OPENSEQ.org - 1490290110 - GREMLIN Submission

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E20 It1

ID:	1490290110	Query Sequence LTANLVCRVALGILANLLCLVPLRLLYHNHELAAVVFILNIEFKNILTIVSALIWRDDNMEDWWAGYGLCDFASFANNFSFGLFDTCMLAIMRNLAHQANLLSAHPSAQRYLIGTLTGCTWTQYPSWPYVVFFALPPLVLSVVVSVLVPYFPVVVTIFIMNHGWIPILSAIPVIVFFGMTKEAINDYRRVLLLPGFADGSFGSSHSAANSGS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	212 (208)
Sequences:	738 (631.7)
Seq/Len:	3.548
Nf(neff/√len):	43.8

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: 3.548).

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	4.049	1.00
127_W	131_V	3.480	1.00
155_V	159_I	2.835	1.00
60_M	116_L	2.758	1.00
174_I	178_G	2.355	1.00
61_E	65_A	2.141	1.00
68_G	72_F	2.052	1.00
110_R	118_G	1.884	1.00
9_V	12_G	1.840	0.99
109_Q	112_L	1.739	0.99
184_I	187_Y	1.683	0.99
9_V	13_I	1.676	0.99
187_Y	191_L	1.647	0.99
64_W	67_Y	1.604	0.98
8_R	12_G	1.596	0.98
25_L	28_H	1.590	0.98
50_V	73_A	1.582	0.98
151_F	155_V	1.579	0.98
47_L	80_S	1.563	0.98
174_I	177_F	1.529	0.97
23_L	45_N	1.521	0.97
110_R	119_C	1.516	0.97
89_L	140_L	1.479	0.97
177_F	187_Y	1.478	0.97
71_D	74_S	1.459	0.96
10_A	14_L	1.448	0.96
32_L	37_F	1.415	0.95
107_S	194_P	1.412	0.95
123_Q	129_Y	1.395	0.95
71_D	110_R	1.388	0.95
89_L	93_R	1.378	0.94
182_E	187_Y	1.370	0.94
22_P	45_N	1.358	0.94
75_F	79_F	1.356	0.94
69_L	73_A	1.355	0.94
35_V	39_L	1.353	0.94
152_P	178_G	1.343	0.93
101_L	104_A	1.340	0.93
83_L	87_C	1.337	0.93
194_P	198_D	1.313	0.92
177_F	182_E	1.302	0.92
8_R	59_N	1.291	0.91
151_F	182_E	1.263	0.90
10_A	13_I	1.257	0.90
35_V	90_A	1.251	0.89
29_N	37_F	1.249	0.89
96_A	102_L	1.245	0.89
177_F	183_A	1.234	0.89
202_G	206_S	1.233	0.89
14_L	18_L	1.231	0.88
105_H	187_Y	1.222	0.88
111_Y	118_G	1.219	0.88
18_L	48_T	1.215	0.88
112_L	122_T	1.213	0.87
5_L	9_V	1.190	0.86
19_C	52_A	1.178	0.85
87_C	92_M	1.168	0.85
138_L	154_V	1.165	0.84
18_L	170_A	1.151	0.83
54_I	58_D	1.137	0.82
81_F	125_P	1.129	0.82
76_A	165_I	1.112	0.80
141_S	150_Y	1.101	0.80
86_T	140_L	1.099	0.79
19_C	24_R	1.095	0.79
79_F	82_G	1.090	0.79
113_I	118_G	1.090	0.79
12_G	59_N	1.088	0.78
186_D	190_V	1.087	0.78
183_A	187_Y	1.084	0.78
203_S	207_A	1.081	0.78
65_A	68_G	1.080	0.78
33_A	41_I	1.075	0.77
68_G	71_D	1.062	0.76
13_I	17_L	1.061	0.76
71_D	75_F	1.060	0.76
17_L	175_V	1.060	0.76
100_N	155_V	1.057	0.76
201_F	204_S	1.053	0.75
48_T	170_A	1.052	0.75
43_F	54_I	1.052	0.75
199_G	202_G	1.048	0.75
187_Y	190_V	1.048	0.75
30_H	33_A	1.048	0.75
33_A	37_F	1.045	0.74
128_P	136_P	1.045	0.74
125_P	130_V	1.041	0.74
102_L	149_P	1.035	0.73
12_G	55_W	1.035	0.73
180_T	183_A	1.029	0.73
108_A	124_Y	1.026	0.72
34_A	58_D	1.023	0.72
34_A	43_F	1.022	0.72
88_M	146_V	1.020	0.72
11_L	163_G	1.019	0.72
194_P	197_A	1.012	0.71
202_G	205_H	1.011	0.71
152_P	177_F	1.002	0.70
111_Y	119_C	1.001	0.70

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
2z73A	2	0.9623	27.6	0.935	Contact Map
4pxzA	1	0.9151	22.2	0.938	Contact Map
4xesA	1	0	21.5	0.938	Contact Map
4n6hA	1	0.9434	20.3	0.939	Contact Map
3oduA	2	0.9481	12.7	0.944	Contact Map
4ea3A	2	0.9434	11.5	0.945	Contact Map
4zwjA	4	0	10.7	0.946	Contact Map
4grvA	1	0.9434	9.6	0.947	Contact Map
4mbsA	2	0.9575	9.2	0.948	Contact Map
3pblA	2	0.9387	8.1	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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