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dcp2

ID: 1502383441 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 300 (250)
Sequences: 289 (177.8)
Seq/Len: 1.156
Nf(neff/√len): 11.2

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: 1.156).

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
110_Q181_L3.0731.00
99_R136_D2.8071.00
101_A144_V2.6451.00
48_F190_R2.2790.99
124_G127_K2.2490.99
105_D109_Q2.1250.98
136_D187_S2.0830.97
101_A152_C2.0300.97
168_G206_T1.9560.96
13_D71_H1.9030.95
132_K199_H1.8760.95
40_Q99_R1.8660.94
32_E89_F1.6950.90
17_A99_R1.6240.87
203_D230_K1.5810.85
103_M112_V1.5490.83
161_F172_R1.5330.82
96_I131_D1.5310.82
96_I169_Q1.5260.82
69_F75_L1.5200.82
183_T209_K1.5050.81
155_R179_I1.4980.80
115_K194_S1.4980.80
98_V127_K1.4920.80
21_L174_Y1.4730.79
117_W191_K1.4640.78
127_K136_D1.4530.77
56_L232_W1.4480.77
141_I150_F1.4380.76
104_L175_I1.4350.76
163_D172_R1.4320.76
30_S89_F1.4150.75
199_H219_F1.3950.73
46_E191_K1.3850.72
105_D181_L1.3720.71
106_M178_G1.3690.71
113_L199_H1.3560.70
105_D110_Q1.3410.69
21_L172_R1.3250.68
175_I236_R1.3120.67
27_E131_D1.3110.66
102_I173_L1.3060.66
189_T224_P1.3010.66
51_A191_K1.2910.65
42_H127_K1.2900.65
15_L39_E1.2890.65
99_R187_S1.2740.63
15_L22_N1.2640.62
33_R39_E1.2550.61
26_E54_D1.2500.61
124_G152_C1.2480.61
99_R130_I1.2070.57
84_E88_D1.1990.56
17_A40_Q1.1950.56
79_S82_H1.1820.55
20_I152_C1.1810.55
12_L222_V1.1810.55
133_D159_N1.1790.54
98_V136_D1.1770.54
39_E44_F1.1760.54
103_M152_C1.1750.54
62_R176_I1.1740.54
110_Q178_G1.1540.52
13_D38_I1.1540.52
59_L91_R1.1520.52
27_E96_I1.1510.52
15_L44_F1.1400.51
39_E93_K1.1400.51
105_D135_S1.1400.51
46_E58_S1.1370.50
62_R157_N1.1350.50
50_R61_L1.1330.50
127_K208_K1.1300.50
174_Y217_N1.1260.49
22_N33_R1.1240.49
248_I252_V1.1170.48
150_F155_R1.1050.47
203_D220_Y1.1040.47
99_R170_N1.0920.46
81_V211_K1.0900.46
105_D196_I1.0880.46
40_Q136_D1.0870.45
22_N39_E1.0860.45
48_F105_D1.0780.45
136_D172_R1.0710.44
150_F185_F1.0670.44
89_F115_K1.0660.43
117_W194_S1.0620.43
6_A111_C1.0570.43
154_S178_G1.0570.43
157_N186_E1.0490.42
114_V193_I1.0430.41
199_H235_K1.0420.41
50_R57_P1.0420.41
75_L191_K1.0410.41
103_M178_G1.0400.41
72_C232_W1.0390.41
113_L124_G1.0380.41
61_L86_F1.0380.41
66_A233_I1.0350.41
28_Q127_K1.0330.40
14_D36_F1.0320.40
96_I135_S1.0280.40
72_C136_D1.0270.40
161_F174_Y1.0260.40
17_A132_K1.0230.39
65_S83_E1.0200.39
243_T248_I1.0190.39
127_K132_K1.0180.39
102_I162_I1.0160.39
37_Q48_F1.0150.39
28_Q98_V1.0140.39
246_K249_S1.0120.38
14_D18_R1.0050.38
91_R150_F1.0020.38
4_T112_V1.0000.37
126_P193_I1.0000.37
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  
2a6tA20.76671000.532Contact Map
2qklB10.31000.699Contact Map
4kg3A30.483399.90.807Contact Map
3o8sA10.426799.70.851Contact Map
4hfqA20.653399.70.86Contact Map
3q1pA20.6499.70.861Contact Map
4ickA20.4599.60.868Contact Map
1vk6A10.799.60.868Contact Map
1f3yA10.4899.60.869Contact Map
1sjyA10.599.60.87Contact 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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