Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114089
Name   oriT_pR18.0409_97k in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain R18.0409
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP100709 (61463..61551 [+], 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_pR18.0409_97k
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9048 GenBank   WP_011264053
Name   nikB_NL735_RS26150_pR18.0409_97k insolico UniProt ID   A0A767TAZ8
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103882.34 Da        Isoelectric Point: 7.4198

>WP_011264053.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
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 A0A767TAZ8


Auxiliary protein

ID   5270 GenBank   WP_001283947
Name   WP_001283947_pR18.0409_97k 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   10475 GenBank   WP_011264051
Name   trbC_NL735_RS26145_pR18.0409_97k 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: 86954.10 Da        Isoelectric Point: 6.7713

>WP_011264051.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 12259..56084

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NL735_RS25890 (NL735_25890) 7321..8388 + 1068 WP_001302629 type IV pilus biogenesis lipoprotein PilL -
NL735_RS25895 (NL735_25895) 8388..8825 + 438 WP_000539807 type IV pilus biogenesis protein PilM -
NL735_RS25900 (NL735_25900) 8839..10521 + 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
NL735_RS25905 (NL735_25905) 10514..11809 + 1296 WP_000752772 type 4b pilus protein PilO2 -
NL735_RS25910 (NL735_25910) 11796..12248 + 453 WP_001247334 type IV pilus biogenesis protein PilP -
NL735_RS25915 (NL735_25915) 12259..13812 + 1554 WP_167651944 GspE/PulE family protein virB11
NL735_RS25920 (NL735_25920) 13825..14922 + 1098 WP_001208805 type II secretion system F family protein -
NL735_RS25925 (NL735_25925) 14940..15554 + 615 WP_000959786 type 4 pilus major pilin -
NL735_RS25930 (NL735_25930) 15564..16124 + 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
NL735_RS25935 (NL735_25935) 16109..16765 + 657 WP_001193553 prepilin peptidase -
NL735_RS25940 (NL735_25940) 16765..18057 + 1293 WP_001417545 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
NL735_RS25945 (NL735_25945) 18054..18302 - 249 WP_001349157 hypothetical protein -
NL735_RS25950 (NL735_25950) 19540..19824 - 285 WP_187642572 pilus assembly protein PilV -
NL735_RS25955 (NL735_25955) 19823..20977 + 1155 WP_001139958 tyrosine-type recombinase/integrase -
NL735_RS25960 (NL735_25960) 21128..21952 + 825 WP_001238929 conjugal transfer protein TraE traE
NL735_RS25965 (NL735_25965) 22038..23240 + 1203 WP_000976353 conjugal transfer protein TraF -
NL735_RS25970 (NL735_25970) 23300..23884 + 585 WP_000977522 histidine phosphatase family protein -
NL735_RS25975 (NL735_25975) 24279..24737 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
NL735_RS25980 (NL735_25980) 24734..25552 + 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
NL735_RS25985 (NL735_25985) 25549..26697 + 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
NL735_RS25990 (NL735_25990) 26694..26984 + 291 WP_001299214 hypothetical protein traK
NL735_RS25995 (NL735_25995) 26999..27550 + 552 WP_000014584 phospholipase D family protein -
NL735_RS26000 (NL735_26000) 27640..31407 + 3768 WP_023518849 LPD7 domain-containing protein -
NL735_RS26005 (NL735_26005) 31425..31772 + 348 WP_001055900 conjugal transfer protein traL
NL735_RS26010 (NL735_26010) 31769..32461 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
NL735_RS26015 (NL735_26015) 32472..33455 + 984 WP_001191880 IncI1-type conjugal transfer protein TraN traN
NL735_RS26020 (NL735_26020) 33458..34747 + 1290 WP_167651943 conjugal transfer protein TraO traO
NL735_RS26025 (NL735_26025) 34747..35451 + 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
NL735_RS26030 (NL735_26030) 35451..35978 + 528 WP_001055569 conjugal transfer protein TraQ traQ
NL735_RS26035 (NL735_26035) 36029..36433 + 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
NL735_RS26040 (NL735_26040) 36497..36685 + 189 WP_001277255 putative conjugal transfer protein TraS -
NL735_RS26045 (NL735_26045) 36669..37469 + 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
NL735_RS26050 (NL735_26050) 37559..40603 + 3045 WP_023518848 IncI1-type conjugal transfer protein TraU traU
NL735_RS26055 (NL735_26055) 40603..41217 + 615 WP_000337399 IncI1-type conjugal transfer protein TraV traV
NL735_RS26060 (NL735_26060) 41184..42386 + 1203 WP_254535113 IncI1-type conjugal transfer protein TraW traW
NL735_RS26065 (NL735_26065) 42415..42999 + 585 WP_254535114 IncI1-type conjugal transfer protein TraX -
NL735_RS26070 (NL735_26070) 43096..45264 + 2169 WP_023518847 DotA/TraY family protein traY
NL735_RS26075 (NL735_26075) 45335..45997 + 663 WP_000644796 plasmid IncI1-type surface exclusion protein ExcA -
NL735_RS26080 (NL735_26080) 46069..46278 - 210 WP_000062603 HEAT repeat domain-containing protein -
NL735_RS26085 (NL735_26085) 46670..46846 + 177 WP_001054897 hypothetical protein -
NL735_RS26450 46911..47006 - 96 WP_000609148 DinQ-like type I toxin DqlB -
NL735_RS26095 (NL735_26095) 47507..47758 + 252 WP_001291964 hypothetical protein -
NL735_RS26100 (NL735_26100) 47830..47982 - 153 WP_001387489 Hok/Gef family protein -
NL735_RS26105 (NL735_26105) 48303..48677 + 375 WP_223349261 hypothetical protein -
NL735_RS26110 (NL735_26110) 48830..50092 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
NL735_RS26115 (NL735_26115) 50416..51561 + 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
NL735_RS26120 (NL735_26120) 51655..52188 + 534 WP_001221666 lipocalin family protein -
NL735_RS26125 (NL735_26125) 52185..52502 - 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
NL735_RS26130 (NL735_26130) 52698..53480 + 783 WP_227496365 protein FinQ -
NL735_RS26135 (NL735_26135) 53787..54995 + 1209 WP_011264049 IncI1-type conjugal transfer protein TrbA trbA
NL735_RS26140 (NL735_26140) 55014..56084 + 1071 WP_011264050 IncI1-type conjugal transfer protein TrbB trbB
NL735_RS26145 (NL735_26145) 56077..58368 + 2292 WP_011264051 F-type conjugative transfer protein TrbC -

Host bacterium

ID   14524 GenBank   NZ_CP100709
Plasmid name   pR18.0409_97k Incompatibility group   IncI1
Plasmid size   97209 bp Coordinate of oriT [Strand]   61463..61551 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain R18.0409

Cargo genes

Drug resistance gene   blaCMY-2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrVA2