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T0809 -force run

ID: 1402085427 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 62 (62)
Sequences: 51 (32.1)
Seq/Len: 0.823
Nf(neff/√len): 4.1

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: 0.823).

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
29_V37_Y2.1470.96
47_K50_D1.9450.92
11_E40_Y1.7890.87
9_L12_V1.7810.87
17_V32_K1.7710.87
13_N41_I1.7010.83
16_Q19_E1.5160.72
9_L51_N1.3970.63
19_E56_N1.3410.59
9_L17_V1.3290.58
13_N51_N1.2760.53
38_T53_L1.2630.52
6_S31_K1.2220.48
41_I54_T1.2040.47
44_Q58_K1.1860.45
26_E50_D1.1830.45
12_V51_N1.1750.44
48_L57_V1.1680.44
30_T34_S1.1620.43
10_Q55_K1.1580.43
24_G28_N1.1550.42
20_A27_I1.1490.42
16_Q56_N1.1450.42
6_S22_I1.0970.38
25_R50_D1.0750.36
18_R59_V1.0720.35
6_S20_A1.0630.35
26_E47_K1.0510.34
2_K59_V1.0330.32
34_S60_V1.0300.32
7_T37_Y1.0280.32
15_D33_D1.0200.31
36_R40_Y1.0190.31
25_R33_D1.0090.31
47_K52_L1.0020.30
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: (06Aug15)
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  
2muyA1199.20.579Contact Map
4m8aA31990.612Contact Map
4co9A40.983928.10.896Contact Map
1r61A2114.20.909Contact Map
2zxqA10.98399.30.916Contact Map
3pgwB20.29037.70.919Contact Map
4cobA20.98396.90.921Contact Map
4cogA40.98396.80.921Contact Map
4m8dA1216.30.922Contact Map
2vxpA20.98396.30.922Contact 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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