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AclwA19027a

ID: 1516321242 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 336 (331)
Sequences: 4119 (2946.2)
Seq/Len: 12.444
Nf(neff/√len): 161.9

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: 12.444).

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
165_S191_T4.5901.00
93_G201_D3.9281.00
318_F329_Y3.5471.00
90_K94_D3.4761.00
252_N262_P3.4471.00
91_T94_D3.3621.00
285_R322_T3.2471.00
281_D320_K3.1591.00
264_T268_R2.9751.00
285_R289_I2.9701.00
233_T272_E2.9141.00
287_A291_L2.8361.00
185_Q188_M2.8041.00
291_L305_Q2.7171.00
317_A321_W2.5651.00
163_H192_E2.5291.00
167_P187_D2.5161.00
139_E166_Y2.4271.00
31_H57_M2.4141.00
237_R282_A2.4111.00
236_I254_V2.3771.00
280_K284_R2.3461.00
251_L262_P2.3281.00
32_V57_M2.2881.00
196_A199_Y2.2751.00
285_R321_W2.2721.00
324_V332_L2.2581.00
251_L266_R2.2161.00
268_R271_A2.2111.00
161_R185_Q2.0681.00
64_D70_D2.0561.00
314_F318_F2.0521.00
24_D27_T2.0511.00
175_Y186_F1.9301.00
85_L98_L1.9211.00
295_P330_R1.8911.00
274_K278_G1.8481.00
146_H150_S1.8441.00
277_Q281_D1.8251.00
31_H61_V1.7681.00
292_L299_L1.7621.00
169_P186_F1.7371.00
254_V276_Y1.7361.00
80_A83_C1.7141.00
239_V257_M1.7101.00
35_E38_L1.6961.00
297_L305_Q1.6931.00
69_F175_Y1.6881.00
216_K220_A1.6681.00
47_S50_Q1.6471.00
102_F220_A1.6461.00
93_G97_E1.6361.00
289_I322_T1.6111.00
239_V254_V1.6111.00
237_R286_D1.6101.00
17_G71_K1.6061.00
5_T45_R1.6031.00
288_A314_F1.5971.00
309_S313_T1.5831.00
300_E311_T1.5751.00
121_A200_L1.5731.00
301_D304_Q1.5661.00
315_H327_G1.5431.00
314_F326_P1.5381.00
295_P302_V1.5381.00
174_E177_A1.5371.00
264_T267_R1.5321.00
120_E194_T1.5281.00
211_L215_L1.5171.00
163_H185_Q1.5161.00
217_A221_Q1.5081.00
231_S272_E1.5031.00
274_K279_V1.4911.00
92_L149_A1.4871.00
299_L311_T1.4781.00
263_Q266_R1.4751.00
121_A197_A1.4671.00
311_T315_H1.4551.00
291_L302_V1.4541.00
297_L302_V1.4311.00
289_I318_F1.4181.00
318_F322_T1.4121.00
232_L236_I1.3660.99
287_A290_H1.3550.99
119_H197_A1.3520.99
168_R186_F1.3410.99
329_Y333_H1.3350.99
290_H294_N1.3320.99
57_M61_V1.3310.99
163_H188_M1.3270.99
236_I279_V1.3260.99
327_G331_Q1.3240.99
93_G116_R1.3180.99
232_L272_E1.3070.99
324_V328_L1.2930.99
81_I219_P1.2860.99
139_E164_F1.2840.99
315_H325_T1.2750.99
281_D308_F1.2740.99
70_D174_E1.2660.99
152_L204_I1.2620.99
160_E196_A1.2590.99
175_Y180_F1.2470.99
138_T191_T1.2460.98
250_T253_D1.2450.98
237_R279_V1.2400.98
258_L265_L1.2350.98
249_P276_Y1.2320.98
239_V258_L1.2100.98
281_D321_W1.1990.98
168_R172_A1.1980.98
122_R192_E1.1970.98
88_H212_E1.1940.98
261_S264_T1.1900.98
240_L280_K1.1870.98
281_D285_R1.1810.98
26_D36_A1.1800.98
289_I293_L1.1740.98
98_L216_K1.1710.98
250_T276_Y1.1630.97
212_E216_K1.1620.97
241_K287_A1.1600.97
171_H174_E1.1470.97
232_L260_L1.1430.97
116_R197_A1.1430.97
121_A195_F1.1310.97
101_Q220_A1.1280.97
89_A212_E1.1220.97
169_P175_Y1.1170.96
53_R57_M1.1060.96
287_A305_Q1.1040.96
161_R194_T1.1040.96
281_D284_R1.1000.96
89_A98_L1.0930.96
308_F317_A1.0930.96
69_F143_M1.0920.96
260_L268_R1.0840.96
122_R194_T1.0840.96
302_V330_R1.0790.95
147_G150_S1.0790.95
301_D305_Q1.0750.95
82_M86_I1.0750.95
98_L212_E1.0750.95
310_E315_H1.0570.95
172_A184_M1.0560.95
91_T201_D1.0490.94
86_I95_A1.0460.94
86_I99_S1.0450.94
199_Y202_L1.0440.94
146_H193_I1.0340.94
291_L297_L1.0300.94
29_L34_I1.0300.94
276_Y280_K1.0270.94
298_T301_D1.0070.93
79_F106_F1.0040.93
84_Q88_H1.0010.92
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  
3mklA20.330499.90.654Contact Map
1bl0A10.318599.90.656Contact Map
3oouA10.309599.90.657Contact Map
3lsgA50.303699.90.661Contact Map
3oioA10.327499.90.661Contact Map
3mn2A20.312599.90.662Contact Map
2k9sA10.315599.90.664Contact Map
1d5yA40.318599.90.671Contact Map
3w6vA10.315599.90.671Contact Map
3gbgA10.681599.90.687Contact 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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