Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113607
Name   oriT_S18BD04295|p73 in_silico
Organism   Shigella sonnei strain S18BD04295
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099768 (49347..49433 [-], 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_S18BD04295|p73
GGGGTGTCGGGGCGAAGCCCTGACCAGGAGGCAATTGTATAATCGCGCGTGCGCGGTTATACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8716 GenBank   WP_024190603
Name   nikB_NHV91_RS00290_S18BD04295|p73 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   5102 GenBank   WP_001281051
Name   WP_001281051_S18BD04295|p73 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   10093 GenBank   WP_024190602
Name   trbC_NHV91_RS00300_S18BD04295|p73 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: 55790..92811

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NHV91_RS00295 52616..53434 + 819 WP_000106194 DUF2971 domain-containing protein -
NHV91_RS00300 53506..55797 - 2292 WP_024190602 F-type conjugative transfer protein TrbC -
NHV91_RS00305 55790..56860 - 1071 WP_000151590 IncI1-type conjugal transfer protein TrbB trbB
NHV91_RS00310 56879..58087 - 1209 WP_251291477 IncI1-type conjugal transfer protein TrbA trbA
NHV91_RS00315 58395..59174 - 780 WP_276312874 protein FinQ -
NHV91_RS00320 59801..59953 + 153 WP_001303307 Hok/Gef family protein -
NHV91_RS00325 60025..60276 - 252 WP_001291965 hypothetical protein -
NHV91_RS00545 60777..60872 + 96 WP_000609148 DinQ-like type I toxin DqlB -
NHV91_RS00335 60937..61221 - 285 WP_172692542 hypothetical protein -
NHV91_RS00340 61515..61724 + 210 WP_000062603 HEAT repeat domain-containing protein -
NHV91_RS00345 61796..62458 - 663 WP_000644795 plasmid IncI1-type surface exclusion protein ExcA -
NHV91_RS00350 62529..64697 - 2169 WP_000698356 DotA/TraY family protein traY
NHV91_RS00355 64794..65378 - 585 WP_001037992 IncI1-type conjugal transfer protein TraX -
NHV91_RS00360 65407..66609 - 1203 WP_001189157 IncI1-type conjugal transfer protein TraW traW
NHV91_RS00365 66576..67190 - 615 WP_032174792 IncI1-type conjugal transfer protein TraV traV
NHV91_RS00370 67190..70234 - 3045 WP_253075082 IncI1-type conjugal transfer protein TraU traU
NHV91_RS00375 70324..71124 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
NHV91_RS00380 71108..71296 - 189 WP_001277255 putative conjugal transfer protein TraS -
NHV91_RS00385 71360..71764 - 405 WP_000086957 IncI1-type conjugal transfer protein TraR traR
NHV91_RS00390 71815..72342 - 528 WP_001055569 conjugal transfer protein TraQ traQ
NHV91_RS00395 72342..73046 - 705 WP_001295718 IncI1-type conjugal transfer protein TraP traP
NHV91_RS00400 73046..74335 - 1290 WP_001271993 conjugal transfer protein TraO traO
NHV91_RS00405 74338..75321 - 984 WP_001191880 IncI1-type conjugal transfer protein TraN traN
NHV91_RS00410 75332..76024 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
NHV91_RS00415 76021..76368 - 348 WP_001055900 conjugal transfer protein traL
NHV91_RS00420 76386..80153 - 3768 WP_001141524 LPD7 domain-containing protein -
NHV91_RS00425 80243..80794 - 552 WP_000014585 phospholipase D family protein -
NHV91_RS00430 80809..81099 - 291 WP_001299214 hypothetical protein traK
NHV91_RS00435 81096..82244 - 1149 WP_001024968 plasmid transfer ATPase TraJ virB11
NHV91_RS00440 82241..83059 - 819 WP_000646093 IncI1-type conjugal transfer lipoprotein TraI traI
NHV91_RS00445 83056..83514 - 459 WP_001079806 IncI1-type conjugal transfer lipoprotein TraH -
NHV91_RS00450 83909..84493 - 585 WP_086200648 histidine phosphatase family protein -
NHV91_RS00455 84553..85755 - 1203 WP_000976355 conjugal transfer protein TraF -
NHV91_RS00460 85841..86665 - 825 WP_001238934 conjugal transfer protein TraE traE
NHV91_RS00555 86816..86923 - 108 Protein_93 shufflon-specific DNA recombinase -
NHV91_RS00465 86906..87169 + 264 Protein_94 transposase -
NHV91_RS00470 87226..88419 - 1194 WP_086200649 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
NHV91_RS00475 88437..89063 - 627 WP_000939938 prepilin peptidase -
NHV91_RS00480 89079..89564 - 486 WP_001080767 lytic transglycosylase domain-containing protein virB1
NHV91_RS00485 89609..90145 - 537 WP_000111522 type 4 pilus major pilin -
NHV91_RS00490 90207..91301 - 1095 WP_000697154 type II secretion system F family protein -
NHV91_RS00495 91303..92811 - 1509 WP_000880806 GspE/PulE family protein virB11
NHV91_RS00500 92914..93372 - 459 WP_000095887 type IV pilus biogenesis protein PilP -
NHV91_RS00505 93362..94657 - 1296 WP_000129884 type 4b pilus protein PilO2 -
NHV91_RS00510 94678..96297 - 1620 WP_001035559 PilN family type IVB pilus formation outer membrane protein -
NHV91_RS00515 96329..96766 - 438 WP_000539951 type IV pilus biogenesis protein PilM -

Host bacterium

ID   14042 GenBank   NZ_CP099768
Plasmid name   S18BD04295|p73 Incompatibility group   IncB/O/K/Z
Plasmid size   101123 bp Coordinate of oriT [Strand]   49347..49433 [-]
Host baterium   Shigella sonnei strain S18BD04295

Cargo genes

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