Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100071
Name   oriT_pNL194 in_silico
Organism   Klebsiella pneumoniae
Sequence Completeness      incomplete
NCBI accession of oriT (coordinates [strand])   NC_014368 (59504..59513 [+], 10 nt)
oriT length   10 nt
IRs (inverted repeats)     _
Location of nic site      5..6
Conserved sequence flanking the
  nic site    		  GGTGT|ATAGC
Note   putative IncN oriT nick site

  oriT sequence  


Download         Length: 10 nt

>oriT_pNL194
GGTGTATAGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Miriagou V et al. (2010) Sequence of pNL194, a 79.3-kilobase IncN plasmid carrying the blaVIM-1 metallo-beta-lactamase gene in Klebsiella pneumoniae. Antimicrob Agents Chemother. 54(10):4497-502. [PMID:20660690]


Relaxase

ID   67 GenBank   YP_003813077
Name   TraI_pNL194 insolico UniProt ID   E2EAU3
Length   1078 a.a. PDB ID   
Note   conjugal nickase and helicase

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120137.33 Da        Isoelectric Point: 6.5766

>YP_003813077.1 TraI (plasmid) [Klebsiella pneumoniae]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(16-287)

AAA domain (AAA_30)

(477-653)

UvrD-like helicase C-terminal domain (UvrD_C_2)

(851-895)


  Protein structure


Source ID Structure
AlphaFold DB E2EAU3

  Reference


[1] Miriagou V et al. (2010) Sequence of pNL194, a 79.3-kilobase IncN plasmid carrying the blaVIM-1 metallo-beta-lactamase gene in Klebsiella pneumoniae. Antimicrob Agents Chemother. 54(10):4497-502. [PMID:20660690]


Auxiliary protein

ID   98 GenBank   YP_003813079
Name   TraK_pNL194 insolico UniProt ID   B6RFQ7
Length   138 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 138 a.a.        Molecular weight: 15332.60 Da        Isoelectric Point: 5.9670

>YP_003813079.1 TraK (plasmid) [Klebsiella pneumoniae]
MPIITAKVSDELLAYIDLVSGGNRSDYLRRCIEAGPGDRESGLKIVADRLSDVNRKLDYLFDRASDADFG
PLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB B6RFQ7

  Reference


[1] Miriagou V et al. (2010) Sequence of pNL194, a 79.3-kilobase IncN plasmid carrying the blaVIM-1 metallo-beta-lactamase gene in Klebsiella pneumoniae. Antimicrob Agents Chemother. 54(10):4497-502. [PMID:20660690]


T4CP

ID   67 GenBank   YP_003813031
Name   TraG_pNL194 insolico UniProt ID   E2EAP7
Length   331 a.a. PDB ID   _
Note   Type IV Secretion System Coupling Protein

  T4CP protein sequence


Download         Length: 331 a.a.        Molecular weight: 36797.61 Da        Isoelectric Point: 6.6007

>YP_003813031.1 TraG (plasmid) [Klebsiella pneumoniae]
MTDAAFYQLGPLREYLEDPTVFEIRINCFQEVICDTFSGRRVVQNAAITADFIRNLAKSLVSSNKLTMQA
INDVILPGGIRGVICLPPAVIDGTTAVAFRKDLAADKNLEQLTSEGIFSDCRKITGSKQSLTDDDFFLKE
LHSSEKWPAFLQTAVEKKRTIVICGETGSGKTVLTRALLKSLHKDERVIILEDVHEVTVDHVVEAVYMMY
GDAGKIGPVSATDALRACMRLTPGRIIMTELRDDAAWDYLKALNTGHPGGVMSTHANSARDAFNRIGLLI
KATPIGRMLDMSDIMRMLYSTIDVVVHMEKRKIKEIYFDPEYKMQCVNGSL

  Protein domains


Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(50-310)

  Protein structure


Source ID Structure
AlphaFold DB E2EAP7

  Reference


[1] Miriagou V et al. (2010) Sequence of pNL194, a 79.3-kilobase IncN plasmid carrying the blaVIM-1 metallo-beta-lactamase gene in Klebsiella pneumoniae. Antimicrob Agents Chemother. 54(10):4497-502. [PMID:20660690]


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2340..12664

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS667_RS00005 1..207 - 207 WP_001749967 hypothetical protein -
HS667_RS00010 (pNL194_p01) 212..859 - 648 WP_015344958 restriction endonuclease -
HS667_RS00015 909..1142 - 234 WP_001191790 hypothetical protein -
HS667_RS00020 (pNL194_p02) 1256..1570 - 315 WP_000734776 TrbM/KikA/MpfK family conjugal transfer protein -
HS667_RS00025 1533..1910 - 378 WP_010999955 hypothetical protein -
HS667_RS00030 (pNL194_p03) 1926..2297 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HS667_RS00035 (pNL194_p04) 2340..3074 + 735 WP_000033783 lytic transglycosylase domain-containing protein virB1
HS667_RS00040 (pNL194_p05) 3083..3364 + 282 WP_000440698 transcriptional repressor KorA -
HS667_RS00045 (pNL194_p06) 3374..3667 + 294 WP_000209137 TrbC/VirB2 family protein virB2
HS667_RS00050 (pNL194_p07) 3717..4028 + 312 WP_010999956 VirB3 family type IV secretion system protein virB3
HS667_RS00055 (pNL194_p08) 4033..6633 + 2601 WP_010999957 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HS667_RS00060 (pNL194_p09) 6651..7364 + 714 WP_013263778 type IV secretion system protein virB5
HS667_RS00065 (pNL194_p10) 7372..7602 + 231 WP_013263779 IncN-type entry exclusion lipoprotein EexN -
HS667_RS00070 (pNL194_p11) 7618..8658 + 1041 WP_013263780 type IV secretion system protein virB6
HS667_RS00075 (pNL194_p13) 8877..9575 + 699 WP_010999962 type IV secretion system protein virB8
HS667_RS00080 (pNL194_p14) 9586..10470 + 885 WP_010999963 TrbG/VirB9 family P-type conjugative transfer protein virB9
HS667_RS00085 (pNL194_p15) 10470..11630 + 1161 WP_010999964 type IV secretion system protein VirB10 virB10
HS667_RS00090 (pNL194_p16) 11669..12664 + 996 WP_010999965 ATPase, T2SS/T4P/T4SS family virB11
HS667_RS00095 (pNL194_p17) 12664..13197 + 534 WP_013263781 phospholipase D family protein -
HS667_RS00100 13327..13687 - 361 Protein_19 hypothetical protein -
HS667_RS00105 (pNL194_p19) 13944..14300 - 357 WP_000215515 cupin domain-containing protein -
HS667_RS00110 (pNL194_p20) 14290..14691 - 402 WP_001293886 DUF86 domain-containing protein -
HS667_RS00115 (pNL194_p21) 14688..14978 - 291 WP_001247892 nucleotidyltransferase -
HS667_RS00120 (pNL194_p22) 15285..15872 - 588 Protein_23 class 1 integron integrase IntI1 -
HS667_RS00125 15875..15940 + 66 Protein_24 EAL domain-containing protein -
HS667_RS00130 (pNL194_p23) 16080..16844 - 765 WP_001389365 IS6-like element IS6100 family transposase -
HS667_RS00135 16962..17027 - 66 Protein_26 EAL domain-containing protein -
HS667_RS00140 (pNL194_p24) 17071..17376 - 306 WP_000130000 PadR family transcriptional regulator -

Host bacterium

ID   67 GenBank   NC_014368
Plasmid name   pNL194 Incompatibility group   IncN
Plasmid size   79307 bp Coordinate of oriT [Strand]   59504..59513 [+]
Host baterium   Klebsiella pneumoniae

Cargo genes

Drug resistance gene   carrying a mosaic structure including blaVIM-1, aacA7, aadA1, aadA2, dfrA1, dfrA12, aphA1, strA, strB, and sul1.
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -