Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102350
Name   oriT_pAR-0410 in_silico
Organism   Salmonella enterica subsp. enterica serovar Infantis strain AR-0410
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_WACL01000005 (283992..284080 [-], 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_pAR-0410
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1781 GenBank   WP_006855641
Name   nikB_F4V22_RS23490_pAR-0410 insolico UniProt ID   A0A620WL05
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104006.42 Da        Isoelectric Point: 7.3526

>WP_006855641.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELDLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVHDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRAQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYRDYIAANSNDDASLPPPEQDKRWEPPSPG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure


Source ID Structure
AlphaFold DB A0A620WL05


Auxiliary protein

ID   701 GenBank   WP_001283947
Name   WP_001283947_pAR-0410 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   1364 GenBank   WP_001289275
Name   trbC_F4V22_RS23495_pAR-0410 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: 86957.15 Da        Isoelectric Point: 6.7713

>WP_001289275.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHLTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 289458..320322

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
F4V22_RS23495 287174..289465 - 2292 WP_001289275 F-type conjugative transfer protein TrbC -
F4V22_RS23500 289458..290528 - 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
F4V22_RS23505 290547..291755 - 1209 WP_001383960 IncI1-type conjugal transfer protein TrbA trbA
F4V22_RS23510 292062..292841 - 780 WP_275450201 protein FinQ -
F4V22_RS23515 293468..293620 + 153 WP_001387489 Hok/Gef family protein -
F4V22_RS23520 293692..293943 - 252 WP_001291964 hypothetical protein -
F4V22_RS25550 294444..294539 + 96 WP_000609148 DinQ-like type I toxin DqlB -
F4V22_RS25120 294604..294780 - 177 WP_001054897 hypothetical protein -
F4V22_RS23530 295172..295381 + 210 WP_000062603 HEAT repeat domain-containing protein -
F4V22_RS23535 295453..296115 - 663 WP_000644796 plasmid IncI1-type surface exclusion protein ExcA -
F4V22_RS23540 296186..298354 - 2169 WP_058649949 DotA/TraY family protein traY
F4V22_RS23545 298451..299035 - 585 WP_001037996 IncI1-type conjugal transfer protein TraX -
F4V22_RS23550 299064..300266 - 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
F4V22_RS23555 300233..300847 - 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
F4V22_RS23560 300847..303891 - 3045 WP_001024776 IncI1-type conjugal transfer protein TraU traU
F4V22_RS23565 303981..304781 - 801 WP_001164792 IncI1-type conjugal transfer protein TraT traT
F4V22_RS23570 304765..304953 - 189 WP_001277255 putative conjugal transfer protein TraS -
F4V22_RS23575 305017..305421 - 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
F4V22_RS23580 305472..305999 - 528 WP_001055569 conjugal transfer protein TraQ traQ
F4V22_RS23585 305999..306703 - 705 WP_023155244 IncI1-type conjugal transfer protein TraP traP
F4V22_RS23590 306703..307992 - 1290 WP_001271994 conjugal transfer protein TraO traO
F4V22_RS23595 307995..308978 - 984 WP_021513963 IncI1-type conjugal transfer protein TraN traN
F4V22_RS23600 308989..309681 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
F4V22_RS23605 309678..310025 - 348 WP_001055900 conjugal transfer protein traL
F4V22_RS23610 310043..313810 - 3768 WP_058649948 LPD7 domain-containing protein -
F4V22_RS23615 313900..314451 - 552 WP_000014584 phospholipase D family protein -
F4V22_RS23620 314466..314756 - 291 WP_001299214 hypothetical protein traK
F4V22_RS23625 314753..315901 - 1149 WP_001024976 plasmid transfer ATPase TraJ virB11
F4V22_RS23630 315898..316716 - 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
F4V22_RS23635 316713..317171 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
F4V22_RS23640 317566..318150 - 585 WP_000977520 histidine phosphatase family protein -
F4V22_RS23645 318210..319412 - 1203 WP_000976353 conjugal transfer protein TraF -
F4V22_RS23650 319498..320322 - 825 WP_058649947 conjugal transfer protein TraE traE
F4V22_RS23655 320473..321627 - 1155 WP_001139955 site-specific integrase -

Host bacterium

ID   2794 GenBank   NZ_WACL01000005
Plasmid name   pAR-0410 Incompatibility group   IncFIB
Plasmid size   321860 bp Coordinate of oriT [Strand]   283992..284080 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Infantis strain AR-0410

Cargo genes

Drug resistance gene   tet(A), sul1, qacE, ant(3'')-Ia, aph(3')-Ia, dfrA14, aac(3)-IVa, aph(4)-Ia, floR, fosA3, blaCTX-M-65
Virulence gene   ybtS, ybtX, ybtQ, ybtP, ybtA, irp2, ybtT, ybtE, fyuA, faeI, faeH, faeF, faeE, faeC
Metal resistance gene   merR, merT, merP, merA, merD, merE, arsA, arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2