OPENSEQ.org - 1496299109 - GREMLIN Submission

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2NW6

ID:	1496299109	Query Sequence ADNYAATRYPIILVHGLTGTDKYAGVLEYWYGIQEDLQQRGATVYVANLSGFQSDDGPNGRGEQLLAYVKTVLAATGATKVNLVGHSQGGLTSRYVAAVAPDLVASVTTIGTPHRGSEFADFVQGVLAYDPTGLSSTVIAAFVNVFGILTSSSNNTNQDALAALKTLTTAQAATYNQNYPSAGLGAPGSCQTGAPTETVGGNTHLLYSWAGTAIQPTISVFGVTGATDTSTIPLVDPANALDPSTLALFGTGTVMVNRGSGQNDGVVSKCSALYGQVLSTSYKWNHLDEINQLLGVRGANAEDPVAVIRTHANRLKLAGV
Length:	320 (301)
Sequences:	896 (518.5)
Seq/Len:	2.977
Nf(neff/√len):	29.9

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: 2.977).

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
90_G	112_T	3.380	1.00
69_V	81_V	2.891	1.00
11_I	312_A	2.850	1.00
18_T	52_F	2.738	1.00
109_T	112_T	2.559	1.00
210_A	272_A	2.542	1.00
55_D	88_Q	2.523	1.00
97_A	107_V	2.392	1.00
30_W	33_I	2.365	1.00
121_D	169_T	2.320	1.00
17_L	163_A	2.158	1.00
50_S	64_Q	2.108	1.00
118_E	268_S	2.068	1.00
98_A	179_Y	2.058	1.00
111_G	289_E	2.045	1.00
9_Y	80_K	2.022	1.00
83_L	93_S	1.993	1.00
90_G	114_H	1.969	1.00
212_T	269_K	1.904	0.99
100_A	103_L	1.885	0.99
117_S	268_S	1.864	0.99
211_G	289_E	1.851	0.99
73_L	78_A	1.827	0.99
14_V	47_A	1.760	0.99
192_T	195_P	1.756	0.99
14_V	92_T	1.755	0.99
80_K	105_A	1.721	0.98
66_L	100_A	1.673	0.98
15_H	19_G	1.671	0.98
62_G	96_V	1.658	0.98
90_G	113_P	1.622	0.98
187_P	191_Q	1.603	0.97
268_S	272_A	1.593	0.97
111_G	211_G	1.580	0.97
12_I	69_V	1.542	0.96
212_T	262_Q	1.506	0.96
99_V	179_Y	1.501	0.96
17_L	52_F	1.496	0.96
9_Y	105_A	1.489	0.95
313_N	317_L	1.465	0.95
59_N	178_N	1.465	0.95
86_H	89_G	1.448	0.94
91_L	172_A	1.446	0.94
14_V	93_S	1.430	0.94
55_D	92_T	1.416	0.93
50_S	53_Q	1.408	0.93
181_S	201_G	1.398	0.93
4_Y	313_N	1.396	0.93
181_S	274_Y	1.380	0.92
207_Y	318_A	1.370	0.92
119_F	266_V	1.365	0.92
269_K	272_A	1.354	0.91
51_G	158_Q	1.354	0.91
124_Q	136_S	1.327	0.90
263_N	271_S	1.327	0.90
273_L	277_V	1.324	0.90
85_G	107_V	1.323	0.90
206_L	274_Y	1.314	0.90
115_R	188_G	1.306	0.89
284_W	307_V	1.305	0.89
186_A	195_P	1.305	0.89
73_L	76_T	1.305	0.89
34_Q	46_V	1.296	0.89
55_D	166_T	1.293	0.89
37_L	42_A	1.289	0.88
47_A	68_Y	1.289	0.88
90_G	109_T	1.268	0.87
3_N	6_A	1.259	0.87
109_T	114_H	1.248	0.86
7_T	82_N	1.245	0.86
42_A	316_K	1.239	0.86
192_T	196_T	1.232	0.85
71_T	75_A	1.223	0.85
185_G	191_Q	1.221	0.84
184_L	194_A	1.218	0.84
91_L	113_P	1.212	0.84
110_I	125_G	1.209	0.84
184_L	188_G	1.205	0.83
28_E	31_Y	1.203	0.83
210_A	269_K	1.198	0.83
187_P	194_A	1.198	0.83
91_L	112_T	1.191	0.82
60_G	64_Q	1.191	0.82
188_G	192_T	1.191	0.82
186_A	192_T	1.184	0.82
211_G	284_W	1.181	0.82
205_L	318_A	1.180	0.82
37_L	44_V	1.179	0.81
37_L	41_G	1.179	0.81
47_A	72_V	1.160	0.80
112_T	307_V	1.155	0.80
297_R	301_A	1.146	0.79
5_A	40_R	1.132	0.78
186_A	194_A	1.130	0.78
34_Q	38_Q	1.120	0.77
69_V	96_V	1.113	0.76
85_G	97_A	1.111	0.76
210_A	277_V	1.106	0.75
9_Y	30_W	1.101	0.75
188_G	195_P	1.093	0.74
277_V	280_T	1.087	0.74
36_D	40_R	1.086	0.73
70_K	100_A	1.080	0.73
217_T	228_D	1.078	0.73
11_I	42_A	1.076	0.73
30_W	113_P	1.076	0.73
186_A	196_T	1.075	0.72
73_L	81_V	1.070	0.72
17_L	117_S	1.067	0.72
20_T	288_D	1.055	0.70
28_E	34_Q	1.049	0.70
248_L	251_T	1.048	0.70
81_V	104_V	1.046	0.69
187_P	195_P	1.038	0.69
192_T	276_Q	1.034	0.68
82_N	266_V	1.032	0.68
166_T	290_I	1.032	0.68
285_N	300_N	1.030	0.68
266_V	272_A	1.028	0.68
39_Q	283_K	1.028	0.68
54_S	162_A	1.025	0.67
66_L	69_V	1.022	0.67
95_Y	175_Y	1.019	0.67
61_R	65_L	1.018	0.66
111_G	272_A	1.017	0.66
47_A	65_L	1.016	0.66
174_T	178_N	1.004	0.65
53_Q	60_G	1.000	0.64

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
4fkbA	2	0.8719	100	0.468	Contact Map
2hihA	2	0.8688	100	0.483	Contact Map
1ex9A	1	0.8812	100	0.528	Contact Map
4hs9A	1	0.8875	100	0.544	Contact Map
1ys1X	1	1	100	0.592	Contact Map
2x5xA	1	0.7063	99.7	0.809	Contact Map
1ei9A	1	0.7625	99.6	0.828	Contact Map
4x90A	4	0.8344	99.6	0.831	Contact Map
4xwgA	1	0	99.5	0.832	Contact Map
3ds8A	1	0.6156	99.5	0.836	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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