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leafs_1ptf_fastRelax_16

ID: 1507536333 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (87)
Sequences: 470 (260.2)
Seq/Len: 5.402
Nf(neff/√len): 27.9

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: 5.402).

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
6_L78_V3.0421.00
25_S80_T2.8211.00
1_G66_Y2.6731.00
44_F81_F2.3141.00
33_F63_L2.1111.00
2_L71_D1.9541.00
20_V47_W1.8451.00
32_L41_W1.7341.00
5_L49_L1.6861.00
28_L37_R1.6601.00
35_L44_F1.6090.99
24_V47_W1.5600.99
15_I24_V1.5450.99
23_Q27_N1.4990.99
36_I41_W1.4810.99
7_L60_L1.4300.98
23_Q38_N1.4020.98
34_V41_W1.3970.98
36_I55_P1.3470.97
37_R55_P1.3320.97
34_V44_F1.3300.97
42_R82_R1.3090.96
17_S51_H1.2150.94
15_I56_R1.1520.91
4_R78_V1.1140.89
9_L85_R1.0980.88
11_P78_V1.0980.88
10_D39_L1.0910.88
20_V84_L1.0880.88
81_F86_I1.0700.87
44_F63_L1.0680.86
36_I57_R1.0650.86
52_S70_E1.0590.86
1_G21_M1.0580.86
75_R78_V1.0360.84
42_R53_L1.0300.84
37_R52_S1.0300.84
7_L64_Y1.0260.83
8_I27_N1.0080.82
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  
1kklH3195.50.836Contact Map
1ka5A1195.50.836Contact Map
3ccdA20.97795.30.838Contact Map
3ihsA20.942595.20.839Contact Map
1ptfA1195.10.84Contact Map
1pchA10.988594.70.844Contact Map
1y51A30.988594.50.845Contact Map
1sphA20.988594.40.846Contact Map
3le1A20.988593.50.852Contact Map
3pqaA40.50578.50.934Contact 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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