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2K5W

ID: 1515673932 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 111 (96)
Sequences: 488 (332.6)
Seq/Len: 5.083
Nf(neff/√len): 33.9

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: 5.083).

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
41_D45_V2.9571.00
98_L102_V2.2941.00
39_A70_L2.1881.00
38_P46_K2.1251.00
95_K103_K2.1121.00
69_R91_E1.9971.00
11_K71_Y1.9881.00
21_E64_K1.9711.00
11_K73_D1.8231.00
14_Y47_K1.7841.00
36_T50_T1.7331.00
63_N66_A1.6370.99
13_V69_R1.5460.99
18_I22_G1.5300.99
22_G66_A1.5150.99
14_Y84_S1.5140.99
63_N92_E1.5030.99
66_A92_E1.4750.98
76_D86_E1.4620.98
34_N50_T1.4400.98
98_L103_K1.4370.98
39_A49_I1.3690.97
37_L51_F1.3630.97
18_I51_F1.2940.95
12_D41_D1.2530.94
62_L90_Y1.2100.93
51_F63_N1.2070.93
16_M68_L1.1970.92
16_M37_L1.1880.92
49_I87_V1.1800.92
39_A72_V1.1770.91
51_F62_L1.1710.91
62_L68_L1.1630.91
14_Y72_V1.1570.91
93_I106_F1.1380.90
53_S63_N1.1330.89
9_I73_D1.1170.88
5_S11_K1.1090.88
68_L92_E1.1080.88
14_Y39_A1.1070.88
71_Y88_K1.1000.87
37_L87_V1.0730.86
25_E34_N1.0660.85
49_I72_V1.0590.84
19_K22_G1.0570.84
4_A84_S1.0380.83
18_I33_R1.0340.83
24_I67_F1.0280.82
15_Y101_K1.0280.82
67_F93_I1.0120.81
30_R93_I1.0050.80
72_V90_Y1.0040.80
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  
2k5wA1199.90.125Contact Map
2k5qA10.846899.90.244Contact Map
3nppA20.774899.90.258Contact Map
2mmpA10.62167.90.914Contact Map
3v9fA40.72977.40.916Contact Map
4a2lA60.729750.922Contact Map
3ottA20.80184.90.922Contact Map
1c8cA10.57664.50.924Contact Map
3u1wA30.68472.90.93Contact Map
4k61A20.65772.80.931Contact 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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