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testelo

ID: 1501325049 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 279 (252)
Sequences: 1854 (1200.1)
Seq/Len: 7.357
Nf(neff/√len): 75.6

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: 7.357).

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
93_C225_C3.2221.00
63_I183_G3.0481.00
249_N253_H2.9951.00
50_M132_K2.8631.00
143_F242_I2.6781.00
77_V173_S2.6291.00
74_L176_V2.5531.00
112_W116_F2.3601.00
174_V204_I2.3561.00
41_F126_V2.2311.00
79_E106_R2.2101.00
67_F183_G2.1311.00
122_L149_P2.1251.00
206_L248_S2.1031.00
206_L244_F2.0901.00
139_F143_F2.0851.00
61_F127_I2.0551.00
70_V180_L2.0171.00
50_M53_R1.9931.00
48_R51_A1.9701.00
73_S121_E1.9671.00
126_V130_L1.9091.00
72_L117_S1.8411.00
245_M249_N1.8071.00
122_L126_V1.7561.00
50_M56_F1.6831.00
46_G129_I1.6451.00
69_L121_E1.6351.00
244_F248_S1.6221.00
128_F137_V1.5711.00
114_F117_S1.5491.00
178_M202_T1.5471.00
116_F120_I1.5431.00
65_Y69_L1.5230.99
19_I25_M1.5100.99
250_F255_Y1.4820.99
63_I186_A1.4800.99
173_S204_I1.4650.99
49_I56_F1.4650.99
173_S177_I1.4640.99
39_V146_S1.4590.99
171_N175_H1.4540.99
74_L78_Y1.4490.99
147_V243_F1.4390.99
177_I204_I1.4340.99
175_H178_M1.4290.99
196_W200_H1.4190.99
37_T41_F1.4030.99
144_H171_N1.3980.99
62_M127_I1.3900.99
114_F148_L1.3810.99
210_V244_F1.3360.98
49_I53_R1.3230.98
202_T205_Q1.3220.98
63_I187_F1.3170.98
175_H205_Q1.3150.98
197_W201_M1.3020.98
171_N179_Y1.3020.98
46_G50_M1.2970.98
58_L130_L1.2880.98
41_F46_G1.2800.98
183_G187_F1.2710.98
76_I117_S1.2700.97
68_S120_I1.2670.97
197_W200_H1.2600.97
138_T142_V1.2500.97
62_M131_R1.2460.97
76_I172_S1.2420.97
144_H175_H1.2340.97
35_L146_S1.2280.97
34_I122_L1.2280.97
252_Y256_T1.2270.97
171_N202_T1.2150.96
50_M55_P1.2150.96
35_L39_V1.2140.96
21_G26_G1.2120.96
115_L119_F1.2010.96
90_T94_D1.1990.96
129_I132_K1.1960.96
175_H202_T1.1950.96
53_R132_K1.1940.96
171_N205_Q1.1570.95
242_I245_M1.1550.95
202_T208_Q1.1510.95
248_S252_Y1.1510.95
166_F211_L1.1500.95
184_L191_A1.1470.95
253_H257_K1.1470.95
40_Y45_L1.1400.94
73_S76_I1.1400.94
251_W255_Y1.1350.94
247_F255_Y1.1140.94
205_Q208_Q1.1050.93
134_D137_V1.0980.93
145_H171_N1.0830.92
45_L49_I1.0820.92
175_H179_Y1.0800.92
27_S30_L1.0780.92
111_A168_A1.0760.92
199_K209_F1.0700.92
171_N178_M1.0660.91
59_R63_I1.0610.91
178_M205_Q1.0580.91
101_S104_A1.0570.91
22_Y112_W1.0560.91
241_T245_M1.0550.91
141_H144_H1.0550.91
113_L116_F1.0500.91
252_Y257_K1.0340.90
70_V121_E1.0240.89
179_Y205_Q1.0210.89
239_Y243_F1.0190.89
141_H145_H1.0140.88
58_L61_F1.0130.88
55_P132_K1.0070.88
53_R56_F1.0000.88
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  
3ze3A60.16854.40.972Contact Map
2ks1B10.13984.20.972Contact Map
2wwbC10.12920.976Contact Map
2jwaA20.13261.50.978Contact Map
2ww9C10.07531.50.978Contact Map
4x5mA30.32261.40.978Contact Map
4hkcB10.02511.40.978Contact Map
3he5B30.11111.40.978Contact Map
2rddB10.13261.30.979Contact Map
2losA10.23661.20.979Contact 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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