Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100331
Name   oriT_pEK499 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_013122 (26046..26495 [-], 450 nt)
oriT length   450 nt
IRs (inverted repeats)      IR1: 201..215, 222..236  (ATTCATTGGTGAATC..GATTCACCAATGAAT)
 IR2: 308..315, 318..325  (GCAAAAAC..GTTTTTGC)
Location of nic site      334..335
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 450 nt

>oriT_pEK499
ATATGTATACCTCTTTATTTTCTTATCGCATCAAATTTATTTCACATATAAAAAAATGACAATTCATCGATGAATCGAATCGTGACGCAAGTTACGAAAATTACGATTCATGCAGCAAATCACATCACGAATTGAATCTAGAGTCAATTCGCTTTAACTCGTTGTTTTATTATTACTGATTCATCTATGAGTTGCGTTAAATTCATTGGTGAATCATATGCGATTCACCAATGAATCCTTTTTATAATGTAAAATAAATTAAAATACATTATTTAAAACATAAGTTAATGATTCAAATAGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCCATCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   402 GenBank   YP_003108353
Name   pEK499_p088_pEK499 insolico UniProt ID   Q0ZKT4
Length   101 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 101 a.a.        Molecular weight: 11477.11 Da        Isoelectric Point: 7.5204

>YP_003108353.1 hypothetical protein pEK499_p088 (plasmid) [Escherichia coli]
MTDKDLYGGLIRLHILHHAAEEPVFGLGIIEELRRHGYEMSAGTVYPMLHGLEKKGYLTSRHERTGRRER
RVYDITEQGRTALADAKTKVKELFGELVEGG

  Protein domains


Predicted by InterproScan.

Transcriptional regulator PadR-like family (PadR)

(15-84)


  Protein structure


Source ID Structure
AlphaFold DB Q0ZKT4


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 25561..36303

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS578_RS00115 (pEK499_p026) 21528..21962 + 435 WP_000845901 conjugation system SOS inhibitor PsiB -
HS578_RS00120 (pEK499_p027) 21959..22721 + 763 Protein_25 plasmid SOS inhibition protein A -
HS578_RS00695 22900..23049 + 150 Protein_26 plasmid maintenance protein Mok -
HS578_RS00125 (pEK499_p029) 22991..23116 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HS578_RS00700 23336..23566 + 231 WP_071587244 hypothetical protein -
HS578_RS00705 23564..23737 - 174 Protein_29 hypothetical protein -
HS578_RS00130 24035..24322 + 288 WP_000107537 hypothetical protein -
HS578_RS00135 (pEK499_p032) 24443..25264 + 822 WP_001234469 DUF932 domain-containing protein -
HS578_RS00140 (pEK499_p033) 25561..26208 - 648 WP_000614282 transglycosylase SLT domain-containing protein virB1
HS578_RS00145 (pEK499_p034) 26494..26877 + 384 WP_001151564 conjugal transfer relaxosome DNA-binding protein TraM -
HS578_RS00150 (pEK499_p035) 27071..27757 + 687 WP_000332487 PAS domain-containing protein -
HS578_RS00155 (pEK499_p036) 27851..28078 + 228 WP_001254388 conjugal transfer relaxosome protein TraY -
HS578_RS00160 (pEK499_p037) 28112..28474 + 363 WP_001098998 type IV conjugative transfer system pilin TraA -
HS578_RS00165 (pEK499_p038) 28479..28790 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HS578_RS00170 (pEK499_p039) 28812..29378 + 567 WP_000399804 type IV conjugative transfer system protein TraE traE
HS578_RS00175 (pEK499_p040) 29365..30093 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HS578_RS00180 (pEK499_p041) 30093..31520 + 1428 WP_000146638 F-type conjugal transfer pilus assembly protein TraB traB
HS578_RS00185 (pEK499_p042) 31510..32094 + 585 WP_000002795 conjugal transfer pilus-stabilizing protein TraP -
HS578_RS00190 (pEK499_p043) 32081..32401 + 321 WP_001057302 conjugal transfer protein TrbD virb4
HS578_RS00195 (pEK499_p044) 32394..32645 + 252 WP_001038341 conjugal transfer protein TrbG -
HS578_RS00200 (pEK499_p045) 32642..33157 + 516 WP_000809893 type IV conjugative transfer system lipoprotein TraV traV
HS578_RS00205 (pEK499_p046) 33292..33513 + 222 WP_001278978 conjugal transfer protein TraR -
HS578_RS00210 (pEK499_p047) 33673..36303 + 2631 WP_012783967 type IV secretion system protein TraC virb4
HS578_RS00215 (pEK499_p048) 36350..37054 + 705 WP_001067855 IS6-like element IS26 family transposase -
HS578_RS00220 (pEK499_p049) 37298..38560 - 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
HS578_RS00225 38742..38960 - 219 WP_001143771 DUF4158 domain-containing protein -
HS578_RS00230 (pEK499_p051) 39124..39681 + 558 WP_001235713 recombinase family protein -
HS578_RS00235 (pEK499_p052) 39864..40676 + 813 WP_172683509 TEM family class A beta-lactamase -

Host bacterium

ID   792 GenBank   NC_013122
Plasmid name   pEK499 Incompatibility group   IncFIA
Plasmid size   117536 bp Coordinate of oriT [Strand]   26046..26495 [-]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   blaTEM-1B, tet(A), aac(6')-Ib-cr, blaOXA-1, blaCTX-M-15, aadA5, sul1, mph(A)
Virulence gene   virulence-associated protein VagC and VagD
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -