Detailed information of oriT

oriT


The information of the oriT region


oriTDB ID   100569
Name   oriT_pHNAH4-1 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_024955 (55669..55778 [-], 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_pHNAH4-1
TCACTTCAGGCTCCTTACGGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTCAGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase


ID   641 GenBank   YP_009060040
Name   NikB_pHNAH4-1 insolico UniProt ID   A0A023UG69
Length   871 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 871 a.a.        Molecular weight: 100815.80 Da        Isoelectric Point: 7.3426

>YP_009060040.1 relaxase/mobilization nuclease domain protein NikB (plasmid) [Escherichia coli]
MTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVDVMKDGCEWVNFYGVTCFHNCTSLETAAA
DMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVRHTLKSLGLADHQYVSAVHTDTDNLHVHV
AVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCWVHAPGNRIVRKTAVERDRQNAWTRGKKQ
TFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGKFLVMDGWDRNREGVQLDSFGPSWCAEKL
MKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETESLQQYACRHLGERLPEMAREGRLENCQA
IHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLTLDNVNQLDGGWQPVPTDIFRQVTPTERF
RGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGYSISHCSPQIEEMITQGEFTWQRCHELFA
QQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEPQAGPFVSAPADLFDRVQPESRYNPELAV
SDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRKPDLRYGERCREIHQACRLRKSHIRAQYD
DPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYPPSYRQWVEIQAAQGDRAAVSQLRGWDYR
DRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGSVRFRDRRTGEFVCTDYGDRVVFRNHHDR
NALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAWHNVTGRTGHEDYRITRPDVDHHREGSER
YYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

(34-286)


  Protein structure


Source ID Structure
AlphaFold DB A0A023UG69


T4SS


T4SS were predicted by using oriTfinder2.

Region 1: 61138..99119

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTC07_RS00365 (orf00089) 58854..61145 - 2292 WP_001289276 F-type conjugative transfer protein TrbC -
HTC07_RS00370 (orf00090) 61138..62208 - 1071 WP_000151582 IncI1-type conjugal transfer protein TrbB trbB
HTC07_RS00375 (orf00091) 62227..63435 - 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
HTC07_RS00380 (orf00093) 63727..63879 + 153 WP_001331364 Hok/Gef family protein -
HTC07_RS00385 63951..64202 - 252 WP_001291964 hypothetical protein -
HTC07_RS00630 64701..64796 + 96 WP_001303310 DinQ-like type I toxin DqlB -
HTC07_RS00390 64861..65145 - 285 WP_001707309 hypothetical protein -
HTC07_RS00395 65435..65638 + 204 WP_242596808 HEAT repeat domain-containing protein -
HTC07_RS00400 (orf00095) 65710..66372 - 663 WP_000644796 plasmid IncI1-type surface exclusion protein ExcA -
HTC07_RS00405 (orf00096) 66443..68611 - 2169 WP_000698354 DotA/TraY family protein traY
HTC07_RS00410 (orf00097) 68708..69292 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
HTC07_RS00415 (orf00098) 69321..70523 - 1203 WP_001385654 IncI1-type conjugal transfer protein TraW traW
HTC07_RS00420 (orf00099) 70490..71104 - 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
HTC07_RS00425 (orf00100) 71104..74148 - 3045 WP_001024780 IncI1-type conjugal transfer protein TraU traU
HTC07_RS00430 (orf00101) 74238..75038 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
HTC07_RS00435 (orf00102) 75022..75210 - 189 WP_001277255 putative conjugal transfer protein TraS -
HTC07_RS00440 (orf00103) 75274..75678 - 405 WP_000086958 IncI1-type conjugal transfer protein TraR traR
HTC07_RS00445 (orf00104) 75729..76256 - 528 WP_001055569 conjugal transfer protein TraQ traQ
HTC07_RS00450 (orf00105) 76256..76960 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
HTC07_RS00455 (orf00106) 76960..78249 - 1290 WP_001272003 conjugal transfer protein TraO traO
HTC07_RS00460 (orf00107) 78252..79235 - 984 WP_001191877 IncI1-type conjugal transfer protein TraN traN
HTC07_RS00465 (orf00108) 79246..79938 - 693 WP_000138550 DotI/IcmL family type IV secretion protein traM
HTC07_RS00470 (orf00109) 79935..80282 - 348 WP_001055900 conjugal transfer protein traL
HTC07_RS00475 (orf00111) 80300..84067 - 3768 WP_031942279 LPD7 domain-containing protein -
HTC07_RS00480 (orf00113) 84157..84708 - 552 WP_000014583 phospholipase D family protein -
HTC07_RS00625 (orf00112) 84723..85013 - 291 WP_001299214 hypothetical protein traK
HTC07_RS00485 (orf00114) 85010..86158 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
HTC07_RS00490 (orf00115) 86155..86973 - 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
HTC07_RS00495 (orf00116) 86970..87428 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
HTC07_RS00500 (orf00117) 87823..88407 - 585 WP_031942280 histidine phosphatase family protein -
HTC07_RS00505 (orf00118) 88467..89669 - 1203 WP_000976353 conjugal transfer protein TraF -
HTC07_RS00510 (orf00119) 89755..90579 - 825 WP_001238927 conjugal transfer protein TraE traE
HTC07_RS00515 (orf00120) 90730..91884 - 1155 WP_001139958 site-specific integrase -
HTC07_RS00520 91883..92194 + 312 WP_000958120 hypothetical protein -
HTC07_RS00530 (orf00122) 93189..94613 - 1425 WP_172685503 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HTC07_RS00535 (orf00123) 94613..95269 - 657 WP_001193554 prepilin peptidase -
HTC07_RS00540 95254..95814 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
HTC07_RS00545 (orf00125) 95824..96438 - 615 WP_000959785 type 4 pilus major pilin -
HTC07_RS00550 (orf00126) 96456..97553 - 1098 WP_001208805 type II secretion system F family protein -
HTC07_RS00555 (orf00127) 97566..99119 - 1554 WP_000362202 ATPase, T2SS/T4P/T4SS family virB11
HTC07_RS00560 (orf00128) 99130..99582 - 453 WP_001247334 type IV pilus biogenesis protein PilP -
HTC07_RS00565 (orf00129) 99569..100864 - 1296 WP_000752772 type 4b pilus protein PilO2 -
HTC07_RS00570 (orf00130) 100857..102539 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
HTC07_RS00575 (orf00131) 102553..102990 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
HTC07_RS00580 (orf00132) 102990..104057 - 1068 WP_001302629 type IV pilus biogenesis lipoprotein PilL -


Host bacterium


ID   1029 GenBank   NC_024955
Plasmid name   pHNAH4-1 Incompatibility group   IncI1
Plasmid size   109191 bp Coordinate of oriT [Strand]   55669..55778 [-]
Host baterium   Escherichia coli

Cargo genes


Drug resistance gene   mph(A), blaCTX-M-123
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -