OPENSEQ.org - 1490273626 - GREMLIN Submission

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E4 it0

ID:	1490273626	Query Sequence LTANLVCRVALGILANLLCLVPLRLLYHNHELAAVVFILNIEFKNILTIVSALIWRDDNMEDWWAGYGLCDFASFANNFSFGLFDTCMLAIMRNLAHQANLLSAHPSAQRYLIGTLTGCTWTQYPSWPYVVFFALPPLVLSVVVSVLVPYFPVVVTIFIMNHGWIPILSAIPVIVFFGMTKEAINDYRRVLLLPGFADGSFGSSHSAANSGS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	212 (211)
Sequences:	338 (293.5)
Seq/Len:	1.602
Nf(neff/√len):	20.2

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: 1.602).

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
110_R	118_G	2.473	1.00
174_I	178_G	2.325	1.00
177_F	187_Y	2.263	0.99
182_E	187_Y	2.141	0.99
174_I	177_F	2.057	0.99
110_R	119_C	2.026	0.98
177_F	182_E	2.021	0.98
68_G	72_F	1.980	0.98
127_W	131_V	1.794	0.96
178_G	187_Y	1.785	0.96
64_W	111_Y	1.768	0.96
151_F	155_V	1.768	0.96
83_L	136_P	1.722	0.95
183_A	187_Y	1.675	0.94
152_P	177_F	1.664	0.93
152_P	178_G	1.641	0.93
111_Y	118_G	1.621	0.92
89_L	140_L	1.563	0.90
164_W	177_F	1.535	0.89
174_I	187_Y	1.510	0.88
177_F	183_A	1.482	0.87
111_Y	119_C	1.479	0.86
13_I	53_L	1.453	0.85
178_G	182_E	1.445	0.85
155_V	159_I	1.444	0.85
109_Q	112_L	1.442	0.84
33_A	41_I	1.424	0.83
68_G	128_P	1.413	0.83
180_T	187_Y	1.411	0.83
6_V	10_A	1.402	0.82
64_W	67_Y	1.402	0.82
69_L	73_A	1.385	0.81
113_I	118_G	1.343	0.78
91_I	152_P	1.342	0.78
170_A	177_F	1.335	0.78
92_M	176_F	1.332	0.77
55_W	66_G	1.331	0.77
187_Y	191_L	1.320	0.77
129_Y	136_P	1.315	0.76
178_G	183_A	1.290	0.74
151_F	182_E	1.287	0.74
20_L	23_L	1.284	0.74
179_M	187_Y	1.269	0.72
6_V	33_A	1.252	0.71
182_E	186_D	1.246	0.70
66_G	70_C	1.231	0.69
45_N	51_S	1.216	0.68
174_I	182_E	1.211	0.67
208_A	211_G	1.209	0.67
15_A	113_I	1.207	0.67
31_E	37_F	1.206	0.67
164_W	178_G	1.194	0.66
177_F	180_T	1.185	0.65
202_G	206_S	1.181	0.64
8_R	36_V	1.178	0.64
21_V	26_L	1.165	0.63
89_L	93_R	1.161	0.63
37_F	55_W	1.154	0.62
68_G	71_D	1.149	0.61
110_R	113_I	1.147	0.61
169_S	173_V	1.144	0.61
164_W	187_Y	1.134	0.60
26_L	31_E	1.128	0.59
170_A	187_Y	1.126	0.59
170_A	178_G	1.118	0.58
152_P	187_Y	1.116	0.58
96_A	102_L	1.111	0.57
22_P	31_E	1.108	0.57
33_A	37_F	1.095	0.56
5_L	9_V	1.090	0.55
119_C	152_P	1.085	0.55
66_G	71_D	1.083	0.55
22_P	37_F	1.071	0.53
54_I	58_D	1.064	0.53
139_V	142_V	1.063	0.52
71_D	74_S	1.061	0.52
113_I	119_C	1.058	0.52
75_F	122_T	1.057	0.52
54_I	66_G	1.052	0.51
136_P	152_P	1.047	0.51
152_P	163_G	1.045	0.51
87_C	172_P	1.044	0.50
54_I	64_W	1.035	0.50
12_G	23_L	1.031	0.49
185_N	192_L	1.028	0.49
86_T	117_T	1.027	0.49
140_L	146_V	1.023	0.48
20_L	148_V	1.019	0.48
36_V	64_W	1.015	0.47
9_V	12_G	1.002	0.46

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	25.9	0.937	Contact Map
2z73A	2	0.9575	19.9	0.941	Contact Map
3oduA	2	0.9528	17.8	0.942	Contact Map
4ea3A	2	0.9387	15.8	0.943	Contact Map
4mbsA	2	0.967	14.4	0.944	Contact Map
4pxzA	1	0.9198	13.5	0.945	Contact Map
4eiyA	1	0.9151	12.7	0.946	Contact Map
4xesA	1	0	12.1	0.946	Contact Map
4zwjA	4	0	11.4	0.947	Contact Map
3emlA	1	0.9528	11.2	0.947	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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