OPENSEQ.org - 1492169250 - GREMLIN Submission

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125-352_p2_x1012 99-330

ID:	1492169250	Query Sequence NNEVSKPLFDMAKGETPFEINSRIGYSGDSSSDISLKPLNYEQKDEKVAFSGGEFQLNADRDGKAISLSGEAQSGRIDAVNEYNQKVQLTFNNLKTDGSSTLASFGERVGNQKLSLEKMTISVEGKELALLEGMEISGKSDLVNDGKTINSQLDYSLNSLKVQNQDLGSGKLTLKVGQIDGEAWHQFSQQYNAQTQALLAQPEIANNPELYQEKVTEAFFSALPLMLKGDPV	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	232 (232)
Sequences:	937 (873)
Seq/Len:	4.039
Nf(neff/√len):	57.3

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: 4.039).

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
133_G	158_N	2.376	1.00
40_N	49_A	2.084	1.00
94_L	116_L	2.021	1.00
118_K	132_E	1.776	0.99
180_D	183_A	1.767	0.99
32_S	57_L	1.743	0.99
68_L	98_G	1.740	0.99
157_L	160_L	1.739	0.99
194_Q	197_A	1.731	0.99
9_F	12_A	1.730	0.99
31_S	58_N	1.701	0.99
180_D	229_G	1.681	0.99
177_G	232_V	1.672	0.99
93_N	99_S	1.664	0.99
11_M	14_G	1.648	0.99
9_F	26_Y	1.607	0.99
107_E	110_G	1.571	0.98
185_H	189_Q	1.563	0.98
1_N	6_K	1.540	0.98
148_T	178_Q	1.530	0.98
93_N	117_E	1.527	0.98
17_P	187_F	1.516	0.98
22_S	32_S	1.511	0.98
26_Y	168_G	1.501	0.98
19_E	35_S	1.478	0.97
6_K	10_D	1.449	0.97
52_G	231_P	1.425	0.96
67_S	99_S	1.410	0.96
70_G	73_Q	1.409	0.96
9_F	168_G	1.405	0.96
211_Y	215_V	1.386	0.96
9_F	13_K	1.378	0.95
39_L	50_F	1.371	0.95
38_P	52_G	1.358	0.95
133_G	136_I	1.343	0.95
28_G	32_S	1.331	0.94
227_L	231_P	1.327	0.94
178_Q	231_P	1.327	0.94
134_M	137_S	1.322	0.94
213_E	216_T	1.320	0.94
136_I	140_S	1.312	0.94
14_G	17_P	1.307	0.94
57_L	68_L	1.303	0.93
16_T	37_K	1.298	0.93
19_E	34_I	1.294	0.93
8_L	11_M	1.293	0.93
191_Y	195_T	1.289	0.93
203_E	206_N	1.287	0.93
226_M	229_G	1.284	0.93
152_Q	175_K	1.284	0.93
89_L	217_E	1.282	0.93
20_I	32_S	1.278	0.93
2_N	5_S	1.271	0.92
55_F	70_G	1.269	0.92
3_E	6_K	1.263	0.92
90_T	120_T	1.263	0.92
194_Q	198_L	1.252	0.91
190_Q	193_A	1.247	0.91
42_E	47_K	1.241	0.91
180_D	225_L	1.239	0.91
197_A	202_P	1.229	0.90
69_S	97_D	1.221	0.90
133_G	138_G	1.210	0.90
131_L	134_M	1.203	0.89
127_E	130_L	1.196	0.89
50_F	231_P	1.191	0.89
8_L	228_K	1.187	0.88
48_V	77_I	1.184	0.88
51_S	73_Q	1.181	0.88
150_N	177_G	1.166	0.87
25_G	29_D	1.164	0.87
12_A	39_L	1.163	0.87
20_I	34_I	1.159	0.87
10_D	14_G	1.152	0.86
94_L	151_S	1.147	0.86
170_G	173_T	1.144	0.86
199_L	202_P	1.143	0.86
108_R	230_D	1.137	0.85
125_G	136_I	1.135	0.85
22_S	30_S	1.124	0.84
3_E	7_P	1.121	0.84
179_I	184_W	1.107	0.83
129_A	132_E	1.104	0.83
5_S	10_D	1.104	0.83
134_M	138_G	1.101	0.83
102_L	105_F	1.094	0.82
51_S	74_S	1.092	0.82
28_G	61_R	1.090	0.82
124_E	128_L	1.090	0.82
66_I	75_G	1.089	0.82
219_F	222_A	1.086	0.81
208_P	212_Q	1.084	0.81
13_K	40_N	1.083	0.81
209_E	218_A	1.082	0.81
95_K	115_S	1.079	0.81
22_S	28_G	1.077	0.81
9_F	14_G	1.070	0.80
129_A	134_M	1.067	0.80
2_N	26_Y	1.066	0.80
178_Q	183_A	1.061	0.79
163_Q	171_K	1.060	0.79
25_G	227_L	1.049	0.78
154_D	173_T	1.049	0.78
183_A	187_F	1.049	0.78
24_I	30_S	1.048	0.78
141_D	144_N	1.048	0.78
12_A	24_I	1.046	0.78
161_K	166_D	1.040	0.77
189_Q	193_A	1.040	0.77
43_Q	46_E	1.039	0.77
37_K	179_I	1.030	0.76
26_Y	32_S	1.028	0.76
50_F	74_S	1.025	0.76
25_G	231_P	1.025	0.76
155_Y	191_Y	1.024	0.76
116_L	119_M	1.024	0.76
37_K	50_F	1.024	0.76
129_A	133_G	1.024	0.76
110_G	226_M	1.022	0.76
50_F	57_L	1.021	0.76
132_E	135_E	1.019	0.75
35_S	54_E	1.018	0.75
34_I	68_L	1.017	0.75
138_G	142_L	1.016	0.75
72_A	75_G	1.013	0.75
30_S	59_A	1.008	0.74
52_G	168_G	1.007	0.74
2_N	186_Q	1.007	0.74

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
2rckA	2	0.8405	3.4	0.94	Contact Map
1gnyA	1	0.6509	3.3	0.94	Contact Map
2mniA	1	0.2888	2.3	0.944	Contact Map
3e8tA	1	0.8017	1.6	0.95	Contact Map
2o6fA	2	0.2759	1.4	0.951	Contact Map
2jnsA	1	0.3707	1.3	0.952	Contact Map
3fz2A	12	0.2328	1.2	0.953	Contact Map
1zoqC	2	0.1336	1.2	0.953	Contact Map
4peuA	1	0.6207	1.2	0.953	Contact Map
3hxiC	1	0.0603	1.1	0.954	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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