OPENSEQ.org - 1402293815 - GREMLIN Submission

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nRGS

ID:	1402293815	Query Sequence MNIQEQGFPLDLGASFTEDAPRPPVPGEEGELVSTDPRPASYSFCSGKGVGIKGETSTATPRRSDLDLGYEPEGSASPTPPYLKWAESLHSLLDDQDGISLFRTFLKQEGCADLLDFWFACTGFRKLEPCDSNEEKRLKLARAIYRKYILDNNGIVSRQTKPATKSFIKGCIMKQLIDPAMFDQAQTEIQATMEENTYPSFLKSDIYLEYTR	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	212 (202)
Sequences:	514 (372.2)
Seq/Len:	2.545
Nf(neff/√len):	26.2

Jackhmmer Results: (2014_04_16)
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: 2.545).

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
92_L	198_Y	2.619	1.00
113_D	159_Q	2.286	1.00
85_W	98_G	2.198	1.00
114_L	196_N	1.977	0.99
114_L	159_Q	1.973	0.99
193_M	197_T	1.799	0.99
118_W	186_Q	1.676	0.97
92_L	98_G	1.653	0.97
98_G	121_C	1.638	0.97
196_N	200_S	1.626	0.97
35_T	38_R	1.602	0.96
124_F	141_A	1.573	0.96
34_S	38_R	1.529	0.95
61_P	65_D	1.509	0.94
114_L	192_T	1.506	0.94
117_F	121_C	1.417	0.91
110_G	114_L	1.402	0.91
39_P	44_F	1.388	0.90
18_E	22_R	1.388	0.90
113_D	196_N	1.387	0.90
37_P	40_A	1.383	0.90
104_T	201_F	1.374	0.90
114_L	200_S	1.367	0.89
93_L	118_W	1.366	0.89
85_W	92_L	1.355	0.89
107_K	112_A	1.349	0.89
35_T	40_A	1.344	0.88
124_F	168_I	1.333	0.88
34_S	37_P	1.333	0.88
45_C	49_G	1.323	0.87
164_T	185_A	1.321	0.87
36_D	40_A	1.320	0.87
85_W	198_Y	1.319	0.87
110_G	113_D	1.280	0.85
20_A	23_P	1.278	0.85
111_C	159_Q	1.277	0.85
114_L	197_T	1.271	0.84
118_W	122_T	1.268	0.84
34_S	40_A	1.263	0.84
172_I	181_M	1.258	0.83
85_W	121_C	1.255	0.83
118_W	193_M	1.252	0.83
111_C	196_N	1.233	0.82
38_R	42_Y	1.225	0.81
122_T	186_Q	1.225	0.81
92_L	121_C	1.210	0.80
121_C	186_Q	1.207	0.80
37_P	42_Y	1.192	0.79
88_S	98_G	1.191	0.79
84_K	87_E	1.186	0.78
110_G	159_Q	1.185	0.78
14_A	17_T	1.184	0.78
29_E	33_V	1.182	0.78
159_Q	192_T	1.157	0.76
109_E	120_A	1.151	0.75
182_F	198_Y	1.148	0.75
159_Q	196_N	1.144	0.75
98_G	109_E	1.137	0.74
24_P	28_E	1.132	0.73
119_F	202_L	1.131	0.73
105_F	200_S	1.129	0.73
45_C	48_K	1.126	0.73
53_K	57_S	1.114	0.72
54_G	61_P	1.111	0.71
124_F	137_R	1.109	0.71
103_R	116_D	1.107	0.71
98_G	198_Y	1.094	0.70
28_E	32_L	1.092	0.70
92_L	202_L	1.090	0.69
106_L	120_A	1.087	0.69
61_P	66_L	1.086	0.69
22_R	29_E	1.081	0.68
42_Y	46_S	1.079	0.68
62_R	65_D	1.077	0.68
115_L	122_T	1.073	0.68
42_Y	45_C	1.073	0.68
35_T	39_P	1.073	0.68
113_D	192_T	1.072	0.68
90_H	190_Q	1.066	0.67
109_E	121_C	1.064	0.67
27_G	32_L	1.060	0.66
98_G	120_A	1.059	0.66
36_D	42_Y	1.058	0.66
85_W	109_E	1.049	0.65
22_R	25_V	1.049	0.65
103_R	112_A	1.036	0.64
46_S	50_V	1.035	0.64
81_P	95_D	1.033	0.63
36_D	39_P	1.032	0.63
10_L	13_G	1.030	0.63
149_I	165_K	1.028	0.63
13_G	16_F	1.026	0.63
111_C	114_L	1.024	0.62
14_A	19_D	1.024	0.62
192_T	197_T	1.016	0.61
21_P	24_P	1.016	0.61
93_L	169_K	1.013	0.61
21_P	28_E	1.006	0.60
103_R	165_K	1.002	0.60
85_W	120_A	1.001	0.60
104_T	194_E	1.000	0.60

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: (29May14)
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
1dk8A	1	0.6509	100	0.35	Contact Map
4iguA	2	0.6179	100	0.37	Contact Map
2ihdA	1	0.5991	100	0.372	Contact Map
1cmzA	1	0.6038	100	0.374	Contact Map
2bv1A	2	0.6179	100	0.374	Contact Map
1zv4X	1	0.6368	100	0.377	Contact Map
2dlvA	1	0.6368	100	0.377	Contact Map
2oj4A	1	0.5991	100	0.377	Contact Map
2pbiA	2	0.9434	100	0.377	Contact Map
2jm5A	1	0.6179	100	0.378	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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