Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102635
Name   oriT_pUMNturkey4_IncI1 in_silico
Organism   Escherichia coli strain UMNturkey4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JRPZ01000051 (12893..12981 [-], 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_pUMNturkey4_IncI1
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1959 GenBank   WP_001306778
Name   nikB_LS40_RS19740_pUMNturkey4_IncI1 insolico UniProt ID   Q79VV7
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 104010.41 Da        Isoelectric Point: 7.4265

>WP_001306778.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIARQAHYAKDDTDPVFHYILSWQSHESPRPEQIYDSVR
HTLKSLGLADHQYVSAVHTDTDNLHVHVAVNRVHPETGYLNRLSWSQEKLSRACRELELKHGFAPDNGCW
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 Q79VV7


Auxiliary protein

ID   784 GenBank   WP_001283947
Name   WP_001283947_pUMNturkey4_IncI1 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   1587 GenBank   WP_001289276
Name   trbC_LS40_RS19745_pUMNturkey4_IncI1 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: 86941.11 Da        Isoelectric Point: 6.7713

>WP_001289276.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 18359..57826

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
LS40_RS19745 (LS40_19735) 16075..18366 - 2292 WP_001289276 F-type conjugative transfer protein TrbC -
LS40_RS19750 (LS40_19740) 18359..19429 - 1071 WP_000151582 IncI1-type conjugal transfer protein TrbB trbB
LS40_RS19755 (LS40_19745) 19448..20656 - 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
LS40_RS19760 (LS40_19750) 20963..21742 - 780 WP_275450201 protein FinQ -
LS40_RS19765 (LS40_19755) 22369..22521 + 153 WP_001303307 Hok/Gef family protein -
LS40_RS19770 (LS40_19760) 22593..22844 - 252 WP_001291965 hypothetical protein -
LS40_RS29845 (LS40_19765) 23768..23944 - 177 WP_001054900 hypothetical protein -
LS40_RS19785 (LS40_19775) 24153..24362 - 210 Protein_28 hemolysin expression modulator Hha -
LS40_RS19790 (LS40_19780) 24460..25074 - 615 WP_000578649 plasmid IncI1-type surface exclusion protein ExcA -
LS40_RS19795 (LS40_19785) 25150..27318 - 2169 WP_000698360 IncI1-type conjugal transfer membrane protein TraY traY
LS40_RS19800 (LS40_19790) 27415..27999 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
LS40_RS19805 (LS40_19795) 28028..29230 - 1203 WP_001189159 IncI1-type conjugal transfer protein TraW traW
LS40_RS19810 (LS40_19800) 29197..29811 - 615 WP_000337394 IncI1-type conjugal transfer protein TraV traV
LS40_RS19815 (LS40_19805) 29811..32855 - 3045 WP_001024752 IncI1-type conjugal transfer protein TraU traU
LS40_RS19820 (LS40_19810) 32945..33745 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
LS40_RS19825 (LS40_19815) 33729..33917 - 189 WP_001277255 putative conjugal transfer protein TraS -
LS40_RS19830 (LS40_19820) 33981..34385 - 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
LS40_RS19835 (LS40_19825) 34436..34963 - 528 WP_001055569 conjugal transfer protein TraQ traQ
LS40_RS19840 (LS40_19830) 34963..35667 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
LS40_RS19845 (LS40_19835) 35667..36956 - 1290 WP_001271997 conjugal transfer protein TraO traO
LS40_RS19850 (LS40_19840) 36959..37942 - 984 WP_001191878 IncI1-type conjugal transfer protein TraN traN
LS40_RS19855 (LS40_19845) 37953..38645 - 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
LS40_RS19860 (LS40_19850) 38642..38989 - 348 WP_001055900 conjugal transfer protein traL
LS40_RS19865 (LS40_19855) 39007..42774 - 3768 WP_001141539 LPD7 domain-containing protein -
LS40_RS19870 (LS40_19860) 42864..43415 - 552 WP_000014584 phospholipase D family protein -
LS40_RS27970 43430..43720 - 291 WP_001299214 hypothetical protein traK
LS40_RS19875 (LS40_19865) 43717..44865 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
LS40_RS19880 (LS40_19870) 44862..45680 - 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
LS40_RS19885 (LS40_19875) 45677..46135 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
LS40_RS19890 (LS40_19880) 46530..47114 - 585 WP_000977522 histidine phosphatase family protein -
LS40_RS19895 (LS40_19885) 47174..48376 - 1203 WP_000976353 conjugal transfer protein TraF -
LS40_RS19900 (LS40_19890) 48462..49286 - 825 WP_001238927 conjugal transfer protein TraE traE
LS40_RS19905 (LS40_19895) 49437..50591 - 1155 WP_047609501 site-specific integrase -
LS40_RS30305 50590..50874 + 285 WP_187642572 pilus assembly protein PilV -
LS40_RS30645 51678..51899 + 222 Protein_55 prepilin -
LS40_RS19920 (LS40_19910) 51896..53320 - 1425 WP_024199048 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
LS40_RS19925 (LS40_19915) 53320..53976 - 657 WP_001389386 prepilin peptidase -
LS40_RS19930 (LS40_19920) 53961..54521 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
LS40_RS19935 (LS40_19925) 54531..55145 - 615 WP_000959786 type 4 pilus major pilin -
LS40_RS19940 (LS40_19930) 55163..56260 - 1098 WP_001208805 type II secretion system F family protein -
LS40_RS19945 (LS40_19935) 56273..57826 - 1554 WP_000362202 ATPase, T2SS/T4P/T4SS family virB11
LS40_RS19950 (LS40_19940) 57837..58289 - 453 WP_001247334 type IV pilus biogenesis protein PilP -
LS40_RS19955 (LS40_19945) 58276..59571 - 1296 WP_000752772 type 4b pilus protein PilO2 -
LS40_RS19960 (LS40_19950) 59564..61246 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
LS40_RS19965 (LS40_19955) 61260..61697 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
LS40_RS19970 (LS40_19960) 61697..62764 - 1068 WP_047609496 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   3079 GenBank   NZ_JRPZ01000051
Plasmid name   pUMNturkey4_IncI1 Incompatibility group   IncI1
Plasmid size   80158 bp Coordinate of oriT [Strand]   12893..12981 [-]
Host baterium   Escherichia coli strain UMNturkey4

Cargo genes

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