Detailed information of oriT

oriT


The information of the oriT region


oriTDB ID   113605
Name   oriT_S15BD07413|p12 in_silico
Organism   Shigella sonnei strain S15BD07413
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099779 (35197..35285 [-], 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_S15BD07413|p12
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase


ID   8714 GenBank   WP_001387486
Name   nikB_NHV80_RS00220_S15BD07413|p12 insolico UniProt ID   D9Z503
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103861.32 Da        Isoelectric Point: 7.4288

>WP_001387486.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNRGGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB D9Z503


Auxiliary protein


ID   5099 GenBank   WP_001283947
Name   WP_001283947_S15BD07413|p12 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   10090 GenBank   WP_001289278
Name   trbC_NHV80_RS00225_S15BD07413|p12 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: 86924.02 Da        Isoelectric Point: 6.7713

>WP_001289278.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILTAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS


T4SS were predicted by using oriTfinder2.

Region 1: 40663..80154

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NHV80_RS00225 38379..40670 - 2292 WP_001289278 F-type conjugative transfer protein TrbC -
NHV80_RS00230 40663..41733 - 1071 WP_000151588 IncI1-type conjugal transfer protein TrbB trbB
NHV80_RS00235 41752..42960 - 1209 WP_000121263 IncI1-type conjugal transfer protein TrbA trbA
NHV80_RS00240 43267..44046 - 780 WP_275450201 protein FinQ -
NHV80_RS00245 44673..44825 + 153 WP_001387489 Hok/Gef family protein -
NHV80_RS00250 44897..45148 - 252 WP_001291964 hypothetical protein -
NHV80_RS00490 45649..45744 + 96 WP_000609148 DinQ-like type I toxin DqlB -
NHV80_RS00260 45809..45985 - 177 WP_001054898 hypothetical protein -
NHV80_RS00265 46168..46377 - 210 WP_001140543 hemolysin expression modulator Hha -
NHV80_RS00270 46475..47089 - 615 WP_000578648 plasmid IncI1-type surface exclusion protein ExcA -
NHV80_RS00275 47165..49333 - 2169 WP_000698360 IncI1-type conjugal transfer membrane protein TraY traY
NHV80_RS00280 49430..50014 - 585 WP_001037983 IncI1-type conjugal transfer protein TraX -
NHV80_RS00285 50043..51245 - 1203 WP_001387490 IncI1-type conjugal transfer protein TraW traW
NHV80_RS00290 51212..51826 - 615 WP_000337395 IncI1-type conjugal transfer protein TraV traV
NHV80_RS00295 51826..54870 - 3045 WP_001024789 IncI1-type conjugal transfer protein TraU traU
NHV80_RS00300 54960..55760 - 801 WP_001164783 IncI1-type conjugal transfer protein TraT traT
NHV80_RS00305 55744..55932 - 189 WP_001277253 putative conjugal transfer protein TraS -
NHV80_RS00310 55996..56400 - 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
NHV80_RS00315 56451..56978 - 528 WP_001055569 conjugal transfer protein TraQ traQ
NHV80_RS00320 56978..57682 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
NHV80_RS00325 57682..58971 - 1290 WP_001271994 conjugal transfer protein TraO traO
NHV80_RS00330 58974..59957 - 984 WP_001191879 IncI1-type conjugal transfer protein TraN traN
NHV80_RS00335 59968..60660 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
NHV80_RS00340 60657..61004 - 348 WP_001055900 conjugal transfer protein traL
NHV80_RS00345 61022..64786 - 3765 WP_001141540 LPD7 domain-containing protein -
NHV80_RS00350 64876..65427 - 552 WP_000014586 phospholipase D family protein -
NHV80_RS00355 65442..65732 - 291 WP_001314267 hypothetical protein traK
NHV80_RS00360 65729..66877 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
NHV80_RS00365 66874..67692 - 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
NHV80_RS00370 67689..68147 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
NHV80_RS00375 68542..69126 - 585 WP_000977522 histidine phosphatase family protein -
NHV80_RS00380 69186..70388 - 1203 WP_000976357 conjugal transfer protein TraF -
NHV80_RS00385 70474..71298 - 825 WP_001238932 conjugal transfer protein TraE traE
NHV80_RS00390 71449..72603 - 1155 WP_001139956 tyrosine-type recombinase/integrase -
NHV80_RS00395 72916..73071 - 156 WP_001302705 hypothetical protein -
NHV80_RS00400 73709..73966 - 258 WP_001302706 hypothetical protein -
NHV80_RS00405 74124..74372 + 249 WP_001349157 hypothetical protein -
NHV80_RS00410 74369..75661 - 1293 WP_001390622 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
NHV80_RS00415 75661..76317 - 657 WP_001193549 A24 family peptidase -
NHV80_RS00420 76302..76862 - 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
NHV80_RS00425 76872..77486 - 615 WP_000908227 type 4 pilus major pilin -
NHV80_RS00430 77503..78588 - 1086 WP_001208802 type II secretion system F family protein -
NHV80_RS00435 78601..80154 - 1554 WP_000362206 GspE/PulE family protein virB11
NHV80_RS00440 80165..80617 - 453 WP_001247337 type IV pilus biogenesis protein PilP -
NHV80_RS00445 80604..81899 - 1296 WP_000752782 type 4b pilus protein PilO2 -
NHV80_RS00450 81892..83574 - 1683 WP_000748144 PilN family type IVB pilus formation outer membrane protein -
NHV80_RS00455 83588..84025 - 438 WP_000539806 type IV pilus biogenesis protein PilM -
NHV80_RS00460 84025..85092 - 1068 WP_001360287 type IV pilus biogenesis lipoprotein PilL -


Host bacterium


ID   14040 GenBank   NZ_CP099779
Plasmid name   S15BD07413|p12 Incompatibility group   IncI1
Plasmid size   89871 bp Coordinate of oriT [Strand]   35197..35285 [-]
Host baterium   Shigella sonnei strain S15BD07413

Cargo genes


Drug resistance gene   blaCTX-M-15, blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2