Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100663
Name   oriT_pKPC-1c5 in_silico
Organism   Pantoea sp. PSNIH1
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP009881 (36381..37007 [+], 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_pKPC-1c5
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTTTTAAACAAAAAATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTGGGTGTTTTTAATACCTAATTATTACCGAATATTGTTGCTATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGGGCGATCTACGTAGGTTAAGGACTAACTGGCTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACAAAAGTACATCAAAATTACATCAAAATTACATCACTTGAAGGTTGACAGTACAACAAAATTACATCATTCTTTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAGTACATCAAAATTACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   735 GenBank   WP_012561166
Name   Relaxase_pKPC-1c5 insolico UniProt ID   A0A0A0Z8W7
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

>WP_012561166.1 MULTISPECIES: MobF family relaxase [Gammaproteobacteria]
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: 11795..22120

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PSNIH1_RS16565 (PSNIH1_18580) 7640..9073 - 1434 WP_001288432 DNA cytosine methyltransferase -
PSNIH1_RS16570 (PSNIH1_18585) 9172..9444 + 273 Protein_10 IS1 family transposase -
PSNIH1_RS21660 9455..9661 - 207 WP_001749967 hypothetical protein -
PSNIH1_RS16575 (PSNIH1_18590) 9666..10313 - 648 WP_012561184 restriction endonuclease -
PSNIH1_RS16580 (PSNIH1_18595) 10363..10674 - 312 WP_001452736 hypothetical protein -
PSNIH1_RS16585 (PSNIH1_18600) 10710..11024 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
PSNIH1_RS16590 (PSNIH1_18605) 11021..11365 - 345 WP_001749964 hypothetical protein -
PSNIH1_RS16595 (PSNIH1_18610) 11381..11686 - 306 WP_000960954 H-NS family nucleoid-associated regulatory protein -
PSNIH1_RS16600 (PSNIH1_18615) 11795..12529 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
PSNIH1_RS16605 (PSNIH1_18620) 12538..12819 + 282 WP_000440698 transcriptional repressor KorA -
PSNIH1_RS16610 (PSNIH1_18625) 12829..13122 + 294 WP_001749962 hypothetical protein virB2
PSNIH1_RS16615 (PSNIH1_18630) 13172..13489 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
PSNIH1_RS16620 (PSNIH1_18635) 13489..16089 + 2601 WP_001749961 VirB4 family type IV secretion/conjugal transfer ATPase virb4
PSNIH1_RS16625 (PSNIH1_18640) 16107..16820 + 714 WP_001749960 type IV secretion system protein virB5
PSNIH1_RS16630 (PSNIH1_18645) 16828..17055 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
PSNIH1_RS16635 (PSNIH1_18650) 17071..18111 + 1041 WP_001749958 type IV secretion system protein virB6
PSNIH1_RS16640 (PSNIH1_18655) 18330..19028 + 699 WP_000646594 type IV secretion system protein virB8
PSNIH1_RS16645 (PSNIH1_18660) 19039..19923 + 885 WP_000735066 TrbG/VirB9 family P-type conjugative transfer protein virB9
PSNIH1_RS16650 (PSNIH1_18665) 19923..21083 + 1161 WP_000101710 type IV secretion system protein VirB10 virB10
PSNIH1_RS16655 (PSNIH1_18670) 21125..22120 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
PSNIH1_RS16660 (PSNIH1_18675) 22120..22653 + 534 WP_000792636 phospholipase D family protein -
PSNIH1_RS22840 22827..22955 - 129 WP_002210551 DUF6710 family protein -
PSNIH1_RS21670 23381..23560 + 180 Protein_31 helix-turn-helix domain-containing protein -
PSNIH1_RS21675 23625..24185 + 561 Protein_32 IS6 family transposase -
PSNIH1_RS16675 (PSNIH1_18690) 24205..26316 - 2112 Protein_33 Tn3-like element Tn3 family transposase -

Host bacterium

ID   1123 GenBank   NZ_CP009881
Plasmid name   pKPC-1c5 Incompatibility group   IncN
Plasmid size   50272 bp Coordinate of oriT [Strand]   36381..37007 [+]
Host baterium   Pantoea sp. PSNIH1

Cargo genes

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