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T0814 180-300

ID: 1404854277 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 121 (119)
Sequences: 225 (198.6)
Seq/Len: 1.891
Nf(neff/√len): 18.2

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: 1.891).

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
65_E113_D2.1270.99
16_I23_L2.1110.99
32_R35_N2.0100.99
40_L58_L1.9650.99
81_V95_L1.9440.98
23_L50_I1.8390.98
19_P24_K1.8170.97
65_E111_D1.8000.97
27_V58_L1.7360.96
28_Y33_R1.6730.95
17_T66_Y1.5220.91
77_N81_V1.5210.91
16_I22_D1.4950.90
4_Q59_I1.4440.88
18_Y21_T1.4250.87
9_I97_T1.4020.86
67_R98_D1.3900.85
7_F25_I1.3490.83
66_Y119_R1.3490.83
5_V113_D1.3180.81
69_M95_L1.3110.80
2_H61_P1.3050.80
9_I19_P1.2990.79
70_E109_D1.2940.79
37_V81_V1.2810.78
8_N83_N1.2780.78
45_I51_S1.2410.75
36_A39_D1.2370.74
43_M111_D1.2370.74
16_I24_K1.2300.74
29_Q35_N1.2280.74
11_N16_I1.2210.73
16_I76_Y1.2080.72
5_V27_V1.1840.70
73_S76_Y1.1710.69
13_N16_I1.1690.68
87_H92_N1.1380.65
37_V40_L1.1340.65
66_Y109_D1.1200.63
72_L112_Q1.1130.63
7_F116_F1.1050.62
44_S51_S1.0980.61
84_I93_V1.0980.61
4_Q54_Y1.0910.60
26_F51_S1.0910.60
54_Y109_D1.0880.60
9_I53_T1.0860.60
70_E110_Q1.0830.60
4_Q67_R1.0780.59
19_P116_F1.0630.58
25_I39_D1.0620.57
71_F93_V1.0600.57
20_Q118_I1.0580.57
9_I18_Y1.0520.56
109_D112_Q1.0450.56
54_Y58_L1.0370.55
11_N47_E1.0190.53
22_D102_D1.0180.53
82_E100_R1.0180.53
66_Y72_L1.0030.51
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  
1avyA30.355410.20.941Contact Map
1k9aA60.64469.90.941Contact Map
2lqnA10.33888.80.943Contact Map
2dm0A10.33067.30.945Contact Map
2cs0A10.35547.20.945Contact Map
2vseA20.80176.20.946Contact Map
2ekxA10.33886.20.946Contact Map
3wa4A10.25625.80.947Contact Map
4oujA20.39675.70.947Contact Map
2bbuA10.35545.40.948Contact 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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