Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105801
Name   oriT_pL4094 in_silico
Organism   Shigella sonnei strain L4094
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP049180 (21373..21461 [+], 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_pL4094
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3918 GenBank   WP_011264053
Name   nikB_G6O64_RS24840_pL4094 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   1764 GenBank   WP_063119516
Name   WP_063119516_pL4094 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   3931 GenBank   WP_011264051
Name   trbC_G6O64_RS24835_pL4094 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: 67..15995

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
G6O64_RS24750 (G6O64_24530) 67..471 + 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
G6O64_RS24755 (G6O64_24535) 535..723 + 189 WP_001277253 putative conjugal transfer protein TraS -
G6O64_RS24760 (G6O64_24540) 707..1507 + 801 WP_107372244 IncI1-type conjugal transfer protein TraT traT
G6O64_RS24765 (G6O64_24545) 1597..4641 + 3045 WP_107372243 IncI1-type conjugal transfer protein TraU traU
G6O64_RS24770 (G6O64_24550) 4641..5255 + 615 WP_000337395 IncI1-type conjugal transfer protein TraV traV
G6O64_RS24775 (G6O64_24555) 5222..6424 + 1203 WP_107372242 IncI1-type conjugal transfer protein TraW traW
G6O64_RS24780 (G6O64_24560) 6453..7037 + 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
G6O64_RS24785 (G6O64_24565) 7134..9302 + 2169 WP_001774191 DotA/TraY family protein traY
G6O64_RS24790 (G6O64_24570) 9376..10026 + 651 WP_001178506 plasmid IncI1-type surface exclusion protein ExcA -
G6O64_RS24795 (G6O64_24575) 10098..10307 - 210 WP_000062603 HEAT repeat domain-containing protein -
G6O64_RS24800 (G6O64_24580) 10673..10849 + 177 WP_001054898 hypothetical protein -
G6O64_RS25330 10914..11009 - 96 WP_000609148 DinQ-like type I toxin DqlB -
G6O64_RS24810 (G6O64_24590) 11510..11761 + 252 WP_001291964 hypothetical protein -
G6O64_RS24815 (G6O64_24595) 11833..11985 - 153 WP_001387489 Hok/Gef family protein -
G6O64_RS24820 (G6O64_24600) 12612..13391 + 780 WP_275450201 protein FinQ -
G6O64_RS24825 (G6O64_24605) 13698..14906 + 1209 WP_107372241 IncI1-type conjugal transfer protein TrbA trbA
G6O64_RS24830 (G6O64_24610) 14925..15995 + 1071 WP_000151590 IncI1-type conjugal transfer protein TrbB trbB
G6O64_RS24835 (G6O64_24615) 15988..18279 + 2292 WP_011264051 F-type conjugative transfer protein TrbC -

Region 2: 62458..85634

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
G6O64_RS25100 (G6O64_24880) 57520..58587 + 1068 WP_001545759 type IV pilus biogenesis lipoprotein PilL -
G6O64_RS25105 (G6O64_24885) 58587..59024 + 438 WP_001545758 type IV pilus biogenesis protein PilM -
G6O64_RS25110 (G6O64_24890) 59038..60720 + 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
G6O64_RS25115 (G6O64_24895) 60713..62008 + 1296 WP_016245572 type 4b pilus protein PilO2 -
G6O64_RS25120 (G6O64_24900) 61995..62447 + 453 WP_001247333 type IV pilus biogenesis protein PilP -
G6O64_RS25125 (G6O64_24905) 62458..64011 + 1554 WP_001545756 ATPase, T2SS/T4P/T4SS family virB11
G6O64_RS25130 (G6O64_24910) 64024..65109 + 1086 WP_001208802 type II secretion system F family protein -
G6O64_RS25135 (G6O64_24915) 65126..65740 + 615 WP_000908227 type 4 pilus major pilin -
G6O64_RS25140 (G6O64_24920) 65750..66310 + 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
G6O64_RS25145 (G6O64_24925) 66295..66951 + 657 WP_001193549 A24 family peptidase -
G6O64_RS25150 (G6O64_24930) 66951..68243 + 1293 WP_001390622 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
G6O64_RS25155 (G6O64_24935) 68240..68488 - 249 WP_001349157 hypothetical protein -
G6O64_RS25160 69657..70010 - 354 WP_001393368 hypothetical protein -
G6O64_RS25165 (G6O64_24950) 70009..71163 + 1155 WP_001139958 site-specific integrase -
G6O64_RS25170 (G6O64_24955) 71314..72138 + 825 WP_001545755 conjugal transfer protein TraE traE
G6O64_RS25175 (G6O64_24960) 72224..73426 + 1203 WP_171776325 conjugal transfer protein TraF -
G6O64_RS25180 (G6O64_24965) 73486..74070 + 585 WP_000977522 histidine phosphatase family protein -
G6O64_RS25185 (G6O64_24970) 74465..74923 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
G6O64_RS25190 (G6O64_24975) 74920..75738 + 819 WP_097763371 IncI1-type conjugal transfer lipoprotein TraI traI
G6O64_RS25195 (G6O64_24980) 75735..76883 + 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
G6O64_RS25200 (G6O64_24985) 76880..77170 + 291 WP_001314267 hypothetical protein traK
G6O64_RS25205 (G6O64_24990) 77185..77736 + 552 WP_000014586 phospholipase D family protein -
G6O64_RS25210 (G6O64_24995) 77826..81590 + 3765 WP_001141540 LPD7 domain-containing protein -
G6O64_RS25215 (G6O64_25000) 81608..81955 + 348 WP_001055900 conjugal transfer protein traL
G6O64_RS25220 (G6O64_25005) 81952..82644 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
G6O64_RS25225 (G6O64_25010) 82655..83638 + 984 WP_001191879 IncI1-type conjugal transfer protein TraN traN
G6O64_RS25230 (G6O64_25015) 83641..84930 + 1290 WP_001271994 conjugal transfer protein TraO traO
G6O64_RS25235 (G6O64_25020) 84930..85634 + 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP

Host bacterium

ID   6238 GenBank   NZ_CP049180
Plasmid name   pL4094 Incompatibility group   IncI1
Plasmid size   86136 bp Coordinate of oriT [Strand]   21373..21461 [+]
Host baterium   Shigella sonnei strain L4094

Cargo genes

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