Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100195
Name   oriT_pIJB1 in_silico
Organism   Burkholderia cepacia
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019378 (_)
oriT length   99 nt
IRs (inverted repeats)      13..31, 34..52  (GTGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCAC)
Location of nic site      60..61
Conserved sequence flanking the
  nic site    		  CATCCTG|C
Note   _

  oriT sequence  


Download         Length: 99 nt

>oriT_pIJB1
GAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   188 GenBank   YP_006965894
Name   TraI_pIJB1 insolico UniProt ID   K4IYE5
Length   730 a.a. PDB ID   
Note   TraI Conjugative transfer protein, DNA relaxase

  Relaxase protein sequence


Download         Length: 730 a.a.        Molecular weight: 80015.48 Da        Isoelectric Point: 10.3609

>YP_006965894.1 TraI Conjugative transfer protein, DNA relaxase (plasmid) [Burkholderia cepacia]
MIAKHVSMKTVQKSDFAGLVKYITDEQAKNERVGYVAVTNCHTDRPEVAITEVLNTQAQNTRSGADKTYH
LIVSFRPGEQPDDATLKAIEARICEGLGFGEHQRVSAVHHDTDNLHIHIAINKIHPTRYTILEPFNAYHT
LGQLCEKLEREYGLERDNHQGNKLVSEGRAQDMERHAGVESLQGWVKRECAADMQAAQSWEALHQVMRDN
GLELRERGNGFVIQAADGLAVKASSIGREFSKAKLEERLGTFEPSAEHLERAAQKPRKQYDKKPVRSRVN
TVELHAKYKADQLTISGSRTAEWEKARAKKDRLIEAAKRSGRLKRSTIKLISGAGVGKKLMYSATSKTMK
SEIEKINKQYLKERQEIHEKYQRRAWADWLRAKAAEGDQEALGALRARDAAQGLKGNTVAGTGPLRPQAA
AAEQDSVTKKGTIIYRVGPTAVRDDGDRLKVSRGADQDGMQAALRMAMDRYGDRISVGGTPAFKEQIAQA
AAASKLPITFDDDALERRRQELLTQATTKENDHDRTDRGRAAGGGISGSGPAIAAIPGAARAGQPRAAAA
GRTTKPNVGRVGRKPPPQSQNRLRRLSQLGVVQLASGSEVLLPRHVPGDVEQQGAKPVDGLRRDIFGPGR
LSPQVAAAADKYIAEREGKRLKGFDIPKHSRYTDGQDGAATFAGIRQVEGQSLALLTRGEEVMVLPVDEP
TARRLKRLAVGDAITVTPQGSIKTTKGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(424-512)

Relaxase/Mobilisation nuclease domain (Relaxase)

(13-250)


  Protein structure


Source ID Structure
AlphaFold DB K4IYE5


Auxiliary protein

ID   266 GenBank   YP_006965895
Name   TraH_pIJB1 insolico UniProt ID   K4J0Y9
Length   108 a.a. PDB ID   _
Note   TraH Conjugative transfer protein, relaxosome stabilization

  Auxiliary protein sequence


Download         Length: 108 a.a.        Molecular weight: 11836.18 Da        Isoelectric Point: 3.8732

>YP_006965895.1 TraH Conjugative transfer protein, relaxosome stabilization (plasmid) [Burkholderia cepacia]
MTEPTEDELLEAALAAVDQPLPQSPEPPEPDSHEPPQPDGPPSPTLAALDESRRPKAKTVCEDCPNSVWF
SSPAEVKCYCRVMFLVTWSNKEPNQLTACDGIFLGQED

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB K4J0Y9

ID   267 GenBank   YP_006965896
Name   TraJ_pIJB1 insolico UniProt ID   Q2VLB1
Length   129 a.a. PDB ID   _
Note   TraJ Conjugative transfer protein, relaxosome protein

  Auxiliary protein sequence


Download         Length: 129 a.a.        Molecular weight: 14479.81 Da        Isoelectric Point: 10.3612

>YP_006965896.1 TraJ Conjugative transfer protein, relaxosome protein (plasmid) [Burkholderia cepacia]
MAKTRNSDDPRMPTRKAGRHLRVPVLPDEEAEIKRLAASVGLPVAAYLRNVGLGYQVPGILDNKRVEELA
RINGDLGRLGGLLKLWLTDDVRTLQFGETTILALLSRIESTQDRMHEVMQEVVTPRVKR

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q2VLB1

ID   268 GenBank   YP_006965897
Name   TraK_pIJB1 insolico UniProt ID   K4JDT7
Length   132 a.a. PDB ID   _
Note   TraK conjugative transfer protein,oriT binding protein

  Auxiliary protein sequence


Download         Length: 132 a.a.        Molecular weight: 14842.04 Da        Isoelectric Point: 10.5392

>YP_006965897.1 TraK Conjugative transfer protein, OriT binding protein (plasmid) [Burkholderia cepacia]
MPKSYPEELAEWVKKREATRPRQDKNVVAFLALKSDVQDAIAAGYSLRTIWEHMHEKGKIPYRYETFLKH
VRRHIKGRPPAVVDGQPSTPPDPPRPPAAGKTAAPRPQQPTKSAPAPAGFKFDSQPKKEDLL

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5338) (DUF5338)

(7-74)


  Protein structure


Source ID Structure
AlphaFold DB K4JDT7


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1821..12421

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTB43_RS00005 (D704_p36) 1..870 - 870 WP_015063508 plasmid replication initiator TrfA -
HTB43_RS00010 (D704_p34) 1191..1568 + 378 WP_011171717 transcriptional regulator -
HTB43_RS00015 (D704_p33) 1821..2783 + 963 WP_011171718 P-type conjugative transfer ATPase TrbB virB11
HTB43_RS00020 (D704_p32) 2795..3223 + 429 WP_011171719 IncP-type conjugal transfer pilin TrbC virB2
HTB43_RS00025 (D704_p31) 3226..3537 + 312 WP_011171720 conjugal transfer protein TrbD virB3
HTB43_RS00030 (D704_p30) 3534..6071 + 2538 WP_015063520 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HTB43_RS00035 (D704_p29) 6068..6844 + 777 WP_015063521 conjugal transfer protein TrbF virB8
HTB43_RS00040 (D704_p28) 6857..7762 + 906 WP_015063522 P-type conjugative transfer protein TrbG virB9
HTB43_RS00045 (D704_p27) 7765..8232 + 468 WP_015063523 TrbH Mating pair formation protein -
HTB43_RS00050 (D704_p26) 8238..9632 + 1395 WP_015063524 TrbI/VirB10 family protein virB10
HTB43_RS00055 (D704_p25) 9651..10424 + 774 WP_015063525 P-type conjugative transfer protein TrbJ virB5
HTB43_RS00060 (D704_p24) 10435..10674 + 240 WP_015063526 entry exclusion lipoprotein TrbK -
HTB43_RS00065 (D704_p35) 10685..12421 + 1737 WP_172685318 P-type conjugative transfer protein TrbL virB6
HTB43_RS00070 (D704_p23) 12441..13034 + 594 WP_015063527 TrbM/KikA/MpfK family conjugal transfer protein -
HTB43_RS00075 (D704_p22) 13048..13653 + 606 WP_015063528 transglycosylase SLT domain-containing protein -
HTB43_RS00080 (D704_p02) 13679..13942 + 264 WP_015063529 hypothetical protein -
HTB43_RS00085 (D704_p01) 13945..14643 + 699 WP_015063530 TraX family protein -
HTB43_RS00090 14644..15000 + 357 WP_258404801 OmpA family protein -
HTB43_RS00095 (D704_p55) 15086..15571 + 486 WP_015063510 thermonuclease family protein -
HTB43_RS00100 (D704_p56) 15556..15975 + 420 WP_172685320 hypothetical protein -
HTB43_RS00105 (D704_p54) 15932..16303 - 372 WP_015063512 resolvase -

Host bacterium

ID   188 GenBank   NC_019378
Plasmid name   pIJB1 Incompatibility group   IncP-1
Plasmid size   99001 bp Coordinate of oriT [Strand]   43131..43230 [+]
Host baterium   Burkholderia cepacia

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   merR1, merT, merP, merA, merB, merR2, merD, merE
Degradation gene   linF
Symbiosis gene   -
Anti-CRISPR   AcrIIA9, AcrIF24