Detailed information of oriT

oriT


The information of the oriT region


oriTDB ID   100576
Name   oriT_pESBL-283 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_024978 (55130..55239 [-], 110 nt)
oriT length   110 nt
IRs (inverted repeats)      IR1: 24..31, 35..42  (GTCGGGGC..GCCCTGAC)
 IR2: 49..65, 72..88  (GCAATTGTAATAGCGTC..GACGGTATTACAATTGC)
Location of nic site      96..97
Conserved sequence flanking the
  nic site  
 
 CATCCTG|T
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 110 nt

>oriT_pESBL-283
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase


ID   648 GenBank   YP_009061483
Name   NikB_pESBL-283 insolico UniProt ID   A0A075UR71
Length   899 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104022.47 Da        Isoelectric Point: 7.4265

>YP_009061483.1 NikB (plasmid) [Escherichia coli]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYAIRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A075UR71


T4SS


T4SS were predicted by using oriTfinder2.

Region 1: 60599..100065

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS294_RS00365 (D616_p128077) 58315..60606 - 2292 WP_001289276 F-type conjugative transfer protein TrbC -
HS294_RS00370 (D616_p128078) 60599..61669 - 1071 WP_000151582 IncI1-type conjugal transfer protein TrbB trbB
HS294_RS00375 (D616_p128079) 61688..62896 - 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
HS294_RS00380 (D616_p128080) 63203..63982 - 780 WP_275450201 protein FinQ -
HS294_RS00385 (D616_p128081) 64609..64761 + 153 WP_001303307 Hok/Gef family protein -
HS294_RS00390 (D616_p128082) 64833..65084 - 252 WP_001291965 hypothetical protein -
HS294_RS00395 66007..66291 - 285 WP_014640317 hypothetical protein -
HS294_RS00400 (D616_p128083) 66392..66601 - 210 Protein_78 hemolysin expression modulator Hha -
HS294_RS00405 (D616_p128084) 66699..67313 - 615 WP_000578649 plasmid IncI1-type surface exclusion protein ExcA -
HS294_RS00410 (D616_p128085) 67389..69557 - 2169 WP_000698360 IncI1-type conjugal transfer membrane protein TraY traY
HS294_RS00415 (D616_p128086) 69654..70238 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
HS294_RS00420 (D616_p128087) 70267..71469 - 1203 WP_001189159 IncI1-type conjugal transfer protein TraW traW
HS294_RS00425 (D616_p128088) 71436..72050 - 615 WP_000337394 IncI1-type conjugal transfer protein TraV traV
HS294_RS00430 (D616_p128089) 72050..75094 - 3045 WP_001024752 IncI1-type conjugal transfer protein TraU traU
HS294_RS00435 (D616_p128090) 75184..75984 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
HS294_RS00440 (D616_p128091) 75968..76156 - 189 WP_001277255 putative conjugal transfer protein TraS -
HS294_RS00445 (D616_p128092) 76220..76624 - 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
HS294_RS00450 (D616_p128093) 76675..77202 - 528 WP_001055569 conjugal transfer protein TraQ traQ
HS294_RS00455 (D616_p128094) 77202..77906 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
HS294_RS00460 (D616_p128095) 77906..79195 - 1290 WP_001271997 conjugal transfer protein TraO traO
HS294_RS00465 (D616_p128096) 79198..80181 - 984 WP_001191878 IncI1-type conjugal transfer protein TraN traN
HS294_RS00470 (D616_p128097) 80192..80884 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
HS294_RS00475 (D616_p128098) 80881..81228 - 348 WP_001055900 conjugal transfer protein traL
HS294_RS00480 (D616_p128099) 81246..85013 - 3768 WP_001141539 LPD7 domain-containing protein -
HS294_RS00485 (D616_p128100) 85103..85654 - 552 WP_000014584 phospholipase D family protein -
HS294_RS00490 (D616_p128101) 85669..85959 - 291 WP_001299214 hypothetical protein traK
HS294_RS00495 (D616_p128102) 85956..87104 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
HS294_RS00500 (D616_p128103) 87101..87919 - 819 WP_025492003 IncI1-type conjugal transfer lipoprotein TraI traI
HS294_RS00505 (D616_p128104) 87916..88374 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
HS294_RS00510 (D616_p128105) 88769..89353 - 585 WP_000977522 histidine phosphatase family protein -
HS294_RS00515 (D616_p128106) 89413..90615 - 1203 WP_031942455 conjugal transfer protein TraF -
HS294_RS00520 (D616_p128107) 90701..91525 - 825 WP_001238927 conjugal transfer protein TraE traE
HS294_RS00525 (D616_p128108) 91676..92830 - 1155 WP_001139958 site-specific integrase -
HS294_RS00530 (D616_p128109) 92814..93140 + 327 WP_001213803 hypothetical protein -
HS294_RS00535 (D616_p128112) 94267..95559 - 1293 WP_024198499 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HS294_RS00540 (D616_p128113) 95559..96215 - 657 WP_001389386 prepilin peptidase -
HS294_RS00545 (D616_p128114) 96200..96760 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
HS294_RS00550 (D616_p128115) 96770..97384 - 615 WP_000959786 type 4 pilus major pilin -
HS294_RS00555 (D616_p128116) 97402..98499 - 1098 WP_001208805 type II secretion system F family protein -
HS294_RS00560 (D616_p128117) 98512..100065 - 1554 WP_025492055 ATPase, T2SS/T4P/T4SS family virB11
HS294_RS00565 (D616_p128118) 100076..100528 - 453 WP_001247334 type IV pilus biogenesis protein PilP -
HS294_RS00570 (D616_p128119) 100515..101810 - 1296 WP_000752772 type 4b pilus protein PilO2 -
HS294_RS00575 (D616_p128120) 101803..103485 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
HS294_RS00580 (D616_p128121) 103499..103936 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
HS294_RS00585 (D616_p128122) 103936..105003 - 1068 WP_001302629 type IV pilus biogenesis lipoprotein PilL -


Host bacterium


ID   1036 GenBank   NC_024978
Plasmid name   pESBL-283 Incompatibility group   IncI1
Plasmid size   110137 bp Coordinate of oriT [Strand]   55130..55239 [-]
Host baterium   Escherichia coli

Cargo genes


Drug resistance gene   sul2, blaCTX-M-1, sul1, qacE, ant(3'')-Ia, dfrA1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2