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fastRelax_offset_7

ID: 1507196406 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (87)
Sequences: 481 (243.4)
Seq/Len: 5.529
Nf(neff/√len): 26.1

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: 5.529).

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
30_R68_D2.9361.00
38_D56_Y2.3631.00
44_I77_V1.9301.00
44_I61_L1.8981.00
14_P66_F1.8061.00
29_H51_H1.7391.00
79_I83_S1.7191.00
2_A71_R1.6541.00
25_L83_S1.5330.99
46_I82_L1.4660.99
34_L77_V1.4170.98
33_F70_A1.4030.98
78_R82_L1.3600.97
25_L36_H1.3490.97
29_H83_S1.3400.97
7_V60_V1.3200.97
36_H40_Y1.3100.96
20_A47_W1.2750.96
4_D78_R1.2600.95
3_L23_A1.2340.95
9_L87_A1.2040.94
18_F83_S1.1940.93
18_F86_V1.1670.92
36_H41_T1.1610.92
33_F39_S1.1510.91
63_V72_E1.1490.91
49_D77_V1.1410.91
14_P85_L1.1380.91
70_A82_L1.1320.91
15_L38_D1.1080.89
10_L18_F1.1040.89
60_V78_R1.1010.89
18_F65_V1.1010.89
1_P17_Q1.0700.87
71_R75_A1.0570.86
11_L48_L1.0450.85
27_R61_L1.0440.85
10_L80_A1.0320.84
2_A62_L1.0320.84
25_L84_H1.0300.84
41_T76_F1.0170.83
5_V49_D1.0070.82
47_W64_L1.0070.82
28_L65_V1.0040.82
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  
1kklH3169.20.891Contact Map
1pchA10.988569.20.891Contact Map
1ka5A1162.30.896Contact Map
1ptfA1160.60.897Contact Map
3ccdA20.97755.70.9Contact Map
1sphA20.988555.50.9Contact Map
1y51A30.988553.80.901Contact Map
3ihsA20.90848.30.904Contact Map
3le1A20.988541.10.908Contact Map
2q8nA30.9773.40.945Contact 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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