Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100052
Name   oriT_pIFM3804 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_023329 (47883..47992 [-], 110 nt)
oriT length   110 nt
IRs (inverted repeats)      8..bp: 24..31, 35..42  (GTCGGGGC..GCCCTGAC)
  17..bp: 49..65, 72..88  (GCAATTGTAATAGCGTC..GACGGTATTACAATTGC)
Location of nic site      96..97
Conserved sequence flanking the
  nic site    		  CATCCTG|T
Note   similar to oriT of plasmid R64

  oriT sequence  


Download         Length: 110 nt

>oriT_pIFM3804
CCTGAAAAACGGGACAGGATGTGCAATTGTAATACCGTCACACGCGACGCTATTACAATTGCCATCTGGTCAGGGCTTCGCCCCGACACCCCGTAAGGAGCCTGAAGTGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Freire Martín I et al. (2014) Sequence analysis of a CTX-M-1 IncI1 plasmid found in Salmonella 4,5,12:i:-, Escherichia coli and Klebsiella pneumoniae on a UK pig farm. J Antimicrob Chemother. 69(8):2098-101. [PMID:24729584]


Relaxase

ID   50 GenBank   YP_008998777
Name   NikB_pIFM3804 insolico UniProt ID   E9LLN1
Length   899 a.a. PDB ID   
Note   Relaxase/Mobilisation nuclease

  Relaxase protein sequence


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

>YP_008998777.1 NikB (plasmid) [Escherichia coli]
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 E9LLN1

  Reference


[1] Freire Martín I et al. (2014) Sequence analysis of a CTX-M-1 IncI1 plasmid found in Salmonella 4,5,12:i:-, Escherichia coli and Klebsiella pneumoniae on a UK pig farm. J Antimicrob Chemother. 69(8):2098-101. [PMID:24729584]


Auxiliary protein

ID   81 GenBank   YP_008998776
Name   NikA_pIFM3804 insolico UniProt ID   C7SA35
Length   110 a.a. PDB ID   _
Note   _

  Auxiliary protein sequence


Download         Length: 110 a.a.        Molecular weight: 12613.57 Da        Isoelectric Point: 10.7463

>YP_008998776.1 NikA (plasmid) [Escherichia coli]
MSDSAVRKKSEVRQKTVVRTLRFSPVEDETIRKKAEDSGLTVSAYIRNAALNKRINSRTDDAFLKELMRL
GRMQKHLFVQGKRTGDKEYAEVLVAITELTNTLRKQLMEG

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB C7SA35


T4CP

ID   50 GenBank   YP_008998778
Name   TrbC_pIFM3804 insolico UniProt ID   E9LLN2
Length   763 a.a. PDB ID   _
Note   nucleotide-binding protein

  T4CP protein sequence


Download         Length: 763 a.a.        Molecular weight: 86941.11 Da        Isoelectric Point: 6.7713

>YP_008998778.1 TrbC (plasmid) [Escherichia coli]
MSEHRVNPELLHRTAWGNPVWNALQSLNIYGFCLVASLVASFIWPLALPACLLFTLITMLVFSLQRWRCP
LRMPMTLECADPSQDRMIKRSLFSFWPTLFQYEVILESPASGIFYVGYQRVRDIGRELWLSMDDLTRHIM
FFATTGGGKTETIFAWAINPLCWARGFTLVDGKAQNDTARTIWYLARRFGREDDVEVINFMNGGKSRSEI
ILSGEKTRPQSNTWNPFCYSTEAFTAETMQSMLPQNVQGGEWQSRAIAMNKALVFGTKFWCVREGKTMSL
QMLREHMTLEGMAKLYCRGLDDQWPEEAIAPLRNYLQDVPGFDLSLVRTPSAWTEEPRKQHAYLSGQFSE
TFSTFTEAFGDIFAEDSGDIDIRDSIHSDRILMVMIPALDTSAHTTSALGRMFITQKSMILARDLGYRLE
GTDSDALEVKKYKGRFPYLCFLDEVGAYYTDRIAVEATQVRSLDFALILMAQDQERIEGQTTATNTATLM
QNTGTKFAGRIVSEGSTARTLKSAAGEEARARMNNLQRQDGIFGESWIDSPQISILMESKINVQELIELH
PGEFFSIFRGETVPSASFFIPDDEKSCSSDPVVINRYISVDAPRLDRLRRLVPRTTQRRIPSPENVSAII
GVLTAKPSRKRRKIRTEPHTIVDTFQQRIAGRQAAMAMLEEYDTDINARESALWETAVNTLKTTTREERR
IRYITLNRPELPETKEENQISVRAERAGINLLTLPQDNNHPTGRPVNGFHHKKTNRPDWDGMY

  Protein domains



No domain identified.


  Protein structure


Source ID Structure
AlphaFold DB E9LLN2


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 53352..94327

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTE28_RS00320 (D616_p112062) 51068..53359 - 2292 WP_001289276 F-type conjugative transfer protein TrbC -
HTE28_RS00325 (D616_p112061) 53352..54422 - 1071 WP_000151582 IncI1-type conjugal transfer protein TrbB trbB
HTE28_RS00330 (D616_p112060) 54441..55649 - 1209 WP_000121273 IncI1-type conjugal transfer protein TrbA trbA
HTE28_RS00335 (D616_p112058) 55941..56093 + 153 WP_001331364 Hok/Gef family protein -
HTE28_RS00340 (D616_p112057) 56165..56416 - 252 WP_001291964 hypothetical protein -
HTE28_RS00620 56914..57009 + 96 WP_001303310 DinQ-like type I toxin DqlB -
HTE28_RS00345 (D616_p112055) 57074..57250 - 177 WP_001054904 hypothetical protein -
HTE28_RS00350 (D616_p112053) 57641..57850 + 210 WP_000062603 HEAT repeat domain-containing protein -
HTE28_RS00355 (D616_p112052) 57922..58404 - 483 WP_001672078 plasmid IncI1-type surface exclusion protein ExcA -
HTE28_RS00360 (D616_p112051) 58645..60813 - 2169 WP_021265679 DotA/TraY family protein traY
HTE28_RS00365 (D616_p112050) 60910..61494 - 585 WP_001037987 IncI1-type conjugal transfer protein TraX -
HTE28_RS00370 (D616_p112049) 61523..62725 - 1203 WP_001189160 IncI1-type conjugal transfer protein TraW traW
HTE28_RS00375 (D616_p112048) 62692..63306 - 615 WP_000337398 IncI1-type conjugal transfer protein TraV traV
HTE28_RS00380 (D616_p112047) 63306..66350 - 3045 WP_021265678 IncI1-type conjugal transfer protein TraU traU
HTE28_RS00385 (D616_p112046) 66440..67240 - 801 WP_001164788 IncI1-type conjugal transfer protein TraT traT
HTE28_RS00390 (D616_p112045) 67224..67412 - 189 WP_001277255 putative conjugal transfer protein TraS -
HTE28_RS00395 (D616_p112044) 67476..67880 - 405 WP_000086958 IncI1-type conjugal transfer protein TraR traR
HTE28_RS00400 (D616_p112043) 67931..68458 - 528 WP_001055569 conjugal transfer protein TraQ traQ
HTE28_RS00405 (D616_p112042) 68458..69162 - 705 WP_000801920 IncI1-type conjugal transfer protein TraP traP
HTE28_RS00410 (D616_p112041) 69162..70451 - 1290 WP_001272003 conjugal transfer protein TraO traO
HTE28_RS00415 (D616_p112040) 70454..71437 - 984 WP_001191877 IncI1-type conjugal transfer protein TraN traN
HTE28_RS00420 (D616_p112039) 71448..72140 - 693 WP_000138550 DotI/IcmL family type IV secretion protein traM
HTE28_RS00425 (D616_p112038) 72137..72484 - 348 WP_001055900 conjugal transfer protein traL
HTE28_RS00430 (D616_p112037) 72502..76269 - 3768 WP_001141527 LPD7 domain-containing protein -
HTE28_RS00435 (D616_p112036) 76358..76909 - 552 WP_000014583 phospholipase D family protein -
HTE28_RS00440 (D616_p112035) 76924..77214 - 291 WP_001299214 hypothetical protein traK
HTE28_RS00445 (D616_p112034) 77211..78359 - 1149 WP_001024972 plasmid transfer ATPase TraJ virB11
HTE28_RS00450 (D616_p112033) 78356..79174 - 819 WP_000646098 IncI1-type conjugal transfer lipoprotein TraI traI
HTE28_RS00455 (D616_p112032) 79171..79629 - 459 WP_001079808 IncI1-type conjugal transfer lipoprotein TraH -
HTE28_RS00460 (D616_p112030) 80024..80608 - 585 WP_000977522 histidine phosphatase family protein -
HTE28_RS00465 (D616_p112029) 80668..81870 - 1203 WP_000976351 conjugal transfer protein TraF -
HTE28_RS00470 (D616_p112028) 81955..82779 - 825 WP_001238939 conjugal transfer protein TraE traE
HTE28_RS00475 (D616_p112027) 82930..84084 - 1155 WP_001139957 site-specific integrase -
HTE28_RS00610 84068..84367 + 300 WP_223873359 pilus assembly protein PilV -
HTE28_RS00485 (D616_p112023) 84878..86140 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
HTE28_RS00490 (D616_p112021) 86428..87303 + 876 WP_013188473 extended-spectrum class A beta-lactamase CTX-M-1 -
HTE28_RS00495 87350..87694 - 345 Protein_97 WbuC family cupin fold metalloprotein -
HTE28_RS00615 87694..87903 + 210 Protein_98 hypothetical protein -
HTE28_RS00505 (D616_p112017) 88397..89821 - 1425 WP_001389385 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HTE28_RS00510 89821..90477 - 657 WP_001193553 prepilin peptidase -
HTE28_RS00515 90462..91022 - 561 WP_000014116 lytic transglycosylase domain-containing protein virB1
HTE28_RS00520 (D616_p112016) 91032..91646 - 615 WP_000959785 type 4 pilus major pilin -
HTE28_RS00525 (D616_p112015) 91664..92761 - 1098 WP_001208805 type II secretion system F family protein -
HTE28_RS00530 (D616_p112014) 92774..94327 - 1554 WP_000362202 ATPase, T2SS/T4P/T4SS family virB11
HTE28_RS00535 (D616_p112013) 94338..94790 - 453 WP_001247334 type IV pilus biogenesis protein PilP -
HTE28_RS00540 (D616_p112012) 94777..96072 - 1296 WP_000752772 type 4b pilus protein PilO2 -
HTE28_RS00545 (D616_p112011) 96065..97747 - 1683 WP_000748143 PilN family type IVB pilus formation outer membrane protein -
HTE28_RS00550 (D616_p112010) 97761..98198 - 438 WP_000539807 type IV pilus biogenesis protein PilM -
HTE28_RS00555 (D616_p112009) 98198..99265 - 1068 WP_001302629 type IV pilus biogenesis lipoprotein PilL -

Host bacterium

ID   50 GenBank   NC_023329
Plasmid name   pIFM3804 Incompatibility group   IncI1
Plasmid size   104399 bp Coordinate of oriT [Strand]   47883..47992 [-]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   sul2, floR, blaCTX-M-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -