OPENSEQ.org - 1448043449 - GREMLIN Submission

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2EVU

ID:	1448043449	Query Sequence MVSLTKRCIAEFIGTFILVFFGAGSAAVTLMIASGGTSPNPFNIGIGLLGGLGDWVAIGLAFGFAIAASIYALGNISGCHINPAVTIGLWSVKKFPGREVVPYIIAQLLGAAFGSFIFLQCAGIGAATVGGLGATAPFPGISYWQAMLAEVVGTFLLMITIMGIAVDERAPKGFAGIIIGLTVAGIITTLGNISGSSLNPARTFGPYLNDMIFAGTDLWNYYSIYVIGPIVGAVLAALTYQYLTSE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	246 (230)
Sequences:	4218 (2585.8)
Seq/Len:	18.339
Nf(neff/√len):	170.5

HHblits Results: (2015_06)
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: 18.339).

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
86_T	100_V	4.143	1.00
90_W	97_G	4.110	1.00
12_F	113_F	3.836	1.00
16_F	117_I	3.610	1.00
151_V	235_L	3.421	1.00
90_W	100_V	3.420	1.00
151_V	231_V	3.377	1.00
8_C	106_A	3.162	1.00
147_M	228_G	3.043	1.00
153_G	190_L	2.888	1.00
16_F	114_G	2.627	1.00
63_G	184_A	2.573	1.00
8_C	102_P	2.496	1.00
22_G	62_F	2.477	1.00
7_R	99_E	2.468	1.00
197_S	203_T	2.463	1.00
12_F	109_L	2.439	1.00
160_T	182_T	2.389	1.00
155_F	236_A	2.346	1.00
147_M	151_V	2.204	1.00
87_I	230_I	2.204	1.00
73_L	81_I	2.141	1.00
187_I	196_S	2.085	1.00
104_I	230_I	2.078	1.00
4_L	8_C	1.918	1.00
222_Y	226_V	1.872	1.00
106_A	110_G	1.841	1.00
91_S	234_V	1.838	1.00
87_I	104_I	1.824	1.00
108_L	204_F	1.732	1.00
204_F	226_V	1.719	1.00
93_K	241_Q	1.651	1.00
186_I	198_L	1.641	1.00
14_G	81_I	1.619	1.00
116_F	209_N	1.611	1.00
230_I	234_V	1.608	1.00
85_V	161_I	1.590	1.00
66_I	183_V	1.575	1.00
146_A	194_S	1.557	1.00
187_I	191_G	1.541	1.00
158_M	233_A	1.528	1.00
115_S	206_P	1.527	1.00
113_F	116_F	1.525	1.00
116_F	120_Q	1.511	1.00
153_G	198_L	1.487	1.00
80_H	103_Y	1.464	1.00
232_G	236_A	1.459	1.00
24_G	118_F	1.454	1.00
25_S	61_A	1.429	1.00
155_F	239_T	1.414	1.00
100_V	104_I	1.409	1.00
95_F	100_V	1.378	0.99
86_T	95_F	1.350	0.99
67_A	180_G	1.349	0.99
204_F	208_L	1.346	0.99
154_T	233_A	1.329	0.99
23_A	115_S	1.318	0.99
150_E	194_S	1.316	0.99
164_I	178_I	1.313	0.99
67_A	177_I	1.299	0.99
88_G	92_V	1.296	0.99
204_F	222_Y	1.295	0.99
149_A	193_I	1.294	0.99
90_W	95_F	1.291	0.99
69_S	73_L	1.290	0.99
86_T	104_I	1.283	0.99
203_T	207_Y	1.278	0.99
15_T	111_A	1.254	0.99
83_P	201_A	1.246	0.98
183_V	198_L	1.245	0.98
17_I	69_S	1.239	0.98
84_A	200_P	1.238	0.98
147_M	224_I	1.237	0.98
11_E	14_G	1.237	0.98
149_A	153_G	1.235	0.98
73_L	79_C	1.227	0.98
14_G	18_L	1.226	0.98
87_I	234_V	1.221	0.98
59_G	188_T	1.218	0.98
110_G	114_G	1.206	0.98
157_L	183_V	1.204	0.98
219_W	222_Y	1.199	0.98
65_A	69_S	1.193	0.98
97_G	100_V	1.170	0.97
21_F	65_A	1.165	0.97
167_D	240_Y	1.164	0.97
101_V	105_I	1.158	0.97
151_V	232_G	1.139	0.97
16_F	113_F	1.133	0.97
223_S	227_I	1.130	0.97
88_G	237_A	1.126	0.97
155_F	235_L	1.121	0.97
89_L	95_F	1.116	0.96
137_P	146_A	1.101	0.96
56_V	60_L	1.095	0.96
144_W	148_L	1.092	0.96
23_A	118_F	1.089	0.96
53_G	57_A	1.088	0.96
115_S	205_G	1.085	0.96
88_G	158_M	1.084	0.96
112_A	204_F	1.083	0.96
70_I	176_G	1.081	0.95
117_I	152_V	1.072	0.95
17_I	156_L	1.069	0.95
18_L	66_I	1.062	0.95
228_G	232_G	1.061	0.95
15_T	19_V	1.055	0.95
221_Y	225_Y	1.049	0.94
20_F	121_C	1.039	0.94
86_T	107_Q	1.031	0.94
63_G	180_G	1.027	0.94
202_R	206_P	1.022	0.93
13_I	239_T	1.013	0.93
5_T	8_C	1.011	0.93
149_A	194_S	1.005	0.93

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
2f2bA	1	0.9959	100	0.054	Contact Map
1ldfA	1	0.9187	100	0.073	Contact Map
3c02A	1	0.9187	100	0.08	Contact Map
3iyzA	1	0.8943	100	0.083	Contact Map
3cn5A	1	0.9228	100	0.086	Contact Map
2zz9A	1	0.8943	100	0.092	Contact Map
3gd8A	1	0.8984	100	0.093	Contact Map
4oj2X	1	0.8862	100	0.093	Contact Map
1j4nA	1	0.9228	100	0.094	Contact Map
3llqA	2	0.9106	100	0.095	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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