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Tsal_Coevolution Analysis_Iterations8 Coverage90RemoveGaps75Eval1E-10HHBlit

ID: 1513840998 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 307 (301)
Sequences: 365 (236.1)
Seq/Len: 1.213
Nf(neff/√len): 13.6

HHblits Results: (2016_02)
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: 1.213).

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
212_V232_C3.3111.00
242_R248_E3.0451.00
63_A80_R2.7511.00
146_H269_R2.6051.00
231_L287_L2.5831.00
199_G202_F2.5261.00
231_L290_T2.5151.00
73_R181_D2.4520.99
89_Q93_L2.3310.99
207_V283_I2.2570.99
42_D107_R2.0900.98
18_F78_H1.9970.97
65_F105_A1.9640.96
213_V242_R1.9310.96
289_D293_Q1.7750.93
214_S225_R1.7400.92
207_V228_V1.7320.92
45_Y169_W1.7260.91
205_F258_S1.7150.91
204_V286_R1.6960.90
50_V91_V1.6140.87
148_I184_A1.6090.87
214_S256_F1.5940.86
227_T294_W1.5890.86
255_I275_L1.5490.84
23_Y93_L1.5430.84
211_A240_E1.5290.83
201_G261_A1.5190.83
56_F227_T1.4940.81
188_V204_V1.4500.78
49_H260_T1.4390.78
26_A130_I1.4140.76
36_W39_G1.4100.76
76_L142_E1.3850.74
203_N222_G1.3790.73
35_D108_G1.3770.73
59_D84_A1.3730.73
66_E80_R1.3700.73
65_F103_M1.3570.72
47_V197_T1.3500.71
79_D82_E1.3490.71
184_A284_S1.3480.71
275_L278_D1.3380.70
16_A23_Y1.3370.70
108_G165_K1.3370.70
151_K178_E1.3330.70
89_Q229_F1.3030.67
35_D42_D1.2940.66
229_F239_W1.2870.66
249_L280_P1.2770.65
280_P288_K1.2770.65
27_G31_I1.2740.65
38_F43_V1.2650.64
87_L127_A1.2560.63
246_A250_R1.2520.63
62_L84_A1.2490.62
188_V276_S1.2390.61
21_G81_G1.2340.61
57_R60_H1.2160.59
57_R227_T1.2060.58
252_A255_I1.2040.58
38_F104_I1.1990.58
224_T252_A1.1990.58
72_L227_T1.1950.57
39_G104_I1.1930.57
46_D263_G1.1910.57
147_L250_R1.1900.57
46_D65_F1.1880.57
125_F244_I1.1730.55
191_D195_L1.1640.54
122_Q285_A1.1600.54
215_P264_V1.1520.53
255_I267_A1.1500.53
165_K170_G1.1490.53
147_L212_V1.1490.53
70_A85_E1.1460.53
250_R271_D1.1430.52
207_V248_E1.1310.51
118_P283_I1.1310.51
23_Y89_Q1.1240.50
279_R286_R1.1200.50
54_A301_A1.1190.50
205_F225_R1.1180.50
244_I255_I1.1160.50
53_G108_G1.1050.49
111_L137_P1.1040.48
32_S112_P1.1040.48
208_K213_V1.1010.48
12_F207_V1.1010.48
29_A225_R1.0990.48
219_A275_L1.0960.48
228_V267_A1.0900.47
22_R267_A1.0870.47
40_K110_P1.0860.47
25_P28_E1.0840.47
278_D281_G1.0810.46
57_R189_L1.0800.46
155_I160_V1.0800.46
293_Q297_E1.0800.46
50_V101_V1.0790.46
52_G108_G1.0750.46
247_D293_Q1.0750.46
73_R218_G1.0740.46
115_P121_M1.0700.45
25_P267_A1.0660.45
8_T11_D1.0640.45
246_A271_D1.0630.45
268_S280_P1.0570.44
76_L212_V1.0560.44
230_D286_R1.0540.44
32_S212_V1.0520.43
233_D239_W1.0510.43
92_R306_Y1.0500.43
157_P249_L1.0500.43
44_T72_L1.0480.43
29_A38_F1.0480.43
57_R73_R1.0390.42
55_F87_L1.0350.42
81_G241_I1.0330.42
51_W263_G1.0310.41
198_E254_E1.0290.41
262_G265_M1.0290.41
44_T259_T1.0260.41
87_L123_N1.0240.41
145_A265_M1.0230.41
45_Y166_N1.0230.41
31_I233_D1.0210.40
196_V223_I1.0200.40
239_W285_A1.0100.39
77_P86_I1.0100.39
62_L87_L1.0090.39
39_G121_M1.0080.39
232_C293_Q1.0080.39
137_P207_V1.0060.39
28_E291_Y1.0050.39
134_D291_Y1.0030.39
209_A244_I1.0030.39
196_V248_E1.0030.39
18_F56_F1.0020.39
122_Q243_A1.0010.39
97_R306_Y1.0010.39
44_T105_A1.0000.39
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: (06Aug15)
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  
4chiA20.99671000.322Contact Map
3u0gA60.95441000.349Contact Map
1iyeA30.95111000.351Contact Map
4cmfA10.9871000.352Contact Map
2eiyA30.95441000.352Contact Map
4tm5A10.91211000.38Contact Map
3daaA20.89251000.385Contact Map
4tviA20.89581000.4Contact Map
4dqnA10.97071000.401Contact Map
4jxuA20.90881000.405Contact 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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