Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100931
Name   oriT_pDCY110-2 in_silico
Organism   Rhodoferax koreense strain DCY-110
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP019238 (36515..36887 [-], 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_pDCY110-2
GCCTCGCCTCGTCTCTCATGCCGGCGGTAGCCGGCTGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAACCCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTACATTTGCGATGAGAGGATTAGATGGACGAACACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1002 GenBank   WP_011117146
Name   TraI_pDCY110-2 insolico UniProt ID   Q0B119
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 Q0B119


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 11336..22013

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RD110_RS26985 (RD110_26985) 6552..6767 - 216 WP_021561443 antitoxin MazE family protein -
RD110_RS26990 (RD110_26990) 7056..7811 + 756 WP_232476757 recombinase family protein -
RD110_RS26995 (RD110_26995) 7813..8487 - 675 WP_011178411 DNA methylase -
RD110_RS27000 (RD110_27000) 8642..9073 - 432 WP_001665065 OmpA family protein -
RD110_RS27005 (RD110_27005) 9089..9787 - 699 WP_011114053 TraX family protein -
RD110_RS27010 (RD110_27010) 9787..10053 - 267 WP_010890140 hypothetical protein -
RD110_RS27015 (RD110_27015) 10082..10717 - 636 WP_011114052 transglycosylase SLT domain-containing protein -
RD110_RS27020 (RD110_27020) 10731..11318 - 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
RD110_RS27025 (RD110_27025) 11336..13054 - 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
RD110_RS27030 (RD110_27030) 13065..13292 - 228 WP_000644148 entry exclusion lipoprotein TrbK -
RD110_RS27035 (RD110_27035) 13302..14066 - 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
RD110_RS27040 (RD110_27040) 14087..15508 - 1422 WP_011114050 TrbI/VirB10 family protein virB10
RD110_RS27045 (RD110_27045) 15513..16001 - 489 WP_006122479 conjugal transfer protein TrbH -
RD110_RS27050 (RD110_27050) 16004..16903 - 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
RD110_RS27055 (RD110_27055) 16921..17703 - 783 WP_006122481 conjugal transfer protein TrbF virB8
RD110_RS27060 (RD110_27060) 17700..20258 - 2559 WP_011114047 VirB4 family type IV secretion/conjugal transfer ATPase virb4
RD110_RS27065 (RD110_27065) 20255..20566 - 312 WP_001207961 conjugal transfer protein TrbD virB3
RD110_RS27070 (RD110_27070) 20570..21034 - 465 WP_011114046 conjugal transfer system pilin TrbC virB2
RD110_RS27075 (RD110_27075) 21051..22013 - 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
RD110_RS27080 (RD110_27080) 22323..22685 - 363 WP_010890126 transcriptional regulator -
RD110_RS27085 (RD110_27085) 22799..23140 + 342 WP_000019167 single-stranded DNA-binding protein -
RD110_RS27090 (RD110_27090) 23187..24407 + 1221 WP_011114072 plasmid replication initiator TrfA -
RD110_RS27105 (RD110_27105) 25730..26044 - 315 WP_011117139 type II toxin-antitoxin system RelE/ParE family toxin -
RD110_RS27110 (RD110_27110) 26041..26310 - 270 WP_001260984 type II toxin-antitoxin system ParD family antitoxin -
RD110_RS27115 (RD110_27115) 26479..26907 + 429 WP_001095942 antirestriction protein -

Host bacterium

ID   1390 GenBank   NZ_CP019238
Plasmid name   pDCY110-2 Incompatibility group   IncP1
Plasmid size   71276 bp Coordinate of oriT [Strand]   36515..36887 [-]
Host baterium   Rhodoferax koreense strain DCY-110

Cargo genes

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