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T0844

ID: 1404750589 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 145 (135)
Sequences: 176 (158.7)
Seq/Len: 1.304
Nf(neff/√len): 13.7

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: 1.304).

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
94_K102_E2.5731.00
47_I86_K2.4981.00
13_E48_Y1.8800.96
23_V123_R1.7910.94
44_S54_L1.7220.92
98_Y101_S1.6860.91
43_L104_N1.6630.90
56_Q95_S1.5480.86
48_Y56_Q1.5370.85
119_V126_I1.5200.84
40_I43_L1.4600.81
39_K91_G1.4380.79
103_Q121_N1.4030.77
61_I112_I1.3720.75
59_S71_L1.3710.75
34_Q104_N1.3680.75
27_I53_I1.3270.71
78_S82_I1.3090.70
110_N116_A1.2850.68
130_H134_G1.2630.66
60_H63_A1.2560.65
87_G101_S1.2330.63
133_K139_Q1.2280.63
37_L48_Y1.2070.61
13_E144_P1.2010.60
58_I111_E1.1960.60
33_I121_N1.1930.59
24_I33_I1.1760.58
12_A142_K1.1750.58
65_P116_A1.1740.58
16_P45_K1.1550.56
86_K101_S1.1440.55
22_E126_I1.1430.54
31_A40_I1.1360.54
23_V95_S1.1330.53
38_E125_T1.1320.53
72_S119_V1.1180.52
13_E16_P1.1060.51
83_G118_K1.0860.49
34_Q107_I1.0830.48
15_L141_V1.0800.48
24_I84_R1.0770.48
43_L133_K1.0740.48
37_L40_I1.0640.47
12_A48_Y1.0560.46
75_I100_I1.0560.46
33_I71_L1.0540.46
70_E115_Y1.0500.45
72_S113_F1.0430.45
24_I89_K1.0310.43
63_A74_R1.0250.43
33_I72_S1.0220.42
57_D81_S1.0220.42
47_I93_I1.0210.42
68_G116_A1.0210.42
51_P93_I1.0180.42
102_E143_M1.0130.42
26_K136_R1.0110.41
16_P136_R1.0100.41
20_E40_I1.0100.41
27_I110_N1.0060.41
30_D125_T1.0050.41
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  
2lnmA10.406943.60.928Contact Map
2llwA10.489731.20.934Contact Map
2llvA10.489717.80.941Contact Map
2zbcA80.53112.40.945Contact Map
3hwsA60.64148.90.949Contact Map
2djwA100.52418.20.949Contact Map
4o4fA10.95176.10.952Contact Map
2oeqA40.4695.80.953Contact Map
2lmdA10.4695.80.953Contact Map
2f4mB10.41385.40.953Contact 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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