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PilT

ID: 1513364057 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 363 (345)
Sequences: 7163 (4405.9)
Seq/Len: 20.762
Nf(neff/√len): 237.2

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: 20.762).

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
119_L263_A3.5181.00
157_L193_A3.1621.00
288_T313_Y3.1001.00
122_L262_R3.0511.00
94_A155_H3.0071.00
117_N147_Y2.9771.00
159_I189_A2.9441.00
273_I332_S2.9061.00
233_S236_Q2.7291.00
128_L227_A2.6351.00
272_R279_I2.6341.00
130_T229_L2.5931.00
294_L306_M2.5551.00
150_R170_K2.5261.00
324_E328_N2.4391.00
52_L95_A2.4221.00
90_R163_I2.4081.00
34_D271_K2.2421.00
233_S304_P2.2261.00
293_N297_E2.2121.00
120_A144_I2.1671.00
265_I284_I2.1301.00
108_E117_N2.1301.00
78_G101_P2.1261.00
321_C325_Y2.0601.00
20_H197_D2.0381.00
287_A292_R2.0221.00
106_T109_E2.0191.00
319_D340_S1.9841.00
85_N196_E1.9701.00
82_F97_F1.9541.00
279_I330_W1.9401.00
206_M215_A1.9231.00
118_R286_I1.9151.00
154_D200_I1.9081.00
94_A175_N1.8931.00
11_M16_A1.8641.00
287_A295_I1.8471.00
116_L144_I1.8341.00
141_L202_M1.8321.00
7_F19_L1.7951.00
291_I303_I1.7891.00
9_K13_D1.7851.00
322_I336_A1.7841.00
129_V140_T1.7711.00
64_F93_V1.7671.00
87_Y177_R1.7461.00
206_M227_A1.7431.00
100_I165_F1.7431.00
238_V261_L1.7271.00
206_M212_I1.7241.00
34_D153_Y1.7201.00
294_L299_K1.7181.00
316_M324_E1.7161.00
16_A31_I1.6651.00
272_R330_W1.6601.00
317_S320_D1.6501.00
321_C324_E1.6381.00
245_F277_G1.6351.00
30_R197_D1.6291.00
121_L147_Y1.6241.00
285_M315_M1.6211.00
141_L226_F1.6191.00
86_Y95_A1.6031.00
154_D172_C1.6031.00
299_K302_Q1.6011.00
201_I218_A1.5961.00
212_I244_A1.5861.00
127_V224_L1.5841.00
146_D150_R1.5821.00
281_A325_Y1.5811.00
323_M327_N1.5721.00
271_K335_E1.5681.00
82_F99_L1.5261.00
209_L213_S1.5251.00
335_E338_I1.5171.00
10_L14_T1.5171.00
11_M19_L1.5101.00
103_K109_E1.5071.00
288_T306_M1.4891.00
290_A313_Y1.4781.00
84_V97_F1.4471.00
20_H30_R1.4381.00
213_S217_E1.4321.00
146_D170_K1.4171.00
26_P37_R1.4151.00
4_L51_M1.4070.99
185_S188_N1.4030.99
89_Q175_N1.3950.99
37_R40_Y1.3910.99
25_N48_L1.3900.99
149_N156_I1.3890.99
68_G88_R1.3720.99
190_L214_L1.3680.99
302_Q305_S1.3570.99
63_R67_Q1.3470.99
191_R208_D1.3450.99
326_L336_A1.3320.99
130_T231_T1.3300.99
133_T198_P1.3280.99
62_K66_E1.3260.99
53_Y61_I1.3250.99
279_I325_Y1.3230.99
331_I335_E1.3200.99
127_V263_A1.3160.99
119_L127_V1.3120.99
193_A201_I1.3100.99
150_R153_Y1.3100.99
107_V143_A1.3070.99
57_P60_I1.2940.99
32_H272_R1.2760.99
159_I179_L1.2750.99
124_R262_R1.2610.99
94_A157_L1.2590.99
177_R193_A1.2540.99
306_M310_G1.2520.99
126_L225_V1.2500.99
306_M313_Y1.2470.99
308_Q320_D1.2340.98
235_A285_M1.2330.98
112_L282_M1.2320.98
212_I241_I1.2320.98
326_L333_P1.2320.98
69_E183_T1.2310.98
331_I336_A1.2260.98
268_T318_L1.2230.98
159_I193_A1.2200.98
327_N330_W1.2190.98
14_T36_Q1.2160.98
147_Y151_M1.2140.98
282_M316_M1.1940.98
148_A226_F1.1930.98
12_V80_A1.1860.98
49_R53_Y1.1850.98
107_V117_N1.1780.98
148_A200_I1.1640.97
29_L38_V1.1610.97
111_G280_V1.1460.97
187_A210_E1.1460.97
153_Y171_N1.1420.97
105_K109_E1.1380.97
108_E147_Y1.1300.97
325_Y330_W1.1300.97
33_G278_R1.1270.97
189_A193_A1.1200.96
19_L29_L1.1190.96
208_D211_T1.1120.96
217_E243_D1.1120.96
15_Q32_H1.0960.96
64_F183_T1.0890.96
37_R152_R1.0850.96
85_N96_A1.0840.96
64_F182_H1.0830.96
235_A304_P1.0770.95
155_H175_N1.0750.95
237_T264_V1.0720.95
316_M321_C1.0700.95
179_L183_T1.0640.95
16_A29_L1.0630.95
258_S295_I1.0600.95
11_M29_L1.0600.95
262_R292_R1.0560.95
264_V285_M1.0530.95
133_T223_H1.0510.94
130_T237_T1.0500.94
276_P331_I1.0490.94
257_L261_L1.0490.94
270_F331_I1.0470.94
28_L37_R1.0450.94
270_F335_E1.0440.94
183_T246_P1.0370.94
297_E302_Q1.0290.94
261_L264_V1.0010.92
285_M291_I1.0000.92
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  
2ewvA10.94211000.282Contact Map
3jvvA30.92841000.306Contact Map
4ksrA301000.345Contact Map
4phtA30.8761000.36Contact Map
1p9rA10.87331000.39Contact Map
2eyuA20.67771000.487Contact Map
2oap120.94211000.54Contact Map
4ihqA30.94211000.563Contact Map
2gzaA30.78241000.614Contact Map
4bloA120.68699.90.727Contact 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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