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1ptf_-13

ID: 1502152810 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 86 (86)
Sequences: 426 (2.6)
Seq/Len: 4.953
Nf(neff/√len): 0.3

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: 4.953).

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
3_A77_I6.2851.00
4_N61_Q4.8901.00
26_S58_S3.3811.00
1_A70_E3.2861.00
39_K51_S2.9131.00
47_D58_S2.8591.00
29_S67_D2.8231.00
55_D58_S2.7991.00
1_A31_Q2.3811.00
19_T23_L2.3291.00
26_S40_S2.2761.00
26_S47_D2.0981.00
26_S44_T1.9391.00
74_A78_A1.8961.00
40_S58_S1.8681.00
3_A59_N1.7631.00
1_A71_D1.6890.99
58_S61_Q1.6110.99
31_Q61_Q1.5920.99
40_S47_D1.5370.99
36_Y58_S1.5350.99
31_Q40_S1.5210.99
4_N31_Q1.4760.98
26_S31_Q1.4540.98
33_E44_T1.2880.95
3_A67_D1.2450.94
27_S40_S1.2400.94
4_N40_S1.2330.93
1_A4_N1.2310.93
1_A33_E1.2090.92
26_S33_E1.1900.92
31_Q58_S1.1810.91
55_D78_A1.1790.91
26_S61_Q1.1260.88
44_T58_S1.1050.87
39_K82_E1.0860.86
58_S67_D1.0530.83
33_E58_S1.0310.82
58_S78_A1.0270.81
35_L77_I1.0050.79
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  
1kklH3199.30.692Contact Map
1ptfA1199.20.694Contact Map
1ka5A1199.20.696Contact Map
1pchA1199.20.697Contact Map
1y51A3199.20.7Contact Map
1sphA2199.20.7Contact Map
3ihsA20.941999.20.7Contact Map
3ccdA20.976799.20.7Contact Map
3le1A20.988499.10.71Contact Map
1yx5B10.755834.50.924Contact 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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