OPENSEQ.org - 1416338811 - GREMLIN Submission

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ompla

ID:	1416338811	Query Sequence MRTLQGWLLPVFMLPMAVYAQEATVKEVHDAPAVRGSIIANMLQEHDNPFTLYPYDTNYLIYTQTSDLNKEAIASYDWAENARKDEVKFQLSLAFPLWRGILGPNSVLGASYTQKSWWQLSNSEESSPFRETNYEPQLFLGFATDYRFAGWTLRDVEMGYNHDSNGRSDPTSRSWNRLYTRLMAENGNWLVEVKPWYVVGNTDDNPDITKYMGYYQLKIGYHLGDAVLSAKGQYNWNTGYGGAELGLSYPITKHVRLYTQVYSGYGESLIDYNFNQTRVGVGVMLNDLF	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	289 (270)
Sequences:	546 (384.5)
Seq/Len:	2.022
Nf(neff/√len):	23.4

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: 2.022).

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	3.347	1.00
242_G	262_Y	3.309	1.00
131_E	270_I	3.163	1.00
88_K	260_Q	3.100	1.00
160_Y	176_N	3.078	1.00
194_K	216_Q	2.959	1.00
231_K	242_G	2.845	1.00
234_Y	239_G	2.790	1.00
191_V	217_L	2.757	1.00
261_V	277_T	2.715	1.00
87_V	120_L	2.606	1.00
159_G	179_Y	2.520	1.00
135_E	161_N	2.418	1.00
116_S	132_T	2.385	1.00
114_Q	134_Y	2.362	1.00
198_V	203_D	2.300	1.00
161_N	179_Y	2.143	0.99
128_P	172_S	1.813	0.98
263_S	275_N	1.803	0.98
189_W	221_Y	1.780	0.97
55_Y	94_A	1.774	0.97
108_L	140_L	1.763	0.97
139_F	159_G	1.734	0.97
210_K	237_N	1.698	0.96
263_S	277_T	1.697	0.96
197_Y	200_G	1.683	0.96
233_Q	242_G	1.630	0.95
106_S	140_L	1.612	0.95
57_T	288_L	1.598	0.94
150_G	186_N	1.563	0.93
111_S	137_Q	1.538	0.93
86_E	130_R	1.464	0.90
244_E	260_Q	1.458	0.90
236_W	239_G	1.446	0.89
246_G	260_Q	1.439	0.89
210_K	238_T	1.396	0.87
71_E	74_A	1.393	0.87
172_S	204_D	1.391	0.86
52_L	285_L	1.361	0.85
111_S	139_F	1.338	0.83
160_Y	178_L	1.338	0.83
89_F	131_E	1.336	0.83
226_A	247_L	1.334	0.83
259_T	279_V	1.334	0.83
139_F	179_Y	1.333	0.83
241_G	262_Y	1.331	0.83
138_L	160_Y	1.326	0.83
61_I	258_Y	1.325	0.83
246_G	258_Y	1.313	0.82
243_A	263_S	1.285	0.80
86_E	119_Q	1.270	0.79
189_W	195_P	1.268	0.79
38_I	53_Y	1.261	0.78
200_G	203_D	1.253	0.78
163_D	255_V	1.246	0.77
128_P	204_D	1.230	0.76
231_K	244_E	1.222	0.75
175_W	196_W	1.207	0.74
157_E	181_R	1.202	0.73
86_E	137_Q	1.196	0.73
98_W	101_I	1.196	0.73
235_N	239_G	1.196	0.73
39_I	96_P	1.191	0.72
117_W	268_S	1.181	0.71
198_V	201_N	1.174	0.71
60_L	110_A	1.165	0.70
267_E	271_D	1.163	0.70
110_A	138_L	1.161	0.70
117_W	278_R	1.153	0.69
177_R	196_W	1.147	0.68
258_Y	284_M	1.146	0.68
94_A	121_S	1.143	0.68
135_E	163_D	1.141	0.68
24_T	30_D	1.135	0.67
228_L	245_L	1.132	0.67
250_P	257_L	1.128	0.66
258_Y	280_G	1.128	0.66
197_Y	201_N	1.125	0.66
38_I	42_M	1.125	0.66
144_T	153_L	1.119	0.65
208_I	271_D	1.118	0.65
159_G	180_T	1.114	0.65
160_Y	199_V	1.109	0.64
116_S	129_F	1.106	0.64
122_N	284_M	1.100	0.63
106_S	179_Y	1.099	0.63
179_Y	194_K	1.096	0.63
201_N	204_D	1.096	0.63
119_Q	130_R	1.096	0.63
83_R	122_N	1.096	0.63
222_H	249_Y	1.096	0.63
118_W	129_F	1.095	0.63
175_W	198_V	1.094	0.63
90_Q	113_T	1.092	0.63
62_Y	65_T	1.080	0.61
52_L	97_L	1.079	0.61
94_A	109_G	1.077	0.61
119_Q	280_G	1.072	0.61
64_Q	68_L	1.068	0.60
201_N	206_P	1.056	0.59
106_S	142_F	1.054	0.59
23_A	26_K	1.049	0.58
244_E	258_Y	1.048	0.58
233_Q	273_N	1.048	0.58
137_Q	179_Y	1.040	0.57
21_Q	26_K	1.040	0.57
132_T	268_S	1.039	0.57
211_Y	245_L	1.038	0.57
259_T	281_V	1.037	0.57
41_N	96_P	1.035	0.57
232_G	236_W	1.027	0.56
55_Y	114_Q	1.023	0.55
40_A	48_N	1.022	0.55
93_L	134_Y	1.021	0.55
163_D	256_R	1.020	0.55
235_N	240_Y	1.020	0.55
219_I	227_V	1.018	0.55
182_L	193_V	1.017	0.55
207_D	248_S	1.008	0.54
108_L	269_L	1.002	0.53
86_E	278_R	1.000	0.53

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

See coupling matrix (for protein design or mutagenesis)
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	0.099	Contact Map
1qd6C	2	0.8304	100	0.144	Contact Map
2x9kA	1	0.4706	65.7	0.961	Contact Map
4e1sA	1	0.564	11.3	0.974	Contact Map
2vveA	2	0.7093	10.8	0.974	Contact Map
3qraA	1	0.526	9.4	0.975	Contact Map
4fqeA	1	0.301	5.7	0.977	Contact Map
1ormA	1	0.5121	4.4	0.979	Contact Map
2o4vA	3	0.3702	3.8	0.979	Contact Map
1p4tA	1	0.5087	3.6	0.979	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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