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BipA

ID: 1517555010 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 195 (188)
Sequences: 29355 (12320.1)
Seq/Len: 156.144
Nf(neff/√len): 898.5

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: 156.144).

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
169_N181_E3.5731.00
24_K170_G3.2211.00
163_V189_A2.8711.00
101_A127_I2.6061.00
126_V165_A2.5781.00
161_P189_A2.5261.00
189_A192_D2.3771.00
13_H109_T2.3611.00
21_L98_V2.3581.00
98_V128_N2.3571.00
96_L126_V2.3291.00
9_A92_V2.2841.00
130_V164_Y2.1281.00
126_V186_L2.0971.00
141_V145_F2.0841.00
141_V164_Y2.0671.00
145_F149_V2.0151.00
62_A69_R1.9921.00
182_D185_P1.9621.00
189_A193_H1.9401.00
128_N167_A1.9341.00
102_F132_R1.9301.00
127_I164_Y1.8821.00
130_V181_E1.8561.00
24_K183_M1.7811.00
97_L113_T1.7781.00
20_T167_A1.7631.00
10_I22_V1.7521.00
10_I96_L1.7391.00
7_N71_N1.7331.00
21_L183_M1.6761.00
60_N71_N1.6141.00
101_A130_V1.6121.00
86_E115_K1.5601.00
144_V148_F1.5581.00
96_L190_I1.5491.00
165_A186_L1.5361.00
110_R147_L1.5191.00
94_S124_I1.5101.00
124_I163_V1.5041.00
188_Q192_D1.4961.00
99_V125_V1.4541.00
142_D146_D1.4481.00
184_T188_Q1.4291.00
64_K69_R1.4101.00
21_L186_L1.4070.99
94_S190_I1.4040.99
5_L71_N1.4000.99
104_G143_Q1.3850.99
124_I189_A1.3790.99
74_D77_G1.3770.99
70_I191_V1.3700.99
96_L124_I1.3630.99
68_Y191_V1.3540.99
107_P110_R1.3190.99
161_P193_H1.3110.99
127_I162_I1.2980.99
143_Q146_D1.2890.99
62_A71_N1.2820.99
185_P188_Q1.2740.99
25_L187_Y1.2540.99
103_D106_M1.2480.99
100_D103_D1.2480.99
185_P189_A1.2460.98
8_I94_S1.2410.98
99_V162_I1.2370.98
183_M187_Y1.2370.98
13_H16_H1.2220.98
136_R139_W1.1850.98
24_K28_Q1.1840.98
108_Q111_F1.1550.97
95_V121_L1.1390.97
125_V162_I1.1280.97
21_L167_A1.1110.96
143_Q147_L1.1080.96
110_R114_K1.0870.96
21_L25_L1.0760.95
105_P108_Q1.0730.95
22_V72_I1.0710.95
96_L186_L1.0640.95
21_L165_A1.0620.95
117_F123_P1.0600.95
60_N73_V1.0410.94
142_D145_F1.0400.94
95_V116_A1.0400.94
84_E88_V1.0320.94
161_P164_Y1.0310.94
126_V163_V1.0170.93
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  
4zciA201000.126Contact Map
2yweA10.77951000.192Contact Map
3cb4D60.74871000.196Contact Map
3vqtA40.86151000.204Contact Map
3j25A10.93331000.206Contact Map
4qjty10.769299.90.221Contact Map
2h5eA20.820599.90.221Contact Map
3tr5A40.943699.90.224Contact Map
4kiyV10.912899.90.228Contact Map
1darA10.815499.90.228Contact 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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