Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105018
Name   oriT_pC2601-5-NDM in_silico
Organism   Klebsiella pneumoniae strain C2601
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP039817 (22286..22368 [-], 83 nt)
oriT length   83 nt
IRs (inverted repeats)      27..34, 37..44  (AGTGCGAT..ATCGCACT)
 13..18, 32..37  (TAAATC..GATTTA)
Location of nic site      55..56
Conserved sequence flanking the
  nic site    		  GGTGTATAGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 83 nt

>oriT_pC2601-5-NDM
TTTTTTGTTTTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3512 GenBank   WP_014014966
Name   mobF_FBF56_RS28395_pC2601-5-NDM insolico UniProt ID   I7CZU5
Length   1068 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1068 a.a.        Molecular weight: 118452.14 Da        Isoelectric Point: 6.4309

>WP_014014966.1 MULTISPECIES: MobF family relaxase [Enterobacterales]
MLDITTITRIDIASVVGYYADAKDDYYSKDSSFTAWHGQGAEALGLSGEVSSQRFKELLVGEIDPFTQMK
RSSGDATKERLGYDLTFSAPKGVSMQALIHGDKAIIAAHEKAVAAAVQEAEKLAQARTTHAGKTITQNTG
NLVVASFRHETSRALDPELHTHAFVMNMTQRGDGQWRALKNDELMRAKMHLGDVYKQELALELTKAGYEL
RYNNKNNTFDMAHFTDEQIRGFSRRSAQIEEGLAAMGLTRETADAQTKSRVSMATRDKKTDDYSREDIHK
EWVNRANELGIDFNDLSWAGKGKDGPQTSMNTVPNFTSPEVKADRAIQFALKSLSERDASFDQSRLLAVA
NKKAIGQASKQDIEAAYYRAVAKGAIIEGEARYTTTTDQRSKDAPPLPAMTKAEWQAQLTDKKGMNNDQA
KALVAEGIKSGRLKKTSHRVTTVEGIRVEKAVLNIEARGRGKVIAALTSEQVTAQLVGKTLKAEQQKSVV
DICTTTDRFVAAHGFAGTGKSYMTMSAKAVLESQGFNVTALAPYGTQKKSLEDEGMPARTVAAFVKAKDK
KIDEKSVVFIDEAGVIPARQMKVLMETIEKAGARAVFLGDTSQTKAVEAGKPFEQLISAGMQTSYMKDIQ
RQKNDVLLEAVKLAAEGHISGSLARLSNISAEKDQDKRLEAVANRWLSFSPEQREGTLIISGTNESRVIL
NSQIREALQLQGKGVEVNFLERVDSTQAERRDSKYYQVGQIIIPEKDYKNGLQRGESYRVLDTGPGNLLT
VAGSDGQKISFSPRTHKNLSVYTSVAAELAVGDKVMVTRNDKTLDVANGDRFTVTGTTEKGTFTLTNAKG
REIELDQKQAAYLSYAYATTVHKAQGLTCDRVLFNIDTRSLTTSKDVFYVGISRARHEVEIFTDDKKRLL
SSASRNSPKTTASEIDRFLGMEERYKDVNRSDGQQEKSYGHDAGHQTEEKENTMKNATEAAHDGPDTSGT
ENTSQDLRQREQEEVNAAIRYEQRQEATPEMEANPYHDYERYADEGPDYGDMQDYSTYEEYERARDVELP
QHEHENHQHDHDKEGYGL

  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 I7CZU5


T4CP

ID   3466 GenBank   WP_014014965
Name   t4cp2_FBF56_RS28390_pC2601-5-NDM 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: 58174.11 Da        Isoelectric Point: 9.7081

>WP_014014965.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MTEQERGLIFLCSLLGPIPFVWFITAKFVYGINSETAHYLVPYLLKNTFNLWPLWVAIIAGAVIGLCGFI
GFIIYDKGRVYKGPRFKRVLRGTKLVRASSLAERTKERGHKQLTVAGVPVPTEYETLHFSIGGATGTGKS
TIIKEAIYSSLKRGRDKRVILDPNGEYVETFYRENDIILNPYDKRSPGWSMFNEIRDEFDYDLYAVSIIQ
ESKERSAEEWYRYGRLLYREVSKKLLTHKRNPSMEEVLYWCNVAEYDKVKDFVKGTPAESLFIKGAERAT
GSARFVLGDKLASHLKMPEGNFSLRDWLEDDKPGTLFITWQEQMKKSLNPLISCWLDIMFSSLLGMGKRD
QRTLFFIDELESLEYLPNLQDLLTKGRKSGASVWAGYQTFSQLVERYGINIAETLLGSMRSGIVMGSSRL
GKATLEHMSRALGEIEGEIERRQGGILQSGPNNRPRIETRTVRAVTPTEISELRNLTGYIYFPGDLPVGK
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: 38583..48865

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FBF56_RS28430 (FBF56_28560) 33936..34748 - 813 WP_004201164 subclass B1 metallo-beta-lactamase NDM-1 -
FBF56_RS28435 34849..35124 - 276 WP_052264168 hypothetical protein -
FBF56_RS28440 (FBF56_28565) 35044..36075 + 1032 WP_001395480 IS630-like element ISEc33 family transposase -
FBF56_RS28445 (FBF56_28570) 36094..36840 - 747 Protein_37 IS30-like element ISAba125 family transposase -
FBF56_RS28450 (FBF56_28575) 37751..38062 - 312 WP_000570332 hypothetical protein -
FBF56_RS28455 (FBF56_28580) 38059..38571 - 513 WP_029697418 phospholipase D family protein -
FBF56_RS28460 (FBF56_28585) 38583..39584 - 1002 WP_001076634 ATPase, T2SS/T4P/T4SS family virB11
FBF56_RS28465 (FBF56_28590) 39635..40774 - 1140 WP_014014945 type IV secretion system protein VirB10 virB10
FBF56_RS28470 (FBF56_28595) 40774..41661 - 888 WP_014014946 TrbG/VirB9 family P-type conjugative transfer protein virB9
FBF56_RS28475 (FBF56_28600) 41672..42367 - 696 WP_014014947 type IV secretion system protein virB8
FBF56_RS29275 (FBF56_28605) 42378..42509 - 132 WP_072000589 conjugal transfer protein TraN -
FBF56_RS28480 (FBF56_28610) 42586..43623 - 1038 WP_014014948 type IV secretion system protein virB6
FBF56_RS28485 (FBF56_28615) 43640..43882 - 243 WP_000858958 EexN family lipoprotein -
FBF56_RS28490 (FBF56_28620) 43892..44593 - 702 WP_014014949 type IV secretion system protein virB5
FBF56_RS28495 (FBF56_28625) 44609..47182 - 2574 WP_014014950 VirB4 family type IV secretion/conjugal transfer ATPase virb4
FBF56_RS28500 (FBF56_28630) 47183..47500 - 318 WP_000462629 VirB3 family type IV secretion system protein virB3
FBF56_RS28505 (FBF56_28635) 47540..47881 - 342 WP_001121032 TrbC/VirB2 family protein virB2
FBF56_RS28510 (FBF56_28645) 48083..48865 - 783 WP_014014952 lytic transglycosylase domain-containing protein virB1
FBF56_RS28515 (FBF56_28650) 48965..49282 + 318 WP_000960955 H-NS family nucleoid-associated regulatory protein -
FBF56_RS28520 (FBF56_28655) 49286..49636 + 351 WP_014014953 hypothetical protein -
FBF56_RS28525 (FBF56_28660) 49633..49971 + 339 WP_000040982 hypothetical protein -
FBF56_RS28530 (FBF56_28665) 49975..50283 + 309 WP_000733764 hypothetical protein -
FBF56_RS28535 (FBF56_28670) 50568..50753 + 186 WP_014014955 ribbon-helix-helix domain-containing protein -
FBF56_RS28540 (FBF56_28675) 50750..51358 - 609 WP_000275218 recombinase family protein -
FBF56_RS28545 (FBF56_28680) 51524..51856 - 333 WP_015060077 hypothetical protein -

Host bacterium

ID   5456 GenBank   NZ_CP039817
Plasmid name   pC2601-5-NDM Incompatibility group   IncN2
Plasmid size   51995 bp Coordinate of oriT [Strand]   22286..22368 [-]
Host baterium   Klebsiella pneumoniae strain C2601

Cargo genes

Drug resistance gene   blaNDM-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -