Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102843
Name   oriT_pXH990_3 in_silico
Organism   Escherichia coli strain XH990
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP019358 (2251..2339 [+], 89 nt)
oriT length   89 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 89 nt

>oriT_pXH990_3
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2116 GenBank   WP_012783930
Name   nikB_BW242_RS01870_pXH990_3 insolico UniProt ID   N0GUP8
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104070.55 Da        Isoelectric Point: 7.3623

>WP_012783930.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSHMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLAERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALVDKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB N0GUP8


Auxiliary protein

ID   855 GenBank   WP_001283947
Name   WP_001283947_pXH990_3 insolico UniProt ID   A0A142CMC2
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12613.57 Da        Isoelectric Point: 10.7463

>WP_001283947.1 MULTISPECIES: IncI1-type relaxosome accessory protein NikA [Enterobacteriaceae]
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A142CMC2


T4CP

ID   1779 GenBank   WP_202036551
Name   trbC_BW242_RS02350_pXH990_3 insolico UniProt ID   _
Length   763 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 763 a.a.        Molecular weight: 86878.96 Da        Isoelectric Point: 6.7713

>WP_202036551.1 F-type conjugative transfer protein TrbC [Escherichia coli]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRVPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILTAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 43833..82901

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BW242_RS02125 (BW242_02405) 38895..39962 + 1068 WP_012783947 type IV pilus biogenesis lipoprotein PilL -
BW242_RS02130 (BW242_02410) 39962..40399 + 438 WP_000539807 type IV pilus biogenesis protein PilM -
BW242_RS02135 (BW242_02415) 40413..42095 + 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
BW242_RS02140 (BW242_02420) 42088..43383 + 1296 WP_012783946 type 4b pilus protein PilO2 -
BW242_RS02145 (BW242_02425) 43370..43822 + 453 WP_012783945 type IV pilus biogenesis protein PilP -
BW242_RS02150 (BW242_02430) 43833..45386 + 1554 WP_001492932 ATPase, T2SS/T4P/T4SS family virB11
BW242_RS02155 (BW242_02435) 45399..46496 + 1098 WP_001492931 type II secretion system F family protein -
BW242_RS02160 (BW242_02440) 46514..47128 + 615 WP_001542527 type 4 pilus major pilin -
BW242_RS02165 (BW242_02445) 47138..47698 + 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
BW242_RS02170 (BW242_02450) 47683..48339 + 657 WP_001193553 prepilin peptidase -
BW242_RS02175 (BW242_02455) 48339..49633 + 1295 Protein_63 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
BW242_RS02180 (BW242_02465) 49626..49877 - 252 WP_236922475 hypothetical protein -
BW242_RS25650 (BW242_02485) 50660..50734 - 75 Protein_65 shufflon protein D' -
BW242_RS02185 (BW242_02490) 50733..51887 + 1155 WP_001139955 site-specific integrase -
BW242_RS02190 (BW242_02495) 52038..52862 + 825 WP_001238932 conjugal transfer protein TraE traE
BW242_RS02195 (BW242_02500) 52948..54150 + 1203 WP_000976353 conjugal transfer protein TraF -
BW242_RS02200 (BW242_02505) 54210..54794 + 585 WP_000977522 histidine phosphatase family protein -
BW242_RS02205 (BW242_02510) 55188..55646 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
BW242_RS02210 (BW242_02515) 55643..56461 + 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
BW242_RS02215 (BW242_02520) 56458..57606 + 1149 WP_001024971 plasmid transfer ATPase TraJ virB11
BW242_RS02220 (BW242_02525) 57603..57893 + 291 WP_001314267 hypothetical protein traK
BW242_RS02225 (BW242_02530) 57908..58459 + 552 WP_012783942 phospholipase D family protein -
BW242_RS02230 (BW242_02535) 58549..62316 + 3768 WP_012783940 LPD7 domain-containing protein -
BW242_RS02235 (BW242_02540) 62334..62681 + 348 WP_001055900 conjugal transfer protein traL
BW242_RS02240 (BW242_02545) 62678..63370 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
BW242_RS02245 (BW242_02550) 63381..64364 + 984 WP_001191880 IncI1-type conjugal transfer protein TraN traN
BW242_RS02250 (BW242_02555) 64367..65656 + 1290 WP_011264042 conjugal transfer protein TraO traO
BW242_RS02255 (BW242_02560) 65656..66360 + 705 WP_001493811 IncI1-type conjugal transfer protein TraP traP
BW242_RS02260 (BW242_02565) 66360..66887 + 528 WP_001055569 conjugal transfer protein TraQ traQ
BW242_RS02265 (BW242_02570) 66938..67342 + 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
BW242_RS02270 (BW242_02575) 67406..67594 + 189 WP_001277255 putative conjugal transfer protein TraS -
BW242_RS02275 (BW242_02580) 67578..68378 + 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
BW242_RS02280 (BW242_02585) 68468..71512 + 3045 WP_012783939 IncI1-type conjugal transfer protein TraU traU
BW242_RS02285 (BW242_02590) 71512..72126 + 615 WP_000337394 IncI1-type conjugal transfer protein TraV traV
BW242_RS02290 (BW242_02595) 72093..73295 + 1203 WP_012783938 IncI1-type conjugal transfer protein TraW traW
BW242_RS02295 (BW242_02600) 73324..73908 + 585 WP_012783937 conjugal transfer protein TraX -
BW242_RS02300 (BW242_02605) 74005..76173 + 2169 WP_015508354 DotA/TraY family protein traY
BW242_RS02305 (BW242_02610) 76244..76906 + 663 WP_012783935 plasmid IncI1-type surface exclusion protein ExcA -
BW242_RS02310 (BW242_02615) 76978..77187 - 210 WP_000062603 HEAT repeat domain-containing protein -
BW242_RS02315 (BW242_02625) 77579..77755 + 177 WP_001054900 hypothetical protein -
BW242_RS25920 77820..77915 - 96 WP_000609148 DinQ-like type I toxin DqlB -
BW242_RS02325 (BW242_02635) 78416..78667 + 252 Protein_94 hypothetical protein -
BW242_RS02330 (BW242_02640) 78739..78891 - 153 WP_001387489 Hok/Gef family protein -
BW242_RS02335 (BW242_02645) 79518..80297 + 780 WP_275450201 protein FinQ -
BW242_RS02340 (BW242_02650) 80604..81812 + 1209 WP_001703845 IncI1-type conjugal transfer protein TrbA trbA
BW242_RS02345 (BW242_02655) 81831..82901 + 1071 WP_012783932 IncI1-type conjugal transfer protein TrbB trbB
BW242_RS02350 (BW242_02660) 82894..85185 + 2292 WP_202036551 F-type conjugative transfer protein TrbC -

Host bacterium

ID   3286 GenBank   NZ_CP019358
Plasmid name   pXH990_3 Incompatibility group   IncI1
Plasmid size   86028 bp Coordinate of oriT [Strand]   2251..2339 [+]
Host baterium   Escherichia coli strain XH990

Cargo genes

Drug resistance gene   blaCTX-M-55
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2