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OPENSEQ.org

4DUR_A 430-791

ID: 1412285718 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 362 (335)
Sequences: 491 (287.2)
Seq/Len: 1.466
Nf(neff/√len): 15.7

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: 1.466).

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
159_C175_C2.9361.00
162_T236_A2.4821.00
251_C318_C2.1300.99
202_Q233_V2.0750.98
163_L227_A2.0540.98
236_A317_V2.0200.98
170_L326_L2.0190.98
54_C57_W1.9800.98
296_L316_L1.9460.97
85_N95_C1.8860.97
346_V351_F1.8040.95
95_C107_C1.7980.95
161_G169_V1.7540.94
332_W343_G1.7050.93
329_V346_V1.7040.93
55_Q62_P1.7010.93
333_G343_G1.6980.93
207_S222_K1.6960.93
38_G41_Y1.6920.93
50_T105_D1.6780.93
133_V136_G1.6480.92
306_D312_S1.6460.92
132_R136_G1.6360.91
54_C83_C1.6170.91
207_S224_S1.6080.90
331_S343_G1.5830.89
251_C342_P1.5820.89
85_N107_C1.5710.89
318_C342_P1.5670.89
33_C54_C1.5610.89
217_D333_G1.5260.87
253_I271_A1.5130.86
78_L85_N1.4700.84
333_G345_Y1.4660.84
168_W172_A1.4470.83
94_W107_C1.4330.82
38_G85_N1.4250.82
119_C146_W1.3990.80
96_Y236_A1.3790.78
331_S345_Y1.3720.78
312_S331_S1.3690.78
306_D345_Y1.3620.77
42_R77_G1.3590.77
160_G172_A1.3590.77
84_R94_W1.3510.76
57_W83_C1.3480.76
332_W345_Y1.3430.76
303_G344_V1.3390.76
316_L342_P1.3360.75
51_G95_C1.3320.75
87_D95_C1.3310.75
81_N84_R1.3300.75
135_G146_W1.3260.75
85_N94_W1.3240.74
189_L206_V1.3220.74
160_G175_C1.3190.74
134_V337_A1.3120.73
172_A175_C1.3100.73
160_G174_H1.3010.73
84_R95_C1.2980.72
171_T176_L1.2970.72
41_Y107_C1.2950.72
143_S270_E1.2850.71
146_W172_A1.2840.71
312_S343_G1.2780.71
83_C94_W1.2750.70
253_I305_T1.2730.70
217_D331_S1.2680.70
306_D343_G1.2660.70
160_G164_I1.2560.69
120_G135_G1.2550.69
147_Q162_T1.2540.69
41_Y95_C1.2390.67
251_C316_L1.2380.67
292_Q295_E1.2320.67
309_Q312_S1.2290.66
119_C136_G1.2270.66
271_A305_T1.2080.64
145_P237_C1.2060.64
89_D106_Y1.2060.64
48_T89_D1.2050.64
122_P171_T1.1990.64
169_V172_A1.1890.63
136_G146_W1.1880.62
87_D107_C1.1870.62
86_P94_W1.1860.62
48_T106_Y1.1860.62
217_D343_G1.1840.62
168_W173_A1.1770.61
43_G46_A1.1760.61
84_R87_D1.1750.61
348_V354_W1.1680.61
147_Q254_T1.1650.60
213_P358_V1.1630.60
149_S157_H1.1590.60
159_C270_E1.1590.60
119_C133_V1.1590.60
150_L304_G1.1590.60
43_G84_R1.1560.59
298_A343_G1.1560.59
191_A201_V1.1540.59
312_S345_Y1.1540.59
120_G146_W1.1530.59
236_A323_K1.1480.59
217_D306_D1.1450.58
295_E332_W1.1400.58
87_D94_W1.1270.56
163_L229_I1.1270.56
176_L211_L1.1240.56
38_G95_C1.1230.56
150_L278_N1.1200.56
43_G85_N1.1130.55
38_G107_C1.1130.55
294_T351_F1.1120.55
144_W254_T1.1100.55
328_G336_C1.1100.55
43_G95_C1.1060.54
174_H312_S1.1050.54
148_V167_E1.1020.54
120_G136_G1.0980.53
306_D331_S1.0970.53
164_I172_A1.0950.53
253_I330_T1.0940.53
48_T95_C1.0890.53
157_H160_G1.0890.53
149_S159_C1.0870.52
83_C112_C1.0840.52
84_R107_C1.0830.52
81_N85_N1.0810.52
222_K349_S1.0790.52
298_A306_D1.0750.51
245_V275_V1.0740.51
273_L316_L1.0720.51
164_I324_Y1.0710.51
51_G105_D1.0710.51
144_W270_E1.0690.50
190_G218_I1.0660.50
189_L227_A1.0660.50
164_I175_C1.0640.50
81_N221_L1.0640.50
273_L326_L1.0600.50
139_A173_A1.0560.49
219_A330_T1.0560.49
329_V352_V1.0540.49
157_H175_C1.0530.49
210_F224_S1.0530.49
122_P252_F1.0530.49
132_R146_W1.0520.49
48_T94_W1.0490.48
130_P317_V1.0440.48
294_T350_R1.0420.48
217_D237_C1.0400.48
217_D312_S1.0400.48
142_H232_K1.0390.47
150_L303_G1.0390.47
43_G54_C1.0370.47
332_W344_V1.0360.47
173_A217_D1.0350.47
168_W174_H1.0340.47
41_Y84_R1.0330.47
132_R135_G1.0320.47
133_V146_W1.0310.47
38_G43_G1.0290.46
168_W220_L1.0280.46
163_L189_L1.0230.46
227_A347_R1.0220.46
160_G315_P1.0220.46
78_L87_D1.0210.46
81_N94_W1.0200.45
87_D105_D1.0170.45
41_Y51_G1.0120.45
229_I235_P1.0100.44
78_L86_P1.0050.44
48_T107_C1.0030.44
348_V351_F1.0010.44
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: (06Sep14)
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  
4durA20.96411000.235Contact Map
3nxpA10.90061000.295Contact Map
4nzqA10.93091000.3Contact Map
4igdA10.95861000.427Contact Map
4kkdA20.97791000.439Contact Map
1gpzA20.90881000.452Contact Map
4j1yA20.90881000.453Contact Map
4f4oC40.76521000.462Contact Map
1zjkA10.95861000.463Contact Map
2f83A10.87571000.471Contact 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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