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PFK2 200-500

ID: 1515201454 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 301 (286)
Sequences: 4219 (1962.8)
Seq/Len: 14.752
Nf(neff/√len): 116.1

HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 14.752).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
29_R50_E4.2041.00
203_G211_I4.0211.00
88_L93_V4.0171.00
98_V104_S3.3311.00
34_M49_K3.2721.00
162_Y290_V3.1291.00
32_V67_I3.0621.00
86_Q90_E3.0311.00
43_G90_E2.8081.00
23_A30_A2.7791.00
199_A245_V2.7561.00
52_H55_D2.7311.00
168_I198_L2.5731.00
172_I245_V2.5311.00
43_G91_A2.4931.00
32_V51_F2.4761.00
38_E42_R2.3421.00
87_H90_E2.3391.00
166_D290_V2.2901.00
165_L198_L2.2831.00
265_K269_D2.2821.00
162_Y166_D2.2801.00
43_G87_H2.2541.00
15_N144_T2.2411.00
190_V245_V2.2311.00
19_I97_I2.1931.00
49_K55_D2.0721.00
109_D113_S2.0711.00
77_K80_G2.0661.00
33_V40_L2.0441.00
266_V269_D1.9951.00
31_F50_E1.9841.00
161_A201_L1.9241.00
35_E183_S1.9151.00
168_I202_A1.8891.00
210_Y227_M1.8491.00
1_A33_V1.8491.00
35_E68_G1.8411.00
37_Y107_G1.8251.00
105_L143_G1.7581.00
175_V188_V1.7531.00
170_K174_Y1.7471.00
73_M76_K1.7301.00
171_A283_V1.7081.00
86_Q89_I1.6921.00
228_C267_L1.6621.00
172_I206_T1.6491.00
81_R114_E1.6161.00
59_W66_N1.5621.00
17_R298_T1.5481.00
187_V263_V1.5461.00
83_L86_Q1.5441.00
82_L86_Q1.5231.00
82_L115_W1.5181.00
98_V108_A1.4811.00
15_N159_I1.4801.00
103_G107_G1.4631.00
20_V56_V1.4611.00
19_I301_G1.4351.00
85_A115_W1.4311.00
252_A256_T1.4151.00
24_I53_W1.4141.00
172_I188_V1.4111.00
164_A198_L1.4040.99
31_F93_V1.3880.99
173_D294_R1.3840.99
196_G215_E1.3820.99
219_T253_A1.3780.99
187_V244_V1.3760.99
261_S265_K1.3680.99
200_L213_I1.3580.99
229_D232_S1.3480.99
31_F91_A1.3390.99
190_V199_A1.3340.99
159_I297_A1.3280.99
88_L96_L1.3260.99
224_Q266_V1.3140.99
73_M103_G1.3100.99
108_A141_I1.3090.99
232_S236_S1.3050.99
38_E72_C1.2930.99
23_A28_C1.2790.99
167_R170_K1.2730.99
78_R82_L1.2710.99
264_H277_I1.2610.99
172_I202_A1.2580.99
179_A186_F1.2570.99
18_A301_G1.2450.98
209_D239_K1.2220.98
165_L168_I1.2180.98
278_T281_G1.2180.98
22_S25_F1.2160.98
268_V274_D1.2020.98
65_T181_S1.1930.98
72_C80_G1.1910.98
99_C146_G1.1890.98
157_A296_L1.1810.98
20_V24_I1.1790.98
262_D266_V1.1790.98
233_K236_S1.1700.97
231_V242_T1.1670.97
167_R174_Y1.1620.97
88_L139_L1.1550.97
149_D193_R1.1300.97
292_Y296_L1.1290.97
196_G214_P1.1090.96
110_L113_S1.1080.96
41_V87_H1.1080.96
291_A295_I1.1070.96
12_M146_G1.0970.96
185_A267_L1.0890.96
264_H275_T1.0860.96
85_A139_L1.0810.95
172_I243_I1.0770.95
41_V72_C1.0740.95
85_A89_I1.0730.95
85_A111_F1.0700.95
16_V99_C1.0660.95
278_T283_V1.0500.94
175_V186_F1.0410.94
112_R141_I1.0370.94
161_A197_W1.0360.94
131_E135_R1.0320.94
88_L140_N1.0300.94
246_V263_V1.0220.93
262_D265_K1.0210.93
229_D233_K1.0210.93
148_I198_L1.0190.93
203_G208_A1.0190.93
31_F48_I1.0130.93
106_T110_L1.0110.93
1_A93_V1.0100.93
110_L114_E1.0070.93
252_A258_I1.0050.93
3_M33_V1.0050.93
68_G240_R1.0000.92
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (06Aug15)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
3o8oB41100-0.015Contact Map
3opyB40.9701100-0.014Contact Map
4xz2A40100-0.008Contact Map
3o8oA40.9934100-0.004Contact Map
3opyA40.96681000Contact Map
4i7eA40.87711000.06Contact Map
1zxxA10.87711000.06Contact Map
1pfkA20.87711000.062Contact Map
3hnoA40.90031000.098Contact Map
2higA20.91031000.099Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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