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T0818

ID: 1402705394 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 166 (153)
Sequences: 275 (264.7)
Seq/Len: 1.797
Nf(neff/√len): 21.4

Jackhmmer Results: (2014_04_16)
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: 1.797).

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
49_D52_K3.6361.00
41_M53_L2.9151.00
68_S73_I1.7440.96
61_M65_Y1.5830.92
54_F73_I1.5290.91
76_L81_D1.5090.90
18_M36_E1.5040.90
82_G86_S1.4610.88
67_D72_E1.4450.87
8_M60_D1.4300.86
12_L125_I1.4160.85
148_C152_N1.4090.85
53_L76_L1.3770.83
45_I50_S1.3770.83
49_D55_D1.3740.83
10_S25_V1.3350.81
144_M147_I1.3170.79
82_G117_T1.3130.79
19_I118_E1.3010.78
4_L23_C1.2580.75
149_K153_W1.2440.74
41_M54_F1.2380.73
69_S73_I1.2360.73
72_E76_L1.2340.73
66_K81_D1.2290.72
150_D153_W1.2260.72
68_S76_L1.2250.72
151_G154_G1.2230.72
15_S18_M1.2140.71
116_T120_G1.2030.70
12_L19_I1.1920.69
146_Q149_K1.1790.68
12_L16_L1.1780.68
12_L59_K1.1670.67
50_S53_L1.1580.66
100_N103_I1.1580.66
17_I62_K1.1550.65
148_C151_G1.1550.65
57_Y61_M1.1520.65
149_K152_N1.1520.65
152_N155_E1.1390.64
127_F132_I1.1360.64
73_I76_L1.1310.63
34_I54_F1.1300.63
145_I148_C1.1290.63
5_V43_E1.1240.62
41_M111_P1.1230.62
65_Y73_I1.1210.62
44_C52_K1.1180.62
45_I53_L1.1130.61
15_S78_E1.1120.61
41_M130_H1.1100.61
84_I134_N1.1060.61
46_V84_I1.1040.60
76_L79_Y1.1030.60
68_S135_E1.1020.60
127_F131_Y1.1000.60
54_F57_Y1.0960.59
118_E123_Y1.0950.59
80_I84_I1.0870.59
110_H115_F1.0860.58
86_S91_G1.0840.58
8_M35_K1.0830.58
139_Y144_M1.0800.58
35_K128_S1.0790.58
57_Y73_I1.0790.58
153_W156_K1.0710.57
149_K155_E1.0630.56
71_D102_G1.0590.56
117_T120_G1.0580.55
46_V113_F1.0530.55
139_Y145_I1.0530.55
117_T123_Y1.0510.55
22_S26_N1.0490.54
18_M132_I1.0450.54
73_I77_F1.0430.54
11_F14_L1.0430.54
115_F119_T1.0400.53
6_K98_A1.0390.53
102_G141_G1.0370.53
21_S142_I1.0320.53
6_K10_S1.0310.53
73_I81_D1.0310.53
67_D71_D1.0280.52
20_F51_E1.0260.52
80_I83_A1.0140.51
7_I11_F1.0130.51
8_M13_A1.0080.50
11_F21_S1.0070.50
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: (07Jun14)
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  
3k7cA40.584393.40.809Contact Map
1vqqA20.75393.40.809Contact Map
2mc8A10.686776.20.853Contact Map
3zbiC140.144670.60.86Contact Map
2ap3A10.728950.40.876Contact Map
3ombA10.554249.40.877Contact Map
3gzbA80.789247.60.878Contact Map
3h51A20.813342.80.881Contact Map
3bb9A60.686740.10.884Contact Map
4jg9A20.6627330.889Contact 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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