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T0812

ID: 1403918320 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 204 (200)
Sequences: 363 (188.6)
Seq/Len: 1.815
Nf(neff/√len): 13.3

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: 1.815).

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
20_L62_L2.5821.00
199_A202_I2.5491.00
4_K62_L2.2120.99
179_I182_I2.1180.99
73_A186_V2.0830.99
4_K20_L1.8270.97
4_K7_I1.8050.97
79_K128_E1.7550.96
66_F161_I1.7130.96
20_L66_F1.6450.94
70_K187_A1.6130.93
101_I161_I1.5870.93
23_V165_L1.5790.92
27_L150_T1.5640.92
62_L66_F1.5410.91
56_E165_L1.5230.91
104_G154_F1.5200.90
82_I170_Y1.4500.87
67_E179_I1.4410.87
17_Q62_L1.4230.86
157_I185_E1.4220.86
4_K11_V1.4200.86
62_L136_W1.4050.85
150_T153_D1.3940.84
71_L159_Y1.3890.84
138_Y149_V1.3860.84
103_G108_H1.3760.83
76_G185_E1.3600.82
22_L140_G1.3440.81
32_T184_M1.3250.80
4_K17_Q1.3220.80
22_L139_Y1.3070.79
17_Q66_F1.3020.78
17_Q20_L1.3020.78
6_L62_L1.2860.77
79_K150_T1.2740.76
54_H58_F1.2710.76
152_E160_D1.2600.75
105_T133_E1.2590.75
16_E135_E1.2490.74
99_V166_I1.2480.74
168_A186_V1.2350.73
4_K66_F1.2320.73
17_Q179_I1.2310.73
196_T199_A1.2310.73
90_T179_I1.2280.73
155_L185_E1.2250.72
89_E149_V1.2170.72
26_A69_K1.2110.71
94_T167_K1.2070.71
73_A181_E1.1980.70
111_I154_F1.1940.69
98_Q167_K1.1890.69
80_Y98_Q1.1860.69
152_E156_D1.1810.68
71_L178_R1.1750.68
7_I62_L1.1660.67
151_R154_F1.1540.66
53_L179_I1.1530.66
62_L164_I1.1440.65
8_R148_T1.1360.64
132_T154_F1.1330.64
60_W136_W1.1300.63
40_P73_A1.1220.62
70_K81_A1.1210.62
104_G159_Y1.1210.62
6_L20_L1.1150.62
153_D201_L1.1080.61
159_Y201_L1.0970.60
66_F136_W1.0950.60
73_A182_I1.0930.59
141_D162_H1.0860.59
61_K83_Y1.0790.58
129_I193_T1.0780.58
22_L169_T1.0720.57
23_V59_Y1.0700.57
77_K130_E1.0680.57
29_H129_I1.0660.57
95_Y179_I1.0660.57
187_A199_A1.0650.56
4_K14_K1.0620.56
14_K62_L1.0590.56
43_V46_M1.0570.56
164_I185_E1.0570.56
82_I89_E1.0420.54
47_D161_I1.0410.54
41_E183_S1.0400.54
89_E175_R1.0380.54
19_I32_T1.0340.53
91_G150_T1.0340.53
111_I115_H1.0330.53
138_Y153_D1.0310.53
7_I20_L1.0290.53
111_I157_I1.0240.52
33_K141_D1.0170.51
57_P77_K1.0150.51
38_Q122_G1.0130.51
56_E71_L1.0110.51
111_I151_R1.0090.50
191_R199_A1.0060.50
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: (21Jun14)
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  
4a0tA30.46575.10.964Contact Map
2brfA10.31864.10.965Contact Map
3kt9A10.32353.80.966Contact Map
1wfxA10.43633.60.966Contact Map
2aqjA10.52943.10.968Contact Map
1cjcA10.48042.50.969Contact Map
2jwkA20.32352.30.97Contact Map
2qa1A10.52.20.97Contact Map
1ujxA10.34312.20.97Contact Map
2pfuA10.4022.20.97Contact 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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