Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103101
Name   oriT_pBU53M1 in_silico
Organism   Shigella dysenteriae
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KT754162 (87352..87440 [-], 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_pBU53M1
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCCTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2323 GenBank   WP_069896299
Name   nikB_HPF87_RS00520_pBU53M1 insolico UniProt ID   A0A142CMC3
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103891.35 Da        Isoelectric Point: 7.4288

>WP_069896299.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKHTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
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 A0A142CMC3


Auxiliary protein

ID   983 GenBank   WP_001283947
Name   WP_001283947_pBU53M1 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


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 790..20036

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HPF87_RS00010 790..1773 - 984 WP_001191880 IncI1-type conjugal transfer protein TraN traN
HPF87_RS00015 1784..2476 - 693 WP_000138551 DotI/IcmL family type IV secretion protein traM
HPF87_RS00020 2473..2820 - 348 WP_001055900 conjugal transfer protein traL
HPF87_RS00025 2838..6605 - 3768 WP_050197986 LPD7 domain-containing protein -
HPF87_RS00030 6695..7246 - 552 WP_000014586 phospholipase D family protein -
HPF87_RS00035 7261..7551 - 291 WP_001299214 hypothetical protein traK
HPF87_RS00040 7548..8696 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
HPF87_RS00045 8693..9511 - 819 WP_032220737 IncI1-type conjugal transfer lipoprotein TraI traI
HPF87_RS00050 9508..9966 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
HPF87_RS00055 10361..10945 - 585 WP_000977525 histidine phosphatase family protein -
HPF87_RS00060 11005..12207 - 1203 WP_000976353 conjugal transfer protein TraF -
HPF87_RS00065 12293..13117 - 825 WP_001690630 conjugal transfer protein TraE traE
HPF87_RS00070 13268..14422 - 1155 WP_001139955 site-specific integrase -
HPF87_RS00075 14473..15543 - 1071 Protein_14 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HPF87_RS00080 15543..16199 - 657 WP_001193549 A24 family peptidase -
HPF87_RS00085 16184..16744 - 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
HPF87_RS00090 16754..17368 - 615 WP_000908226 type 4 pilus major pilin -
HPF87_RS00095 17385..18470 - 1086 WP_001208802 type II secretion system F family protein -
HPF87_RS00100 18483..20036 - 1554 WP_032220709 ATPase, T2SS/T4P/T4SS family virB11
HPF87_RS00105 20047..20499 - 453 WP_001247337 type IV pilus biogenesis protein PilP -
HPF87_RS00110 20486..21781 - 1296 WP_050197975 type 4b pilus protein PilO2 -
HPF87_RS00115 21774..23456 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
HPF87_RS00120 23470..23907 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
HPF87_RS00125 23907..24974 - 1068 WP_001360287 type IV pilus biogenesis lipoprotein PilL -

Region 2: 92817..111171

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HPF87_RS00525 90494..92824 - 2331 WP_171265250 F-type conjugative transfer protein TrbC -
HPF87_RS00530 92817..93887 - 1071 WP_050197982 IncI1-type conjugal transfer protein TrbB trbB
HPF87_RS00535 93906..95114 - 1209 WP_000121263 IncI1-type conjugal transfer protein TrbA trbA
HPF87_RS00540 95421..96200 - 780 WP_275450201 protein FinQ -
HPF87_RS00545 96827..96979 + 153 WP_001387489 Hok/Gef family protein -
HPF87_RS00550 97051..97302 - 252 WP_001291964 hypothetical protein -
HPF87_RS00650 97803..97898 + 96 WP_000609148 DinQ-like type I toxin DqlB -
HPF87_RS00560 97963..98139 - 177 WP_001054900 hypothetical protein -
HPF87_RS00565 98470..98679 + 210 WP_000062603 HEAT repeat domain-containing protein -
HPF87_RS00570 98751..99413 - 663 WP_042078443 plasmid IncI1-type surface exclusion protein ExcA -
HPF87_RS00575 99657..99866 - 210 WP_001140543 hemolysin expression modulator Hha -
HPF87_RS00580 99964..100578 - 615 WP_000578648 plasmid IncI1-type surface exclusion protein ExcA -
HPF87_RS00585 100654..102822 - 2169 WP_000698360 IncI1-type conjugal transfer membrane protein TraY traY
HPF87_RS00590 102919..103503 - 585 WP_050197983 IncI1-type conjugal transfer protein TraX -
HPF87_RS00595 103532..104734 - 1203 WP_012783938 IncI1-type conjugal transfer protein TraW traW
HPF87_RS00600 104701..105315 - 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
HPF87_RS00605 105315..108359 - 3045 WP_050197984 IncI1-type conjugal transfer protein TraU traU
HPF87_RS00610 108449..109249 - 801 WP_001493813 IncI1-type conjugal transfer protein TraT traT
HPF87_RS00615 109233..109421 - 189 WP_001277255 putative conjugal transfer protein TraS -
HPF87_RS00620 109485..109889 - 405 WP_025769131 IncI1-type conjugal transfer protein TraR traR
HPF87_RS00625 109940..110467 - 528 WP_001055569 conjugal transfer protein TraQ traQ
HPF87_RS00630 110467..111171 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP

Host bacterium

ID   3544 GenBank   NZ_KT754162
Plasmid name   pBU53M1 Incompatibility group   IncI1
Plasmid size   111673 bp Coordinate of oriT [Strand]   87352..87440 [-]
Host baterium   Shigella dysenteriae

Cargo genes

Drug resistance gene   blaTEM-1D, sul1, qacE, ant(3'')-Ia, dfrA1, catA1
Virulence gene   -
Metal resistance gene   merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2