OPENSEQ.org - 1447330067 - GREMLIN Submission

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11 -force run

ID:	1447330067	Query Sequence GQLAGGVAHDFNNLLTAIQLRLDELLHRHPVGDPSYEGLNEIRQTGVRAADLVRKLLAFSRKQTVQREVLDLGELISEFEVLLRRLLREDVKLITDYGRDLPQVRADKSQLETAVMNLAVNARDAVRAAKGGGVVRIRTARLTRDEAIQLGFPAADGDTAFIEVSDDGPGIPPDVMGKIFDPFFTTKPVGEGTGLGLATVYGIVKQSDGWIHVHSRPNEGAAFRIFLPVYEAPAGAVAVQ	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	240 (211)
Sequences:	150 (48.1)
Seq/Len:	0.711
Nf(neff/√len):	3.3

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: 0.711).

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	3.204	1.00
165_S	217_P	2.632	0.99
31_V	204_V	1.952	0.90
164_V	174_D	1.809	0.85
22_L	102_P	1.728	0.81
111_L	213_V	1.682	0.79
104_V	171_I	1.642	0.77
171_I	199_T	1.635	0.76
72_L	104_V	1.600	0.74
186_T	200_V	1.569	0.72
128_A	167_D	1.554	0.71
126_V	167_D	1.546	0.70
70_L	104_V	1.542	0.70
118_L	164_V	1.534	0.69
5_G	63_Q	1.511	0.68
89_E	124_D	1.487	0.66
137_I	223_F	1.485	0.66
161_F	224_R	1.453	0.63
5_G	195_L	1.450	0.63
135_V	206_Q	1.444	0.63
13_N	187_K	1.413	0.60
217_P	222_A	1.411	0.60
176_M	187_K	1.377	0.57
154_A	177_G	1.377	0.57
124_D	167_D	1.368	0.56
72_L	82_L	1.355	0.55
89_E	92_K	1.345	0.55
20_L	200_V	1.334	0.54
66_Q	164_V	1.332	0.53
195_L	199_T	1.324	0.53
63_Q	225_I	1.322	0.53
164_V	206_Q	1.318	0.52
36_Y	179_I	1.315	0.52
13_N	19_Q	1.311	0.52
108_K	135_V	1.303	0.51
13_N	200_V	1.282	0.49
70_L	77_S	1.276	0.49
47_V	208_D	1.269	0.48
120_V	186_T	1.269	0.48
124_D	127_R	1.264	0.48
126_V	211_I	1.253	0.47
12_N	45_T	1.241	0.46
65_V	124_D	1.237	0.45
50_A	188_P	1.228	0.45
19_Q	176_M	1.222	0.44
173_P	215_S	1.219	0.44
39_L	60_S	1.211	0.43
90_D	110_Q	1.208	0.43
48_R	164_V	1.206	0.43
19_Q	200_V	1.206	0.43
47_V	70_L	1.204	0.43
115_V	225_I	1.200	0.42
42_I	63_Q	1.199	0.42
115_V	135_V	1.195	0.42
19_Q	187_K	1.189	0.41
94_I	171_I	1.182	0.41
19_Q	50_A	1.182	0.41
22_L	72_L	1.180	0.41
135_V	229_V	1.166	0.40
72_L	224_R	1.165	0.39
75_L	171_I	1.161	0.39
104_V	199_T	1.160	0.39
198_A	203_I	1.146	0.38
11_F	18_I	1.142	0.38
60_S	198_A	1.137	0.37
23_D	207_S	1.135	0.37
124_D	169_P	1.125	0.36
186_T	214_H	1.123	0.36
140_A	161_F	1.112	0.35
164_V	201_Y	1.107	0.35
47_V	68_E	1.105	0.35
72_L	102_P	1.101	0.34
160_A	171_I	1.097	0.34
233_P	236_A	1.095	0.34
13_N	20_L	1.094	0.34
153_P	177_G	1.092	0.34
42_I	195_L	1.088	0.33
38_G	135_V	1.087	0.33
40_N	225_I	1.075	0.32
71_D	211_I	1.063	0.32
13_N	123_R	1.063	0.32
30_P	187_K	1.059	0.31
30_P	186_T	1.058	0.31
206_Q	217_P	1.056	0.31
158_D	222_A	1.052	0.31
162_I	217_P	1.047	0.30
47_V	171_I	1.047	0.30
5_G	179_I	1.046	0.30
55_K	58_A	1.033	0.29
19_Q	123_R	1.026	0.29
119_A	174_D	1.023	0.29
64_T	137_I	1.019	0.28
12_N	46_G	1.014	0.28
123_R	187_K	1.012	0.28
4_A	160_A	1.009	0.28
13_N	50_A	1.008	0.28
48_R	211_I	1.006	0.28
140_A	224_R	1.004	0.27
54_R	99_R	1.004	0.27
70_L	171_I	1.003	0.27
60_S	207_S	1.003	0.27
5_G	42_I	1.000	0.27

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

See coupling matrix (for protein design or mutagenesis)
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	0.644	Contact Map
4bixA	2	0.8542	100	0.65	Contact Map
4gczA	2	0.925	100	0.65	Contact Map
3jz3A	2	0.65	100	0.655	Contact Map
4ctiA	4	0.7208	100	0.662	Contact Map
3a0rA	1	0.8542	100	0.663	Contact Map
4q20A	2	0.875	100	0.665	Contact Map
3d36A	2	0.875	100	0.666	Contact Map
4mpcA	1	0.8833	100	0.667	Contact Map
2q8gA	1	0.9	100	0.668	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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