Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102426
Name   oriT_SMG006F1|unnamed1 in_silico
Organism   Escherichia coli strain SMG006F1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAKVTA010000022 (61283..61371 [+], 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_SMG006F1|unnamed1
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1814 GenBank   WP_242425780
Name   nikB_ML405_RS20005_SMG006F1|unnamed1 insolico UniProt ID   _
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103997.62 Da        Isoelectric Point: 7.3372

>WP_242425780.1 IncI1-type relaxase NikB [Escherichia coli]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELEMKHGFSPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKQTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAEKLMKKMGDYTPVPKDIFSQVDAPGRYNPDFIAADVRPEKIAETE
SLQQYACRHLGERLPEMAREGRLENCQAIHRTLAEAGLWMRVQHGHLVICDGYDHNQTPVRADSVWSLLT
LDNVNQLDGGWQPVPTDIFRQVTPTERFRGRRMESCPATDKEWHRMRTGTGPQGAIKRELFSDKESLWGY
SISHCSPQIEEMITQGEFTWQRCHELFAQQGLMLQKQHHGLVVVDAFNHEQTPVKASSIHPDLTLGRAEP
QAGPFVSAPADLFDRVQPESRYNPELAVSDRYGVSSKRDPMLRRQRREARAEARADLRARYLAWREQWRK
PDLRYGERCREIHQACRLRKSHIRTQYDDPALRKLHYHIAEVQRMQALIRLKEDIRDERQKLIADGKWYP
PSYRQWVEIQAAQGDRAAVSQLRGWDYRDRRKDKSRTTTTDRCVVLCEPGGTPVYGNTGDLEARLQKNGS
VRFRDRRTGEFVCTDYGDRVVFRNHHDRNALADKLDLIAPVLFGRDPRMGFEPEGNDKQFNQVFAEMVAW
HNVTGRTGHEDYRITRPDVDHHREGSERYYSDYIAANSNDEITLPSLELEKQWEPPKPM

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(62-314)


  Protein structure



No available structure.




Auxiliary protein

ID   735 GenBank   WP_001283947
Name   WP_001283947_SMG006F1|unnamed1 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   1401 GenBank   WP_242425779
Name   trbC_ML405_RS19990_SMG006F1|unnamed1 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: 86981.19 Da        Isoelectric Point: 6.8156

>WP_242425779.1 F-type conjugative transfer protein TrbC [Escherichia coli]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVIMESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPHLNRLRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRTERIGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 24382..54474

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ML405_RS19815 (ML405_19815) 19444..20511 + 1068 WP_012565251 type IV pilus biogenesis lipoprotein PilL -
ML405_RS19820 (ML405_19820) 20511..20948 + 438 WP_000539810 type IV pilus biogenesis protein PilM -
ML405_RS19825 (ML405_19825) 20962..22644 + 1683 WP_000733118 PilN family type IVB pilus formation outer membrane protein -
ML405_RS19830 (ML405_19830) 22637..23932 + 1296 WP_000752781 type 4b pilus protein PilO2 -
ML405_RS19835 (ML405_19835) 23919..24371 + 453 WP_001247329 type IV pilus biogenesis protein PilP -
ML405_RS19840 (ML405_19840) 24382..25935 + 1554 WP_112912660 ATPase, T2SS/T4P/T4SS family virB11
ML405_RS19845 (ML405_19845) 25948..27045 + 1098 WP_001208806 type II secretion system F family protein -
ML405_RS19850 (ML405_19850) 27063..27677 + 615 WP_242425773 type 4 pilus major pilin -
ML405_RS19855 (ML405_19855) 27687..28247 + 561 WP_064198679 lytic transglycosylase domain-containing protein virB1
ML405_RS19860 (ML405_19860) 28232..28888 + 657 WP_001193553 prepilin peptidase -
ML405_RS19865 (ML405_19865) 28888..30180 + 1293 WP_064198708 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
ML405_RS19870 (ML405_19870) 30237..30362 - 126 Protein_35 RNA-guided endonuclease TnpB family protein -
ML405_RS19875 (ML405_19875) 30570..31394 + 825 WP_064198681 conjugal transfer protein TraE traE
ML405_RS19880 (ML405_19880) 31480..32682 + 1203 WP_000976347 conjugal transfer protein TraF -
ML405_RS19885 (ML405_19885) 32742..33326 + 585 WP_001611722 histidine phosphatase family protein -
ML405_RS19890 (ML405_19890) 33721..34179 + 459 WP_001079805 IncI1-type conjugal transfer lipoprotein TraH -
ML405_RS19895 (ML405_19895) 34176..34994 + 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
ML405_RS19900 (ML405_19900) 34991..36139 + 1149 WP_001024975 plasmid transfer ATPase TraJ virB11
ML405_RS19905 (ML405_19905) 36136..36426 + 291 WP_001314267 hypothetical protein traK
ML405_RS19910 (ML405_19910) 36441..36992 + 552 WP_000014581 phospholipase D family protein -
ML405_RS19915 (ML405_19915) 37082..40849 + 3768 WP_242425774 LPD7 domain-containing protein -
ML405_RS19920 (ML405_19920) 40867..41214 + 348 WP_001055900 conjugal transfer protein traL
ML405_RS19925 (ML405_19925) 41211..41903 + 693 WP_242425775 DotI/IcmL family type IV secretion protein traM
ML405_RS19930 (ML405_19930) 41972..44446 + 2475 Protein_47 IncI1-type conjugal transfer protein TraU -
ML405_RS19935 (ML405_19935) 44446..45060 + 615 WP_001542516 IncI1-type conjugal transfer protein TraV traV
ML405_RS19940 (ML405_19940) 45027..46229 + 1203 WP_001749185 IncI1-type conjugal transfer protein TraW traW
ML405_RS19945 (ML405_19945) 46258..46842 + 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
ML405_RS19950 (ML405_19950) 46939..49107 + 2169 WP_242425776 DotA/TraY family protein traY
ML405_RS19955 (ML405_19955) 49178..49840 + 663 WP_000644796 plasmid IncI1-type surface exclusion protein ExcA -
ML405_RS19960 (ML405_19960) 49938..50147 + 210 WP_242425777 hemolysin expression modulator Hha -
ML405_RS19965 (ML405_19965) 50265..50507 + 243 WP_000504400 hypothetical protein -
ML405_RS25210 50572..50667 - 96 WP_000609148 DinQ-like type I toxin DqlB -
ML405_RS19970 (ML405_19970) 51410..51661 + 252 WP_024196888 hypothetical protein -
ML405_RS19975 (ML405_19975) 51733..51885 - 153 WP_023156060 Hok/Gef family protein -
ML405_RS19980 (ML405_19980) 52177..53385 + 1209 WP_001611760 IncI1-type conjugal transfer protein TrbA trbA
ML405_RS19985 (ML405_19985) 53404..54474 + 1071 WP_242425778 IncI1-type conjugal transfer protein TrbB trbB
ML405_RS19990 (ML405_19990) 54467..56758 + 2292 WP_242425779 F-type conjugative transfer protein TrbC -
ML405_RS19995 (ML405_19995) 56946..57500 - 555 WP_181186628 GNAT family N-acetyltransferase -
ML405_RS20000 (ML405_20000) 57484..57807 - 324 WP_001419663 DUF1778 domain-containing protein -

Host bacterium

ID   2870 GenBank   NZ_JAKVTA010000022
Plasmid name   SMG006F1|unnamed1 Incompatibility group   IncI1
Plasmid size   89955 bp Coordinate of oriT [Strand]   61283..61371 [+]
Host baterium   Escherichia coli strain SMG006F1

Cargo genes

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