OPENSEQ.org
4euu gremlin

ID: 1516522185 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 306 (289)
Sequences: 13301 (7774.7)
Seq/Len: 46.024
Nf(neff/√len): 457.3

HHblits Results: (2016_02)
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
116_L211_F4.6571.00
286_E291_K4.0391.00
142_M156_T3.9741.00
13_D25_R3.5791.00
25_R34_L3.5451.00
283_N293_W3.2381.00
123_M207_I3.1871.00
26_G35_F3.1421.00
26_G37_I2.9981.00
28_H31_T2.9591.00
63_N69_K2.9191.00
122_G155_L2.9131.00
136_I210_T2.7601.00
204_L284_I2.7401.00
120_V207_I2.6981.00
288_D291_K2.6831.00
37_I85_I2.6121.00
87_E154_K2.5981.00
14_I22_N2.5791.00
124_N128_E2.5731.00
95_Y139_G2.4311.00
27_R34_L2.3061.00
116_L207_I2.2911.00
14_I17_Q2.2721.00
64_H125_H2.2331.00
112_F215_A2.1141.00
25_R88_F2.0951.00
137_K176_T2.0831.00
71_F87_E2.0751.00
33_D71_F2.0711.00
141_I153_Y2.0651.00
12_S27_R2.0111.00
14_I24_F1.9761.00
175_G180_L1.9191.00
141_I210_T1.9021.00
135_D140_N1.8731.00
181_H202_V1.8001.00
27_R32_G1.7871.00
118_D153_Y1.7821.00
69_K87_E1.7771.00
108_P111_E1.7711.00
23_V36_A1.7671.00
109_E270_S1.7291.00
211_F280_V1.7271.00
117_R121_G1.7171.00
10_L29_K1.7051.00
66_N121_G1.6951.00
213_H219_L1.6791.00
179_Y213_H1.6401.00
93_S96_T1.6341.00
119_V141_I1.6321.00
24_F39_V1.6141.00
115_V153_Y1.5861.00
233_V237_I1.5801.00
70_L84_L1.5761.00
279_P283_N1.5641.00
283_N286_E1.5561.00
181_H184_M1.5321.00
131_I161_A1.5281.00
61_K163_E1.5101.00
123_M136_I1.5091.00
138_P179_Y1.4901.00
124_N296_D1.4881.00
58_V161_A1.4831.00
136_I155_L1.4781.00
109_E274_Q1.4621.00
119_V153_Y1.4621.00
201_T294_G1.4511.00
198_Y202_V1.4341.00
35_F71_F1.4301.00
68_V86_M1.4251.00
89_C154_K1.4141.00
28_H33_D1.4010.99
125_H129_N1.3900.99
12_S25_R1.3710.99
135_D159_G1.3710.99
10_L27_R1.3690.99
35_F85_I1.3580.99
212_Y216_T1.3500.99
137_K140_N1.3260.99
215_A273_L1.3180.99
209_V219_L1.3090.99
67_I126_L1.3040.99
112_F214_A1.2950.99
280_V284_I1.2930.99
208_G284_I1.2820.99
134_R174_Y1.2800.99
118_D150_Q1.2770.99
11_L24_F1.2730.99
95_Y99_E1.2700.99
39_V83_V1.2700.99
89_C142_M1.2630.99
204_L295_F1.2490.99
59_L70_L1.2130.98
90_P147_E1.2110.98
68_V89_C1.1980.98
61_K129_N1.1970.98
42_N75_E1.1920.98
97_V107_L1.1860.98
62_L125_H1.1860.98
62_L126_L1.1840.98
98_L213_H1.1790.98
121_G124_N1.1560.97
59_L86_M1.1480.97
130_G200_A1.1450.97
114_I118_D1.1430.97
18_G21_A1.1400.97
16_G23_V1.1360.97
34_L88_F1.1330.97
293_W297_Q1.1310.97
95_Y213_H1.1250.97
26_G85_I1.1210.97
93_S139_G1.1190.96
119_V210_T1.0990.96
34_L90_P1.0960.96
74_E85_I1.0960.96
68_V156_T1.0940.96
37_I83_V1.0930.96
294_G297_Q1.0870.96
65_K121_G1.0870.96
270_S274_Q1.0810.95
110_S113_L1.0660.95
123_M127_R1.0610.95
119_V122_G1.0480.94
64_H67_I1.0420.94
109_E112_F1.0420.94
284_I293_W1.0420.94
146_G150_Q1.0390.94
283_N297_Q1.0250.93
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  
4im0A10.9151000.076Contact Map
4euuA20.99671000.098Contact Map
4kikA20.94121000.192Contact Map
4ic7A20.92481000.224Contact Map
3utoA20.86931000.228Contact Map
4aojA30.82031000.236Contact Map
4aszA10.84641000.236Contact Map
3zonA10.82681000.236Contact Map
5a46A201000.236Contact Map
4qoxA10.85291000.237Contact 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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