Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106340
Name   oriT_SJTUF11216|unnamedB in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain SJTUF11216
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP047524 (44810..44898 [-], 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_SJTUF11216|unnamedB
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4241 GenBank   WP_012783930
Name   nikB_DXN15_RS25410_SJTUF11216|unnamedB insolico UniProt ID   N0GUP8
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104070.55 Da        Isoelectric Point: 7.3623

>WP_012783930.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSHMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLAERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWLPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDRSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALVDKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB N0GUP8


Auxiliary protein

ID   1889 GenBank   WP_001283947
Name   WP_001283947_SJTUF11216|unnamedB 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   4264 GenBank   WP_012783931
Name   trbC_DXN15_RS25415_SJTUF11216|unnamedB 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: 50276..84413

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
DXN15_RS25415 (DXN15_025360) 47992..50283 - 2292 WP_012783931 F-type conjugative transfer protein TrbC -
DXN15_RS25420 (DXN15_025365) 50276..51346 - 1071 WP_012783932 IncI1-type conjugal transfer protein TrbB trbB
DXN15_RS25425 (DXN15_025370) 51365..52573 - 1209 WP_001703845 IncI1-type conjugal transfer protein TrbA trbA
DXN15_RS25430 (DXN15_025375) 52880..53659 - 780 WP_275450201 protein FinQ -
DXN15_RS25435 (DXN15_025380) 54286..54438 + 153 WP_001387489 Hok/Gef family protein -
DXN15_RS25440 (DXN15_025385) 54510..54761 - 252 WP_001291964 hypothetical protein -
DXN15_RS25670 55262..55357 + 96 WP_000609148 DinQ-like type I toxin DqlB -
DXN15_RS25450 55422..55598 - 177 WP_001054900 hypothetical protein -
DXN15_RS25455 (DXN15_025395) 55990..56199 + 210 WP_000062603 HEAT repeat domain-containing protein -
DXN15_RS25460 (DXN15_025400) 56271..56933 - 663 WP_012783935 plasmid IncI1-type surface exclusion protein ExcA -
DXN15_RS25465 (DXN15_025405) 57004..59172 - 2169 WP_015508354 DotA/TraY family protein traY
DXN15_RS25470 (DXN15_025410) 59269..59853 - 585 WP_001037998 conjugal transfer protein TraX -
DXN15_RS25475 (DXN15_025415) 59882..61084 - 1203 WP_001690627 IncI1-type conjugal transfer protein TraW traW
DXN15_RS25480 (DXN15_025420) 61051..61665 - 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
DXN15_RS25485 (DXN15_025425) 61665..64709 - 3045 WP_023518848 IncI1-type conjugal transfer protein TraU traU
DXN15_RS25490 (DXN15_025430) 64799..65599 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
DXN15_RS25495 (DXN15_025435) 65583..65771 - 189 WP_001277255 putative conjugal transfer protein TraS -
DXN15_RS25500 (DXN15_025440) 65835..66239 - 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
DXN15_RS25505 (DXN15_025445) 66290..66817 - 528 WP_001055569 conjugal transfer protein TraQ traQ
DXN15_RS25510 (DXN15_025450) 66817..67521 - 705 WP_064198837 IncI1-type conjugal transfer protein TraP traP
DXN15_RS25515 (DXN15_025455) 67521..68810 - 1290 WP_001271994 conjugal transfer protein TraO traO
DXN15_RS25520 (DXN15_025460) 68813..69796 - 984 WP_001191880 IncI1-type conjugal transfer protein TraN traN
DXN15_RS25525 (DXN15_025465) 69807..70499 - 693 WP_000138551 DotI/IcmL family type IV secretion protein traM
DXN15_RS25530 (DXN15_025470) 70496..70843 - 348 WP_001055900 conjugal transfer protein traL
DXN15_RS25535 (DXN15_025475) 70861..74625 - 3765 WP_064198838 LPD7 domain-containing protein -
DXN15_RS25540 (DXN15_025480) 74715..75266 - 552 WP_000014586 phospholipase D family protein -
DXN15_RS25545 (DXN15_025485) 75281..75571 - 291 WP_001299214 hypothetical protein traK
DXN15_RS25550 (DXN15_025490) 75568..76716 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
DXN15_RS25555 (DXN15_025495) 76713..77531 - 819 WP_032220737 IncI1-type conjugal transfer lipoprotein TraI traI
DXN15_RS25560 (DXN15_025500) 77528..77986 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
DXN15_RS25565 (DXN15_025505) 78402..79061 - 660 Protein_92 IS5 family transposase -
DXN15_RS25570 (DXN15_025510) 79096..79971 - 876 WP_001617865 extended-spectrum class A beta-lactamase CTX-M-14 -
DXN15_RS25575 (DXN15_025515) 80221..81483 - 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
DXN15_RS25580 (DXN15_025520) 81636..82241 - 606 WP_064198839 lipopolysaccharide core heptose(II)-phosphate phosphatase -
DXN15_RS25585 (DXN15_025525) 82301..83503 - 1203 WP_000976353 conjugal transfer protein TraF -
DXN15_RS25590 (DXN15_025530) 83589..84413 - 825 WP_001690630 conjugal transfer protein TraE traE
DXN15_RS25595 (DXN15_025535) 84564..85718 - 1155 WP_001139955 site-specific integrase -
DXN15_RS25600 (DXN15_025540) 86738..86986 + 249 WP_001349157 hypothetical protein -

Host bacterium

ID   6777 GenBank   NZ_CP047524
Plasmid name   SJTUF11216|unnamedB Incompatibility group   IncI
Plasmid size   87292 bp Coordinate of oriT [Strand]   44810..44898 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain SJTUF11216

Cargo genes

Drug resistance gene   blaCTX-M-14
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2