OPENSEQ.org - 1504790096 - GREMLIN Submission

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2wvoA

ID:	1504790096	Query Sequence MSEPFEIVAGALGVAGLFNNCVACFEYVQLGRHFGRDYERCQLRLDIAKVRLSRWGEAVQINDDPRFHSSAPIDKSVQLAKSIVEEILLLFESAQKTSKRYELVADQQDLVVFEDKDMKPIGRALHRRLKDLVSRRQKQTSLAKKTAWALYDGKSLEKIVDQVAGFVDELEKAFPIEAVCHKLAENEIEEVEDEASLTILKDAAGGIDAAMSDAAAQKIDAIVGRNSHHHHHH	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	233 (207)
Sequences:	1195 (937.3)
Seq/Len:	5.773
Nf(neff/√len):	65.1

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: 5.773).

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 > 50% 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
3_E	6_E	4.141	1.00
37_D	153_G	2.373	1.00
5_F	9_A	2.282	1.00
2_S	7_I	2.244	1.00
10_G	13_G	2.227	1.00
4_P	8_V	2.215	1.00
16_G	19_N	1.879	1.00
56_G	60_Q	1.713	1.00
48_A	167_V	1.658	1.00
44_R	162_Q	1.648	1.00
16_G	20_N	1.631	1.00
88_L	92_E	1.625	0.99
48_A	164_A	1.606	0.99
44_R	165_G	1.601	0.99
87_I	163_V	1.572	0.99
48_A	169_E	1.472	0.99
1_M	4_P	1.435	0.98
5_F	10_G	1.433	0.98
18_F	56_G	1.433	0.98
2_S	6_E	1.424	0.98
51_R	172_K	1.411	0.98
9_A	13_G	1.407	0.98
25_F	163_V	1.402	0.98
127_R	130_K	1.391	0.98
161_D	165_G	1.388	0.98
51_R	171_E	1.375	0.98
6_E	10_G	1.369	0.98
197_L	200_L	1.358	0.98
1_M	13_G	1.356	0.98
3_E	7_I	1.348	0.97
34_F	38_Y	1.329	0.97
153_G	157_E	1.329	0.97
193_D	196_S	1.324	0.97
27_Y	149_A	1.320	0.97
51_R	168_D	1.312	0.97
3_E	13_G	1.296	0.96
31_G	34_F	1.274	0.96
52_L	57_E	1.252	0.95
194_E	198_T	1.235	0.95
6_E	9_A	1.229	0.95
25_F	167_V	1.229	0.95
51_R	56_G	1.219	0.95
124_A	131_D	1.218	0.95
151_Y	163_V	1.218	0.95
195_A	199_I	1.207	0.94
188_I	192_E	1.205	0.94
125_L	132_L	1.205	0.94
55_W	87_I	1.197	0.94
13_G	16_G	1.196	0.94
48_A	177_E	1.184	0.93
26_E	154_K	1.168	0.93
44_R	164_A	1.168	0.93
152_D	155_S	1.167	0.93
41_C	48_A	1.166	0.93
5_F	14_V	1.165	0.93
34_F	37_D	1.164	0.93
190_E	195_A	1.157	0.92
167_V	170_L	1.145	0.92
35_G	137_Q	1.144	0.92
51_R	55_W	1.135	0.91
18_F	80_A	1.134	0.91
41_C	160_V	1.121	0.91
6_E	13_G	1.116	0.90
3_E	8_V	1.107	0.90
192_E	195_A	1.098	0.89
141_S	145_K	1.096	0.89
101_Y	152_D	1.088	0.89
4_P	7_I	1.087	0.89
162_Q	169_E	1.085	0.89
193_D	197_L	1.084	0.89
152_D	156_L	1.084	0.89
8_V	11_A	1.084	0.89
55_W	80_A	1.080	0.88
184_A	210_A	1.080	0.88
56_G	61_I	1.079	0.88
7_I	13_G	1.076	0.88
147_A	152_D	1.071	0.88
80_A	174_F	1.069	0.88
128_R	131_D	1.062	0.87
77_V	80_A	1.059	0.87
47_I	83_I	1.059	0.87
121_I	125_L	1.058	0.87
184_A	205_G	1.051	0.86
180_C	205_G	1.048	0.86
34_F	97_T	1.048	0.86
9_A	14_V	1.048	0.86
193_D	205_G	1.045	0.86
144_K	152_D	1.045	0.86
164_A	168_D	1.039	0.86
36_R	89_L	1.038	0.86
195_A	206_G	1.036	0.85
183_L	191_V	1.034	0.85
110_L	113_F	1.032	0.85
182_K	205_G	1.031	0.85
189_E	210_A	1.029	0.85
188_I	193_D	1.026	0.85
118_M	121_I	1.025	0.85
18_F	21_C	1.025	0.85
124_A	127_R	1.024	0.85
152_D	163_V	1.019	0.84
122_G	126_H	1.017	0.84
90_L	163_V	1.014	0.84
115_D	118_M	1.013	0.84
126_H	132_L	1.010	0.83
38_Y	148_W	1.008	0.83
15_A	45_L	1.006	0.83
55_W	60_Q	1.003	0.83

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
2wvqA	2	0.9142	100	0.121	Contact Map
4btfA	1	0.6524	17.8	0.909	Contact Map
2msvA	1	0.6052	13.7	0.914	Contact Map
4ogqG	1	0.1502	6.2	0.926	Contact Map
1q90G	1	0.1202	5.1	0.929	Contact Map
4abxA	4	0.515	4.3	0.932	Contact Map
2kncB	1	0.2918	2.4	0.94	Contact Map
5rubA	2	0.2446	2.3	0.941	Contact Map
2ifoA	1	0.1073	2.2	0.941	Contact Map
1y14A	2	0.412	2.1	0.941	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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