GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
AAC

ID: 1505232275 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 298 (294)
Sequences: 13392 (7618.1)
Seq/Len: 45.551
Nf(neff/√len): 444.3

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: 45.551).

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
262_A270_F3.5361.00
165_F173_L3.2771.00
62_P70_F3.0041.00
256_D260_K2.9161.00
261_I269_A2.8771.00
162_I166_K2.7971.00
159_D163_K2.7451.00
59_V63_K2.7271.00
259_R263_K2.6691.00
260_K264_D2.6241.00
163_K167_S2.4951.00
56_D60_R2.4551.00
164_I172_G2.4211.00
155_H159_D2.3791.00
258_W270_F2.3191.00
95_Y122_A2.3001.00
265_E269_A2.2221.00
234_V258_W2.1631.00
60_R64_E2.1041.00
237_R265_E2.0951.00
161_I173_L2.0831.00
33_K37_Q1.9621.00
226_L274_A1.9131.00
61_I69_S1.9061.00
253_G256_D1.8941.00
251_Y257_C1.8831.00
154_F160_C1.8631.00
121_G185_I1.8471.00
140_R168_D1.8361.00
95_Y126_T1.8191.00
91_F95_Y1.7981.00
262_A267_A1.7651.00
168_D172_G1.7491.00
252_T256_D1.7171.00
30_E33_K1.7031.00
117_L189_A1.6981.00
194_V223_V1.6981.00
251_Y256_D1.6921.00
293_E296_K1.6901.00
290_L294_I1.6821.00
58_V70_F1.6781.00
35_L65_Q1.6631.00
38_V143_A1.6561.00
99_F119_S1.6501.00
286_F290_L1.6431.00
27_A31_R1.6341.00
17_V294_I1.6161.00
235_R239_M1.6051.00
65_Q72_R1.5891.00
156_G159_D1.5881.00
51_Y57_C1.5861.00
168_D175_Q1.5751.00
265_E272_K1.5681.00
93_D96_K1.5631.00
202_L216_I1.5601.00
159_D162_I1.5561.00
255_V259_R1.5501.00
197_T201_M1.5421.00
195_Y292_D1.5271.00
154_F159_D1.5261.00
87_L91_F1.4951.00
56_D59_V1.4721.00
31_R35_L1.4651.00
165_F170_L1.4581.00
51_Y56_D1.4501.00
52_K56_D1.4351.00
136_F140_R1.4221.00
96_K196_D1.4151.00
32_V58_V1.4101.00
95_Y119_S1.4030.99
132_Y136_F1.4030.99
94_K98_L1.4000.99
99_F122_A1.3950.99
15_G19_A1.3900.99
21_V290_L1.3900.99
197_T200_G1.3890.99
255_V258_W1.3550.99
216_I220_V1.3380.99
114_A118_A1.3290.99
158_G162_I1.3200.99
163_K166_K1.3010.99
121_G189_A1.2990.99
170_L174_Y1.2860.99
208_V212_V1.2770.99
190_A227_V1.2750.99
177_F181_V1.2750.99
229_Y277_N1.2750.99
198_A216_I1.2710.99
61_I65_Q1.2670.99
138_R142_A1.2540.99
74_N78_V1.2480.99
38_V236_R1.2470.99
65_Q69_S1.2380.98
160_C164_I1.2340.98
194_V198_A1.2300.98
17_V21_V1.2290.98
251_Y260_K1.2100.98
217_A220_V1.2100.98
27_A71_W1.2090.98
13_L16_G1.2050.98
198_A219_S1.2000.98
169_G172_G1.1990.98
120_G189_A1.1910.98
179_V254_T1.1900.98
84_T88_N1.1880.98
137_A161_I1.1850.98
94_K97_Q1.1620.97
256_D259_R1.1580.97
9_L13_L1.1560.97
187_Y224_A1.1430.97
24_T74_N1.1400.97
229_Y233_T1.1340.97
190_A194_V1.1330.97
55_I59_V1.1270.97
122_A126_T1.1260.97
262_A265_E1.1210.97
292_D295_K1.1160.96
232_D235_R1.1130.96
91_F126_T1.1020.96
20_A78_V1.1010.96
267_A271_F1.0970.96
260_K263_K1.0960.96
221_T232_D1.0940.96
266_G269_A1.0900.96
95_Y99_F1.0860.96
271_F274_A1.0810.95
120_G124_G1.0790.95
139_T240_M1.0720.95
129_C177_F1.0660.95
209_H212_V1.0630.95
125_A181_V1.0630.95
214_W217_A1.0630.95
118_A122_A1.0580.95
257_C260_K1.0570.95
83_P86_A1.0480.94
196_D199_K1.0430.94
191_Y288_L1.0410.94
290_L293_E1.0340.94
257_C261_I1.0340.94
184_I187_Y1.0330.94
234_V257_C1.0320.94
215_M219_S1.0270.94
291_Y295_K1.0240.93
14_A18_A1.0110.93
62_P67_F1.0100.93
59_V62_P1.0040.93
284_G287_V1.0000.92
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  
1okcA10.97991000.054Contact Map
4c9gA10.88591000.1Contact Map
2lckA10.93961000.123Contact Map
4i5lB20.241617.60.95Contact Map
1fa2A10.26512.20.967Contact Map
2xfrA10.24831.60.97Contact Map
3lo3A280.21811.60.97Contact Map
2kygA20.15441.50.97Contact Map
4jjfA20.30871.40.97Contact Map
2l5rA10.07721.40.971Contact 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 0.0446 seconds.