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ID: 1513879389 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 307 (290)
Sequences: 12766 (7339.2)
Seq/Len: 44.021
Nf(neff/√len): 431.0

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: 44.021).

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
259_F267_F3.3791.00
165_A173_L3.3251.00
66_V74_L2.8191.00
253_N257_K2.8101.00
162_R166_T2.8091.00
258_V266_A2.7701.00
159_N163_I2.6911.00
256_M260_T2.6321.00
257_K261_N2.6221.00
63_T67_K2.5871.00
163_I167_T2.5491.00
164_I172_G2.4211.00
60_G64_A2.3901.00
99_V122_T2.3351.00
255_A267_F2.2721.00
155_T159_N2.2491.00
64_A68_T2.2281.00
161_Y173_L2.1351.00
236_V255_A2.0981.00
262_E266_A2.0661.00
239_R262_E2.0241.00
121_L185_V1.9921.00
228_A271_L1.9691.00
99_V126_V1.9551.00
291_Q294_R1.8781.00
250_S253_N1.8431.00
95_L99_V1.8311.00
38_K42_Q1.7881.00
65_V73_K1.7801.00
202_F218_S1.7261.00
117_I189_C1.7221.00
284_I288_C1.7161.00
154_Y160_A1.7151.00
288_C292_L1.7081.00
249_K253_N1.7081.00
248_Y254_C1.7041.00
62_I74_L1.6961.00
259_F264_P1.6791.00
248_Y253_N1.6711.00
197_L201_A1.6661.00
140_R168_E1.6631.00
40_R69_E1.6621.00
168_E172_G1.6551.00
103_L119_A1.6421.00
156_G159_N1.6351.00
194_T225_C1.6261.00
252_P256_M1.6181.00
159_N162_R1.5981.00
22_I292_L1.5911.00
32_F36_T1.5871.00
35_D38_K1.5781.00
43_V143_A1.5721.00
99_V119_A1.5641.00
55_Y61_T1.5401.00
262_E269_K1.5211.00
60_G63_T1.5191.00
69_E76_S1.5131.00
98_T102_F1.4941.00
168_E175_K1.4791.00
154_Y159_N1.4761.00
136_V140_R1.4611.00
195_Y290_E1.4501.00
237_K241_I1.4281.00
197_L200_E1.4251.00
165_A170_L1.4181.00
56_K60_G1.4151.00
26_L288_C1.4131.00
91_L95_L1.4081.00
100_Q196_D1.4081.00
198_M221_I1.3960.99
103_L122_T1.3940.99
220_L279_G1.3920.99
158_Y162_R1.3720.99
114_G118_L1.3600.99
37_A62_I1.3520.99
97_D100_Q1.3380.99
55_Y60_G1.3250.99
132_Q136_V1.3200.99
65_V69_E1.3190.99
36_T40_R1.3180.99
20_A24_A1.3150.99
190_T229_M1.3110.99
163_I166_T1.3010.99
121_L189_C1.2860.99
179_P251_V1.2710.99
252_P255_A1.2700.99
160_A164_I1.2630.99
137_V161_Y1.2520.99
22_I26_L1.2320.98
198_M218_S1.2290.98
187_I226_A1.2260.98
177_T181_L1.2250.98
170_L174_W1.2210.98
292_L296_L1.2210.98
194_T198_M1.2090.98
29_V78_L1.2020.98
122_T126_V1.1980.98
169_G172_G1.1860.98
43_V238_T1.1800.98
78_L82_L1.1760.98
253_N256_M1.1710.98
69_E73_K1.1690.97
125_G181_L1.1590.97
118_L122_T1.1550.97
264_P268_F1.1520.97
217_V220_L1.1410.97
248_Y257_K1.1400.97
59_L63_T1.1390.97
129_F177_T1.1350.97
138_K142_Q1.1340.97
14_G18_F1.1300.97
231_S235_V1.1280.97
190_T194_T1.1280.97
18_F21_G1.1280.97
211_D214_C1.1260.97
98_T101_E1.1240.97
191_E286_F1.1200.96
257_K260_T1.1190.96
120_G124_G1.1160.96
290_E293_K1.1050.96
25_C82_L1.0970.96
120_G189_C1.0940.96
288_C291_Q1.0890.96
263_G266_A1.0870.96
268_F271_L1.0850.96
259_F262_E1.0850.96
278_L282_N1.0820.96
95_L126_V1.0770.95
231_S274_S1.0760.95
57_G60_G1.0760.95
201_A204_K1.0680.95
99_V102_F1.0680.95
19_S23_A1.0530.95
87_S90_S1.0500.94
19_S292_L1.0490.94
281_W285_M1.0460.94
66_V71_R1.0450.94
234_D237_K1.0450.94
32_F75_Y1.0420.94
97_D293_K1.0330.94
217_V221_I1.0250.93
88_S92_R1.0220.93
221_I225_C1.0200.93
254_C257_K1.0050.93
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  
2lckA10.95441000.156Contact Map
1okcA10.91861000.175Contact Map
4c9gA10.84361000.177Contact Map
4i5lB20.244311.60.958Contact Map
1u7gA10.37792.90.968Contact Map
3j9xA5802.80.968Contact Map
4rdqA50.21822.20.97Contact Map
3tguG20.24762.20.97Contact Map
2kygA20.16292.10.97Contact Map
1pp9G20.2412.10.97Contact 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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