GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
ECD_L

ID: 1513199600 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 261 (254)
Sequences: 298 (234.2)
Seq/Len: 1.173
Nf(neff/√len): 14.7

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: 1.173).

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
125_D128_Y3.1451.00
26_N119_E2.5111.00
119_E254_G2.4860.99
51_K119_E2.3610.99
94_P123_S2.1910.98
235_P238_E2.0780.98
26_N254_G1.9740.96
232_V239_I1.8880.95
146_W165_G1.8200.94
149_I188_F1.7180.91
51_K254_G1.7130.91
129_P132_D1.6920.90
117_V236_T1.6860.90
54_G238_E1.6580.89
51_K233_T1.6510.88
102_T249_K1.6490.88
26_N51_K1.6120.87
61_G85_N1.5970.86
224_G228_Y1.5900.86
118_S236_T1.5900.86
133_V137_F1.5700.85
122_L232_V1.5680.85
119_E234_G1.5610.84
141_D253_V1.4730.79
54_G235_P1.4650.79
104_K126_R1.4530.78
126_R135_N1.4500.78
93_H157_K1.4380.77
22_L188_F1.4230.76
121_Y124_Y1.4120.75
123_S150_E1.4100.75
237_K248_V1.3870.73
111_T241_R1.3740.72
121_Y254_G1.3680.72
51_K234_G1.3610.71
56_K236_T1.3500.70
21_A24_M1.3460.70
68_F220_V1.3420.69
45_T248_V1.3380.69
116_T253_V1.3270.68
62_N129_P1.3240.68
58_A257_E1.3210.68
164_L192_L1.2940.65
234_G254_G1.2790.64
123_S189_I1.2750.64
149_I166_Y1.2540.62
128_Y254_G1.2510.62
49_L61_G1.2410.61
140_Y232_V1.2390.60
55_T58_A1.2280.59
141_D238_E1.2220.59
227_V249_K1.2190.59
123_S152_E1.2160.58
20_V49_L1.2130.58
130_T230_S1.2090.58
152_E228_Y1.2080.58
192_L217_L1.2080.58
150_E231_V1.1930.56
94_P249_K1.1890.56
117_V235_P1.1860.55
126_R136_K1.1800.55
25_P146_W1.1780.55
22_L105_A1.1770.55
114_E131_K1.1730.54
57_T152_E1.1660.54
136_K245_N1.1650.53
41_F128_Y1.1640.53
88_G248_V1.1590.53
120_V192_L1.1500.52
54_G143_S1.1500.52
201_W205_I1.1470.52
113_P258_L1.1470.52
127_A221_E1.1460.52
110_S245_N1.1430.51
123_S249_K1.1430.51
54_G232_V1.1420.51
123_S227_V1.1410.51
129_P226_N1.1390.51
141_D248_V1.1380.51
96_N253_V1.1310.50
25_P165_G1.1280.50
40_L66_E1.1160.49
199_E211_L1.1120.48
132_D254_G1.1110.48
129_P237_K1.1090.48
145_L166_Y1.1020.47
187_Q220_V1.1010.47
192_L243_L1.1010.47
153_K250_S1.1000.47
43_M138_K1.0890.46
11_E64_R1.0880.46
122_L188_F1.0870.46
152_E235_P1.0820.45
110_S240_Q1.0800.45
8_T18_V1.0780.45
137_F144_F1.0780.45
188_F192_L1.0740.45
61_G106_E1.0680.44
112_L116_T1.0670.44
79_Y236_T1.0660.44
113_P215_N1.0640.44
117_V233_T1.0630.44
137_F247_S1.0590.43
192_L195_M1.0590.43
114_E123_S1.0420.42
253_V256_V1.0410.42
154_N238_E1.0360.41
114_E117_V1.0350.41
61_G87_T1.0330.41
103_A166_Y1.0330.41
138_K242_M1.0330.41
231_V234_G1.0320.41
109_L206_S1.0300.40
247_S251_A1.0290.40
30_D42_G1.0280.40
112_L255_E1.0250.40
124_Y230_S1.0250.40
14_E120_V1.0240.40
41_F164_L1.0140.39
102_T250_S1.0140.39
150_E227_V1.0090.39
97_K131_K1.0080.38
84_V92_T1.0050.38
195_M225_V1.0020.38
165_G229_G1.0000.38
192_L206_S1.0000.38
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  
2ki0A10.12647.60.961Contact Map
3pmcA20.29124.50.964Contact Map
3edyA10.46363.80.966Contact Map
3pmdA10.3183.60.966Contact Map
4i0uA100.26823.60.966Contact Map
4ev6A50.27593.40.967Contact Map
2c71A10.44442.80.968Contact Map
1oefA10.0922.70.968Contact Map
1t1eA10.47132.50.969Contact Map
2r91A40.25292.40.969Contact 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.

Page generated in 0.0392 seconds.