Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111102
Name   oriT_pCVM44454 in_silico
Organism   Salmonella enterica subsp. enterica serovar Infantis strain CVM44454 isolate 2014am-3028
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP016413 (233452..233540 [+], 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_pCVM44454
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7287 GenBank   WP_006855641
Name   nikB_BAR51_RS25105_pCVM44454 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   4052 GenBank   WP_001283947
Name   WP_001283947_pCVM44454 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   8301 GenBank   WP_001289275
Name   trbC_BAR51_RS25100_pCVM44454 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: 189185..228074

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BAR51_RS24875 184247..185314 + 1068 WP_001360287 type IV pilus biogenesis lipoprotein PilL -
BAR51_RS24880 (BAR51_23745) 185314..185751 + 438 WP_000539807 type IV pilus biogenesis protein PilM -
BAR51_RS24885 (BAR51_23750) 185765..187447 + 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
BAR51_RS24890 (BAR51_23755) 187440..188735 + 1296 WP_058649964 type 4b pilus protein PilO2 -
BAR51_RS24895 (BAR51_23760) 188722..189174 + 453 WP_058649963 type IV pilus biogenesis protein PilP -
BAR51_RS24900 (BAR51_23765) 189185..190738 + 1554 WP_000362204 ATPase, T2SS/T4P/T4SS family virB11
BAR51_RS24905 (BAR51_23770) 190751..191836 + 1086 WP_001208803 type II secretion system F family protein -
BAR51_RS24910 (BAR51_23775) 191853..192467 + 615 WP_000908228 type 4 pilus major pilin -
BAR51_RS24915 (BAR51_23780) 192477..193037 + 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
BAR51_RS24920 (BAR51_23785) 193022..193678 + 657 WP_001193551 A24 family peptidase -
BAR51_RS24925 (BAR51_23790) 193678..194970 + 1293 WP_039719938 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
BAR51_RS26830 194967..195215 - 249 WP_001349157 hypothetical protein -
BAR51_RS24940 (BAR51_23795) 195905..197059 + 1155 WP_001139955 site-specific integrase -
BAR51_RS24945 (BAR51_23800) 197210..198034 + 825 WP_058649947 conjugal transfer protein TraE traE
BAR51_RS24950 (BAR51_23805) 198120..199322 + 1203 WP_000976353 conjugal transfer protein TraF -
BAR51_RS24955 (BAR51_23810) 199382..199966 + 585 WP_000977520 histidine phosphatase family protein -
BAR51_RS24960 (BAR51_23815) 200361..200819 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
BAR51_RS24965 (BAR51_23820) 200816..201634 + 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
BAR51_RS24970 (BAR51_23825) 201631..202779 + 1149 WP_001024976 plasmid transfer ATPase TraJ virB11
BAR51_RS24975 202776..203066 + 291 WP_001299214 hypothetical protein traK
BAR51_RS24980 (BAR51_23830) 203081..203632 + 552 WP_000014584 phospholipase D family protein -
BAR51_RS24985 (BAR51_23835) 203722..207489 + 3768 WP_058649948 LPD7 domain-containing protein -
BAR51_RS24990 (BAR51_23840) 207507..207854 + 348 WP_001055900 conjugal transfer protein traL
BAR51_RS24995 (BAR51_23845) 207851..208543 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
BAR51_RS25000 (BAR51_23850) 208554..209537 + 984 WP_021513963 IncI1-type conjugal transfer protein TraN traN
BAR51_RS25005 (BAR51_23855) 209540..210829 + 1290 WP_001271994 conjugal transfer protein TraO traO
BAR51_RS25010 (BAR51_23860) 210829..211533 + 705 WP_023155244 IncI1-type conjugal transfer protein TraP traP
BAR51_RS25015 (BAR51_23865) 211533..212060 + 528 WP_001055569 conjugal transfer protein TraQ traQ
BAR51_RS25020 (BAR51_23870) 212111..212515 + 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
BAR51_RS25025 (BAR51_23875) 212579..212767 + 189 WP_001277255 putative conjugal transfer protein TraS -
BAR51_RS25030 (BAR51_23880) 212751..213551 + 801 WP_001164792 IncI1-type conjugal transfer protein TraT traT
BAR51_RS25035 (BAR51_23885) 213641..216685 + 3045 WP_001024776 IncI1-type conjugal transfer protein TraU traU
BAR51_RS25040 216685..217299 + 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
BAR51_RS25045 (BAR51_23890) 217266..218468 + 1203 WP_001189156 IncI1-type conjugal transfer protein TraW traW
BAR51_RS25050 (BAR51_23895) 218497..219081 + 585 WP_001037996 IncI1-type conjugal transfer protein TraX -
BAR51_RS25055 (BAR51_23900) 219178..221346 + 2169 WP_058649949 DotA/TraY family protein traY
BAR51_RS25060 (BAR51_23905) 221417..222079 + 663 WP_000644796 plasmid IncI1-type surface exclusion protein ExcA -
BAR51_RS25065 (BAR51_23910) 222151..222360 - 210 WP_000062603 HEAT repeat domain-containing protein -
BAR51_RS26835 222752..222928 + 177 WP_001054897 hypothetical protein -
BAR51_RS27145 222993..223088 - 96 WP_000609148 DinQ-like type I toxin DqlB -
BAR51_RS25075 (BAR51_23920) 223589..223840 + 252 WP_001291964 hypothetical protein -
BAR51_RS25080 (BAR51_23925) 223912..224064 - 153 WP_001387489 Hok/Gef family protein -
BAR51_RS25085 (BAR51_23930) 224691..225470 + 780 WP_275450201 protein FinQ -
BAR51_RS25090 (BAR51_23935) 225777..226985 + 1209 WP_001383960 IncI1-type conjugal transfer protein TrbA trbA
BAR51_RS25095 (BAR51_23940) 227004..228074 + 1071 WP_000151583 IncI1-type conjugal transfer protein TrbB trbB
BAR51_RS25100 (BAR51_23945) 228067..230358 + 2292 WP_001289275 F-type conjugative transfer protein TrbC -

Host bacterium

ID   11537 GenBank   NZ_CP016413
Plasmid name   pCVM44454 Incompatibility group   IncFIB
Plasmid size   316160 bp Coordinate of oriT [Strand]   233452..233540 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Infantis strain CVM44454 isolate 2014am-3028

Cargo genes

Drug resistance gene   ant(3'')-Ia, qacE, sul1, tet(A), blaCTX-M-65, floR, aph(4)-Ia, aac(3)-IVa, dfrA14
Virulence gene   -
Metal resistance gene   merE, merD, merA, merP, merT, merR, arsH, arsA
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2