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Jerome CLAIN

ID: 1514367964 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 282 (280)
Sequences: 14110 (9749.1)
Seq/Len: 50.393
Nf(neff/√len): 582.6

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: 50.393).

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
95_R113_A4.2841.00
142_K159_V4.0871.00
47_F66_V3.8621.00
189_Q208_Q3.6361.00
209_Y214_K3.3311.00
160_Y165_N3.1771.00
114_Y119_K3.0561.00
67_Y72_D2.7681.00
88_C136_C2.6021.00
237_S254_F2.2721.00
40_G89_G2.2701.00
255_F260_N2.2581.00
135_M183_A2.1981.00
189_Q210_Q2.0871.00
136_C145_V2.0861.00
131_R158_E2.0661.00
95_R115_D2.0071.00
89_G98_C1.9881.00
159_V168_E1.9801.00
47_F68_D1.9671.00
142_K161_E1.9641.00
19_L24_Q1.9611.00
66_V77_S1.9521.00
159_V170_F1.9431.00
182_A231_A1.9351.00
113_A124_V1.9341.00
90_V143_I1.9191.00
113_A122_V1.9151.00
137_V190_I1.8611.00
84_R112_E1.8591.00
208_Q219_L1.8441.00
81_N112_E1.8301.00
42_A96_I1.7911.00
134_A145_V1.7711.00
33_S65_E1.7591.00
237_S256_S1.7361.00
191_Y208_Q1.6911.00
208_Q217_Q1.6791.00
128_N158_E1.6771.00
41_S50_V1.6591.00
94_G117_R1.6311.00
44_L91_T1.6021.00
97_Y113_A1.5741.00
88_C134_A1.5671.00
90_V136_C1.5651.00
92_S138_A1.5551.00
141_N163_K1.5501.00
115_D118_M1.5491.00
144_Y159_V1.5421.00
135_M181_G1.5311.00
66_V75_Y1.5261.00
87_N98_C1.5121.00
183_A192_V1.4931.00
42_A89_G1.4751.00
188_N212_F1.4661.00
99_I143_I1.4611.00
49_Y66_V1.4491.00
18_L29_C1.4421.00
46_N70_L1.4381.00
175_L207_E1.4361.00
183_A190_I1.4341.00
111_V124_V1.4191.00
171_P214_K1.4141.00
40_G87_N1.4121.00
231_A240_I1.4060.99
68_D71_R1.3970.99
131_R156_S1.3940.99
103_D108_I1.3740.99
209_Y216_W1.3590.99
146_I157_I1.3540.99
184_F233_T1.3510.99
114_Y121_W1.3490.99
139_F211_P1.3410.99
84_R110_N1.3360.99
43_V69_R1.3320.99
55_N61_L1.3310.99
99_I111_V1.3230.99
184_F238_Y1.3100.99
178_R207_E1.3100.99
97_Y111_V1.3090.99
90_V138_A1.3070.99
161_E164_M1.3040.99
125_A165_N1.3000.99
78_S119_K1.2850.99
178_R205_S1.2800.99
181_G192_V1.2770.99
67_Y74_W1.2740.99
139_F185_N1.2700.99
51_F89_G1.2690.99
182_A229_F1.2640.99
42_A91_T1.2630.99
229_F240_I1.2580.99
49_Y96_I1.2580.99
223_P253_H1.2490.99
136_C143_I1.2460.98
36_K65_E1.2370.98
210_Q213_N1.2320.98
137_V183_A1.2300.98
44_L116_H1.2270.98
184_F231_A1.2220.98
197_D203_L1.2220.98
207_E218_F1.2200.98
193_V206_V1.2200.98
239_I254_F1.2180.98
143_I162_E1.2180.98
51_F64_T1.2160.98
112_E123_E1.2150.98
50_V74_W1.2130.98
51_F96_I1.2090.98
150_N154_L1.2090.98
138_A162_E1.2090.98
144_Y157_I1.2040.98
91_T116_H1.2020.98
64_T114_Y1.1870.98
256_S259_T1.1850.98
124_V165_N1.1780.98
144_Y190_I1.1780.98
158_E169_Q1.1720.98
178_R181_G1.1700.97
137_V185_N1.1600.97
226_K253_H1.1570.97
146_I190_I1.1460.97
97_Y143_I1.1420.97
92_S162_E1.1290.97
64_T77_S1.1250.97
226_K243_G1.1250.97
96_I116_H1.1240.97
186_Y233_T1.1200.96
170_F214_K1.1190.96
41_S48_L1.1170.96
102_Y132_S1.1020.96
84_R87_N1.0980.96
99_I136_C1.0970.96
65_E76_V1.0950.96
193_V231_A1.0910.96
2_F18_L1.0860.96
89_G96_I1.0830.96
30_T72_D1.0820.96
107_I132_S1.0730.95
111_V160_Y1.0700.95
36_K63_E1.0630.95
254_F265_G1.0620.95
206_V219_L1.0570.95
49_Y64_T1.0570.95
220_N260_N1.0540.95
231_A238_Y1.0470.94
254_F263_Q1.0420.94
157_I170_F1.0410.94
128_N167_W1.0220.93
48_L69_R1.0070.93
77_S119_K1.0060.93
190_I211_P1.0040.93
94_G116_H1.0010.92
226_K251_S1.0010.92
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  
4yy8A21100-0.003Contact Map
1zgkA10.98231000.044Contact Map
3ii7A10.97521000.05Contact Map
4chbA20.98581000.053Contact Map
2vpjA10.98941000.063Contact Map
2wozA10.95391000.126Contact Map
4ascA10.95041000.127Contact Map
2uvkA20.91841000.166Contact Map
1k3iA10.97521000.202Contact Map
2zwaA20.90071000.226Contact 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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