Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107561
Name   oriT_pSH4469 in_silico
Organism   Shigella sonnei strain SS084469
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KJ406378 (36351..36439 [-], 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_pSH4469
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5075 GenBank   WP_012783930
Name   nikB_HPF50_RS00235_pSH4469 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   2328 GenBank   WP_001283947
Name   WP_001283947_pSH4469 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   5291 GenBank   WP_012783931
Name   trbC_HPF50_RS00240_pSH4469 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: 41817..81047

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HPF50_RS00240 39533..41824 - 2292 WP_012783931 F-type conjugative transfer protein TrbC -
HPF50_RS00245 41817..42887 - 1071 WP_012783932 IncI1-type conjugal transfer protein TrbB trbB
HPF50_RS00250 42906..44114 - 1209 WP_001703845 IncI1-type conjugal transfer protein TrbA trbA
HPF50_RS00255 44421..45200 - 780 WP_275450201 protein FinQ -
HPF50_RS00260 45827..45979 + 153 WP_001387489 Hok/Gef family protein -
HPF50_RS00265 46051..46302 - 252 WP_001291964 hypothetical protein -
HPF50_RS00530 46803..46898 + 96 WP_000609148 DinQ-like type I toxin DqlB -
HPF50_RS00275 46963..47247 - 285 WP_014640317 hypothetical protein -
HPF50_RS00280 47531..47740 + 210 WP_000062603 HEAT repeat domain-containing protein -
HPF50_RS00285 47812..48474 - 663 WP_012783935 plasmid IncI1-type surface exclusion protein ExcA -
HPF50_RS00290 48545..50713 - 2169 WP_015508354 DotA/TraY family protein traY
HPF50_RS00295 50810..51394 - 585 WP_012783937 conjugal transfer protein TraX -
HPF50_RS00300 51423..52625 - 1203 WP_012783938 IncI1-type conjugal transfer protein TraW traW
HPF50_RS00305 52592..53206 - 615 WP_000337394 IncI1-type conjugal transfer protein TraV traV
HPF50_RS00310 53206..56250 - 3045 WP_012783939 IncI1-type conjugal transfer protein TraU traU
HPF50_RS00315 56340..57140 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
HPF50_RS00320 57124..57312 - 189 WP_001277255 putative conjugal transfer protein TraS -
HPF50_RS00325 57376..57780 - 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
HPF50_RS00330 57831..58358 - 528 WP_001055569 conjugal transfer protein TraQ traQ
HPF50_RS00335 58358..59062 - 705 WP_001493811 IncI1-type conjugal transfer protein TraP traP
HPF50_RS00340 59062..60351 - 1290 WP_011264042 conjugal transfer protein TraO traO
HPF50_RS00345 60354..61337 - 984 WP_001191880 IncI1-type conjugal transfer protein TraN traN
HPF50_RS00350 61348..62040 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
HPF50_RS00355 62037..62384 - 348 WP_001055900 conjugal transfer protein traL
HPF50_RS00360 62402..66168 - 3767 Protein_70 LPD7 domain-containing protein -
HPF50_RS00370 66258..66809 - 552 WP_012783942 phospholipase D family protein -
HPF50_RS00375 66824..67114 - 291 WP_001314267 hypothetical protein traK
HPF50_RS00380 67111..68259 - 1149 WP_001024971 plasmid transfer ATPase TraJ virB11
HPF50_RS00385 68256..69074 - 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
HPF50_RS00390 69071..69529 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
HPF50_RS00395 69923..70507 - 585 WP_000977522 histidine phosphatase family protein -
HPF50_RS00400 70567..71769 - 1203 WP_000976353 conjugal transfer protein TraF -
HPF50_RS00405 71855..72679 - 825 WP_001238932 conjugal transfer protein TraE traE
HPF50_RS00410 72830..73984 - 1155 WP_001139955 site-specific integrase -
HPF50_RS00415 74589..74846 - 258 WP_001302706 hypothetical protein -
HPF50_RS00535 74896..75120 + 225 Protein_81 hypothetical protein -
HPF50_RS00425 75117..76541 - 1425 WP_001389385 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HPF50_RS00430 76541..77197 - 657 WP_001193553 prepilin peptidase -
HPF50_RS00435 77182..77742 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
HPF50_RS00440 77752..78366 - 615 WP_001542527 type 4 pilus major pilin -
HPF50_RS00445 78384..79481 - 1098 WP_001492931 type II secretion system F family protein -
HPF50_RS00450 79494..81047 - 1554 WP_001492932 ATPase, T2SS/T4P/T4SS family virB11
HPF50_RS00455 81058..81510 - 453 WP_012783945 type IV pilus biogenesis protein PilP -
HPF50_RS00460 81497..82792 - 1296 WP_012783946 type 4b pilus protein PilO2 -
HPF50_RS00465 82785..84467 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
HPF50_RS00470 84481..84917 - 437 Protein_91 type IV pilus biogenesis protein PilM -
HPF50_RS00475 84917..85984 - 1068 WP_012783947 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   7996 GenBank   NZ_KJ406378
Plasmid name   pSH4469 Incompatibility group   IncI1
Plasmid size   91109 bp Coordinate of oriT [Strand]   36351..36439 [-]
Host baterium   Shigella sonnei strain SS084469

Cargo genes

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