GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
scEMC3

ID: 1504851071 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 253 (243)
Sequences: 304 (182.1)
Seq/Len: 1.251
Nf(neff/√len): 11.7

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: 1.251).

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
60_I228_M2.2210.99
8_K11_V2.0630.98
3_L11_V1.9860.97
27_Q195_G1.8720.95
55_W60_I1.7850.93
163_G176_S1.6890.91
18_V135_W1.5600.85
162_T165_I1.5520.85
194_I232_L1.5490.85
248_V252_Y1.5360.84
148_L166_C1.5140.83
3_L8_K1.5100.83
3_L193_L1.4760.81
4_D14_P1.4760.81
71_F237_H1.4690.80
11_V193_L1.4690.80
204_Q237_H1.4610.80
71_F74_K1.4550.80
154_A173_W1.4340.78
13_L41_A1.4220.77
38_A48_T1.4160.77
67_S239_T1.4060.76
49_E129_Q1.4060.76
153_T179_W1.3940.75
117_N121_G1.3860.75
23_G27_Q1.3840.75
118_M122_N1.3710.74
155_K171_V1.3540.72
12_L129_Q1.3520.72
13_L20_V1.3480.72
19_M131_I1.3470.72
78_L81_D1.3380.71
59_L232_L1.3270.70
78_L88_L1.3210.70
174_V181_F1.3150.69
19_M139_F1.3050.68
74_K77_F1.2940.67
10_W14_P1.2830.66
143_F176_S1.2780.66
46_K218_Q1.2770.66
129_Q139_F1.2630.65
149_P152_L1.2630.65
111_M114_A1.2610.64
20_V122_N1.2550.64
122_N188_N1.2470.63
153_T175_S1.2370.62
23_G128_P1.2290.61
132_I183_S1.2260.61
70_A137_N1.2220.61
12_L148_L1.2180.60
58_L66_L1.2160.60
159_M232_L1.2160.60
133_M231_D1.2130.60
23_G26_K1.2100.60
175_S179_W1.2070.59
59_L63_G1.2020.59
135_W153_T1.1990.59
128_P183_S1.1950.58
15_I135_W1.1880.58
244_V248_V1.1870.58
6_Q88_L1.1720.56
34_T66_L1.1690.56
157_K173_W1.1670.56
164_I190_V1.1650.55
28_Y226_H1.1570.55
42_Q244_V1.1550.54
171_V177_I1.1520.54
12_L49_E1.1500.54
49_E148_L1.1460.54
4_D15_I1.1460.54
136_V157_K1.1460.54
187_L191_Y1.1410.53
15_I153_T1.1390.53
66_L172_R1.1370.53
241_L245_E1.1320.52
185_L220_Q1.1240.51
105_P132_I1.1200.51
12_L15_I1.1190.51
171_V174_V1.1180.51
62_N71_F1.1170.51
88_L213_P1.1140.50
45_V126_F1.1090.50
91_A113_N1.1080.50
12_L16_S1.1070.50
123_M176_S1.1070.50
71_F118_M1.1040.49
145_L225_M1.1010.49
149_P161_Q1.1010.49
12_L18_V1.1000.49
55_W172_R1.0980.49
71_F160_L1.0970.49
248_V251_Q1.0900.48
128_P132_I1.0890.48
127_I172_R1.0800.47
53_L228_M1.0750.47
11_V14_P1.0690.46
239_T242_D1.0690.46
19_M23_G1.0680.46
121_G169_L1.0670.46
111_M117_N1.0650.46
119_A164_I1.0650.46
134_W144_I1.0600.45
138_H184_V1.0560.45
122_N131_I1.0530.44
53_L248_V1.0510.44
56_A229_A1.0470.44
78_L249_L1.0470.44
154_A170_D1.0470.44
124_A131_I1.0460.44
243_N248_V1.0440.44
81_D88_L1.0420.43
160_L175_S1.0420.43
221_V224_A1.0410.43
150_F156_F1.0410.43
143_F193_L1.0370.43
7_L162_T1.0340.43
129_Q171_V1.0320.42
6_Q155_K1.0260.42
182_I234_I1.0220.41
175_S181_F1.0200.41
66_L102_V1.0190.41
190_V194_I1.0170.41
29_I232_L1.0140.41
13_L197_N1.0120.40
53_L157_K1.0110.40
125_S128_P1.0100.40
105_P115_M1.0090.40
13_L181_F1.0070.40
152_L156_F1.0070.40
82_L86_R1.0070.40
22_T207_I1.0020.39
31_T47_L1.0010.39
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  
4wrtB10.27277.50.975Contact Map
4wsbB10.276760.976Contact Map
3wcaA40.32813.30.979Contact Map
4bj1A10.26482.60.98Contact Map
4g9qA10.27272.40.981Contact Map
2mkbA10.09492.30.981Contact Map
2y9yB10.19372.30.981Contact Map
1nvpB10.13442.20.981Contact Map
3vfzA20.09882.20.981Contact Map
2hfrA10.106720.981Contact 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.

Page generated in 0.0427 seconds.