Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100580
Name   oriT_pAAA83 in_silico
Organism   Paracidovorax avenae
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_024998 (9191..9563 [-], 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_pAAA83
GCCTCGCCTCGTCTCTCATGCCGGCGGTAGCCGGCTGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAACCCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTACATTTGCGATGAGAGGATTAGATGGACGAACACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   652 GenBank   YP_009062664
Name   Relaxase_pAAA83 insolico UniProt ID   A0A077KSK4
Length   746 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 746 a.a.        Molecular weight: 82038.71 Da        Isoelectric Point: 10.7900

>YP_009062664.1 DNA relaxase (plasmid) [Acidovorax avenae subsp. avenae]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQSLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
IQAINKQFQQERTALYAEHSRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRIAGGSEVLLPRDVPRHVEQQGTQ
PDHALRRGISRPGTGVGQTPPGVAAADKYIAEREAKRLKGFDIPKHSRYTAGDGALTFQGTRTIEGQALA
LLKRGDEVMVMPIDQATARRLTRIAVGDAVSITAKGSIKTSKGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(422-508)

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-251)


  Protein structure


Source ID Structure
AlphaFold DB A0A077KSK4


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 34256..44933

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXD03_RS00165 (LW57_p31) 29514..30305 + 792 Protein_32 universal stress protein -
HXD03_RS00170 (LW57_p32) 30322..30657 + 336 WP_011518936 molecular chaperone DnaK -
HXD03_RS00175 (LW57_p33) 30733..31491 - 759 WP_012805979 hypothetical protein -
HXD03_RS00180 (LW57_p34) 31562..31993 - 432 WP_001665065 OmpA family protein -
HXD03_RS00185 (LW57_p35) 32009..32707 - 699 WP_011114053 TraX family protein -
HXD03_RS00190 (LW57_p36) 32707..32973 - 267 WP_010890140 hypothetical protein -
HXD03_RS00195 (LW57_p37) 33002..33637 - 636 WP_011114052 transglycosylase SLT domain-containing protein -
HXD03_RS00200 (LW57_p38) 33651..34238 - 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
HXD03_RS00205 (LW57_p39) 34256..35974 - 1719 WP_027814021 P-type conjugative transfer protein TrbL virB6
HXD03_RS00210 (LW57_p40) 35985..36212 - 228 WP_000644148 entry exclusion lipoprotein TrbK -
HXD03_RS00215 (LW57_p41) 36222..36986 - 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
HXD03_RS00220 (LW57_p42) 37007..38428 - 1422 WP_011114050 TrbI/VirB10 family protein virB10
HXD03_RS00225 (LW57_p43) 38433..38921 - 489 WP_006122479 conjugal transfer protein TrbH -
HXD03_RS00230 (LW57_p44) 38924..39823 - 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
HXD03_RS00235 (LW57_p45) 39841..40623 - 783 WP_006122481 conjugal transfer protein TrbF virB8
HXD03_RS00240 (LW57_p46) 40620..43178 - 2559 WP_011114047 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HXD03_RS00245 (LW57_p47) 43175..43486 - 312 WP_001207961 conjugal transfer protein TrbD virB3
HXD03_RS00250 (LW57_p48) 43490..43954 - 465 WP_011114046 conjugal transfer system pilin TrbC virB2
HXD03_RS00255 (LW57_p49) 43971..44933 - 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
HXD03_RS00260 (LW57_p50) 45243..45605 - 363 WP_010890126 transcriptional regulator -
HXD03_RS00265 (LW57_p51) 45719..46060 + 342 WP_000019167 single-stranded DNA-binding protein -
HXD03_RS00270 (LW57_p52) 46107..47327 + 1221 WP_011114072 plasmid replication initiator TrfA -
HXD03_RS00345 47759..47962 - 204 WP_027814028 EAL domain-containing protein -

Host bacterium

ID   1040 GenBank   NC_024998
Plasmid name   pAAA83 Incompatibility group   IncP1
Plasmid size   59534 bp Coordinate of oriT [Strand]   9191..9563 [-]
Host baterium   Paracidovorax avenae

Cargo genes

Drug resistance gene   aac(2')-IIa, aph(3'')-Ib, aph(6)-Id
Virulence gene   -
Metal resistance gene   merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -