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GApi

ID: 1507524259 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 333 (332)
Sequences: 4352 (1858.2)
Seq/Len: 13.108
Nf(neff/√len): 102.0

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: 13.108).

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
163_H221_E4.8451.00
169_V248_E3.5811.00
273_G289_H3.5741.00
160_K164_D3.5301.00
203_N282_S3.2291.00
135_H328_H3.1831.00
179_I201_L3.0931.00
77_E82_K3.0391.00
79_D82_K2.9071.00
166_F259_V2.8951.00
260_V293_F2.8701.00
291_S310_S2.8511.00
165_N262_Q2.7961.00
238_V284_F2.7761.00
231_F240_V2.6921.00
290_S321_R2.6571.00
178_A235_T2.6521.00
145_I329_M2.5791.00
250_P304_H2.5461.00
105_K108_A2.5171.00
237_N285_N2.5101.00
51_H237_N2.4201.00
170_E246_R2.3831.00
204_I231_F2.3691.00
131_M135_H2.3281.00
127_P142_L2.2781.00
273_G287_D2.2561.00
256_I306_V2.1631.00
102_T105_K2.1601.00
116_R143_K2.1551.00
120_S322_V2.1011.00
274_Y295_A2.1001.00
321_R324_D2.0901.00
258_K262_Q2.0401.00
118_I326_M2.0301.00
80_P100_F2.0291.00
159_A222_L2.0121.00
261_K276_E2.0041.00
107_G111_Q1.9821.00
247_L306_V1.9801.00
227_T299_I1.9731.00
216_G223_N1.9611.00
278_Q296_G1.9581.00
96_S120_S1.9391.00
46_Q277_H1.9011.00
94_V326_M1.8771.00
257_K298_G1.8441.00
3_K27_D1.8101.00
49_S202_Q1.8061.00
217_K223_N1.7921.00
101_T119_I1.7891.00
84_K87_D1.7691.00
81_S108_A1.7671.00
261_K274_Y1.7571.00
279_V284_F1.7391.00
169_V304_H1.7221.00
166_F247_L1.7081.00
185_T200_A1.7071.00
106_A119_I1.6451.00
73_T87_D1.6341.00
169_V246_R1.6281.00
75_F88_A1.6271.00
158_L310_S1.6261.00
171_G226_L1.5951.00
159_A168_I1.5931.00
181_A186_V1.5691.00
83_I88_A1.5631.00
297_A309_I1.5631.00
199_G202_Q1.4981.00
20_A28_I1.4851.00
94_V322_V1.4741.00
182_T190_S1.4631.00
249_K255_D1.4621.00
49_S282_S1.4481.00
275_T284_F1.4421.00
103_M107_G1.4391.00
181_A188_G1.4371.00
290_S324_D1.4351.00
196_D207_A1.4271.00
127_P137_K1.4211.00
163_H219_I1.4131.00
79_D108_A1.4121.00
158_L291_S1.4010.99
182_T196_D1.3940.99
53_K287_D1.3880.99
193_L196_D1.3640.99
251_A259_V1.3530.99
253_Y298_G1.3340.99
170_E304_H1.3340.99
316_F320_N1.3250.99
275_T279_V1.3210.99
130_V148_A1.3100.99
289_H292_T1.3090.99
92_Y326_M1.3010.99
246_R304_H1.2980.99
92_Y118_I1.2970.99
64_K71_P1.2940.99
21_F54_F1.2920.99
247_L251_A1.2860.99
229_M309_I1.2830.99
161_V272_L1.2750.99
240_V309_I1.2720.99
202_Q236_A1.2630.99
102_T124_A1.2490.99
318_Y322_V1.2440.98
288_T320_N1.2280.98
242_D307_K1.2230.98
184_K188_G1.2160.98
73_T88_A1.2050.98
138_Y143_K1.2040.98
50_T237_N1.2030.98
154_C241_V1.2020.98
107_G110_L1.2020.98
176_V231_F1.1990.98
194_W197_G1.1990.98
96_S322_V1.1930.98
119_I123_S1.1900.98
81_S111_Q1.1890.98
282_S285_N1.1700.97
162_I308_L1.1670.97
161_V259_V1.1630.97
17_T67_I1.1620.97
129_F142_L1.1620.97
165_N259_V1.1560.97
258_K261_K1.1510.97
286_S316_F1.1440.97
251_A255_D1.1420.97
252_K255_D1.1410.97
167_G247_L1.1330.97
195_R294_D1.1290.97
288_T316_F1.1280.97
300_A306_V1.1280.97
91_E115_K1.1280.97
50_T236_A1.1230.97
287_D292_T1.1210.97
162_I260_V1.1200.96
40_Y194_W1.1180.96
51_H285_N1.1170.96
118_I145_I1.1130.96
116_R138_Y1.1130.96
259_V262_Q1.1110.96
27_D70_N1.1100.96
162_I245_C1.1090.96
128_M217_K1.1060.96
166_F251_A1.1050.96
166_F256_I1.1040.96
250_P303_D1.0980.96
47_Y277_H1.0900.96
170_E305_F1.0860.96
51_H286_S1.0860.96
165_N169_V1.0850.96
139_D142_L1.0840.96
131_M328_H1.0830.96
238_V285_N1.0820.96
66_V71_P1.0780.95
251_A300_A1.0760.95
274_Y293_F1.0750.95
45_F56_G1.0740.95
5_G83_I1.0600.95
43_Y197_G1.0560.95
268_L272_L1.0500.94
163_H248_E1.0480.94
155_L173_M1.0470.94
19_A320_N1.0410.94
103_M126_A1.0390.94
253_Y257_K1.0330.94
129_F138_Y1.0290.94
46_Q53_K1.0210.93
64_K73_T1.0120.93
131_M271_I1.0060.93
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  
4boyA20.9941000.196Contact Map
3idsC411000.203Contact Map
1rm4O30.9941000.208Contact Map
4o59O40.9971000.211Contact Map
3docA40.9941000.212Contact Map
4lsmA20.9911000.212Contact Map
3pymA20.9971000.215Contact Map
2x5jO40.9761000.219Contact Map
1obfO20.9881000.219Contact Map
3cpsA20.9941000.221Contact 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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