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GS - Cfa

ID: 1501864347 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 136 (133)
Sequences: 322 (275.7)
Seq/Len: 2.421
Nf(neff/√len): 23.9

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: 2.421).

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
5_D19_G3.6261.00
68_A74_F3.1501.00
104_I107_R2.6181.00
21_I44_I2.5941.00
127_L132_L2.2721.00
31_Y41_T1.8780.99
7_E17_P1.6920.97
119_G124_H1.6400.97
62_D102_V1.6390.97
46_Q119_G1.6030.96
66_I74_F1.5770.95
42_Q122_K1.5350.94
120_V124_H1.5330.94
24_E27_E1.5220.94
87_I90_R1.4620.92
57_E65_I1.4560.92
50_R134_A1.4290.91
1_C72_H1.4260.91
10_T41_T1.4090.90
81_M134_A1.3760.89
100_L117_D1.3400.87
34_D40_Y1.3360.87
104_I110_L1.3170.86
2_L6_T1.2890.84
50_R117_D1.2880.84
53_Q68_A1.2760.84
60_L64_S1.2710.83
8_I128_L1.2640.83
103_K106_S1.2600.82
83_P86_E1.2500.82
126_F134_A1.2390.81
94_L103_K1.2150.79
18_I30_V1.1970.78
56_F107_R1.1730.76
120_V133_V1.1730.76
120_V126_F1.1720.76
40_Y123_D1.1690.75
84_I90_R1.1180.71
56_F117_D1.0990.69
58_Y104_I1.0900.68
32_T123_D1.0820.67
55_V67_R1.0790.67
89_E104_I1.0790.67
124_H134_A1.0770.67
10_T14_G1.0730.66
63_G79_G1.0710.66
30_V44_I1.0650.65
125_N133_V1.0610.65
18_I118_I1.0590.65
104_I131_G1.0550.64
19_G69_T1.0520.64
57_E108_K1.0470.63
21_I75_M1.0380.62
25_R28_C1.0380.62
29_T41_T1.0350.62
73_K116_Y1.0320.62
131_G135_S1.0300.61
33_V127_L1.0260.61
70_K119_G1.0200.60
17_P20_K1.0180.60
81_M135_S1.0170.60
8_I95_K1.0150.60
31_Y43_P1.0090.59
56_F84_I1.0000.58
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  
3nzmA10.96321000.149Contact Map
2imzA20.94851000.154Contact Map
2in0A10.97061000.154Contact Map
4o1rA10.96321000.168Contact Map
1mi8A10.97061000.173Contact Map
4e2uA10.97061000.204Contact Map
4kl5A20.97791000.204Contact Map
1am2A10.94851000.208Contact Map
2lcjA10.977999.90.222Contact Map
2jmzA10.985399.90.243Contact 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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