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RB_cycD

ID: 1504662760 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 52 (52)
Sequences: 71 (34.7)
Seq/Len: 1.365
Nf(neff/√len): 4.8

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: 1.365).

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
39_M51_C1.7030.92
37_P49_E1.6380.90
36_L42_I1.6270.90
38_S42_I1.6050.89
37_P43_V1.4790.83
39_M47_M1.4710.83
43_V51_C1.4460.81
39_M43_V1.4230.80
38_S41_K1.3170.72
43_V47_M1.2990.70
38_S48_L1.2940.70
45_T52_E1.2190.63
36_L44_A1.2140.63
36_L45_T1.2020.62
41_K45_T1.1610.58
41_K51_C1.1290.54
47_M51_C1.1180.53
41_K52_E1.0910.51
43_V49_E1.0910.51
23_C26_L1.0830.50
37_P51_C1.0650.48
7_F15_A1.0490.46
44_A48_L1.0370.45
42_I52_E1.0160.43
5_S31_P1.0050.42
5_S29_E1.0020.42
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  
4ellA20.807797.70.527Contact Map
4eljA10.846297.60.538Contact Map
4yozA1097.50.553Contact Map
2r7gA20.807797.40.559Contact Map
2b9rA20.846248.80.794Contact Map
1w98B11420.802Contact Map
2pk2A40.826941.60.802Contact Map
4eojB20.884638.60.805Contact Map
1f5qB20.923136.90.808Contact Map
2i53A10.846235.70.809Contact 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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