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PhD

ID: 1516009600 Query Sequence

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We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 128 (125)
Sequences: 3108 (2416.1)
Seq/Len: 24.864
Nf(neff/√len): 216.1

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: 24.864).

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
12_S120_D3.1691.00
53_F99_G3.0901.00
38_Y41_G2.6151.00
23_S26_L2.1091.00
20_P36_K2.0971.00
71_E125_R1.9721.00
22_Y34_R1.8391.00
52_V124_L1.8261.00
27_Q32_C1.8131.00
34_R57_S1.7871.00
99_G103_F1.7421.00
54_L68_Y1.6451.00
51_S103_F1.6141.00
7_V121_T1.5481.00
36_K55_E1.5461.00
35_L126_F1.5331.00
70_V100_Y1.5201.00
25_P32_C1.5161.00
109_L115_L1.4951.00
6_F37_V1.4481.00
34_R55_E1.4441.00
23_S33_W1.4211.00
109_L122_V1.3770.99
9_E121_T1.3730.99
97_C101_N1.3650.99
10_N13_T1.3430.99
104_F109_L1.2960.99
42_N97_C1.2870.99
74_H113_G1.2770.99
55_E97_C1.2700.99
31_L56_L1.2220.98
37_V50_L1.1990.98
4_A23_S1.1970.98
8_L12_S1.1950.98
43_G47_G1.1820.98
68_Y88_F1.1770.98
31_L49_Y1.1660.97
29_S33_W1.1620.97
49_Y105_R1.1610.97
49_Y102_R1.1600.97
5_T125_R1.1500.97
5_T123_I1.1470.97
106_L110_A1.1380.97
6_F10_N1.1360.97
6_F23_S1.1300.97
97_C100_Y1.1190.96
105_R108_L1.0850.96
41_G51_S1.0790.95
42_N53_F1.0780.95
22_Y55_E1.0690.95
75_Q116_N1.0600.95
68_Y99_G1.0570.95
90_S98_W1.0560.95
35_L124_L1.0560.95
113_G116_N1.0540.95
51_S99_G1.0490.94
41_G53_F1.0340.94
52_V70_V1.0310.94
30_G33_W1.0310.94
37_V52_V1.0270.94
4_A26_L1.0250.93
75_Q123_I1.0180.93
73_V125_R1.0170.93
93_E96_E1.0170.93
6_F11_F1.0140.93
98_W102_R1.0130.93
72_M104_F1.0060.93
45_V49_Y1.0020.92
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  
1flkA20.968899.80.088Contact Map
4ghuA10.968899.80.095Contact Map
2f1zA20.945399.80.1Contact Map
3ivvA10.976699.80.101Contact Map
3zjbA30.984499.80.105Contact Map
1lb6A10.984499.80.107Contact Map
1ca9A60.960999.80.109Contact Map
1d00A80.960999.80.111Contact Map
3hqiA20.945399.80.125Contact Map
4gwmA20.945399.80.126Contact 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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