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T0822 -force run

ID: 1403035131 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 121 (112)
Sequences: 61 (56.3)
Seq/Len: 0.545
Nf(neff/√len): 5.3

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: 0.545).

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
78_D98_H3.8261.00
49_E52_T1.8310.80
58_A62_G1.7640.77
13_T43_T1.7220.74
10_H42_L1.7000.73
66_L108_L1.6430.69
7_N95_Q1.5860.65
52_T98_H1.5530.63
29_S32_K1.4350.54
62_G113_Y1.4030.51
11_D42_L1.3720.49
37_Y67_V1.3700.49
11_D14_A1.3630.48
11_D110_Y1.3570.48
9_V17_T1.3370.46
10_H62_G1.3240.45
26_G100_I1.2980.43
59_P111_M1.2890.42
27_N51_A1.2520.40
5_A55_S1.2420.39
52_T102_K1.2370.38
81_K103_A1.2360.38
12_F26_G1.2290.38
38_N67_V1.2290.38
12_F46_L1.2030.36
59_P62_G1.2000.36
48_M75_A1.1960.35
104_D109_F1.1930.35
63_K92_D1.1930.35
74_T103_A1.1720.34
64_L75_A1.1680.33
77_V113_Y1.1610.33
50_T101_T1.1410.32
57_T114_A1.1240.30
73_A113_Y1.1080.29
19_S99_T1.1030.29
25_A88_I1.0900.28
26_G102_K1.0840.28
7_N112_E1.0810.28
37_Y64_L1.0780.27
54_I77_V1.0720.27
29_S93_L1.0700.27
63_K90_T1.0670.27
38_N112_E1.0620.26
29_S45_C1.0550.26
72_A84_A1.0540.26
4_V103_A1.0510.26
71_A93_L1.0450.25
49_E102_K1.0410.25
22_Y85_S1.0340.25
18_S31_S1.0310.25
7_N60_S1.0290.24
26_G48_M1.0250.24
57_T97_A1.0240.24
42_L62_G1.0180.24
6_G91_V1.0170.24
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  
2wz8A10.84347.90.908Contact Map
2zxqA10.925641.90.911Contact Map
3wnoA20.933925.60.92Contact Map
3ecqA20.9256220.923Contact Map
2bgoA10.793419.10.925Contact Map
4bhrA20.388413.70.93Contact Map
4kmqA10.925610.60.933Contact Map
3zm8A10.8768.40.936Contact Map
3w5mA10.79347.60.937Contact Map
4g5aA20.66127.40.937Contact 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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