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8_1qqvpdb

ID: 1516869680 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 67 (65)
Sequences: 614 (399.6)
Seq/Len: 9.446
Nf(neff/√len): 49.6

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: 9.446).

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
19_D29_K2.1751.00
59_N63_E2.1471.00
9_L13_V1.8761.00
44_M52_L1.8321.00
54_L57_Q1.7961.00
9_L37_D1.7191.00
7_F12_L1.6521.00
21_P24_V1.6081.00
8_P11_V1.6031.00
35_D46_R1.5821.00
33_L38_F1.5141.00
31_N50_A1.4631.00
30_E61_K1.3980.99
38_F49_F1.3460.99
59_N62_K1.3060.99
18_E29_K1.2480.98
26_P29_K1.2420.98
50_A57_Q1.2020.98
9_L65_G1.1570.97
48_A51_N1.1540.97
46_R50_A1.1490.97
38_F42_F1.1450.97
52_L60_L1.1400.97
6_T46_R1.1370.96
9_L41_V1.1260.96
11_V23_G1.0810.95
21_P29_K1.0730.95
62_K65_G1.0680.95
28_R31_N1.0610.94
22_R48_A1.0580.94
54_L58_Q1.0310.93
35_D39_K1.0190.93
34_S38_F1.0040.92
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  
1yu8X10.955299.9-0.023Contact Map
1ujsA1199.90.018Contact Map
1qzpA10.985199.90.023Contact Map
2k6mS10.955299.90.049Contact Map
1undA10.537399.40.361Contact Map
1wy3A10.507599.30.397Contact Map
2pnwA10.388117.10.871Contact Map
3czbA20.35829.80.885Contact Map
3j7yf10.31349.50.885Contact Map
2g5dA10.67167.70.89Contact 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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