GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
TMEM41B

ID: 1513722570 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 291 (246)
Sequences: 342 (220)
Seq/Len: 1.390
Nf(neff/√len): 14.0

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: 1.390).

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
144_P148_A2.3220.99
161_S226_L2.1160.99
136_S244_A1.9440.97
256_T259_E1.8590.96
142_L219_S1.8510.96
203_F214_F1.6520.91
207_T215_I1.6350.90
148_A157_G1.5980.89
124_L155_C1.5550.87
204_L212_N1.5340.86
207_T210_L1.5300.86
126_T162_F1.5260.86
83_R94_D1.4920.84
204_L214_F1.4850.84
215_I233_T1.4690.83
218_T224_V1.4520.82
160_A163_C1.4420.81
274_V278_L1.4360.81
210_L240_P1.4110.79
143_Y218_T1.3970.78
86_M235_L1.3880.78
124_L136_S1.3450.75
148_A224_V1.3340.74
148_A165_M1.3300.73
136_S155_C1.3210.73
170_V189_Q1.3190.73
91_D150_F1.3160.72
201_I232_G1.3140.72
136_S240_P1.3050.71
237_V241_S1.3030.71
211_P216_N1.2960.71
220_P247_A1.2890.70
136_S241_S1.2870.70
58_V282_F1.2840.70
125_Q208_P1.2720.69
213_W220_P1.2720.69
87_K149_L1.2660.68
90_R94_D1.2650.68
207_T232_G1.2530.67
124_L215_I1.2500.67
156_S240_P1.2390.66
190_V197_L1.2370.65
124_L200_Y1.2330.65
222_I242_F1.2310.65
50_A54_L1.2300.65
93_D190_V1.2230.64
155_C240_P1.2220.64
217_I222_I1.2180.64
183_A187_S1.2160.64
121_Y171_G1.2120.63
182_K220_P1.2030.62
62_L107_D1.1950.62
262_S277_I1.1930.61
224_V240_P1.1920.61
129_I142_L1.1880.61
186_W240_P1.1700.59
124_L233_T1.1670.59
133_I210_L1.1620.58
65_A278_L1.1550.58
95_A245_I1.1510.57
89_P138_L1.1470.57
125_Q131_G1.1470.57
95_A141_F1.1450.57
240_P244_A1.1430.56
65_A123_F1.1420.56
136_S210_L1.1420.56
144_P272_L1.1420.56
186_W241_S1.1390.56
94_D257_A1.1360.56
276_S279_P1.1350.56
180_T212_N1.1330.55
135_L139_S1.1330.55
203_F207_T1.1310.55
161_S191_E1.1270.55
95_A138_L1.1230.54
130_P159_G1.1200.54
136_S268_I1.1170.54
282_F285_K1.1150.54
187_S287_K1.1120.53
127_F245_I1.1110.53
125_Q130_P1.1030.52
136_S186_W1.1000.52
190_V222_I1.0970.52
60_I281_I1.0930.51
155_C244_A1.0860.51
155_C213_W1.0850.51
61_F187_S1.0850.51
149_L190_V1.0770.50
188_Q198_I1.0730.49
143_Y202_I1.0680.49
132_S246_K1.0650.49
120_T165_M1.0630.48
201_I215_I1.0630.48
68_M161_S1.0620.48
130_P140_G1.0620.48
186_W237_V1.0600.48
154_L287_K1.0540.47
237_V240_P1.0540.47
48_G51_R1.0500.47
124_L145_F1.0490.47
121_Y220_P1.0470.47
150_F154_L1.0460.47
46_E53_S1.0420.46
87_K94_D1.0340.45
117_Y139_S1.0330.45
180_T221_V1.0300.45
52_M55_L1.0280.45
99_G133_I1.0250.45
200_Y207_T1.0250.45
193_H209_F1.0200.44
118_F214_F1.0190.44
123_F170_V1.0180.44
121_Y164_Y1.0130.43
121_Y125_Q1.0120.43
72_Y171_G1.0120.43
126_T201_I1.0120.43
224_V252_Y1.0100.43
286_L289_K1.0100.43
208_P229_F1.0070.43
49_S52_M1.0070.43
186_W207_T1.0060.43
175_V198_I1.0020.42
183_A228_V1.0010.42
149_L241_S1.0000.42
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  
4k0jA60.848854.50.96Contact Map
3w9iA60.872923.10.967Contact Map
4dx5A30.876320.20.968Contact Map
4mt1A10.838519.40.968Contact Map
4j05A20.618614.30.97Contact Map
3ne5A10.879713.60.971Contact Map
4tkrA20.560112.60.971Contact Map
3effK40.41249.70.972Contact Map
3o7qA10.64959.30.973Contact Map
4q4hB10.59459.20.973Contact 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 0.0342 seconds.