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HST

ID: 1499265671 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 337 (325)
Sequences: 750 (464.2)
Seq/Len: 2.308
Nf(neff/√len): 25.7

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: 2.308).

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
224_E232_R3.3751.00
193_K197_D2.7541.00
215_A220_R2.7271.00
120_T124_R2.5961.00
116_K173_L2.4261.00
95_Y206_K2.3911.00
62_L252_V2.3591.00
103_K224_E2.2911.00
107_F111_Q2.2501.00
192_F214_L2.2281.00
187_G190_G2.0620.99
227_C241_C2.0070.99
185_Y190_G1.9950.99
7_R40_V1.9560.99
293_L297_D1.9460.99
9_C19_C1.8990.99
15_E18_K1.8470.99
22_F26_M1.7930.98
185_Y197_D1.7730.98
61_T251_V1.7670.98
151_A170_L1.7630.98
65_G249_H1.7520.98
42_K47_D1.7390.98
116_K219_D1.7170.97
12_S18_K1.6710.97
171_C174_C1.6560.96
39_C48_C1.6390.96
120_T125_S1.6160.96
124_R188_Y1.6130.96
120_T127_G1.5930.95
122_L162_A1.5850.95
171_C179_C1.5830.95
237_E240_D1.5660.95
22_F270_A1.5580.95
292_D295_F1.5380.94
42_K51_A1.5290.94
285_F297_D1.5280.94
120_T188_Y1.5040.93
206_K209_T1.4970.93
219_D222_Q1.4960.93
187_G191_A1.4950.93
295_F302_F1.4850.93
121_G124_R1.4430.91
282_F285_F1.4360.91
156_G172_Q1.4360.91
10_A16_A1.4350.91
130_I244_A1.4290.91
127_G131_P1.4250.90
161_C174_C1.4160.90
102_K198_G1.4150.90
13_E41_K1.4050.90
120_T206_K1.4030.89
8_W15_E1.3690.88
49_I70_A1.3630.88
188_Y206_K1.3550.87
194_C241_C1.3540.87
9_C18_K1.3430.87
9_C48_C1.3390.86
97_A130_I1.3260.86
285_F295_F1.3250.86
225_L242_H1.3190.85
112_L202_V1.3110.85
108_Q111_Q1.3050.84
287_S297_D1.3000.84
47_D51_A1.2980.84
120_T126_A1.2970.84
15_E19_C1.2920.83
157_S170_L1.2830.83
183_N243_L1.2800.83
207_H238_Y1.2700.82
122_L159_A1.2660.82
12_S15_E1.2610.81
321_T325_N1.2490.81
183_N186_F1.2470.80
8_W18_K1.2380.80
71_Y311_A1.2380.80
189_S213_N1.2310.79
118_C194_C1.2290.79
67_V250_T1.2260.79
158_C190_G1.2260.79
98_V207_H1.2230.79
192_F213_N1.2230.79
9_C39_C1.2220.79
64_A249_H1.2220.79
226_L232_R1.2120.78
26_M270_A1.2040.77
178_G184_Q1.2010.77
59_A254_R1.1890.76
116_K201_D1.1820.75
284_L287_S1.1750.75
16_A20_Q1.1700.74
18_K295_F1.1680.74
158_C174_C1.1680.74
170_L174_C1.1670.74
6_V59_A1.1560.73
97_A127_G1.1540.73
64_A188_Y1.1540.73
224_E234_P1.1470.72
188_Y244_A1.1460.72
292_D297_D1.1420.72
95_Y120_T1.1420.72
96_Y207_H1.1410.72
241_C247_P1.1250.70
282_F287_S1.1210.70
95_Y244_A1.1130.69
229_D232_R1.1110.69
22_F37_V1.1100.68
132_I150_V1.1080.68
19_C39_C1.1070.68
117_S154_F1.1060.68
160_P174_C1.1060.68
228_L318_E1.1050.68
293_L298_S1.1030.68
194_C200_G1.0980.67
125_S188_Y1.0950.67
95_Y188_Y1.0910.67
233_K237_E1.0900.66
52_I60_V1.0830.66
97_A120_T1.0820.66
124_R186_F1.0750.65
35_P266_L1.0630.64
43_A205_V1.0530.63
135_L205_V1.0490.62
244_A249_H1.0490.62
104_D197_D1.0460.62
209_T249_H1.0450.62
76_N255_S1.0410.61
125_S133_G1.0400.61
117_S120_T1.0350.61
36_S55_N1.0350.61
19_C48_C1.0340.60
150_V154_F1.0320.60
226_L229_D1.0310.60
116_K188_Y1.0290.60
32_S286_S1.0240.59
225_L238_Y1.0230.59
117_S155_S1.0210.59
49_I62_L1.0200.59
282_F295_F1.0200.59
188_Y249_H1.0140.58
7_R132_I1.0130.58
125_S129_N1.0080.58
263_I267_L1.0050.57
295_F299_A1.0050.57
118_C227_C1.0030.57
102_K115_K1.0020.57
174_C179_C1.0020.57
132_I147_E1.0010.57
210_I235_V1.0000.57
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  
1cb6A10.99111000.168Contact Map
1blfA10.97631000.18Contact Map
1h45A10.92881000.2Contact Map
1ryoA10.96141000.212Contact Map
2d3iA10.94961000.212Contact Map
3v83A60.9971000.216Contact Map
3mc2A40.95551000.218Contact Map
3todA10.91391000.227Contact Map
3skpA10.93181000.246Contact Map
1iejA10.93471000.284Contact 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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