Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101559
Name   oriT_EC-28|unnamed2 in_silico
Organism   Escherichia coli strain EC-28
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAWLTU010000003 (32829..32917 [-], 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_EC-28|unnamed2
GGGGTGTCGGGGCGAAGCCCTGACCAGATGGTAATTGTAATAGCGTCGCGTGTGACGGTATTACAATTACACATCCTGTCCCGTTTTTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1382 GenBank   WP_052974688
Name   nikB_V6E60_RS25220_EC-28|unnamed2 insolico UniProt ID   A0A0F7KZP4
Length   899 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 899 a.a.        Molecular weight: 103875.39 Da        Isoelectric Point: 7.5153

>WP_052974688.1 MULTISPECIES: IncI1-type relaxase NikB [Enterobacteriaceae]
MNAVIPKKRRDGKSSFEDLVSYVSVRDDMTDEELNLSSSSQAEQPHRSRFSRLVDYATRLRNESFVALVD
VMKDGCEWVNFYGVTCFHNCTSLETAAADMEYIAQQAHYAKDNTDPVFHYILSWQAHESPRPEQIYDSVR
HTLKSLGLGEHQYVSAVHTDTDNLHVHVAVNRVHPVTGYLNCLSWSQEKLSRACRELELKHGFAPDNGCW
VHAPGNRIVRKTAVERDRQNAWTRGKKHTFREYVAQTAVAGLRSEPVNDWLSLHRRLAEDGLYLSQMDGK
FLVMDGWDRNREGVQLDSFGPSWCAVKLMKKMGDYTPVPKDIFSQVEAPGRYNPDFIAADIRPEKIAETE
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 A0A0F7KZP4


Auxiliary protein

ID   501 GenBank   WP_001283947
Name   WP_001283947_EC-28|unnamed2 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   1014 GenBank   WP_072121498
Name   trbC_V6E60_RS25225_EC-28|unnamed2 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: 86896.07 Da        Isoelectric Point: 6.7712

>WP_072121498.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTAKTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKIDVQELIELH
PGEFFSIFRGETVPSASFFIPDNEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTAQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKNNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 38295..76591

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
V6E60_RS25225 36011..38302 - 2292 WP_072121498 F-type conjugative transfer protein TrbC -
V6E60_RS25230 38295..39365 - 1071 WP_052974687 IncI1-type conjugal transfer protein TrbB trbB
V6E60_RS25235 39384..40592 - 1209 WP_052974686 IncI1-type conjugal transfer protein TrbA trbA
V6E60_RS25240 40881..41036 + 156 WP_000249068 Hok/Gef family protein -
V6E60_RS25245 41108..41359 - 252 WP_001291967 hypothetical protein -
V6E60_RS25250 41858..41953 + 96 WP_001303310 DinQ-like type I toxin DqlB -
V6E60_RS25255 42018..42194 - 177 WP_001054898 hypothetical protein -
V6E60_RS25260 42586..42795 + 210 WP_000062603 HEAT repeat domain-containing protein -
V6E60_RS25265 42867..43529 - 663 WP_012783935 plasmid IncI1-type surface exclusion protein ExcA -
V6E60_RS25270 43600..45768 - 2169 WP_052974685 DotA/TraY family protein traY
V6E60_RS25275 45865..46449 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
V6E60_RS25280 46478..47680 - 1203 WP_001189160 IncI1-type conjugal transfer protein TraW traW
V6E60_RS25285 47647..48261 - 615 WP_000337394 IncI1-type conjugal transfer protein TraV traV
V6E60_RS25290 48261..51305 - 3045 WP_052974684 IncI1-type conjugal transfer protein TraU traU
V6E60_RS25295 51395..52195 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
V6E60_RS25300 52179..52367 - 189 WP_001277255 putative conjugal transfer protein TraS -
V6E60_RS25305 52431..52835 - 405 WP_000086965 IncI1-type conjugal transfer protein TraR traR
V6E60_RS25310 52886..53413 - 528 WP_001055569 conjugal transfer protein TraQ traQ
V6E60_RS25315 53413..54117 - 705 WP_052974683 IncI1-type conjugal transfer protein TraP traP
V6E60_RS25320 54117..55406 - 1290 WP_001744085 conjugal transfer protein TraO traO
V6E60_RS25325 55409..56392 - 984 WP_001191879 IncI1-type conjugal transfer protein TraN traN
V6E60_RS25330 56403..57095 - 693 WP_000138549 DotI/IcmL family type IV secretion protein traM
V6E60_RS25335 57092..57439 - 348 WP_001055900 conjugal transfer protein traL
V6E60_RS25340 57457..61224 - 3768 WP_085453269 LPD7 domain-containing protein -
V6E60_RS25345 61314..61865 - 552 WP_000014584 phospholipase D family protein -
V6E60_RS25350 61880..62170 - 291 WP_001330823 hypothetical protein traK
V6E60_RS25355 62167..63315 - 1149 WP_001024975 plasmid transfer ATPase TraJ virB11
V6E60_RS25360 63312..64130 - 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
V6E60_RS25365 64127..64585 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
V6E60_RS25370 64980..65564 - 585 WP_000977522 histidine phosphatase family protein -
V6E60_RS25375 65624..66826 - 1203 WP_000976351 conjugal transfer protein TraF -
V6E60_RS25380 66911..67735 - 825 WP_001238939 conjugal transfer protein TraE traE
V6E60_RS25385 67886..69040 - 1155 WP_001139955 site-specific integrase -
V6E60_RS25390 70561..70809 + 249 WP_001349157 hypothetical protein -
V6E60_RS25395 70806..72098 - 1293 WP_001619585 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
V6E60_RS25400 72098..72754 - 657 WP_001193549 A24 family peptidase -
V6E60_RS25405 72739..73299 - 561 WP_000014005 lytic transglycosylase domain-containing protein virB1
V6E60_RS25410 73309..73923 - 615 WP_000908226 type 4 pilus major pilin -
V6E60_RS25415 73940..75025 - 1086 WP_001208802 type II secretion system F family protein -
V6E60_RS25420 75038..76591 - 1554 WP_000362206 ATPase, T2SS/T4P/T4SS family virB11
V6E60_RS25425 76602..77054 - 453 WP_001247337 type IV pilus biogenesis protein PilP -
V6E60_RS25430 77041..78336 - 1296 WP_000752780 type 4b pilus protein PilO2 -
V6E60_RS25435 78329..80011 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
V6E60_RS25440 80025..80462 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
V6E60_RS25445 80462..81529 - 1068 WP_042012078 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   2003 GenBank   NZ_JAWLTU010000003
Plasmid name   EC-28|unnamed2 Incompatibility group   IncI1
Plasmid size   86354 bp Coordinate of oriT [Strand]   32829..32917 [-]
Host baterium   Escherichia coli strain EC-28

Cargo genes

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