WP_008324137 hypothetical protein -
CfB38_RS25085 (CfB38_5032) 39019..39204 - 186 WP_008324139 hypothetical protein -
CfB38_RS25090 (CfB38_5033) 39208..39432 - 225 WP_008324141 TraR/DksA C4-type zinc finger protein -
CfB38_RS25095 (CfB38_5034) 39552..40091 - 540 WP_058659925 type IV conjugative transfer system lipoprotein TraV traV
CfB38_RS25100 (CfB38_5035) 40113..41507 - 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
CfB38_RS25105 (CfB38_5036) 41494..42237 - 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
CfB38_RS25110 (CfB38_5037) 42224..42790 - 567 WP_008324158 type IV conjugative transfer system protein TraE traE
CfB38_RS25115 (CfB38_5038) 42805..43110 - 306 WP_008324160 type IV conjugative transfer system protein TraL traL
CfB38_RS25120 (CfB38_5039) 43261..43611 - 351 WP_016247536 type IV conjugative transfer system pilin TraA -
CfB38_RS25125 (CfB38_5040) 43669..43893 - 225 WP_008324165 TraY domain-containing protein -
CfB38_RS25130 (CfB38_5041) 43980..44669 - 690 WP_008324166 hypothetical protein -
CfB38_RS25135 (CfB38_5042) 44858..45250 - 393 WP_065945173 conjugal transfer relaxosome DNA-binding protein TraM -
CfB38_RS25140 (CfB38_5043) 45682..46158 + 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
CfB38_RS25145 (CfB38_5044) 46205..46735 - 531 WP_008324170 antirestriction protein -
CfB38_RS25150 (CfB38_5045) 47362..48192 - 831 WP_065945174 N-6 DNA methylase -
CfB38_RS25155 (CfB38_5046) 48235..48498 - 264 WP_008324174 hypothetical protein -
CfB38_RS25160 (CfB38_5047) 48584..48928 - 345 WP_008324177 hypothetical protein -
CfB38_RS25165 (CfB38_5048) 48975..49262 - 288 WP_008324178 hypothetical protein -
CfB38_RS25170 (CfB38_5049) 49316..49690 - 375 WP_008324180 hypothetical protein -
CfB38_RS25175 (CfB38_5050) 50317..50676 - 360 WP_008324181 hypothetical protein -
CfB38_RS25180 (CfB38_5051) 50738..51061 - 324 WP_008324183 hypothetical protein -

Host bacterium

ID   21006 GenBank   NZ_CP016763
Plasmid name   pOZ172 Incompatibility group   IncFII
Plasmid size   127005 bp Coordinate of oriT [Strand]   45508..45610 [-]
Host baterium   Citrobacter freundii strain B38

Cargo genes

Drug resistance gene   mcr-10, blaIMP-4, aph(3')-XV
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -