OPENSEQ.org - 1447340508 - GREMLIN Submission

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ID:	1447340508	Query Sequence GQLAGGVAHDFNNLLTAIQLRLDELLHRHPVGDPSYEGLNEIRQTGVRAADLVRKLLAFSRKQTVQREVLDLGELISEFEVLLRRLLREDVKLITDYGRDLPQVRADKSQLETAVMNLAVNARDAVRAAKGGGVVRIRTARLTRDEAIQLGFPAADGDTAFIEVSDDGPGIPPDVMGKIFDPFFTTKPVGEGTGLGLATVYGIVKQSDGWIHVHSRPNEGAAFRIFLPVYEAPAGAVAVQ	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	240 (221)
Sequences:	90365 (68825.7)
Seq/Len:	408.891
Nf(neff/√len):	4629.7

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: 408.891).

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
165_S	222_A	3.025	1.00
212_H	224_R	2.938	1.00
70_L	106_A	2.791	1.00
159_T	226_F	2.789	1.00
166_D	170_G	2.739	1.00
201_Y	205_K	2.603	1.00
163_E	222_A	2.585	1.00
163_E	224_R	2.412	1.00
126_V	167_D	2.390	1.00
161_F	224_R	2.346	1.00
106_A	207_S	2.323	1.00
161_F	226_F	2.283	1.00
138_R	163_E	2.191	1.00
176_M	215_S	2.180	1.00
172_P	175_V	2.152	1.00
19_Q	47_V	2.076	1.00
216_R	219_E	1.974	1.00
214_H	224_R	1.970	1.00
22_L	42_I	1.938	1.00
69_V	105_R	1.930	1.00
114_A	204_V	1.924	1.00
19_Q	46_G	1.910	1.00
213_V	223_F	1.909	1.00
214_H	222_A	1.907	1.00
178_K	184_F	1.883	1.00
134_V	167_D	1.877	1.00
200_V	211_I	1.861	1.00
176_M	213_V	1.845	1.00
204_V	209_G	1.841	1.00
136_R	165_S	1.833	1.00
180_F	211_I	1.795	1.00
140_A	161_F	1.776	1.00
173_P	176_M	1.768	1.00
210_W	226_F	1.766	1.00
171_I	179_I	1.734	1.00
175_V	178_K	1.713	1.00
120_V	124_D	1.693	1.00
94_I	136_R	1.692	1.00
138_R	165_S	1.687	1.00
140_A	163_E	1.678	1.00
71_D	74_E	1.678	1.00
153_P	229_V	1.678	1.00
178_K	181_D	1.655	1.00
50_A	54_R	1.653	1.00
78_E	112_E	1.644	1.00
19_Q	50_A	1.639	1.00
69_V	103_Q	1.627	1.00
212_H	226_F	1.621	1.00
114_A	200_V	1.570	1.00
96_D	138_R	1.566	1.00
94_I	134_V	1.559	1.00
175_V	184_F	1.555	1.00
18_I	46_G	1.536	1.00
171_I	175_V	1.525	1.00
204_V	225_I	1.511	1.00
106_A	111_L	1.475	1.00
215_S	221_A	1.470	1.00
114_A	203_I	1.468	1.00
175_V	186_T	1.409	1.00
133_G	167_D	1.394	0.99
171_I	221_A	1.393	0.99
43_R	47_V	1.388	0.99
205_K	210_W	1.368	0.99
107_D	110_Q	1.362	0.99
10_D	113_T	1.327	0.99
96_D	136_R	1.326	0.99
172_P	217_P	1.314	0.99
92_K	134_V	1.313	0.99
126_V	133_G	1.301	0.99
181_D	184_F	1.290	0.99
115_V	162_I	1.289	0.99
110_Q	206_Q	1.286	0.99
203_I	207_S	1.282	0.99
73_G	77_S	1.272	0.99
83_L	116_M	1.269	0.99
110_Q	113_T	1.255	0.99
26_L	43_R	1.254	0.99
22_L	43_R	1.253	0.99
19_Q	43_R	1.247	0.99
68_E	108_K	1.247	0.99
160_A	229_V	1.236	0.98
12_N	54_R	1.228	0.98
180_F	213_V	1.224	0.98
17_A	21_R	1.200	0.98
17_A	45_T	1.195	0.98
67_R	105_R	1.192	0.98
108_K	112_E	1.180	0.98
23_D	43_R	1.174	0.98
154_A	161_F	1.158	0.97
117_N	200_V	1.141	0.97
6_G	182_P	1.136	0.97
21_R	38_G	1.130	0.97
126_V	135_V	1.127	0.97
159_T	210_W	1.126	0.97
73_G	139_T	1.121	0.97
162_I	225_I	1.117	0.96
209_G	227_L	1.108	0.96
71_D	103_Q	1.105	0.96
179_I	213_V	1.102	0.96
26_L	40_N	1.091	0.96
170_G	221_A	1.080	0.95
21_R	41_E	1.078	0.95
45_T	48_R	1.077	0.95
51_D	109_S	1.076	0.95
78_E	108_K	1.072	0.95
166_D	221_A	1.064	0.95
215_S	219_E	1.042	0.94
209_G	225_I	1.042	0.94
202_G	205_K	1.041	0.94
204_V	211_I	1.039	0.94
136_R	167_D	1.023	0.93
111_L	207_S	1.021	0.93
215_S	218_N	1.020	0.93
110_Q	203_I	1.013	0.93
202_G	206_Q	1.011	0.93

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
4i5sA	2	0.8583	100	0.093	Contact Map
3jz3A	2	0.6542	100	0.109	Contact Map
3a0rA	1	0.8625	100	0.112	Contact Map
3d36A	2	0.875	100	0.113	Contact Map
4gczA	2	0.925	100	0.113	Contact Map
4q20A	2	0.875	100	0.123	Contact Map
4mpcA	1	0.875	100	0.132	Contact Map
4e01A	1	0.8875	100	0.14	Contact Map
2q8gA	1	0.8875	100	0.141	Contact Map
4bixA	2	0.8542	100	0.151	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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