OPENSEQ.org - 1487851499 - GREMLIN Submission

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c2

ID:	1487851499	Query Sequence WLDRTLIKLCQKYADYNKDDPQSFRLAPNFSLYPQFTYYLRRSQFLSVFNNSPDETAFYRHIFTREDTTNSLIMIQPTLTSFSMEDDPQPVLLDSISVKPNTILLLDTFFFILIYHGEQIAQWRKAGYQDDPQYADFKALLEEPKLEAAELLVDRFPLPRFIDTEAGGSQARFLLSKLNPSDNYQDMARGGSTIVLTDDVSLQNFMTHLQQVAVSGQA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	218 (217)
Sequences:	350 (194)
Seq/Len:	1.613
Nf(neff/√len):	13.2

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: 1.613).

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.

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.

i	j	Scaled score	Prob
66_E	70_N	2.543	1.00
161_F	166_A	2.100	0.99
4_R	8_K	2.087	0.99
82_F	147_E	1.982	0.98
4_R	19_D	1.793	0.96
95_S	182_D	1.749	0.95
127_G	130_D	1.727	0.95
115_Y	166_A	1.704	0.94
164_T	176_S	1.682	0.94
142_E	146_L	1.655	0.93
81_S	102_T	1.582	0.91
78_T	151_L	1.575	0.91
197_T	209_L	1.567	0.90
137_F	141_L	1.557	0.90
136_D	140_L	1.523	0.89
129_Q	137_F	1.518	0.88
121_A	125_K	1.511	0.88
4_R	7_I	1.510	0.88
17_N	20_D	1.505	0.88
94_D	179_N	1.464	0.86
178_L	195_V	1.413	0.83
48_V	51_N	1.394	0.82
5_T	14_A	1.389	0.82
203_Q	210_Q	1.364	0.80
113_L	162_I	1.362	0.80
120_I	140_L	1.360	0.80
112_I	167_G	1.348	0.79
198_D	201_S	1.345	0.79
45_F	74_M	1.338	0.78
115_Y	178_L	1.302	0.75
198_D	209_L	1.297	0.75
116_H	163_D	1.294	0.75
154_D	210_Q	1.294	0.75
117_G	157_P	1.282	0.74
8_K	19_D	1.276	0.73
24_F	173_F	1.275	0.73
135_A	138_K	1.266	0.72
24_F	35_Q	1.264	0.72
122_Q	168_G	1.262	0.72
174_L	202_L	1.256	0.72
108_T	118_E	1.250	0.71
161_F	210_Q	1.249	0.71
204_N	212_V	1.248	0.71
50_N	111_F	1.222	0.69
208_H	212_V	1.215	0.68
121_A	165_E	1.213	0.68
58_F	62_I	1.212	0.68
7_I	16_Y	1.191	0.66
124_R	165_E	1.191	0.66
51_N	56_T	1.186	0.65
171_A	198_D	1.182	0.65
115_Y	131_D	1.179	0.65
185_Q	204_N	1.174	0.64
38_Y	134_Y	1.172	0.64
65_R	83_S	1.170	0.64
95_S	161_F	1.169	0.64
30_F	46_L	1.161	0.63
108_T	162_I	1.153	0.62
170_Q	173_F	1.152	0.62
61_H	115_Y	1.152	0.62
172_R	180_P	1.146	0.61
67_D	112_I	1.142	0.61
183_N	212_V	1.140	0.61
33_Y	37_T	1.139	0.61
173_F	199_D	1.130	0.60
182_D	185_Q	1.125	0.59
178_L	196_L	1.119	0.59
183_N	186_D	1.116	0.58
84_M	140_L	1.108	0.57
50_N	114_I	1.107	0.57
11_Q	17_N	1.107	0.57
203_Q	206_M	1.105	0.57
27_A	31_S	1.105	0.57
64_T	190_G	1.093	0.56
49_F	110_F	1.088	0.55
164_T	168_G	1.088	0.55
172_R	199_D	1.087	0.55
166_A	193_T	1.077	0.54
184_Y	210_Q	1.077	0.54
108_T	127_G	1.075	0.54
50_N	53_P	1.068	0.53
40_L	50_N	1.067	0.53
211_Q	215_S	1.067	0.53
30_F	71_S	1.065	0.53
47_S	211_Q	1.063	0.53
46_L	71_S	1.062	0.53
5_T	9_L	1.057	0.52
33_Y	46_L	1.054	0.52
202_L	208_H	1.054	0.52
87_D	147_E	1.053	0.52
10_C	215_S	1.052	0.52
9_L	15_D	1.051	0.51
70_N	153_V	1.051	0.51
51_N	168_G	1.048	0.51
50_N	93_L	1.041	0.50
174_L	179_N	1.041	0.50
150_E	153_V	1.038	0.50
167_G	170_Q	1.037	0.50
35_Q	49_F	1.030	0.49
57_A	162_I	1.027	0.49
173_F	177_K	1.025	0.49
11_Q	217_Q	1.024	0.49
91_V	100_P	1.023	0.48
197_T	205_F	1.021	0.48
38_Y	116_H	1.021	0.48
204_N	208_H	1.020	0.48
177_K	199_D	1.019	0.48
94_D	181_S	1.017	0.48
182_D	187_M	1.014	0.48
200_V	208_H	1.012	0.47
4_R	213_A	1.010	0.47
15_D	88_P	1.007	0.47

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)).

Text file of contact predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

NEW Features

Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.

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
1m2oA	2	0.9358	100	0.2	Contact Map
2nutA	1	0.9083	100	0.215	Contact Map
3efoB	1	0.9312	100	0.576	Contact Map
3eh1A	1	0.9083	100	0.59	Contact Map
3eh2A	3	0.9266	100	0.613	Contact Map
1pcxA	1	0.8761	100	0.627	Contact Map
1m2vB	1	0.8165	100	0.627	Contact Map
1svqA	1	0.4128	93	0.929	Contact Map
1kcqA	1	0.4587	89.9	0.935	Contact Map
1d0nA	2	0.7706	71.7	0.947	Contact 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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