Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115370
Name   oriT_pCL053-1 in_silico
Organism   Shigella sonnei strain CL-053
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OR237799 (38200..38288 [-], 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_pCL053-1
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9832 GenBank   WP_031942444
Name   nikB_RI193_RS00265_pCL053-1 insolico UniProt ID   A0A075UES7
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104017.50 Da        Isoelectric Point: 7.2816

>WP_031942444.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSHMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLAERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESCYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALVDKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A075UES7


Auxiliary protein

ID   5758 GenBank   WP_001283947
Name   WP_001283947_pCL053-1 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   11456 GenBank   WP_012783931
Name   trbC_RI193_RS00270_pCL053-1 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: 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: 43666..83168

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RI193_RS00270 (pCL053-1_00050) 41382..43673 - 2292 WP_012783931 F-type conjugative transfer protein TrbC -
RI193_RS00275 (pCL053-1_00051) 43666..44736 - 1071 WP_031942445 IncI1-type conjugal transfer protein TrbB trbB
RI193_RS00280 (pCL053-1_00052) 44755..45963 - 1209 WP_001703845 IncI1-type conjugal transfer protein TrbA trbA
RI193_RS00285 (pCL053-1_00053) 46269..47048 - 780 WP_275542888 protein FinQ -
RI193_RS00290 (pCL053-1_00054) 47675..47827 + 153 WP_001331364 Hok/Gef family protein -
RI193_RS00295 (pCL053-1_00055) 47899..48150 - 252 WP_001291964 hypothetical protein -
RI193_RS00300 48651..48746 + 96 WP_000609148 DinQ-like type I toxin DqlB -
RI193_RS00305 (pCL053-1_00057) 48811..49053 - 243 WP_001420340 hypothetical protein -
RI193_RS00310 (pCL053-1_00058) 49170..49379 - 210 WP_001140543 hemolysin expression modulator Hha -
RI193_RS00315 (pCL053-1_00059) 49477..50091 - 615 WP_000578648 plasmid IncI1-type surface exclusion protein ExcA -
RI193_RS00320 (pCL053-1_00060) 50167..52335 - 2169 WP_031942447 IncI1-type conjugal transfer membrane protein TraY traY
RI193_RS00325 (pCL053-1_00061) 52432..53016 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
RI193_RS00330 (pCL053-1_00062) 53045..54247 - 1203 WP_031942448 IncI1-type conjugal transfer protein TraW traW
RI193_RS00335 (pCL053-1_00063) 54214..54828 - 615 WP_031942449 IncI1-type conjugal transfer protein TraV traV
RI193_RS00340 (pCL053-1_00064) 54828..57872 - 3045 WP_001024789 IncI1-type conjugal transfer protein TraU traU
RI193_RS00345 (pCL053-1_00065) 57962..58762 - 801 WP_001164783 IncI1-type conjugal transfer protein TraT traT
RI193_RS00350 (pCL053-1_00066) 58746..58934 - 189 WP_001277253 putative conjugal transfer protein TraS -
RI193_RS00355 (pCL053-1_00067) 58998..59402 - 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
RI193_RS00360 (pCL053-1_00068) 59453..59980 - 528 WP_001055569 conjugal transfer protein TraQ traQ
RI193_RS00365 (pCL053-1_00069) 59980..60684 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
RI193_RS00370 (pCL053-1_00070) 60684..61973 - 1290 WP_001271994 conjugal transfer protein TraO traO
RI193_RS00375 (pCL053-1_00071) 61976..62959 - 984 WP_001191879 IncI1-type conjugal transfer protein TraN traN
RI193_RS00380 (pCL053-1_00072) 62970..63662 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
RI193_RS00385 (pCL053-1_00073) 63659..64006 - 348 WP_001055900 conjugal transfer protein traL
RI193_RS00390 (pCL053-1_00074) 64024..67788 - 3765 WP_001141540 LPD7 domain-containing protein -
RI193_RS00395 (pCL053-1_00075) 67878..68429 - 552 WP_052987786 phospholipase D family protein -
RI193_RS00400 (pCL053-1_00076) 68444..68734 - 291 WP_001314267 hypothetical protein traK
RI193_RS00405 (pCL053-1_00077) 68731..69879 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
RI193_RS00410 (pCL053-1_00078) 69876..70694 - 819 WP_031942450 IncI1-type conjugal transfer lipoprotein TraI traI
RI193_RS00415 (pCL053-1_00079) 70691..71149 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
RI193_RS00420 (pCL053-1_00080) 71544..72128 - 585 WP_000977522 histidine phosphatase family protein -
RI193_RS00425 (pCL053-1_00081) 72188..73390 - 1203 WP_000976351 conjugal transfer protein TraF -
RI193_RS00430 (pCL053-1_00082) 73475..74299 - 825 WP_001238939 conjugal transfer protein TraE traE
RI193_RS00435 (pCL053-1_00083) 74450..75604 - 1155 WP_001139957 tyrosine-type recombinase/integrase -
RI193_RS00440 76450..76605 - 156 WP_001302705 hypothetical protein -
RI193_RS00445 76733..76990 + 258 WP_001302706 hypothetical protein -
RI193_RS00450 77125..77373 + 249 WP_001349157 hypothetical protein -
RI193_RS00455 (pCL053-1_00085) 77370..78662 - 1293 WP_001417545 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
RI193_RS00460 (pCL053-1_00086) 78662..79318 - 657 WP_001193553 prepilin peptidase -
RI193_RS00465 (pCL053-1_00087) 79303..79863 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
RI193_RS00470 (pCL053-1_00088) 79873..80487 - 615 WP_000959785 type 4 pilus major pilin -
RI193_RS00475 (pCL053-1_00089) 80505..81602 - 1098 WP_001208805 type II secretion system F family protein -
RI193_RS00480 (pCL053-1_00090) 81615..83168 - 1554 WP_000362202 GspE/PulE family protein virB11
RI193_RS00485 (pCL053-1_00091) 83179..83631 - 453 WP_001247336 type IV pilus biogenesis protein PilP -
RI193_RS00490 (pCL053-1_00092) 83618..84913 - 1296 WP_021560540 type 4b pilus protein PilO2 -
RI193_RS00495 (pCL053-1_00093) 84906..86588 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
RI193_RS00500 (pCL053-1_00094) 86602..87039 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
RI193_RS00505 (pCL053-1_00095) 87039..88106 - 1068 WP_031942452 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   15803 GenBank   NZ_OR237799
Plasmid name   pCL053-1 Incompatibility group   IncI1
Plasmid size   93766 bp Coordinate of oriT [Strand]   38200..38288 [-]
Host baterium   Shigella sonnei strain CL-053

Cargo genes

Drug resistance gene   blaCTX-M-15, aac(3)-IId, blaTEM-1B
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2