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1k30A_EvalDCA_aln

ID: 1500066090 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 234 (216)
Sequences: 3485 (2361.6)
Seq/Len: 16.134
Nf(neff/√len): 160.7

Jackhmmer Results: (2016_04)
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: 16.134).

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
17_K200_P4.2291.00
13_D197_S3.0481.00
14_I17_K2.8061.00
24_V117_L2.6591.00
109_L113_G2.5211.00
144_S148_N2.3831.00
166_A199_A2.2931.00
42_L198_V2.1321.00
26_L117_L2.0371.00
165_L198_V1.9731.00
218_R222_S1.9541.00
65_D68_C1.8761.00
222_S226_F1.8041.00
59_G125_G1.7851.00
60_D64_A1.7531.00
224_A228_S1.7501.00
223_K227_D1.7271.00
106_E109_L1.6631.00
13_D195_G1.6581.00
24_V163_F1.6551.00
58_A63_L1.6331.00
23_N115_S1.6211.00
206_E224_A1.5681.00
108_A112_R1.5551.00
70_P74_G1.5361.00
60_D93_T1.5061.00
219_E222_S1.4901.00
219_E223_K1.4861.00
220_A224_A1.4821.00
127_D130_D1.4781.00
221_Y224_A1.4651.00
110_L116_Q1.4571.00
138_P141_F1.4531.00
151_R155_H1.4531.00
217_V222_S1.4511.00
142_D145_S1.4401.00
11_F193_G1.4301.00
113_G116_Q1.4281.00
111_L152_L1.4221.00
215_E218_R1.4201.00
31_Q126_R1.4081.00
159_P203_S1.3920.99
148_N153_I1.3770.99
55_I116_Q1.3660.99
105_K108_A1.3650.99
97_R100_N1.3600.99
28_S165_L1.3490.99
69_K73_I1.3480.99
178_Q181_I1.3430.99
181_I184_G1.3300.99
217_V221_Y1.3180.99
102_R105_K1.3140.99
126_R130_D1.3130.99
36_P40_S1.3120.99
218_R221_Y1.3000.99
217_V220_A1.2920.99
99_A102_R1.2890.99
110_L118_I1.2860.99
78_I110_L1.2820.99
62_V72_S1.2750.99
66_P69_K1.2660.99
26_L163_F1.2640.99
207_I224_A1.2520.99
134_G137_Y1.2510.99
54_T119_W1.2400.98
14_I18_L1.2260.98
164_P201_E1.2240.98
63_L79_C1.2150.98
39_I167_L1.2140.98
220_A223_K1.2090.98
222_S225_L1.2080.98
19_Q22_H1.2040.98
178_Q182_E1.1960.98
106_E110_L1.1950.98
141_F146_V1.1910.98
28_S119_W1.1890.98
179_V182_E1.1840.98
107_M118_I1.1710.98
147_D150_R1.1680.97
31_Q169_C1.1680.97
26_L43_L1.1660.97
216_E220_A1.1590.97
157_D208_A1.1580.97
58_A77_L1.1520.97
108_A156_S1.1500.97
62_V68_C1.1480.97
177_S180_E1.1480.97
104_L108_A1.1440.97
19_Q24_V1.1390.97
72_S77_L1.1350.97
104_L152_L1.1340.97
94_E100_N1.1290.97
80_V100_N1.1180.96
162_L204_F1.1100.96
67_L70_P1.1090.96
107_M152_L1.1030.96
226_F229_V1.1020.96
39_I165_L1.1000.96
25_V152_L1.0990.96
96_K99_A1.0960.96
228_S231_M1.0960.96
70_P73_I1.0870.96
223_K226_F1.0850.96
176_P180_E1.0840.96
31_Q170_H1.0700.95
182_E185_E1.0670.95
228_S232_Q1.0650.95
57_V118_I1.0630.95
224_A227_D1.0620.95
141_F145_S1.0610.95
171_D192_N1.0510.94
148_N152_L1.0510.94
59_G62_V1.0380.94
149_M153_I1.0370.94
169_C174_P1.0360.94
25_V120_I1.0360.94
218_R226_F1.0350.94
147_D151_R1.0350.94
105_K109_L1.0320.94
141_F144_S1.0240.93
111_L158_V1.0230.93
98_K101_T1.0230.93
32_T123_S1.0190.93
39_I121_A1.0010.92
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  
1iuqA10.95731000.199Contact Map
1pn9A20.367550.955Contact Map
3einA10.3593.40.959Contact Map
3ay8A10.38463.40.959Contact Map
2hdcA10.15813.10.959Contact Map
1r5aA10.37613.10.959Contact Map
1axdA20.337630.96Contact Map
1ewqA20.40172.90.96Contact Map
4pngA202.80.96Contact Map
4w20Z10.49152.70.96Contact 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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