OPENSEQ.org - 1408540418 - GREMLIN Submission

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BubR1 -force run 1-200 -force run

ID:	1408540418	Query Sequence MAAVKKEGGALSEAMSLEGDEWELSKENVQPLRQGRIMSTLQGALAQESACNNTLQQQKRAFEYEIRFYTGNDPLDVWDRYISWTEQNYPQGGKESNMSTLLERAVEALQGEKRYYSDPRFLNLWLKLGRLCNEPLDMYSYLHNQGIGVSLAQFYISWAEEYEARENFRKADAIFQEGIQQKAEPLERLQSQHRQFQARV	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	200 (186)
Sequences:	175 (127.4)
Seq/Len:	0.941
Nf(neff/√len):	9.3

HHblits Results: (2013_03)
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: 0.941).

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
156_I	188_R	2.400	0.99
159_A	196_F	2.091	0.96
63_E	81_Y	1.983	0.95
32_L	36_R	1.905	0.93
163_E	199_R	1.882	0.92
63_E	151_L	1.846	0.91
177_E	181_Q	1.622	0.82
119_P	151_L	1.617	0.82
62_F	104_R	1.615	0.82
86_E	127_K	1.585	0.80
122_L	179_I	1.550	0.78
27_E	35_G	1.505	0.75
66_I	117_S	1.478	0.74
27_E	36_R	1.462	0.72
111_G	137_D	1.423	0.69
105_A	124_L	1.418	0.69
32_L	35_G	1.411	0.69
27_E	32_L	1.410	0.68
101_L	166_E	1.409	0.68
63_E	104_R	1.404	0.68
29_V	45_L	1.372	0.65
45_L	48_E	1.371	0.65
66_I	158_W	1.369	0.65
196_F	199_R	1.362	0.65
82_I	124_L	1.348	0.63
27_E	41_L	1.341	0.63
65_E	80_R	1.338	0.63
172_D	193_H	1.312	0.60
72_N	188_R	1.276	0.57
23_E	26_K	1.263	0.56
26_K	41_L	1.238	0.54
90_P	183_A	1.226	0.53
85_T	101_L	1.218	0.52
121_F	162_Y	1.212	0.51
70_T	152_A	1.209	0.51
30_Q	95_E	1.209	0.51
82_I	105_A	1.205	0.51
162_Y	167_N	1.205	0.51
135_P	163_E	1.199	0.50
106_V	175_F	1.199	0.50
148_G	171_A	1.198	0.50
23_E	27_E	1.192	0.49
22_W	129_G	1.190	0.49
76_D	80_R	1.189	0.49
129_G	151_L	1.187	0.49
31_P	92_G	1.183	0.49
22_W	157_S	1.177	0.48
22_W	29_V	1.176	0.48
22_W	25_S	1.176	0.48
117_S	139_Y	1.175	0.48
89_Y	96_S	1.175	0.48
84_W	96_S	1.159	0.46
26_K	32_L	1.156	0.46
197_Q	200_V	1.156	0.46
26_K	35_G	1.154	0.46
174_I	182_K	1.153	0.46
179_I	189_L	1.153	0.46
152_A	160_E	1.153	0.46
90_P	96_S	1.149	0.46
28_N	32_L	1.146	0.45
124_L	181_Q	1.146	0.45
78_W	158_W	1.146	0.45
192_Q	195_Q	1.143	0.45
85_T	166_E	1.142	0.45
73_D	120_R	1.135	0.44
189_L	196_F	1.126	0.43
121_F	125_W	1.124	0.43
133_N	170_K	1.120	0.43
125_W	155_Y	1.119	0.43
151_L	178_G	1.119	0.43
171_A	199_R	1.099	0.41
137_D	145_Q	1.099	0.41
99_S	138_M	1.097	0.41
28_N	35_G	1.093	0.41
92_G	96_S	1.093	0.41
151_L	188_R	1.092	0.40
28_N	41_L	1.083	0.40
117_S	151_L	1.083	0.40
72_N	156_I	1.076	0.39
109_L	121_F	1.072	0.39
153_Q	156_I	1.069	0.38
15_M	18_E	1.059	0.38
178_G	189_L	1.055	0.37
22_W	38_M	1.055	0.37
91_Q	96_S	1.054	0.37
119_P	129_G	1.052	0.37
35_G	41_L	1.050	0.37
142_L	159_A	1.045	0.36
66_I	138_M	1.043	0.36
122_L	125_W	1.037	0.36
82_I	195_Q	1.035	0.36
32_L	41_L	1.035	0.36
41_L	45_L	1.034	0.35
176_Q	180_Q	1.033	0.35
102_L	135_P	1.032	0.35
74_P	84_W	1.032	0.35
148_G	189_L	1.029	0.35
45_L	90_P	1.028	0.35
59_K	126_L	1.027	0.35
28_N	36_R	1.024	0.35
59_K	178_G	1.017	0.34
36_R	41_L	1.015	0.34
163_E	171_A	1.014	0.34
36_R	183_A	1.010	0.33
22_W	37_I	1.007	0.33
110_Q	137_D	1.000	0.33

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: (17Jul14)
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
4aezC	3	0.93	100	0.266	Contact Map
4a1gA	4	0.735	100	0.415	Contact Map
2wviA	1	0.7	100	0.544	Contact Map
3eslA	2	0.765	100	0.586	Contact Map
4b94A	4	0.63	99.9	0.721	Contact Map
4h7yA	4	0.63	99.8	0.753	Contact Map
4ggdC	2	0.04	98.4	0.873	Contact Map
2ondA	2	0.61	96.6	0.91	Contact Map
2ooeA	1	0.935	95.4	0.919	Contact Map
2uy1A	1	0.565	92.9	0.928	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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