Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107592
Name   oriT_pSPE55_vir in_silico
Organism   Salmonella enterica subsp. enterica serovar Infantis strain SPE55
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP040066 (219575..219663 [+], 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_pSPE55_vir
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5102 GenBank   WP_001299212
Name   nikB_EXT34_RS23645_pSPE55_vir insolico UniProt ID   A0A5T4AK12
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103956.40 Da        Isoelectric Point: 7.2642

>WP_001299212.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWINFYGVTCFHNCTSLETAAADMEYIALQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVSDWLSLHRRLAEDGLYLSQMDGK
YLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A5T4AK12


Auxiliary protein

ID   2335 GenBank   WP_001283947
Name   WP_001283947_pSPE55_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   5323 GenBank   WP_001289276
Name   trbC_EXT34_RS23640_pSPE55_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: 86941.11 Da        Isoelectric Point: 6.7713

>WP_001289276.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 178055..214197

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EXT34_RS23435 (EXT34_23890) 173117..174184 + 1068 WP_001360287 type IV pilus biogenesis lipoprotein PilL -
EXT34_RS23440 (EXT34_23895) 174184..174621 + 438 WP_000539807 type IV pilus biogenesis protein PilM -
EXT34_RS23445 (EXT34_23900) 174635..176317 + 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
EXT34_RS23450 (EXT34_23905) 176310..177605 + 1296 WP_001545757 type 4b pilus protein PilO2 -
EXT34_RS23455 (EXT34_23910) 177592..178044 + 453 WP_001247331 type IV pilus biogenesis protein PilP -
EXT34_RS23460 (EXT34_23915) 178055..179608 + 1554 WP_000362206 ATPase, T2SS/T4P/T4SS family virB11
EXT34_RS23465 (EXT34_23920) 179621..180706 + 1086 WP_001208802 type II secretion system F family protein -
EXT34_RS23470 (EXT34_23925) 180723..181337 + 615 WP_000908226 type 4 pilus major pilin -
EXT34_RS23475 (EXT34_23930) 181347..181907 + 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
EXT34_RS23480 (EXT34_23935) 181892..182548 + 657 WP_001193549 A24 family peptidase -
EXT34_RS23485 (EXT34_23940) 182548..183840 + 1293 WP_001350014 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
EXT34_RS23490 (EXT34_23945) 183896..184021 - 126 Protein_175 RNA-guided endonuclease TnpB family protein -
EXT34_RS23495 (EXT34_23950) 184229..185053 + 825 WP_001238942 conjugal transfer protein TraE traE
EXT34_RS23500 (EXT34_23955) 185139..186341 + 1203 WP_000976348 conjugal transfer protein TraF -
EXT34_RS23505 (EXT34_23960) 186401..186985 + 585 WP_000977522 histidine phosphatase family protein -
EXT34_RS23510 (EXT34_23965) 187380..187838 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
EXT34_RS23515 (EXT34_23970) 187835..188653 + 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
EXT34_RS23520 (EXT34_23975) 188650..189798 + 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
EXT34_RS23525 (EXT34_23980) 189795..190085 + 291 WP_001299214 hypothetical protein traK
EXT34_RS23530 (EXT34_23985) 190100..190651 + 552 WP_000014584 phospholipase D family protein -
EXT34_RS23535 (EXT34_23990) 190741..194508 + 3768 WP_001141542 LPD7 domain-containing protein -
EXT34_RS23540 (EXT34_23995) 194526..194873 + 348 WP_001055900 conjugal transfer protein traL
EXT34_RS23545 (EXT34_24000) 194870..195562 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
EXT34_RS23550 (EXT34_24005) 195573..196556 + 984 WP_001191878 IncI1-type conjugal transfer protein TraN traN
EXT34_RS23555 (EXT34_24010) 196559..197848 + 1290 WP_001271997 conjugal transfer protein TraO traO
EXT34_RS23560 (EXT34_24015) 197848..198552 + 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
EXT34_RS23565 (EXT34_24020) 198552..199079 + 528 WP_001055569 conjugal transfer protein TraQ traQ
EXT34_RS23570 (EXT34_24025) 199130..199534 + 405 WP_000086961 IncI1-type conjugal transfer protein TraR traR
EXT34_RS23575 (EXT34_24030) 199598..199786 + 189 WP_001277255 putative conjugal transfer protein TraS -
EXT34_RS23580 (EXT34_24035) 199770..200570 + 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
EXT34_RS23585 (EXT34_24040) 200660..203704 + 3045 WP_001024780 IncI1-type conjugal transfer protein TraU traU
EXT34_RS23590 (EXT34_24045) 203704..204318 + 615 WP_000337400 IncI1-type conjugal transfer protein TraV traV
EXT34_RS23595 (EXT34_24050) 204285..205487 + 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
EXT34_RS23600 (EXT34_24055) 205516..206100 + 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
EXT34_RS23605 (EXT34_24060) 206197..208365 + 2169 WP_000698357 DotA/TraY family protein traY
EXT34_RS23610 (EXT34_24065) 208439..209089 + 651 WP_001178506 plasmid IncI1-type surface exclusion protein ExcA -
EXT34_RS23615 (EXT34_24070) 209161..209370 - 210 WP_000062603 HEAT repeat domain-containing protein -
EXT34_RS23620 209762..209938 + 177 WP_001054904 hypothetical protein -
EXT34_RS24495 210003..210098 - 96 WP_001303310 DinQ-like type I toxin DqlB -
EXT34_RS23625 (EXT34_24075) 210730..211638 + 909 WP_000055084 hypothetical protein -
EXT34_RS23630 (EXT34_24080) 211900..213108 + 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
EXT34_RS23635 (EXT34_24085) 213127..214197 + 1071 WP_000151577 IncI1-type conjugal transfer protein TrbB trbB
EXT34_RS23640 (EXT34_24090) 214190..216481 + 2292 WP_001289276 F-type conjugative transfer protein TrbC -

Host bacterium

ID   8027 GenBank   NZ_CP040066
Plasmid name   pSPE55_vir Incompatibility group   IncFIB
Plasmid size   287479 bp Coordinate of oriT [Strand]   219575..219663 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Infantis strain SPE55

Cargo genes

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