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T0808 19-150

ID: 1405534291 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 132 (127)
Sequences: 156 (148)
Seq/Len: 1.228
Nf(neff/√len): 13.1

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: 1.228).

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
68_G97_V3.1541.00
89_I99_I2.2120.99
55_L117_L1.8300.94
48_P94_A1.7870.93
40_S100_D1.7650.93
53_L78_S1.7260.92
51_A97_V1.4860.81
6_V124_G1.4780.81
76_L82_T1.4160.76
58_K79_N1.3910.75
58_K97_V1.3850.74
47_Q120_D1.3430.71
46_H101_L1.3310.70
36_K60_H1.3260.70
45_L119_A1.3220.69
9_V39_V1.3080.68
57_A76_L1.2930.67
27_R98_R1.2890.66
25_T28_G1.2740.65
31_H37_S1.2720.65
65_V117_L1.2260.61
100_D113_E1.2050.59
55_L76_L1.1840.57
52_D98_R1.1780.56
22_A86_V1.1760.56
9_V78_S1.1630.55
60_H107_S1.1560.54
8_G11_G1.1510.53
58_K84_V1.1490.53
94_A122_V1.1480.53
43_F86_V1.1440.53
61_S76_L1.1430.53
29_V61_S1.1360.52
17_R91_I1.1280.51
97_V105_S1.1270.51
4_Q9_V1.1250.51
53_L70_K1.1250.51
48_P85_P1.1180.50
99_I122_V1.1140.50
6_V15_V1.1120.50
43_F99_I1.1040.49
61_S112_G1.0950.48
116_Q120_D1.0940.48
34_N103_G1.0930.48
72_F102_Q1.0890.47
20_D108_G1.0850.47
113_E116_Q1.0830.47
17_R57_A1.0730.46
19_Q23_R1.0630.45
64_K119_A1.0630.45
56_Y116_Q1.0630.45
40_S43_F1.0500.44
98_R106_K1.0500.44
10_S115_K1.0420.43
36_K101_L1.0410.43
61_S117_L1.0400.43
9_V12_N1.0370.42
21_G25_T1.0370.42
27_R83_K1.0320.42
88_S101_L1.0310.42
28_G45_L1.0240.41
31_H103_G1.0240.41
52_D124_G1.0170.40
12_N65_V1.0120.40
33_T63_I1.0100.40
20_D71_G1.0090.40
43_F53_L1.0090.40
93_Q125_K1.0090.40
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  
3zm8A10.94799.40.449Contact Map
2vzsA2099.40.45Contact Map
2wz8A10.871299.40.453Contact Map
4kmqA10.893999.40.459Contact Map
2cdpA40.886499.30.467Contact Map
2bgoA10.840999.30.479Contact Map
2y8kA10.886499.30.479Contact Map
3wnoA20.984899.30.486Contact Map
2w87A20.924299.30.491Contact Map
2w47A10.916799.20.498Contact 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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