Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113939
Name   oriT_pSBO53_vir in_silico
Organism   Salmonella enterica subsp. enterica serovar Infantis strain SBO53
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP040062 (206318..206406 [+], 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_pSBO53_vir
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8953 GenBank   WP_006855641
Name   nikB_EXT33_RS23630_pSBO53_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   5238 GenBank   WP_001283947
Name   WP_001283947_pSBO53_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   10399 GenBank   WP_001289275
Name   trbC_EXT33_RS23625_pSBO53_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: 162051..200940

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EXT33_RS23400 (EXT33_23895) 157113..158180 + 1068 WP_001360287 type IV pilus biogenesis lipoprotein PilL -
EXT33_RS23405 (EXT33_23900) 158180..158617 + 438 WP_000539807 type IV pilus biogenesis protein PilM -
EXT33_RS23410 (EXT33_23905) 158631..160313 + 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
EXT33_RS23415 (EXT33_23910) 160306..161601 + 1296 WP_058649964 type 4b pilus protein PilO2 -
EXT33_RS23420 (EXT33_23915) 161588..162040 + 453 WP_058649963 type IV pilus biogenesis protein PilP -
EXT33_RS23425 (EXT33_23920) 162051..163604 + 1554 WP_000362204 GspE/PulE family protein virB11
EXT33_RS23430 (EXT33_23925) 163617..164702 + 1086 WP_001208803 type II secretion system F family protein -
EXT33_RS23435 (EXT33_23930) 164719..165333 + 615 WP_000908228 type 4 pilus major pilin -
EXT33_RS23440 (EXT33_23935) 165343..165903 + 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
EXT33_RS23445 (EXT33_23940) 165888..166544 + 657 WP_001193551 A24 family peptidase -
EXT33_RS23450 (EXT33_23945) 166532..167968 + 1437 WP_015058913 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
EXT33_RS24820 (EXT33_23950) 167965..168189 - 225 Protein_168 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
EXT33_RS24825 168462..168731 - 270 Protein_169 hypothetical protein -
EXT33_RS23460 (EXT33_23960) 168771..169925 + 1155 WP_001139955 tyrosine-type recombinase/integrase -
EXT33_RS23465 (EXT33_23965) 170076..170900 + 825 WP_058649947 conjugal transfer protein TraE traE
EXT33_RS23470 (EXT33_23970) 170986..172188 + 1203 WP_000976353 conjugal transfer protein TraF -
EXT33_RS23475 (EXT33_23975) 172248..172832 + 585 WP_000977520 histidine phosphatase family protein -
EXT33_RS23480 (EXT33_23980) 173227..173685 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
EXT33_RS23485 (EXT33_23985) 173682..174500 + 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
EXT33_RS23490 (EXT33_23990) 174497..175645 + 1149 WP_001024976 plasmid transfer ATPase TraJ virB11
EXT33_RS23495 (EXT33_23995) 175642..175932 + 291 WP_001299214 hypothetical protein traK
EXT33_RS23500 (EXT33_24000) 175947..176498 + 552 WP_000014584 phospholipase D family protein -
EXT33_RS23505 (EXT33_24005) 176588..180355 + 3768 WP_058649948 LPD7 domain-containing protein -
EXT33_RS23510 (EXT33_24010) 180373..180720 + 348 WP_001055900 conjugal transfer protein traL
EXT33_RS23515 (EXT33_24015) 180717..181409 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
EXT33_RS23520 (EXT33_24020) 181420..182403 + 984 WP_021513963 IncI1-type conjugal transfer protein TraN traN
EXT33_RS23525 (EXT33_24025) 182406..183695 + 1290 WP_001271994 conjugal transfer protein TraO traO
EXT33_RS23530 (EXT33_24030) 183695..184399 + 705 WP_023155244 IncI1-type conjugal transfer protein TraP traP
EXT33_RS23535 (EXT33_24035) 184399..184926 + 528 WP_001055569 conjugal transfer protein TraQ traQ
EXT33_RS23540 (EXT33_24040) 184977..185381 + 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
EXT33_RS23545 (EXT33_24045) 185445..185633 + 189 WP_001277255 putative conjugal transfer protein TraS -
EXT33_RS23550 (EXT33_24050) 185617..186417 + 801 WP_001164792 IncI1-type conjugal transfer protein TraT traT
EXT33_RS23555 (EXT33_24055) 186507..189551 + 3045 WP_001024776 IncI1-type conjugal transfer protein TraU traU
EXT33_RS23560 (EXT33_24060) 189551..190165 + 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
EXT33_RS23565 (EXT33_24065) 190132..191334 + 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
EXT33_RS23570 (EXT33_24070) 191363..191947 + 585 WP_001037996 IncI1-type conjugal transfer protein TraX -
EXT33_RS23575 (EXT33_24075) 192044..194212 + 2169 WP_058649949 DotA/TraY family protein traY
EXT33_RS23580 (EXT33_24080) 194283..194945 + 663 WP_000644796 plasmid IncI1-type surface exclusion protein ExcA -
EXT33_RS23585 (EXT33_24085) 195017..195226 - 210 WP_000062603 HEAT repeat domain-containing protein -
EXT33_RS23590 195618..195794 + 177 WP_001054897 hypothetical protein -
EXT33_RS24705 195859..195954 - 96 WP_000609148 DinQ-like type I toxin DqlB -
EXT33_RS23600 (EXT33_24095) 196455..196706 + 252 WP_001291964 hypothetical protein -
EXT33_RS23605 (EXT33_24100) 196778..196930 - 153 WP_001387489 Hok/Gef family protein -
EXT33_RS23610 (EXT33_24105) 197557..198336 + 780 WP_275450201 protein FinQ -
EXT33_RS23615 (EXT33_24110) 198643..199851 + 1209 WP_001383960 IncI1-type conjugal transfer protein TrbA trbA
EXT33_RS23620 (EXT33_24115) 199870..200940 + 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
EXT33_RS23625 (EXT33_24120) 200933..203224 + 2292 WP_001289275 F-type conjugative transfer protein TrbC -

Host bacterium

ID   14374 GenBank   NZ_CP040062
Plasmid name   pSBO53_vir Incompatibility group   IncFIB
Plasmid size   320846 bp Coordinate of oriT [Strand]   206318..206406 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Infantis strain SBO53

Cargo genes

Drug resistance gene   ant(3'')-Ia, qacE, sul1, tet(A), blaCTX-M-65, fosA3, floR, aph(4)-Ia, aac(3)-IVa, dfrA14
Virulence gene   faeC, faeE, faeF, faeH, faeI, ybtS, ybtX, ybtQ, ybtP, ybtA, irp2, irp1, ybtU, ybtT, ybtE, fyuA
Metal resistance gene   merE, merD, merA, merP, merT, merR, arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2