OPENSEQ.org - 1491223302 - GREMLIN Submission

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Pa_5_3510

ID:	1491223302	Query Sequence MAKKTYILAPNFTTSPSSLRLGDILPDPLSPDLIPLNRKSRLPINPDDLLPPTTVTSFSSMRKDLLTGRFGLWTTLLAGLNLPMGADLGLFLERGSNDVIQVPELETGEFVATEEYIQRVSEQDDVKGYLTERKYRVPVYIVTGVKIARGASVSLERTLEVDARVGVSGPEGVAEVKPLLQIGRNRLQGVAFDTASEFVLAFQVRRIKFARGRMQHELSLKGTSMLGDEREDVQEWKVESVDDFVGEEDEVEVLEDSDGVQWAVAREFED	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	270 (231)
Sequences:	289 (261.9)
Seq/Len:	1.251
Nf(neff/√len):	17.2

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: 1.251).

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
107_T	146_K	3.293	1.00
28_P	204_V	2.960	1.00
6_Y	146_K	2.456	1.00
151_A	198_F	2.285	0.99
5_T	8_L	1.963	0.97
6_Y	107_T	1.910	0.96
6_Y	10_P	1.796	0.94
149_R	197_E	1.786	0.93
100_I	200_L	1.767	0.93
24_I	141_I	1.716	0.92
25_L	204_V	1.703	0.91
138_P	206_R	1.664	0.90
57_S	193_D	1.657	0.90
139_V	151_A	1.641	0.89
120_V	141_I	1.629	0.89
115_E	125_D	1.580	0.86
87_D	147_I	1.569	0.86
55_V	195_A	1.516	0.83
147_I	197_E	1.510	0.83
31_P	202_F	1.456	0.80
88_L	123_Q	1.431	0.78
9_A	23_D	1.404	0.76
13_T	146_K	1.399	0.76
71_G	179_L	1.366	0.73
7_I	201_A	1.357	0.73
21_L	110_F	1.354	0.72
137_V	200_L	1.349	0.72
28_P	31_P	1.345	0.72
8_L	76_L	1.336	0.71
76_L	100_I	1.331	0.70
143_T	206_R	1.314	0.69
28_P	140_Y	1.309	0.69
7_I	202_F	1.304	0.68
151_A	222_G	1.299	0.68
71_G	178_P	1.291	0.67
4_K	89_G	1.288	0.67
27_D	148_A	1.279	0.66
7_I	25_L	1.274	0.66
7_I	117_I	1.274	0.66
191_A	199_V	1.258	0.64
170_P	173_V	1.256	0.64
74_T	86_A	1.238	0.62
41_R	71_G	1.229	0.61
21_L	94_R	1.229	0.61
72_L	97_N	1.225	0.61
23_D	120_V	1.205	0.59
6_Y	11_N	1.198	0.59
89_G	199_V	1.193	0.58
6_Y	109_E	1.192	0.58
112_A	197_E	1.179	0.57
106_E	149_R	1.172	0.56
46_P	128_G	1.172	0.56
183_G	199_V	1.172	0.56
101_Q	152_S	1.165	0.55
147_I	185_N	1.162	0.55
12_F	23_D	1.151	0.54
206_R	217_E	1.142	0.53
63_K	187_L	1.139	0.53
25_L	223_T	1.138	0.53
122_E	191_A	1.138	0.53
105_L	148_A	1.131	0.52
6_Y	37_N	1.130	0.52
120_V	142_V	1.128	0.52
73_W	192_F	1.124	0.51
94_R	162_D	1.120	0.51
64_D	113_T	1.119	0.51
164_R	202_F	1.106	0.50
13_T	224_S	1.105	0.49
67_T	75_T	1.101	0.49
20_R	118_Q	1.099	0.49
106_E	179_L	1.094	0.48
19_L	78_A	1.092	0.48
17_S	202_F	1.088	0.48
140_Y	197_E	1.086	0.48
124_D	140_Y	1.086	0.48
110_F	223_T	1.083	0.47
6_Y	93_E	1.080	0.47
121_S	200_L	1.080	0.47
116_Y	120_V	1.078	0.47
114_E	118_Q	1.075	0.47
74_T	84_M	1.069	0.46
126_V	208_K	1.067	0.46
147_I	194_T	1.067	0.46
103_P	152_S	1.066	0.46
42_L	90_L	1.066	0.46
73_W	177_K	1.056	0.45
142_V	149_R	1.052	0.44
21_L	75_T	1.051	0.44
8_L	25_L	1.048	0.44
105_L	207_I	1.046	0.44
86_A	118_Q	1.044	0.44
19_L	49_L	1.044	0.44
37_N	141_I	1.043	0.43
141_I	217_E	1.043	0.43
24_I	231_E	1.040	0.43
36_L	137_V	1.039	0.43
35_P	136_R	1.039	0.43
44_I	110_F	1.036	0.43
140_Y	225_M	1.036	0.43
147_I	154_S	1.029	0.42
198_F	221_K	1.025	0.42
75_T	114_E	1.023	0.41
24_I	207_I	1.023	0.41
10_P	83_P	1.022	0.41
113_T	156_E	1.020	0.41
14_T	53_T	1.019	0.41
68_G	140_Y	1.019	0.41
73_W	207_I	1.017	0.41
76_L	199_V	1.015	0.41
86_A	167_V	1.013	0.41
146_K	219_S	1.009	0.40
24_I	142_V	1.009	0.40
28_P	203_Q	1.007	0.40
108_G	218_L	1.005	0.40
11_N	107_T	1.000	0.39
77_L	130_L	1.000	0.39

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
1rl2A	2	0.3704	3.6	0.972	Contact Map
4kxqB	1	0.0852	3.5	0.972	Contact Map
4rb6D	1	0.6222	3	0.973	Contact Map
3bboE	1	0.6222	2.7	0.974	Contact Map
2iu4A	2	0.2259	2.7	0.974	Contact Map
3tk2A	1	0.1704	2.6	0.974	Contact Map
1v54J	2	0.2037	2.5	0.974	Contact Map
2f1eA	1	0.3222	2.2	0.975	Contact Map
1tzaA	2	0.3296	2.2	0.975	Contact Map
4v06A	2	0.2852	2	0.975	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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