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190

ID: 1500058671 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 190 (190)
Sequences: 452 (312.9)
Seq/Len: 2.379
Nf(neff/√len): 22.7

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: 2.379).

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
66_R69_L1.8460.99
28_E32_Y1.8000.98
124_F127_N1.7550.98
145_V149_L1.7050.97
58_T62_S1.6470.97
20_Q26_D1.6420.96
140_A144_L1.6360.96
187_E190_D1.6250.96
100_E105_L1.5950.96
98_Q101_M1.5900.96
59_P62_S1.5810.95
139_S144_L1.5590.95
127_N130_I1.5500.95
22_Y46_S1.5400.94
49_I52_K1.5270.94
181_L185_A1.5240.94
96_A101_M1.4980.93
19_V22_Y1.4880.93
50_W53_F1.4730.93
50_W55_L1.3980.90
103_T106_L1.3890.89
23_F55_L1.3880.89
115_F118_D1.3870.89
59_P63_P1.3540.88
52_K55_L1.3310.86
30_N33_Q1.3270.86
31_F36_Q1.3200.86
30_N36_Q1.3190.86
162_P165_A1.3130.85
45_P52_K1.3070.85
146_S149_L1.3020.85
29_E32_Y1.3000.85
159_S162_P1.2980.85
30_N35_Q1.2790.83
98_Q102_V1.2650.82
48_D53_F1.2590.82
61_L64_S1.2540.82
145_V148_K1.2500.81
97_D101_M1.2360.80
21_P56_L1.2360.80
99_L106_L1.2330.80
106_L130_I1.2270.80
138_F144_L1.2250.80
145_V150_A1.2140.79
48_D55_L1.1960.77
24_Y137_G1.1960.77
58_T65_R1.1940.77
57_P62_S1.1920.77
98_Q103_T1.1780.76
169_S175_S1.1750.75
114_S117_C1.1730.75
31_F34_Q1.1540.74
97_D100_E1.1520.73
12_Y16_Y1.1500.73
107_G115_F1.1490.73
113_Q117_C1.1490.73
50_W134_M1.1490.73
45_P48_D1.1310.71
180_D183_A1.1300.71
29_E34_Q1.1270.71
19_V25_C1.1250.71
143_K149_L1.1200.70
101_M104_E1.1140.70
34_Q37_Q1.1050.69
30_N34_Q1.1030.69
18_S24_Y1.1000.68
94_S98_Q1.0990.68
171_C174_S1.0980.68
22_Y44_A1.0970.68
59_P65_R1.0890.67
47_E52_K1.0880.67
36_Q39_E1.0750.66
161_S167_G1.0720.65
46_S49_I1.0700.65
153_Q156_R1.0690.65
61_L66_R1.0660.65
95_T98_Q1.0610.64
164_P168_H1.0550.64
174_S179_Q1.0470.63
146_S150_A1.0460.63
186_S190_D1.0450.63
32_Y36_Q1.0420.62
99_L102_V1.0410.62
48_D52_K1.0400.62
110_M113_Q1.0400.62
47_E51_K1.0380.62
169_S174_S1.0370.62
31_F38_S1.0370.62
102_V105_L1.0360.62
24_Y54_E1.0190.60
129_I140_A1.0190.60
103_T108_G1.0140.59
76_A81_S1.0110.59
31_F35_Q1.0090.59
13_D21_P1.0080.58
60_P63_P1.0070.58
157_K163_N1.0040.58
166_R169_S1.0030.58
99_L103_T1.0020.58
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  
2xl1A10.07892.10.969Contact Map
2yuhA10.37891.20.973Contact Map
4okvE20.33160.90.975Contact Map
1x9uA20.23160.90.975Contact Map
4bjoA20.13160.90.976Contact Map
1n0uA10.31580.80.976Contact Map
2mcmA10.20.80.977Contact Map
1noaA10.20530.80.977Contact Map
4qhwA10.31580.70.977Contact Map
1akpA10.20530.70.977Contact 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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