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RB_CyclinD_corr

ID: 1504665730 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 53 (53)
Sequences: 62 (38.6)
Seq/Len: 1.170
Nf(neff/√len): 5.3

HHblits Results: (2016_02)
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: 1.170).

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
32_P38_V1.6620.89
47_E52_E1.4530.78
43_L50_K1.4020.74
36_K52_E1.3570.71
31_L36_K1.2810.64
32_P52_E1.2700.63
34_M43_L1.2630.63
45_V49_Q1.2170.58
10_T27_T1.2000.57
32_P36_K1.1990.57
31_L40_T1.1880.56
34_M46_C1.1740.54
48_E52_E1.1600.53
44_E53_E1.1540.52
44_E48_E1.1220.49
6_L10_T1.1050.48
40_T50_K1.0910.46
36_K40_T1.0720.44
27_T30_K1.0670.44
37_I52_E1.0490.42
26_D29_N1.0410.41
31_L37_I1.0270.40
38_V43_L1.0230.40
26_D30_K1.0210.40
38_V48_E1.0150.39
39_A46_C1.0050.38
2_F14_T1.0020.38
2_F6_L1.0010.38
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  
2f2cA10.962383.60.714Contact Map
1f5qB20.905780.80.723Contact Map
2b9rA20.924579.90.725Contact Map
1g3nC20.962378.80.728Contact Map
2w96A10.905777.40.732Contact Map
3g33B20.905777.40.732Contact Map
1w98B10.962376.50.734Contact Map
4eojB20.9623740.739Contact Map
2pk2A40.849172.10.743Contact Map
2ivxA20.849170.80.745Contact 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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