OPENSEQ.org - 1424268691 - GREMLIN Submission

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SYNTH235-345 ACT608-702 filtered manually

ID:	1424268691	Query Sequence GREKHLYSIYCKMVLKEQRFHSIMDIYAFRVIVNDSDTCYRVLGQMHSLYKPRPGRVKDYIAIPKANGYQSLHTSMIGPHGVPVEVQIRTEDMDQMAEMGVAAHWAYKEHGEPEKFMAVEWDKETAQEFITEIKVEMFNHQGALANLTAAINTTTSNIQSLNTEEKDGRVYSAFIRLTARDRVHLANIMRKIRVMPDVIKVTRNRN	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	206 (206)
Sequences:	625 (435.7)
Seq/Len:	3.034
Nf(neff/√len):	30.4

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: 3.034).

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
189_M	201_V	3.527	1.00
37_D	41_R	3.302	1.00
35_D	38_T	2.828	1.00
161_L	175_I	2.561	1.00
18_Q	23_I	2.024	1.00
4_K	12_K	2.004	1.00
12_K	85_E	1.794	0.99
182_R	186_A	1.756	0.99
34_N	91_E	1.706	0.98
33_V	42_V	1.672	0.98
142_G	157_N	1.561	0.97
34_N	38_T	1.553	0.97
133_I	189_M	1.535	0.96
40_Y	47_H	1.519	0.96
47_H	74_T	1.481	0.95
135_V	192_I	1.443	0.94
43_L	47_H	1.430	0.94
91_E	95_Q	1.420	0.94
27_Y	82_V	1.416	0.94
94_D	98_E	1.416	0.94
145_A	148_T	1.416	0.94
2_R	8_S	1.414	0.94
10_Y	52_P	1.401	0.93
137_M	143_A	1.367	0.92
40_Y	44_G	1.363	0.92
4_K	25_D	1.358	0.92
38_T	42_V	1.346	0.91
158_I	175_I	1.345	0.91
2_R	12_K	1.340	0.91
1_G	71_S	1.335	0.91
73_H	89_R	1.314	0.90
151_I	156_S	1.290	0.89
56_R	75_S	1.284	0.88
151_I	158_I	1.254	0.87
73_H	87_Q	1.233	0.86
25_D	85_E	1.226	0.85
40_Y	43_L	1.217	0.85
177_L	188_I	1.216	0.85
9_I	12_K	1.214	0.84
186_A	190_R	1.213	0.84
28_A	75_S	1.211	0.84
53_R	57_V	1.207	0.84
4_K	85_E	1.207	0.84
30_R	87_Q	1.206	0.84
12_K	25_D	1.197	0.83
43_L	88_I	1.191	0.83
156_S	184_H	1.186	0.82
4_K	104_H	1.185	0.82
179_A	184_H	1.183	0.82
4_K	9_I	1.178	0.82
2_R	85_E	1.169	0.81
22_S	141_Q	1.166	0.81
30_R	85_E	1.166	0.81
8_S	85_E	1.161	0.81
40_Y	74_T	1.159	0.80
102_A	142_G	1.159	0.80
43_L	57_V	1.150	0.80
50_Y	68_G	1.149	0.80
8_S	12_K	1.142	0.79
52_P	62_A	1.129	0.78
140_H	146_N	1.126	0.78
12_K	30_R	1.122	0.77
4_K	87_Q	1.121	0.77
47_H	61_I	1.115	0.77
2_R	108_K	1.114	0.77
132_E	176_R	1.111	0.76
36_S	48_S	1.108	0.76
40_Y	62_A	1.107	0.76
47_H	57_V	1.103	0.76
12_K	28_A	1.101	0.75
14_V	153_T	1.101	0.75
71_S	89_R	1.100	0.75
29_F	33_V	1.093	0.75
182_R	190_R	1.093	0.75
140_H	143_A	1.084	0.74
40_Y	61_I	1.068	0.72
42_V	88_I	1.064	0.72
65_K	69_Y	1.058	0.71
184_H	188_I	1.057	0.71
27_Y	83_P	1.055	0.71
63_I	76_M	1.054	0.71
13_M	20_F	1.052	0.71
2_R	30_R	1.051	0.71
28_A	85_E	1.051	0.71
188_I	195_M	1.046	0.70
43_L	74_T	1.046	0.70
47_H	62_A	1.041	0.69
75_S	96_M	1.041	0.69
24_M	29_F	1.037	0.69
110_H	126_A	1.035	0.69
30_R	89_R	1.034	0.69
139_N	146_N	1.032	0.69
6_L	62_A	1.030	0.68
65_K	73_H	1.022	0.67
3_E	27_Y	1.021	0.67
12_K	87_Q	1.020	0.67
137_M	173_A	1.019	0.67
131_T	139_N	1.017	0.67
183_V	186_A	1.014	0.67
56_R	104_H	1.011	0.66
141_Q	155_T	1.010	0.66
104_H	108_K	1.010	0.66
4_K	28_A	1.006	0.66
3_E	76_M	1.005	0.66
31_V	133_I	1.001	0.65

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	0.419	Contact Map
3l9dA	2	0.7087	100	0.503	Contact Map
2be3A	2	0.7233	100	0.514	Contact Map
1y7pA	3	0.3835	99.1	0.841	Contact Map
2ko1A	2	0.3883	99	0.846	Contact Map
2lvwA	2	0.4078	98.8	0.854	Contact Map
2pc6A	4	0.3786	98.8	0.859	Contact Map
2fgcA	1	0.3786	98.7	0.86	Contact Map
2f1fA	2	0.3738	98.7	0.861	Contact Map
1zpvA	3	0.3835	98.4	0.874	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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