OPENSEQ.org - 1516831203 - GREMLIN Submission

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IFNa21b

ID:	1516831203	Query Sequence CDLPQTHSLGNRRALILLAQMGRISPFSCLKDRHDFGFPQEEFDGNQFQKAQAISVLHEMIQQTFNLFSTKDSSATWEQSLLEKFSTELNQQLNDLEACVIQEVGVEETPLMNVDSILAVKKYFQRITLYLTEKKYSPCAWEVVRAEIMRSFSLSKIFQERLRRKE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	166 (157)
Sequences:	399 (230.9)
Seq/Len:	2.541
Nf(neff/√len):	18.4

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: 2.541).

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	2.718	1.00
142_E	145_R	2.616	1.00
59_E	121_K	1.948	0.99
65_F	97_E	1.664	0.97
140_A	144_V	1.656	0.97
13_R	86_S	1.589	0.96
85_F	152_F	1.564	0.96
77_W	145_R	1.552	0.95
78_E	132_T	1.521	0.95
131_L	140_A	1.507	0.94
30_L	33_R	1.496	0.94
18_L	123_Y	1.439	0.92
99_C	142_E	1.427	0.92
99_C	124_F	1.419	0.92
36_F	123_Y	1.404	0.91
124_F	142_E	1.384	0.90
50_K	143_V	1.363	0.89
14_A	61_I	1.345	0.88
159_Q	162_L	1.325	0.87
90_N	100_V	1.301	0.86
46_N	90_N	1.295	0.86
59_E	63_Q	1.292	0.86
77_W	142_E	1.291	0.85
113_N	117_I	1.266	0.84
38_F	99_C	1.264	0.84
97_E	118_L	1.258	0.83
135_K	154_L	1.255	0.83
141_W	145_R	1.252	0.83
21_M	99_C	1.244	0.82
61_I	86_S	1.215	0.80
52_Q	62_Q	1.199	0.79
123_Y	147_E	1.196	0.79
91_Q	127_I	1.190	0.78
90_N	132_T	1.182	0.78
26_P	43_F	1.176	0.77
158_F	163_R	1.168	0.77
160_E	164_R	1.160	0.76
20_Q	147_E	1.159	0.76
159_Q	163_R	1.154	0.75
161_R	164_R	1.150	0.75
160_E	163_R	1.148	0.75
111_L	114_V	1.143	0.74
17_L	127_I	1.140	0.74
67_L	111_L	1.134	0.74
22_G	86_S	1.129	0.73
98_A	109_T	1.114	0.72
32_D	54_I	1.114	0.72
131_L	141_W	1.114	0.72
134_K	143_V	1.107	0.71
114_V	120_V	1.104	0.71
58_H	97_E	1.096	0.70
23_R	120_V	1.096	0.70
133_E	142_E	1.092	0.70
58_H	65_F	1.090	0.69
79_Q	126_R	1.086	0.69
70_T	128_T	1.077	0.68
108_E	115_D	1.076	0.68
127_I	147_E	1.072	0.67
85_F	106_V	1.072	0.67
156_K	159_Q	1.067	0.67
85_F	113_N	1.067	0.67
34_H	51_A	1.057	0.66
42_E	55_S	1.054	0.66
156_K	163_R	1.049	0.65
112_M	115_D	1.046	0.65
46_N	113_N	1.044	0.64
13_R	94_N	1.042	0.64
23_R	37_G	1.040	0.64
158_F	161_R	1.037	0.64
26_P	78_E	1.037	0.64
17_L	141_W	1.028	0.63
126_R	146_A	1.025	0.62
49_Q	108_E	1.023	0.62
41_E	108_E	1.023	0.62
110_P	113_N	1.019	0.62
43_F	152_F	1.019	0.62
145_R	152_F	1.015	0.61
124_F	151_S	1.014	0.61
36_F	147_E	1.010	0.61
66_N	83_E	1.002	0.60
25_S	86_S	1.002	0.60
18_L	68_F	1.000	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	0.018	Contact Map
1b5lA	1	0.9157	100	0.018	Contact Map
3oq3A	1	1	100	0.018	Contact Map
3s9dA	2	0.7651	100	0.024	Contact Map
1au1A	2	0.9819	100	0.033	Contact Map
1wu3I	1	0.9518	100	0.064	Contact Map
3piwA	1	0.9036	100	0.102	Contact Map
3pivA	2	0.9157	100	0.133	Contact Map
4gmoA	1	0.7169	11.4	0.95	Contact Map
2d48A	1	0.7108	10.7	0.951	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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