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PEX5S full length N-term

ID: 1513945443 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 285 (284)
Sequences: 536 (431.3)
Seq/Len: 1.887
Nf(neff/√len): 25.6

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: 1.887).

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
102_R106_V3.7011.00
137_W141_F3.1821.00
115_W118_E2.8521.00
60_V64_L2.6731.00
230_L234_F2.6461.00
248_W252_Q2.5331.00
102_R105_G2.5271.00
251_L255_L2.4841.00
137_W140_E2.4421.00
207_L211_E2.2571.00
115_W119_F2.1180.99
217_W221_F2.0660.99
103_A106_V2.0010.99
266_H269_L1.9910.99
195_A198_F1.9420.98
79_F84_L1.8770.98
84_L87_E1.7440.96
116_A119_F1.6520.95
252_Q255_L1.6500.95
195_A199_V1.4890.90
181_W185_Y1.4830.90
265_A269_L1.4820.90
131_D134_E1.4800.89
198_F201_K1.4660.89
199_V203_D1.4630.89
250_K254_E1.4550.88
250_K257_E1.4520.88
252_Q256_E1.4480.88
156_W159_E1.4410.88
252_Q267_P1.4400.88
9_G15_M1.4400.88
138_S141_F1.4380.88
130_Q133_N1.4110.86
195_A203_D1.4010.86
247_F251_L1.3860.85
134_E138_S1.3820.85
268_W272_Y1.3780.84
21_F25_K1.3780.84
76_P84_L1.3660.84
113_E118_E1.3600.83
79_F87_E1.3410.82
232_M235_E1.3360.82
195_A200_A1.3330.82
112_S116_A1.3290.81
267_P270_S1.3280.81
193_H199_V1.3270.81
251_L254_E1.3240.81
248_W254_E1.3210.81
10_G15_M1.2970.79
250_K253_A1.2930.79
105_G109_L1.2700.77
85_L88_M1.2680.77
15_M19_G1.2460.75
130_Q137_W1.2460.75
207_L210_S1.2380.74
118_E122_A1.2340.74
252_Q259_A1.2220.73
24_D30_E1.2010.71
181_W184_E1.2010.71
268_W271_D1.1980.71
24_D28_R1.1960.71
25_K28_R1.1920.70
247_F254_E1.1900.70
87_E91_I1.1880.70
244_D248_W1.1870.70
8_C12_N1.1840.70
46_A49_K1.1830.70
248_W258_M1.1820.70
8_C284_Y1.1790.69
251_L260_K1.1730.69
269_L272_Y1.1720.69
248_W251_L1.1720.69
113_E116_A1.1710.68
200_A214_S1.1710.68
195_A207_L1.1650.68
76_P79_F1.1650.68
100_P103_A1.1630.68
15_M22_T1.1610.68
190_D193_H1.1550.67
205_P209_N1.1510.67
9_G22_T1.1440.66
9_G60_V1.1420.66
159_E162_E1.1310.65
9_G21_F1.1270.64
133_N136_D1.1260.64
5_E19_G1.1240.64
208_A211_E1.1140.63
35_G39_P1.1100.62
250_K258_M1.1100.62
200_A203_D1.1100.62
78_T84_L1.1100.62
157_A160_Y1.1060.62
255_L258_M1.0980.61
16_K19_G1.0980.61
84_L89_Q1.0980.61
112_S118_E1.0960.61
131_D136_D1.0950.61
167_K172_E1.0940.61
127_D132_Y1.0920.61
251_L259_A1.0900.60
17_L23_Q1.0890.60
189_E205_P1.0850.60
244_D247_F1.0840.60
203_D206_K1.0800.59
104_P107_A1.0800.59
158_E162_E1.0790.59
7_E235_E1.0790.59
128_V131_D1.0790.59
77_Q81_M1.0770.59
114_N117_Q1.0730.59
30_E33_R1.0720.58
129_T133_N1.0710.58
25_K29_Q1.0670.58
15_M26_A1.0610.57
214_S217_W1.0600.57
209_N212_G1.0580.57
7_E10_G1.0560.57
272_Y277_S1.0550.57
102_R109_L1.0550.57
19_G22_T1.0530.56
252_Q258_M1.0510.56
255_L259_A1.0510.56
195_A211_E1.0500.56
19_G63_F1.0470.56
256_E260_K1.0440.55
104_P109_L1.0340.54
105_G108_D1.0260.53
175_G178_T1.0250.53
114_N118_E1.0240.53
81_M88_M1.0230.53
255_L260_K1.0190.53
195_A202_V1.0180.53
9_G17_L1.0160.52
249_D255_L1.0140.52
254_E259_A1.0130.52
254_E257_E1.0130.52
190_D195_A1.0130.52
21_F32_L1.0130.52
39_P60_V1.0090.52
79_F88_M1.0030.51
81_M87_E1.0020.51
264_E268_W1.0000.51
8_C14_L1.0000.51
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  
1rlhA10.14391.80.961Contact Map
2p7nA10.15791.40.963Contact Map
4aneA60.17541.10.966Contact Map
1bf5A10.15091.10.966Contact Map
1ag7A10.07721.10.966Contact Map
2okrC20.07371.10.966Contact Map
3zf7Y10.059610.966Contact Map
3fmuA10.16840.80.968Contact Map
4rl1A10.17890.80.968Contact Map
2xz2A10.09120.80.968Contact 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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