OPENSEQ.org
NanR 25-255

ID: 1517460237 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 231 (227)
Sequences: 18336 (12293.2)
Seq/Len: 80.775
Nf(neff/√len): 815.9

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: 80.775).

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
128_A206_R4.0101.00
113_R214_D3.5461.00
209_D212_E3.2781.00
26_G29_E3.2291.00
19_M24_E2.9181.00
135_S199_I2.6281.00
99_H162_P2.5821.00
106_F110_S2.5631.00
19_M40_F2.5401.00
34_E45_R2.4011.00
17_E58_K2.2641.00
126_L154_V2.2621.00
13_E54_A2.2341.00
105_L222_N2.1721.00
62_Q72_S2.1691.00
12_V43_V2.0831.00
204_A212_E2.0691.00
123_Q160_G2.0671.00
102_Q114_Y2.0601.00
12_V41_F2.0471.00
120_T123_Q1.9711.00
157_E165_M1.9361.00
117_E210_P1.9271.00
131_L202_V1.8691.00
124_I206_R1.8291.00
63_I69_A1.8071.00
15_E19_M1.8011.00
212_E216_A1.7981.00
152_H198_H1.7911.00
109_S218_Q1.7811.00
197_Q223_S1.7371.00
6_K14_E1.7051.00
154_V157_E1.7011.00
203_D207_R1.6981.00
109_S214_D1.6861.00
214_D218_Q1.6851.00
103_L167_I1.6741.00
200_A216_A1.6111.00
37_L48_V1.5851.00
113_R210_P1.5771.00
110_S113_R1.5721.00
207_R212_E1.5451.00
18_Q22_R1.5401.00
199_I203_D1.5301.00
153_R169_V1.5291.00
130_A147_S1.5221.00
112_V213_A1.4791.00
119_A124_I1.4771.00
105_L218_Q1.4631.00
105_L225_S1.4521.00
156_A168_H1.4471.00
64_N67_E1.4411.00
128_A132_E1.4361.00
128_A202_V1.4291.00
113_R211_D1.4261.00
140_N143_A1.4111.00
166_A170_A1.4091.00
215_R219_S1.3980.99
131_L199_I1.3970.99
11_M15_E1.3930.99
35_R39_A1.3820.99
133_I150_D1.3740.99
123_Q158_I1.3730.99
13_E58_K1.3720.99
36_E40_F1.3670.99
119_A208_H1.3330.99
64_N70_R1.3280.99
129_K133_I1.3230.99
210_P214_D1.3140.99
148_D152_H1.3110.99
15_E18_Q1.3110.99
126_L157_E1.3030.99
105_L109_S1.3020.99
99_H163_I1.2970.99
163_I174_W1.2940.99
155_L205_I1.2880.99
109_S113_R1.2850.99
159_P165_M1.2680.99
104_R108_E1.2650.99
15_E41_F1.2590.99
19_M41_F1.2460.98
197_Q220_H1.2450.98
102_Q161_N1.2420.98
124_I208_H1.2330.98
30_Q70_R1.2260.98
130_A154_V1.2090.98
202_V206_R1.2080.98
133_I147_S1.2010.98
124_I202_V1.2000.98
153_R157_E1.2000.98
150_D154_V1.1760.98
146_R150_D1.1700.97
111_L156_A1.1550.97
212_E215_R1.1460.97
148_D198_H1.1420.97
112_V116_A1.1410.97
218_Q222_N1.1390.97
98_A225_S1.1280.97
25_F71_V1.1280.97
99_H161_N1.1240.97
211_D215_R1.1200.96
119_A158_I1.1200.96
64_N68_R1.1130.96
154_V158_I1.1110.96
7_K10_E1.1090.96
112_V217_L1.0970.96
62_Q70_R1.0960.96
143_A146_R1.0960.96
110_S214_D1.0890.96
200_A212_E1.0800.95
119_A205_I1.0780.95
6_K11_M1.0770.95
200_A219_S1.0690.95
196_Q200_A1.0680.95
135_S195_Y1.0680.95
56_K63_I1.0610.95
151_F202_V1.0580.95
56_K61_V1.0580.95
33_S36_E1.0550.95
108_E152_H1.0360.94
114_Y118_H1.0300.94
119_A123_Q1.0280.94
198_H220_H1.0160.93
126_L129_K1.0120.93
102_Q118_H1.0060.93
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  
3c7jA20.90481000.103Contact Map
4p96A20.9741000.109Contact Map
3sxyA20.85281000.113Contact Map
2di3A20.9611000.115Contact Map
2hs5A10.87881000.126Contact Map
3ihuA20.87011000.128Contact Map
4p9fA20.90041000.14Contact Map
1hw1A20.95671000.152Contact Map
3ic7A20.480599.80.496Contact Map
3by6A50.523899.80.497Contact 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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