Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100620
Name   oriT_pUMAF0158 in_silico
Organism   Pseudomonas syringae UMAF0158
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP005971 (20885..21030 [+], 146 nt)
oriT length   146 nt
IRs (inverted repeats)      IR1: 38..43, 52..57  (AAAAAG..CTTTTT)
  IR2: 72..83, 87..98  (GTGCCAAAGGGG..CCCCTTTGAAAC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 146 nt

>oriT_pUMAF0158
CGAATTCGTTAAACAGGCACGTTACCGATTGTCTACAAAAAAGAGCTTCGCCTTTTTCGTAGCCAATCGACGTGCCAAAGGGGATACCCCTTTGAAACCCCGCAGAGCGGGAAAGCGTTGTTGTTGTCGTTGTTGGTTGTCGTCAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   692 GenBank   WP_080376851
Name   Relaxase_pUMAF0158 insolico UniProt ID   _
Length   1247 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1247 a.a.        Molecular weight: 138237.53 Da        Isoelectric Point: 8.2634

>WP_080376851.1 LPD7 domain-containing protein [Pseudomonas syringae]
MLIRVSGYNTGAQEYLEQGNKSGREFTRDELDHRLIIEGQLSVTRAIYESIPDHGQDRYLTFTLSFKEDT
VSPELLKAVTTDFKNFFMHAYKPEEFNLYAEAHLPKMKTVTDRKTGEVIDRKPHIHIIIPRINLLSGNEA
NPVDVYKNHEKYFEAFQEHINQKYGLSSPRENVRADITDAASVLSRYKGDDFYGKNRQFKQQLVEQVIER
GVTSRADFYALVAEHGETRIRNEGKDNEYISVKLPGDAKGTNLKDTIFQDDFIVRRELRKPPLEASVIQE
RLLAWPQRAREIKYVNKATPKFRKQYSQASPEERVRLLAERETNFYRAHGDDYESVHTWQRQRDNQRSPA
ETTGRRTAAPADGLQDLSVSDVADHRQAGPTRSRDGALLLPSDAHVHVGQSQPGGDSGLRSSVPGGGGGG
RRVGSTAERGRGGSQPAAVSQETKGTATPAGATGRRRAGAGKPRNTRVRAGRLVPPYAQNPHRVATIADI
EERGRRLFDPLKRPSDNALVFYRSSSHPQVADQLPQATAATTTSVQSTAGRRPRTSGKPRPPRQWRPGSV
VPPYAKNPHRVATVADIEQRARMLFDPLKRPADKALVFKRASIKALTLNKHASTVAAYFTRQAQHNQIAP
AHRWAIRRIDQQYFALRRAVFSDQRLTRQDKAQLVSVLTFERLKAREQFHKSQPNIEVNLMGSAAIRNLL
DDEKEDPGFSISGARGPGREGVRDQVKRIMDRFAKQVDPAAASERARDLSAKDLYTRKAKFSQNVHYLDK
QTDKTLFVDTGTTISMRRTGITEAGVSVALQLARERFGSTLTINGTAEFKKLVIEAVAKNGLDVHFTDKA
MNQSLADRRAELDIERGGQSIGPATDLPRHVDDATRDVRDQADRLDVTVPIEALYGQGKTADQVSQALAA
QLDTVPESERIAFVETVAITLAIPERGEPKGDQAFAQWQAQRAQPAADSAATATAETQTRVPTPSGAAPE
PLIPEAAKPALANDPALQSPSELVRLEAQWRRDFPMSEADVRASDTVMGLRGEDHAVWIIATNDKTPEAA
AMLTAYMENDSYREAFKASIVAAYKQVENSPKLVDDLDHLTAMAAQIVNEVEDRLYPAPQASSESTNKII
EGTLIEHGEAPYQHNDDNQMSYFVTLKPEGSKPRTVWGVGLAEAMSEADLKQGDQVRLQDLGTQPVVVQV
IEEDGTVTDKTVNRREWSAQPVAPEREVAETTPKGQAAAAGTPELSSPDEDDGMSVD

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(762-847)

Relaxase/Mobilisation nuclease domain (Relaxase)

(40-256)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1864..12213

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PSYRMG_RS26755 171..386 + 216 WP_080376848 hypothetical protein -
PSYRMG_RS26760 396..680 - 285 WP_223123953 helix-turn-helix transcriptional regulator -
PSYRMG_RS25210 (PSYRMG_25710) 987..1520 + 534 WP_060708976 transcription termination/antitermination NusG family protein -
PSYRMG_RS25215 (PSYRMG_25715) 1609..1851 + 243 WP_060708977 hypothetical protein -
PSYRMG_RS25220 (PSYRMG_25720) 1864..2571 + 708 WP_060708978 lytic transglycosylase domain-containing protein virB1
PSYRMG_RS25225 (PSYRMG_25725) 2571..2906 + 336 WP_055010259 hypothetical protein -
PSYRMG_RS25230 (PSYRMG_25730) 2919..3407 + 489 WP_060708979 VirB3 family type IV secretion system protein virB3
PSYRMG_RS25235 (PSYRMG_25735) 3310..5808 + 2499 WP_226995511 conjugal transfer protein virb4
PSYRMG_RS25240 (PSYRMG_25740) 5805..6491 + 687 WP_060708981 P-type DNA transfer protein VirB5 -
PSYRMG_RS25245 (PSYRMG_25745) 6524..6877 + 354 WP_060708982 hypothetical protein -
PSYRMG_RS25250 (PSYRMG_25750) 6888..7820 + 933 WP_060708983 type IV secretion system protein virB6
PSYRMG_RS25255 (PSYRMG_25755) 8228..9016 + 789 WP_060708984 type IV secretion system protein virB8
PSYRMG_RS25260 (PSYRMG_25760) 9006..9815 + 810 WP_060708985 P-type conjugative transfer protein VirB9 virB9
PSYRMG_RS25265 (PSYRMG_25765) 9802..11172 + 1371 WP_060708986 TrbI/VirB10 family protein virB10
PSYRMG_RS25270 (PSYRMG_25770) 11182..12213 + 1032 WP_060708987 P-type DNA transfer ATPase VirB11 virB11
PSYRMG_RS25275 (PSYRMG_25775) 12223..12579 + 357 WP_060708988 hypothetical protein -
PSYRMG_RS25280 (PSYRMG_25780) 12706..12936 + 231 WP_054073146 hypothetical protein -
PSYRMG_RS25285 (PSYRMG_25785) 12936..14588 + 1653 WP_060708989 type IV secretory system conjugative DNA transfer family protein -
PSYRMG_RS25290 (PSYRMG_25790) 14630..14992 + 363 WP_060708990 TrbM/KikA/MpfK family conjugal transfer protein -
PSYRMG_RS25295 (PSYRMG_25795) 15020..17185 + 2166 WP_060708991 type IA DNA topoisomerase -

Host bacterium

ID   1080 GenBank   NZ_CP005971
Plasmid name   pUMAF0158 Incompatibility group   _
Plasmid size   63004 bp Coordinate of oriT [Strand]   20885..21030 [+]
Host baterium   Pseudomonas syringae UMAF0158

Cargo genes

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