OPENSEQ.org - 1490791966 - GREMLIN Submission

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ID:	1490791966	Query Sequence MSEPFEIVAGALGVAGLFNNCVACFEYVQLGRHFGRDYERCQLRLDIAKVRLSRWGEAVQINDDPRFHSSAPIDKSVQLAKSIVEEILLLFESAQKTSKRYELVADQQDLVVFEDKDMKPIGRALHRRLKDLVSRRQKQTSLAKKTAWALYDGKSLEKIVDQVAGFVDELEKAFPIEAVCHKLAENEIEEVEDEASLTILKDAAGGIDAAMSDAAAQKIDAIVGRNSA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	228 (220)
Sequences:	411 (340.5)
Seq/Len:	1.868
Nf(neff/√len):	23.0

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: 1.868).

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
25_F	167_V	2.246	1.00
5_F	10_G	2.210	1.00
19_N	23_A	2.156	0.99
48_A	167_V	2.072	0.99
51_R	168_D	2.034	0.99
25_F	163_V	2.001	0.99
47_I	83_I	1.903	0.98
100_R	147_A	1.865	0.98
52_L	56_G	1.709	0.96
35_G	133_V	1.644	0.94
37_D	153_G	1.630	0.94
91_F	174_F	1.620	0.94
80_A	174_F	1.570	0.92
45_L	74_D	1.568	0.92
98_S	103_L	1.561	0.92
35_G	137_Q	1.557	0.92
18_F	56_G	1.540	0.92
3_E	6_E	1.538	0.91
26_E	154_K	1.504	0.90
101_Y	152_D	1.487	0.90
25_F	45_L	1.475	0.89
56_G	60_Q	1.467	0.89
37_D	80_A	1.451	0.88
6_E	10_G	1.425	0.87
97_T	103_L	1.389	0.85
123_R	200_L	1.378	0.84
155_S	215_A	1.375	0.84
138_K	144_K	1.375	0.84
34_F	37_D	1.339	0.82
52_L	55_W	1.315	0.80
163_V	167_V	1.311	0.80
51_R	171_E	1.307	0.80
31_G	213_D	1.295	0.79
215_A	218_K	1.286	0.78
45_L	163_V	1.285	0.78
187_E	208_D	1.280	0.78
14_V	17_L	1.273	0.77
28_V	38_Y	1.272	0.77
4_P	8_V	1.271	0.77
141_S	145_K	1.269	0.77
97_T	155_S	1.268	0.77
36_R	39_E	1.266	0.76
51_R	56_G	1.263	0.76
37_D	148_W	1.262	0.76
154_K	200_L	1.235	0.74
52_L	204_A	1.228	0.73
28_V	73_I	1.219	0.73
15_A	141_S	1.219	0.73
44_R	165_G	1.215	0.72
153_G	220_D	1.212	0.72
55_W	170_L	1.207	0.71
159_I	162_Q	1.203	0.71
97_T	102_E	1.202	0.71
131_D	160_V	1.200	0.71
44_R	162_Q	1.190	0.70
80_A	169_E	1.189	0.70
22_V	143_A	1.181	0.69
101_Y	173_A	1.179	0.69
54_R	132_L	1.178	0.69
28_V	142_L	1.175	0.69
59_V	83_I	1.175	0.69
184_A	205_G	1.174	0.68
182_K	185_E	1.167	0.68
160_V	200_L	1.166	0.68
2_S	6_E	1.156	0.67
10_G	13_G	1.149	0.66
188_I	192_E	1.147	0.66
51_R	91_F	1.145	0.66
93_S	201_K	1.144	0.66
64_D	160_V	1.137	0.65
52_L	61_I	1.136	0.65
54_R	208_D	1.126	0.64
193_D	197_L	1.119	0.63
20_N	45_L	1.113	0.62
212_S	216_A	1.112	0.62
80_A	125_L	1.109	0.62
35_G	140_T	1.105	0.62
153_G	157_E	1.101	0.61
9_A	156_L	1.099	0.61
42_Q	160_V	1.099	0.61
158_K	162_Q	1.095	0.61
24_C	48_A	1.094	0.60
41_C	152_D	1.090	0.60
160_V	168_D	1.089	0.60
56_G	61_I	1.087	0.60
43_L	54_R	1.085	0.59
40_R	43_L	1.079	0.59
21_C	52_L	1.078	0.59
21_C	101_Y	1.077	0.59
14_V	203_A	1.076	0.59
29_Q	32_R	1.075	0.58
4_P	7_I	1.074	0.58
33_H	37_D	1.071	0.58
93_S	102_E	1.061	0.57
100_R	158_K	1.059	0.57
100_R	157_E	1.052	0.56
41_C	48_A	1.037	0.54
79_L	83_I	1.037	0.54
28_V	93_S	1.036	0.54
11_A	46_D	1.026	0.53
11_A	96_K	1.025	0.53
3_E	10_G	1.023	0.53
193_D	196_S	1.021	0.53
23_A	160_V	1.021	0.53
33_H	68_H	1.019	0.52
1_M	8_V	1.016	0.52
212_S	218_K	1.014	0.52
40_R	86_E	1.014	0.52
188_I	191_V	1.006	0.51
97_T	156_L	1.004	0.51
30_L	48_A	1.001	0.50
102_E	155_S	1.001	0.50
20_N	130_K	1.000	0.50

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	0.9342	100	0.187	Contact Map
2msvA	1	0.6184	38.9	0.927	Contact Map
4btfA	1	0.6228	12.9	0.942	Contact Map
3he4A	4	0.1974	9	0.946	Contact Map
4abxA	4	0.5132	5.6	0.951	Contact Map
2uytA	1	0.2149	4.2	0.953	Contact Map
4y21A	1	0	3.9	0.954	Contact Map
1w3iA	4	0.4254	2.9	0.957	Contact Map
2k9jB	1	0.1491	2.9	0.957	Contact Map
2b1eA	1	0.6798	2.8	0.958	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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