Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103872
Name   oriT_pk88 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhi strain 311189_268103
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP029903 (33967..34055 [-], 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_pk88
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2876 GenBank   WP_001387486
Name   nikB_SM268103_RS24915_pk88 insolico UniProt ID   D9Z503
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103861.32 Da        Isoelectric Point: 7.4288

>WP_001387486.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRNRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNRGGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
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 D9Z503


Auxiliary protein

ID   1192 GenBank   WP_001283947
Name   WP_001283947_pk88 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   2718 GenBank   WP_001289278
Name   trbC_SM268103_RS24920_pk88 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: 86924.02 Da        Isoelectric Point: 6.7713

>WP_001289278.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILTAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 39433..78924

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SM268103_RS24920 (SM268103_07029) 37149..39440 - 2292 WP_001289278 F-type conjugative transfer protein TrbC -
SM268103_RS24925 (SM268103_07040) 39433..40503 - 1071 WP_000151588 IncI1-type conjugal transfer protein TrbB trbB
SM268103_RS24930 (SM268103_07046) 40522..41730 - 1209 WP_000121263 IncI1-type conjugal transfer protein TrbA trbA
SM268103_RS24935 (SM268103_07137) 42037..42816 - 780 WP_275450201 protein FinQ -
SM268103_RS24940 (SM268103_07023) 43443..43595 + 153 WP_001387489 Hok/Gef family protein -
SM268103_RS24945 (SM268103_07043) 43667..43918 - 252 WP_001291964 hypothetical protein -
SM268103_RS25805 44419..44514 + 96 WP_000609148 DinQ-like type I toxin DqlB -
SM268103_RS25380 (SM268103_07125) 44579..44755 - 177 WP_001054898 hypothetical protein -
SM268103_RS24955 44938..45147 - 210 WP_001140543 hemolysin expression modulator Hha -
SM268103_RS24960 (SM268103_07051) 45245..45859 - 615 WP_000578648 plasmid IncI1-type surface exclusion protein ExcA -
SM268103_RS24965 (SM268103_07127) 45935..48103 - 2169 WP_000698360 IncI1-type conjugal transfer membrane protein TraY traY
SM268103_RS24970 (SM268103_07055) 48200..48784 - 585 WP_001037983 IncI1-type conjugal transfer protein TraX -
SM268103_RS24975 (SM268103_07059) 48813..50015 - 1203 WP_001387490 IncI1-type conjugal transfer protein TraW traW
SM268103_RS24980 49982..50596 - 615 WP_000337395 IncI1-type conjugal transfer protein TraV traV
SM268103_RS24985 (SM268103_07062) 50596..53640 - 3045 WP_001024789 IncI1-type conjugal transfer protein TraU traU
SM268103_RS24990 (SM268103_07054) 53730..54530 - 801 WP_001164783 IncI1-type conjugal transfer protein TraT traT
SM268103_RS24995 (SM268103_07050) 54514..54702 - 189 WP_001277253 putative conjugal transfer protein TraS -
SM268103_RS25000 (SM268103_07057) 54766..55170 - 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
SM268103_RS25005 (SM268103_07048) 55221..55748 - 528 WP_001055569 conjugal transfer protein TraQ traQ
SM268103_RS25010 (SM268103_07063) 55748..56452 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
SM268103_RS25015 (SM268103_07060) 56452..57741 - 1290 WP_001271994 conjugal transfer protein TraO traO
SM268103_RS25020 (SM268103_07047) 57744..58727 - 984 WP_001191879 IncI1-type conjugal transfer protein TraN traN
SM268103_RS25025 (SM268103_07068) 58738..59430 - 693 WP_000138552 DotI/IcmL family type IV secretion protein -
SM268103_RS25030 (SM268103_07061) 59427..59774 - 348 WP_001055900 conjugal transfer protein traL
SM268103_RS25035 (SM268103_07044) 59792..63556 - 3765 WP_001141540 LPD7 domain-containing protein -
SM268103_RS25040 (SM268103_07049) 63646..64197 - 552 WP_000014586 phospholipase D family protein -
SM268103_RS25045 (SM268103_07066) 64212..64502 - 291 WP_001314267 hypothetical protein traK
SM268103_RS25050 (SM268103_07069) 64499..65647 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
SM268103_RS25055 (SM268103_07053) 65644..66462 - 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
SM268103_RS25060 (SM268103_07067) 66459..66917 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
SM268103_RS25065 (SM268103_07073) 67312..67896 - 585 WP_000977522 histidine phosphatase family protein -
SM268103_RS25070 (SM268103_07071) 67956..69158 - 1203 WP_000976357 conjugal transfer protein TraF -
SM268103_RS25075 (SM268103_07064) 69244..70068 - 825 WP_001238932 conjugal transfer protein TraE traE
SM268103_RS25080 (SM268103_07076) 70219..71373 - 1155 WP_001139956 site-specific integrase -
SM268103_RS25865 71956..72180 + 225 Protein_78 hypothetical protein -
SM268103_RS25100 72177..72425 - 249 WP_001349157 hypothetical protein -
SM268103_RS25120 (SM268103_07135) 73061..74443 - 1383 WP_023383831 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
SM268103_RS25125 (SM268103_07075) 74431..75087 - 657 WP_001193549 A24 family peptidase -
SM268103_RS25130 (SM268103_07079) 75072..75632 - 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
SM268103_RS25135 (SM268103_07065) 75642..76256 - 615 WP_000908227 type 4 pilus major pilin -
SM268103_RS25140 (SM268103_07070) 76273..77358 - 1086 WP_001208802 type II secretion system F family protein -
SM268103_RS25145 (SM268103_07084) 77371..78924 - 1554 WP_000362206 ATPase, T2SS/T4P/T4SS family virB11
SM268103_RS25150 (SM268103_07082) 78935..79387 - 453 WP_001247337 type IV pilus biogenesis protein PilP -
SM268103_RS25155 (SM268103_07072) 79374..80669 - 1296 WP_000752782 type 4b pilus protein PilO2 -
SM268103_RS25160 (SM268103_07083) 80662..82344 - 1683 WP_000748144 PilN family type IVB pilus formation outer membrane protein -
SM268103_RS25165 (SM268103_07086) 82358..82795 - 438 WP_000539806 type IV pilus biogenesis protein PilM -
SM268103_RS25170 (SM268103_07078) 82795..83862 - 1068 WP_001360287 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   4312 GenBank   NZ_CP029903
Plasmid name   pk88 Incompatibility group   IncI1
Plasmid size   88544 bp Coordinate of oriT [Strand]   33967..34055 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhi strain 311189_268103

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2