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T0806

ID: 1403287152 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 258 (256)
Sequences: 1627 (1188)
Seq/Len: 6.355
Nf(neff/√len): 74.2

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: 6.355).

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
30_N150_I3.9451.00
52_I56_L3.4951.00
92_Q95_T2.9551.00
142_D145_Q2.6221.00
241_D244_S2.6161.00
81_L101_F2.5681.00
60_N63_R2.5361.00
100_D221_E2.4311.00
217_R221_E2.4071.00
226_K229_Q2.3791.00
149_D153_N2.3561.00
104_A220_I2.3521.00
47_S54_D2.3441.00
100_D223_R2.2721.00
17_L77_R2.2171.00
168_I219_I2.2161.00
241_D253_K2.1751.00
4_L167_V2.1511.00
10_T84_K2.1331.00
97_S100_D2.1231.00
137_N140_G2.1101.00
3_I219_I2.0651.00
244_S253_K1.9661.00
61_A65_H1.9611.00
187_E248_G1.9241.00
96_F217_R1.9011.00
228_E231_T1.8591.00
246_S249_E1.8021.00
13_Y82_A1.7561.00
196_E255_Y1.7341.00
131_M178_S1.7131.00
26_E154_K1.6911.00
105_Q121_L1.6831.00
103_F107_H1.6661.00
194_L253_K1.6651.00
96_F100_D1.6621.00
8_A11_L1.6401.00
151_I178_S1.6361.00
219_I224_L1.6151.00
5_I87_V1.6041.00
219_I230_L1.6041.00
100_D220_I1.6011.00
5_I216_S1.5971.00
31_S67_W1.5750.99
96_F101_F1.5710.99
38_A64_F1.5700.99
59_I63_R1.5490.99
214_L236_E1.5420.99
192_V249_E1.5350.99
104_A216_S1.5260.99
26_E158_A1.5140.99
109_R158_A1.5080.99
231_T250_L1.5060.99
58_G62_A1.4910.99
96_F104_A1.4750.99
5_I108_L1.4620.99
37_E135_L1.4490.99
227_P250_L1.4110.99
151_I179_V1.4100.99
86_D206_F1.3910.98
103_F220_I1.3910.98
141_K145_Q1.3810.98
2_L165_N1.3650.98
191_P250_L1.3540.98
15_S77_R1.3530.98
90_G210_K1.3520.98
46_I52_I1.3500.98
4_L155_L1.3400.98
208_A212_R1.3270.98
196_E201_F1.3250.98
18_T81_L1.2970.97
168_I191_P1.2800.97
240_F250_L1.2650.97
12_D84_K1.2650.97
75_N125_Q1.2610.96
154_K157_E1.2580.96
62_A66_D1.2520.96
224_L229_Q1.2480.96
81_L96_F1.2430.96
216_S220_I1.2300.96
76_A123_L1.2150.95
84_K94_E1.2140.95
144_Y177_K1.2080.95
99_D223_R1.2050.95
113_G131_M1.2040.95
52_I57_A1.2020.95
91_L216_S1.2010.95
221_E235_S1.1970.95
77_R82_A1.1940.95
28_L70_D1.1910.95
83_F118_L1.1900.95
225_T229_Q1.1890.95
201_F253_K1.1880.95
207_Y254_R1.1580.94
37_E41_L1.1510.93
96_F221_E1.1330.93
80_I91_L1.1260.92
148_G180_K1.1160.92
47_S57_A1.1140.92
196_E199_G1.1070.91
12_D77_R1.1040.91
118_L124_M1.0890.90
30_N139_R1.0880.90
47_S52_I1.0840.90
239_F255_Y1.0780.90
35_I114_L1.0590.89
31_S35_I1.0570.89
166_V227_P1.0560.89
27_L154_K1.0510.88
82_A126_P1.0490.88
111_L179_V1.0430.88
13_Y124_M1.0410.88
190_K249_E1.0260.87
53_S56_L1.0240.86
37_E137_N1.0220.86
159_L186_A1.0210.86
195_D205_S1.0180.86
32_Q36_H1.0160.86
31_S146_F1.0150.86
194_L201_F1.0140.86
168_I230_L1.0120.86
102_D106_Q1.0080.85
41_L46_I1.0070.85
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: (14Jun14)
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  
4glxA10.325623.50.962Contact Map
3eyiA20.240318.70.964Contact Map
4gfjA10.073612.50.967Contact Map
2yfvC10.22099.60.968Contact Map
3bbnB10.47679.50.968Contact Map
4ou0A10.22878.60.969Contact Map
3hixA30.33337.10.97Contact Map
2duyA10.24816.40.971Contact Map
3sgiA106.40.971Contact Map
4a1qA20.25975.80.971Contact 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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