GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
RB_CycD

ID: 1504661053 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 43 (42)
Sequences: 174 (111.6)
Seq/Len: 4.143
Nf(neff/√len): 17.2

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: 4.143).

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
17_N35_L1.7210.99
9_R12_Y1.6910.99
19_I36_M1.6510.99
37_W40_D1.6440.99
39_L42_Q1.6280.99
9_R28_S1.5420.98
7_F10_K1.5250.98
8_L17_N1.4780.97
38_L42_Q1.4560.97
4_Q7_F1.3770.96
37_W41_F1.3640.95
10_K22_L1.3380.95
10_K14_L1.3270.94
3_Q12_Y1.2800.93
3_Q6_L1.2520.92
13_T17_N1.1450.86
2_P12_Y1.0960.83
7_F41_F1.0880.82
13_T21_K1.0800.82
6_L9_R1.0600.80
2_P10_K1.0590.80
14_L30_A1.0580.80
13_T19_I1.0570.80
9_R23_C1.0230.76
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  
4ellA20.976798.90.1Contact Map
4yozA1098.90.102Contact Map
4eljA10.976798.80.127Contact Map
2r7gA20.976798.80.138Contact Map
2qdjA10.651224.80.76Contact Map
3opyI40.62796.70.814Contact Map
3hhwK50.97673.20.84Contact Map
1czaN10.69773.20.84Contact Map
2jexA10.41863.10.842Contact Map
4cr2O10.97672.50.849Contact 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.

Page generated in 0.0316 seconds.