Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113940
Name   oriT_pSPE102_vir in_silico
Organism   Salmonella enterica subsp. enterica serovar Infantis strain SPE102
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP040165 (236957..237045 [+], 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_pSPE102_vir
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8954 GenBank   WP_006855641
Name   nikB_EXT36_RS23620_pSPE102_vir insolico UniProt ID   A0A620WL05
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104006.42 Da        Isoelectric Point: 7.3526

>WP_006855641.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A620WL05


Auxiliary protein

ID   5239 GenBank   WP_001283947
Name   WP_001283947_pSPE102_vir 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   10400 GenBank   WP_001289275
Name   trbC_EXT36_RS23615_pSPE102_vir 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: 86957.15 Da        Isoelectric Point: 6.7713

>WP_001289275.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHLTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 192690..231579

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EXT36_RS23390 (EXT36_23875) 187752..188819 + 1068 WP_001360287 type IV pilus biogenesis lipoprotein PilL -
EXT36_RS23395 (EXT36_23880) 188819..189256 + 438 WP_000539807 type IV pilus biogenesis protein PilM -
EXT36_RS23400 (EXT36_23885) 189270..190952 + 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
EXT36_RS23405 (EXT36_23890) 190945..192240 + 1296 WP_058649964 type 4b pilus protein PilO2 -
EXT36_RS23410 (EXT36_23895) 192227..192679 + 453 WP_058649963 type IV pilus biogenesis protein PilP -
EXT36_RS23415 (EXT36_23900) 192690..194243 + 1554 WP_000362204 GspE/PulE family protein virB11
EXT36_RS23420 (EXT36_23905) 194256..195341 + 1086 WP_001208803 type II secretion system F family protein -
EXT36_RS23425 (EXT36_23910) 195358..195972 + 615 WP_000908228 type 4 pilus major pilin -
EXT36_RS23430 (EXT36_23915) 195982..196542 + 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
EXT36_RS23435 (EXT36_23920) 196527..197183 + 657 WP_001193551 A24 family peptidase -
EXT36_RS23440 (EXT36_23925) 197171..198607 + 1437 WP_015058913 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
EXT36_RS24680 (EXT36_23930) 198604..198828 - 225 Protein_190 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
EXT36_RS24685 199101..199370 - 270 Protein_191 hypothetical protein -
EXT36_RS23450 (EXT36_23940) 199410..200564 + 1155 WP_001139955 tyrosine-type recombinase/integrase -
EXT36_RS23455 (EXT36_23945) 200715..201539 + 825 WP_058649947 conjugal transfer protein TraE traE
EXT36_RS23460 (EXT36_23950) 201625..202827 + 1203 WP_000976353 conjugal transfer protein TraF -
EXT36_RS23465 (EXT36_23955) 202887..203471 + 585 WP_000977520 histidine phosphatase family protein -
EXT36_RS23470 (EXT36_23960) 203866..204324 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
EXT36_RS23475 (EXT36_23965) 204321..205139 + 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
EXT36_RS23480 (EXT36_23970) 205136..206284 + 1149 WP_001024976 plasmid transfer ATPase TraJ virB11
EXT36_RS23485 (EXT36_23975) 206281..206571 + 291 WP_001299214 hypothetical protein traK
EXT36_RS23490 (EXT36_23980) 206586..207137 + 552 WP_000014584 phospholipase D family protein -
EXT36_RS23495 (EXT36_23985) 207227..210994 + 3768 WP_058649948 LPD7 domain-containing protein -
EXT36_RS23500 (EXT36_23990) 211012..211359 + 348 WP_001055900 conjugal transfer protein traL
EXT36_RS23505 (EXT36_23995) 211356..212048 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
EXT36_RS23510 (EXT36_24000) 212059..213042 + 984 WP_021513963 IncI1-type conjugal transfer protein TraN traN
EXT36_RS23515 (EXT36_24005) 213045..214334 + 1290 WP_001271994 conjugal transfer protein TraO traO
EXT36_RS23520 (EXT36_24010) 214334..215038 + 705 WP_023155244 IncI1-type conjugal transfer protein TraP traP
EXT36_RS23525 (EXT36_24015) 215038..215565 + 528 WP_001055569 conjugal transfer protein TraQ traQ
EXT36_RS23530 (EXT36_24020) 215616..216020 + 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
EXT36_RS23535 (EXT36_24025) 216084..216272 + 189 WP_001277255 putative conjugal transfer protein TraS -
EXT36_RS23540 (EXT36_24030) 216256..217056 + 801 WP_001164792 IncI1-type conjugal transfer protein TraT traT
EXT36_RS23545 (EXT36_24035) 217146..220190 + 3045 WP_001024776 IncI1-type conjugal transfer protein TraU traU
EXT36_RS23550 (EXT36_24040) 220190..220804 + 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
EXT36_RS23555 (EXT36_24045) 220771..221973 + 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
EXT36_RS23560 (EXT36_24050) 222002..222586 + 585 WP_001037996 IncI1-type conjugal transfer protein TraX -
EXT36_RS23565 (EXT36_24055) 222683..224851 + 2169 WP_058649949 DotA/TraY family protein traY
EXT36_RS23570 (EXT36_24060) 224922..225584 + 663 WP_000644796 plasmid IncI1-type surface exclusion protein ExcA -
EXT36_RS23575 (EXT36_24065) 225656..225865 - 210 WP_000062603 HEAT repeat domain-containing protein -
EXT36_RS23580 226257..226433 + 177 WP_001054897 hypothetical protein -
EXT36_RS24580 226498..226593 - 96 WP_000609148 DinQ-like type I toxin DqlB -
EXT36_RS23590 (EXT36_24075) 227094..227345 + 252 WP_001291964 hypothetical protein -
EXT36_RS23595 (EXT36_24080) 227417..227569 - 153 WP_001387489 Hok/Gef family protein -
EXT36_RS23600 (EXT36_24085) 228196..228975 + 780 WP_275450201 protein FinQ -
EXT36_RS23605 (EXT36_24090) 229282..230490 + 1209 WP_001383960 IncI1-type conjugal transfer protein TrbA trbA
EXT36_RS23610 (EXT36_24095) 230509..231579 + 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
EXT36_RS23615 (EXT36_24100) 231572..233863 + 2292 WP_001289275 F-type conjugative transfer protein TrbC -

Host bacterium

ID   14375 GenBank   NZ_CP040165
Plasmid name   pSPE102_vir Incompatibility group   IncFIB
Plasmid size   324798 bp Coordinate of oriT [Strand]   236957..237045 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Infantis strain SPE102

Cargo genes

Drug resistance gene   ant(3'')-Ia, qacE, sul1, tet(A), blaCTX-M-65, floR, aph(4)-Ia, aac(3)-IVa, dfrA14, aph(3')-Ia
Virulence gene   faeC, faeE, faeF, faeH, faeI, fyuA, ybtE, ybtT, ybtU, irp1, irp2, ybtA, ybtP, ybtQ, ybtX, ybtS
Metal resistance gene   merE, merD, merA, merP, merT, merR, arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2