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OPENSEQ.org
Q9HYR3_1Z1S
ID: 1404255386 Query Sequence

 Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 141 (135)
Sequences: 289 (249.5)
Seq/Len: 2.141
Nf(neff/√len): 21.5
HHblits Results: (2013_03)
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: 2.141).

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
106_R114_L2.5161.00
108_R113_L2.1761.00
28_P48_R2.0220.99
47_G50_T1.9800.99
83_E118_F1.8500.98
4_K8_V1.8360.98
31_V47_G1.8200.98
36_Y99_Q1.8010.98
10_S22_W1.7840.98
18_D21_G1.7540.97
27_H113_L1.6180.95
78_D108_R1.5500.94
79_L106_R1.4970.92
28_P49_E1.4900.92
132_E135_A1.4810.91
83_E116_R1.4760.91
74_T77_P1.4650.91
24_D110_G1.4230.89
30_G51_I1.4150.89
32_L120_N1.3970.88
84_F101_Y1.3920.88
61_H93_S1.3660.86
7_L105_L1.3560.86
24_D97_L1.3110.83
18_D118_F1.2980.82
5_E70_Q1.2720.80
106_R113_L1.2590.79
3_A107_T1.2330.77
29_E47_G1.2180.76
34_F119_W1.2130.76
18_D24_D1.2080.75
5_E112_I1.1910.74
88_G128_L1.1850.73
83_E104_V1.1810.73
97_L117_D1.1800.73
12_R49_E1.1550.71
103_S115_Y1.1460.70
4_K18_D1.1340.69
54_H115_Y1.1300.68
68_D85_H1.1280.68
13_L18_D1.1210.67
42_K116_R1.1200.67
7_L80_A1.1190.67
40_G120_N1.1190.67
26_F65_R1.1010.65
101_Y119_W1.0980.65
77_P80_A1.0960.65
54_H121_P1.0790.63
66_F86_G1.0760.63
85_H98_A1.0690.62
49_E53_A1.0640.61
103_S117_D1.0640.61
4_K76_D1.0610.61
33_E44_R1.0610.61
13_L24_D1.0600.61
55_M98_A1.0590.61
45_F115_Y1.0330.58
26_F115_Y1.0200.57
56_R82_G1.0070.55
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: (28Jun14)
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  
1z1sA10.914999.90.276Contact Map
1s5aA40.957499.90.328Contact Map
3jumA20.985899.90.364Contact Map
3dm8A10.907899.90.365Contact Map
3fgyA20.92299.90.374Contact Map
3ff0A20.985899.90.374Contact Map
3f9sA20.907899.90.381Contact Map
3grdA20.900799.90.385Contact Map
3ec9A20.900799.90.387Contact Map
1sjwA10.929199.90.392Contact 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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