Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100661
Name   oriT_pKPC-56a in_silico
Organism   Pantoea sp. PSNIH2
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP009867 (40048..40674 [+], 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-56a
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTTTTAAACAAAAAATTGGGATCTAACAAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTGGGTGTTTTTAATACCTAATTATTACCGAATATTGTTGCTATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGGGCGATCTACGTAGGTTAAGGACTAACTGGCTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACAAAAGTACATCAAAATTACATCAAAATTACATCACTTGAAGGTTGACAGTACAACAAAATTACATCATTCTTTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAGTACATCAAAATTACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   733 GenBank   WP_012561166
Name   Relaxase_pKPC-56a insolico UniProt ID   A0A0A1B5M6
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: 11794..25787

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PSNIH2_RS19775 (PSNIH2_19775) 7639..9072 - 1434 WP_001288432 DNA cytosine methyltransferase -
PSNIH2_RS19780 (PSNIH2_19780) 9171..9443 + 273 Protein_13 IS1 family transposase -
PSNIH2_RS24345 9454..9660 - 207 WP_001749967 hypothetical protein -
PSNIH2_RS19785 (PSNIH2_19785) 9665..10153 - 489 WP_064577928 restriction endonuclease -
PSNIH2_RS19790 (PSNIH2_19790) 10362..10673 - 312 WP_001452736 hypothetical protein -
PSNIH2_RS19795 (PSNIH2_19795) 10709..11023 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
PSNIH2_RS19800 (PSNIH2_19800) 11020..11364 - 345 WP_001749964 hypothetical protein -
PSNIH2_RS19805 (PSNIH2_19805) 11380..11730 - 351 WP_024129965 H-NS family nucleoid-associated regulatory protein -
PSNIH2_RS19810 (PSNIH2_19810) 11794..12528 + 735 WP_001749963 lytic transglycosylase domain-containing protein virB1
PSNIH2_RS19815 (PSNIH2_19815) 12537..12818 + 282 WP_000440698 transcriptional repressor KorA -
PSNIH2_RS19820 (PSNIH2_19820) 12828..13121 + 294 WP_001749962 hypothetical protein virB2
PSNIH2_RS19825 (PSNIH2_19825) 13171..13488 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
PSNIH2_RS19830 (PSNIH2_19830) 13488..16070 + 2583 WP_040126168 VirB4 family type IV secretion/conjugal transfer ATPase virb4
PSNIH2_RS19835 (PSNIH2_19835) 16086..16691 - 606 WP_000509966 recombinase family protein -
PSNIH2_RS19840 (PSNIH2_19840) 16786..19683 + 2898 WP_040126169 Tn3-like element Tn5403 family transposase -
PSNIH2_RS19845 (PSNIH2_19845) 19775..20488 + 714 WP_001749960 type IV secretion system protein virB5
PSNIH2_RS19850 (PSNIH2_19850) 20496..20723 + 228 WP_001749959 IncN-type entry exclusion lipoprotein EexN -
PSNIH2_RS19855 (PSNIH2_19855) 20739..21779 + 1041 WP_001749958 type IV secretion system protein virB6
PSNIH2_RS24350 21862..22008 + 147 WP_001257173 conjugal transfer protein TraN -
PSNIH2_RS19860 (PSNIH2_19860) 21998..22696 + 699 WP_000646594 type IV secretion system protein virB8
PSNIH2_RS19865 (PSNIH2_19865) 22770..23591 + 822 WP_019706045 TrbG/VirB9 family P-type conjugative transfer protein virB9
PSNIH2_RS19870 23591..24750 + 1160 Protein_33 conjugal transfer protein TraF -
PSNIH2_RS19875 (PSNIH2_19875) 24792..25787 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
PSNIH2_RS19880 (PSNIH2_19880) 25787..26320 + 534 WP_000792636 phospholipase D family protein -
PSNIH2_RS25440 26602..26781 - 180 Protein_36 hypothetical protein -
PSNIH2_RS24355 27048..27227 + 180 Protein_37 helix-turn-helix domain-containing protein -
PSNIH2_RS24360 27292..27852 + 561 Protein_38 IS6 family transposase -
PSNIH2_RS19895 (PSNIH2_19895) 27872..29983 - 2112 Protein_39 Tn3-like element Tn3 family transposase -

Host bacterium

ID   1121 GenBank   NZ_CP009867
Plasmid name   pKPC-56a Incompatibility group   IncN
Plasmid size   54000 bp Coordinate of oriT [Strand]   40048..40674 [+]
Host baterium   Pantoea sp. PSNIH2

Cargo genes

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