OPENSEQ.org - 1490239013 - GREMLIN Submission

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E4 it2

ID:	1490239013	Query Sequence LTANLVCRVALGILANLLCLVPLRLLYHNHELAAVVFILNIEFKNILTIVSALIWRDDNMEDWWAGYGLCDFASFANNFSFGLFDTCMLAIMRNLAHQANLLSAHPSAQRYLIGTLTGCTWTQYPSWPYVVFFALPPLVLSVVVSVLVPYFPVVVTIFIMNHGWIPILSAIPVIVFFGMTKEAINDYRRVLLLPGFADGSFGSSHSAANSGS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	212 (208)
Sequences:	759 (650.1)
Seq/Len:	3.649
Nf(neff/√len):	45.1

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: 3.649).

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
64_W	111_Y	3.953	1.00
127_W	131_V	3.516	1.00
155_V	159_I	2.924	1.00
60_M	116_L	2.766	1.00
174_I	178_G	2.389	1.00
61_E	65_A	2.129	1.00
68_G	72_F	1.899	1.00
110_R	118_G	1.887	1.00
9_V	12_G	1.795	0.99
9_V	13_I	1.761	0.99
109_Q	112_L	1.667	0.99
184_I	187_Y	1.666	0.99
187_Y	191_L	1.663	0.99
151_F	155_V	1.633	0.99
64_W	67_Y	1.617	0.98
8_R	12_G	1.605	0.98
47_L	80_S	1.601	0.98
50_V	73_A	1.561	0.98
25_L	28_H	1.547	0.98
177_F	187_Y	1.510	0.97
89_L	140_L	1.499	0.97
71_D	110_R	1.492	0.97
23_L	45_N	1.485	0.97
32_L	37_F	1.471	0.97
71_D	74_S	1.471	0.97
182_E	187_Y	1.468	0.97
174_I	177_F	1.459	0.96
110_R	119_C	1.443	0.96
101_L	104_A	1.414	0.95
123_Q	129_Y	1.411	0.95
10_A	14_L	1.407	0.95
75_F	79_F	1.401	0.95
83_L	87_C	1.381	0.95
89_L	93_R	1.369	0.94
69_L	73_A	1.357	0.94
35_V	39_L	1.346	0.94
22_P	45_N	1.337	0.93
8_R	59_N	1.330	0.93
177_F	182_E	1.316	0.93
152_P	178_G	1.287	0.91
29_N	37_F	1.284	0.91
35_V	90_A	1.283	0.91
194_P	198_D	1.262	0.90
14_L	18_L	1.258	0.90
107_S	194_P	1.242	0.89
18_L	48_T	1.242	0.89
10_A	13_I	1.241	0.89
202_G	206_S	1.238	0.89
19_C	52_A	1.236	0.89
111_Y	118_G	1.224	0.89
112_L	122_T	1.203	0.87
86_T	140_L	1.202	0.87
96_A	102_L	1.200	0.87
76_A	165_I	1.195	0.87
87_C	92_M	1.187	0.86
177_F	183_A	1.183	0.86
151_F	182_E	1.182	0.86
183_A	187_Y	1.173	0.86
105_H	187_Y	1.152	0.84
5_L	9_V	1.151	0.84
18_L	170_A	1.147	0.84
13_I	17_L	1.143	0.83
81_F	125_P	1.140	0.83
100_N	155_V	1.123	0.82
186_D	190_V	1.110	0.81
180_T	183_A	1.106	0.81
138_L	154_V	1.097	0.80
203_S	207_A	1.085	0.79
33_A	41_I	1.077	0.78
113_I	118_G	1.076	0.78
54_I	58_D	1.072	0.78
174_I	182_E	1.071	0.78
65_A	68_G	1.070	0.78
152_P	177_F	1.070	0.78
201_F	204_S	1.066	0.77
79_F	82_G	1.059	0.76
199_G	202_G	1.058	0.76
11_L	163_G	1.055	0.76
178_G	183_A	1.052	0.76
71_D	75_F	1.051	0.76
178_G	182_E	1.051	0.76
43_F	54_I	1.046	0.75
48_T	170_A	1.040	0.75
12_G	59_N	1.040	0.75
30_H	33_A	1.039	0.75
70_C	119_C	1.039	0.75
88_M	146_V	1.037	0.74
34_A	43_F	1.036	0.74
33_A	37_F	1.035	0.74
19_C	24_R	1.034	0.74
46_I	50_V	1.033	0.74
102_L	149_P	1.024	0.73
202_G	205_H	1.024	0.73
194_P	197_A	1.023	0.73
108_A	112_L	1.022	0.73
164_W	177_F	1.022	0.73
195_G	198_D	1.015	0.72
34_A	58_D	1.009	0.71
12_G	23_L	1.003	0.71

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
4n6hA	1	0.9481	21.6	0.938	Contact Map
2z73A	2	0.9623	20.8	0.939	Contact Map
4xesA	1	0	19.9	0.939	Contact Map
4l6rA	1	0.934	19.4	0.939	Contact Map
4pxzA	1	0.9245	18.1	0.94	Contact Map
3oduA	2	0.9528	12.4	0.945	Contact Map
4ea3A	2	0.9481	12	0.945	Contact Map
4grvA	1	0.9434	9.8	0.947	Contact Map
4mbsA	2	0.9575	9.6	0.947	Contact Map
4mqsA	1	0.816	8.2	0.949	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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