OPENSEQ.org - 1473079569 - GREMLIN Submission

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1thf

ID:	1473079569	Query Sequence MLAKRIIACLDVKDGRVVKGSNFENLRDSGDPVELGKFYSEIGIDELVFLDITASVEKRKTMLELVEKVAEQIDIPFTVGGGIHDFETASELILRGADKVSINTAAVENPSLITQIAQTFGSQAVVVAIDAKRVDGEFMVFTYSGKKNTGILLRDWVVEVEKRGAGEILLTSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAFLAGADAALAASVFHFREIDVRELKEYLKKHGVNVRLEGL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	253 (229)
Sequences:	2918 (1650.5)
Seq/Len:	12.742
Nf(neff/√len):	109.1

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: 12.742).

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
89_A	116_I	3.395	1.00
109_N	115_Q	2.806	1.00
161_E	196_L	2.763	1.00
129_I	157_V	2.694	1.00
143_Y	147_K	2.540	1.00
85_D	88_T	2.485	1.00
37_K	41_E	2.352	1.00
127_V	160_V	2.351	1.00
159_E	163_R	2.310	1.00
114_T	163_R	2.299	1.00
208_E	211_L	2.278	1.00
18_V	178_T	2.127	1.00
37_K	72_Q	2.083	1.00
108_E	143_Y	2.082	1.00
89_A	125_V	2.059	1.00
139_M	148_N	2.029	1.00
83_I	92_L	2.019	1.00
90_S	94_L	2.005	1.00
116_I	125_V	2.002	1.00
38_F	42_I	1.885	1.00
31_D	34_E	1.880	1.00
128_A	169_L	1.869	1.00
139_M	152_L	1.854	1.00
139_M	150_G	1.846	1.00
99_K	126_V	1.837	1.00
179_K	231_E	1.831	1.00
40_S	74_D	1.813	1.00
31_D	68_K	1.813	1.00
208_E	212_E	1.798	1.00
86_F	116_I	1.792	1.00
90_S	119_T	1.770	1.00
223_A	226_V	1.725	1.00
207_M	232_I	1.719	1.00
47_L	75_I	1.705	1.00
170_L	186_M	1.703	1.00
161_E	195_T	1.698	1.00
204_A	213_A	1.657	1.00
226_V	232_I	1.650	1.00
13_K	28_D	1.636	1.00
107_V	142_T	1.630	1.00
223_A	227_F	1.626	1.00
159_E	162_K	1.618	1.00
206_K	209_H	1.594	1.00
46_E	99_K	1.571	1.00
11_D	53_T	1.570	1.00
64_E	67_E	1.560	1.00
63_L	91_E	1.542	1.00
4_K	46_E	1.528	1.00
105_A	112_L	1.526	1.00
111_S	115_Q	1.522	1.00
102_I	105_A	1.518	1.00
158_V	193_L	1.514	1.00
141_F	148_N	1.495	1.00
213_A	218_A	1.473	1.00
152_L	155_D	1.471	1.00
104_T	108_E	1.436	1.00
151_I	159_E	1.427	1.00
56_V	146_K	1.419	1.00
89_A	100_V	1.406	0.99
128_A	171_T	1.404	0.99
22_N	56_V	1.400	0.99
131_A	170_L	1.394	0.99
62_M	65_L	1.388	0.99
93_I	124_A	1.379	0.99
21_S	24_E	1.378	0.99
67_E	71_E	1.371	0.99
172_S	183_D	1.362	0.99
170_L	190_V	1.345	0.99
68_K	71_E	1.344	0.99
188_R	192_P	1.332	0.99
66_V	79_V	1.331	0.99
5_R	44_I	1.331	0.99
210_F	226_V	1.328	0.99
214_F	221_A	1.324	0.99
191_R	198_I	1.316	0.99
142_T	147_K	1.300	0.99
184_T	212_E	1.276	0.99
166_G	197_P	1.255	0.99
70_A	77_F	1.251	0.99
189_F	193_L	1.249	0.99
114_T	118_Q	1.238	0.98
108_E	142_T	1.227	0.98
55_S	104_T	1.221	0.98
169_L	222_L	1.218	0.98
49_F	69_V	1.216	0.98
33_V	65_L	1.188	0.98
153_L	157_V	1.187	0.98
2_L	46_E	1.186	0.98
111_S	114_T	1.185	0.98
13_K	30_G	1.181	0.98
42_I	233_D	1.176	0.98
187_I	191_R	1.166	0.97
87_E	90_S	1.164	0.97
157_V	190_V	1.147	0.97
86_F	115_Q	1.139	0.97
153_L	190_V	1.135	0.97
108_E	147_K	1.130	0.97
190_V	198_I	1.115	0.96
210_F	223_A	1.113	0.96
19_K	178_T	1.101	0.96
107_V	151_I	1.098	0.96
126_V	169_L	1.090	0.96
54_A	61_T	1.088	0.96
67_E	95_R	1.082	0.96
184_T	188_R	1.080	0.95
29_S	35_L	1.076	0.95
66_V	97_A	1.073	0.95
157_V	194_T	1.067	0.95
161_E	194_T	1.066	0.95
213_A	221_A	1.060	0.95
182_Y	204_A	1.058	0.95
79_V	92_L	1.053	0.95
50_L	169_L	1.053	0.95
38_F	41_E	1.048	0.94
86_F	119_T	1.046	0.94
46_E	126_V	1.018	0.93
112_L	116_I	1.013	0.93
106_A	127_V	1.011	0.93
126_V	167_E	1.008	0.93
14_D	35_L	1.007	0.93
35_L	38_F	1.002	0.92
225_S	229_F	1.000	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
2agkA	1	0.8458	100	0.278	Contact Map
1jvnA	2	0.9447	100	0.285	Contact Map
1qo2A	2	0.9289	100	0.44	Contact Map
4gj1A	1	0.8893	100	0.46	Contact Map
1thfD	1	0.9881	100	0.475	Contact Map
2y88A	1	0.9289	100	0.495	Contact Map
4evzA	2	0.9881	100	0.501	Contact Map
2w6rA	1	0.8419	100	0.507	Contact Map
4u28A	1	0.9051	100	0.515	Contact Map
1h5yA	2	0.9763	100	0.516	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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