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ID: 1501847578 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 226 (211)
Sequences: 4889 (2728.1)
Seq/Len: 23.171
Nf(neff/√len): 187.8

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: 23.171).

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
117_F176_E4.2051.00
29_H208_Y2.9541.00
41_L70_M2.8651.00
58_F66_P2.7661.00
173_K177_A2.7151.00
122_Q140_E2.6151.00
71_T91_F2.5071.00
124_L168_V2.4921.00
43_D47_R2.4561.00
44_N76_H2.2881.00
25_R204_W2.2871.00
131_P158_V2.2681.00
102_D189_K2.2261.00
130_H133_S2.2091.00
128_W139_I2.1971.00
126_A138_N2.0971.00
119_V122_Q2.0931.00
56_K60_D2.0691.00
114_N194_T2.0221.00
29_H204_W2.0131.00
54_L57_T1.9811.00
71_T100_A1.9671.00
131_P155_E1.9441.00
121_K169_V1.8641.00
187_R194_T1.8631.00
58_F63_K1.8411.00
44_N49_T1.8361.00
57_T61_Q1.8101.00
165_P169_V1.7781.00
180_E184_E1.7321.00
50_E53_V1.7001.00
133_S153_T1.6901.00
146_T149_I1.6651.00
135_R152_L1.6421.00
113_L197_G1.6391.00
50_E54_L1.6251.00
150_D153_T1.6131.00
176_E180_E1.6051.00
38_G42_R1.5691.00
130_H153_T1.5631.00
44_N73_L1.5531.00
204_W208_Y1.5341.00
160_R163_D1.5301.00
128_W159_Q1.5281.00
22_V207_V1.5141.00
33_K77_E1.5101.00
196_S199_E1.4991.00
130_H150_D1.4761.00
170_K173_K1.4761.00
117_F169_V1.4591.00
102_D185_Y1.4411.00
102_D186_Y1.4271.00
117_F173_K1.3960.99
112_N183_L1.3960.99
138_N141_F1.3960.99
14_A175_Y1.3860.99
67_D97_Q1.3820.99
175_Y179_T1.3770.99
8_R86_W1.3660.99
44_N47_R1.3610.99
117_F172_L1.3600.99
18_G21_T1.3350.99
54_L72_R1.3330.99
25_R28_K1.3180.99
208_Y212_Q1.3110.99
184_E188_K1.3000.99
24_S28_K1.3000.99
99_E102_D1.2940.99
96_P99_E1.2920.99
66_P69_V1.2870.99
129_I136_V1.2830.99
95_L99_E1.2630.99
12_M183_L1.2480.99
206_H209_A1.2480.99
126_A139_I1.2370.98
144_P151_D1.2270.98
133_S150_D1.2190.98
77_E80_N1.2190.98
184_E187_R1.2100.98
49_T52_G1.2050.98
20_G89_D1.2040.98
145_K151_D1.2000.98
172_L176_E1.1920.98
16_G124_L1.1910.98
41_L45_M1.1880.98
199_E206_H1.1720.98
100_A103_R1.1270.97
205_P209_A1.1260.97
110_V192_L1.1230.97
45_M59_I1.1100.96
199_E203_I1.0870.96
11_I23_S1.0730.95
22_V204_W1.0520.95
17_S115_V1.0400.94
135_R142_N1.0390.94
75_L104_A1.0380.94
35_L40_L1.0360.94
92_P97_Q1.0300.94
199_E205_P1.0290.94
72_R75_L1.0280.94
45_M56_K1.0220.93
26_I207_V1.0210.93
40_L44_N1.0200.93
48_G53_V1.0160.93
125_T165_P1.0090.93
77_E82_T1.0010.92
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  
1zd8A10.93811000.336Contact Map
4qbgB10.92921000.354Contact Map
3be4A10.92041000.359Contact Map
3gmtA20.84511000.364Contact Map
4pzlA40.94691000.367Contact Map
2xb4A10.91151000.37Contact Map
3tlxA40.94251000.374Contact Map
4jzkA20.91151000.378Contact Map
1akyA10.92921000.379Contact Map
1ak2A10.94251000.386Contact 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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