Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100496
Name   oriT_pNCPPB880-40 in_silico
Organism   Pseudomonas syringae
Sequence Completeness      incomplete
NCBI accession of oriT (coordinates [strand])   NC_019341 (11647..11676 [+], 30 nt)
oriT length   30 nt
IRs (inverted repeats)     _
Location of nic site      14..15
Conserved sequence flanking the
  nic site    		  GGTGT|ATAGC
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 30 nt

>oriT_pNCPPB880-40
ATTGCGTATGGTGTATAGCTCGTTAAGGGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   567 GenBank   YP_006964196
Name   TraI_pNCPPB880-40 insolico UniProt ID   I3W2D2
Length   989 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 989 a.a.        Molecular weight: 109917.12 Da        Isoelectric Point: 9.4933

>YP_006964196.1 putative TraI protein (plasmid) [Pseudomonas syringae]
MIDITTITRQSFGKVVSYYADGADDYYAKDGTAMQWQGEGAEALGLSGEVDQKRFRELLEGKIDERTHLK
RSSSEGTNKERIGYDLTFSAPKGVSLQALVDGDQRIIAAHDKAVTAAVREAEMLAKARHTVNKKTSVEDT
KNLVVAKFRHETSRALDPDLHSHAFVMNMTQRADGEWRALMNDAIVNSSMHIGNVYKAELAKELEKAGFV
LRYERNGTFDLAHFSDHQIKEFSARSQQIEAWLEKKGLDRSTASHAEKNQAALATRDKKAPNIDREELRK
VWQARSRDLGIDYKSREWAGEGGRGPDDKGRSPTPSPQLEKPLEWHADKTLEFAIQSLTERKAVITVKEL
MDTAMKHGFGRLNVDDIRAGIERRLESGHLIKEEPLYSAGNAENDKAGKTRKGAEKPAKAPVLLSRKEWV
DQLVKSGRTRSEAVKLVESGIKSGRLKKGDTRFTTHIAQRRERDILALERMGRGKFESTISPEKVKGFLD
DRTLNAEQGKAVSQIVQGRNQFMAVQGYAGVGKSFMTTAARDLLEENGYKVTALAPYGSQKKALEEEGIE
ARTVASFLKAQDKKIDKDTVVFIDEAGVIPARQMNEIMKVIEQAGARAVFLGDTAQTKAIEAGKPFEQLM
KAGMETARMEDIQRQKNPVLLEAVKLAAAGDARGSLEKIAKITEVKEDGDRYSQIVQSYVSLPKAERDNA
LVITGTNDSRQQINAGIRRGLELEGKGQDFHLLNRLDTTQAERRHSKYYEKGAIIVPEQDYKNGLMRGEQ
YKVLDTGPGNRLTVENATGDRIQFSPAQCTKLSVYRNEKSELAVGDWVKITRNDKTLDLANGDRFIVSEV
RDGKIILTDGKPGSEDPERKLGRVEIDASQSMFIGYAYASTVHSAQGLTCDKVLVNLETESKTTAKDVYY
VAVSRARHEAEIYTDSAAKLGNAVSRLNIKDAALDIKQLSKYAQPKTKTIENSTPEKQVKETGVAHSKRQ
KGDDRSIGL

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(14-288)

AAA domain (AAA_30)

(493-676)

UvrD-like helicase C-terminal domain (UvrD_C_2)

(876-920)


  Protein structure


Source ID Structure
AlphaFold DB I3W2D2


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1..11175

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS937_RS00005 (D708_p3001) 1..708 + 708 WP_015062512 type IV secretion system protein virB5
HS937_RS00010 (D708_p3002) 710..916 + 207 WP_015062513 EexN family lipoprotein -
HS937_RS00015 (D708_p3003) 931..1983 + 1053 WP_015062514 type IV secretion system protein virB6
HS937_RS00020 (D708_p3004) 2085..2270 + 186 WP_015062515 hypothetical protein -
HS937_RS00025 (D708_p3005) 2267..3007 + 741 WP_015062516 type IV secretion system protein virB8
HS937_RS00030 (D708_p3006) 3010..3921 + 912 WP_015062517 TrbG/VirB9 family P-type conjugative transfer protein virB9
HS937_RS00035 (D708_p3007) 3918..5066 + 1149 WP_015062518 type IV secretion system protein VirB10 virB10
HS937_RS00040 (D708_p3008) 5023..6090 + 1068 WP_228857561 ATPase, T2SS/T4P/T4SS family virB11
HS937_RS00045 (D708_p3009) 6080..6607 + 528 WP_015062520 phospholipase D-like domain-containing protein -
HS937_RS00050 (D708_p3010) 6656..9625 - 2970 WP_015062521 MobF family relaxase -
HS937_RS00055 (D708_p3011) 9622..11175 - 1554 WP_015062522 type IV secretion system DNA-binding domain-containing protein virb4
HS937_RS00060 (D708_p3012) 11178..11528 - 351 WP_172684885 hypothetical protein -
HS937_RS00065 (D708_p3013) 11942..12391 + 450 WP_015062524 hypothetical protein -
HS937_RS00070 (D708_p3014) 12399..13106 + 708 WP_015062525 StbB family protein -
HS937_RS00075 (D708_p3015) 13110..13493 + 384 WP_015062526 plasmid stabilization protein StbC -
HS937_RS00080 (D708_p3016) 13749..14543 + 795 WP_015062527 SprT-like domain-containing protein -
HS937_RS00085 (D708_p3017) 14575..14994 - 420 WP_015062528 hypothetical protein -
HS937_RS00090 (D708_p3018) 15084..15422 - 339 WP_015062529 hypothetical protein -

Region 2: 33781..41721

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS937_RS00210 (D708_p3045) 29529..29741 - 213 WP_015062556 hypothetical protein -
HS937_RS00215 29771..30034 - 264 WP_103750672 hypothetical protein -
HS937_RS00220 30031..30345 - 315 WP_172684892 hypothetical protein -
HS937_RS00225 (D708_p3047) 30391..30744 - 354 WP_015062558 hypothetical protein -
HS937_RS00230 (D708_p3048) 30785..31012 - 228 WP_015062559 hypothetical protein -
HS937_RS00235 (D708_p3049) 31114..31659 - 546 WP_015062560 restriction endonuclease -
HS937_RS00240 (D708_p3050) 31707..32168 - 462 WP_172684893 hypothetical protein -
HS937_RS00245 (D708_p3052) 32670..32987 - 318 WP_015062563 hypothetical protein -
HS937_RS00250 (D708_p3053) 33080..33508 - 429 WP_015062564 hypothetical protein -
HS937_RS00255 (D708_p3054) 33512..33757 - 246 WP_015062565 H-NS histone family protein -
HS937_RS00260 (D708_p3055) 33781..34599 + 819 WP_172684894 lytic transglycosylase domain-containing protein virB1
HS937_RS00265 (D708_p3056) 34596..34928 + 333 WP_015062567 hypothetical protein -
HS937_RS00270 (D708_p3057) 34912..35208 + 297 WP_015062568 TrbC/VirB2 family protein virB2
HS937_RS00275 (D708_p3058) 35254..35565 + 312 WP_015062569 VirB3 family type IV secretion system protein virB3
HS937_RS00280 (D708_p3059) 35565..36977 + 1413 WP_015062570 VirB4 family type IV secretion system protein virb4
HS937_RS00285 (D708_p3060) 37090..38319 - 1230 WP_015062536 IS91 family transposase -
HS937_RS00290 (D708_p3061) 38300..38581 - 282 WP_015062535 hypothetical protein -
HS937_RS00295 (D708_p3062) 38651..39280 + 630 WP_015062571 type IV secretion system DNA-binding domain-containing protein virb4
HS937_RS00300 (D708_p3063) 39454..40683 - 1230 WP_015062536 IS91 family transposase -
HS937_RS00305 (D708_p3064) 40664..40945 - 282 WP_015062535 hypothetical protein -
HS937_RS00310 (D708_p3065) 40987..41721 + 735 WP_015062572 ATPase provides energy for both assembly of type IV secretion complex and secretion of T-DNA complex (VirB4) virb4

Host bacterium

ID   957 GenBank   NC_019341
Plasmid name   pNCPPB880-40 Incompatibility group   _
Plasmid size   41724 bp Coordinate of oriT [Strand]   11647..11676 [+]
Host baterium   Pseudomonas syringae

Cargo genes

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