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T0829

ID: 1403547770 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 70 (69)
Sequences: 398 (336.8)
Seq/Len: 5.768
Nf(neff/√len): 40.5

Jackhmmer Results: (2014_04_16)
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: 5.768).

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_R24_E3.3271.00
24_E34_Q2.9821.00
42_A55_F2.7251.00
45_N55_F2.2611.00
40_E44_Q2.0661.00
37_G65_L1.7211.00
56_F61_K1.5990.99
3_R26_Q1.5100.99
6_V14_I1.4360.98
3_R13_S1.4220.98
42_A64_F1.3930.98
26_Q32_T1.3920.98
43_H47_M1.2920.96
14_I46_F1.2640.96
36_L65_L1.2250.95
39_P64_F1.2170.94
53_G61_K1.2130.94
34_Q67_R1.2120.94
9_S53_G1.2000.94
8_S53_G1.1880.94
13_S34_Q1.1690.93
57_D61_K1.1590.92
41_R45_N1.1520.92
27_F53_G1.1500.92
9_S51_S1.1400.92
27_F56_F1.1280.91
36_L67_R1.1220.91
11_I56_F1.1070.90
11_I14_I1.1060.90
26_Q34_Q1.0910.89
23_L35_Y1.0830.89
39_P42_A1.0730.88
23_L60_I1.0310.85
13_S24_E1.0120.84
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: (21Jun14)
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  
4hs5A20.957120.40.886Contact Map
4jpdA10.971417.90.889Contact Map
2x8nA10.942917.90.889Contact Map
3k8rA20.857117.60.89Contact Map
3nv7A10.5143170.89Contact Map
1ew4A10.971411.90.898Contact Map
3oeqA10.957110.50.9Contact Map
4f3rA30.510.20.901Contact Map
2ji4A10.842910.20.901Contact Map
1ej2A10.65718.30.905Contact 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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