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BepA 15-235

ID: 1507223372 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 221 (205)
Sequences: 2363 (1650.1)
Seq/Len: 11.527
Nf(neff/√len): 115.2

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: 11.527).

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
51_T72_L4.0911.00
135_I197_Q2.9811.00
55_C147_F2.5171.00
72_L109_L2.4271.00
142_N155_Q2.3481.00
119_K133_E2.1421.00
108_G111_R2.1131.00
139_N187_V2.0871.00
132_S197_Q2.0561.00
152_G156_R2.0521.00
76_P102_G1.8961.00
56_H59_Q1.8361.00
110_Q114_Q1.7811.00
104_E107_E1.7471.00
105_I144_L1.7391.00
116_L162_L1.6931.00
104_E108_G1.6671.00
73_R77_F1.6451.00
145_H152_G1.6371.00
176_T179_R1.6291.00
180_M184_S1.6171.00
136_E193_L1.6071.00
56_H60_Q1.6061.00
186_A195_P1.6051.00
21_N24_A1.5671.00
142_N152_G1.5631.00
36_A63_K1.5571.00
145_H153_R1.5251.00
155_Q159_F1.4991.00
198_H202_D1.4971.00
106_Q110_Q1.4831.00
51_T106_Q1.4761.00
134_A200_F1.4691.00
73_R105_I1.4351.00
36_A39_N1.4331.00
47_E53_Y1.4281.00
50_D53_Y1.4171.00
114_Q118_E1.4121.00
59_Q63_K1.4121.00
33_T61_L1.4091.00
68_W71_Y1.3840.99
55_C71_Y1.3620.99
130_F166_A1.3530.99
17_Y28_K1.3420.99
109_L113_D1.3330.99
149_E153_R1.3090.99
209_I213_K1.3070.99
99_F152_G1.3000.99
7_Y11_T1.2950.99
107_E110_Q1.2710.99
79_F149_E1.2650.99
176_T206_P1.2630.99
111_R114_Q1.2620.99
102_G106_Q1.2620.99
60_Q63_K1.2620.99
29_C66_F1.2610.99
51_T113_D1.2530.99
54_L158_F1.2440.98
143_Q188_A1.2410.98
5_Y10_T1.2340.98
112_L144_L1.2320.98
36_A60_Q1.2210.98
182_V186_A1.2170.98
112_L137_L1.1990.98
100_A108_G1.1930.98
138_F200_F1.1770.98
134_A163_A1.1750.98
52_A56_H1.1740.98
157_L160_E1.1580.97
141_L155_Q1.1530.97
36_A64_N1.1380.97
109_L144_L1.1310.97
57_I154_T1.1200.96
139_N193_L1.1180.96
210_R213_K1.1000.96
205_N209_I1.0990.96
133_E162_L1.0880.96
138_F180_M1.0840.96
54_L147_F1.0770.95
141_L154_T1.0750.95
130_F168_H1.0730.95
76_P98_A1.0620.95
138_F159_F1.0510.94
136_E140_S1.0460.94
113_D158_F1.0420.94
119_K137_L1.0390.94
68_W74_H1.0370.94
105_I146_P1.0360.94
51_T110_Q1.0340.94
186_A192_D1.0340.94
135_I196_M1.0260.94
54_L113_D1.0230.93
145_H149_E1.0220.93
7_Y10_T1.0220.93
30_S34_A1.0200.93
129_E132_S1.0130.93
179_R202_D1.0110.93
5_Y13_L1.0030.93
108_G144_L1.0010.92
36_A40_L1.0000.92
185_V189_E1.0000.92
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  
4n67A10.96381000.168Contact Map
4npsA10.95481000.168Contact Map
2jk8A20.99551000.173Contact Map
4m16A10.97291000.192Contact Map
4py3A1001000.192Contact Map
3zc7A10.90051000.207Contact Map
3shgA10.86881000.23Contact Map
4u04A20.88691000.384Contact Map
3cucA20.92311000.398Contact Map
4rglA10.90051000.411Contact 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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