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OPENSEQ.org

PON1

ID: 1389840621 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 355 (354)
Sequences: 489 (347.1)
Seq/Len: 1.381
Nf(neff/√len): 18.4

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: 1.381).

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
130_L172_A2.4631.00
168_N184_H2.4341.00
268_V282_V2.0780.98
67_S86_L2.0540.98
181_T226_I1.9790.97
115_H134_H1.9440.97
271_I280_L1.8650.96
208_Y213_V1.8600.96
53_E270_N1.8530.96
53_E269_D1.8240.95
53_E224_N1.7160.93
7_L10_L1.6930.92
52_S67_S1.6930.92
64_F85_I1.6490.91
131_V146_F1.6440.91
168_N269_D1.6060.89
53_E115_H1.5090.85
78_N85_I1.5030.85
274_D277_T1.5020.85
6_A22_S1.4810.83
247_V257_T1.4630.82
168_N224_N1.4380.81
9_L17_F1.4360.81
12_M15_A1.4300.80
168_N332_T1.4220.80
10_L13_G1.4200.80
5_I17_F1.4180.80
8_T14_L1.4120.79
128_Y145_K1.4070.79
227_N271_I1.4040.79
237_I256_L1.3960.78
114_P131_V1.3910.78
20_H24_Y1.3880.78
53_E168_N1.3850.77
66_S114_P1.3820.77
168_N183_D1.3790.77
180_G206_V1.3600.76
156_L299_P1.3480.75
4_L14_L1.3460.74
224_N270_N1.3330.73
3_K12_M1.3300.73
10_L14_L1.3280.73
235_V351_L1.3260.73
1_M4_L1.3170.72
205_V223_A1.3120.72
132_V170_I1.3120.72
58_L64_F1.3110.72
11_G14_L1.3000.71
7_L11_G1.2950.70
12_M22_S1.2940.70
3_K24_Y1.2940.70
281_W320_V1.2880.70
308_Q316_K1.2870.70
5_I8_T1.2830.69
191_L195_E1.2830.69
174_G245_I1.2820.69
5_I12_M1.2750.69
127_M148_E1.2700.68
53_E116_G1.2690.68
173_V179_Y1.2640.68
5_I10_L1.2620.68
302_S331_S1.2590.67
115_H270_N1.2590.67
116_G269_D1.2550.67
51_G114_P1.2540.67
215_V218_E1.2530.67
7_L12_M1.2510.67
5_I9_L1.2480.66
4_L9_L1.2430.66
226_I235_V1.2410.66
222_F240_L1.2370.65
2_A19_N1.2330.65
179_Y250_K1.2290.65
51_G169_D1.2230.64
18_R24_Y1.2210.64
2_A20_H1.2190.64
19_N24_Y1.2180.63
304_V324_N1.2130.63
176_E185_Y1.2100.63
33_E36_P1.2070.62
2_A24_Y1.2050.62
19_N23_S1.2030.62
26_T30_A1.2020.62
174_G232_G1.1980.62
287_N290_K1.1970.62
83_G114_P1.1910.61
18_R25_Q1.1890.61
233_K251_H1.1880.61
18_R21_Q1.1870.61
3_K9_L1.1850.60
236_Y247_V1.1830.60
3_K10_L1.1830.60
215_V223_A1.1810.60
169_D346_V1.1810.60
71_Y74_I1.1790.60
63_A230_P1.1750.59
198_L231_D1.1720.59
18_R28_L1.1540.57
104_G248_Y1.1540.57
236_Y245_I1.1520.57
274_D279_D1.1510.57
140_T158_T1.1500.57
6_A24_Y1.1440.56
63_A195_E1.1400.56
14_L17_F1.1330.55
17_F22_S1.1320.55
281_W341_L1.1280.55
143_L339_G1.1260.55
2_A22_S1.1260.55
4_L16_L1.1230.54
16_L20_H1.1230.54
183_D320_V1.1220.54
167_L180_G1.1200.54
266_T284_C1.1180.54
180_G344_G1.1180.54
233_K342_L1.1170.54
84_K283_G1.1060.53
17_F21_Q1.1050.52
2_A8_T1.1050.52
222_F239_E1.0980.52
17_F26_T1.0950.51
23_S26_T1.0950.51
17_F20_H1.0950.51
236_Y284_C1.0910.51
10_L21_Q1.0910.51
25_Q31_L1.0900.51
115_H222_F1.0880.51
217_A256_L1.0820.50
5_I24_Y1.0760.49
54_D118_S1.0720.49
20_H23_S1.0710.49
115_H225_G1.0690.49
6_A16_L1.0670.49
152_S219_G1.0650.48
115_H224_N1.0650.48
10_L17_F1.0640.48
52_S344_G1.0630.48
22_S26_T1.0620.48
50_T283_G1.0620.48
306_R319_Q1.0610.48
281_W336_V1.0600.48
21_Q27_R1.0590.48
13_G22_S1.0580.48
205_V226_I1.0530.47
20_H28_L1.0500.47
99_E341_L1.0460.46
3_K7_L1.0460.46
314_E317_V1.0440.46
220_F226_I1.0440.46
6_A21_Q1.0430.46
19_N25_Q1.0410.46
350_A353_C1.0370.46
3_K8_T1.0360.45
54_D270_N1.0350.45
28_L34_V1.0340.45
266_T315_P1.0330.45
12_M35_Q1.0310.45
22_S31_L1.0300.45
3_K14_L1.0280.45
9_L23_S1.0270.45
117_I143_L1.0240.44
21_Q25_Q1.0240.44
274_D350_A1.0240.44
170_I303_E1.0230.44
21_Q24_Y1.0200.44
2_A23_S1.0200.44
179_Y291_I1.0200.44
279_D306_R1.0190.44
3_K6_A1.0170.44
175_P253_N1.0130.43
126_A346_V1.0120.43
133_N166_N1.0080.43
118_S346_V1.0080.43
20_H26_T1.0060.42
284_C305_L1.0050.42
179_Y229_S1.0040.42
289_M347_F1.0030.42
151_K245_I1.0030.42
51_G66_S1.0030.42
52_S345_T1.0020.42
121_T230_P1.0020.42
24_Y28_L1.0020.42
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: (08Feb14)
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  
3sreA10.92681000.535Contact Map
2fp8A20.79151000.674Contact Map
2p4oA10.777599.80.761Contact Map
1pjxA10.788799.80.774Contact Map
3dr2A20.899.70.779Contact Map
3q6kA20.828299.70.779Contact Map
2qe8A20.774699.70.779Contact Map
2g8sA20.783199.70.791Contact Map
2dg1A60.816999.70.791Contact Map
3a9gA10.76999.70.791Contact 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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