Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100371
Name   oriT_pALIDE02 in_silico
Organism   Alicycliphilus denitrificans BC
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_014911 (12434..12806 [+], 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_pALIDE02
GCCTCGCCTCGTCTCTCATGCCGGCGGTAGCCGGCTGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAAACCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTACATTTGCGATGAGAGGATTAGATGGACGAACACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   442 GenBank   WP_011137971
Name   TraI_pALIDE02 insolico UniProt ID   E8U2N9
Length   746 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 746 a.a.        Molecular weight: 82068.74 Da        Isoelectric Point: 10.7900

>WP_011137971.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Comamonadaceae]
MIAKHVPMRSLGKSDFAGLANYITDAQSKDHRLGHVQATNCEAGSIQDAITEVLATQHTNTRAKGDKTYH
LIVSFRAGEQPSADTLRAIEERICVGLGYGEHQRISAVHNDTDNLHIHIAINKIHPTRHTMHEPYYPHRA
LAELCTALERDYGLERDNHEPRKRGAEGRAADMERHAGVESLVGWIKRECLDEIKGAQSWQELHQVMRDN
GMELRVRANGLVFEAGDGTMVKASTVARDLSKPSLEARLGPFEASPERQAQTTAKRQYRKDPIRLRVNTV
ELYAKYKAEQQSLTTARAQALERARHRKDRLIEAAKRSNRLRRATIKVVGEGRANKKLLYAQASKALRSE
LQAINKQFQQERTALYAEHSRRTWADWLKKEAQHGGADALAALRAREAAQGLKGNTIRGEGQAKPGHAPA
VDNITKKGTIIFRAGMSAVRDDGDRLQVSREATREGLQEALRLAMQRYGNRITVNGTVEFKAQMIRAAVD
SQLPITFTDPALESRRQALLNKENTHERTERPEHRGRTGRGAGGPGQRPAADQHATGAAAVARAGDGRPA
AGRGDRADAGLHAATVHRKPDVGRLGRKPPPQSQHRLRALSELGVVRITGGSEVLLPRDVPRHVEQQGTQ
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



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 47484..58161

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ALIDE_RS22745 (Alide_4467) 43016..43678 - 663 WP_013521175 peroxiredoxin-like family protein -
ALIDE_RS22750 (Alide_4468) 44017..44298 - 282 WP_013521176 type II toxin-antitoxin system YafQ family toxin -
ALIDE_RS22755 (Alide_4469) 44285..44551 - 267 WP_013521177 type II toxin-antitoxin system RelB/DinJ family antitoxin -
ALIDE_RS22760 (Alide_4470) 45090..46310 - 1221 WP_011114072 plasmid replication initiator TrfA -
ALIDE_RS22765 (Alide_4471) 46357..46698 - 342 WP_000019167 single-stranded DNA-binding protein -
ALIDE_RS22770 (Alide_4472) 46812..47174 + 363 WP_011137961 transcriptional regulator -
ALIDE_RS22775 (Alide_4473) 47484..48446 + 963 WP_011137962 P-type conjugative transfer ATPase TrbB virB11
ALIDE_RS22780 (Alide_4474) 48463..48927 + 465 WP_011114046 conjugal transfer system pilin TrbC virB2
ALIDE_RS22785 (Alide_4475) 48931..49242 + 312 WP_001207961 conjugal transfer protein TrbD virB3
ALIDE_RS22790 (Alide_4476) 49239..51797 + 2559 WP_011114047 VirB4 family type IV secretion/conjugal transfer ATPase virb4
ALIDE_RS22795 (Alide_4477) 51794..52576 + 783 WP_006122481 conjugal transfer protein TrbF virB8
ALIDE_RS22800 (Alide_4478) 52594..53493 + 900 WP_013521178 P-type conjugative transfer protein TrbG virB9
ALIDE_RS22805 (Alide_4479) 53496..53984 + 489 WP_006122479 conjugal transfer protein TrbH -
ALIDE_RS22810 (Alide_4480) 53989..55410 + 1422 WP_011114050 TrbI/VirB10 family protein virB10
ALIDE_RS22815 (Alide_4481) 55431..56195 + 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
ALIDE_RS22820 (Alide_4482) 56205..56432 + 228 WP_000644148 entry exclusion lipoprotein TrbK -
ALIDE_RS22825 (Alide_4483) 56443..58161 + 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
ALIDE_RS22830 (Alide_4484) 58179..58766 + 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
ALIDE_RS22835 (Alide_4485) 58780..59415 + 636 WP_011114052 transglycosylase SLT domain-containing protein -
ALIDE_RS22840 (Alide_4486) 59444..59710 + 267 WP_010890140 hypothetical protein -
ALIDE_RS22845 (Alide_4487) 59710..60408 + 699 WP_011114053 TraX family protein -
ALIDE_RS22850 (Alide_4488) 60424..60855 + 432 WP_001665065 OmpA family protein -
ALIDE_RS22855 (Alide_4489) 61008..61583 - 576 WP_001173919 recombinase family protein -
ALIDE_RS22860 (Alide_4490) 61710..61946 - 237 WP_013521179 type II toxin-antitoxin system YafQ family toxin -

Host bacterium

ID   832 GenBank   NC_014911
Plasmid name   pALIDE02 Incompatibility group   IncP1
Plasmid size   78982 bp Coordinate of oriT [Strand]   12434..12806 [+]
Host baterium   Alicycliphilus denitrificans BC

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   merE, merD, merA, merF, merP, merT, merR2
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -