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T0806

ID: 1401990630 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 258 (257)
Sequences: 947 (715.4)
Seq/Len: 3.685
Nf(neff/√len): 44.6

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: 3.685).

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
52_I56_L3.6611.00
30_N150_I3.5441.00
142_D145_Q3.0371.00
60_N63_R2.6601.00
100_D223_R2.5901.00
241_D244_S2.5261.00
47_S54_D2.4071.00
81_L101_F2.3641.00
226_K229_Q2.2801.00
187_E248_G2.2631.00
100_D221_E2.2431.00
104_A220_I2.2351.00
61_A65_H2.1931.00
217_R221_E2.1901.00
92_Q95_T2.1751.00
3_I219_I2.1721.00
168_I219_I2.1611.00
4_L167_V2.1551.00
228_E231_T2.1471.00
17_L77_R2.1461.00
96_F100_D2.0821.00
10_T84_K1.9681.00
241_D253_K1.9681.00
137_N140_G1.8971.00
149_D153_N1.8651.00
38_A64_F1.8411.00
5_I216_S1.8411.00
103_F107_H1.8340.99
151_I178_S1.8110.99
97_S100_D1.8090.99
227_P250_L1.7900.99
246_S249_E1.7110.99
96_F101_F1.6890.99
231_T250_L1.6850.99
104_A216_S1.6840.99
194_L253_K1.6810.99
100_D220_I1.6770.99
5_I108_L1.6630.99
96_F217_R1.6630.99
26_E154_K1.6570.99
5_I87_V1.6300.99
86_D206_F1.6300.99
59_I63_R1.6080.98
46_I52_I1.5940.98
13_Y82_A1.5900.98
219_I224_L1.5570.98
31_S67_W1.5190.97
244_S253_K1.5110.97
105_Q121_L1.5040.97
58_G62_A1.4970.97
195_D205_S1.4880.97
15_S77_R1.4360.96
90_G210_K1.4090.95
52_I57_A1.4020.95
103_F220_I1.3820.95
81_L96_F1.3660.94
201_F253_K1.3570.94
10_T89_T1.3570.94
141_K145_Q1.3420.94
76_A123_L1.3400.94
208_A212_R1.3360.93
28_L70_D1.3240.93
196_E255_Y1.3220.93
219_I230_L1.3030.92
109_R158_A1.2950.92
113_G131_M1.2910.92
91_L216_S1.2820.91
214_L236_E1.2820.91
96_F104_A1.2790.91
168_I191_P1.2580.90
247_N250_L1.2570.90
196_E256_E1.2560.90
87_V206_F1.2420.90
240_F250_L1.2300.89
191_P250_L1.2240.89
99_D223_R1.2230.89
26_E158_A1.2210.89
192_V249_E1.2180.88
62_A66_D1.2080.88
151_I179_V1.2020.88
31_S146_F1.1880.87
84_K89_T1.1790.86
8_A11_L1.1740.86
207_Y254_R1.1590.85
37_E135_L1.1430.84
149_D180_K1.1370.83
2_L165_N1.1220.82
224_L229_Q1.1190.82
22_Y73_P1.1180.82
37_E41_L1.1010.80
35_I114_L1.1000.80
18_T81_L1.0980.80
95_T217_R1.0960.80
42_T45_Q1.0890.79
84_K94_E1.0880.79
4_L155_L1.0860.79
87_V204_I1.0820.79
95_T221_E1.0770.78
154_K157_E1.0680.78
79_A88_Y1.0640.77
131_M175_Y1.0470.76
221_E235_S1.0430.75
27_L196_E1.0410.75
148_G151_I1.0390.75
216_S220_I1.0360.75
166_V187_E1.0350.74
239_F255_Y1.0330.74
77_R82_A1.0280.74
173_D190_K1.0280.74
12_D82_A1.0260.74
113_G130_E1.0230.73
47_S52_I1.0160.72
155_L184_L1.0070.72
250_L253_K1.0030.71
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: (29May14)
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  
3eyiA20.240314.80.966Contact Map
4glxA10.32567.80.97Contact Map
4a1qA20.25977.70.97Contact Map
1wrdA10.26746.60.971Contact Map
4ou0A10.22876.10.972Contact Map
2duyA10.24815.70.972Contact Map
2yfvC10.22095.30.972Contact Map
3hixA30.33335.30.972Contact Map
1pavA10.29844.40.974Contact Map
1wgrA10.28684.30.974Contact 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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