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T0812

ID: 1403919122 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 204 (200)
Sequences: 315 (164)
Seq/Len: 1.575
Nf(neff/√len): 11.6

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: 1.575).

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
199_A202_I5.5691.00
200_D203_E2.8161.00
20_L62_L2.4001.00
199_A203_E2.2820.99
66_F161_I2.2050.99
179_I182_I2.1520.99
73_A186_V2.0680.99
20_L66_F1.9340.98
62_L66_F1.8890.97
4_K62_L1.7290.95
197_P201_L1.6710.93
111_I154_F1.6390.92
104_G154_F1.6310.92
17_Q66_F1.6260.92
101_I117_A1.6020.91
101_I161_I1.5340.89
22_L140_G1.4860.86
98_Q167_K1.4520.85
99_V166_I1.4400.84
56_E165_L1.4330.84
58_F197_P1.4120.82
94_T167_K1.4080.82
17_Q62_L1.3900.81
70_K81_A1.3700.80
32_T184_M1.3420.78
62_L136_W1.3280.77
6_L62_L1.3190.76
157_I185_E1.2990.74
111_I149_V1.2950.74
73_A101_I1.2720.72
126_R202_I1.2720.72
17_Q136_W1.2690.72
99_V165_L1.2670.72
89_E149_V1.2540.71
79_K128_E1.2390.69
73_A181_E1.2240.68
74_Y97_P1.2200.68
17_Q20_L1.2150.67
108_H111_I1.2100.67
7_I20_L1.2040.66
23_V59_Y1.2040.66
58_F119_P1.1990.66
152_E160_D1.1950.65
4_K20_L1.1930.65
38_Q73_A1.1870.65
79_K147_R1.1720.63
27_L150_T1.1620.62
7_I62_L1.1610.62
80_Y110_R1.1610.62
164_I185_E1.1590.62
118_A125_T1.1550.61
67_E179_I1.1530.61
59_Y195_M1.1510.61
76_G84_F1.1470.61
71_L199_A1.1450.60
59_Y131_M1.1390.60
168_A186_V1.1380.60
132_T154_F1.1330.59
38_Q122_G1.1260.59
90_T179_I1.1210.58
64_E150_T1.1160.57
96_N169_T1.1110.57
9_T20_L1.1040.56
103_G106_P1.1040.56
103_G155_L1.0920.55
105_T133_E1.0880.55
23_V104_G1.0840.54
24_D174_M1.0810.54
104_G124_L1.0770.53
169_T177_S1.0730.53
138_Y149_V1.0720.53
16_E135_E1.0710.53
134_K164_I1.0670.52
4_K7_I1.0670.52
77_K130_E1.0650.52
76_G81_A1.0620.52
7_I66_F1.0570.51
76_G185_E1.0540.51
105_T164_I1.0510.51
16_E37_F1.0460.50
132_T136_W1.0380.49
22_L82_I1.0360.49
43_V46_M1.0330.49
44_A48_L1.0300.49
129_I193_T1.0300.49
14_K20_L1.0160.47
26_A161_I1.0100.46
86_A174_M1.0060.46
152_E156_D1.0060.46
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  
3gm8A10.46579.90.96Contact Map
1fjjA10.65695.20.965Contact Map
2d7nA10.36272.90.969Contact Map
4a0tA30.45592.80.969Contact Map
3n08A20.62752.50.97Contact Map
3achA10.61272.40.97Contact Map
1lyqA20.41182.10.971Contact Map
2qygA40.26961.90.972Contact Map
3abdX20.0981.90.972Contact Map
3g3tA10.27941.90.972Contact 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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