Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111003
Name   oriT_S15BD09164|p20 in_silico
Organism   Shigella sonnei strain S15BD09164
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099778 (31005..31093 [-], 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_S15BD09164|p20
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7240 GenBank   WP_012783930
Name   nikB_NHV78_RS00215_S15BD09164|p20 insolico UniProt ID   N0GUP8
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104070.55 Da        Isoelectric Point: 7.3623

>WP_012783930.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSHMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLAERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALVDKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB N0GUP8


Auxiliary protein

ID   4037 GenBank   WP_001283947
Name   WP_001283947_S15BD09164|p20 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   8245 GenBank   WP_012783931
Name   trbC_NHV78_RS00220_S15BD09164|p20 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: 86911.02 Da        Isoelectric Point: 6.7713

>WP_012783931.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILTAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 36471..76202

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NHV78_RS00220 34187..36478 - 2292 WP_012783931 F-type conjugative transfer protein TrbC -
NHV78_RS00225 36471..37541 - 1071 WP_012783932 IncI1-type conjugal transfer protein TrbB trbB
NHV78_RS00230 37560..38768 - 1209 WP_001703845 IncI1-type conjugal transfer protein TrbA trbA
NHV78_RS00235 39075..39854 - 780 WP_275450201 protein FinQ -
NHV78_RS00240 40481..40633 + 153 WP_001387489 Hok/Gef family protein -
NHV78_RS00245 40705..40956 - 252 WP_001291964 hypothetical protein -
NHV78_RS00490 41457..41552 + 96 WP_000609148 DinQ-like type I toxin DqlB -
NHV78_RS00255 41617..41901 - 285 WP_014640317 hypothetical protein -
NHV78_RS00260 42185..42394 + 210 WP_000062603 HEAT repeat domain-containing protein -
NHV78_RS00265 42466..43128 - 663 WP_012783935 plasmid IncI1-type surface exclusion protein ExcA -
NHV78_RS00270 43199..45367 - 2169 WP_015508354 DotA/TraY family protein traY
NHV78_RS00275 45464..46048 - 585 WP_012783937 conjugal transfer protein TraX -
NHV78_RS00280 46077..47279 - 1203 WP_012783938 IncI1-type conjugal transfer protein TraW traW
NHV78_RS00285 47246..47860 - 615 WP_000337394 IncI1-type conjugal transfer protein TraV traV
NHV78_RS00290 47860..50904 - 3045 WP_012783939 IncI1-type conjugal transfer protein TraU traU
NHV78_RS00295 50994..51794 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
NHV78_RS00300 51778..51966 - 189 WP_001277255 putative conjugal transfer protein TraS -
NHV78_RS00305 52030..52434 - 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
NHV78_RS00310 52485..53012 - 528 WP_001055569 conjugal transfer protein TraQ traQ
NHV78_RS00315 53012..53716 - 705 WP_001493811 IncI1-type conjugal transfer protein TraP traP
NHV78_RS00320 53716..55005 - 1290 WP_011264042 conjugal transfer protein TraO traO
NHV78_RS00325 55008..55991 - 984 WP_001191880 IncI1-type conjugal transfer protein TraN traN
NHV78_RS00330 56002..56694 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
NHV78_RS00335 56691..57038 - 348 WP_001055900 conjugal transfer protein traL
NHV78_RS00340 57056..60823 - 3768 WP_012783940 LPD7 domain-containing protein -
NHV78_RS00345 60913..61464 - 552 WP_012783942 phospholipase D family protein -
NHV78_RS00350 61479..61769 - 291 WP_001314267 hypothetical protein traK
NHV78_RS00355 61766..62914 - 1149 WP_001024971 plasmid transfer ATPase TraJ virB11
NHV78_RS00360 62911..63729 - 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
NHV78_RS00365 63726..64184 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
NHV78_RS00370 64578..65162 - 585 WP_000977522 histidine phosphatase family protein -
NHV78_RS00375 65222..66424 - 1203 WP_000976353 conjugal transfer protein TraF -
NHV78_RS00380 66509..67333 - 825 WP_001238939 conjugal transfer protein TraE traE
NHV78_RS00385 67484..68638 - 1155 WP_001139957 site-specific integrase -
NHV78_RS00390 68622..68990 + 369 WP_015059923 hypothetical protein -
NHV78_RS00395 69813..69968 - 156 WP_001302705 hypothetical protein -
NHV78_RS00400 70272..71696 - 1425 WP_001389385 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
NHV78_RS00405 71696..72352 - 657 WP_001193553 prepilin peptidase -
NHV78_RS00410 72337..72897 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
NHV78_RS00415 72907..73521 - 615 WP_000959785 type 4 pilus major pilin -
NHV78_RS00420 73539..74636 - 1098 WP_001208805 type II secretion system F family protein -
NHV78_RS00425 74649..76202 - 1554 WP_000362202 ATPase, T2SS/T4P/T4SS family virB11
NHV78_RS00430 76213..76665 - 453 WP_001247336 type IV pilus biogenesis protein PilP -
NHV78_RS00435 76652..77947 - 1296 WP_000752774 type 4b pilus protein PilO2 -
NHV78_RS00440 77940..79622 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
NHV78_RS00445 79636..80073 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
NHV78_RS00450 80073..81140 - 1068 WP_000742600 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   11438 GenBank   NZ_CP099778
Plasmid name   S15BD09164|p20 Incompatibility group   IncI1
Plasmid size   86718 bp Coordinate of oriT [Strand]   31005..31093 [-]
Host baterium   Shigella sonnei strain S15BD09164

Cargo genes

Drug resistance gene   blaCTX-M-55
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2