OPENSEQ.org - 1424275273 - GREMLIN Submission

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SYNTH235-345 ACT608-702 Enriched second highest filter

ID:	1424275273	Query Sequence GREKHLYSIYCKMVLKEQRFHSIMDIYAFRVIVNDSDTCYRVLGQMHSLYKPRPGRVKDYIAIPKANGYQSLHTSMIGPHGVPVEVQIRTEDMDQMAEMGVAAHWAYKEHGEPEKFMAVEWDKETAQEFITEIKVEMFNHQGALANLTAAINTTTSNIQSLNTEEKDGRVYSAFIRLTARDRVHLANIMRKIRVMPDVIKVTRNRN	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	206 (205)
Sequences:	596 (415.6)
Seq/Len:	2.907
Nf(neff/√len):	29.0

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: 2.907).

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 > 50% 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
189_M	201_V	3.572	1.00
37_D	41_R	3.222	1.00
35_D	38_T	2.782	1.00
161_L	175_I	2.582	1.00
18_Q	23_I	2.130	1.00
4_K	12_K	1.935	0.99
12_K	85_E	1.853	0.99
34_N	91_E	1.668	0.98
182_R	186_A	1.641	0.98
133_I	189_M	1.582	0.97
33_V	42_V	1.579	0.97
142_G	157_N	1.573	0.97
158_I	175_I	1.525	0.96
135_V	192_I	1.475	0.95
43_L	47_H	1.466	0.95
34_N	38_T	1.461	0.94
27_Y	82_V	1.437	0.94
40_Y	47_H	1.436	0.94
94_D	98_E	1.418	0.93
91_E	95_Q	1.413	0.93
177_L	188_I	1.411	0.93
137_M	143_A	1.389	0.92
2_R	8_S	1.387	0.92
47_H	74_T	1.386	0.92
4_K	85_E	1.370	0.92
4_K	25_D	1.370	0.92
2_R	12_K	1.345	0.91
73_H	87_Q	1.340	0.90
1_G	71_S	1.332	0.90
10_Y	52_P	1.320	0.89
38_T	42_V	1.294	0.88
145_A	148_T	1.291	0.88
151_I	156_S	1.273	0.87
56_R	75_S	1.263	0.87
40_Y	44_G	1.262	0.86
2_R	108_K	1.254	0.86
102_A	142_G	1.251	0.86
2_R	85_E	1.244	0.85
156_S	184_H	1.243	0.85
179_A	184_H	1.234	0.85
73_H	89_R	1.232	0.85
8_S	85_E	1.221	0.84
22_S	141_Q	1.216	0.84
28_A	75_S	1.216	0.84
36_S	48_S	1.196	0.82
186_A	190_R	1.193	0.82
53_R	57_V	1.181	0.81
40_Y	43_L	1.175	0.81
25_D	85_E	1.169	0.80
2_R	30_R	1.162	0.80
4_K	104_H	1.162	0.80
8_S	12_K	1.159	0.79
52_P	62_A	1.158	0.79
40_Y	74_T	1.130	0.77
50_Y	68_G	1.129	0.77
75_S	96_M	1.129	0.77
30_R	85_E	1.125	0.76
40_Y	62_A	1.124	0.76
71_S	89_R	1.121	0.76
4_K	87_Q	1.103	0.74
132_E	176_R	1.095	0.74
30_R	87_Q	1.095	0.74
30_R	89_R	1.093	0.74
29_F	101_V	1.093	0.74
14_V	153_T	1.092	0.73
42_V	88_I	1.092	0.73
142_G	158_I	1.092	0.73
26_I	29_F	1.089	0.73
110_H	126_A	1.089	0.73
151_I	158_I	1.088	0.73
12_K	25_D	1.083	0.73
43_L	74_T	1.081	0.72
13_M	60_Y	1.073	0.72
184_H	188_I	1.072	0.71
182_R	190_R	1.067	0.71
9_I	12_K	1.066	0.71
47_H	62_A	1.065	0.71
32_I	130_I	1.065	0.71
4_K	9_I	1.061	0.70
56_R	104_H	1.058	0.70
69_Y	73_H	1.057	0.70
188_I	195_M	1.053	0.69
12_K	28_A	1.052	0.69
140_H	146_N	1.049	0.69
43_L	57_V	1.049	0.69
2_R	28_A	1.046	0.69
6_L	62_A	1.043	0.68
141_Q	155_T	1.042	0.68
65_K	73_H	1.040	0.68
38_T	201_V	1.037	0.68
28_A	85_E	1.032	0.67
43_L	88_I	1.029	0.67
140_H	147_L	1.029	0.67
65_K	69_Y	1.022	0.66
47_H	57_V	1.017	0.66
183_V	186_A	1.015	0.65
44_G	47_H	1.015	0.65
8_S	73_H	1.007	0.64
104_H	108_K	1.006	0.64
66_A	86_V	1.004	0.64
8_S	87_Q	1.004	0.64
4_K	28_A	1.003	0.64
91_E	133_I	1.001	0.64

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: (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
1vj7A	2	0.5291	100	0.417	Contact Map
3l9dA	2	0.6893	100	0.497	Contact Map
2be3A	2	0.699	100	0.506	Contact Map
1y7pA	3	0.3835	99	0.846	Contact Map
2ko1A	2	0.3883	99	0.849	Contact Map
2lvwA	2	0.4078	98.8	0.858	Contact Map
2pc6A	4	0.3786	98.7	0.862	Contact Map
2f1fA	2	0.3738	98.7	0.864	Contact Map
2fgcA	1	0.3786	98.7	0.865	Contact Map
1zpvA	3	0.3835	98.4	0.876	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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