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T0811

ID: 1402339849 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 255 (246)
Sequences: 2387 (1661.8)
Seq/Len: 9.703
Nf(neff/√len): 106.0

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: 9.703).

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
189_D228_H3.8361.00
44_I65_G3.6361.00
138_E181_I3.3801.00
142_A191_R3.1121.00
109_D148_R2.6231.00
15_N74_A2.5561.00
141_E144_T2.5491.00
47_F81_I2.5011.00
146_L191_R2.2941.00
86_L91_L2.2801.00
116_T128_I2.2011.00
119_A124_L2.1781.00
240_D243_G2.1701.00
158_E162_R2.1241.00
215_V232_L2.0531.00
136_Q141_E1.9951.00
9_G127_L1.9791.00
77_W104_H1.9591.00
151_E198_V1.9581.00
134_L138_E1.9051.00
217_P243_G1.8651.00
48_T81_I1.8551.00
128_I153_A1.8541.00
7_W167_L1.8501.00
16_K20_E1.8351.00
136_Q145_V1.8331.00
130_I146_L1.8321.00
134_L181_I1.8151.00
69_M119_A1.7581.00
143_D194_L1.7271.00
112_V128_I1.7101.00
69_M83_P1.7081.00
57_L64_V1.6901.00
44_I95_E1.6841.00
186_D226_Q1.6731.00
94_V119_A1.6161.00
8_V224_I1.6151.00
95_E127_L1.5931.00
147_K194_L1.5911.00
193_R197_E1.5901.00
40_Q208_P1.5861.00
143_D190_A1.5731.00
9_G42_F1.5641.00
41_R248_L1.5611.00
188_A223_L1.5521.00
7_W42_F1.5471.00
120_V166_V1.5461.00
72_D114_L1.5451.00
196_G209_V1.5411.00
109_D152_G1.5281.00
54_K64_V1.5091.00
63_K92_D1.5091.00
68_N105_F1.4951.00
24_F241_V1.4921.00
133_T173_V1.4851.00
188_A226_Q1.4781.00
45_P67_Q1.4621.00
73_D121_K1.4601.00
71_W114_L1.4521.00
66_A86_L1.4321.00
25_A53_V1.4321.00
108_T111_T1.4321.00
185_A222_E1.4211.00
188_A229_I1.4180.99
133_T136_Q1.4170.99
220_C224_I1.4140.99
215_V224_I1.4120.99
136_Q148_R1.4060.99
130_I173_V1.4030.99
21_A49_A1.3890.99
199_A207_V1.3740.99
118_A121_K1.3710.99
50_A66_A1.3620.99
220_C247_I1.3520.99
69_M96_L1.3430.99
164_A206_K1.3200.99
147_K151_E1.3160.99
113_G117_A1.3130.99
46_P49_A1.3120.99
45_P53_V1.3100.99
44_I127_L1.3100.99
66_A94_V1.3080.99
137_R187_Y1.2900.99
218_Q243_G1.2890.99
68_N80_E1.2780.99
185_A188_A1.2750.99
200_E205_V1.2720.99
92_D125_V1.2670.99
70_H105_F1.2650.99
16_K21_A1.2640.99
145_V173_V1.2620.99
94_V124_L1.2540.98
5_G40_Q1.2540.98
72_D77_W1.2130.98
223_L229_I1.2110.98
130_I150_V1.2070.98
189_D227_P1.2070.98
71_W105_F1.1960.98
113_G156_F1.1860.98
215_V234_I1.1740.97
93_I125_V1.1720.97
182_P223_L1.1650.97
187_Y190_A1.1590.97
27_G242_G1.1440.97
42_F93_I1.1370.97
73_D122_H1.1210.96
158_E161_A1.1210.96
4_S230_D1.1140.96
125_V165_P1.1130.96
71_W111_T1.1110.96
17_T49_A1.1050.96
186_D190_A1.1050.96
21_A53_V1.0940.96
51_R55_E1.0920.96
70_H118_A1.0900.95
6_L224_I1.0800.95
103_E133_T1.0780.95
137_R190_A1.0760.95
151_E202_A1.0760.95
226_Q229_I1.0750.95
17_T20_E1.0710.95
83_P118_A1.0680.95
144_T147_K1.0530.94
54_K57_L1.0520.94
159_G204_G1.0500.94
6_L208_P1.0480.94
80_E105_F1.0470.94
23_V27_G1.0470.94
69_M94_V1.0380.94
133_T145_V1.0380.94
7_W210_L1.0380.94
57_L62_V1.0320.93
52_Q55_E1.0220.93
117_A121_K1.0100.92
118_A122_H1.0100.92
197_E201_R1.0090.92
28_L241_V1.0060.92
162_R165_P1.0030.92
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  
2j27A20.96081000.024Contact Map
4mvaA20.98041000.024Contact Map
3ta6A20.97651000.027Contact Map
4g1kA40.97251000.027Contact Map
1m6jA20.98431000.027Contact Map
1aw2A80.97651000.027Contact Map
1yyaA20.96471000.028Contact Map
3m9yA20.96861000.028Contact Map
2btmA20.96471000.029Contact Map
1b9bA20.98041000.029Contact 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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