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T0808 150-418 -force run

ID: 1405031266 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 269 (265)
Sequences: 108 (93)
Seq/Len: 0.408
Nf(neff/√len): 5.7

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: 0.408).

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
77_N80_E2.3290.92
71_S106_S2.2030.89
126_M140_A2.0740.84
90_L156_F2.0120.82
24_E127_Q1.9790.80
204_T252_C1.9710.80
128_I165_Y1.9260.78
25_W141_Y1.8700.75
210_H246_M1.7730.69
66_L109_Q1.7710.69
41_S96_V1.7120.65
188_F234_L1.7100.65
120_N144_A1.6650.62
214_A222_Y1.6590.62
25_W167_R1.5900.57
202_R252_C1.5820.56
14_L186_V1.5480.54
156_F218_V1.5450.53
179_Q237_G1.4790.49
61_T86_K1.4730.48
26_F168_P1.4230.45
31_T121_T1.4120.44
45_A124_F1.3930.42
30_I179_Q1.3650.40
193_A257_K1.3620.40
122_Y142_F1.3530.40
40_H236_M1.3520.39
5_W223_Q1.3480.39
125_L200_W1.3360.38
38_T237_G1.3090.37
10_P180_G1.3040.36
14_L206_A1.3020.36
44_M66_L1.2940.36
71_S81_I1.2770.34
126_M165_Y1.2700.34
62_E174_N1.2660.34
254_P257_K1.2650.34
65_I186_V1.2600.33
5_W87_I1.2530.33
23_T83_D1.2460.32
83_D132_G1.2440.32
82_P103_N1.2340.32
40_H43_Y1.2220.31
45_A65_I1.2180.31
257_K262_D1.2140.30
8_R224_G1.2110.30
160_K237_G1.2010.30
99_G103_N1.1960.29
134_G263_W1.1850.29
24_E129_R1.1820.28
188_F243_S1.1790.28
40_H76_Q1.1770.28
25_W203_L1.1760.28
30_I260_E1.1740.28
260_E264_E1.1730.28
27_Y192_W1.1650.27
135_N157_L1.1630.27
71_S75_T1.1610.27
37_E40_H1.1560.27
19_P208_F1.1550.27
122_Y161_T1.1550.27
184_R232_F1.1540.27
76_Q166_K1.1440.26
66_L111_Y1.1430.26
16_Y28_N1.1420.26
10_P221_D1.1380.26
74_D230_N1.1370.26
169_H263_W1.1270.25
37_E57_Y1.1260.25
98_I166_K1.1260.25
188_F195_S1.1250.25
28_N234_L1.1230.25
55_M83_D1.1210.25
255_T265_A1.1190.25
46_A66_L1.1110.24
65_I212_A1.1090.24
50_E163_T1.1020.24
183_S235_K1.1010.24
66_L154_A1.1000.24
131_D134_G1.1000.24
33_P37_E1.1000.24
6_G71_S1.0990.24
84_D88_K1.0960.24
21_G167_R1.0940.23
253_K258_E1.0930.23
55_M65_I1.0910.23
204_T256_G1.0880.23
77_N143_Y1.0870.23
178_E250_F1.0860.23
137_T160_K1.0860.23
24_E186_V1.0850.23
35_E148_K1.0820.23
47_G67_F1.0810.23
185_E228_K1.0810.23
83_D260_E1.0800.23
14_L103_N1.0800.23
28_N188_F1.0760.23
213_T250_F1.0730.22
29_E219_R1.0710.22
248_T254_P1.0700.22
53_F206_A1.0680.22
71_S78_P1.0680.22
117_K264_E1.0660.22
262_D265_A1.0650.22
205_D251_Y1.0640.22
39_M246_M1.0620.22
128_I135_N1.0580.22
103_N152_L1.0570.22
17_A258_E1.0550.22
255_T264_E1.0530.21
170_S206_A1.0450.21
108_G119_G1.0450.21
164_W213_T1.0420.21
207_T215_S1.0380.21
14_L53_F1.0370.21
141_Y167_R1.0370.21
21_G195_S1.0360.21
103_N106_S1.0360.21
189_G262_D1.0360.21
90_L167_R1.0350.21
260_E265_A1.0350.21
3_D202_R1.0340.20
71_S100_E1.0320.20
81_I106_S1.0320.20
183_S205_D1.0320.20
194_R258_E1.0320.20
30_I247_G1.0300.20
58_N64_R1.0260.20
165_Y168_P1.0240.20
4_Y161_T1.0240.20
30_I197_E1.0230.20
134_G234_L1.0210.20
43_Y193_A1.0200.20
180_G221_D1.0200.20
172_L237_G1.0140.20
40_H211_D1.0130.20
131_D216_A1.0130.20
39_M264_E1.0120.19
112_L153_I1.0100.19
4_Y250_F1.0090.19
192_W200_W1.0090.19
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: (05Jul14)
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  
2ww6A30.092911.10.975Contact Map
4h62V10.02976.10.978Contact Map
3ii7A10.46845.50.978Contact Map
4ascA10.56885.50.978Contact Map
1yo8A10.5133.20.981Contact Map
3owtC10.04093.10.981Contact Map
1zg2A10.32342.80.981Contact Map
3uzeC20.04092.60.982Contact Map
3l3fX10.15242.50.982Contact Map
3obaA40.44982.50.982Contact 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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