OPENSEQ.org - 1464786735 - GREMLIN Submission

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Eelco Tromer

ID:	1464786735	Query Sequence YTLREFIDEVGVGFLDTKLIDDLDKKVNFPLNSLNLMEIQRIDNVLSAYYIDIPILEVEAFRCKELWRSINESKNKFKDFETQIDRSHPPLLLQEYFSSSEKMKQLMKDQLQLVKGYSKLEAAMEWYEWRKKQLNGLELIL	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	141 (137)
Sequences:	257 (176)
Seq/Len:	1.876
Nf(neff/√len):	15.0

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: 1.876).

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
77_F	89_P	1.830	0.97
23_L	26_K	1.796	0.97
1_Y	9_E	1.612	0.94
89_P	133_Q	1.579	0.93
126_W	129_W	1.542	0.92
65_E	68_R	1.519	0.91
115_K	126_W	1.506	0.90
41_R	100_S	1.504	0.90
132_K	136_G	1.461	0.88
1_Y	112_Q	1.379	0.84
84_I	104_K	1.378	0.84
12_V	71_N	1.330	0.81
64_K	136_G	1.308	0.80
119_K	136_G	1.295	0.79
62_R	111_L	1.294	0.79
122_A	125_E	1.265	0.76
82_T	137_L	1.243	0.75
56_L	90_P	1.242	0.75
11_G	19_L	1.230	0.74
123_A	133_Q	1.222	0.73
51_I	125_E	1.219	0.73
36_L	46_L	1.211	0.72
82_T	98_S	1.199	0.71
15_L	18_K	1.198	0.71
82_T	93_L	1.178	0.69
3_L	118_S	1.172	0.68
107_M	111_L	1.169	0.68
70_I	93_L	1.164	0.68
7_I	121_E	1.162	0.67
65_E	129_W	1.156	0.67
100_S	135_N	1.151	0.66
19_L	55_I	1.150	0.66
1_Y	110_Q	1.146	0.66
67_W	110_Q	1.144	0.66
96_Y	134_L	1.144	0.66
31_L	64_K	1.143	0.66
2_T	85_D	1.131	0.64
26_K	118_S	1.130	0.64
69_S	133_Q	1.130	0.64
5_E	104_K	1.125	0.64
110_Q	122_A	1.125	0.64
13_G	64_K	1.116	0.63
5_E	116_G	1.114	0.63
94_Q	97_F	1.107	0.62
132_K	139_L	1.100	0.61
24_D	74_K	1.098	0.61
62_R	129_W	1.097	0.61
49_Y	114_V	1.090	0.60
91_L	122_A	1.084	0.60
90_P	96_Y	1.081	0.59
114_V	136_G	1.079	0.59
43_D	102_K	1.078	0.59
2_T	6_F	1.076	0.59
13_G	42_I	1.073	0.58
32_N	118_S	1.071	0.58
77_F	112_Q	1.068	0.58
56_L	79_D	1.067	0.58
120_L	130_R	1.066	0.58
84_I	121_E	1.066	0.58
8_D	11_G	1.065	0.57
101_E	118_S	1.065	0.57
13_G	81_E	1.064	0.57
65_E	130_R	1.063	0.57
22_D	26_K	1.055	0.56
52_D	77_F	1.054	0.56
16_D	45_V	1.048	0.56
1_Y	23_L	1.045	0.55
68_R	118_S	1.043	0.55
66_L	126_W	1.039	0.55
3_L	6_F	1.033	0.54
71_N	137_L	1.031	0.54
65_E	80_F	1.027	0.53
56_L	129_W	1.027	0.53
17_T	119_K	1.026	0.53
66_L	111_L	1.024	0.53
28_N	34_L	1.024	0.53
66_L	129_W	1.022	0.53
66_L	123_A	1.020	0.53
4_R	31_L	1.016	0.52
100_S	139_L	1.016	0.52
7_I	113_L	1.013	0.52
9_E	97_F	1.013	0.52
11_G	95_E	1.010	0.52
24_D	93_L	1.009	0.51
78_K	128_E	1.004	0.51

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
2ve7C	2	0.8652	8.9	0.93	Contact Map
3nfqA	2	0.4326	7.9	0.931	Contact Map
3fhnA	4	0.922	7	0.933	Contact Map
4ociA	1	0.617	6.6	0.934	Contact Map
4d1eA	1	0.5674	5.7	0.936	Contact Map
3d5aX	1	0.4326	5.1	0.937	Contact Map
4jo7E	4	0.5603	4	0.94	Contact Map
3ghgA	4	0.8652	3.8	0.941	Contact Map
1gl2D	1	0.3901	3.7	0.941	Contact Map
3q5iA	1	0.5957	3.5	0.942	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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