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coconut

ID: 1513834416 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 183 (177)
Sequences: 195 (144.2)
Seq/Len: 1.102
Nf(neff/√len): 10.8

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: 1.102).

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
175_I178_I2.9421.00
76_Y94_Q2.7141.00
99_G102_P2.3650.99
59_P64_G2.2970.99
94_Q166_Y2.0430.97
97_I125_I1.8990.95
165_T173_S1.8700.94
90_T163_K1.8550.94
147_R154_L1.7560.91
157_I174_R1.7540.91
134_Y149_D1.7200.90
151_L157_I1.6980.89
56_W59_P1.6940.89
56_W64_G1.5800.84
160_I164_A1.5470.82
62_F68_M1.4690.77
18_L30_G1.4650.77
69_A127_M1.4620.77
133_K163_K1.4240.74
107_I129_E1.4030.72
58_L132_W1.3960.72
58_L62_F1.3840.71
57_K159_Y1.3560.69
55_Y160_I1.3530.69
163_K177_E1.3450.68
125_I132_W1.3380.67
143_R150_F1.3220.66
154_L164_A1.3170.66
18_L58_L1.2810.62
75_K124_E1.2630.61
144_T180_M1.2550.60
162_I183_A1.2500.60
27_T30_G1.2350.58
62_F72_G1.2080.56
136_G162_I1.2030.55
15_I97_I1.1950.54
99_G103_T1.1910.54
73_K126_E1.1910.54
68_M142_H1.1860.54
154_L162_I1.1750.53
126_E181_E1.1610.51
149_D152_D1.1530.50
136_G149_D1.1480.50
149_D153_I1.1450.50
14_T54_F1.1410.49
59_P62_F1.1390.49
56_W132_W1.1360.49
153_I164_A1.1300.48
127_M180_M1.1270.48
97_I157_I1.1230.48
129_E147_R1.1180.47
142_H151_L1.1120.47
97_I112_M1.1070.46
39_V54_F1.1010.45
165_T174_R1.0990.45
148_E152_D1.0960.45
76_Y93_P1.0960.45
22_A78_I1.0950.45
3_I6_W1.0930.45
95_V148_E1.0900.44
129_E154_L1.0850.44
81_E94_Q1.0820.44
125_I129_E1.0780.43
161_L181_E1.0770.43
125_I131_E1.0770.43
102_P134_Y1.0750.43
21_E25_H1.0730.43
67_L137_D1.0720.43
23_L36_P1.0650.42
153_I161_L1.0650.42
16_L181_E1.0550.41
76_Y163_K1.0530.41
99_G153_I1.0480.41
76_Y166_Y1.0460.40
97_I160_I1.0460.40
75_K182_V1.0350.39
63_E170_M1.0250.38
69_A72_G1.0250.38
53_P94_Q1.0140.37
12_E175_I1.0130.37
69_A182_V1.0110.37
85_E96_I1.0090.37
62_F89_S1.0080.37
92_N100_G1.0060.37
134_Y152_D1.0060.37
72_G95_V1.0050.37
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  
4yepA201000.232Contact Map
4yeqU101000.239Contact Map
3ov1A10.25684.20.959Contact Map
4a0tA30.4592.60.963Contact Map
4mkqC20.04922.50.964Contact Map
1nrvA20.25682.20.964Contact Map
1r1pA40.284220.965Contact Map
1lkkA10.256820.965Contact Map
3q3eA20.27871.90.966Contact Map
2ichA20.38251.70.967Contact 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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