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T0833

ID: 1403812340 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 136 (133)
Sequences: 1031 (948.1)
Seq/Len: 7.752
Nf(neff/√len): 82.2

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: 7.752).

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
66_N70_K7.2071.00
97_D101_G6.6701.00
118_S122_Q4.9781.00
37_E41_K4.5851.00
95_Q104_K3.1311.00
64_Q73_E2.6061.00
116_N125_I2.0821.00
101_G121_V2.0681.00
107_Y111_D1.7981.00
77_F81_R1.6771.00
63_F71_V1.5491.00
94_Y102_E1.4980.99
65_Y71_V1.4620.99
34_D42_I1.4440.99
104_K114_K1.4260.99
95_Q103_I1.3490.99
61_Y74_K1.3370.99
122_Q129_T1.3130.98
123_N126_I1.3030.98
92_I108_G1.2900.98
128_S131_Y1.2660.98
128_S132_E1.1930.96
15_F18_M1.1750.96
107_Y113_K1.1530.95
9_S13_L1.1440.95
13_L18_M1.1200.94
5_V10_I1.1180.94
94_Y105_T1.1140.94
4_S8_K1.1030.94
84_D87_V1.0870.93
3_T13_L1.0840.93
4_S13_L1.0770.93
11_L18_M1.0730.92
35_T44_S1.0680.92
3_T8_K1.0560.92
5_V9_S1.0560.92
5_V11_L1.0550.92
12_A15_F1.0480.91
102_E105_T1.0430.91
13_L17_F1.0400.91
64_Q72_S1.0370.91
4_S10_I1.0350.91
9_S12_A1.0320.90
34_D45_K1.0320.90
4_S9_S1.0290.90
10_I15_F1.0290.90
53_G56_N1.0260.90
52_N57_K1.0230.90
8_K14_V1.0190.90
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  
3mswA10.808898.90.548Contact Map
4iglB20.786898.60.594Contact Map
4o9xA10.904498.30.623Contact Map
4iglA20.87596.70.725Contact Map
4ghbA20.8676900.798Contact Map
4a2lA60.757445.30.86Contact Map
3nokA20.7868190.885Contact Map
3zbiC140.205914.70.89Contact Map
3vgzA40.713214.50.891Contact Map
2ecfA10.772113.40.892Contact 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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