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T0818 30-163 -force run

ID: 1405477686 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 134 (125)
Sequences: 76 (69.3)
Seq/Len: 0.608
Nf(neff/√len): 6.2

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: 0.608).

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_L2.4930.98
104_W110_Y1.8900.85
89_E94_Y1.8580.84
44_I118_I1.8280.83
59_N113_I1.8280.83
104_W107_H1.6740.74
17_V51_I1.6330.72
53_G89_E1.5860.69
45_R110_Y1.5570.66
51_I55_I1.5430.65
21_S45_R1.5240.64
52_D86_F1.5110.63
64_G73_G1.3880.53
15_C24_L1.3850.53
52_D58_Y1.3510.50
15_C23_K1.3490.50
53_G94_Y1.3250.48
22_E38_D1.3090.47
47_L116_I1.3000.46
41_L44_I1.2980.46
110_Y116_I1.2790.45
33_K36_Y1.2750.44
16_I19_K1.2740.44
30_K55_I1.2470.42
20_D25_F1.2350.41
25_F40_S1.2350.41
29_N107_H1.2300.41
58_Y118_I1.2200.40
71_N109_E1.1940.38
119_C123_N1.1940.38
16_I47_L1.1860.37
55_I105_N1.1860.37
12_M93_E1.1810.37
39_S44_I1.1800.37
22_E45_R1.1780.37
88_T109_E1.1780.37
24_L53_G1.1570.35
34_D37_K1.1510.35
50_Y118_I1.1510.35
30_K45_R1.1490.34
41_L86_F1.1480.34
16_I118_I1.1480.34
53_G88_T1.1450.34
16_I44_I1.1310.33
29_N32_M1.1210.32
7_E113_I1.1190.32
84_F96_I1.1120.32
75_I103_I1.0970.31
16_I120_K1.0900.30
17_V55_I1.0690.29
43_E114_N1.0680.29
55_I58_Y1.0600.28
55_I71_N1.0580.28
35_N105_N1.0580.28
51_I65_G1.0530.28
21_S26_D1.0460.27
12_M95_T1.0410.27
12_M54_A1.0300.26
48_F119_C1.0210.26
104_W113_I1.0200.26
91_G125_G1.0170.26
110_Y113_I1.0170.26
108_P111_E1.0110.25
21_S110_Y1.0110.25
105_N116_I1.0050.25
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  
2mc8A10.746379.40.874Contact Map
3hx8A40.858239.20.904Contact Map
3robA40.888138.60.904Contact Map
3cu3A10.985131.40.909Contact Map
4i4kA20.910431.30.909Contact Map
1tuhA10.9328310.909Contact Map
3g0kA10.813430.10.909Contact Map
3g8zA10.910426.40.912Contact Map
2a15A10.895524.50.913Contact Map
3d9rA40.7836190.917Contact 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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