Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111001
Name   oriT_pCf-N3 in_silico
Organism   Citrobacter freundii strain Cf-Emp
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP110779 (12123..12212 [-], 90 nt)
oriT length   90 nt
IRs (inverted repeats)      34..41, 44..51  (AGTGCGAT..ATCGCACT)
 20..25, 39..44  (TAAATC..GATTTA)
Location of nic site      62..63
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 90 nt

>oriT_pCf-N3
TATTTCATTTTTTGTTTTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7238 GenBank   WP_050136475
Name   mobF_OPR78_RS27300_pCf-N3 insolico UniProt ID   _
Length   1072 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1072 a.a.        Molecular weight: 118873.51 Da        Isoelectric Point: 6.4635

>WP_050136475.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGDIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDVEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNDSQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGYNVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGTTEKGTFTLTNSKG
REIELDQKQAAYLSYAYATTVHKAQGLTCDRVLFNIDTRSLTTSKDVFYVGISRARHEVEIFTDDKKRLL
SSASRNSPKTTASEIDRFLGMEERYKDVNRSYGHSDGQQEKSYGHDAGHQTEEKENTMKNATEAAHDGPD
TSGTENTSQDLRQREQEEVNAAIRYEQRQEATPEMEANPYHDYERYADEGPDYGDMQDYSTYEEYERARD
VELPQHEHENHQHDHDKEGYGL

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(16-288)

AAA domain (AAA_30)

(480-656)

UvrD-like helicase C-terminal domain (UvrD_C_2)

(855-899)


  Protein structure



No available structure.




T4CP

ID   8242 GenBank   WP_040223430
Name   t4cp2_OPR78_RS27295_pCf-N3 insolico UniProt ID   _
Length   510 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 510 a.a.        Molecular weight: 57917.09 Da        Isoelectric Point: 9.6871

>WP_040223430.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MTEQERGLIFLCSLLGPIPFVWFITAKFTYGINSETAHYLVPYLLKNTFNLWPLWAAIIAGVVIGLCGFI
GFIIYDKGRVYKGPRFKRILRGTKLARASTLAEKTKERGKKQLMIAGVPVPTEYETLHFSIGGATGTGKS
TVIKEAIYSSLKRGTDKRIVLDPNGEYVETFYRPGDVILSPYDKRSPGWSMFNEIRDDFDYDLYAVSIIQ
ESKERSAEEWYRYGRLIYREVSKKLLTLKRNPTMEEVMHWCTIVENDKLKEFVKGTPAEALFIKGAERAT
GSARFVLGDKLAPHLKMPAGDFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTYSQLIERYGINIAETLLGSMRSGIVMGSSRL
GKETLEQMSRALGEIEGEVEHKQGNPFQAGIGNRPRIETRTVRAVTPTEISELKNLTGYVYFPGDLPVGK
FKTKYVKYTRKNPVPGIIMR

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(113-492)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 12783..30292

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
OPR78_RS27255 (OPR78_27245) 8570..9247 + 678 WP_050136486 DUF5417 domain-containing protein -
OPR78_RS27260 (OPR78_27250) 9428..9634 + 207 WP_048987680 DUF905 family protein -
OPR78_RS27265 (OPR78_27255) 9709..9891 + 183 WP_040223426 hypothetical protein -
OPR78_RS27270 (OPR78_27260) 9950..10300 - 351 WP_227660645 hypothetical protein -
OPR78_RS27275 (OPR78_27265) 10364..10732 - 369 WP_040223427 plasmid stabilization protein StbC -
OPR78_RS27280 (OPR78_27270) 10735..11451 - 717 WP_040223428 StbB family protein -
OPR78_RS27285 (OPR78_27275) 11460..11891 - 432 WP_040223429 plasmid stabilization protein StbA -
OPR78_RS27290 (OPR78_27280) 12358..12783 + 426 WP_227660646 traK protein -
OPR78_RS27295 (OPR78_27285) 12783..14315 + 1533 WP_040223430 type IV secretion system DNA-binding domain-containing protein virb4
OPR78_RS27300 (OPR78_27290) 14320..17538 + 3219 WP_050136475 MobF family relaxase -
OPR78_RS27305 (OPR78_27295) 17535..18200 + 666 WP_283523261 DUF6710 family protein -
OPR78_RS27310 (OPR78_27300) 18193..18555 + 363 WP_024561906 hypothetical protein -
OPR78_RS27315 (OPR78_27305) 19175..19486 - 312 WP_040223418 hypothetical protein -
OPR78_RS27320 (OPR78_27310) 19483..19950 - 468 WP_050136493 phospholipase D family protein -
OPR78_RS27325 (OPR78_27315) 20007..21008 - 1002 WP_058672984 ATPase, T2SS/T4P/T4SS family virB11
OPR78_RS27330 (OPR78_27320) 21059..22192 - 1134 WP_040223416 type IV secretion system protein VirB10 virB10
OPR78_RS27335 (OPR78_27325) 22192..23079 - 888 WP_040223415 TrbG/VirB9 family P-type conjugative transfer protein virB9
OPR78_RS27340 (OPR78_27330) 23090..23785 - 696 WP_040223414 type IV secretion system protein virB8
OPR78_RS27345 (OPR78_27335) 24004..25041 - 1038 WP_040223413 type IV secretion system protein virB6
OPR78_RS27350 (OPR78_27340) 25058..25300 - 243 WP_040223412 EexN family lipoprotein -
OPR78_RS27355 (OPR78_27345) 25310..26020 - 711 WP_040223411 type IV secretion system protein virB5
OPR78_RS27360 (OPR78_27350) 26036..28609 - 2574 WP_040223410 VirB4 family type IV secretion/conjugal transfer ATPase virb4
OPR78_RS27365 (OPR78_27355) 28610..28927 - 318 WP_040223409 VirB3 family type IV secretion system protein virB3
OPR78_RS27370 (OPR78_27360) 28967..29263 - 297 WP_015060075 TrbC/VirB2 family protein virB2
OPR78_RS27375 (OPR78_27365) 29510..30292 - 783 WP_014014952 lytic transglycosylase domain-containing protein virB1
OPR78_RS27380 (OPR78_27370) 30392..30709 + 318 WP_000960955 H-NS family nucleoid-associated regulatory protein -
OPR78_RS27385 (OPR78_27375) 30713..31063 + 351 WP_014014953 hypothetical protein -
OPR78_RS27390 (OPR78_27380) 31060..31398 + 339 WP_000040982 hypothetical protein -
OPR78_RS27395 (OPR78_27385) 31402..31710 + 309 WP_000733764 hypothetical protein -
OPR78_RS27400 (OPR78_27390) 32078..33082 - 1005 WP_047642113 IS110-like element IS4321 family transposase -
OPR78_RS27405 (OPR78_27395) 33167..33247 - 81 WP_227538286 hypothetical protein -
OPR78_RS27410 (OPR78_27400) 33522..34274 - 753 WP_004729622 alpha/beta hydrolase -

Host bacterium

ID   11436 GenBank   NZ_CP110779
Plasmid name   pCf-N3 Incompatibility group   IncN3
Plasmid size   74000 bp Coordinate of oriT [Strand]   12123..12212 [-]
Host baterium   Citrobacter freundii strain Cf-Emp

Cargo genes

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