OPENSEQ.org - 1490307277 - GREMLIN Submission

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ID:	1490307277	Query Sequence LTANLVCRVALGILANLLCLVPLRLLYHNHELAAVVFILNIEFKNILTIVSALIWRDDNMEDWWAGYGLCDFASFANNFSFGLFDTCMLAIMRNLAHQANLLSAHPSAQRYLIGTLTGCTWTQYPSWPYVVFFALPPLVLSVVVSVLVPYFPVVVTIFIMNHGWIPILSAIPVIVFFGMTKEAINDYRRVLLLPGFADGSFGSSHSAANSGS	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	212 (205)
Sequences:	485 (407.4)
Seq/Len:	2.366
Nf(neff/√len):	28.5

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: 2.366).

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
127_W	131_V	3.119	1.00
64_W	111_Y	3.107	1.00
155_V	159_I	2.583	1.00
68_G	72_F	2.140	1.00
177_F	187_Y	2.067	0.99
110_R	118_G	1.964	0.99
107_S	194_P	1.873	0.99
61_E	65_A	1.870	0.99
174_I	178_G	1.845	0.99
50_V	73_A	1.805	0.98
60_M	116_L	1.803	0.98
187_Y	191_L	1.691	0.97
174_I	177_F	1.643	0.96
110_R	119_C	1.581	0.95
182_E	187_Y	1.574	0.95
89_L	93_R	1.551	0.95
177_F	182_E	1.534	0.94
151_F	155_V	1.533	0.94
8_R	12_G	1.524	0.94
23_L	45_N	1.515	0.94
152_P	178_G	1.480	0.93
9_V	12_G	1.470	0.92
14_L	18_L	1.445	0.91
109_Q	112_L	1.432	0.91
9_V	13_I	1.431	0.91
130_V	158_F	1.418	0.90
13_I	17_L	1.416	0.90
22_P	45_N	1.415	0.90
10_A	14_L	1.413	0.90
69_L	73_A	1.395	0.89
174_I	182_E	1.380	0.89
178_G	187_Y	1.374	0.89
68_G	71_D	1.342	0.87
5_L	9_V	1.335	0.87
177_F	183_A	1.331	0.86
83_L	136_P	1.325	0.86
164_W	177_F	1.324	0.86
11_L	90_A	1.316	0.85
202_G	206_S	1.315	0.85
19_C	52_A	1.308	0.85
112_L	122_T	1.307	0.85
64_W	67_Y	1.298	0.84
8_R	59_N	1.263	0.82
47_L	51_S	1.252	0.81
33_A	41_I	1.241	0.81
178_G	182_E	1.240	0.81
32_L	37_F	1.232	0.80
183_A	187_Y	1.225	0.79
129_Y	136_P	1.219	0.79
89_L	140_L	1.218	0.79
91_I	152_P	1.205	0.78
87_C	92_M	1.204	0.78
151_F	182_E	1.173	0.75
86_T	167_I	1.170	0.75
87_C	179_M	1.156	0.74
92_M	176_F	1.146	0.73
123_Q	129_Y	1.146	0.73
110_R	113_I	1.143	0.72
113_I	118_G	1.141	0.72
11_L	55_W	1.140	0.72
152_P	177_F	1.136	0.72
25_L	28_H	1.135	0.72
170_A	178_G	1.115	0.70
108_A	146_V	1.113	0.70
111_Y	118_G	1.109	0.69
194_P	198_D	1.107	0.69
18_L	48_T	1.098	0.68
87_C	137_P	1.096	0.68
105_H	171_I	1.090	0.67
138_L	154_V	1.085	0.67
15_A	113_I	1.084	0.67
140_L	146_V	1.084	0.67
128_P	134_A	1.078	0.66
46_I	50_V	1.076	0.66
6_V	33_A	1.071	0.65
75_F	122_T	1.070	0.65
78_N	151_F	1.070	0.65
170_A	177_F	1.069	0.65
33_A	37_F	1.068	0.65
12_G	59_N	1.054	0.63
47_L	80_S	1.050	0.63
178_G	183_A	1.048	0.63
86_T	140_L	1.048	0.63
8_R	36_V	1.044	0.62
71_D	74_S	1.042	0.62
29_N	32_L	1.042	0.62
174_I	187_Y	1.041	0.62
79_F	164_W	1.041	0.62
202_G	205_H	1.038	0.62
86_T	117_T	1.035	0.61
36_V	64_W	1.034	0.61
16_N	52_A	1.034	0.61
72_F	75_F	1.032	0.61
167_I	170_A	1.032	0.61
75_F	167_I	1.019	0.60
180_T	187_Y	1.018	0.59
181_K	188_R	1.017	0.59
108_A	112_L	1.017	0.59
111_Y	119_C	1.014	0.59
82_G	136_P	1.014	0.59
131_V	135_L	1.011	0.59
18_L	170_A	1.006	0.58
24_R	45_N	1.005	0.58

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	27.2	0.939	Contact Map
4pxzA	1	0.9151	24.3	0.94	Contact Map
4l6rA	1	0.9198	22.9	0.941	Contact Map
4xesA	1	0	22.4	0.941	Contact Map
4n6hA	1	0.934	20.8	0.942	Contact Map
4mbsA	2	0.967	20.5	0.942	Contact Map
3oduA	2	0.9528	17.8	0.944	Contact Map
3emlA	1	0.9623	14.6	0.946	Contact Map
4eiyA	1	0.9198	13.6	0.947	Contact Map
4ea3A	2	0.9575	11.8	0.948	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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