OPENSEQ.org - 1510929708 - GREMLIN Submission

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Elodie Laine

ID:	1510929708	Query Sequence VHQVLYRALVSTKWLAESVRAGKVGPGLRVLDASWYSPGTREARKEYLERHVPGASFFDIEECRDKASPYEVMLPSEAGFADYVGSLGISNDTHVVVYNGDDLGSFYAPRVWWMFRVFGHRTVSVLNGGFRNWLKEGHPVTSEPSRPEPAIFKATLNRSLLKTYEQVLENLESKRFQLVDSRAQGRYLGTQPEPDAVGLDSGHIRGSVNMPFMDFLTENGFEKSPEELRAMFEAKKVDLTKPLIATCRKGVTACHIALAAYLCGKPDVAIYDGSWFEWFHRAPPETWVSQGKG	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	293 (274)
Sequences:	2926 (1843.5)
Seq/Len:	10.679
Nf(neff/√len):	111.4

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: 10.679).

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
10_V	14_W	4.406	1.00
94_H	124_S	4.062	1.00
50_R	134_L	3.232	1.00
132_N	136_E	3.166	1.00
223_K	227_E	3.039	1.00
185_G	190_T	3.022	1.00
15_L	126_L	3.005	1.00
29_R	93_T	2.813	1.00
80_F	84_V	2.546	1.00
11_S	127_N	2.488	1.00
185_G	191_Q	2.448	1.00
257_A	270_I	2.411	1.00
12_T	132_N	2.411	1.00
31_L	56_S	2.366	1.00
12_T	136_E	2.360	1.00
224_S	227_E	2.331	1.00
204_I	207_S	2.306	1.00
50_R	142_S	2.292	1.00
184_Q	188_L	2.276	1.00
16_A	138_H	2.275	1.00
81_A	85_G	2.273	1.00
273_G	277_E	2.210	1.00
253_A	270_I	2.195	1.00
74_L	117_V	2.181	1.00
31_L	89_I	2.152	1.00
84_V	115_F	2.150	1.00
15_L	30_V	2.149	1.00
85_G	150_A	2.116	1.00
13_K	17_E	2.111	1.00
184_Q	209_N	2.068	1.00
76_S	79_G	2.065	1.00
120_H	152_F	2.054	1.00
162_K	269_A	2.025	1.00
74_L	114_M	2.025	1.00
164_Y	281_R	2.016	1.00
163_T	166_Q	1.968	1.00
80_F	115_F	1.960	1.00
223_K	231_M	1.949	1.00
186_R	252_T	1.919	1.00
162_K	167_V	1.914	1.00
41_R	46_E	1.908	1.00
229_R	233_E	1.830	1.00
225_P	229_R	1.800	1.00
164_Y	168_L	1.784	1.00
12_T	138_H	1.733	1.00
50_R	140_V	1.732	1.00
130_F	140_V	1.696	1.00
162_K	166_Q	1.666	1.00
125_V	258_L	1.661	1.00
177_Q	241_K	1.648	1.00
77_E	81_A	1.643	1.00
33_A	97_V	1.634	1.00
141_T	145_S	1.627	1.00
80_F	118_F	1.592	1.00
91_N	153_K	1.580	1.00
109_P	254_C	1.566	1.00
176_F	244_I	1.534	1.00
10_V	15_L	1.516	1.00
90_S	93_T	1.485	1.00
167_V	244_I	1.461	1.00
82_D	86_S	1.425	1.00
42_E	45_K	1.401	0.99
36_Y	100_G	1.369	0.99
89_I	95_V	1.367	0.99
200_D	279_F	1.367	0.99
134_L	140_V	1.359	0.99
217_T	221_F	1.346	0.99
223_K	228_L	1.316	0.99
97_V	111_V	1.313	0.99
275_W	279_F	1.310	0.99
85_G	151_I	1.309	0.99
112_W	257_A	1.305	0.99
243_L	260_A	1.304	0.99
14_W	18_S	1.298	0.99
276_F	279_F	1.296	0.99
238_D	241_K	1.275	0.99
254_C	270_I	1.274	0.99
12_T	16_A	1.249	0.99
242_P	267_D	1.239	0.98
52_V	133_W	1.227	0.98
162_K	244_I	1.195	0.98
245_A	260_A	1.191	0.98
9_L	222_E	1.182	0.98
112_W	261_Y	1.168	0.97
58_F	87_L	1.165	0.97
228_L	232_F	1.162	0.97
81_A	154_A	1.159	0.97
79_G	83_Y	1.157	0.97
97_V	123_V	1.151	0.97
90_S	150_A	1.143	0.97
47_Y	51_H	1.142	0.97
112_W	116_R	1.141	0.97
89_I	115_F	1.138	0.97
230_A	234_A	1.135	0.97
11_S	14_W	1.132	0.97
132_N	221_F	1.124	0.97
85_G	90_S	1.121	0.97
183_A	213_M	1.119	0.96
97_V	115_F	1.116	0.96
132_N	138_H	1.116	0.96
227_E	230_A	1.108	0.96
81_A	153_K	1.107	0.96
167_V	178_L	1.104	0.96
91_N	120_H	1.091	0.96
242_P	269_A	1.086	0.96
36_Y	41_R	1.079	0.95
183_A	186_R	1.070	0.95
228_L	263_C	1.060	0.95
27_G	94_H	1.056	0.95
15_L	28_L	1.053	0.95
192_P	201_S	1.053	0.95
210_M	235_K	1.045	0.94
58_F	111_V	1.040	0.94
177_Q	242_P	1.039	0.94
16_A	132_N	1.037	0.94
10_V	124_S	1.032	0.94
257_A	268_V	1.029	0.94
109_P	258_L	1.025	0.93
130_F	134_L	1.024	0.93
177_Q	243_L	1.020	0.93
210_M	231_M	1.012	0.93
181_S	256_I	1.005	0.93
109_P	125_V	1.002	0.92
186_R	193_E	1.001	0.92
9_L	258_L	1.001	0.92
230_A	233_E	1.000	0.92

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
1rhsA	1	0.9966	100	0.263	Contact Map
4jgtA	3	0.9522	100	0.301	Contact Map
1urhA	2	0.884	100	0.303	Contact Map
3utnX	1	0.9625	100	0.318	Contact Map
1e0cA	1	0.9181	100	0.324	Contact Map
1uarA	1	0.9147	100	0.33	Contact Map
3aayA	2	0.9215	100	0.338	Contact Map
1okgA	1	0.9352	100	0.344	Contact Map
3hzuA	1	0.9352	100	0.347	Contact Map
2wlrA	1	0.9522	100	0.355	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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