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T0826 1-220

ID: 1403988800 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 220 (213)
Sequences: 376 (292.7)
Seq/Len: 1.765
Nf(neff/√len): 20.1

HHblits Results: (2013_03)
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: 1.765).

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
131_G135_A2.6451.00
173_Q177_Y2.5541.00
216_Q219_M2.4391.00
62_N162_S2.2481.00
87_A127_I2.1380.99
91_Q118_L2.0200.99
79_P135_A1.9990.99
52_T177_Y1.9460.98
91_Q99_F1.9440.98
103_M106_N1.9010.98
79_P138_Y1.8820.98
104_L203_K1.8020.97
68_I77_L1.7870.97
203_K220_A1.7710.96
82_L138_Y1.7510.96
71_P75_K1.7500.96
62_N158_L1.6600.94
55_V168_G1.5950.93
59_F165_C1.5530.91
20_S27_L1.5520.91
31_F35_V1.5410.91
75_K79_P1.4750.88
129_C136_L1.4700.88
92_E99_F1.4660.88
97_I199_A1.4450.87
100_N103_M1.4240.86
62_N213_P1.4200.85
22_Y27_L1.4170.85
31_F185_K1.3820.83
170_A183_N1.3780.83
49_F177_Y1.3460.81
111_T139_I1.3340.80
117_R188_T1.3310.80
23_S65_F1.3100.78
79_P139_I1.2980.77
127_I160_A1.2910.77
108_L203_K1.2850.76
120_T155_R1.2850.76
93_I192_V1.2710.75
180_F195_N1.2690.75
151_E155_R1.2650.75
63_F163_F1.2620.75
21_L58_F1.2530.74
26_V147_V1.2460.73
99_F214_Y1.2460.73
128_V160_A1.2440.73
23_S81_I1.2420.73
80_L152_L1.2290.72
161_V168_G1.2270.72
19_L138_Y1.2230.71
188_T198_G1.2190.71
211_N214_Y1.2140.70
94_F138_Y1.2100.70
95_F110_T1.1930.69
21_L144_K1.1920.68
80_L161_V1.1870.68
185_K194_S1.1860.68
15_L138_Y1.1640.66
104_L175_Q1.1580.65
92_E95_F1.1530.65
174_Y178_A1.1450.64
49_F105_N1.1400.63
95_F153_L1.1400.63
30_A183_N1.1360.63
128_V132_V1.1330.63
92_E195_N1.1280.62
126_W130_L1.1230.62
71_P190_L1.1180.61
54_P177_Y1.1170.61
31_F192_V1.1150.61
155_R194_S1.1140.61
175_Q183_N1.1140.61
190_L195_N1.1100.60
164_L167_L1.1080.60
122_G217_L1.1030.60
95_F211_N1.0940.59
25_L185_K1.0900.58
88_V196_F1.0820.57
174_Y183_N1.0820.57
83_V137_A1.0720.56
160_A165_C1.0720.56
192_V198_G1.0710.56
174_Y191_I1.0690.56
174_Y184_N1.0680.56
60_L199_A1.0670.56
207_W220_A1.0670.56
31_F187_V1.0660.56
83_V140_A1.0620.55
86_A150_K1.0590.55
31_F53_M1.0520.54
63_F159_A1.0480.54
19_L22_Y1.0410.53
39_H104_L1.0400.53
31_F198_G1.0400.53
129_C146_R1.0390.53
98_Y190_L1.0370.53
60_L133_L1.0310.52
57_L194_S1.0300.52
86_A130_L1.0240.51
111_T188_T1.0200.51
91_Q214_Y1.0200.51
56_V165_C1.0160.50
137_A143_V1.0140.50
109_Q117_R1.0090.50
112_A202_S1.0040.49
71_P196_F1.0020.49
104_L108_L1.0010.49
57_L108_L1.0010.49
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: (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  
1fmeA10.10454.30.966Contact Map
1oisA10.21823.40.968Contact Map
3owqA40.05911.50.973Contact Map
1fftB20.51.50.973Contact Map
2m7gA10.27731.10.975Contact Map
3b55A10.17731.10.975Contact Map
2hi2A10.30451.10.975Contact Map
2ww9C10.09551.10.975Contact Map
2a65A10.58641.10.976Contact Map
3mtlA10.21821.10.976Contact 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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