Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120404
Name   oriT_p07B16020_B_KPC in_silico
Organism   Citrobacter freundii strain 07B16CRGN020
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OQ821030 (42860..42959 [-], 100 nt)
oriT length   100 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: 100 nt

>oriT_p07B16020_B_KPC
TATTGAATGTTTTATTCTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATCAGTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12843 GenBank   WP_020323154
Name   mobF_SLH58_RS00260_p07B16020_B_KPC insolico UniProt ID   A0A0R8CGS3
Length   1072 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1072 a.a.        Molecular weight: 118689.40 Da        Isoelectric Point: 6.4933

>WP_020323154.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGEIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDIEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNNGQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGFHVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGATEKGTFTLTNAKG
REIELDQKQAAYLSYAYATTVHKAQGLTCDRVLFNIDTRSLTTSKDVFYVGISRARHEVEIFTDDKGRLL
SSASRNSPKTTASEIDRFLGMEERYKDVNRSYGHDDGQQAKSYGHEAGQQTGEKENTMKNATEAAHDGPD
TSGTENTSQDLRQREQEEVNAAIRYEQRQEATPEMEANPYHDYERYADEGPDYGDMQDYSTYEEYERARD
VELPQHEHENHQHDYDKEGYGL

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(16-288)

UvrD-like helicase C-terminal domain (UvrD_C_2)

(855-899)

AAA domain (AAA_30)

(480-656)


  Protein structure


Source ID Structure
AlphaFold DB A0A0R8CGS3


T4CP

ID   15089 GenBank   WP_020323171
Name   t4cp2_SLH58_RS00255_p07B16020_B_KPC 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: 58208.12 Da        Isoelectric Point: 9.7037

>WP_020323171.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVSIIAGSVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAEKTKERGHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
TIIKEAIYSSLKRGRDKRVILDPNGEYVETFYRENDIILNPYDKRSPGWSMFNEIRDEFDYDLYAVSIIQ
ESKERSAEEWYRYGRLLYREVSKKLLTHKRNPSMEEVLYWCNVAEYDKVKDFVKGTPAESLFIKGAERAT
GSARFVLGDKLASHLKMPEGNFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTFSQLVERYGINIAETLLGSMRSGIVMGSSRL
GKATLEHMSRALGEIEGEIERRQGSLLQSGPNNRPRIETRTVRAVTPTEISELRNLTGYIYFPGDLPVGK
FKTKHVQYTRKNPVPGIIMR

  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: 43530..61026

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SLH58_RS00215 (GFOBKLCA_00044) 39200..39994 + 795 WP_053075878 DUF5417 domain-containing protein -
SLH58_RS00220 (GFOBKLCA_00045) 40176..40382 + 207 WP_020323152 DUF905 family protein -
SLH58_RS00225 (GFOBKLCA_00046) 40456..40638 + 183 WP_000170167 hypothetical protein -
SLH58_RS00230 (GFOBKLCA_00047) 40697..41068 - 372 WP_227665545 hypothetical protein -
SLH58_RS00235 (GFOBKLCA_00048) 41111..41479 - 369 WP_032416596 plasmid stabilization protein StbC -
SLH58_RS00240 (GFOBKLCA_00049) 41482..42198 - 717 WP_020323147 StbB family protein -
SLH58_RS00245 (GFOBKLCA_00050) 42207..42638 - 432 WP_020323173 plasmid stabilization protein StbA -
SLH58_RS00250 (GFOBKLCA_00051) 43054..43530 + 477 WP_223226686 traK protein -
SLH58_RS00255 (GFOBKLCA_00052) 43530..45062 + 1533 WP_020323171 type IV secretion system DNA-binding domain-containing protein virb4
SLH58_RS00260 (GFOBKLCA_00053) 45067..48285 + 3219 WP_020323154 MobF family relaxase -
SLH58_RS00265 (GFOBKLCA_00054) 48282..48947 + 666 WP_020323157 DUF6710 family protein -
SLH58_RS00270 (GFOBKLCA_00055) 48940..49302 + 363 WP_020323170 hypothetical protein -
SLH58_RS00275 (GFOBKLCA_00056) 49918..50229 - 312 WP_032416518 hypothetical protein -
SLH58_RS00280 (GFOBKLCA_00057) 50226..50693 - 468 WP_046092601 phospholipase D family protein -
SLH58_RS00285 (GFOBKLCA_00058) 50750..51751 - 1002 WP_020323165 ATPase, T2SS/T4P/T4SS family virB11
SLH58_RS00290 (GFOBKLCA_00059) 51802..52935 - 1134 WP_020323153 type IV secretion system protein VirB10 virB10
SLH58_RS00295 (GFOBKLCA_00060) 52935..53822 - 888 WP_020323166 TrbG/VirB9 family P-type conjugative transfer protein virB9
SLH58_RS00300 (GFOBKLCA_00061) 53833..54528 - 696 WP_001208352 type IV secretion system protein virB8
SLH58_RS00375 (GFOBKLCA_00062) 54539..54670 - 132 WP_032493177 hypothetical protein -
SLH58_RS00305 (GFOBKLCA_00063) 54747..55784 - 1038 WP_020323169 type IV secretion system protein virB6
SLH58_RS00310 (GFOBKLCA_00064) 55801..56043 - 243 WP_000858958 EexN family lipoprotein -
SLH58_RS00315 (GFOBKLCA_00065) 56053..56754 - 702 WP_020323143 type IV secretion system protein virB5
SLH58_RS00320 (GFOBKLCA_00066) 56770..59343 - 2574 WP_020323176 VirB4 family type IV secretion/conjugal transfer ATPase virb4
SLH58_RS00325 (GFOBKLCA_00067) 59344..59661 - 318 WP_000462629 type IV secretion system protein VirB3 virB3
SLH58_RS00330 (GFOBKLCA_00068) 59701..60042 - 342 WP_001121032 TrbC/VirB2 family protein virB2
SLH58_RS00335 (GFOBKLCA_00070) 60244..61026 - 783 WP_032416587 lytic transglycosylase domain-containing protein virB1
SLH58_RS00340 (GFOBKLCA_00071) 61090..61443 + 354 WP_223598071 H-NS histone family protein -
SLH58_RS00345 (GFOBKLCA_00072) 61447..61797 + 351 WP_032416642 hypothetical protein -
SLH58_RS00350 (GFOBKLCA_00073) 61776..62132 + 357 WP_227665546 hypothetical protein -
SLH58_RS00355 (GFOBKLCA_00074) 62136..62444 + 309 WP_032416643 hypothetical protein -
SLH58_RS00360 (GFOBKLCA_00075) 62729..62914 + 186 WP_006118530 ribbon-helix-helix domain-containing protein -
SLH58_RS00365 (GFOBKLCA_00076) 62911..63519 - 609 WP_032449362 recombinase family protein -
SLH58_RS00370 (GFOBKLCA_00077) 63685..64017 - 333 WP_020323168 hypothetical protein -

Host bacterium

ID   20833 GenBank   NZ_OQ821030
Plasmid name   p07B16020_B_KPC Incompatibility group   IncN3
Plasmid size   64156 bp Coordinate of oriT [Strand]   42860..42959 [-]
Host baterium   Citrobacter freundii strain 07B16CRGN020

Cargo genes

Drug resistance gene   blaKPC-2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -