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GREMLIN_2ibn

ID: 1515511975 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 235 (234)
Sequences: 424 (178.7)
Seq/Len: 1.812
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: 1.812).

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
73_D227_K3.6361.00
168_L172_A3.5991.00
78_V172_A3.4751.00
147_V193_L2.8991.00
128_D132_S2.8051.00
135_L140_P2.7181.00
68_A211_F2.5931.00
170_P197_Q2.4651.00
35_K234_S2.4131.00
18_V137_M2.3741.00
42_V58_A2.3251.00
135_L192_Q2.2160.99
200_A203_P2.1260.99
73_D228_Y2.0730.99
223_G227_K1.9830.99
108_R134_E1.9720.99
157_M161_M1.8120.97
157_M176_I1.8050.97
104_P149_M1.7630.96
69_H72_K1.7060.95
78_V168_L1.6350.94
11_L15_H1.6250.94
73_D77_L1.5990.93
144_L193_L1.5590.92
164_N233_L1.5290.91
14_T122_D1.5030.90
218_R222_Q1.4960.89
24_K27_Q1.4790.89
140_P192_Q1.4740.88
3_D7_T1.4680.88
65_I75_F1.4320.86
184_W205_V1.4200.86
116_C119_T1.4200.86
75_F175_M1.4160.86
18_V148_L1.4150.86
77_L228_Y1.4030.85
104_P110_Q1.3900.84
184_W202_L1.3790.84
19_D22_R1.3590.82
21_V105_V1.3380.81
75_F207_E1.3360.81
222_Q226_D1.3340.81
7_T10_K1.3320.81
35_K232_I1.3170.79
25_H148_L1.3100.79
144_L147_V1.2980.78
18_V131_Y1.2960.78
226_D231_G1.2930.78
134_E192_Q1.2880.77
65_I79_G1.2870.77
73_D223_G1.2850.77
38_V84_L1.2740.76
197_Q201_M1.2740.76
191_Q199_L1.2670.76
104_P107_C1.2570.75
135_L141_H1.2260.72
225_I235_W1.2190.72
84_L160_V1.2130.71
8_T12_M1.2030.70
160_V235_W1.1990.70
10_K14_T1.1910.69
12_M183_P1.1760.68
40_E43_D1.1710.67
2_M6_F1.1670.67
104_P201_M1.1620.66
141_H193_L1.1580.66
109_P113_V1.1550.66
46_D78_V1.1400.64
190_Y198_D1.1380.64
42_V80_L1.1210.62
215_D218_R1.1040.61
61_T79_G1.0990.60
108_R133_T1.0970.60
21_V148_L1.0970.60
221_Y228_Y1.0880.59
109_P126_L1.0770.58
194_C199_L1.0750.57
46_D55_S1.0740.57
54_N64_G1.0720.57
65_I175_M1.0640.56
209_N213_L1.0610.56
38_V193_L1.0490.55
42_V56_F1.0460.54
188_R206_R1.0460.54
5_V9_Y1.0440.54
3_D6_F1.0390.54
77_L81_L1.0350.53
145_D195_S1.0270.52
20_F97_A1.0240.52
120_F150_S1.0120.51
182_Y185_H1.0080.50
179_H182_Y1.0060.50
83_D101_D1.0050.50
172_A176_I1.0040.50
145_D178_F1.0000.49
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  
2huoA111000.018Contact Map
2ibnA211000.027Contact Map
3ccgA10.651195.80.946Contact Map
4mlmA20.621395.40.947Contact Map
2o08A20.642695.30.947Contact Map
2ogiA20.651193.50.952Contact Map
4n6wA10.693.50.952Contact Map
4mcwA20.783890.957Contact Map
4r8zA20.689487.10.958Contact Map
3tm8A20.761781.90.961Contact 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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