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T0848 35-150

ID: 1404967668 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 116 (110)
Sequences: 281 (236.1)
Seq/Len: 2.555
Nf(neff/√len): 22.5

HHblits Results: (2013_03)
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: 2.555).

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
32_Q95_V3.3141.00
18_Y35_L3.2061.00
42_K87_S2.5201.00
14_K40_A2.1841.00
41_V44_T2.1461.00
30_D95_V1.9240.99
10_Q46_K1.8980.99
33_L99_G1.6820.97
38_N91_N1.6230.97
31_D95_V1.6140.97
40_A89_E1.5560.95
9_A44_T1.5010.94
36_K91_N1.4750.93
32_Q84_A1.3460.89
37_V67_D1.3420.88
106_Y109_E1.3310.88
7_D30_D1.3300.88
19_T51_V1.3160.87
65_M68_T1.3150.87
45_G65_M1.2820.85
15_D103_E1.2750.85
37_V41_V1.2660.84
11_V24_Y1.2600.84
31_D86_K1.2300.82
7_D105_N1.2240.81
103_E108_P1.2190.81
13_I93_F1.2190.81
46_K103_E1.1960.79
76_K99_G1.1810.78
103_E109_E1.1770.78
56_F106_Y1.1720.77
52_D70_P1.1600.76
48_P83_N1.1390.74
8_I44_T1.1380.74
9_A49_L1.1130.72
93_F104_L1.1120.72
57_T91_N1.1060.71
59_Y93_F1.0970.70
41_V89_E1.0950.70
19_T35_L1.0900.69
11_V15_D1.0770.68
35_L99_G1.0710.68
14_K38_N1.0710.68
12_K42_K1.0620.67
83_N86_K1.0580.66
36_K93_F1.0570.66
16_V92_L1.0560.66
48_P90_G1.0550.66
77_L89_E1.0460.65
5_S9_A1.0370.64
62_D98_K1.0310.63
9_A97_D1.0240.62
51_V94_F1.0190.62
16_V37_V1.0120.61
7_D10_Q1.0120.61
48_P81_T1.0070.61
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: (05Jul14)
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  
3cfuA20.974199.80.262Contact Map
4lesA10.991499.70.327Contact Map
2llgA10.939798.20.654Contact Map
3qfgA20.939796.80.737Contact Map
3nrfA20.887992.40.797Contact Map
1lmiA10.939791.30.803Contact Map
3isyA10.81990.50.806Contact Map
4phzA30.9138900.809Contact Map
4eaeA20.991488.90.813Contact Map
2x3cA10.732887.10.818Contact 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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