OPENSEQ.org - 1453971206 - GREMLIN Submission

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1fcy

ID:	1453971206	Query Sequence ASPQLEELITKVSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERAITLKMEIPGPMPPLIREMLE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	236 (221)
Sequences:	2121 (1238.1)
Seq/Len:	9.597
Nf(neff/√len):	83.3

HHblits Results: (2015_06)
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: 9.597).

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
143_D	183_Y	2.671	1.00
230_L	233_E	2.350	1.00
165_E	168_K	1.968	1.00
70_F	73_L	1.802	1.00
70_F	78_Q	1.690	1.00
146_E	194_M	1.611	1.00
77_D	163_L	1.605	1.00
142_M	146_E	1.528	1.00
14_K	18_E	1.518	1.00
16_H	19_T	1.517	1.00
65_K	78_Q	1.489	1.00
23_L	26_L	1.450	1.00
210_T	214_E	1.431	1.00
9_I	15_A	1.408	0.99
12_V	15_A	1.391	0.99
64_A	70_F	1.391	0.99
211_K	215_R	1.387	0.99
18_E	21_P	1.382	0.99
199_L	203_T	1.382	0.99
61_V	65_K	1.364	0.99
17_Q	20_F	1.360	0.99
200_M	203_T	1.350	0.99
14_K	17_Q	1.349	0.99
57_I	63_F	1.343	0.99
79_I	83_K	1.333	0.99
150_L	153_I	1.332	0.99
35_A	38_R	1.332	0.99
14_K	19_T	1.328	0.99
142_M	198_M	1.328	0.99
36_D	39_V	1.324	0.99
65_K	70_F	1.310	0.99
9_I	16_H	1.302	0.99
15_A	18_E	1.283	0.99
129_L	132_A	1.278	0.99
21_P	26_L	1.277	0.99
12_V	16_H	1.272	0.99
35_A	39_V	1.265	0.99
9_I	17_Q	1.262	0.99
22_S	25_Q	1.258	0.98
7_E	10_T	1.257	0.98
7_E	14_K	1.237	0.98
184_A	194_M	1.235	0.98
17_Q	23_L	1.229	0.98
57_I	86_C	1.229	0.98
88_D	206_R	1.227	0.98
13_S	17_Q	1.217	0.98
10_T	13_S	1.212	0.98
10_T	19_T	1.212	0.98
12_V	22_S	1.210	0.98
9_I	13_S	1.207	0.98
145_T	183_Y	1.206	0.98
9_I	22_S	1.206	0.98
218_T	222_E	1.206	0.98
7_E	17_Q	1.204	0.98
10_T	18_E	1.203	0.98
22_S	26_L	1.192	0.98
18_E	25_Q	1.188	0.98
13_S	18_E	1.183	0.97
127_T	148_G	1.179	0.97
14_K	21_P	1.179	0.97
169_V	173_Q	1.173	0.97
11_K	15_A	1.169	0.97
11_K	17_Q	1.164	0.97
10_T	35_A	1.158	0.97
9_I	12_V	1.158	0.97
10_T	14_K	1.154	0.97
16_H	22_S	1.150	0.97
78_Q	81_L	1.137	0.97
21_P	39_V	1.134	0.97
20_F	23_L	1.131	0.96
21_P	25_Q	1.127	0.96
10_T	21_P	1.119	0.96
8_L	16_H	1.110	0.96
65_K	75_I	1.110	0.96
73_L	77_D	1.105	0.96
12_V	17_Q	1.105	0.96
196_P	200_M	1.091	0.95
23_L	39_V	1.090	0.95
77_D	81_L	1.088	0.95
11_K	38_R	1.088	0.95
180_L	195_F	1.087	0.95
13_S	16_H	1.084	0.95
163_L	169_V	1.083	0.95
11_K	22_S	1.083	0.95
17_Q	21_P	1.082	0.95
18_E	26_L	1.080	0.95
12_V	18_E	1.070	0.95
15_A	19_T	1.069	0.95
19_T	22_S	1.068	0.95
10_T	17_Q	1.064	0.95
17_Q	24_C	1.060	0.94
11_K	20_F	1.059	0.94
25_Q	40_Q	1.058	0.94
10_T	20_F	1.057	0.94
11_K	18_E	1.055	0.94
15_A	20_F	1.054	0.94
63_F	98_Y	1.051	0.94
13_S	19_T	1.049	0.94
11_K	14_K	1.047	0.94
93_R	151_S	1.047	0.94
36_D	40_Q	1.045	0.94
10_T	16_H	1.041	0.94
18_E	22_S	1.038	0.94
201_K	204_D	1.035	0.93
20_F	25_Q	1.035	0.93
77_D	169_V	1.032	0.93
10_T	39_V	1.032	0.93
229_P	233_E	1.032	0.93
38_R	41_L	1.030	0.93
7_E	13_S	1.027	0.93
70_F	77_D	1.027	0.93
21_P	24_C	1.026	0.93
8_L	19_T	1.026	0.93
217_I	222_E	1.025	0.93
199_L	206_R	1.025	0.93
10_T	36_D	1.024	0.93
23_L	38_R	1.021	0.93
78_Q	82_L	1.019	0.93
17_Q	25_Q	1.017	0.93
13_S	20_F	1.017	0.93
21_P	38_R	1.013	0.92
7_E	23_L	1.012	0.92
7_E	18_E	1.012	0.92
24_C	35_A	1.011	0.92
114_N	117_Q	1.011	0.92
35_A	40_Q	1.009	0.92
8_L	17_Q	1.007	0.92
160_R	164_E	1.007	0.92
17_Q	22_S	1.001	0.92

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
1fcyA	1	1	100	0.151	Contact Map
3kmrA	1	0.9915	100	0.16	Contact Map
1xdkB	2	0.9915	100	0.17	Contact Map
3ilzA	1	0.9831	100	0.185	Contact Map
1n83A	1	0.9873	100	0.187	Contact Map
1nq7A	1	0.9915	100	0.195	Contact Map
4wlbA	2	0.9831	100	0.203	Contact Map
4ymqA	1	0	100	0.203	Contact Map
3b0tA	1	1	100	0.211	Contact Map
2o4jA	1	0.9661	100	0.211	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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