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p5cr

ID: 1505113320 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 263 (260)
Sequences: 13232 (8345.7)
Seq/Len: 50.892
Nf(neff/√len): 517.6

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: 50.892).

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
139_D143_K3.4781.00
105_R134_D3.1721.00
71_E95_T2.7401.00
4_Y58_D2.7121.00
2_N26_R2.6311.00
70_M88_A2.5701.00
188_D191_E2.5411.00
4_Y54_E2.1861.00
132_E136_R2.1671.00
109_V122_S2.0251.00
8_G29_I2.0181.00
149_V194_A2.0151.00
2_N28_Y1.9991.00
31_N36_K1.9591.00
171_V200_F1.9191.00
2_N59_D1.9011.00
139_D150_W1.8871.00
64_A87_V1.8811.00
63_L84_V1.8771.00
131_S134_D1.8541.00
147_L194_A1.8531.00
119_L205_A1.8301.00
34_A38_E1.8221.00
179_Q193_R1.8201.00
136_R139_D1.8101.00
71_E75_K1.8081.00
60_V83_L1.8031.00
41_E49_S1.7971.00
174_L244_I1.7961.00
183_I189_M1.7911.00
126_A135_R1.7881.00
121_V147_L1.7341.00
29_I46_V1.6921.00
135_R150_W1.6721.00
85_L138_A1.6651.00
5_F16_A1.6571.00
205_A209_Q1.6521.00
249_C253_R1.6381.00
69_D72_A1.6071.00
83_L138_A1.6041.00
172_F203_A1.5921.00
83_L134_D1.5811.00
37_R49_S1.5731.00
175_L207_A1.5711.00
28_Y50_A1.5641.00
167_G199_T1.5541.00
28_Y47_E1.5541.00
216_K220_N1.5451.00
197_L208_E1.5261.00
250_A253_R1.5251.00
201_K205_A1.5161.00
28_Y57_S1.5121.00
38_E42_K1.5101.00
63_L70_M1.5091.00
15_V145_V1.4961.00
190_A194_A1.4801.00
143_K148_T1.4611.00
11_M87_V1.4231.00
30_A52_L1.4111.00
36_K39_R1.4081.00
65_V73_A1.4060.99
5_F12_A1.3790.99
62_I85_L1.3750.99
109_V142_M1.3670.99
212_E220_N1.3650.99
140_R143_K1.3360.99
132_E150_W1.3360.99
5_F62_I1.3350.99
236_R241_A1.3310.99
158_H255_S1.3250.99
2_N57_S1.3190.99
38_E41_E1.3170.99
254_R257_E1.3150.99
17_G43_E1.3130.99
54_E58_D1.3040.99
16_A27_I1.3020.99
86_S96_L1.3020.99
31_N37_R1.2940.99
35_E38_E1.2820.99
60_V85_L1.2570.99
174_L240_V1.2540.99
229_H233_E1.2530.99
97_S101_G1.2500.99
135_R139_D1.2480.99
107_V138_A1.2380.98
123_G160_I1.2090.98
216_K219_K1.2080.98
242_E246_E1.1970.98
246_E250_A1.1940.98
62_I87_V1.1900.98
28_Y58_D1.1900.98
213_D216_K1.1880.98
32_R69_D1.1860.98
182_A192_A1.1840.98
149_V191_E1.1690.97
72_A75_K1.1680.97
237_R246_E1.1680.97
153_D156_K1.1650.97
60_V137_I1.1620.97
33_G36_K1.1580.97
18_G21_K1.1550.97
3_V19_L1.1500.97
75_K99_Y1.1480.97
205_A208_E1.1230.97
252_V256_Q1.1190.96
18_G145_V1.1170.96
253_R257_E1.1150.96
4_Y30_A1.1130.96
17_G44_L1.0910.96
39_R42_K1.0800.95
230_E233_E1.0790.95
234_A237_R1.0780.95
15_V19_L1.0700.95
15_V64_A1.0690.95
12_A16_A1.0660.95
180_N189_M1.0650.95
13_A36_K1.0630.95
193_R197_L1.0610.95
74_C84_V1.0600.95
13_A39_R1.0590.95
137_I140_R1.0560.95
180_N241_A1.0550.95
180_N183_I1.0450.94
130_V134_D1.0420.94
65_V88_A1.0400.94
158_H256_Q1.0380.94
182_A187_F1.0360.94
63_L74_C1.0360.94
114_P120_G1.0350.94
198_A201_K1.0330.94
53_P56_H1.0320.94
55_L61_L1.0290.94
191_E194_A1.0260.94
170_Y231_A1.0240.93
98_R102_G1.0220.93
171_V174_L1.0210.93
184_R245_S1.0200.93
152_D156_K1.0100.93
1_M25_Y1.0040.93
75_K78_R1.0020.92
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  
2ahrA50.96581000.241Contact Map
1yqgA10.99241000.245Contact Map
2izzA50.98861000.247Contact Map
2rcyA50.95821000.255Contact Map
3triA20.99241000.265Contact Map
3gt0A10.78331000.313Contact Map
4kqwA20.96961000.393Contact Map
4wjiA10.9621000.403Contact Map
4d3sA80.965899.90.411Contact Map
4d3dA20.96299.90.413Contact 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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