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T0815

ID: 1402513597 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 106 (105)
Sequences: 203 (181.7)
Seq/Len: 1.933
Nf(neff/√len): 17.7

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: 1.933).

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_V48_W2.7931.00
28_P42_V1.6850.96
11_F74_V1.6080.94
10_Y93_F1.6070.94
20_D46_L1.5430.92
35_E52_A1.5030.91
94_T102_R1.4790.90
62_P74_V1.4740.90
35_E39_H1.4690.89
76_A86_P1.4550.89
35_E48_W1.4510.89
82_F89_L1.4330.88
4_P95_I1.3490.83
35_E78_V1.3450.83
27_A101_A1.3420.83
35_E89_L1.3250.82
56_A83_P1.3180.81
57_S81_R1.3130.81
40_Q67_V1.3040.80
49_W53_K1.2890.79
78_V86_P1.2810.79
56_A91_Y1.2550.77
56_A82_F1.2470.76
80_G83_P1.2440.76
5_D81_R1.2410.75
66_T99_R1.2340.75
59_V63_L1.2180.73
17_N105_I1.1960.71
94_T101_A1.1810.70
11_F85_S1.1740.69
80_G86_P1.1730.69
84_G103_L1.1560.68
46_L50_V1.1430.66
32_V35_E1.1420.66
7_V23_S1.1230.64
61_E77_K1.1120.63
13_A101_A1.1100.63
38_R59_V1.1020.62
6_I43_V1.1020.62
84_G87_V1.0740.59
79_S85_S1.0610.58
19_T74_V1.0590.58
12_D27_A1.0540.57
63_L98_G1.0440.56
35_E84_G1.0430.56
35_E82_F1.0330.55
31_V44_A1.0330.55
2_D106_Q1.0280.54
7_V72_A1.0220.54
24_E37_A1.0170.53
23_S47_R1.0170.53
24_E69_G1.0100.52
32_V62_P1.0020.52
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: (07Jun14)
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  
3mg1A2199.30.627Contact Map
4h3uA2199.20.637Contact Map
4mjdA20.981199.20.651Contact Map
3dm8A1199.10.658Contact Map
3g16A2199.10.659Contact Map
3ff2A1199.10.659Contact Map
2k54A1199.10.66Contact Map
2a15A10.981199.10.66Contact Map
1ohpA40.990699.10.662Contact Map
3dmcA21990.668Contact 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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