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dcp2 1-98

ID: 1502389065 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 98 (97)
Sequences: 303 (201.7)
Seq/Len: 3.124
Nf(neff/√len): 20.5

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: 3.124).

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
13_D71_H2.5481.00
26_E54_D2.2381.00
32_E89_F2.1051.00
17_A40_Q1.8930.99
69_F75_L1.8700.99
38_I61_L1.4890.96
61_L86_F1.4700.95
39_E93_K1.4700.95
84_E88_D1.4310.94
16_S68_L1.4290.94
65_S83_E1.4250.94
35_C85_A1.3600.92
39_E44_F1.3600.92
43_W47_D1.3580.92
79_S82_H1.3570.92
60_G86_F1.3320.91
8_F11_V1.3170.90
20_I23_L1.2770.89
24_P97_P1.2710.88
30_S89_F1.2540.87
37_Q48_F1.2460.87
27_E33_R1.2390.87
81_V84_E1.2350.86
50_R57_P1.2080.85
16_S72_C1.2000.84
2_S5_N1.1890.83
27_E96_I1.1740.82
29_S57_P1.1560.81
3_F6_A1.1430.80
23_L37_Q1.1380.79
11_V42_H1.1370.79
10_Q31_V1.1170.78
46_E58_S1.1090.77
22_N48_F1.0920.75
18_R36_F1.0870.75
14_D18_R1.0850.75
3_F55_Q1.0820.74
13_D38_I1.0730.74
32_E98_V1.0680.73
83_E87_D1.0600.72
37_Q94_T1.0580.72
29_S63_V1.0500.71
9_S77_K1.0480.71
7_T98_V1.0370.70
8_F57_P1.0360.70
54_D81_V1.0310.69
8_F14_D1.0310.69
29_S66_A1.0290.69
2_S6_A1.0290.69
44_F49_I1.0280.69
53_N76_W1.0220.68
53_N59_L1.0100.67
95_R98_V1.0060.67
80_K84_E1.0030.66
3_F38_I1.0010.66
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  
2qklB10.91841000.055Contact Map
2a6tA20.96941000.265Contact Map
1h2vC10.79598.30.93Contact Map
1h7dA10.37767.90.931Contact Map
2r09A20.87767.70.931Contact Map
3gcgB10.959260.935Contact Map
3trkA10.91845.80.935Contact Map
3o8sA10.0515.80.935Contact Map
2hfiA10.64295.40.936Contact Map
2hwkA10.91845.40.936Contact 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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