OPENSEQ.org - 1416337960 - GREMLIN Submission

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ompla

ID:	1416337960	Query Sequence MRTLQGWLLPVFMLPMAVYAQEATVKEVHDAPAVRGSIIANMLQEHDNPFTLYPYDTNYLIYTQTSDLNKEAIASYDWAENARKDEVKFQLSLAFPLWRGILGPNSVLGASYTQKSWWQLSNSEESSPFRETNYEPQLFLGFATDYRFAGWTLRDVEMGYNHDSNGRSDPTSRSWNRLYTRLMAENGNWLVEVKPWYVVGNTDDNPDITKYMGYYQLKIGYHLGDAVLSAKGQYNWNTGYGGAELGLSYPITKHVRLYTQVYSGYGESLIDYNFNQTRVGVGVMLNDLF	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	289 (272)
Sequences:	456 (327.7)
Seq/Len:	1.676
Nf(neff/√len):	19.9

Jackhmmer Results: (2014_04_16)
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: 1.676).

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
249_Y	257_L	3.621	1.00
242_G	262_Y	3.538	1.00
88_K	260_Q	3.533	1.00
131_E	270_I	3.498	1.00
194_K	216_Q	3.293	1.00
87_V	120_L	3.051	1.00
234_Y	239_G	2.987	1.00
231_K	242_G	2.958	1.00
159_G	179_Y	2.614	1.00
198_V	203_D	2.546	1.00
161_N	179_Y	2.539	1.00
114_Q	134_Y	2.449	1.00
261_V	277_T	2.428	1.00
191_V	217_L	2.198	0.99
160_Y	176_N	2.184	0.99
135_E	161_N	2.169	0.99
55_Y	94_A	1.925	0.98
128_P	172_S	1.914	0.98
116_S	132_T	1.870	0.97
189_W	221_Y	1.847	0.97
108_L	140_L	1.813	0.97
197_Y	200_G	1.793	0.96
263_S	277_T	1.772	0.96
106_S	140_L	1.758	0.96
139_F	159_G	1.732	0.95
263_S	275_N	1.722	0.95
210_K	237_N	1.678	0.94
150_G	186_N	1.678	0.94
57_T	288_L	1.655	0.94
236_W	239_G	1.629	0.93
233_Q	242_G	1.608	0.92
241_G	262_Y	1.555	0.90
52_L	285_L	1.544	0.90
172_S	204_D	1.510	0.89
160_Y	178_L	1.476	0.87
61_I	258_Y	1.445	0.86
94_A	121_S	1.395	0.83
244_E	260_Q	1.382	0.82
198_V	201_N	1.382	0.82
98_W	101_I	1.363	0.81
144_T	153_L	1.361	0.81
71_E	74_A	1.339	0.79
117_W	278_R	1.320	0.78
250_P	257_L	1.314	0.77
52_L	97_L	1.310	0.77
128_P	204_D	1.297	0.76
163_D	255_V	1.281	0.75
228_L	245_L	1.280	0.75
111_S	137_Q	1.279	0.75
39_I	96_P	1.267	0.74
210_K	238_T	1.262	0.73
38_I	53_Y	1.257	0.73
139_F	179_Y	1.234	0.71
88_K	267_E	1.230	0.70
138_L	160_Y	1.227	0.70
226_A	247_L	1.223	0.70
135_E	163_D	1.223	0.70
230_A	243_A	1.219	0.69
189_W	195_P	1.206	0.68
60_L	110_A	1.194	0.67
159_G	180_T	1.188	0.67
197_Y	201_N	1.185	0.66
157_E	181_R	1.177	0.65
83_R	122_N	1.174	0.65
235_N	239_G	1.173	0.65
231_K	244_E	1.170	0.65
86_E	130_R	1.161	0.64
232_G	236_W	1.161	0.64
133_N	270_I	1.145	0.62
246_G	260_Q	1.134	0.61
56_D	137_Q	1.129	0.61
41_N	96_P	1.126	0.60
122_N	284_M	1.126	0.60
18_V	22_E	1.123	0.60
267_E	271_D	1.122	0.60
88_K	117_W	1.118	0.60
110_A	138_L	1.113	0.59
221_Y	228_L	1.112	0.59
258_Y	280_G	1.100	0.58
24_T	30_D	1.099	0.58
38_I	42_M	1.094	0.57
86_E	119_Q	1.094	0.57
106_S	142_F	1.080	0.56
61_I	121_S	1.076	0.55
203_D	206_P	1.075	0.55
188_N	221_Y	1.070	0.55
219_I	227_V	1.056	0.53
243_A	263_S	1.056	0.53
259_T	281_V	1.052	0.53
111_S	139_F	1.051	0.53
160_Y	199_V	1.049	0.52
201_N	204_D	1.047	0.52
262_Y	278_R	1.047	0.52
18_V	21_Q	1.046	0.52
187_G	209_T	1.045	0.52
163_D	175_W	1.043	0.52
91_L	283_V	1.041	0.52
23_A	26_K	1.036	0.51
211_Y	245_L	1.035	0.51
182_L	193_V	1.030	0.50
249_Y	288_L	1.027	0.50
55_Y	114_Q	1.022	0.49
198_V	206_P	1.019	0.49
90_Q	113_T	1.018	0.49
21_Q	26_K	1.017	0.49
64_Q	68_L	1.014	0.49
96_P	107_V	1.014	0.49
106_S	179_Y	1.013	0.49
117_W	268_S	1.007	0.48
119_Q	130_R	1.004	0.48
55_Y	286_N	1.002	0.47
204_D	235_N	1.000	0.47
144_T	150_G	1.000	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: (06Sep14)
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
1qd5A	1	0.8893	100	0.119	Contact Map
1qd6C	2	0.8304	100	0.163	Contact Map
2x9kA	1	0.4671	52	0.966	Contact Map
4e1sA	1	0.564	8.4	0.977	Contact Map
3qraA	1	0.526	7.8	0.977	Contact Map
4fqeA	1	0.301	5.8	0.978	Contact Map
2vveA	2	0.7266	3.9	0.98	Contact Map
2o4vA	3	0.3702	3.9	0.98	Contact Map
1p4tA	1	0.5087	3.3	0.981	Contact Map
1rblM	8	0.2042	3	0.981	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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