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BipA

ID: 1504741287 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 196 (187)
Sequences: 31281 (13144.8)
Seq/Len: 167.278
Nf(neff/√len): 961.2

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: 167.278).

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
169_N181_E3.3581.00
163_V189_A3.2681.00
24_K170_G3.1791.00
126_V165_A2.6751.00
101_A127_I2.6011.00
161_P189_A2.5301.00
96_L126_V2.3781.00
13_H109_T2.3401.00
9_A92_V2.3331.00
98_V128_N2.3321.00
189_A192_D2.2981.00
21_L98_V2.2361.00
130_V164_Y2.1651.00
126_V186_L2.0811.00
141_V164_Y2.0761.00
189_A193_H2.0411.00
141_V145_F1.9971.00
62_A69_R1.9861.00
102_F132_R1.9291.00
182_D185_P1.9281.00
97_L113_T1.9241.00
145_F149_V1.8991.00
130_V181_E1.8771.00
127_I164_Y1.8161.00
24_K183_M1.8101.00
128_N167_A1.7991.00
7_N71_N1.7701.00
110_R147_L1.7151.00
20_T167_A1.7111.00
10_I96_L1.6781.00
60_N71_N1.6631.00
10_I22_V1.6591.00
94_S124_I1.6551.00
64_K69_R1.6491.00
21_L183_M1.5891.00
101_A130_V1.5631.00
96_L190_I1.5461.00
165_A186_L1.5231.00
144_V148_F1.5071.00
86_E115_K1.5051.00
124_I163_V1.5001.00
21_L186_L1.4741.00
99_V125_V1.4661.00
124_I189_A1.4551.00
5_L71_N1.4231.00
74_D77_G1.4191.00
188_Q192_D1.4181.00
68_Y191_V1.4050.99
96_L124_I1.3680.99
161_P193_H1.3640.99
104_G143_Q1.3590.99
142_D146_D1.3430.99
136_R139_W1.3390.99
184_T188_Q1.3330.99
99_V162_I1.3240.99
6_R194_V1.3240.99
62_A71_N1.3080.99
185_P189_A1.2760.99
183_M187_Y1.2710.99
70_I191_V1.2680.99
127_I162_I1.2540.99
100_D103_D1.2420.98
94_S190_I1.2380.98
143_Q146_D1.2350.98
8_I94_S1.2090.98
185_P188_Q1.2070.98
94_S194_V1.2060.98
25_L187_Y1.1760.98
13_H16_H1.1750.98
95_V116_A1.1670.97
103_D106_M1.1620.97
24_K28_Q1.1620.97
143_Q147_L1.1550.97
96_L186_L1.1280.97
125_V162_I1.1230.97
60_N73_V1.1050.96
21_L165_A1.0940.96
131_D166_S1.0910.96
95_V121_L1.0770.95
22_V72_I1.0750.95
187_Y190_I1.0710.95
108_Q111_F1.0650.95
117_F123_P1.0640.95
161_P164_Y1.0490.94
110_R114_K1.0440.94
107_P110_R1.0360.94
105_P108_Q1.0300.94
21_L167_A1.0220.93
23_D32_F1.0170.93
140_V143_Q1.0100.93
12_A17_G1.0080.93
188_Q191_V1.0060.93
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  
4zciA201000.119Contact Map
2yweA10.78061000.179Contact Map
3cb4D60.751000.184Contact Map
3vqtA40.86221000.188Contact Map
3j25A10.93371000.194Contact Map
4qjty10.770499.90.208Contact Map
2h5eA20.821499.90.21Contact Map
3tr5A40.943999.90.21Contact Map
2c78A10.979699.90.214Contact Map
4kiyV10.913399.90.218Contact 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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