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PR01229

Identifier
GFLUORESCENT  [View Relations]  [View Alignment]  
Accession
PR01229
No. of Motifs
11
Creation Date
01-NOV-1999
Title
Green fluorescent protein signature
Database References

PFAM; PF01353 GFP
INTERPRO; IPR000786
PDB; 1GFL
SCOP; 1GFL
CATH; 1GFL
Literature References
1. CODY, C.W., PRASHER, D.C., WESTLER, W.M., PRENDERGAST, F.G. AND WARD, W.W.
Chemical structure of the hexapeptide chromophore of the Aequorea green-
fluorescent protein.
BIOCHEMISTRY 32 1212-1218 (1993).
 
2. YANG, F., MOSS, L.G. AND PHILLIPS, G.N. JR.
The molecular structure of green fluorescent protein.
NAT.BIOTECH. 14 1246-1251 (1996). 
 
3. ORMO, M., CUBITT, A.B., KALLIO, K., GROSS, L.A., TSIEN, R.Y.
AND REMINGTON, S.J.
Crystal structure of the Aequorea victoria green fluorescent protein.
SCIENCE 273 1392-1395 (1996). 

Documentation
Green-fluorescent proteins (GFP) are involved in bioluminescence of many
jelly fish (cnidaria) [1]. GFPs serve as energy-transfer acceptors, receiving
energy from either a luciferase-oxyluciferin complex or a Ca(2+)-activated
photoprotein depending on the organism [1]. Following mechanical stimulation
of the organism, GFP emits green light spectrally identical to its 
fluorescence emission. The unique properties of these highly fluorescent
proteins arise from the chemical nature of the covalently attached 
chromophore, which contains modified amino acid residues within the 
polypeptide [1]. 
 
The crystal structure of recombinant wild-type GFP has been solved to 1.9A
resolution [2]. The protein fold forms a cylinder, comprising an 11-stranded
beta-barrel, with a co-axial helix within the cylinder and short helical
segments at the cylinder ends [2] - this represents a new protein fold, 
which has been termed the `beta-can' [2]. In the crystal, two protomers
pack together to form a dimer. The fluorophores, resulting from spontaneous
cyclisation and oxidation of the sequence -Ser65/Thr65-Tyr66-Gly67-, require
the native protein fold for both formation and fluorescence emission [3].
 
GFLUORESCENT is an 11-element fingerprint that provides a signature for
green fluorescent proteins. The fingerprint was derived from an initial
alignment of 5 sequences: the motifs were drawn from conserved regions
spanning the full alignment length - motif 1 spans alpha-helix 1 and beta-
strand 1; motif 2 spans strands 2 and 3; motif 3 includes helices 2 and 3; 
motif 4 encompasses helices 4-6; motif 5 includes strand 4; motif 6 spans
the C-terminal portion of strand 5 and strand 6; motif 8 spans strands 7 and
8 and helix 7 between them; and motifs 9-11 encode strands 9-11 respectively.
A single iteration on SPTR37_10f was required to reach convergence, no
further sequences being identified beyond the starting set.
Summary Information
5 codes involving 11 elements
0 codes involving 10 elements
0 codes involving 9 elements
0 codes involving 8 elements
0 codes involving 7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
1155555555555
1000000000000
900000000000
800000000000
700000000000
600000000000
500000000000
400000000000
300000000000
200000000000
1234567891011
True Positives
GFP_AEQVI     O09206        Q17104        Q27903        
Q93125
Sequence Titles
GFP_AEQVI   GREEN FLUORESCENT PROTEIN - AEQUOREA VICTORIA (JELLYFISH). 
O09206 GREEN FLUORESCENT PROTEIN, S65T VARIANT - UNIDENTIFIED.
Q17104 GREEN-FLUORESCENT PROTEIN - AEQUOREA VICTORIA (JELLYFISH).
Q27903 GREEN FLUORESCENT PROTEIN - AEQUOREA VICTORIA (JELLYFISH).
Q93125 GREEN FLUORESCENT PROTEIN MUTANT 3 - AEQUOREA VICTORIA (JELLYFISH).
Scan History
SPTR37_10f 1  20   NSINGLE    
Initial Motifs
Motif 1  width=25
Element Seqn Id St Int Rpt
KGEELFTGVVPILVELDGDVNGHKF GFP_AEQVI 3 3 -
KGEELFTGVVPILVELDGDVNGQKF Q17104 3 3 -
KGEELFTGVVPILVELDGDVNGHKF Q27903 3 3 -
KGEELFTGVVPILVELDGDVNGHKF O09206 4 4 -
KGEELFTGVVPILVELDGDVNGHKF Q93125 3 3 -

Motif 2 width=21
Element Seqn Id St Int Rpt
SVSGEGEGDATYGKLTLKFIC GFP_AEQVI 28 0 -
SVSGEGEGDATYGKLTLKFIC Q17104 28 0 -
SVSGEGEGDATYGKLTLKFIC Q27903 28 0 -
SVSGEGEGDATYGKLTLKFIC O09206 29 0 -
SVSGEGEGDATYGKLTLKFIC Q93125 28 0 -

Motif 3 width=21
Element Seqn Id St Int Rpt
TTGKLPVPWPTLVTTFSYGVQ GFP_AEQVI 49 0 -
TTGKLPVPWPTLVTTFSYGVQ Q17104 49 0 -
TTGKLPVPWPTLVTTFSYGVQ Q27903 49 0 -
TTGKLPVPWPTLVTTFTYGVQ O09206 50 0 -
TTGKLPVPWPTLVTTFGYGVQ Q93125 49 0 -

Motif 4 width=16
Element Seqn Id St Int Rpt
CFSRYPDHMKQHDFFK GFP_AEQVI 70 0 -
CFSRYPDHMKQHDFFK Q17104 70 0 -
CFSRYPDHMKRHDFFK Q27903 70 0 -
CFSRYPDHMKQHDFFK O09206 71 0 -
CFARYPDHMKQHDFFK Q93125 70 0 -

Motif 5 width=23
Element Seqn Id St Int Rpt
SAMPEGYVQERTIFFKDDGNYKT GFP_AEQVI 86 0 -
SAMPEGYVQERTIFYKDDGNYKT Q17104 86 0 -
SAMPEGYVQERTIFFKDDGNYKT Q27903 86 0 -
SAMPEGYVQERTIFFKDDGNYKT O09206 87 0 -
SAMPEGYVQERTIFFKDDGNYKT Q93125 86 0 -

Motif 6 width=21
Element Seqn Id St Int Rpt
RAEVKFEGDTLVNRIELKGID GFP_AEQVI 109 0 -
RAEVKFEGDTLVNRIELKGID Q17104 109 0 -
RAEVKFEGDTLVNRIELKGID Q27903 109 0 -
RAEVKFEGDTLVNRIELKGID O09206 110 0 -
RAEVKFEGDTLVNRIELKGID Q93125 109 0 -

Motif 7 width=20
Element Seqn Id St Int Rpt
FKEDGNILGHKLEYNYNSHN GFP_AEQVI 130 0 -
FKEDGNILGHKMEYNYNSHN Q17104 130 0 -
FKEDGNILGHKLEYNYNSHN Q27903 130 0 -
FKEDGNILGHKLEYNYNSHN O09206 131 0 -
FKEDGNILGHKLEYNYNSHN Q93125 130 0 -

Motif 8 width=22
Element Seqn Id St Int Rpt
VYIMADKQKNGIKVNFKIRHNI GFP_AEQVI 150 0 -
VYIMADKPKNGIKVNFKIRHNI Q17104 150 0 -
VYIMADKQKNGIKVNFKIRHNI Q27903 150 0 -
VYIMADKQKNGIKVNFKIRHNI O09206 151 0 -
VYIMADKQKNGIKVNFKIRHNI Q93125 150 0 -

Motif 9 width=20
Element Seqn Id St Int Rpt
DGSVQLADHYQQNTPIGDGP GFP_AEQVI 173 1 -
DGSVQLADHYQQNTPIGDGP Q17104 173 1 -
DGSVQLADHYQQNTPIGDGP Q27903 173 1 -
DGSVQLADHYQQNTPIGDGP O09206 174 1 -
DGSVQLADHYQQNTPIGDGP Q93125 173 1 -

Motif 10 width=19
Element Seqn Id St Int Rpt
VLLPDNHYLSTQSALSKDP GFP_AEQVI 193 0 -
VLLPDNHYLSTQSALSKDP Q17104 193 0 -
VLLPDNHYLSTQSALSKDP Q27903 193 0 -
VLLPDNHYLSTQSALSKDP O09206 194 0 -
VLLPDNHYLSTQSALSKDP Q93125 193 0 -

Motif 11 width=24
Element Seqn Id St Int Rpt
KRDHMVLLEFVTAAGITHGMDELY GFP_AEQVI 214 2 -
KRDHMILLEFVTAAGITHGMDELY Q17104 214 2 -
KRDHMVLLEFVTAAGITHGMDELY Q27903 214 2 -
KRDHMVLLEFVTAAGITLGMDELY O09206 215 2 -
KRDHMVLLEFVTAAGITHGMDELY Q93125 214 2 -
Final Motifs
Motif 1  width=25
Element Seqn Id St Int Rpt
KGEELFTGVVPILVELDGDVNGHKF GFP_AEQVI 3 3 -
KGEELFTGVVPILVELDGDVNGQKF Q17104 3 3 -
KGEELFTGVVPILVELDGDVNGHKF Q27903 3 3 -
KGEELFTGVVPILVELDGDVNGHKF O09206 4 4 -
KGEELFTGVVPILVELDGDVNGHKF Q93125 3 3 -

Motif 2 width=21
Element Seqn Id St Int Rpt
SVSGEGEGDATYGKLTLKFIC GFP_AEQVI 28 0 -
SVSGEGEGDATYGKLTLKFIC Q17104 28 0 -
SVSGEGEGDATYGKLTLKFIC Q27903 28 0 -
SVSGEGEGDATYGKLTLKFIC O09206 29 0 -
SVSGEGEGDATYGKLTLKFIC Q93125 28 0 -

Motif 3 width=21
Element Seqn Id St Int Rpt
TTGKLPVPWPTLVTTFSYGVQ GFP_AEQVI 49 0 -
TTGKLPVPWPTLVTTFSYGVQ Q17104 49 0 -
TTGKLPVPWPTLVTTFSYGVQ Q27903 49 0 -
TTGKLPVPWPTLVTTFTYGVQ O09206 50 0 -
TTGKLPVPWPTLVTTFGYGVQ Q93125 49 0 -

Motif 4 width=16
Element Seqn Id St Int Rpt
CFSRYPDHMKQHDFFK GFP_AEQVI 70 0 -
CFSRYPDHMKQHDFFK Q17104 70 0 -
CFSRYPDHMKRHDFFK Q27903 70 0 -
CFSRYPDHMKQHDFFK O09206 71 0 -
CFARYPDHMKQHDFFK Q93125 70 0 -

Motif 5 width=23
Element Seqn Id St Int Rpt
SAMPEGYVQERTIFFKDDGNYKT GFP_AEQVI 86 0 -
SAMPEGYVQERTIFYKDDGNYKT Q17104 86 0 -
SAMPEGYVQERTIFFKDDGNYKT Q27903 86 0 -
SAMPEGYVQERTIFFKDDGNYKT O09206 87 0 -
SAMPEGYVQERTIFFKDDGNYKT Q93125 86 0 -

Motif 6 width=21
Element Seqn Id St Int Rpt
RAEVKFEGDTLVNRIELKGID GFP_AEQVI 109 0 -
RAEVKFEGDTLVNRIELKGID Q17104 109 0 -
RAEVKFEGDTLVNRIELKGID Q27903 109 0 -
RAEVKFEGDTLVNRIELKGID O09206 110 0 -
RAEVKFEGDTLVNRIELKGID Q93125 109 0 -

Motif 7 width=20
Element Seqn Id St Int Rpt
FKEDGNILGHKLEYNYNSHN GFP_AEQVI 130 0 -
FKEDGNILGHKMEYNYNSHN Q17104 130 0 -
FKEDGNILGHKLEYNYNSHN Q27903 130 0 -
FKEDGNILGHKLEYNYNSHN O09206 131 0 -
FKEDGNILGHKLEYNYNSHN Q93125 130 0 -

Motif 8 width=22
Element Seqn Id St Int Rpt
VYIMADKQKNGIKVNFKIRHNI GFP_AEQVI 150 0 -
VYIMADKPKNGIKVNFKIRHNI Q17104 150 0 -
VYIMADKQKNGIKVNFKIRHNI Q27903 150 0 -
VYIMADKQKNGIKVNFKIRHNI O09206 151 0 -
VYIMADKQKNGIKVNFKIRHNI Q93125 150 0 -

Motif 9 width=20
Element Seqn Id St Int Rpt
DGSVQLADHYQQNTPIGDGP GFP_AEQVI 173 1 -
DGSVQLADHYQQNTPIGDGP Q17104 173 1 -
DGSVQLADHYQQNTPIGDGP Q27903 173 1 -
DGSVQLADHYQQNTPIGDGP O09206 174 1 -
DGSVQLADHYQQNTPIGDGP Q93125 173 1 -

Motif 10 width=19
Element Seqn Id St Int Rpt
VLLPDNHYLSTQSALSKDP GFP_AEQVI 193 0 -
VLLPDNHYLSTQSALSKDP Q17104 193 0 -
VLLPDNHYLSTQSALSKDP Q27903 193 0 -
VLLPDNHYLSTQSALSKDP O09206 194 0 -
VLLPDNHYLSTQSALSKDP Q93125 193 0 -

Motif 11 width=24
Element Seqn Id St Int Rpt
KRDHMVLLEFVTAAGITHGMDELY GFP_AEQVI 214 2 -
KRDHMILLEFVTAAGITHGMDELY Q17104 214 2 -
KRDHMVLLEFVTAAGITHGMDELY Q27903 214 2 -
KRDHMVLLEFVTAAGITLGMDELY O09206 215 2 -
KRDHMVLLEFVTAAGITHGMDELY Q93125 214 2 -