Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100654
Name   oriT_pBII_1 in_silico
Organism   Burkholderia ambifaria AMMD
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP009797 (31606..31978 [+], 373 nt)
oriT length   373 nt
IRs (inverted repeats)      IR1: 64..68, 72..76  (GCGCC..GGCGC)
  IR2: 89..107, 110..128  (GTGAAGATAGATAACCGGC..GCCGGTTAGCTAACTTCAC)
Location of nic site      136..137
Conserved sequence flanking the
  nic site    		  CATCCTG|C
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 373 nt

>oriT_pBII_1
GCCTCGCCTCGTCTCTCATGCCGGCGGTAGCCGGCTGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAACCCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTACATTTGCGATGAGAGGATTAGATGGACGAACACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   726 GenBank   WP_011117146
Name   TraI_pBII_1 insolico UniProt ID   A0A1P8K551
Length   746 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 746 a.a.        Molecular weight: 82120.82 Da        Isoelectric Point: 10.8213

>WP_011117146.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Pseudomonadota]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWVKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQNLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
IQAINKQFQQERTALYAEHRRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQ
PDHALRRGISRPGTGVGQTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALA
LLKRGDEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)

Large polyvalent protein-associated domain 7 (LPD7)

(422-508)


  Protein structure


Source ID Structure
AlphaFold DB A0A1P8K551


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2899..13576

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CH72_RS00005 (CH72_6645) 505..1725 - 1221 WP_011114072 plasmid replication initiator TrfA -
CH72_RS00010 (CH72_6646) 1772..2113 - 342 WP_000019167 single-stranded DNA-binding protein -
CH72_RS00015 2227..2589 + 363 WP_010890126 transcriptional regulator -
CH72_RS00020 (CH72_6647) 2899..3861 + 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
CH72_RS00025 (CH72_6648) 3878..4342 + 465 WP_011114046 conjugal transfer system pilin TrbC virB2
CH72_RS00030 (CH72_6649) 4346..4657 + 312 WP_001207961 conjugal transfer protein TrbD virB3
CH72_RS00035 (CH72_6650) 4654..7212 + 2559 WP_011114047 VirB4 family type IV secretion/conjugal transfer ATPase virb4
CH72_RS00040 (CH72_6651) 7209..7991 + 783 WP_006122481 conjugal transfer protein TrbF virB8
CH72_RS00045 (CH72_6652) 8009..8908 + 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
CH72_RS00050 (CH72_6653) 8911..9399 + 489 WP_006122479 conjugal transfer protein TrbH -
CH72_RS00055 (CH72_6654) 9404..10825 + 1422 WP_011114050 TrbI/VirB10 family protein virB10
CH72_RS00060 (CH72_6655) 10846..11610 + 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
CH72_RS00065 (CH72_6656) 11620..11847 + 228 WP_000644148 entry exclusion lipoprotein TrbK -
CH72_RS00070 (CH72_6657) 11858..13576 + 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
CH72_RS00075 (CH72_6658) 13594..14181 + 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
CH72_RS00080 (CH72_6659) 14195..14830 + 636 WP_011114052 transglycosylase SLT domain-containing protein -
CH72_RS00085 (CH72_6660) 14859..15125 + 267 WP_010890140 hypothetical protein -
CH72_RS00090 (CH72_6661) 15125..15823 + 699 WP_011114053 TraX family protein -
CH72_RS00095 (CH72_6662) 15839..16270 + 432 WP_001665065 OmpA family protein -
CH72_RS00100 (CH72_6663) 16425..16922 + 498 WP_011655360 SAM-dependent methyltransferase -
CH72_RS00105 (CH72_6664) 17008..17388 + 381 WP_011655359 hypothetical protein -

Host bacterium

ID   1114 GenBank   NZ_CP009797
Plasmid name   pBII_1 Incompatibility group   IncP1
Plasmid size   43581 bp Coordinate of oriT [Strand]   31606..31978 [+]
Host baterium   Burkholderia ambifaria AMMD

Cargo genes

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