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Quinton Dowling

ID: 1515093355 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 357 (339)
Sequences: 367 (216.9)
Seq/Len: 1.083
Nf(neff/√len): 11.8

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: 1.083).

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
270_Y274_N2.5240.99
270_Y273_K1.9010.94
314_C325_F1.8590.94
253_K269_A1.8430.93
244_C248_C1.7340.90
205_L228_W1.6730.88
63_V253_K1.6390.86
150_T164_Q1.6350.86
236_E270_Y1.6300.86
151_S228_W1.6140.85
267_I314_C1.6120.85
47_F75_L1.6090.85
264_G298_I1.6060.85
147_V229_V1.6040.85
62_E69_F1.6040.85
147_V151_S1.5810.83
59_E273_K1.5770.83
164_Q250_S1.5650.83
164_Q229_V1.5620.82
251_M298_I1.5460.82
148_G164_Q1.5380.81
246_R253_K1.5240.80
344_T347_L1.5130.80
246_R269_A1.5070.79
70_E164_Q1.5060.79
229_V253_K1.4880.78
148_G246_R1.4710.77
69_F269_A1.4660.77
29_I36_I1.4490.75
252_L302_F1.4310.74
245_R280_C1.4160.73
66_P298_I1.4100.73
44_E47_F1.3980.72
41_E317_Y1.3980.72
70_E273_K1.3840.71
272_L276_L1.3790.70
69_F270_Y1.3760.70
229_V250_S1.3750.70
231_S253_K1.3590.69
161_F314_C1.3340.66
195_V199_K1.3330.66
271_H325_F1.3110.64
164_Q253_K1.2980.63
147_V150_T1.2960.63
314_C323_D1.2890.63
268_S272_L1.2870.62
305_L314_C1.2830.62
146_M248_C1.2800.62
340_V347_L1.2780.62
255_L258_R1.2650.60
70_E253_K1.2550.59
275_L304_Q1.2540.59
341_W344_T1.2530.59
120_S135_C1.2510.59
17_A56_G1.2500.59
236_E253_K1.2440.58
63_V231_S1.2360.58
61_V231_S1.2290.57
134_A284_P1.2260.57
68_E253_K1.2240.57
70_E269_A1.2220.56
205_L245_R1.2210.56
343_L347_L1.2180.56
62_E67_N1.2180.56
68_E208_K1.2170.56
314_C324_M1.2160.56
120_S233_F1.2110.55
22_T317_Y1.2030.55
70_E274_N1.1820.53
65_S252_L1.1810.53
269_A273_K1.1770.52
149_D228_W1.1760.52
66_P236_E1.1710.52
106_S207_S1.1680.51
118_L209_E1.1680.51
29_I69_F1.1680.51
274_N280_C1.1660.51
56_G66_P1.1650.51
148_G253_K1.1560.50
245_R248_C1.1540.50
35_D42_L1.1510.50
196_A349_T1.1510.50
275_L279_E1.1470.49
56_G148_G1.1420.49
308_C316_H1.1420.49
87_G101_R1.1400.49
9_R13_E1.1390.49
342_R346_E1.1390.49
68_E166_T1.1320.48
163_V252_L1.1320.48
340_V344_T1.1310.48
289_W297_R1.1310.48
289_W294_I1.1290.48
189_W286_D1.1280.48
248_C297_R1.1270.47
123_I322_L1.1260.47
147_V153_V1.1250.47
205_L325_F1.1240.47
153_V231_S1.1220.47
313_R321_A1.1190.47
340_V343_L1.1170.47
344_T348_L1.1170.47
316_H319_L1.1160.46
129_T139_V1.1160.46
165_I228_W1.1140.46
68_E270_Y1.1140.46
68_E229_V1.1140.46
71_I310_Q1.1120.46
167_P319_L1.1100.46
153_V159_E1.1090.46
240_L249_L1.1040.45
68_E273_K1.1000.45
23_A40_V1.0990.45
255_L263_P1.0990.45
36_I118_L1.0980.45
118_L201_E1.0970.45
70_E270_Y1.0970.45
75_L118_L1.0960.45
93_A111_F1.0920.44
289_W318_F1.0860.44
185_P196_A1.0860.44
196_A285_R1.0850.43
17_A153_V1.0840.43
17_A22_T1.0810.43
71_I277_L1.0810.43
61_V90_P1.0770.43
279_E297_R1.0770.43
7_M66_P1.0760.43
69_F253_K1.0760.43
40_V202_G1.0730.42
153_V235_A1.0730.42
167_P206_L1.0720.42
245_R297_R1.0720.42
104_S151_S1.0720.42
333_L337_A1.0720.42
233_F237_N1.0690.42
85_D180_A1.0680.42
164_Q231_S1.0670.42
96_K312_R1.0660.42
240_L246_R1.0650.42
135_C334_E1.0530.41
20_Y42_L1.0530.41
24_T131_V1.0530.41
133_Q168_A1.0520.40
19_M250_S1.0520.40
44_E323_D1.0500.40
277_L290_D1.0480.40
120_S124_R1.0440.40
17_A62_E1.0440.40
118_L322_L1.0410.39
201_E238_R1.0400.39
68_E269_A1.0400.39
13_E321_A1.0330.39
17_A308_C1.0330.39
116_G334_E1.0320.39
146_M293_C1.0290.38
52_V118_L1.0290.38
277_L314_C1.0240.38
75_L125_A1.0210.38
123_I167_P1.0210.38
71_I87_G1.0210.38
45_P102_K1.0160.37
32_I277_L1.0160.37
28_E229_V1.0140.37
240_L291_E1.0100.37
112_I302_F1.0100.37
68_E164_Q1.0100.37
304_Q308_C1.0100.37
35_D240_L1.0090.37
284_P289_W1.0080.37
62_E269_A1.0070.36
150_T166_T1.0060.36
133_Q235_A1.0040.36
153_V229_V1.0030.36
249_L276_L1.0000.36
66_P69_F1.0000.36
66_P270_Y1.0000.36
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  
4woyA20.85991000.333Contact Map
4oagA20.85431000.343Contact Map
4o6aA20.92161000.343Contact Map
4levA20.92441000.348Contact Map
4xj5A1099.20.852Contact Map
4xj6A1099.10.859Contact Map
1px5A20.784398.80.875Contact Map
4s3nA10.770398.70.878Contact Map
4xq7A1098.70.879Contact Map
1r89A10.700395.50.929Contact 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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