Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113601
Name   oriT_S15BD02407|p5 in_silico
Organism   Shigella sonnei strain S15BD02407
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099781 (44351..44437 [-], 87 nt)
oriT length   87 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 87 nt

>oriT_S15BD02407|p5
GGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8710 GenBank   WP_024190603
Name   nikB_NHV77_RS00280_S15BD02407|p5 insolico UniProt ID   A0A291RBE5
Length   900 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 900 a.a.        Molecular weight: 104187.69 Da        Isoelectric Point: 7.3424

>WP_024190603.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPYRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVDAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWVRVQHGHLVICDGYEHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKLWEPPSPMR

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A291RBE5


Auxiliary protein

ID   5094 GenBank   WP_001281051
Name   WP_001281051_S15BD02407|p5 insolico UniProt ID   A0A3U8I0C6
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12646.44 Da        Isoelectric Point: 10.4030

>WP_001281051.1 MULTISPECIES: plasmid mobilization protein MobA [Enterobacteriaceae]
MSDKRQRSGSERRQKTILRAVRFSPDEDETICKNAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB A0A3U8I0C6


T4CP

ID   10085 GenBank   WP_024190602
Name   trbC_NHV77_RS00290_S15BD02407|p5 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: 86944.10 Da        Isoelectric Point: 6.4493

>WP_024190602.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRIRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMARLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRIRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTQEERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNTPPTERPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 50794..87815

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NHV77_RS00285 47620..48438 + 819 WP_000106194 DUF2971 domain-containing protein -
NHV77_RS00290 48510..50801 - 2292 WP_024190602 F-type conjugative transfer protein TrbC -
NHV77_RS00295 50794..51864 - 1071 WP_000151590 IncI1-type conjugal transfer protein TrbB trbB
NHV77_RS00300 51883..53091 - 1209 WP_001295719 IncI1-type conjugal transfer protein TrbA trbA
NHV77_RS00305 53399..54178 - 780 WP_276312874 protein FinQ -
NHV77_RS00310 54805..54957 + 153 WP_001303307 Hok/Gef family protein -
NHV77_RS00315 55029..55280 - 252 WP_001291965 hypothetical protein -
NHV77_RS00535 55781..55876 + 96 WP_000609148 DinQ-like type I toxin DqlB -
NHV77_RS00325 55941..56225 - 285 WP_172692542 hypothetical protein -
NHV77_RS00330 56519..56728 + 210 WP_000062603 HEAT repeat domain-containing protein -
NHV77_RS00335 56800..57462 - 663 WP_253075078 plasmid IncI1-type surface exclusion protein ExcA -
NHV77_RS00340 57533..59701 - 2169 WP_000698356 DotA/TraY family protein traY
NHV77_RS00345 59798..60382 - 585 WP_001037992 IncI1-type conjugal transfer protein TraX -
NHV77_RS00350 60411..61613 - 1203 WP_001189157 IncI1-type conjugal transfer protein TraW traW
NHV77_RS00355 61580..62194 - 615 WP_032174792 IncI1-type conjugal transfer protein TraV traV
NHV77_RS00360 62194..65238 - 3045 WP_001024771 IncI1-type conjugal transfer protein TraU traU
NHV77_RS00365 65328..66128 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
NHV77_RS00370 66112..66300 - 189 WP_001277255 putative conjugal transfer protein TraS -
NHV77_RS00375 66364..66768 - 405 WP_000086957 IncI1-type conjugal transfer protein TraR traR
NHV77_RS00380 66819..67346 - 528 WP_001055569 conjugal transfer protein TraQ traQ
NHV77_RS00385 67346..68050 - 705 WP_001295718 IncI1-type conjugal transfer protein TraP traP
NHV77_RS00390 68050..69339 - 1290 WP_001271993 conjugal transfer protein TraO traO
NHV77_RS00395 69342..70325 - 984 WP_001191880 IncI1-type conjugal transfer protein TraN traN
NHV77_RS00400 70336..71028 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
NHV77_RS00405 71025..71372 - 348 WP_001055900 conjugal transfer protein traL
NHV77_RS00410 71390..75157 - 3768 WP_001141524 LPD7 domain-containing protein -
NHV77_RS00415 75247..75798 - 552 WP_000014585 phospholipase D family protein -
NHV77_RS00420 75813..76103 - 291 WP_001299214 hypothetical protein traK
NHV77_RS00425 76100..77248 - 1149 WP_001024968 plasmid transfer ATPase TraJ virB11
NHV77_RS00430 77245..78063 - 819 WP_000646093 IncI1-type conjugal transfer lipoprotein TraI traI
NHV77_RS00435 78060..78518 - 459 WP_001079806 IncI1-type conjugal transfer lipoprotein TraH -
NHV77_RS00440 78913..79497 - 585 WP_086200648 histidine phosphatase family protein -
NHV77_RS00445 79557..80759 - 1203 WP_000976355 conjugal transfer protein TraF -
NHV77_RS00450 80845..81669 - 825 WP_001238934 conjugal transfer protein TraE traE
NHV77_RS00540 81820..81927 - 108 Protein_90 shufflon-specific DNA recombinase -
NHV77_RS00455 81910..82173 + 264 Protein_91 transposase -
NHV77_RS00460 82230..83423 - 1194 WP_086200649 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
NHV77_RS00465 83441..84067 - 627 WP_000939938 prepilin peptidase -
NHV77_RS00470 84083..84568 - 486 WP_001080767 lytic transglycosylase domain-containing protein virB1
NHV77_RS00475 84613..85149 - 537 WP_000111522 type 4 pilus major pilin -
NHV77_RS00480 85211..86305 - 1095 WP_000697154 type II secretion system F family protein -
NHV77_RS00485 86307..87815 - 1509 WP_000880806 GspE/PulE family protein virB11
NHV77_RS00490 87918..88376 - 459 WP_000095887 type IV pilus biogenesis protein PilP -
NHV77_RS00495 88366..89661 - 1296 WP_000129884 type 4b pilus protein PilO2 -
NHV77_RS00500 89682..91301 - 1620 WP_001035559 PilN family type IVB pilus formation outer membrane protein -
NHV77_RS00505 91333..91770 - 438 WP_000539951 type IV pilus biogenesis protein PilM -

Host bacterium

ID   14036 GenBank   NZ_CP099781
Plasmid name   S15BD02407|p5 Incompatibility group   IncB/O/K/Z
Plasmid size   96127 bp Coordinate of oriT [Strand]   44351..44437 [-]
Host baterium   Shigella sonnei strain S15BD02407

Cargo genes

Drug resistance gene   qnrS1, blaCTX-M-15
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2