OPENSEQ.org - 1498053053 - GREMLIN Submission

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ID:	1498053053	Query Sequence AEEKDDYEAETKKGEIIHTIQETAQSSARARLKAAEGVERMVGMHQMYDRDEAILNKVEQQLDESKHQARLAHAHLDNLDAANSSLFNLAANSKGKLAERSARKAQSEREREIDRDALREEQALRKRELEAATAQVGRPTLGFNKADRSKWAFEDNDGEQEELNNQIDDDMTEIALSVSTMNMLAKGFSVRTDAQINQVTRLTVKSDAAKDKVRAQNNRMKAEYSP	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	226 (222)
Sequences:	638 (406.8)
Seq/Len:	2.874
Nf(neff/√len):	27.3

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: 2.874).

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
59_E	201_R	3.019	1.00
38_V	180_T	2.694	1.00
27_S	170_D	2.671	1.00
63_D	205_K	2.558	1.00
34_A	177_S	2.352	1.00
28_A	166_Q	2.280	1.00
102_A	106_Q	2.245	1.00
182_N	186_K	2.178	1.00
35_A	173_E	2.112	1.00
24_A	27_S	1.809	0.99
189_S	193_D	1.797	0.99
23_T	27_S	1.778	0.99
41_M	184_L	1.760	0.99
24_A	163_L	1.752	0.99
216_Q	220_M	1.672	0.98
29_R	32_L	1.643	0.98
171_M	178_V	1.625	0.97
30_A	174_I	1.606	0.97
26_S	31_R	1.544	0.96
168_D	171_M	1.534	0.96
26_S	29_R	1.518	0.96
38_V	184_L	1.453	0.94
39_E	42_V	1.443	0.94
180_T	184_L	1.429	0.93
15_E	18_H	1.415	0.93
59_E	198_Q	1.411	0.93
52_E	191_R	1.404	0.93
18_H	21_Q	1.394	0.92
16_I	19_T	1.366	0.91
27_S	31_R	1.354	0.91
202_L	210_K	1.350	0.91
56_N	198_Q	1.342	0.90
61_Q	64_E	1.341	0.90
55_L	199_V	1.334	0.90
81_A	84_S	1.329	0.90
118_L	146_A	1.314	0.89
191_R	195_Q	1.280	0.87
54_I	213_V	1.265	0.86
33_K	37_G	1.265	0.86
17_I	20_I	1.246	0.85
218_N	221_K	1.244	0.85
16_I	20_I	1.218	0.83
19_T	23_T	1.217	0.83
202_L	206_S	1.217	0.83
179_S	185_A	1.214	0.83
26_S	37_G	1.209	0.83
55_L	202_L	1.208	0.83
41_M	44_M	1.207	0.83
52_E	56_N	1.207	0.83
215_A	219_R	1.205	0.83
122_Q	126_K	1.204	0.82
174_I	177_S	1.199	0.82
84_S	87_F	1.190	0.81
220_M	223_E	1.190	0.81
41_M	52_E	1.165	0.80
37_G	41_M	1.165	0.80
183_M	186_K	1.163	0.79
211_D	222_A	1.152	0.78
185_A	188_F	1.146	0.78
161_E	164_N	1.142	0.78
198_Q	201_R	1.139	0.77
14_G	18_H	1.134	0.77
172_T	176_L	1.131	0.77
203_T	206_S	1.129	0.77
57_K	60_Q	1.116	0.75
65_S	76_L	1.114	0.75
83_N	87_F	1.114	0.75
31_R	146_A	1.105	0.74
12_K	17_I	1.105	0.74
48_Y	196_I	1.103	0.74
189_S	196_I	1.099	0.74
168_D	194_A	1.098	0.74
182_N	217_N	1.094	0.73
48_Y	151_W	1.093	0.73
184_L	188_F	1.092	0.73
53_A	184_L	1.090	0.73
111_R	114_D	1.089	0.73
120_E	124_L	1.087	0.73
38_V	43_G	1.081	0.72
152_A	161_E	1.074	0.71
59_E	205_K	1.073	0.71
167_I	174_I	1.073	0.71
28_A	170_D	1.069	0.71
13_K	16_I	1.061	0.70
175_A	200_T	1.050	0.69
34_A	219_R	1.048	0.69
58_V	62_L	1.047	0.69
133_T	138_R	1.047	0.69
37_G	200_T	1.045	0.68
36_E	40_R	1.044	0.68
6_D	10_E	1.043	0.68
41_M	53_A	1.041	0.68
2_E	5_D	1.036	0.67
52_E	68_Q	1.032	0.67
9_A	13_K	1.025	0.66
207_D	210_K	1.023	0.66
72_A	216_Q	1.022	0.66
182_N	208_A	1.022	0.66
29_R	55_L	1.022	0.66
38_V	170_D	1.020	0.66
81_A	174_I	1.019	0.65
43_G	46_Q	1.018	0.65
47_M	50_R	1.010	0.64
131_A	138_R	1.005	0.64
212_K	220_M	1.004	0.64
217_N	224_Y	1.001	0.63

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
3j96M	1	0.5796	100	0.337	Contact Map
1l4aC	1	0.323	99.6	0.664	Contact Map
3b5nC	3	0.3097	99.6	0.665	Contact Map
1n7sC	1	0.3496	99.6	0.668	Contact Map
4wy4C	1	0.3451	99.6	0.674	Contact Map
1l4aD	1	0.3319	99.4	0.708	Contact Map
1sfcD	3	0.3274	99.4	0.711	Contact Map
3b5nD	3	0.2832	99.3	0.72	Contact Map
1n7sD	1	0.292	99.3	0.722	Contact Map
1nhlA	1	0.2389	99.2	0.738	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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