Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100493
Name   oriT_pKV29 in_silico
Organism   Delftia sp. KV29
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019312 (21259..21631 [-], 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_pKV29
GCCTCGCCTCGTCTCTCATGCCGGCGGTAGCCGGCTGCCTCGCAGAGCAGGATGACCCGTTGAGCGCCCCCGGCGCGAATAAGGGACAGTGAAGATAGATAACCGGCTCGCCGGTTAGCTAACTTCACACATCCTGCCCGCCTTACGGCGTTAATAACACCAAGGAAAGTCTACACCAGCCATTACGATTTATCCGCAACTATCGCGCTATCAGGCCGCAAAAGCAGCAACGGATATAGCGAAACCCGCCACAATGGCCCATAATGCCGCTATCGAAGCGTGCCAATGCACGCCGATAGCGGACTTTTTGCGTTTCCGTAGCGCCGCTTAGTAGCGTTACATTTGCGATGAGAGGATTAGATGGACGAACACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   564 GenBank   YP_006962526
Name   TraI_pKV29 insolico UniProt ID   I1Z101
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

>YP_006962526.1 conjugal transfer relaxase TraI (plasmid) [Delftia sp. KV29]
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 I1Z101


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 49819..60496

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS888_RS00220 (pKV29_47) 46322..47185 + 864 WP_015061195 SDR family oxidoreductase -
HS888_RS00225 (pKV29_48) 47425..47934 + 510 WP_003725286 hypothetical protein -
HS888_RS00235 (pKV29_49) 48027..48224 + 198 WP_262351525 winged helix-turn-helix domain-containing protein -
HS888_RS00240 (pKV29_50) 48315..48536 - 222 WP_015061197 hypothetical protein -
HS888_RS00245 (pKV29_51) 48565..49200 - 636 WP_011114052 transglycosylase SLT domain-containing protein -
HS888_RS00250 (pKV29_52) 49214..49801 - 588 WP_010890138 TrbM/KikA/MpfK family conjugal transfer protein -
HS888_RS00255 (pKV29_53) 49819..51537 - 1719 WP_011114051 P-type conjugative transfer protein TrbL virB6
HS888_RS00260 (pKV29_54) 51548..51775 - 228 WP_000644148 entry exclusion lipoprotein TrbK -
HS888_RS00265 (pKV29_55) 51785..52549 - 765 WP_010890135 P-type conjugative transfer protein TrbJ virB5
HS888_RS00270 (pKV29_56) 52570..53991 - 1422 WP_011114050 TrbI/VirB10 family protein virB10
HS888_RS00275 (pKV29_57) 53996..54484 - 489 WP_006122479 conjugal transfer protein TrbH -
HS888_RS00280 (pKV29_58) 54487..55386 - 900 WP_006122480 P-type conjugative transfer protein TrbG virB9
HS888_RS00285 (pKV29_59) 55404..56186 - 783 WP_006122481 conjugal transfer protein TrbF virB8
HS888_RS00290 (pKV29_60) 56183..58741 - 2559 WP_173026318 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HS888_RS00295 (pKV29_61) 58738..59049 - 312 WP_001207961 conjugal transfer protein TrbD virB3
HS888_RS00300 (pKV29_62) 59053..59517 - 465 WP_011114046 conjugal transfer system pilin TrbC virB2
HS888_RS00305 (pKV29_63) 59534..60496 - 963 WP_000132020 P-type conjugative transfer ATPase TrbB virB11
HS888_RS00310 (pKV29_64) 60806..61168 - 363 WP_010890126 transcriptional regulator -
HS888_RS00315 (pKV29_65) 61282..61623 + 342 WP_000019167 single-stranded DNA-binding protein -

Host bacterium

ID   954 GenBank   NC_019312
Plasmid name   pKV29 Incompatibility group   IncP1
Plasmid size   61669 bp Coordinate of oriT [Strand]   21259..21631 [-]
Host baterium   Delftia sp. KV29

Cargo genes

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