OPENSEQ.org - 1425980311 - GREMLIN Submission

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Epsilon

ID:	1425980311	Query Sequence LDGEPSMNYLEDVYVGKALLTNDTQQEQKLKSQSFTCKNTDTVTATTTHTVGTSIQATAKFTVPFNETGVSLTTSYSFANTNTNTNSKEITHNVPSQDILVPANTTVEVIAYLKKVNVKGNVKLVGQVSGSEWGEIPSYLAFPRDGYKFSLSDTVNKSDLNEDGTININGKGNYSAVMGDELIVKVRNLNTNNVQEYVIP	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	200 (193)
Sequences:	193 (172.4)
Seq/Len:	1.000
Nf(neff/√len):	12.4

Jackhmmer Results: (2015_01_07)
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: 1.000).

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
52_G	75_S	2.600	0.99
56_Q	71_S	2.547	0.99
60_K	67_E	2.540	0.99
38_K	89_E	2.436	0.99
44_T	83_T	2.370	0.99
20_L	30_L	2.368	0.99
46_T	81_T	2.260	0.98
48_T	79_A	2.257	0.98
122_V	170_G	2.234	0.98
124_L	170_G	2.009	0.96
27_E	100_L	1.952	0.95
24_T	28_Q	1.938	0.94
107_V	188_N	1.867	0.93
27_E	103_A	1.864	0.93
107_V	186_V	1.763	0.90
63_V	177_V	1.463	0.74
142_F	146_G	1.408	0.70
57_A	104_N	1.380	0.68
34_S	113_L	1.365	0.67
130_G	172_G	1.347	0.65
20_L	109_V	1.339	0.64
20_L	124_L	1.334	0.64
179_G	184_V	1.322	0.63
124_L	176_A	1.318	0.63
29_K	98_D	1.301	0.61
96_S	99_I	1.289	0.60
12_D	172_G	1.280	0.59
124_L	174_Y	1.274	0.59
21_T	24_T	1.258	0.57
92_H	113_L	1.238	0.55
113_L	188_N	1.237	0.55
123_K	169_N	1.231	0.55
49_H	78_F	1.228	0.55
79_A	113_L	1.210	0.53
105_T	188_N	1.206	0.53
32_S	51_V	1.191	0.51
29_K	63_V	1.188	0.51
46_T	83_T	1.178	0.50
56_Q	86_N	1.171	0.49
78_F	170_G	1.169	0.49
113_L	182_L	1.168	0.49
8_N	11_E	1.164	0.49
61_F	67_E	1.153	0.48
188_N	191_T	1.151	0.47
29_K	36_T	1.146	0.47
59_A	93_N	1.146	0.47
20_L	32_S	1.145	0.47
46_T	60_K	1.143	0.47
16_G	111_A	1.140	0.46
61_F	178_M	1.138	0.46
62_T	129_S	1.136	0.46
105_T	190_N	1.133	0.46
128_V	168_I	1.133	0.46
76_Y	183_I	1.128	0.45
36_T	91_T	1.126	0.45
16_G	170_G	1.114	0.44
107_V	190_N	1.108	0.43
34_S	99_I	1.103	0.43
103_A	150_S	1.101	0.43
191_T	194_V	1.100	0.43
44_T	185_K	1.099	0.43
20_L	120_G	1.096	0.42
149_F	171_K	1.088	0.42
83_T	97_Q	1.084	0.41
34_S	126_G	1.076	0.41
25_Q	104_N	1.074	0.40
54_S	87_S	1.072	0.40
127_Q	167_N	1.072	0.40
20_L	35_F	1.066	0.40
16_G	35_F	1.061	0.39
71_S	105_T	1.059	0.39
35_F	170_G	1.056	0.39
129_S	147_Y	1.053	0.39
148_K	151_L	1.050	0.38
67_E	126_G	1.047	0.38
54_S	89_E	1.045	0.38
40_T	85_T	1.037	0.37
54_S	73_T	1.030	0.37
99_I	132_E	1.028	0.36
126_G	170_G	1.027	0.36
69_G	184_V	1.023	0.36
40_T	45_A	1.022	0.36
96_S	111_A	1.020	0.36
18_A	114_K	1.017	0.35
21_T	108_E	1.015	0.35
42_T	181_E	1.014	0.35

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: (31Jan15)
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
3zjxA	4	1	100	0.235	Contact Map
2d42A	2	0.965	100	0.303	Contact Map
1w3fA	1	0.775	99.8	0.604	Contact Map
2ztbA	2	0.89	99.7	0.627	Contact Map
3g4nA	2	0.875	99.6	0.645	Contact Map
4jp0A	1	0.845	91.1	0.888	Contact Map
2j42A	1	0.765	65.6	0.915	Contact Map
3t5oA	1	0.78	19.3	0.938	Contact Map
3wa1A	1	0.76	17	0.939	Contact Map
3zx7A	1	0.835	15.5	0.94	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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