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T0812

ID: 1402433122 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 204 (199)
Sequences: 549 (318.9)
Seq/Len: 2.759
Nf(neff/√len): 22.6

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: 2.759).

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_I2.2661.00
80_Y98_Q2.1021.00
4_K7_I1.9961.00
62_L164_I1.9961.00
101_I161_I1.9520.99
20_L62_L1.9320.99
101_I129_I1.9160.99
152_E156_D1.8490.99
62_L66_F1.7850.99
73_A186_V1.7500.98
77_K130_E1.7130.98
94_T167_K1.7090.98
4_K11_V1.6800.98
62_L136_W1.6800.98
79_K128_E1.6580.98
179_I182_I1.6500.97
4_K20_L1.5970.97
104_G154_F1.5950.97
43_V46_M1.5370.96
93_S167_K1.5350.96
4_K62_L1.5290.96
76_G80_Y1.5270.96
78_L184_M1.5230.95
76_G185_E1.5200.95
167_K181_E1.4980.95
150_T153_D1.4590.94
131_M184_M1.4560.94
196_T199_A1.4430.93
71_L178_R1.4310.93
129_I193_T1.4010.92
99_V182_I1.3970.92
159_Y201_L1.3720.91
111_I149_V1.3660.91
24_D28_Q1.3610.90
4_K9_T1.3510.90
166_I170_Y1.3350.89
104_G159_Y1.3320.89
22_L169_T1.3090.88
79_K150_T1.3070.88
118_A125_T1.3050.88
136_W176_Q1.2810.87
169_T177_S1.2600.85
78_L99_V1.2590.85
138_Y153_D1.2530.85
17_Q20_L1.2450.84
111_I154_F1.2320.84
23_V165_L1.2320.84
26_A161_I1.2080.82
114_R157_I1.2050.82
157_I185_E1.1970.81
155_L175_R1.1970.81
58_F105_T1.1960.81
4_K14_K1.1900.80
44_A97_P1.1900.80
80_Y166_I1.1890.80
61_K82_I1.1820.80
168_A186_V1.1820.80
154_F164_I1.1790.80
56_E165_L1.1770.79
149_V154_F1.1750.79
20_L66_F1.1650.79
127_H169_T1.1590.78
17_Q66_F1.1500.77
70_K120_L1.1490.77
101_I162_H1.1490.77
67_E184_M1.1470.77
101_I193_T1.1450.77
104_G164_I1.1420.77
81_A124_L1.1290.75
82_I89_E1.1180.74
89_E149_V1.1120.74
85_E175_R1.1100.74
138_Y149_V1.1080.73
196_T200_D1.1050.73
38_Q45_H1.1030.73
60_W155_L1.1030.73
103_G108_H1.0970.72
76_G84_F1.0880.72
71_L176_Q1.0870.71
4_K17_Q1.0850.71
97_P110_R1.0850.71
132_T136_W1.0840.71
111_I157_I1.0810.71
153_D201_L1.0710.70
60_W136_W1.0690.70
154_F161_I1.0670.69
103_G150_T1.0590.69
85_E177_S1.0540.68
99_V129_I1.0540.68
86_A185_E1.0510.68
71_L200_D1.0500.68
5_G8_R1.0450.67
3_A6_L1.0440.67
17_Q62_L1.0400.67
100_I128_E1.0300.65
60_W182_I1.0290.65
42_I102_R1.0280.65
66_F161_I1.0260.65
16_E30_T1.0250.65
14_K20_L1.0240.65
125_T136_W1.0210.64
69_K84_F1.0150.64
77_K204_K1.0010.62
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  
1wfxA10.446180.957Contact Map
2d7nA10.35783.10.965Contact Map
1cjcA10.47552.50.967Contact Map
2llzA10.41672.40.967Contact Map
2jovA10.37252.20.968Contact Map
2fo3A10.51962.20.968Contact Map
4a0tA30.42652.10.968Contact Map
2qa1A10.49512.10.968Contact Map
3zxuB20.45120.968Contact Map
3achA10.61271.90.968Contact 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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