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T0806

ID: 1401993600 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 258 (256)
Sequences: 1178 (858.9)
Seq/Len: 4.602
Nf(neff/√len): 53.7

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: 4.602).

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_I4.1591.00
52_I56_L3.5711.00
142_D145_Q2.8451.00
17_L77_R2.8241.00
60_N63_R2.7391.00
100_D223_R2.7331.00
47_S54_D2.5791.00
241_D244_S2.5651.00
81_L101_F2.4661.00
4_L167_V2.4491.00
168_I219_I2.4481.00
92_Q95_T2.3871.00
100_D221_E2.3841.00
149_D153_N2.3641.00
241_D253_K2.1581.00
104_A220_I2.1011.00
187_E248_G2.0821.00
10_T84_K2.0801.00
228_E231_T2.0601.00
3_I219_I2.0321.00
151_I178_S2.0321.00
217_R221_E1.9601.00
96_F217_R1.9351.00
226_K229_Q1.9111.00
244_S253_K1.9001.00
13_Y82_A1.8681.00
109_R158_A1.8351.00
59_I63_R1.8261.00
61_A65_H1.8181.00
137_N140_G1.7981.00
194_L253_K1.7941.00
15_S77_R1.7561.00
246_S249_E1.7160.99
38_A64_F1.7080.99
96_F101_F1.6930.99
168_I230_L1.6530.99
31_S67_W1.6320.99
196_E255_Y1.6300.99
96_F104_A1.6230.99
231_T250_L1.6190.99
18_T81_L1.6150.99
5_I108_L1.6080.99
5_I216_S1.5950.99
192_V249_E1.5600.99
219_I230_L1.5580.99
141_K145_Q1.5530.99
151_I179_V1.5450.99
5_I87_V1.5380.99
26_E154_K1.5330.98
227_P250_L1.5320.98
58_G62_A1.5230.98
214_L236_E1.5140.98
219_I224_L1.5100.98
46_I52_I1.5020.98
103_F107_H1.5020.98
105_Q121_L1.5000.98
168_I191_P1.4910.98
8_A11_L1.4820.98
97_S100_D1.4790.98
37_E135_L1.4720.98
26_E158_A1.4700.98
52_I57_A1.4660.98
224_L229_Q1.4590.98
100_D220_I1.4490.98
76_A123_L1.4460.98
31_S146_F1.4350.97
34_L137_N1.4110.97
81_L96_F1.3990.97
104_A216_S1.3900.97
191_P250_L1.3700.96
80_I91_L1.3610.96
103_F220_I1.3370.96
96_F100_D1.3350.96
195_D205_S1.3330.96
96_F221_E1.3300.95
221_E235_S1.3280.95
47_S52_I1.3280.95
4_L155_L1.3230.95
47_S57_A1.2950.95
240_F250_L1.2940.95
86_D206_F1.2840.94
216_S220_I1.2720.94
75_N125_Q1.2490.93
99_D223_R1.2460.93
84_K94_E1.2460.93
35_I114_L1.2340.92
166_V187_E1.2330.92
166_V227_P1.2290.92
27_L154_K1.2270.92
207_Y254_R1.2210.92
62_A66_D1.2210.92
35_I46_I1.2160.92
13_Y124_M1.1950.91
229_Q232_G1.1930.91
31_S35_I1.1840.90
37_E41_L1.1750.90
30_N139_R1.1720.90
43_P61_A1.1690.90
93_A96_F1.1680.90
192_V203_I1.1580.89
103_F224_L1.1530.89
201_F253_K1.1390.88
38_A41_L1.1340.88
148_G180_K1.1200.87
225_T229_Q1.1090.86
28_L70_D1.0920.85
159_L186_A1.0910.85
71_F75_N1.0880.85
144_Y177_K1.0870.84
12_D84_K1.0840.84
190_K249_E1.0690.83
72_T75_N1.0640.83
93_A217_R1.0620.83
195_D254_R1.0530.82
239_F255_Y1.0500.82
154_K157_E1.0490.81
149_D180_K1.0480.81
10_T89_T1.0430.81
117_V154_K1.0380.81
2_L165_N1.0290.80
153_N183_K1.0140.78
37_E137_N1.0110.78
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  
4a1qA20.259710.10.973Contact Map
3eyiA20.24039.90.973Contact Map
2kyaA10.13185.80.975Contact Map
2vqeB10.47295.60.976Contact Map
1wrdA10.26365.30.976Contact Map
3bbnB10.49225.20.976Contact Map
2ddhA10.41474.80.976Contact Map
4kiyB10.45744.60.977Contact Map
1wy3A10.13184.60.977Contact Map
3arcU20.35274.30.977Contact 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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