Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105935
Name   oriT_pCF10-KPC in_silico
Organism   Citrobacter youngae strain CF10
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP102504 (11378..11467 [-], 90 nt)
oriT length   90 nt
IRs (inverted repeats)      34..41, 44..51  (AGTGCGAT..ATCGCACT)
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_pCF10-KPC
TATTTCATTTTTTGTTTTTTTAATCAGTTAGTTAGTGCGATTCATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4003 GenBank   WP_024561907
Name   mobF_NUG39_RS26365_pCF10-KPC insolico UniProt ID   H1ZMV6
Length   1072 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1072 a.a.        Molecular weight: 118896.59 Da        Isoelectric Point: 6.4636

>WP_024561907.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGEIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDIEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNNDQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGFNVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGTTEKGTFTLTNAKG
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


Source ID Structure
AlphaFold DB H1ZMV6


T4CP

ID   4009 GenBank   WP_032493179
Name   t4cp2_NUG39_RS26360_pCF10-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: 57912.96 Da        Isoelectric Point: 9.5127

>WP_032493179.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVAIIAGAVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAEKTKERDHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
TIIKEAIYSSLKRGTDKRIVLDPNGEYVETFYRPGDVILSPYDKRSPGWSMFNEIRDDFDYDLYAVSIIQ
ESKERSAEEWYRYGRLIYREVSKKLLTLKRSPTMEEVMHWCTIVENEKLKEFVKGTPAEALFIKGAERAT
GSARFVLGDKLAPHLKMPAGDFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTYSQLIERYGINIAETLLGSMRSGIVMGSSRL
GKETLEQMSRALGEIEGEVEHKQGNPFQAGIGNRPRIETRTVRAVTPTEISELKNLTGYVYFPGDLPVGK
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: 39359..45122

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NUG39_RS26465 (NUG39_26465) 35499..36647 + 1149 WP_257749372 CMY-1/MOX family class C beta-lactamase -
NUG39_RS26470 (NUG39_26470) 36940..37725 + 786 Protein_43 MFS transporter -
NUG39_RS26475 (NUG39_26475) 37909..38250 - 342 WP_011918360 hypothetical protein -
NUG39_RS26480 (NUG39_26480) 38260..38544 - 285 WP_257749375 phosphoribulokinase -
NUG39_RS26485 (NUG39_26485) 38608..39312 - 705 WP_001067855 IS6-like element IS26 family transposase -
NUG39_RS26490 (NUG39_26490) 39359..39880 - 522 WP_257749376 type IV secretion system protein virB6
NUG39_RS26495 (NUG39_26495) 39897..40139 - 243 WP_000858958 EexN family lipoprotein -
NUG39_RS26500 (NUG39_26500) 40149..40850 - 702 WP_014014949 type IV secretion system protein virB5
NUG39_RS26505 (NUG39_26505) 40866..43439 - 2574 WP_032493176 VirB4 family type IV secretion/conjugal transfer ATPase virb4
NUG39_RS26510 (NUG39_26510) 43440..43757 - 318 WP_000462629 VirB3 family type IV secretion system protein virB3
NUG39_RS26515 (NUG39_26515) 43797..44093 - 297 WP_015060075 TrbC/VirB2 family protein virB2
NUG39_RS26520 (NUG39_26520) 44340..45122 - 783 WP_024562119 lytic transglycosylase domain-containing protein virB1
NUG39_RS26525 (NUG39_26525) 45222..45539 + 318 WP_000960955 H-NS family nucleoid-associated regulatory protein -
NUG39_RS26530 (NUG39_26530) 45543..45893 + 351 WP_024562120 hypothetical protein -
NUG39_RS26535 (NUG39_26535) 45890..46228 + 339 WP_032493175 hypothetical protein -
NUG39_RS26540 (NUG39_26540) 46232..46540 + 309 WP_000733764 hypothetical protein -
NUG39_RS26545 (NUG39_26545) 46825..47010 + 186 WP_024562121 ribbon-helix-helix domain-containing protein -
NUG39_RS26550 (NUG39_26550) 47007..47615 - 609 WP_000275218 recombinase family protein -
NUG39_RS26555 (NUG39_26555) 47802..48134 - 333 WP_045723726 hypothetical protein -
NUG39_RS26560 (NUG39_26560) 48206..48400 - 195 WP_050136673 hypothetical protein -
NUG39_RS26565 (NUG39_26565) 48487..49116 - 630 WP_064754415 hypothetical protein -

Host bacterium

ID   6372 GenBank   NZ_CP102504
Plasmid name   pCF10-KPC Incompatibility group   IncN3
Plasmid size   49302 bp Coordinate of oriT [Strand]   11378..11467 [-]
Host baterium   Citrobacter youngae strain CF10

Cargo genes

Drug resistance gene   blaKPC-2, blaMOX-3
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -