Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100607
Name   oriT_pECN580 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_025183 (51527..52153 [+], 627 nt)
oriT length   627 nt
IRs (inverted repeats)      IR1: 198..207, 211..220  (ATTGGGTGTT..AATACCTAAT)
 IR2:319..324, 330..335  (AAAAAA..TTTTTT)
  IR3: 393..402, 405..414  (GTATTCATGC..GCATGAATAC)
Location of nic site      301..302
Conserved sequence flanking the
  nic site    		  GGTGT|ATAGC
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 627 nt

>oriT_pECN580
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTTTTAAACAAAAAATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTGGGTGTTTTTAATACCTAATTATTACCGAATATTGTTGCTATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGGGCGATCTACGTAGGTTAAGGACTAACTGGCTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACAAAAGTACATCAAAATTACATCAAAATTACATCACTTGAAGGTTGACAGTACAACAAAATTACATCATTCTTTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAGTACATCAAAATTACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   679 GenBank   YP_009071521
Name   TraI_pECN580 insolico UniProt ID   _
Length   1078 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120141.30 Da        Isoelectric Point: 6.5229

>YP_009071521.1 TraI (plasmid) [Escherichia coli]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATMADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKNEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI

  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



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 15388..25713

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTC05_RS00075 (D616_p156015) 11233..12666 - 1434 WP_001288432 DNA cytosine methyltransferase -
HTC05_RS00080 (D616_p156016) 12765..13037 + 273 Protein_16 IS1 family transposase -
HTC05_RS00085 (D616_p156017) 13048..13254 - 207 WP_001749967 hypothetical protein -
HTC05_RS00090 (D616_p156018) 13259..13906 - 648 WP_015344958 restriction endonuclease -
HTC05_RS00095 (D616_p156019) 13956..14189 - 234 WP_001191790 hypothetical protein -
HTC05_RS00100 (D616_p156020) 14303..14617 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HTC05_RS00105 (D616_p156021) 14614..14958 - 345 WP_001749964 hypothetical protein -
HTC05_RS00110 (D616_p156022) 14974..15345 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HTC05_RS00115 (D616_p156023) 15388..16122 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
HTC05_RS00120 (D616_p156024) 16131..16412 + 282 WP_000440698 transcriptional repressor KorA -
HTC05_RS00125 (D616_p156025) 16422..16715 + 294 WP_001749962 hypothetical protein virB2
HTC05_RS00130 (D616_p156026) 16765..17082 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HTC05_RS00135 (D616_p156027) 17082..19682 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTC05_RS00140 (D616_p156028) 19700..20413 + 714 WP_001749960 type IV secretion system protein virB5
HTC05_RS00145 (D616_p156029) 20421..20648 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
HTC05_RS00150 (D616_p156030) 20664..21704 + 1041 WP_001749958 type IV secretion system protein virB6
HTC05_RS00155 (D616_p156031) 21775..21933 + 159 WP_012561180 hypothetical protein -
HTC05_RS00160 (D616_p156032) 21923..22621 + 699 WP_000646594 type IV secretion system protein virB8
HTC05_RS00165 (D616_p156033) 22632..23516 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTC05_RS00170 (D616_p156034) 23516..24676 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
HTC05_RS00175 (D616_p156035) 24718..25713 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HTC05_RS00180 (D616_p156036) 25713..26246 + 534 WP_000792636 phospholipase D family protein -
HTC05_RS00185 (D616_p156037) 26420..26548 - 129 WP_002210551 DUF6710 family protein -
HTC05_RS00200 (D616_p156041) 27804..29195 - 1392 WP_014839878 ISKra4-like element ISKpn19 family transposase -
HTC05_RS00205 (D616_p156042) 29232..29804 - 573 WP_001493762 recombinase family protein -
HTC05_RS00210 (D616_p156043) 29941..30486 - 546 WP_001493763 plasmid pRiA4b ORF-3 family protein -

Host bacterium

ID   1067 GenBank   NC_025183
Plasmid name   pECN580 Incompatibility group   IncN
Plasmid size   64935 bp Coordinate of oriT [Strand]   51527..52153 [+]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   blaKPC-2, dfrA14, qnrS1, aac(6')-Ib-cr, ARR-3, blaTEM-1B, blaCTX-M-3
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -