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T0759 sub_alignment
ID: 1400107596 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 109 (97)
Sequences: 129 (94.4)
Seq/Len: 1.330
Nf(neff/√len): 9.6
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: 1.330).

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
76_E101_L1.6340.90
68_S97_S1.6200.89
99_Q103_V1.5110.84
13_V24_P1.4870.83
55_G62_V1.4590.81
72_F101_L1.4500.81
25_E38_F1.4190.79
21_E44_Q1.4090.78
49_E57_N1.4000.77
62_V74_I1.3560.74
77_A97_S1.3320.72
59_E74_I1.3240.72
23_S26_E1.3060.70
68_S80_S1.3020.70
16_P58_G1.3010.70
63_I100_E1.2940.69
12_V21_E1.2920.69
36_N39_V1.2730.67
19_G30_A1.2610.66
65_D76_E1.2600.66
70_K84_T1.2550.66
14_I37_M1.2530.66
75_E79_Q1.2340.64
32_L71_K1.2300.63
28_H33_I1.2160.62
13_V76_E1.2150.62
32_L81_G1.2150.62
55_G58_G1.2000.61
95_D98_I1.1900.60
33_I38_F1.1880.59
14_I21_E1.1880.59
25_E39_V1.1630.57
62_V88_Y1.1580.57
37_M44_Q1.1360.54
35_W42_R1.1360.54
45_E50_E1.1130.52
84_T99_Q1.1100.52
11_M21_E1.1020.51
71_K94_K1.0980.51
74_I90_R1.0960.50
58_G62_V1.0940.50
21_E26_E1.0740.48
15_H40_K1.0630.47
19_G62_V1.0630.47
81_G94_K1.0510.46
33_I43_S1.0480.46
21_E37_M1.0380.45
74_I86_A1.0310.44
23_S44_Q1.0310.44
29_R34_D1.0230.43
63_I88_Y1.0190.43
11_M14_I1.0090.42
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: (10May14)
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  
1lm5A20.834999.30.522Contact Map
1lm7A20.889999.30.522Contact Map
4mouA30.917433.20.886Contact Map
3isaA60.880732.90.886Contact Map
3gkbA30.917429.30.889Contact Map
4jylA60.880727.60.89Contact Map
1sg4A30.94526.60.891Contact Map
4gm2A70.357826.10.892Contact Map
3r9qA30.8807240.894Contact Map
3h0uA30.935823.90.894Contact 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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