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P21156 test

ID: 1502090861 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 302 (301)
Sequences: 1189 (435.5)
Seq/Len: 3.950
Nf(neff/√len): 25.1

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: 3.950).

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
10_R200_L5.5551.00
93_P97_A4.4191.00
263_Q267_E4.3301.00
199_W266_P4.1611.00
78_R82_A3.6981.00
61_L122_A3.6651.00
213_E241_K3.2381.00
45_H48_R3.2201.00
242_R259_E2.8011.00
31_V61_L2.7521.00
74_E78_R2.6321.00
56_L85_C2.5281.00
151_F181_I2.3521.00
18_H171_Y2.2671.00
32_M43_M2.2541.00
20_I132_F2.2331.00
264_T267_E2.1751.00
218_E223_L2.1711.00
90_H122_A2.1681.00
43_M132_F2.1661.00
219_R237_E2.1391.00
101_N104_V2.1231.00
243_M261_N2.1051.00
218_E240_K2.0931.00
90_H126_Y2.0821.00
48_R83_Y2.0271.00
79_T82_A1.9401.00
31_V122_A1.8761.00
261_N267_E1.8591.00
196_Q273_L1.8491.00
26_E173_G1.8381.00
213_E243_M1.8281.00
215_P241_K1.7340.99
49_K201_E1.7220.99
31_V131_A1.7210.99
27_F173_G1.7060.99
175_I181_I1.6840.99
243_M263_Q1.6670.99
218_E221_G1.6600.99
157_R298_R1.6260.99
95_G114_M1.6140.99
79_T83_Y1.6130.99
23_V130_A1.6090.99
78_R204_D1.6060.99
284_V287_R1.5860.98
95_G118_G1.5650.98
27_F130_A1.5630.98
61_L88_L1.5490.98
283_R287_R1.4870.97
148_I171_Y1.4590.97
205_I210_L1.4570.97
100_I121_Q1.4500.97
68_K72_M1.4470.97
270_E274_V1.4460.97
151_F175_I1.4400.97
8_H196_Q1.4320.96
123_L131_A1.4010.96
90_H125_K1.3470.94
283_R289_Q1.3410.94
112_D117_E1.3370.94
222_M256_G1.3180.94
217_L226_I1.3090.93
68_K115_K1.3080.93
103_F231_I1.2800.92
297_K302_F1.2790.92
42_V194_I1.2440.91
282_G290_A1.2350.90
233_L237_E1.2140.89
114_M254_L1.2070.89
36_I206_V1.2050.89
210_L265_L1.2020.89
287_R290_A1.2010.89
199_W269_I1.1960.88
94_E98_M1.1950.88
19_I148_I1.1950.88
267_E270_E1.1930.88
63_V90_H1.1890.88
7_T10_R1.1850.88
80_A300_G1.1850.88
70_R74_E1.1820.88
283_R288_D1.1770.87
110_H254_L1.1580.86
120_K157_R1.1500.86
104_V232_D1.1360.85
149_Y183_V1.1340.85
127_G175_I1.1340.85
277_T282_G1.1300.84
66_G91_K1.1270.84
151_F180_S1.1220.84
74_E82_A1.1210.84
47_A58_F1.1170.83
283_R290_A1.1160.83
24_A27_F1.1110.83
43_M186_L1.1060.83
44_L79_T1.1020.82
208_L249_L1.1000.82
227_D230_R1.0990.82
218_E239_I1.0960.82
17_I186_L1.0940.82
217_L236_G1.0840.81
26_E149_Y1.0760.80
295_L298_R1.0750.80
159_D162_N1.0710.80
60_L85_C1.0710.80
111_T254_L1.0670.79
114_M118_G1.0640.79
20_I23_V1.0620.79
48_R79_T1.0610.79
222_M284_V1.0600.79
110_H251_C1.0600.79
233_L239_I1.0490.78
217_L232_D1.0470.77
24_A132_F1.0440.77
48_R56_L1.0420.77
123_L180_S1.0420.77
66_G96_V1.0400.77
216_V223_L1.0400.77
44_L60_L1.0350.76
297_K301_Y1.0290.76
82_A204_D1.0260.75
149_Y173_G1.0240.75
151_F179_E1.0240.75
124_N156_H1.0220.75
218_E242_R1.0190.75
273_L278_S1.0180.75
7_T274_V1.0160.74
93_P99_G1.0160.74
29_N127_G1.0140.74
263_Q266_P1.0090.74
95_G101_N1.0070.74
232_D239_I1.0030.73
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  
1zunA10.65561000.353Contact Map
4bwvA20.70861000.648Contact Map
2oq2A40.76161000.655Contact Map
2wsiA10.68871000.694Contact Map
3fwkA10.7021000.695Contact Map
2goyA80.69211000.7Contact Map
2o8vA10.67221000.704Contact Map
1surA10.63251000.747Contact Map
3bl5A60.625899.80.817Contact Map
2ywbA40.735199.80.821Contact 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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