OPENSEQ.org - 1445535775 - GREMLIN Submission

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1152d1

ID:	1445535775	Query Sequence SMQQDIVNDHQEEAQGWKWEQIKEIIESGELARLKRSRQMTDKYHEHKKRTAGLDMNQYVLQKLGWSLDEPQLENAAAKAFSSSTLYAVRANDFPYNFEPGVVHLVLWSKVALPVHSPDKAVREAARARMNAFLQAQPLLRPLLSSGHVAWFVNYPELQSVARIFHAHVLLFFPRERYSAEQVKTTVDDILSHGFEPLA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	199 (176)
Sequences:	310 (245.4)
Seq/Len:	1.761
Nf(neff/√len):	18.5

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: 1.761).

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
128_A	132_A	2.707	1.00
87_Y	133_F	2.245	1.00
154_N	158_L	2.156	0.99
141_R	181_E	2.025	0.99
10_H	13_E	1.883	0.98
89_V	137_Q	1.817	0.97
66_W	110_K	1.741	0.96
166_H	169_V	1.696	0.95
175_R	178_Y	1.683	0.95
11_Q	39_Q	1.669	0.94
20_E	23_K	1.652	0.94
99_E	175_R	1.615	0.93
121_A	127_R	1.584	0.92
14_A	56_M	1.569	0.92
176_E	184_K	1.526	0.90
12_E	20_E	1.475	0.88
152_F	158_L	1.463	0.87
63_K	94_F	1.443	0.86
122_V	130_M	1.442	0.86
101_G	173_F	1.431	0.86
18_K	25_I	1.398	0.84
62_Q	65_G	1.398	0.84
177_R	182_Q	1.398	0.84
54_L	94_F	1.395	0.84
20_E	89_V	1.357	0.82
98_F	170_L	1.348	0.81
40_M	43_K	1.327	0.79
101_G	172_F	1.326	0.79
46_E	50_R	1.326	0.79
63_K	90_R	1.312	0.78
18_K	28_S	1.303	0.78
154_N	160_S	1.282	0.76
35_K	159_Q	1.269	0.75
38_R	97_N	1.259	0.74
81_F	133_F	1.244	0.73
60_V	88_A	1.223	0.71
41_T	54_L	1.222	0.71
131_N	136_A	1.214	0.70
159_Q	162_A	1.198	0.69
113_L	124_E	1.193	0.68
100_P	106_V	1.186	0.68
18_K	37_S	1.179	0.67
23_K	78_A	1.176	0.67
31_L	158_L	1.163	0.66
37_S	40_M	1.157	0.65
160_S	168_H	1.151	0.64
47_H	51_T	1.145	0.64
22_I	159_Q	1.140	0.63
152_F	160_S	1.135	0.63
43_K	97_N	1.133	0.63
112_A	156_P	1.132	0.63
34_L	159_Q	1.130	0.62
134_L	149_V	1.123	0.62
68_L	113_L	1.109	0.60
151_W	154_N	1.108	0.60
60_V	164_I	1.108	0.60
122_V	139_L	1.102	0.59
48_K	94_F	1.100	0.59
29_G	155_Y	1.100	0.59
15_Q	61_L	1.100	0.59
69_D	134_L	1.091	0.58
80_A	86_L	1.091	0.58
124_E	128_A	1.082	0.57
89_V	109_S	1.079	0.57
29_G	121_A	1.077	0.57
22_I	26_I	1.074	0.57
56_M	61_L	1.074	0.57
123_R	181_E	1.072	0.56
138_P	153_V	1.068	0.56
30_E	33_R	1.067	0.56
31_L	159_Q	1.066	0.56
123_R	153_V	1.052	0.54
99_E	148_H	1.051	0.54
174_P	178_Y	1.051	0.54
96_Y	104_H	1.049	0.54
34_L	163_R	1.044	0.53
120_K	125_A	1.043	0.53
131_N	135_Q	1.035	0.52
24_E	50_R	1.030	0.52
155_Y	158_L	1.028	0.52
89_V	107_L	1.019	0.51
178_Y	181_E	1.019	0.51
126_A	129_R	1.018	0.51
147_G	173_F	1.017	0.50
99_E	124_E	1.016	0.50
22_I	34_L	1.014	0.50
45_H	131_N	1.004	0.49
63_K	122_V	1.002	0.49

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
2eo4A	1	0.603	51.3	0.946	Contact Map
3r6fA	1	0.598	47.9	0.947	Contact Map
3imiA	4	0.6382	46.9	0.947	Contact Map
3o0mA	2	0.5879	34.2	0.951	Contact Map
1y23A	5	0.6231	23.5	0.955	Contact Map
4ndhA	2	0.6482	16.6	0.958	Contact Map
4xbaA	2	0	13.1	0.96	Contact Map
1fitA	1	0.5578	12.9	0.96	Contact Map
3i24A	2	0.5829	11.8	0.961	Contact Map
3oj7A	1	0.5276	9.6	0.962	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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