Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105024
Name   oriT_pC2972-5-NDM in_silico
Organism   Klebsiella pneumoniae strain C2972
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP039806 (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_pC2972-5-NDM
TTTTTTGTTTTTTAAATCAGTTAGTTAGTGCGATTTATCGCACTGCGTTAGGTGTATAGCAGGTTAAGGGCTAAAAAATAATC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3516 GenBank   WP_014014966
Name   mobF_FBF57_RS28975_pC2972-5-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   3475 GenBank   WP_014014965
Name   t4cp2_FBF57_RS28970_pC2972-5-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
FBF57_RS29010 (FBF57_29150) 33936..34748 - 813 WP_004201164 subclass B1 metallo-beta-lactamase NDM-1 -
FBF57_RS29015 34849..35124 - 276 WP_052264168 hypothetical protein -
FBF57_RS29020 (FBF57_29155) 35044..36075 + 1032 WP_001395480 IS630-like element ISEc33 family transposase -
FBF57_RS29025 (FBF57_29160) 36094..36840 - 747 Protein_37 IS30-like element ISAba125 family transposase -
FBF57_RS29030 (FBF57_29165) 37751..38062 - 312 WP_000570332 hypothetical protein -
FBF57_RS29035 (FBF57_29170) 38059..38571 - 513 WP_029697418 phospholipase D family protein -
FBF57_RS29040 (FBF57_29175) 38583..39584 - 1002 WP_001076634 ATPase, T2SS/T4P/T4SS family virB11
FBF57_RS29045 (FBF57_29180) 39635..40774 - 1140 WP_014014945 type IV secretion system protein VirB10 virB10
FBF57_RS29050 (FBF57_29185) 40774..41661 - 888 WP_014014946 TrbG/VirB9 family P-type conjugative transfer protein virB9
FBF57_RS29055 (FBF57_29190) 41672..42367 - 696 WP_014014947 type IV secretion system protein virB8
FBF57_RS29845 (FBF57_29195) 42378..42509 - 132 WP_072000589 conjugal transfer protein TraN -
FBF57_RS29060 (FBF57_29200) 42586..43623 - 1038 WP_014014948 type IV secretion system protein virB6
FBF57_RS29065 (FBF57_29205) 43640..43882 - 243 WP_000858958 EexN family lipoprotein -
FBF57_RS29070 (FBF57_29210) 43892..44593 - 702 WP_014014949 type IV secretion system protein virB5
FBF57_RS29075 (FBF57_29215) 44609..47182 - 2574 WP_014014950 VirB4 family type IV secretion/conjugal transfer ATPase virb4
FBF57_RS29080 (FBF57_29220) 47183..47500 - 318 WP_000462629 VirB3 family type IV secretion system protein virB3
FBF57_RS29085 (FBF57_29225) 47540..47881 - 342 WP_001121032 TrbC/VirB2 family protein virB2
FBF57_RS29090 (FBF57_29235) 48083..48865 - 783 WP_014014952 lytic transglycosylase domain-containing protein virB1
FBF57_RS29095 (FBF57_29240) 48965..49282 + 318 WP_000960955 H-NS family nucleoid-associated regulatory protein -
FBF57_RS29100 (FBF57_29245) 49286..49636 + 351 WP_014014953 hypothetical protein -
FBF57_RS29105 (FBF57_29250) 49633..49971 + 339 WP_000040982 hypothetical protein -
FBF57_RS29110 (FBF57_29255) 49975..50283 + 309 WP_000733764 hypothetical protein -
FBF57_RS29115 (FBF57_29260) 50568..50753 + 186 WP_014014955 ribbon-helix-helix domain-containing protein -
FBF57_RS29120 (FBF57_29265) 50750..51358 - 609 WP_000275218 recombinase family protein -
FBF57_RS29125 (FBF57_29270) 51524..51856 - 333 WP_015060077 hypothetical protein -

Host bacterium

ID   5462 GenBank   NZ_CP039806
Plasmid name   pC2972-5-NDM Incompatibility group   IncN2
Plasmid size   51995 bp Coordinate of oriT [Strand]   22286..22368 [-]
Host baterium   Klebsiella pneumoniae strain C2972

Cargo genes

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