OPENSEQ.org - 1490017029 - GREMLIN Submission

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1uak

ID:	1490017029	Query Sequence SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNSLE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	250 (243)
Sequences:	4665 (2611)
Seq/Len:	19.198
Nf(neff/√len):	167.5

Jackhmmer Results: (2016_04)
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: 19.198).

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
202_H	205_E	4.213	1.00
213_Q	216_Q	3.931	1.00
188_V	193_T	3.626	1.00
67_Q	71_D	3.090	1.00
122_E	126_Q	3.090	1.00
96_L	101_V	2.907	1.00
74_H	190_E	2.843	1.00
43_F	75_T	2.821	1.00
45_F	71_D	2.781	1.00
205_E	208_K	2.764	1.00
127_T	192_L	2.672	1.00
89_L	112_L	2.475	1.00
39_N	42_D	2.452	1.00
85_K	107_N	2.448	1.00
8_I	40_P	2.426	1.00
135_I	149_T	2.409	1.00
33_L	155_A	2.336	1.00
100_G	103_E	2.334	1.00
100_G	131_E	2.273	1.00
145_L	149_T	2.262	1.00
16_K	20_E	2.253	1.00
7_V	151_I	2.249	1.00
100_G	133_W	2.237	1.00
211_L	235_Q	2.234	1.00
85_K	131_E	2.221	1.00
96_L	153_A	2.174	1.00
204_E	207_R	2.146	1.00
94_R	131_E	2.119	1.00
94_R	100_G	2.082	1.00
138_Y	149_T	2.061	1.00
6_G	38_W	2.038	1.00
188_V	191_G	1.978	1.00
70_R	189_L	1.959	1.00
25_G	29_K	1.885	1.00
216_Q	220_L	1.847	1.00
46_D	50_T	1.815	1.00
4_W	34_K	1.800	1.00
193_T	196_P	1.794	1.00
141_T	152_D	1.782	1.00
101_V	153_A	1.738	1.00
73_I	128_E	1.732	1.00
6_G	109_K	1.731	1.00
96_L	150_L	1.720	1.00
92_Q	217_R	1.718	1.00
212_K	241_E	1.717	1.00
150_L	154_V	1.714	1.00
70_R	128_E	1.704	1.00
13_E	21_F	1.698	1.00
151_I	155_A	1.694	1.00
103_E	131_E	1.663	1.00
226_L	229_L	1.639	1.00
6_G	36_E	1.628	1.00
56_Y	187_E	1.575	1.00
70_R	190_E	1.550	1.00
98_Q	157_F	1.549	1.00
54_R	185_R	1.532	1.00
99_G	102_T	1.524	1.00
187_E	193_T	1.520	1.00
15_F	148_M	1.510	1.00
204_E	208_K	1.508	1.00
112_L	150_L	1.499	1.00
50_T	65_M	1.493	1.00
135_I	138_Y	1.482	1.00
132_E	221_R	1.480	1.00
13_E	16_K	1.479	1.00
38_W	43_F	1.475	1.00
97_D	100_G	1.472	1.00
89_L	150_L	1.471	1.00
162_L	168_A	1.464	1.00
102_T	174_A	1.461	1.00
126_Q	192_L	1.451	1.00
40_P	64_M	1.417	1.00
94_R	97_D	1.412	1.00
217_R	221_R	1.397	0.99
55_P	63_L	1.395	0.99
70_R	74_H	1.369	0.99
83_G	108_Q	1.369	0.99
168_A	171_D	1.358	0.99
56_Y	194_V	1.330	0.99
181_P	213_Q	1.315	0.99
88_Y	120_I	1.305	0.99
84_A	111_I	1.281	0.99
229_L	235_Q	1.277	0.99
4_W	36_E	1.264	0.99
88_Y	113_V	1.261	0.99
18_I	148_M	1.256	0.99
179_D	182_H	1.211	0.98
166_A	169_E	1.178	0.98
46_D	65_M	1.174	0.98
13_E	39_N	1.166	0.97
133_W	150_L	1.160	0.97
216_Q	242_A	1.133	0.97
211_L	229_L	1.130	0.97
23_V	26_R	1.124	0.97
112_L	147_A	1.122	0.97
5_I	151_I	1.122	0.97
69_L	113_V	1.115	0.96
6_G	111_I	1.105	0.96
212_K	245_E	1.104	0.96
5_I	33_L	1.101	0.96
20_E	28_V	1.092	0.96
74_H	128_E	1.086	0.96
32_L	161_V	1.082	0.96
208_K	212_K	1.074	0.95
88_Y	125_I	1.068	0.95
90_S	132_E	1.064	0.95
64_M	120_I	1.063	0.95
42_D	49_K	1.062	0.95
211_L	215_L	1.050	0.94
86_V	130_D	1.049	0.94
212_K	238_L	1.048	0.94
95_K	137_D	1.044	0.94
66_V	70_R	1.033	0.94
120_I	124_L	1.032	0.94
187_E	199_M	1.022	0.93
238_L	242_A	1.022	0.93
104_L	133_W	1.021	0.93
219_W	226_L	1.017	0.93
122_E	125_I	1.011	0.93
173_F	225_L	1.008	0.93
5_I	155_A	1.006	0.93
69_L	124_L	1.004	0.93
38_W	76_A	1.004	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
4h3zA	2	0.992	100	0.027	Contact Map
3ky7A	1	0.912	100	0.029	Contact Map
4yvgA	1	0	100	0.034	Contact Map
1oy5A	3	0.872	100	0.042	Contact Map
3knuA	4	0.804	100	0.052	Contact Map
3iefA	2	0.896	100	0.053	Contact Map
3quvA	2	0.872	100	0.062	Contact Map
3aiaA	2	0.536	90.6	0.953	Contact Map
1to0A	8	0.576	88.4	0.955	Contact Map
4fakA	1	0.608	87.5	0.956	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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