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blast alignment

ID: 1515171076 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 69 (69)
Sequences: 1477 (1060.5)
Seq/Len: 21.406
Nf(neff/√len): 127.7

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: 21.406).

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
26_R41_E3.0451.00
5_E55_V2.5281.00
16_E19_K2.4991.00
56_K61_F2.2871.00
49_Y69_P2.2441.00
31_K37_Y2.1301.00
56_K59_E2.1291.00
35_M65_Q2.0551.00
35_M52_K2.0471.00
54_W61_F1.9051.00
16_E64_L1.7701.00
29_K39_T1.6521.00
30_A38_L1.5991.00
10_A25_F1.5641.00
64_L67_F1.5181.00
35_M54_W1.5021.00
28_V48_L1.4621.00
6_I30_A1.3090.99
17_H21_E1.2780.99
37_Y50_E1.2600.99
42_A49_Y1.2340.98
6_I9_L1.2100.98
28_V41_E1.1910.98
34_T57_P1.1480.97
42_A47_K1.1360.97
10_A40_L1.1210.97
10_A38_L1.1180.96
54_W59_E1.0910.96
23_L44_D1.0900.96
7_E11_R1.0820.96
12_F64_L1.0790.95
9_L55_V1.0380.94
11_R15_D1.0230.93
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  
2kxgA1199.20.194Contact Map
3ul5A4199.10.211Contact Map
1eqkA1199.10.221Contact Map
2l4vA1199.10.222Contact Map
1yvbI11990.238Contact Map
5a0oB20990.24Contact Map
4lziA11990.241Contact Map
2ch9A11990.243Contact Map
4n6tA11990.25Contact Map
4n6oB11990.252Contact 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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