Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100245
Name   oriT_pPSR1 in_silico
Organism   Pseudomonas syringae pv. syringae
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_005205 (66771..66916 [+], 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_pPSR1
CGAATTCGCTAAACAGGCACGTTACCGATTGTCTACAAAAAAGAGCTTCGCCTTTTTCGTATCCAATCGACGTGCCAAAGGGGATACCCCTTTGAAACCCCGCGGAGCGGGAAAGCGTTGTCGTTGTCGTTGTTGGTTGTTGTCAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   316 GenBank   NP_940739
Name   Orf54_pPSR1 insolico UniProt ID   Q6VE73
Length   1249 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1249 a.a.        Molecular weight: 138583.89 Da        Isoelectric Point: 8.9877

>NP_940739.1 Orf54 (plasmid) [Pseudomonas syringae pv. syringae]
MLIRVSGYNTGAQEYLEQGNKSGREFTRDELDHRLIIEGQLSVTRAIYESIPDHGQDRYLTFTLSFKEDT
VSPELLKAVTTDFKNFFMHAYKPEEFNLYAEAHLPKMKTVTDRKTGEVIDRKPHIHIIIPRINLLSGNEA
NPVDVYKNHEKYFEAFQEHINQKYGLSSPRENVRADITDAASVLSRYKGDDFYGKNRQFKQQLVKQVIER
GVTSRADFYALVAEHGETRIRNEGKDNEYISVKLPGDAKGTNLKDTIFQDDFIVRRELRKPPLEASVIQE
RLLAWPQRAREIKYVNKATPKFRKQYSQASPEERVRLLAERETNFYRAHGEDYETVHTGQRQRDHQRSPA
ETTGRRTAAPADGVQDLSVSDVADHRQAGPTRSRDGALLLPSDAHVHVGQSQPGGDSGLRSSVPGGGRGR
RAGSTAERGRGGRQPAAVSQETKGTATPAGATGRRRAGAGKPRNTRVRAGRVVPPYAQNPHRVATIADIE
ERGRRLFDPLKRPSDNALVFYRSSSHPQVADQLPQARAATTTPVQSTAGRRPRSSGKPRPPRQWRPGAVP
PYAKNPHRVATVADIEQRARMLFDPLKRPADKVLVFKRASIKALTVNKHASTVAAYFTRQAQHNQIAPAH
RRAIRRIDQQYFALRRAVFSDQRLTRQDKAQLVSVLTFERLKAREQFHNPKPNIEVNLMGSAAIRNLLDD
EKEDPGFSISGARGPGPEGVRERVKRVMDRFAKQVDPVAASERARDLSAKDLYTRKAKFSQNVHYLDKQT
DKTLFVDTGTTISMRRTGITEAGVSVALQLARERFGSTLTINGTAEFKKLVIEAVAKNGLDVHFTDKSMN
QSLADRRAELDIERDGQSIGPATDLPRHVDDATRDVRDQADRLGATVPIEALYGQGKTADQVSQALTAQL
DTVPESERIAFVETVAITLGIPERGQPKGDEAFAQWQAQRAQPAANSVASATSEAQANVPTPSDAVPEPV
NPEAAKPALANDPDLQSPSELVRLEAQWRRDFPMSEADVRASDTVMGLRGEDHAIWIIATDDKTPEAAAL
LTAYMENDSYREAFKASIVAAYKQVENSPQSVDDLDHLTAMAAQIVNEVEERLFPTPQAATGQTAPSRSK
VIEGTLIDHGEAPYQHNDDNQMSYFVTLKPEGGKPRTVWGVGLEEAMSDADLKQGDQVRLQDLGTQPVVV
QVLEEDGTVTDKTVNRREWSAQPVAPEREVAETTPKGQAAAAGTPELSSPDEEDGMNMD

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(40-257)

Large polyvalent protein-associated domain 7 (LPD7)

(760-846)


  Protein structure


Source ID Structure
AlphaFold DB Q6VE73


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 47681..58028

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS292_RS00225 43033..43263 - 231 Protein_48 transposase domain-containing protein -
HS292_RS00230 43490..43828 + 339 Protein_49 tyrosine-type recombinase/integrase -
HS292_RS00235 43989..44471 + 483 WP_054081655 hypothetical protein -
HS292_RS00240 45047..45433 - 387 WP_228409379 hypothetical protein -
HS292_RS00245 (pPSR1_p35) 45673..46143 - 471 WP_011152902 DUF6392 family protein -
HS292_RS00250 (pPSR1_p36) 46230..46502 - 273 WP_230081992 helix-turn-helix transcriptional regulator -
HS292_RS00255 (pPSR1_p37) 46844..47371 + 528 WP_011152904 transcription termination/antitermination NusG family protein -
HS292_RS00260 47443..47652 + 210 WP_223812427 hypothetical protein -
HS292_RS00265 (pPSR1_p38) 47681..48388 + 708 WP_011152905 lytic transglycosylase domain-containing protein virB1
HS292_RS00270 (pPSR1_p39) 48388..48723 + 336 WP_173479888 conjugal transfer protein -
HS292_RS00275 (pPSR1_p40) 48736..49224 + 489 WP_011152907 VirB3 family type IV secretion system protein virB3
HS292_RS00280 (pPSR1_p41) 49127..51619 + 2493 WP_228409383 conjugal transfer protein virb4
HS292_RS00285 (pPSR1_p42) 51622..52308 + 687 WP_011152909 P-type DNA transfer protein VirB5 -
HS292_RS00290 52342..52695 + 354 WP_054081656 hypothetical protein -
HS292_RS00295 (pPSR1_p43) 52706..53638 + 933 WP_011152910 type IV secretion system protein virB6
HS292_RS00300 (pPSR1_p45) 54046..54834 + 789 WP_011152912 type IV secretion system protein virB8
HS292_RS00305 (pPSR1_p46) 54824..55633 + 810 WP_011152913 P-type conjugative transfer protein VirB9 virB9
HS292_RS00310 (pPSR1_p47) 55620..56987 + 1368 WP_011152914 TrbI/VirB10 family protein virB10
HS292_RS00315 (pPSR1_p48) 56997..58028 + 1032 WP_011152915 P-type DNA transfer ATPase VirB11 virB11
HS292_RS00320 58038..58394 + 357 WP_010217013 hypothetical protein -
HS292_RS00325 58584..58814 + 231 WP_054081657 hypothetical protein -
HS292_RS00330 (pPSR1_p49) 58814..60472 + 1659 WP_011152916 type IV secretory system conjugative DNA transfer family protein -
HS292_RS00335 60513..60875 + 363 WP_054081658 TrbM/KikA/MpfK family conjugal transfer protein -

Host bacterium

ID   707 GenBank   NC_005205
Plasmid name   pPSR1 Incompatibility group   _
Plasmid size   72601 bp Coordinate of oriT [Strand]   66771..66916 [+]
Host baterium   Pseudomonas syringae pv. syringae

Cargo genes

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