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T0803 1-90

ID: 1401826419 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 90 (78)
Sequences: 796 (618.2)
Seq/Len: 10.205
Nf(neff/√len): 70.0

HHblits Results: (2013_03)
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: 10.205).

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
11_V57_D3.4811.00
23_L50_E3.4301.00
28_D48_Y3.1811.00
55_K61_E2.2951.00
63_K73_L2.2701.00
57_D62_Y2.1191.00
25_Y37_D2.0151.00
44_V47_T1.8311.00
60_G79_G1.6461.00
2_N5_K1.6181.00
10_S14_D1.6141.00
25_Y41_G1.6051.00
25_Y31_K1.6011.00
3_I7_K1.5941.00
14_D62_Y1.4111.00
49_M53_P1.4030.99
63_K75_I1.3660.99
31_K37_D1.3300.99
4_N7_K1.3220.99
8_V11_V1.3210.99
11_V58_I1.3070.99
18_I49_M1.2760.99
35_T66_K1.2540.99
23_L32_I1.1810.98
2_N24_S1.1800.98
65_I69_N1.1520.97
67_V71_L1.1450.97
19_K72_V1.0950.96
14_D18_I1.0890.96
9_A13_S1.0750.95
29_T47_T1.0510.94
17_S24_S1.0390.94
11_V62_Y1.0180.93
22_A72_V1.0090.93
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: (24May14)
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  
1t92A20.988999.90.178Contact Map
3gn9A30.988999.90.202Contact Map
2kepA10.988999.80.205Contact Map
3g20A20.988999.70.336Contact Map
2m7gA10.493.90.781Contact Map
4ixjA20.944492.60.792Contact Map
2hi2A10.966775.20.837Contact Map
2m3kA10.866763.50.85Contact Map
1x6zA10.944456.30.856Contact Map
1qveA20.966746.10.865Contact 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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