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T0830 1-340

ID: 1405373854 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 340 (317)
Sequences: 2621 (2122.3)
Seq/Len: 8.268
Nf(neff/√len): 119.2

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: 8.268).

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
121_V167_C3.4571.00
117_L163_G3.3241.00
126_A135_A3.1431.00
96_G106_Q2.9481.00
167_C195_A2.9311.00
199_A207_G2.8191.00
114_S163_G2.6791.00
142_L148_W2.6081.00
193_W236_G2.5361.00
113_L117_L2.5121.00
103_G106_Q2.4081.00
197_G243_I2.3501.00
118_G166_S2.2881.00
158_D203_K2.1891.00
97_Y107_A2.1781.00
200_I240_M2.1341.00
88_F202_T2.1281.00
61_E64_R2.1111.00
171_F195_A2.0591.00
96_G110_A1.9911.00
125_A173_L1.9861.00
119_I139_G1.9731.00
126_A138_T1.9381.00
114_S160_T1.9041.00
67_F98_E1.8791.00
226_G229_R1.8751.00
308_R311_V1.8551.00
97_Y102_L1.8501.00
164_V202_T1.8251.00
128_R174_M1.8131.00
123_M139_G1.8091.00
131_G134_A1.8031.00
115_G152_A1.7821.00
171_F188_W1.7761.00
96_G100_F1.7611.00
175_G189_M1.7561.00
119_I142_L1.7561.00
135_A139_G1.7491.00
193_W197_G1.7341.00
118_G163_G1.7331.00
67_F94_V1.7131.00
207_G211_P1.7101.00
171_F191_A1.7011.00
95_V99_L1.6981.00
62_I82_Y1.6681.00
127_R135_A1.6451.00
64_R68_A1.6331.00
144_A296_W1.5871.00
43_F116_L1.5761.00
56_E108_R1.5741.00
71_D254_R1.5541.00
105_W109_L1.5181.00
122_S142_L1.4861.00
127_R132_A1.4800.99
38_A119_I1.4490.99
85_K91_W1.4490.99
43_F112_A1.4390.99
326_I330_A1.4270.99
173_L323_M1.4160.99
85_K203_K1.4120.99
305_T309_A1.4110.99
194_A243_I1.4090.99
121_V163_G1.4060.99
283_F287_P1.4040.99
85_K270_R1.3940.99
46_L112_A1.3920.99
249_Y253_V1.3880.99
86_P203_K1.3850.99
92_V160_T1.3810.99
164_V198_V1.3780.99
238_V242_V1.3680.99
118_G148_W1.3640.99
271_Y334_F1.3640.99
160_T202_T1.3570.99
128_R177_H1.3540.99
59_Y157_L1.3450.99
190_V235_L1.3340.99
63_S93_T1.3320.99
119_I143_L1.3310.99
152_A159_M1.3310.99
96_G109_L1.3260.99
61_E65_E1.3100.98
135_A138_T1.2990.98
26_A29_G1.2670.98
248_F262_F1.2600.98
170_A174_M1.2590.98
115_G148_W1.2570.98
168_V196_M1.2530.98
65_E76_R1.2510.98
195_A198_V1.2510.98
280_G284_Y1.2410.98
246_P250_L1.2400.98
176_Q218_Y1.2270.97
123_M135_A1.2270.97
129_W173_L1.2260.97
106_Q110_A1.2230.97
245_V249_Y1.2230.97
304_W308_R1.2160.97
84_E266_E1.2060.97
88_F198_V1.2030.97
124_M170_A1.2020.97
89_H157_L1.1970.97
40_V44_V1.1910.97
89_H160_T1.1800.97
82_Y266_E1.1730.96
71_D76_R1.1730.96
82_Y157_L1.1660.96
165_M207_G1.1600.96
243_I246_P1.1480.96
122_S138_T1.1470.96
227_L230_R1.1460.96
39_L43_F1.1400.96
115_G142_L1.1300.95
125_A166_S1.1300.95
188_W191_A1.1280.95
164_V199_A1.1250.95
122_S126_A1.1090.95
75_I90_M1.1060.95
242_V246_P1.1050.94
100_F109_L1.1050.94
107_A155_N1.1010.94
126_A129_W1.0950.94
186_R190_V1.0860.94
29_G32_V1.0840.94
106_Q109_L1.0830.94
201_L247_W1.0820.94
223_R226_G1.0790.94
124_M128_R1.0770.93
72_W94_V1.0670.93
34_F38_A1.0630.93
63_S97_Y1.0590.93
92_V96_G1.0580.93
226_G230_R1.0520.92
102_L107_A1.0440.92
287_P290_I1.0400.92
126_A130_F1.0320.91
91_W201_L1.0260.91
89_H93_T1.0200.91
222_T322_L1.0150.90
85_K247_W1.0130.90
271_Y338_S1.0130.90
169_L323_M1.0120.90
83_F255_N1.0090.90
69_S76_R1.0090.90
329_I333_V1.0090.90
320_P324_A1.0080.90
308_R312_E1.0060.90
280_G285_F1.0060.90
97_Y106_Q1.0060.90
298_G302_K1.0050.90
172_M215_L1.0050.90
111_V155_N1.0030.90
239_V243_I1.0020.90
286_L332_F1.0020.90
164_V195_A1.0010.90
94_V98_E1.0010.90
262_F267_H1.0000.90
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: (12Jul14)
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  
3wajA10.82941000.617Contact Map
3rceA10.797199.90.67Contact Map
3dh4A40.14126.90.967Contact Map
2xq2A10.18246.60.967Contact Map
2z73A20.70594.70.969Contact Map
1zrtD20.17653.50.971Contact Map
2m8rA10.15293.20.972Contact Map
3rkoL20.38822.80.973Contact Map
1fftA202.60.973Contact Map
4p02B10.32942.30.974Contact 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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