Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113936
Name   oriT_pSPE100_vir in_silico
Organism   Salmonella enterica subsp. enterica serovar Infantis strain SPE100
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP040064 (232558..232646 [+], 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_pSPE100_vir
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8950 GenBank   WP_006855641
Name   nikB_EXT35_RS23675_pSPE100_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   5237 GenBank   WP_001283947
Name   WP_001283947_pSPE100_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   10398 GenBank   WP_001289275
Name   trbC_EXT35_RS23670_pSPE100_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: 188291..227180

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EXT35_RS23445 (EXT35_23955) 183353..184420 + 1068 WP_001360287 type IV pilus biogenesis lipoprotein PilL -
EXT35_RS23450 (EXT35_23960) 184420..184857 + 438 WP_000539807 type IV pilus biogenesis protein PilM -
EXT35_RS23455 (EXT35_23965) 184871..186553 + 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
EXT35_RS23460 (EXT35_23970) 186546..187841 + 1296 WP_058649964 type 4b pilus protein PilO2 -
EXT35_RS23465 (EXT35_23975) 187828..188280 + 453 WP_058649963 type IV pilus biogenesis protein PilP -
EXT35_RS23470 (EXT35_23980) 188291..189844 + 1554 WP_000362204 GspE/PulE family protein virB11
EXT35_RS23475 (EXT35_23985) 189857..190942 + 1086 WP_001208803 type II secretion system F family protein -
EXT35_RS23480 (EXT35_23990) 190959..191573 + 615 WP_000908228 type 4 pilus major pilin -
EXT35_RS23485 (EXT35_23995) 191583..192143 + 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
EXT35_RS23490 (EXT35_24000) 192128..192784 + 657 WP_001193551 A24 family peptidase -
EXT35_RS23495 (EXT35_24005) 192784..194076 + 1293 WP_039719938 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
EXT35_RS23500 (EXT35_24010) 194073..194321 - 249 WP_001349157 hypothetical protein -
EXT35_RS24820 194702..194971 - 270 Protein_187 hypothetical protein -
EXT35_RS23505 (EXT35_24020) 195011..196165 + 1155 WP_001139955 tyrosine-type recombinase/integrase -
EXT35_RS23510 (EXT35_24025) 196316..197140 + 825 WP_058649947 conjugal transfer protein TraE traE
EXT35_RS23515 (EXT35_24030) 197226..198428 + 1203 WP_000976353 conjugal transfer protein TraF -
EXT35_RS23520 (EXT35_24035) 198488..199072 + 585 WP_000977520 histidine phosphatase family protein -
EXT35_RS23525 (EXT35_24040) 199467..199925 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
EXT35_RS23530 (EXT35_24045) 199922..200740 + 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
EXT35_RS23535 (EXT35_24050) 200737..201885 + 1149 WP_001024976 plasmid transfer ATPase TraJ virB11
EXT35_RS23540 (EXT35_24055) 201882..202172 + 291 WP_001299214 hypothetical protein traK
EXT35_RS23545 (EXT35_24060) 202187..202738 + 552 WP_000014584 phospholipase D family protein -
EXT35_RS23550 (EXT35_24065) 202828..206595 + 3768 WP_058649948 LPD7 domain-containing protein -
EXT35_RS23555 (EXT35_24070) 206613..206960 + 348 WP_001055900 conjugal transfer protein traL
EXT35_RS23560 (EXT35_24075) 206957..207649 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
EXT35_RS23565 (EXT35_24080) 207660..208643 + 984 WP_021513963 IncI1-type conjugal transfer protein TraN traN
EXT35_RS23570 (EXT35_24085) 208646..209935 + 1290 WP_001271994 conjugal transfer protein TraO traO
EXT35_RS23575 (EXT35_24090) 209935..210639 + 705 WP_023155244 IncI1-type conjugal transfer protein TraP traP
EXT35_RS23580 (EXT35_24095) 210639..211166 + 528 WP_001055569 conjugal transfer protein TraQ traQ
EXT35_RS23585 (EXT35_24100) 211217..211621 + 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
EXT35_RS23590 (EXT35_24105) 211685..211873 + 189 WP_001277255 putative conjugal transfer protein TraS -
EXT35_RS23595 (EXT35_24110) 211857..212657 + 801 WP_001164792 IncI1-type conjugal transfer protein TraT traT
EXT35_RS23600 (EXT35_24115) 212747..215791 + 3045 WP_001024776 IncI1-type conjugal transfer protein TraU traU
EXT35_RS23605 (EXT35_24120) 215791..216405 + 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
EXT35_RS23610 (EXT35_24125) 216372..217574 + 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
EXT35_RS23615 (EXT35_24130) 217603..218187 + 585 WP_001037996 IncI1-type conjugal transfer protein TraX -
EXT35_RS23620 (EXT35_24135) 218284..220452 + 2169 WP_058649949 DotA/TraY family protein traY
EXT35_RS23625 (EXT35_24140) 220523..221185 + 663 WP_000644796 plasmid IncI1-type surface exclusion protein ExcA -
EXT35_RS23630 (EXT35_24145) 221257..221466 - 210 WP_000062603 HEAT repeat domain-containing protein -
EXT35_RS23635 221858..222034 + 177 WP_001054897 hypothetical protein -
EXT35_RS24690 222099..222194 - 96 WP_000609148 DinQ-like type I toxin DqlB -
EXT35_RS23645 (EXT35_24155) 222695..222946 + 252 WP_001291964 hypothetical protein -
EXT35_RS23650 (EXT35_24160) 223018..223170 - 153 WP_001387489 Hok/Gef family protein -
EXT35_RS23655 (EXT35_24165) 223797..224576 + 780 WP_275450201 protein FinQ -
EXT35_RS23660 (EXT35_24170) 224883..226091 + 1209 WP_001383960 IncI1-type conjugal transfer protein TrbA trbA
EXT35_RS23665 (EXT35_24175) 226110..227180 + 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
EXT35_RS23670 (EXT35_24180) 227173..229464 + 2292 WP_001289275 F-type conjugative transfer protein TrbC -

Host bacterium

ID   14371 GenBank   NZ_CP040064
Plasmid name   pSPE100_vir Incompatibility group   IncFIB
Plasmid size   326004 bp Coordinate of oriT [Strand]   232558..232646 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Infantis strain SPE100

Cargo genes

Drug resistance gene   ant(3'')-Ia, qacE, sul1, tet(A), fosA3, floR, aph(4)-Ia, aac(3)-IVa, dfrA14, blaCTX-M-65, 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