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Plasmid Files

ΦX174

Complete annotated DNA sequence of bacteriophage phiX174.

 
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phiX174.dna
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BssHII (5348) DraIII (5188) DrdI (5177) BaeGI - Bme1580I (4783) ApaLI (4779) BsiEI (4604) StuI (4488) MfeI (3939) BspQI - SapI (3752) SexAI * (3499) AleI (2916) SacII (2862) AatII (2786) PstI (0) FspI (157) AvaI - BsoBI - PaeR7I - XhoI (162) BmeT110I (163) BsrBI (532) SspI (1009) PshAI (1698) AhdI (1765) Bts α I (2210) PsiI (2306) ZraI (2784) Φ X174 5386 bp
BssHII  (5348)
1 site
G C G C G C C G C G C G

BssHII is typically used at 50°C, but is 75% active at 37°C.
DraIII  (5188)
1 site
C A C N N N G T G G T G N N N C A C

Sticky ends from different DraIII sites may not be compatible.
DrdI  (5177)
1 site
G A C N N N N N N G T C C T G N N N N N N C A G

Sticky ends from different DrdI sites may not be compatible.
BaeGI  (4783)
1 site
G K G C M C C M C G K G

Sticky ends from different BaeGI sites may not be compatible.
Bme1580I  (4783)
1 site
G K G C M C C M C G K G

Sticky ends from different Bme1580I sites may not be compatible.
ApaLI  (4779)
1 site
G T G C A C C A C G T G
BsiEI  (4604)
1 site
C G R Y C G G C Y R G C

Sticky ends from different BsiEI sites may not be compatible.
StuI  (4488)
1 site
A G G C C T T C C G G A
MfeI  (3939)
1 site
C A A T T G G T T A A C
BspQI  (3752)
1 site
G C T C T T C N C G A G A A G N N N N

Sticky ends from different BspQI sites may not be compatible.
SapI  (3752)
1 site
G C T C T T C N C G A G A A G N N N N

Sticky ends from different SapI sites may not be compatible.
SapI gradually settles in solution, so a tube of SapI should be mixed before removing an aliquot.
SexAI  (3499)
1 site
A C C W G G T T G G W C C A
* Blocked by Dcm methylation.
Sticky ends from different SexAI sites may not be compatible.
AleI  (2916)
1 site
C A C N N N N G T G G T G N N N N C A C
SacII  (2862)
1 site
C C G C G G G G C G C C

Efficient cleavage requires at least two copies of the SacII recognition sequence.
AatII  (2786)
1 site
G A C G T C C T G C A G
PstI  (0)
1 site
C T G C A G G A C G T C
FspI  (157)
1 site
T G C G C A A C G C G T
AvaI  (162)
1 site
C Y C G R G G R G C Y C

Sticky ends from different AvaI sites may not be compatible.
BsoBI  (162)
1 site
C Y C G R G G R G C Y C

Sticky ends from different BsoBI sites may not be compatible.
BsoBI is typically used at 37°C, but can be used at temperatures up to 65°C.
PaeR7I  (162)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
XhoI  (162)
1 site
C T C G A G G A G C T C
BmeT110I  (163)
1 site
C Y C G R G G R G C Y C
BsrBI  (532)
1 site
C C G C T C G G C G A G

This recognition sequence is asymmetric, so ligating blunt ends generated by BsrBI will not always regenerate a BsrBI site.
BsrBI is typically used at 37°C, but can be used at temperatures up to 50°C.
SspI  (1009)
1 site
A A T A T T T T A T A A
PshAI  (1698)
1 site
G A C N N N N G T C C T G N N N N C A G

PshAI quickly loses activity at 37°C, but can be used at 25°C for long incubations.
AhdI  (1765)
1 site
G A C N N N N N G T C C T G N N N N N C A G

The 1-base overhangs produced by AhdI may be hard to ligate.
Sticky ends from different AhdI sites may not be compatible.
BtsαI  (2210)
1 site
G C A G T G N N C G T C A C

Sticky ends from different BtsαI sites may not be compatible.
PsiI  (2306)
1 site
T T A T A A A A T A T T
ZraI  (2784)
1 site
G A C G T C C T G C A G
F
358 .. 3975  =  3618 bp
F
358 .. 3975  =  3618 bp
A
3981 .. 5386  =  1406 bp
468 amino acids  =  53.8 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: DNA replication initiation protein gpA
Function: viral strand synthesis
rf replication
A
3981 .. 5386  =  1406 bp
468 amino acids  =  53.8 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: DNA replication initiation protein gpA
Function: viral strand synthesis
rf replication
K
51 .. 221  =  171 bp
56 amino acids  =  6.4 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: protein K
Non-essential protein.  In the absence of protein K burst size is reduced 3 to 6-fold.
K
51 .. 221  =  171 bp
56 amino acids  =  6.4 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: protein K
Non-essential protein.  In the absence of protein K burst size is reduced 3 to 6-fold.
F
1001 .. 2284  =  1284 bp
427 amino acids  =  48.5 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: capsid protein
60 copies of protein F form the icosahedral capsid of Microviruses. other names: protein F, gpF; function: phage structural protein
F
1001 .. 2284  =  1284 bp
427 amino acids  =  48.5 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: capsid protein
60 copies of protein F form the icosahedral capsid of Microviruses. other names: protein F, gpF; function: phage structural protein
H
2931 .. 3917  =  987 bp
328 amino acids  =  34.4 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: minor spike protein
Function: adsorption
One molecule of protein H is located at each of the 12 vertices with 5-fold symmetry.  Binds to LPS and is involved in particle adsorption to host cells.  Several protein H molecules enter the host cytoplasm with the phage genome. other names: protein H, gpH, DNA pilot protein; function: phage minor structural protein, adsorption, DNA injection
H
2931 .. 3917  =  987 bp
328 amino acids  =  34.4 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: minor spike protein
Function: adsorption
One molecule of protein H is located at each of the 12 vertices with 5-fold symmetry.  Binds to LPS and is involved in particle adsorption to host cells.  Several protein H molecules enter the host cytoplasm with the phage genome. other names: protein H, gpH, DNA pilot protein; function: phage minor structural protein, adsorption, DNA injection
A
4497 .. 5386  =  890 bp
296 amino acids  =  33.9 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: protein A*
Function: shut off host DNA synthesis
Synthesized from the larger A gene by internal translation initiation in the same frame as protein A. May be involved in host DNA replication shut off.
A
4497 .. 5386  =  890 bp
296 amino acids  =  33.9 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: protein A*
Function: shut off host DNA synthesis
Synthesized from the larger A gene by internal translation initiation in the same frame as protein A. May be involved in host DNA replication shut off.
D
358 .. 991  =  634 bp
D
358 .. 991  =  634 bp
G
2395 .. 2922  =  528 bp
175 amino acids  =  19.0 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: major spike protein
A total of 60 copies of protein G are present at the 12 vertices with 5-fold symmetry of Microvirus capsids. other names: protein G, gpG; function: phage minor structural protein
G
2395 .. 2922  =  528 bp
175 amino acids  =  19.0 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: major spike protein
A total of 60 copies of protein G are present at the 12 vertices with 5-fold symmetry of Microvirus capsids. other names: protein G, gpG; function: phage minor structural protein
A
1 .. 136  =  136 bp
44 amino acids  =  4.8 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: DNA replication initiation protein gpA
Function: viral strand synthesis
rf replication
A
1 .. 136  =  136 bp
44 amino acids  =  4.8 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: DNA replication initiation protein gpA
Function: viral strand synthesis
rf replication
origin of viral strand synthesis
4306 .. 4306  =  1 bp
origin of viral strand synthesis
origin of viral strand synthesis
4306 .. 4306  =  1 bp
origin of viral strand synthesis
D
390 .. 848  =  459 bp
152 amino acids  =  16.9 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: external scaffolding protein
Function: capsid morphogenesis
240 molecules of protein D form an external scaffold required for the formation of Microvirus procapsid. Not present in mature particles. other names: protein D, gpD; function: morphogenesis
D
390 .. 848  =  459 bp
152 amino acids  =  16.9 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: external scaffolding protein
Function: capsid morphogenesis
240 molecules of protein D form an external scaffold required for the formation of Microvirus procapsid. Not present in mature particles. other names: protein D, gpD; function: morphogenesis
B
5075 .. 5386  =  312 bp
104 amino acids  =  11.8 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: internal scaffolding protein
Function: capsid morphogenesis
Protein B is required for the assembly of the basic building block of the Microvirus capsid and is incorporated into the procapsid.  Protein B is displaced by the protein J/ssDNA complex during assembly and is therefore not part of the mature virion. Other names: protein B, gpB. Function: morphogenesis.
B
5075 .. 5386  =  312 bp
104 amino acids  =  11.8 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: internal scaffolding protein
Function: capsid morphogenesis
Protein B is required for the assembly of the basic building block of the Microvirus capsid and is incorporated into the procapsid.  Protein B is displaced by the protein J/ssDNA complex during assembly and is therefore not part of the mature virion. Other names: protein B, gpB. Function: morphogenesis.
A
1 .. 136  =  136 bp
44 amino acids  =  4.8 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: protein A*
Function: shut off host DNA synthesis
Synthesized from the larger A gene by internal translation initiation in the same frame as protein A. May be involved in host DNA replication shut off.
A
1 .. 136  =  136 bp
44 amino acids  =  4.8 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: protein A*
Function: shut off host DNA synthesis
Synthesized from the larger A gene by internal translation initiation in the same frame as protein A. May be involved in host DNA replication shut off.
E
568 .. 843  =  276 bp
91 amino acids  =  10.6 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: cell lysis protein
Function: cell lysis
Microvirus cell lysis protein is a membrane protein that inhibits MraY, an enzyme required for murein synthesis, and promotes cell lysis in a manner analogous to cell wall synthesis inhibitors like penicillin.  A host factor (slyD) is required for stability of protein E. other names: protein E, gpE; function: phage release by lysis
E
568 .. 843  =  276 bp
91 amino acids  =  10.6 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: cell lysis protein
Function: cell lysis
Microvirus cell lysis protein is a membrane protein that inhibits MraY, an enzyme required for murein synthesis, and promotes cell lysis in a manner analogous to cell wall synthesis inhibitors like penicillin.  A host factor (slyD) is required for stability of protein E. other names: protein E, gpE; function: phage release by lysis
phiX174p05
133 .. 393  =  261 bp
86 amino acids  =  10.1 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: C
DNA maturation
phiX174p05
133 .. 393  =  261 bp
86 amino acids  =  10.1 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: C
DNA maturation
J
848 .. 964  =  117 bp
38 amino acids  =  4.2 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: DNA packaging protein
core protein; Protein J binds to ssDNA Microvirus genomes and is packaged with the DNA into procapsids. During packaging it displaces the internal scaffold protein. other names: core protein, protein J; function: DNA packaging, DNA binding
J
848 .. 964  =  117 bp
38 amino acids  =  4.2 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: DNA packaging protein
core protein; Protein J binds to ssDNA Microvirus genomes and is packaged with the DNA into procapsids. During packaging it displaces the internal scaffold protein. other names: core protein, protein J; function: DNA packaging, DNA binding
B
1 .. 51  =  51 bp
16 amino acids  =  2.0 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: internal scaffolding protein
Function: capsid morphogenesis
Protein B is required for the assembly of the basic building block of the Microvirus capsid and is incorporated into the procapsid.  Protein B is displaced by the protein J/ssDNA complex during assembly and is therefore not part of the mature virion. Other names: protein B, gpB. Function: morphogenesis.
B
1 .. 51  =  51 bp
16 amino acids  =  2.0 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: internal scaffolding protein
Function: capsid morphogenesis
Protein B is required for the assembly of the basic building block of the Microvirus capsid and is incorporated into the procapsid.  Protein B is displaced by the protein J/ssDNA complex during assembly and is therefore not part of the mature virion. Other names: protein B, gpB. Function: morphogenesis.
ORF:  133 .. 393  =  261 bp
ORF:  86 amino acids  =  10.1 kDa
ORF:  568 .. 843  =  276 bp
ORF:  91 amino acids  =  10.6 kDa
ORF:  2395 .. 2922  =  528 bp
ORF:  175 amino acids  =  19.0 kDa
ORF:  3076 .. 3684  =  609 bp
ORF:  202 amino acids  =  24.0 kDa
ORF:  3946 .. 4263  =  318 bp
ORF:  105 amino acids  =  12.1 kDa
ORF:  4621 .. 4857  =  237 bp
ORF:  78 amino acids  =  8.6 kDa
ORF:  1001 .. 2284  =  1284 bp
ORF:  427 amino acids  =  48.5 kDa
ORF:  5075 .. 51  =  363 bp
ORF:  120 amino acids  =  13.8 kDa
ORF:  390 .. 848  =  459 bp
ORF:  152 amino acids  =  16.9 kDa
ORF:  1998 .. 2234  =  237 bp
ORF:  78 amino acids  =  9.0 kDa
ORF:  2931 .. 3917  =  987 bp
ORF:  328 amino acids  =  34.4 kDa
ORF:  3954 .. 136  =  1569 bp
ORF:  522 amino acids  =  59.7 kDa
ORF:  818 .. 1051  =  234 bp
ORF:  77 amino acids  =  8.7 kDa
ORF:  1094 .. 1651  =  558 bp
ORF:  185 amino acids  =  21.0 kDa
ORF:  1772 .. 2167  =  396 bp
ORF:  131 amino acids  =  15.7 kDa
ORF:  2518 .. 2742  =  225 bp
ORF:  74 amino acids  =  8.4 kDa
ORF:  3921 .. 4211  =  291 bp
ORF:  96 amino acids  =  11.2 kDa
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