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2wvoA

ID: 1504789307 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 233 (223)
Sequences: 374 (316.8)
Seq/Len: 1.677
Nf(neff/√len): 21.2

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: 1.677).

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
25_F167_V2.2300.99
5_F10_G2.2190.99
48_A167_V2.2030.99
19_N23_A2.0550.99
51_R168_D2.0490.99
3_E6_E1.9970.98
52_L56_G1.9560.98
47_I83_I1.9440.98
25_F163_V1.8380.97
35_G133_V1.8030.96
26_E154_K1.7780.96
45_L74_D1.7760.96
80_A174_F1.6360.93
4_P8_V1.5830.91
91_F174_F1.5740.91
123_R200_L1.5580.91
55_W170_L1.5540.90
37_D80_A1.5470.90
97_T103_L1.5230.89
155_S215_A1.4970.88
98_S103_L1.4900.88
28_V142_L1.4440.86
101_Y152_D1.4400.85
18_F56_G1.4400.85
21_C101_Y1.4320.85
37_D153_G1.4290.85
93_S201_K1.3740.81
100_R147_A1.3720.81
6_E10_G1.3680.81
52_L204_A1.3670.81
25_F45_L1.3570.80
51_R171_E1.3500.80
31_G213_D1.3470.80
14_V17_L1.3290.78
3_E10_G1.3280.78
37_D148_W1.3260.78
153_G220_D1.3100.77
138_K144_K1.3060.77
45_L163_V1.3020.76
101_Y173_A1.3020.76
28_V73_I1.2990.76
141_S145_K1.2910.76
56_G60_Q1.2810.75
4_P7_I1.2800.75
35_G137_Q1.2560.73
158_K162_Q1.2470.72
97_T155_S1.2430.72
7_I174_F1.2410.71
44_R165_G1.2380.71
20_N130_K1.2380.71
34_F37_D1.2340.71
12_L146_T1.2270.70
5_F8_V1.2270.70
154_K200_L1.2210.70
159_I162_Q1.2200.70
15_A141_S1.2160.69
2_S6_E1.1950.67
187_E208_D1.1940.67
54_R208_D1.1920.67
51_R91_F1.1850.66
41_C102_E1.1800.66
29_Q32_R1.1790.66
60_Q170_L1.1700.65
160_V200_L1.1700.65
52_L61_I1.1700.65
56_G61_I1.1650.64
215_A218_K1.1640.64
193_D197_L1.1560.63
153_G157_E1.1540.63
51_R56_G1.1460.62
140_T145_K1.1460.62
28_V38_Y1.1420.62
133_V137_Q1.1420.62
80_A169_E1.1420.62
163_V167_V1.1380.62
14_V203_A1.1250.60
184_A205_G1.1210.60
4_P154_K1.1130.59
55_W60_Q1.1130.59
188_I192_E1.1090.59
43_L52_L1.1080.59
41_C152_D1.1070.58
93_S102_E1.0980.58
24_C48_A1.0870.56
64_D160_V1.0860.56
22_V143_A1.0830.56
40_R86_E1.0770.55
131_D160_V1.0760.55
21_C50_V1.0740.55
43_L54_R1.0690.55
20_N45_L1.0650.54
44_R162_Q1.0640.54
35_G140_T1.0610.54
97_T102_E1.0610.54
59_V83_I1.0590.53
21_C168_D1.0580.53
44_R97_T1.0570.53
51_R197_L1.0520.53
52_L55_W1.0480.52
17_L20_N1.0350.51
9_A156_L1.0300.50
160_V186_N1.0300.50
26_E32_R1.0280.50
30_L48_A1.0280.50
97_T156_L1.0240.50
145_K159_I1.0200.49
82_S140_T1.0140.49
13_G16_G1.0100.48
80_A125_L1.0090.48
122_G126_H1.0060.48
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  
2wvqA20.91421000.134Contact Map
2msvA10.6052250.931Contact Map
4btfA10.63099.90.943Contact Map
3he4A40.19317.50.946Contact Map
2uytA10.21035.50.949Contact Map
3pltA30.781150.95Contact Map
4abxA40.50214.60.951Contact Map
2k9jB10.14593.20.954Contact Map
1hy5A20.39062.80.956Contact Map
2fywA30.31762.50.957Contact 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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