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salbiii

ID: 1513976230 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 134 (126)
Sequences: 11857 (8277.2)
Seq/Len: 94.103
Nf(neff/√len): 737.4

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: 94.103).

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
107_T116_S2.8531.00
27_V52_R2.6581.00
83_L102_A2.6001.00
22_D25_A2.5061.00
32_E48_R2.3351.00
31_T115_D2.2231.00
86_E99_K2.0551.00
37_E118_R2.0461.00
84_A99_K2.0151.00
8_K12_A1.9801.00
69_H84_A1.9651.00
35_T116_S1.8901.00
34_A51_Q1.7721.00
16_R20_E1.7531.00
9_E13_E1.7411.00
13_E16_R1.7171.00
10_I108_L1.6961.00
27_V48_R1.6851.00
78_S107_T1.6451.00
83_L104_D1.6261.00
25_A28_E1.6121.00
47_G50_A1.6061.00
104_D119_V1.5951.00
30_F34_A1.5881.00
21_G59_V1.5751.00
13_E29_M1.5731.00
24_D52_R1.5641.00
80_A105_V1.5261.00
70_L78_S1.5071.00
52_R56_N1.5011.00
6_K9_E1.4831.00
33_N115_D1.4541.00
109_T115_D1.4511.00
110_P115_D1.4311.00
35_T46_E1.4291.00
37_E116_S1.4000.99
7_R108_L1.3960.99
37_E44_V1.3700.99
23_V27_V1.3480.99
49_A53_E1.3270.99
86_E97_R1.3170.99
70_L82_A1.3060.99
23_V56_N1.2640.99
84_A101_N1.2500.99
31_T109_T1.2480.99
53_E56_N1.2460.98
72_A80_A1.2400.98
12_A16_R1.2380.98
53_E57_S1.1870.98
104_D117_M1.1800.98
78_S105_V1.1710.98
66_E86_E1.1700.97
79_V108_L1.1670.97
24_D27_V1.1500.97
13_E25_A1.1420.97
68_G84_A1.1330.97
38_D119_V1.1260.97
30_F117_M1.1250.97
11_V79_V1.1070.96
30_F51_Q1.1060.96
13_E28_E1.0990.96
7_R79_V1.0830.96
88_T94_N1.0820.96
77_K110_P1.0790.95
107_T115_D1.0770.95
68_G86_E1.0620.95
36_I117_M1.0610.95
49_A52_R1.0580.95
11_V106_F1.0520.95
82_A118_R1.0480.94
7_R73_G1.0440.94
57_S61_A1.0340.94
109_T113_K1.0180.93
106_F114_I1.0000.92
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  
3rgaA10.970199.70.137Contact Map
3wmdA20.970199.70.151Contact Map
1ohpA40.932899.70.167Contact Map
1oh0A20.940399.70.181Contact Map
1tuhA10.940399.70.188Contact Map
2gexA20.970199.70.192Contact Map
2f99A40.962799.70.197Contact Map
3ebtA10.932899.60.201Contact Map
3kkgA10.977699.60.201Contact Map
3g8zA10.917999.60.204Contact 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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