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mTRPM8

ID: 1513653160 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 245 (233)
Sequences: 1758 (1125.2)
Seq/Len: 7.545
Nf(neff/√len): 73.7

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: 7.545).

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
50_E61_Y3.6451.00
50_E53_Q2.9101.00
241_N244_V2.5731.00
53_Q67_N2.3961.00
67_N70_D2.3241.00
61_Y67_N2.2901.00
134_D138_F1.9701.00
50_E67_N1.9471.00
177_L180_F1.9401.00
241_N245_A1.8481.00
21_A108_T1.7711.00
237_I241_N1.7511.00
82_V86_H1.7431.00
70_D110_R1.6821.00
66_W70_D1.6681.00
16_F43_V1.6651.00
48_C75_F1.6561.00
38_I42_L1.6251.00
81_I85_L1.6061.00
149_F153_R1.5761.00
240_V245_A1.5711.00
42_L45_V1.5631.00
72_L106_I1.5611.00
75_F81_I1.5571.00
13_Y17_L1.5561.00
237_I243_L1.5491.00
126_I129_Q1.5491.00
75_F79_A1.5401.00
53_Q70_D1.5291.00
2_P5_V1.5241.00
228_V238_L1.5201.00
12_F16_F1.5090.99
178_A182_Q1.4600.99
184_P187_V1.4500.99
237_I240_V1.4340.99
37_L40_Y1.4280.99
176_Y180_F1.4250.99
107_F110_R1.4170.99
149_F178_A1.4130.99
36_E84_R1.3870.99
75_F92_S1.3670.99
231_Y240_V1.3440.99
79_A133_I1.3390.98
112_I122_G1.3190.98
40_Y81_I1.3160.98
178_A231_Y1.3120.98
80_G100_F1.3000.98
18_L22_Y1.2900.98
237_I244_V1.2850.98
180_F183_V1.2640.98
103_D107_F1.2610.97
177_L182_Q1.2130.97
66_W110_R1.2050.96
5_V9_N1.2030.96
19_L35_P1.1910.96
96_G100_F1.1770.96
227_L243_L1.1670.96
166_W171_V1.1670.96
152_A238_L1.1570.95
69_M106_I1.1500.95
231_Y245_A1.1480.95
3_F7_S1.1420.95
76_Y103_D1.1370.95
114_I118_S1.1370.95
47_F74_L1.1370.95
15_A22_Y1.1360.95
15_A72_L1.1350.95
124_K127_M1.1330.94
53_Q61_Y1.1270.94
240_V244_V1.1260.94
149_F182_Q1.1250.94
127_M241_N1.1230.94
12_F42_L1.1210.94
50_E70_D1.1080.94
41_A90_K1.1000.93
211_L214_H1.0990.93
79_A99_I1.0940.93
237_I242_L1.0910.93
115_F140_F1.0880.93
239_L243_L1.0860.93
103_D135_V1.0700.92
136_F227_L1.0700.92
125_I129_Q1.0700.92
85_L89_N1.0620.92
32_P37_L1.0570.91
180_F185_S1.0530.91
150_G157_L1.0450.91
113_H153_R1.0410.91
65_L68_V1.0340.90
95_S99_I1.0340.90
61_Y71_T1.0290.90
124_K149_F1.0250.90
119_R142_F1.0240.90
218_R239_L1.0230.89
22_Y26_M1.0230.89
117_V123_P1.0190.89
195_S200_S1.0180.89
70_D77_F1.0180.89
182_Q188_D1.0110.89
40_Y230_I1.0110.89
3_F61_Y1.0100.89
111_L131_M1.0050.88
149_F152_A1.0040.88
151_V168_F1.0030.88
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  
3j9pD40.82861000.377Contact Map
3j5pB40.85311000.412Contact Map
4dxwA40.820499.50.67Contact Map
3rvyA20.812299.40.695Contact Map
4bgnA20.775599.20.718Contact Map
2r9rB20.869498.70.772Contact Map
3behA40.812298.50.781Contact Map
4ltoA40.359297.40.835Contact Map
4cbcA40.355196.70.851Contact Map
1orqC10.787894.60.873Contact 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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