OPENSEQ.org - 1490277902 - GREMLIN Submission

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ID:	1490277902	Query Sequence MDKCWFTLDNAHYPPPSLDSMRSGHPISPASLGHLIPSLAHLDQIINAKAIEPFPATMDIHGPTIIEDFKWDHSHEYSLSLGGKVPIPLAPAGVPFVDLNVGLGGAFSRSVANYWEFDRLERYIMQPTRSYVQKCIERDEVKRWIAKNKSMMMMGRWEVYMITGIIVARGGGRKKKEKTTGKEFSVEVTVEVPLIVEAGPGGKRNTARQKTWGTSQTGDFVWAVRLAKITKSGLHSDWKMETVFGKTSSFRGQKAIF	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	257 (238)
Sequences:	330 (298.3)
Seq/Len:	1.387
Nf(neff/√len):	19.3

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: 1.387).

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
122_R	166_I	4.037	1.00
39_L	226_L	2.617	1.00
35_L	161_M	2.194	0.99
171_G	220_F	2.013	0.98
169_R	219_D	1.997	0.98
3_K	6_F	1.900	0.97
39_L	42_L	1.802	0.95
167_V	219_D	1.755	0.94
36_I	226_L	1.740	0.94
4_C	7_T	1.705	0.93
102_G	167_V	1.696	0.92
130_S	140_E	1.638	0.91
158_E	228_K	1.598	0.89
115_W	222_W	1.590	0.89
6_F	223_A	1.521	0.86
63_P	221_V	1.518	0.85
35_L	229_I	1.511	0.85
68_D	215_S	1.508	0.85
82_G	200_P	1.484	0.84
189_T	221_V	1.480	0.83
164_G	225_R	1.458	0.82
168_A	224_V	1.436	0.81
5_W	166_I	1.428	0.80
16_P	28_S	1.406	0.79
39_L	160_Y	1.398	0.78
103_L	138_R	1.396	0.78
159_V	171_G	1.386	0.78
63_P	68_D	1.374	0.77
98_D	175_K	1.369	0.76
32_L	125_M	1.357	0.75
42_L	47_N	1.345	0.75
118_D	172_G	1.329	0.73
136_I	222_W	1.321	0.73
7_T	36_I	1.300	0.71
135_C	161_M	1.289	0.70
5_W	124_I	1.281	0.69
6_F	36_I	1.279	0.69
45_I	163_T	1.273	0.69
157_W	222_W	1.273	0.69
5_W	9_D	1.254	0.67
46_I	127_P	1.241	0.66
146_A	160_Y	1.240	0.66
8_L	158_E	1.237	0.65
6_F	12_H	1.235	0.65
34_H	219_D	1.225	0.64
121_E	169_R	1.222	0.64
120_L	163_T	1.221	0.64
190_V	236_S	1.218	0.64
72_D	194_L	1.218	0.64
131_Y	135_C	1.212	0.63
66_I	217_T	1.210	0.63
3_K	223_A	1.208	0.63
5_W	122_R	1.208	0.63
85_V	89_L	1.198	0.62
123_Y	145_I	1.186	0.61
8_L	11_A	1.186	0.61
32_L	109_R	1.176	0.60
165_I	221_V	1.176	0.60
188_V	200_P	1.167	0.59
193_P	206_T	1.155	0.58
32_L	122_R	1.151	0.57
100_N	237_D	1.134	0.55
34_H	135_C	1.122	0.54
32_L	86_P	1.114	0.53
101_V	193_P	1.114	0.53
8_L	30_A	1.111	0.53
249_S	254_K	1.095	0.52
56_A	229_I	1.094	0.51
101_V	239_K	1.093	0.51
170_G	221_V	1.089	0.51
35_L	135_C	1.081	0.50
144_W	195_I	1.078	0.50
15_P	132_V	1.078	0.50
52_E	105_G	1.077	0.50
163_T	228_K	1.075	0.49
131_Y	164_G	1.074	0.49
220_F	225_R	1.073	0.49
140_E	172_G	1.068	0.49
200_P	246_K	1.065	0.48
71_W	219_D	1.061	0.48
43_D	242_T	1.056	0.48
124_I	187_E	1.055	0.47
42_L	224_V	1.055	0.47
11_A	34_H	1.054	0.47
184_F	205_N	1.054	0.47
34_H	51_I	1.053	0.47
245_G	250_F	1.051	0.47
184_F	194_L	1.050	0.47
168_A	219_D	1.050	0.47
74_S	209_Q	1.049	0.47
28_S	165_I	1.044	0.46
30_A	226_L	1.044	0.46
251_R	254_K	1.043	0.46
108_S	172_G	1.042	0.46
86_P	89_L	1.040	0.46
48_A	162_I	1.038	0.46
69_F	193_P	1.037	0.46
161_M	241_E	1.035	0.45
167_V	216_Q	1.034	0.45
28_S	45_I	1.032	0.45
64_T	121_E	1.031	0.45
101_V	147_K	1.030	0.45
82_G	201_G	1.030	0.45
42_L	88_P	1.030	0.45
201_G	211_T	1.029	0.45
213_G	217_T	1.027	0.45
81_L	186_V	1.026	0.45
170_G	229_I	1.020	0.44
160_Y	250_F	1.019	0.44
205_N	221_V	1.017	0.44
35_L	162_I	1.013	0.43
13_Y	70_K	1.010	0.43
32_L	90_A	1.009	0.43
142_K	146_A	1.002	0.42
82_G	132_V	1.002	0.42
72_D	172_G	1.000	0.42

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
2f1eA	1	0.2335	3.7	0.964	Contact Map
1tzaA	2	0.2451	3.2	0.965	Contact Map
4v06A	2	0.2957	2.8	0.966	Contact Map
1xq4A	4	0.2451	2.7	0.967	Contact Map
1xvsA	2	0.249	2.7	0.967	Contact Map
4jrfA	1	0.2802	2.6	0.967	Contact Map
3tk2A	1	0.1829	2.2	0.968	Contact Map
4afkA	1	0.2451	2.1	0.968	Contact Map
2e2cA	1	0.2529	1.7	0.97	Contact Map
1tteA	1	0.4514	1.6	0.971	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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