Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120626
Name   oriT_pKPC-c9fd in_silico
Organism   Citrobacter freundii complex sp. CFNIH4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP026232 (48243..48342 [-], 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_pKPC-c9fd
TATTGAATGTTTTATTCTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATCAGTTTGGTAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12994 GenBank   WP_020323154
Name   mobF_C2U41_RS26205_pKPC-c9fd 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   15256 GenBank   WP_020323171
Name   t4cp2_C2U41_RS26200_pKPC-c9fd 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: 48913..62137

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C2U41_RS29390 44700..45377 + 678 WP_020323167 DUF5417 domain-containing protein -
C2U41_RS26165 (C2U41_26135) 45559..45765 + 207 WP_020323152 DUF905 family protein -
C2U41_RS26170 (C2U41_26140) 45839..46021 + 183 WP_000170167 hypothetical protein -
C2U41_RS29845 46080..46430 - 351 WP_223226687 hypothetical protein -
C2U41_RS26180 (C2U41_26150) 46494..46862 - 369 WP_032416596 plasmid stabilization protein StbC -
C2U41_RS26185 (C2U41_26155) 46865..47581 - 717 WP_020323147 StbB family protein -
C2U41_RS29850 47590..48021 - 432 WP_020323173 plasmid stabilization protein StbA -
C2U41_RS29855 48488..48913 + 426 WP_223831802 traK protein -
C2U41_RS26200 (C2U41_26170) 48913..50445 + 1533 WP_020323171 type IV secretion system DNA-binding domain-containing protein virb4
C2U41_RS26205 (C2U41_26175) 50450..53668 + 3219 WP_020323154 MobF family relaxase -
C2U41_RS26210 (C2U41_26180) 53665..54330 + 666 WP_020323157 DUF6710 family protein -
C2U41_RS26215 (C2U41_26185) 54323..54685 + 363 WP_020323170 hypothetical protein -
C2U41_RS26220 (C2U41_26190) 55301..55612 - 312 WP_032416518 hypothetical protein -
C2U41_RS26225 (C2U41_26195) 55609..56076 - 468 WP_046092601 phospholipase D family protein -
C2U41_RS26230 (C2U41_26200) 56133..57134 - 1002 WP_020323165 ATPase, T2SS/T4P/T4SS family virB11
C2U41_RS26235 (C2U41_26205) 57185..58318 - 1134 WP_020323153 type IV secretion system protein VirB10 virB10
C2U41_RS26240 (C2U41_26210) 58318..59205 - 888 WP_020323166 TrbG/VirB9 family P-type conjugative transfer protein virB9
C2U41_RS26245 (C2U41_26215) 59216..59911 - 696 WP_001208352 type IV secretion system protein virB8
C2U41_RS30045 (C2U41_26220) 59922..60053 - 132 WP_032493177 hypothetical protein -
C2U41_RS26255 (C2U41_26225) 60130..61167 - 1038 WP_020323169 type IV secretion system protein virB6
C2U41_RS26260 (C2U41_26230) 61184..61426 - 243 WP_000858958 EexN family lipoprotein -
C2U41_RS26265 (C2U41_26235) 61436..62137 - 702 WP_020323143 type IV secretion system protein virB5

Host bacterium

ID   21055 GenBank   NZ_CP026232
Plasmid name   pKPC-c9fd Incompatibility group   IncN3
Plasmid size   62590 bp Coordinate of oriT [Strand]   48243..48342 [-]
Host baterium   Citrobacter freundii complex sp. CFNIH4

Cargo genes

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