Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108837
Name   oriT_p2075-2 in_silico
Organism   Citrobacter freundii strain 2075
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP119167 (45330..45432 [+], 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_p2075-2
CTCACCACCAAAAGCTCCACACCCCACGCAAAATTAAAGTTTTGCTGATTGGGTATTCAAATCATGCAGTTAGTGAAAAAGTAATGTGAAATAATTTATTTTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5924 GenBank   WP_057064462
Name   traI_P0S03_RS25090_p2075-2 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   6373 GenBank   WP_008324134
Name   traC_P0S03_RS25015_p2075-2 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   6374 GenBank   WP_057064463
Name   traD_P0S03_RS25085_p2075-2 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: 44782..69570

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
P0S03_RS24905 (P0S03_24905) 39880..40203 + 324 WP_008324183 hypothetical protein -
P0S03_RS24910 (P0S03_24910) 40265..40624 + 360 WP_015493069 hypothetical protein -
P0S03_RS24915 (P0S03_24915) 41250..41624 + 375 WP_008324180 hypothetical protein -
P0S03_RS24920 (P0S03_24920) 41678..41965 + 288 WP_008324178 hypothetical protein -
P0S03_RS24925 (P0S03_24925) 42012..42356 + 345 WP_008324177 hypothetical protein -
P0S03_RS24930 (P0S03_24930) 42442..42705 + 264 WP_008324174 hypothetical protein -
P0S03_RS24935 (P0S03_24935) 42748..43578 + 831 WP_008324171 N-6 DNA methylase -
P0S03_RS24940 (P0S03_24940) 44205..44735 + 531 WP_008324170 antirestriction protein -
P0S03_RS24945 (P0S03_24945) 44782..45258 - 477 WP_008324168 transglycosylase SLT domain-containing protein virB1
P0S03_RS24950 (P0S03_24950) 45690..46082 + 393 WP_008324167 conjugal transfer relaxosome DNA-binding protein TraM -
P0S03_RS24955 (P0S03_24955) 46271..46960 + 690 WP_008324166 hypothetical protein -
P0S03_RS24960 (P0S03_24960) 47047..47271 + 225 WP_008324165 TraY domain-containing protein -
P0S03_RS24965 (P0S03_24965) 47329..47679 + 351 WP_016247536 type IV conjugative transfer system pilin TraA -
P0S03_RS24970 (P0S03_24970) 47830..48135 + 306 WP_008324160 type IV conjugative transfer system protein TraL traL
P0S03_RS24975 (P0S03_24975) 48150..48716 + 567 WP_016247535 type IV conjugative transfer system protein TraE traE
P0S03_RS24980 (P0S03_24980) 48703..49446 + 744 WP_008324157 type-F conjugative transfer system secretin TraK traK
P0S03_RS24985 (P0S03_24985) 49433..50827 + 1395 WP_008324156 F-type conjugal transfer pilus assembly protein TraB traB
P0S03_RS24990 (P0S03_24990) 50849..51388 + 540 WP_016247533 type IV conjugative transfer system lipoprotein TraV traV
P0S03_RS24995 (P0S03_24995) 51508..51732 + 225 WP_016247532 TraR/DksA C4-type zinc finger protein -
P0S03_RS25000 (P0S03_25000) 51736..51921 + 186 WP_008324139 hypothetical protein -
P0S03_RS25005 (P0S03_25005) 51905..52306 + 402 WP_008324137 hypothetical protein -
P0S03_RS25010 (P0S03_25010) 52296..52862 + 567 WP_008324135 conjugal transfer pilus-stabilizing protein TraP -
P0S03_RS25015 (P0S03_25015) 52855..55485 + 2631 WP_008324134 type IV secretion system protein TraC virb4
P0S03_RS25020 (P0S03_25020) 55482..55829 + 348 WP_008324133 type-F conjugative transfer system protein TrbI -
P0S03_RS25025 (P0S03_25025) 55829..56476 + 648 WP_008324132 type-F conjugative transfer system protein TraW traW
P0S03_RS25030 (P0S03_25030) 56479..57465 + 987 WP_032160671 conjugal transfer pilus assembly protein TraU traU
P0S03_RS25035 (P0S03_25035) 57482..58111 + 630 WP_008324130 type-F conjugative transfer system pilin assembly protein TrbC trbC
P0S03_RS25040 (P0S03_25040) 58108..59961 + 1854 WP_283903510 type-F conjugative transfer system mating-pair stabilization protein TraN traN
P0S03_RS25045 (P0S03_25045) 59993..60181 + 189 WP_008324128 conjugal transfer protein TrbE -
P0S03_RS25050 (P0S03_25050) 60212..60961 + 750 WP_008324127 type-F conjugative transfer system pilin assembly protein TraF traF
P0S03_RS25055 (P0S03_25055) 60978..61226 + 249 WP_045379412 type-F conjugative transfer system pilin chaperone TraQ -
P0S03_RS25060 (P0S03_25060) 61216..61761 + 546 WP_045379409 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
P0S03_RS25065 (P0S03_25065) 61800..63134 + 1335 WP_230199841 conjugal transfer pilus assembly protein TraH traH
P0S03_RS25070 (P0S03_25070) 63134..65956 + 2823 WP_045379403 conjugal transfer mating-pair stabilization protein TraG traG
P0S03_RS25075 (P0S03_25075) 65970..66446 + 477 WP_071886900 hypothetical protein -
P0S03_RS25080 (P0S03_25080) 66483..67283 + 801 WP_226999298 hypothetical protein -
P0S03_RS25085 (P0S03_25085) 67402..69570 + 2169 WP_057064463 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   9272 GenBank   NZ_CP119167
Plasmid name   p2075-2 Incompatibility group   IncFII
Plasmid size   81274 bp Coordinate of oriT [Strand]   45330..45432 [+]
Host baterium   Citrobacter freundii strain 2075

Cargo genes

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