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D3

ID: 1501854333 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 53 (52)
Sequences: 219 (114.3)
Seq/Len: 4.212
Nf(neff/√len): 15.9

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: 4.212).

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
8_V31_D2.1851.00
40_Q45_M1.8981.00
12_E15_A1.8321.00
26_T41_S1.7190.99
9_Q37_L1.3110.94
20_C49_C1.2770.93
28_V37_L1.2760.93
11_T30_N1.2600.92
17_S49_C1.2420.92
9_Q30_N1.2380.91
34_S41_S1.2340.91
24_I33_A1.2250.91
12_E33_A1.1950.89
18_K39_K1.1900.89
28_V33_A1.1780.89
6_C14_S1.1700.88
19_T36_R1.1540.87
36_R51_A1.1470.87
15_A40_Q1.1440.87
10_T39_K1.1420.86
9_Q39_K1.1250.85
22_M43_L1.1230.85
17_S20_C1.1220.85
8_V24_I1.1140.85
4_A50_E1.0750.82
22_M29_T1.0700.81
13_W16_C1.0610.80
22_M26_T1.0550.80
6_C9_Q1.0470.79
4_A40_Q1.0470.79
18_K34_S1.0390.78
29_T46_V1.0320.78
29_T32_N1.0160.76
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  
4hqfA10.0377970.688Contact Map
3ghmA1196.90.694Contact Map
4okrA20.886896.50.706Contact Map
3r6bA10.962396.50.709Contact Map
1vexA10.924596.30.712Contact Map
2rjqA10.150996.30.715Contact Map
1szlA10.981196.20.715Contact Map
4okuA20.8868960.72Contact Map
1lslA10.9434960.72Contact Map
1w0rA2195.50.732Contact 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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