OPENSEQ.org
IFNa21b

ID: 1516831203 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 166 (157)
Sequences: 399 (230.9)
Seq/Len: 2.541
Nf(neff/√len): 18.4

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: 2.541).

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
29_C139_C2.7181.00
142_E145_R2.6161.00
59_E121_K1.9480.99
65_F97_E1.6640.97
140_A144_V1.6560.97
13_R86_S1.5890.96
85_F152_F1.5640.96
77_W145_R1.5520.95
78_E132_T1.5210.95
131_L140_A1.5070.94
30_L33_R1.4960.94
18_L123_Y1.4390.92
99_C142_E1.4270.92
99_C124_F1.4190.92
36_F123_Y1.4040.91
124_F142_E1.3840.90
50_K143_V1.3630.89
14_A61_I1.3450.88
159_Q162_L1.3250.87
90_N100_V1.3010.86
46_N90_N1.2950.86
59_E63_Q1.2920.86
77_W142_E1.2910.85
113_N117_I1.2660.84
38_F99_C1.2640.84
97_E118_L1.2580.83
135_K154_L1.2550.83
141_W145_R1.2520.83
21_M99_C1.2440.82
61_I86_S1.2150.80
52_Q62_Q1.1990.79
123_Y147_E1.1960.79
91_Q127_I1.1900.78
90_N132_T1.1820.78
26_P43_F1.1760.77
158_F163_R1.1680.77
160_E164_R1.1600.76
20_Q147_E1.1590.76
159_Q163_R1.1540.75
161_R164_R1.1500.75
160_E163_R1.1480.75
111_L114_V1.1430.74
17_L127_I1.1400.74
67_L111_L1.1340.74
22_G86_S1.1290.73
98_A109_T1.1140.72
32_D54_I1.1140.72
131_L141_W1.1140.72
134_K143_V1.1070.71
114_V120_V1.1040.71
58_H97_E1.0960.70
23_R120_V1.0960.70
133_E142_E1.0920.70
58_H65_F1.0900.69
79_Q126_R1.0860.69
70_T128_T1.0770.68
108_E115_D1.0760.68
127_I147_E1.0720.67
85_F106_V1.0720.67
156_K159_Q1.0670.67
85_F113_N1.0670.67
34_H51_A1.0570.66
42_E55_S1.0540.66
156_K163_R1.0490.65
112_M115_D1.0460.65
46_N113_N1.0440.64
13_R94_N1.0420.64
23_R37_G1.0400.64
158_F161_R1.0370.64
26_P78_E1.0370.64
17_L141_W1.0280.63
126_R146_A1.0250.62
49_Q108_E1.0230.62
41_E108_E1.0230.62
110_P113_N1.0190.62
43_F152_F1.0190.62
145_R152_F1.0150.61
124_F151_S1.0140.61
36_F147_E1.0100.61
66_N83_E1.0020.60
25_S86_S1.0020.60
18_L68_F1.0000.60
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  
3se4B10.85541000.018Contact Map
1b5lA10.91571000.018Contact Map
3oq3A111000.018Contact Map
3s9dA20.76511000.024Contact Map
1au1A20.98191000.033Contact Map
1wu3I10.95181000.064Contact Map
3piwA10.90361000.102Contact Map
3pivA20.91571000.133Contact Map
4gmoA10.716911.40.95Contact Map
2d48A10.710810.70.951Contact 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.

Page generated in 0.0184 seconds.