Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100452
Name   oriT_pKC396 in_silico
Organism   Escherichia coli O25b:H4-ST131
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019087 (32363..33021 [+], 659 nt)
oriT length   659 nt
IRs (inverted repeats)      IR1: 198..207, 210..219  (ATTGGGTGTT..AATACCTAAT)
 IR2:318..323, 329..334  (AAAAAA..TTTTTT)
  IR3: 392..401, 404..413  (GTATTCATGC..GCATGAATAC)
Location of nic site      300..301
Conserved sequence flanking the
  nic site    		  GGTGT|ATAGC
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 659 nt

>oriT_pKC396
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTCTTAAACAAAAAATTGGGATCTAACCAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTGGGTGTTTTAATACCTAATTATTACCGGATATTGACGCTATTTATTTTTTTATTTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGAGCGAACTACGTAGGTTAAGGACTAACTGGCTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACACTATTACAACAAAAGTACATCAAAATTACATCAAAATTACATCACTTGAAGGTTGACAGTACAACAGAATTACATCATTATCTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAATACATCATAAATACATCATAAATACATCAGAAATACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   523 GenBank   YP_006953736
Name   PutativerelaxaseofpKC396 insolico UniProt ID   D7RVP6
Length   1076 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1076 a.a.        Molecular weight: 119897.16 Da        Isoelectric Point: 6.6071

>YP_006953736.1 conjugal transfer protein (plasmid) [Escherichia coli O25b:H4-ST131]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
ISGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEEGGHEI

  Protein domains


Predicted by InterproScan.

UvrD-like helicase C-terminal domain (UvrD_C_2)

(851-895)

TrwC relaxase (TrwC)

(16-287)

AAA domain (AAA_30)

(477-653)


  Protein structure


Source ID Structure
AlphaFold DB D7RVP6


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 8217..18542

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS703_RS00020 (pKC396-004) 4069..5502 - 1434 WP_001288433 DNA cytosine methyltransferase -
HS703_RS00025 5596..5867 + 272 Protein_4 IS1 family transposase -
HS703_RS00030 (pKC396-006) 5887..6084 - 198 WP_013188474 hypothetical protein -
HS703_RS00035 (pKC396-007) 6089..6736 - 648 WP_001532074 restriction endonuclease -
HS703_RS00040 (pKC396-008) 6786..7019 - 234 WP_001191790 hypothetical protein -
HS703_RS00045 (pKC396-009) 7133..7447 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HS703_RS00050 (pKC396-010) 7410..7787 - 378 WP_000504250 hypothetical protein -
HS703_RS00055 (pKC396-011) 7803..8174 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HS703_RS00060 (pKC396-012) 8217..8951 + 735 WP_000033783 lytic transglycosylase domain-containing protein virB1
HS703_RS00065 (pKC396-013) 8960..9241 + 282 WP_000440698 transcriptional repressor KorA -
HS703_RS00070 (pKC396-014) 9251..9544 + 294 WP_000209137 TrbC/VirB2 family protein virB2
HS703_RS00075 (pKC396-015) 9594..9911 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HS703_RS00080 (pKC396-016) 9911..12511 + 2601 WP_001200711 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HS703_RS00085 (pKC396-017) 12529..13242 + 714 WP_000749362 type IV secretion system protein virB5
HS703_RS00090 (pKC396-018) 13250..13477 + 228 WP_000734973 IncN-type entry exclusion lipoprotein EexN -
HS703_RS00095 (pKC396-019) 13493..14533 + 1041 WP_000886022 type IV secretion system protein virB6
HS703_RS00100 (pKC396-020) 14604..14762 + 159 WP_012561180 hypothetical protein -
HS703_RS00105 (pKC396-021) 14752..15450 + 699 WP_000646594 type IV secretion system protein virB8
HS703_RS00110 (pKC396-022) 15461..16345 + 885 WP_000735067 TrbG/VirB9 family P-type conjugative transfer protein virB9
HS703_RS00115 (pKC396-023) 16345..17505 + 1161 WP_000101712 type IV secretion system protein VirB10 virB10
HS703_RS00120 (pKC396-024) 17547..18542 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HS703_RS00125 (pKC396-025) 18542..19075 + 534 WP_000731968 phospholipase D family protein -
HS703_RS00130 19243..20757 - 1515 Protein_25 Tn3-like element TnAs1 family transposase -
HS703_RS00135 (pKC396-026) 20823..21527 + 705 WP_001067855 IS6-like element IS26 family transposase -
HS703_RS00140 (pKC396-027) 21684..22244 - 561 WP_003124096 recombinase family protein -
HS703_RS00145 22509..23045 + 537 Protein_28 PAS domain-containing protein -

Host bacterium

ID   913 GenBank   NC_019087
Plasmid name   pKC396 Incompatibility group   IncN
Plasmid size   44216 bp Coordinate of oriT [Strand]   32363..33021 [+]
Host baterium   Escherichia coli O25b:H4-ST131

Cargo genes

Drug resistance gene   blaCTX-M-65
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -