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T0818 30-163 -force run

ID: 1405480510 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 134 (126)
Sequences: 79 (74)
Seq/Len: 0.627
Nf(neff/√len): 6.6

Jackhmmer Results: (2014_04_16)
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: 0.627).

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_F41_L2.3030.96
104_W110_Y1.8930.86
51_I55_I1.7190.78
89_E94_Y1.6780.75
104_W107_H1.6780.75
59_N113_I1.6310.72
52_D86_F1.6030.71
16_I116_I1.5470.67
52_D90_T1.5370.66
17_V51_I1.5280.65
53_G89_E1.5190.65
45_R110_Y1.5080.64
44_I118_I1.4750.61
48_F59_N1.4240.57
84_F96_I1.4140.56
15_C24_L1.3680.53
21_S45_R1.3650.52
15_C23_K1.3610.52
16_I120_K1.3580.52
3_G6_K1.3470.51
20_D73_G1.3460.51
34_D37_K1.3050.48
58_Y118_I1.3020.47
48_F78_Y1.2940.47
43_E114_N1.2930.47
25_F40_S1.2630.44
51_I65_G1.2360.42
16_I47_L1.2350.42
108_P111_E1.2320.42
33_K36_Y1.2320.42
55_I58_Y1.2290.41
39_S44_I1.2250.41
6_K58_Y1.2090.40
88_T109_E1.2070.40
22_E71_N1.1930.39
75_I103_I1.1900.38
16_I118_I1.1890.38
41_L44_I1.1880.38
16_I19_K1.1800.38
21_S34_D1.1720.37
53_G88_T1.1700.37
74_I108_P1.1600.36
47_L116_I1.1530.35
52_D58_Y1.1470.35
49_E65_G1.1320.34
20_D25_F1.1240.33
34_D85_D1.1180.33
12_M93_E1.1130.33
66_G113_I1.1070.32
33_K105_N1.1040.32
30_K55_I1.0960.31
29_N107_H1.0820.30
24_L75_I1.0800.30
119_C123_N1.0790.30
124_W127_K1.0770.30
32_M36_Y1.0660.29
11_R17_V1.0640.29
81_H113_I1.0620.29
104_W113_I1.0570.29
16_I44_I1.0520.28
64_G73_G1.0500.28
30_K45_R1.0460.28
105_N116_I1.0350.27
12_M109_E1.0250.27
76_C116_I1.0230.26
22_E38_D1.0130.26
22_E45_R1.0090.26
50_Y118_I1.0080.25
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: (12Jul14)
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  
2mc8A10.753784.40.862Contact Map
3hx8A40.880644.90.896Contact Map
3cu3A10.985135.90.902Contact Map
3robA40.888131.10.905Contact Map
2a15A10.9104310.905Contact Map
4i4kA20.910428.50.907Contact Map
3g0kA10.80627.80.907Contact Map
3wmdA20.925426.50.908Contact Map
3g8zA10.90325.70.909Contact Map
1tuhA10.925424.60.91Contact 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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