Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115369
Name   oriT_pCL059-1 in_silico
Organism   Shigella sonnei strain CL-059
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OR237801 (32192..32280 [-], 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_pCL059-1
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9831 GenBank   WP_011264053
Name   nikB_RI192_RS00230_pCL059-1 insolico UniProt ID   A0A767TAZ8
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103882.34 Da        Isoelectric Point: 7.4198

>WP_011264053.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A767TAZ8


Auxiliary protein

ID   5757 GenBank   WP_063119516
Name   WP_063119516_pCL059-1 insolico UniProt ID   _
Length   110 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12585.55 Da        Isoelectric Point: 10.6897

>WP_063119516.1 MULTISPECIES: IncI1-type relaxosome accessory protein NikA [Enterobacteriaceae]
MSDSAVKKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG

  Protein domains



No domain identified.



  Protein structure



No available structure.




T4CP

ID   11455 GenBank   WP_011264051
Name   trbC_RI192_RS00235_pCL059-1 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: 86954.10 Da        Isoelectric Point: 6.7713

>WP_011264051.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 37658..77340

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RI192_RS00235 (pCL059-1_00046) 35374..37665 - 2292 WP_011264051 F-type conjugative transfer protein TrbC -
RI192_RS00240 (pCL059-1_00047) 37658..38728 - 1071 WP_000151590 IncI1-type conjugal transfer protein TrbB trbB
RI192_RS00245 (pCL059-1_00048) 38747..39955 - 1209 WP_107372241 IncI1-type conjugal transfer protein TrbA trbA
RI192_RS00250 (pCL059-1_00049) 40262..41041 - 780 WP_275450201 protein FinQ -
RI192_RS00255 (pCL059-1_00050) 41668..41820 + 153 WP_001387489 Hok/Gef family protein -
RI192_RS00260 (pCL059-1_00051) 41892..42143 - 252 WP_001291964 hypothetical protein -
RI192_RS00265 42644..42739 + 96 WP_000609148 DinQ-like type I toxin DqlB -
RI192_RS00270 (pCL059-1_00053) 42804..42980 - 177 WP_001054898 hypothetical protein -
RI192_RS00275 (pCL059-1_00054) 43346..43555 + 210 WP_000062603 HEAT repeat domain-containing protein -
RI192_RS00280 (pCL059-1_00055) 43627..44301 - 675 WP_223866377 plasmid IncI1-type surface exclusion protein ExcA -
RI192_RS00285 (pCL059-1_00056) 44351..46519 - 2169 WP_001774191 DotA/TraY family protein traY
RI192_RS00290 (pCL059-1_00057) 46616..47200 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
RI192_RS00295 (pCL059-1_00058) 47229..48431 - 1203 WP_107372242 IncI1-type conjugal transfer protein TraW traW
RI192_RS00300 (pCL059-1_00059) 48398..49012 - 615 WP_000337395 IncI1-type conjugal transfer protein TraV traV
RI192_RS00305 (pCL059-1_00060) 49012..52056 - 3045 WP_107372243 IncI1-type conjugal transfer protein TraU traU
RI192_RS00310 (pCL059-1_00061) 52146..52946 - 801 WP_107372244 IncI1-type conjugal transfer protein TraT traT
RI192_RS00315 (pCL059-1_00062) 52930..53118 - 189 WP_001277253 putative conjugal transfer protein TraS -
RI192_RS00320 (pCL059-1_00063) 53182..53586 - 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
RI192_RS00325 (pCL059-1_00064) 53637..54164 - 528 WP_001055569 conjugal transfer protein TraQ traQ
RI192_RS00330 (pCL059-1_00065) 54164..54868 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
RI192_RS00335 (pCL059-1_00066) 54868..56157 - 1290 WP_001271994 conjugal transfer protein TraO traO
RI192_RS00340 (pCL059-1_00067) 56160..57143 - 984 WP_001191879 IncI1-type conjugal transfer protein TraN traN
RI192_RS00345 (pCL059-1_00068) 57154..57846 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
RI192_RS00350 (pCL059-1_00069) 57843..58190 - 348 WP_001055900 conjugal transfer protein traL
RI192_RS00355 (pCL059-1_00070) 58208..61972 - 3765 WP_001141540 LPD7 domain-containing protein -
RI192_RS00360 (pCL059-1_00071) 62062..62613 - 552 WP_000014586 phospholipase D family protein -
RI192_RS00365 (pCL059-1_00072) 62628..62918 - 291 WP_001314267 hypothetical protein traK
RI192_RS00370 (pCL059-1_00073) 62915..64063 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
RI192_RS00375 (pCL059-1_00074) 64060..64878 - 819 WP_097763371 IncI1-type conjugal transfer lipoprotein TraI traI
RI192_RS00380 (pCL059-1_00075) 64875..65333 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
RI192_RS00385 (pCL059-1_00076) 65728..66312 - 585 WP_000977522 histidine phosphatase family protein -
RI192_RS00390 (pCL059-1_00077) 66372..67574 - 1203 WP_000976353 conjugal transfer protein TraF -
RI192_RS00395 (pCL059-1_00078) 67660..68484 - 825 WP_001545755 conjugal transfer protein TraE traE
RI192_RS00400 (pCL059-1_00079) 68635..69789 - 1155 WP_001139958 tyrosine-type recombinase/integrase -
RI192_RS00405 69773..70072 + 300 WP_223873359 pilus assembly protein PilV -
RI192_RS00410 70385..70642 + 258 WP_001302706 hypothetical protein -
RI192_RS00415 71310..71558 + 249 WP_001349157 hypothetical protein -
RI192_RS00420 (pCL059-1_00082) 71555..72847 - 1293 WP_001390622 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
RI192_RS00425 (pCL059-1_00083) 72847..73503 - 657 WP_001193549 A24 family peptidase -
RI192_RS00430 (pCL059-1_00084) 73488..74048 - 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
RI192_RS00435 (pCL059-1_00085) 74058..74672 - 615 WP_000908227 type 4 pilus major pilin -
RI192_RS00440 (pCL059-1_00086) 74689..75774 - 1086 WP_001208802 type II secretion system F family protein -
RI192_RS00445 (pCL059-1_00087) 75787..77340 - 1554 WP_001545756 GspE/PulE family protein virB11
RI192_RS00450 (pCL059-1_00088) 77351..77803 - 453 WP_001247333 type IV pilus biogenesis protein PilP -
RI192_RS00455 (pCL059-1_00089) 77790..79085 - 1296 WP_016245572 type 4b pilus protein PilO2 -
RI192_RS00460 (pCL059-1_00090) 79078..80760 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
RI192_RS00465 (pCL059-1_00091) 80774..81211 - 438 WP_001545758 type IV pilus biogenesis protein PilM -
RI192_RS00470 (pCL059-1_00092) 81211..82278 - 1068 WP_001545759 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   15802 GenBank   NZ_OR237801
Plasmid name   pCL059-1 Incompatibility group   IncI1
Plasmid size   87510 bp Coordinate of oriT [Strand]   32192..32280 [-]
Host baterium   Shigella sonnei strain CL-059

Cargo genes

Drug resistance gene   blaCTX-M-3
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2