Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113603
Name   oriT_S17BD08233|p55 in_silico
Organism   Shigella sonnei strain S17BD08233
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP099772 (48989..49077 [-], 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_S17BD08233|p55
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8712 GenBank   WP_024143648
Name   nikB_NH235_RS00320_S17BD08233|p55 insolico UniProt ID   A0A023JAU0
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104010.41 Da        Isoelectric Point: 7.4265

>WP_024143648.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNNDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A023JAU0


Auxiliary protein

ID   5096 GenBank   WP_001283947
Name   WP_001283947_S17BD08233|p55 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   10087 GenBank   WP_001289276
Name   trbC_NH235_RS00325_S17BD08233|p55 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: 86941.11 Da        Isoelectric Point: 6.7713

>WP_001289276.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 54455..97567

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NH235_RS00325 52171..54462 - 2292 WP_001289276 F-type conjugative transfer protein TrbC -
NH235_RS00330 54455..55525 - 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
NH235_RS00335 55544..56752 - 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
NH235_RS00340 57044..57196 + 153 WP_001331364 Hok/Gef family protein -
NH235_RS00345 57342..58139 - 798 WP_000544828 IS21-like element IS21 family helper ATPase IstB -
NH235_RS00350 58139..59311 - 1173 WP_000952382 IS21-like element IS21 family transposase -
NH235_RS00355 59393..59653 - 261 WP_159381058 hypothetical protein -
NH235_RS00610 60152..60247 + 96 WP_001303310 DinQ-like type I toxin DqlB -
NH235_RS00365 60312..60596 - 285 WP_031942457 hypothetical protein -
NH235_RS00370 60880..61089 + 210 WP_000062603 HEAT repeat domain-containing protein -
NH235_RS00375 61161..61835 - 675 WP_223866377 plasmid IncI1-type surface exclusion protein ExcA -
NH235_RS00380 61885..64053 - 2169 WP_021537350 DotA/TraY family protein traY
NH235_RS00385 64150..64734 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
NH235_RS00390 64763..65965 - 1203 WP_001189160 IncI1-type conjugal transfer protein TraW traW
NH235_RS00395 65932..66546 - 615 WP_000337398 IncI1-type conjugal transfer protein TraV traV
NH235_RS00400 66546..69590 - 3045 WP_021265678 IncI1-type conjugal transfer protein TraU traU
NH235_RS00405 69680..70480 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
NH235_RS00410 70464..70652 - 189 WP_001277255 putative conjugal transfer protein TraS -
NH235_RS00415 70716..71120 - 405 WP_000086958 IncI1-type conjugal transfer protein TraR traR
NH235_RS00420 71171..71698 - 528 WP_001055569 conjugal transfer protein TraQ traQ
NH235_RS00425 71698..72402 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
NH235_RS00430 72402..73691 - 1290 WP_001272003 conjugal transfer protein TraO traO
NH235_RS00435 73694..74677 - 984 WP_001191877 IncI1-type conjugal transfer protein TraN traN
NH235_RS00440 74688..75380 - 693 WP_000138550 DotI/IcmL family type IV secretion protein traM
NH235_RS00445 75377..75724 - 348 WP_001055900 conjugal transfer protein traL
NH235_RS00450 75742..79509 - 3768 WP_001141527 LPD7 domain-containing protein -
NH235_RS00455 79598..80149 - 552 WP_000014583 phospholipase D family protein -
NH235_RS00460 80164..80454 - 291 WP_001299214 hypothetical protein traK
NH235_RS00465 80451..81599 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
NH235_RS00470 81596..82414 - 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
NH235_RS00475 82411..82869 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
NH235_RS00480 83264..83848 - 585 WP_000977522 histidine phosphatase family protein -
NH235_RS00485 83908..85110 - 1203 WP_000976351 conjugal transfer protein TraF -
NH235_RS00490 85195..86019 - 825 WP_001238939 conjugal transfer protein TraE traE
NH235_RS00495 86170..87324 - 1155 WP_001139957 tyrosine-type recombinase/integrase -
NH235_RS00500 87642..87851 - 210 Protein_101 hypothetical protein -
NH235_RS00505 87851..88195 + 345 Protein_102 WbuC family cupin fold metalloprotein -
NH235_RS00510 88242..89117 - 876 WP_013188473 extended-spectrum class A beta-lactamase CTX-M-1 -
NH235_RS00515 89405..90667 - 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
NH235_RS00520 91769..93061 - 1293 WP_001417545 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
NH235_RS00525 93061..93717 - 657 WP_001193553 prepilin peptidase -
NH235_RS00530 93702..94262 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
NH235_RS00535 94272..94886 - 615 WP_000959785 type 4 pilus major pilin -
NH235_RS00540 94904..96001 - 1098 WP_001208805 type II secretion system F family protein -
NH235_RS00545 96014..97567 - 1554 WP_000362202 GspE/PulE family protein virB11
NH235_RS00550 97578..98030 - 453 WP_001247334 type IV pilus biogenesis protein PilP -
NH235_RS00555 98017..99312 - 1296 WP_000752772 type 4b pilus protein PilO2 -
NH235_RS00560 99305..100987 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
NH235_RS00565 101001..101438 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
NH235_RS00570 101438..102505 - 1068 WP_001302629 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   14038 GenBank   NZ_CP099772
Plasmid name   S17BD08233|p55 Incompatibility group   IncI1
Plasmid size   108048 bp Coordinate of oriT [Strand]   48989..49077 [-]
Host baterium   Shigella sonnei strain S17BD08233

Cargo genes

Drug resistance gene   tet(A), sul2, blaCTX-M-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -