Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116779
Name   oriT_pEF-1 in_silico
Organism   Escherichia fergusonii strain EF21023765
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP137856 (72269..72357 [+], 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_pEF-1
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGCAAACGGAATATCGTCGCGGGTGACGGTATTACATTTGCACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10705 GenBank   WP_001306778
Name   nikB_R9X46_RS21440_pEF-1 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   6302 GenBank   WP_001283947
Name   WP_001283947_pEF-1 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   12504 GenBank   WP_001289276
Name   trbC_R9X46_RS21435_pEF-1 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: 27424..66891

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
R9X46_RS21215 22486..23553 + 1068 WP_001302629 type IV pilus biogenesis lipoprotein PilL -
R9X46_RS21220 23553..23990 + 438 WP_000539807 type IV pilus biogenesis protein PilM -
R9X46_RS21225 24004..25686 + 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
R9X46_RS21230 25679..26974 + 1296 WP_000752772 type 4b pilus protein PilO2 -
R9X46_RS21235 26961..27413 + 453 WP_001247334 type IV pilus biogenesis protein PilP -
R9X46_RS21240 27424..28977 + 1554 WP_000362202 GspE/PulE family protein virB11
R9X46_RS21245 28990..30087 + 1098 WP_001208805 type II secretion system F family protein -
R9X46_RS21250 30105..30719 + 615 WP_000959786 type 4 pilus major pilin -
R9X46_RS21255 30729..31289 + 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
R9X46_RS21260 31274..31930 + 657 WP_001389386 prepilin peptidase -
R9X46_RS21265 31930..33354 + 1425 WP_024199048 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
R9X46_RS21270 33351..33575 - 225 Protein_37 hypothetical protein -
R9X46_RS21275 34659..35813 + 1155 WP_001139958 tyrosine-type recombinase/integrase -
R9X46_RS21280 35964..36788 + 825 WP_001238927 conjugal transfer protein TraE traE
R9X46_RS21285 36874..38076 + 1203 WP_000976349 conjugal transfer protein TraF -
R9X46_RS21290 38136..38720 + 585 WP_000977522 histidine phosphatase family protein -
R9X46_RS21295 39115..39573 + 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
R9X46_RS21300 39570..40388 + 819 WP_000646097 IncI1-type conjugal transfer lipoprotein TraI traI
R9X46_RS21305 40385..41533 + 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
R9X46_RS21310 41530..41820 + 291 WP_001299214 hypothetical protein traK
R9X46_RS21315 41835..42386 + 552 WP_000014584 phospholipase D family protein -
R9X46_RS21320 42476..46243 + 3768 WP_001141539 LPD7 domain-containing protein -
R9X46_RS21325 46261..46608 + 348 WP_001055900 conjugal transfer protein traL
R9X46_RS21330 46605..47297 + 693 WP_000138552 DotI/IcmL family type IV secretion protein traM
R9X46_RS21335 47308..48291 + 984 WP_001191878 IncI1-type conjugal transfer protein TraN traN
R9X46_RS21340 48294..49583 + 1290 WP_001271997 conjugal transfer protein TraO traO
R9X46_RS21345 49583..50287 + 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
R9X46_RS21350 50287..50814 + 528 WP_001055569 conjugal transfer protein TraQ traQ
R9X46_RS21355 50865..51269 + 405 WP_000086960 IncI1-type conjugal transfer protein TraR traR
R9X46_RS21360 51333..51521 + 189 WP_001277255 putative conjugal transfer protein TraS -
R9X46_RS21365 51505..52305 + 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
R9X46_RS21370 52395..55439 + 3045 WP_001024752 IncI1-type conjugal transfer protein TraU traU
R9X46_RS21375 55439..56053 + 615 WP_000337394 IncI1-type conjugal transfer protein TraV traV
R9X46_RS21380 56020..57222 + 1203 WP_001189159 IncI1-type conjugal transfer protein TraW traW
R9X46_RS21385 57251..57835 + 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
R9X46_RS21390 57932..60100 + 2169 WP_000698360 IncI1-type conjugal transfer membrane protein TraY traY
R9X46_RS21395 60176..60790 + 615 WP_318651842 plasmid IncI1-type surface exclusion protein ExcA -
R9X46_RS21400 60888..61097 + 210 Protein_63 hemolysin expression modulator Hha -
R9X46_RS21405 61306..61482 + 177 WP_001054900 hypothetical protein -
R9X46_RS21410 62406..62657 + 252 WP_001291965 hypothetical protein -
R9X46_RS21415 62729..62881 - 153 WP_001303307 Hok/Gef family protein -
R9X46_RS21420 63508..64287 + 780 WP_275450201 protein FinQ -
R9X46_RS21425 64594..65802 + 1209 WP_187796788 IncI1-type conjugal transfer protein TrbA trbA
R9X46_RS21430 65821..66891 + 1071 WP_000151582 IncI1-type conjugal transfer protein TrbB trbB
R9X46_RS21435 66884..69175 + 2292 WP_001289276 F-type conjugative transfer protein TrbC -

Host bacterium

ID   17212 GenBank   NZ_CP137856
Plasmid name   pEF-1 Incompatibility group   IncI1
Plasmid size   90746 bp Coordinate of oriT [Strand]   72269..72357 [+]
Host baterium   Escherichia fergusonii strain EF21023765

Cargo genes

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