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bbs_7_sheet1-force-run

ID: 1505422497 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 130 (128)
Sequences: 286 (214.5)
Seq/Len: 2.234
Nf(neff/√len): 19.0

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: 2.234).

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
15_D118_Y2.6721.00
94_E126_H1.9200.99
39_V86_L1.8640.99
19_L125_L1.7240.97
55_N80_Q1.6940.97
100_L120_I1.6530.96
36_I79_C1.6300.96
23_D89_K1.6080.95
44_D99_T1.5870.95
6_S9_P1.5620.94
95_G98_G1.5250.93
65_D68_S1.5170.93
73_L106_P1.4630.91
11_F114_Q1.4430.91
93_I96_Q1.4210.90
17_F90_I1.4000.89
123_L126_H1.3620.87
92_S124_S1.3570.87
36_I82_N1.3040.84
79_C83_T1.2910.83
7_A24_A1.2650.81
76_T83_T1.2570.80
114_Q122_P1.2550.80
8_V11_F1.2460.80
97_Y122_P1.2450.79
103_Y113_C1.2430.79
57_A78_R1.2280.78
5_K8_V1.2270.78
37_D107_R1.2270.78
37_D58_V1.2230.78
95_G122_P1.2200.78
49_L80_Q1.2180.77
85_R94_E1.2120.77
24_A109_Q1.2060.76
75_A110_P1.1890.75
46_P96_Q1.1820.74
47_I73_L1.1800.74
94_E98_G1.1760.74
40_L103_Y1.1750.74
24_A91_R1.1730.74
106_P112_T1.1720.73
51_D71_N1.1700.73
12_S112_T1.1330.70
97_Y104_V1.1300.70
44_D84_T1.1270.69
95_G126_H1.1270.69
69_N90_I1.1260.69
94_E124_S1.1250.69
31_E111_K1.1250.69
38_N105_T1.1210.69
103_Y106_P1.1190.68
75_A78_R1.1150.68
4_A8_V1.1140.68
72_F96_Q1.1110.68
122_P126_H1.1090.67
17_F28_L1.1080.67
20_N27_S1.1000.67
57_A80_Q1.0940.66
120_I124_S1.0910.66
104_V108_I1.0660.63
107_R127_Q1.0640.63
35_A47_I1.0600.62
6_S13_V1.0580.62
15_D116_R1.0570.62
17_F48_D1.0570.62
42_Q89_K1.0420.60
95_G124_S1.0360.60
120_I123_L1.0270.59
73_L89_K1.0190.58
57_A60_S1.0130.57
11_F17_F1.0110.57
35_A82_N1.0050.56
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  
4iknA10.915410.80.943Contact Map
3l81A10.923180.947Contact Map
4p6zM10.91547.10.948Contact Map
4en2M20.91545.30.951Contact Map
1i31A10.80774.20.953Contact Map
2vglM10.861540.954Contact Map
4dacA40.23.90.954Contact Map
3ml6A60.84623.60.955Contact Map
3k2tA10.13082.90.957Contact Map
2l0lA10.07692.60.958Contact 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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