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OPENSEQ.org

pnpla3 -force run

ID: 1446682721 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 481 (383)
Sequences: 309 (176)
Seq/Len: 0.807
Nf(neff/√len): 9.0

HHblits Results: (2015_06)
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: 0.807).

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 > 50% 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
105_N109_L3.2511.00
120_R123_D2.2650.97
118_L129_V2.1620.96
117_S126_N2.0770.95
137_E160_R1.9120.91
375_W382_D1.8100.88
16_G21_Y1.7810.87
50_A146_C1.6610.81
375_W385_W1.6560.81
17_F21_Y1.6560.81
45_G49_G1.6210.79
19_G22_H1.5920.77
107_H135_K1.5830.76
105_N108_Q1.5800.76
173_V209_K1.5720.76
197_V221_L1.5460.74
168_G226_F1.5320.73
186_P193_I1.5000.71
375_W380_P1.4960.70
11_S15_C1.4200.65
118_L127_V1.4160.64
189_G194_C1.4160.64
84_F128_L1.4110.64
91_S152_S1.4030.63
380_P385_W1.3750.61
241_G244_D1.3740.61
18_L21_Y1.3710.61
377_P382_D1.3680.60
189_G193_I1.3500.59
14_G157_P1.3400.58
382_D385_W1.3400.58
183_T186_P1.3340.57
12_F17_F1.3250.57
194_C218_N1.3200.56
14_G25_A1.3120.56
12_F21_Y1.3070.55
376_L385_W1.2970.54
181_T218_N1.2850.53
141_A144_C1.2820.53
28_C246_F1.2810.53
34_P40_A1.2800.53
311_P316_I1.2740.52
327_A331_E1.2670.52
130_S134_S1.2650.51
120_R127_V1.2620.51
351_M354_V1.2500.50
119_T126_N1.2420.49
189_G195_P1.2380.49
157_P172_N1.2320.49
151_Y161_G1.2240.48
11_S21_Y1.2210.48
130_S135_K1.2140.47
153_G161_G1.2130.47
380_P401_L1.2060.46
182_I185_S1.1990.46
31_E141_A1.1980.46
259_Q262_L1.1980.46
195_P218_N1.1970.46
28_C234_L1.1900.45
144_C160_R1.1840.44
187_F193_I1.1790.44
81_I114_I1.1780.44
376_L380_P1.1750.44
183_T189_G1.1750.44
193_I218_N1.1720.43
181_T229_P1.1720.43
11_S17_F1.1720.43
371_R382_D1.1710.43
119_T132_F1.1700.43
110_I113_K1.1700.43
331_E352_S1.1690.43
112_G123_D1.1650.43
15_C46_A1.1640.43
192_D195_P1.1620.42
172_N182_I1.1570.42
76_A88_F1.1510.42
153_G189_G1.1470.41
30_S240_R1.1450.41
378_D382_D1.1430.41
168_G207_I1.1410.41
10_L247_R1.1380.40
183_T193_I1.1350.40
32_H242_Y1.1340.40
57_L110_I1.1300.40
344_N366_I1.1300.40
142_L245_A1.1260.39
165_V190_E1.1260.39
123_D127_V1.1220.39
322_P363_E1.1220.39
302_L305_L1.1190.39
73_V128_L1.1160.39
131_D160_R1.1090.38
33_A199_S1.1090.38
119_T137_E1.1080.38
155_I163_R1.1060.38
132_F248_F1.1050.38
103_P132_F1.1040.38
387_Q391_S1.1020.37
94_L143_V1.1010.37
104_A135_K1.1010.37
373_V387_Q1.1000.37
181_T189_G1.1000.37
244_D248_F1.0990.37
190_E194_C1.0970.37
128_L202_F1.0910.37
291_A295_R1.0850.36
372_L376_L1.0840.36
120_R157_P1.0820.36
113_K186_P1.0820.36
328_L331_E1.0800.36
348_I358_C1.0800.36
189_G192_D1.0800.36
167_G174_P1.0790.36
186_P195_P1.0790.36
183_T248_F1.0790.36
116_I233_V1.0780.36
8_W40_A1.0760.35
82_G156_P1.0750.35
41_R116_I1.0730.35
337_G352_S1.0720.35
277_S292_L1.0710.35
107_H161_G1.0700.35
144_C153_G1.0700.35
72_L172_N1.0700.35
387_Q390_T1.0690.35
326_T340_S1.0690.35
264_S354_V1.0680.35
168_G225_A1.0660.35
181_T193_I1.0640.34
50_A105_N1.0630.34
11_S16_G1.0610.34
171_D181_T1.0600.34
34_P144_C1.0600.34
123_D211_S1.0600.34
157_P164_Y1.0590.34
352_S368_I1.0560.34
43_L168_G1.0560.34
387_Q401_L1.0540.34
321_S326_T1.0530.34
13_A95_R1.0520.33
54_V125_E1.0510.33
376_L382_D1.0510.33
241_G245_A1.0510.33
51_L245_A1.0480.33
379_M391_S1.0470.33
372_L378_D1.0470.33
371_R375_W1.0460.33
232_K242_Y1.0460.33
46_A49_G1.0420.33
267_E336_G1.0420.33
182_I186_P1.0410.33
225_A229_P1.0400.33
141_A149_P1.0400.33
193_I248_F1.0390.32
306_R309_I1.0380.32
129_V159_F1.0380.32
79_R85_H1.0370.32
189_G249_L1.0360.32
30_S59_G1.0350.32
310_L326_T1.0340.32
141_A184_V1.0330.32
156_P248_F1.0320.32
190_E195_P1.0320.32
89_N147_F1.0290.32
11_S18_L1.0290.32
303_D306_R1.0280.32
185_S244_D1.0280.32
73_V225_A1.0280.32
20_F54_V1.0270.32
39_D148_I1.0270.32
58_S106_V1.0270.32
183_T218_N1.0270.32
75_K78_S1.0260.31
193_I249_L1.0240.31
318_D369_V1.0230.31
183_T195_P1.0210.31
15_C19_G1.0200.31
167_G195_P1.0160.31
54_V108_Q1.0160.31
123_D164_Y1.0150.31
375_W378_D1.0140.31
98_L134_S1.0140.31
103_P161_G1.0130.30
311_P323_R1.0130.30
210_L238_C1.0090.30
84_F122_S1.0080.30
156_P249_L1.0080.30
327_A333_K1.0070.30
84_F249_L1.0060.30
153_G194_C1.0060.30
26_T56_V1.0050.30
119_T139_V1.0050.30
19_G26_T1.0030.30
181_T194_C1.0030.30
174_P195_P1.0020.30
387_Q392_Q1.0020.30
372_L385_W1.0020.30
302_L306_R1.0010.30
269_M339_M1.0000.30
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  
4qmkA20.70271000.808Contact Map
3tu3B10.7361000.845Contact Map
4akfA10.744399.90.852Contact Map
4pk9A10.563499.90.855Contact Map
1cjyA20.6549970.958Contact Map
3is3A10.328525.60.982Contact Map
3bxpA20.397121.40.983Contact Map
3uceA40.311915.70.984Contact Map
3h3eA10.2113.60.984Contact Map
3u5tA40.28913.40.984Contact 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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