OPENSEQ.org - 1503708302 - GREMLIN Submission

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IFNa4

ID:	1503708302	Query Sequence CDLPQTHSLGNRRALILLAQMGRISHFSCLKDRHDFGFPEEEFDGHQFQKAQAISVLHEMIQQTFNLFSTEDSSAAWEQSLLEKFSTELYQQLNDLEACVIQEVGVEETPLMNEDSILAVRKYFQRITLYLTEKKYSPCAWEVVRAEIMRSLSFSTNLQKRLRRKD	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	166 (157)
Sequences:	395 (228.9)
Seq/Len:	2.516
Nf(neff/√len):	18.3

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: 2.516).

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
29_C	139_C	2.769	1.00
142_E	145_R	2.491	1.00
77_W	145_R	1.929	0.99
59_E	121_R	1.896	0.99
140_A	144_V	1.817	0.99
65_F	97_E	1.722	0.98
85_F	152_L	1.608	0.96
124_F	142_E	1.552	0.95
30_L	33_R	1.527	0.95
77_W	142_E	1.520	0.95
18_L	123_Y	1.514	0.94
131_L	140_A	1.502	0.94
99_C	142_E	1.494	0.94
78_E	132_T	1.451	0.93
36_F	123_Y	1.421	0.91
156_T	159_Q	1.377	0.90
13_R	86_S	1.359	0.89
97_E	118_L	1.356	0.89
14_A	61_I	1.349	0.88
99_C	124_F	1.339	0.88
38_F	99_C	1.334	0.88
61_I	86_S	1.315	0.87
113_N	117_I	1.305	0.86
50_K	143_V	1.290	0.85
158_L	161_R	1.279	0.85
21_M	99_C	1.266	0.84
46_H	90_Y	1.241	0.82
59_E	63_Q	1.238	0.82
23_R	37_G	1.230	0.81
141_W	145_R	1.207	0.80
90_Y	100_V	1.199	0.79
52_Q	62_Q	1.198	0.79
123_Y	147_E	1.195	0.79
90_Y	132_T	1.177	0.77
85_F	106_V	1.171	0.77
22_G	86_S	1.170	0.77
90_Y	128_T	1.170	0.77
159_Q	162_L	1.167	0.76
133_E	142_E	1.161	0.76
91_Q	127_I	1.135	0.73
161_R	164_R	1.130	0.73
42_E	55_S	1.126	0.73
43_F	152_L	1.118	0.72
131_L	141_W	1.115	0.72
70_T	128_T	1.101	0.70
67_L	111_L	1.094	0.69
79_Q	126_R	1.088	0.69
41_E	108_E	1.088	0.69
20_Q	147_E	1.087	0.69
160_K	164_R	1.082	0.68
25_S	86_S	1.078	0.68
158_L	163_R	1.071	0.67
33_R	73_S	1.062	0.66
110_P	113_N	1.061	0.66
127_I	147_E	1.061	0.66
135_K	154_F	1.058	0.66
156_T	163_R	1.056	0.65
84_K	94_N	1.048	0.65
27_F	51_A	1.043	0.64
160_K	163_R	1.043	0.64
111_L	114_E	1.042	0.64
40_E	120_V	1.038	0.64
13_R	94_N	1.038	0.64
114_E	120_V	1.033	0.63
23_R	120_V	1.030	0.63
85_F	113_N	1.030	0.63
27_F	63_Q	1.029	0.63
124_F	151_S	1.024	0.62
57_L	89_L	1.022	0.62
92_Q	96_L	1.020	0.62
36_F	147_E	1.019	0.61
49_Q	85_F	1.018	0.61
108_E	115_D	1.017	0.61
49_Q	105_G	1.017	0.61
41_E	85_F	1.016	0.61
61_I	85_F	1.014	0.61
159_Q	163_R	1.010	0.60
87_T	101_I	1.009	0.60
71_E	101_I	1.009	0.60
47_Q	60_M	1.005	0.60
58_H	97_E	1.004	0.60
17_L	141_W	1.003	0.60

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
3se4B	1	0.8554	100	0.019	Contact Map
3oq3A	1	1	100	0.019	Contact Map
1b5lA	1	0.9157	100	0.019	Contact Map
3s9dA	2	0.7651	100	0.024	Contact Map
1au1A	2	0.9819	100	0.036	Contact Map
1wu3I	1	0.9518	100	0.068	Contact Map
3piwA	1	0.9036	100	0.104	Contact Map
3pivA	2	0.9157	100	0.136	Contact Map
4gmoA	1	0.7169	12.6	0.949	Contact Map
2r17C	2	0.6506	11.4	0.95	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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