Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105808
Name   oriT_p6607-69 in_silico
Organism   Shigella sonnei strain 6607.69
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP045527 (28195..28283 [+], 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_p6607-69
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3921 GenBank   WP_171803589
Name   nikB_GE169_RS24725_p6607-69 insolico UniProt ID   _
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104055.54 Da        Isoelectric Point: 7.2859

>WP_171803589.1 IncI1-type relaxase NikB [Shigella sonnei]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEILSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSHMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLAERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALVDKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure



No available structure.




Auxiliary protein

ID   1766 GenBank   WP_001283947
Name   WP_001283947_p6607-69 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   3933 GenBank   WP_012783931
Name   trbC_GE169_RS24720_p6607-69 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: 914..22817

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GE169_RS24595 (GE169_25475) 914..1261 + 348 WP_001055900 conjugal transfer protein traL
GE169_RS24600 (GE169_25480) 1258..1950 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
GE169_RS24605 (GE169_25485) 1961..2944 + 984 WP_001191880 IncI1-type conjugal transfer protein TraN traN
GE169_RS24610 (GE169_25490) 2947..4236 + 1290 WP_011264042 conjugal transfer protein TraO traO
GE169_RS24615 (GE169_25495) 4236..4940 + 705 WP_001493811 IncI1-type conjugal transfer protein TraP traP
GE169_RS24620 (GE169_25500) 4940..5467 + 528 WP_001055569 conjugal transfer protein TraQ traQ
GE169_RS24625 (GE169_25505) 5518..5922 + 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
GE169_RS24630 (GE169_25510) 5986..6174 + 189 WP_001277255 putative conjugal transfer protein TraS -
GE169_RS24635 (GE169_25515) 6158..6958 + 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
GE169_RS24640 (GE169_25520) 7048..10092 + 3045 WP_012783939 IncI1-type conjugal transfer protein TraU traU
GE169_RS24645 (GE169_25525) 10092..10706 + 615 WP_000337394 IncI1-type conjugal transfer protein TraV traV
GE169_RS24650 (GE169_25530) 10673..11875 + 1203 WP_012783938 IncI1-type conjugal transfer protein TraW traW
GE169_RS24655 (GE169_25535) 11904..12488 + 585 WP_012783937 conjugal transfer protein TraX -
GE169_RS24660 (GE169_25540) 12585..13238 + 654 Protein_14 DotA/TraY family protein -
GE169_RS24665 (GE169_25545) 13329..14557 + 1229 WP_088895425 IS3-like element IS2 family transposase -
GE169_RS24670 (GE169_25550) 14569..16089 + 1521 Protein_16 DotA/TraY family protein -
GE169_RS24675 (GE169_25555) 16160..16822 + 663 WP_012783935 plasmid IncI1-type surface exclusion protein ExcA -
GE169_RS24680 (GE169_25560) 16894..17103 - 210 WP_000062603 HEAT repeat domain-containing protein -
GE169_RS24685 (GE169_25565) 17495..17671 + 177 WP_001054900 hypothetical protein -
GE169_RS25170 17736..17831 - 96 WP_000609148 DinQ-like type I toxin DqlB -
GE169_RS24695 (GE169_25575) 18332..18583 + 252 WP_001291964 hypothetical protein -
GE169_RS24700 (GE169_25580) 18655..18807 - 153 WP_001387489 Hok/Gef family protein -
GE169_RS24705 (GE169_25585) 19434..20213 + 780 WP_275450201 protein FinQ -
GE169_RS24710 (GE169_25590) 20520..21728 + 1209 WP_001703845 IncI1-type conjugal transfer protein TrbA trbA
GE169_RS24715 (GE169_25595) 21747..22817 + 1071 WP_012783932 IncI1-type conjugal transfer protein TrbB trbB
GE169_RS24720 (GE169_25600) 22810..25101 + 2292 WP_012783931 F-type conjugative transfer protein TrbC -

Region 2: 72098..86321

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GE169_RS24980 (GE169_25070) 67160..68227 + 1068 WP_012783947 type IV pilus biogenesis lipoprotein PilL -
GE169_RS24985 (GE169_25075) 68227..68664 + 438 WP_000539807 type IV pilus biogenesis protein PilM -
GE169_RS24990 (GE169_25080) 68678..70360 + 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
GE169_RS24995 (GE169_25085) 70353..71648 + 1296 WP_012783946 type 4b pilus protein PilO2 -
GE169_RS25000 (GE169_25090) 71635..72087 + 453 WP_012783945 type IV pilus biogenesis protein PilP -
GE169_RS25005 (GE169_25095) 72098..73651 + 1554 WP_001492932 ATPase, T2SS/T4P/T4SS family virB11
GE169_RS25010 (GE169_25100) 73664..74761 + 1098 WP_001492931 type II secretion system F family protein -
GE169_RS25015 (GE169_25105) 74779..75393 + 615 WP_001542527 type 4 pilus major pilin -
GE169_RS25020 (GE169_25110) 75403..75963 + 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
GE169_RS25025 (GE169_25115) 75948..76604 + 657 WP_001193553 prepilin peptidase -
GE169_RS25030 (GE169_25120) 76604..78028 + 1425 WP_001389385 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
GE169_RS25240 (GE169_25680) 78025..78249 - 225 Protein_91 hypothetical protein -
GE169_RS25035 (GE169_25140) 79161..80315 + 1155 WP_001139955 site-specific integrase -
GE169_RS25040 (GE169_25145) 80466..81290 + 825 WP_001238932 conjugal transfer protein TraE traE
GE169_RS25045 (GE169_25150) 81376..82578 + 1203 WP_000976353 conjugal transfer protein TraF -
GE169_RS25050 (GE169_25155) 82638..83222 + 585 WP_000977522 histidine phosphatase family protein -
GE169_RS25055 (GE169_25160) 83616..84074 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
GE169_RS25060 (GE169_25685) 84071..84889 + 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
GE169_RS25065 (GE169_25690) 84886..86034 + 1149 WP_001024971 plasmid transfer ATPase TraJ virB11
GE169_RS25070 (GE169_25170) 86031..86321 + 291 WP_001314267 hypothetical protein traK
GE169_RS25075 (GE169_25175) 86336..86887 + 552 WP_012783942 phospholipase D family protein -

Host bacterium

ID   6245 GenBank   NZ_CP045527
Plasmid name   p6607-69 Incompatibility group   IncI1
Plasmid size   89848 bp Coordinate of oriT [Strand]   28195..28283 [+]
Host baterium   Shigella sonnei strain 6607.69

Cargo genes

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