OPENSEQ.org - 1500938940 - GREMLIN Submission

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EB Split 2

ID:	1500938940	Query Sequence MKISDAVVSAHIDDEVVLLHLQTGTYFGLDAVGSRIWSLLEEGKRPEEIVDAICAEYSVDRPTVERDLRDFLRALANKELLEGYADEAMKLRLADLQLIAKAWSDLILIDRRLSHEGLDPILIKIESEAAPPQDVSREHLRLARRYARRIALAAHICPVGARCLHRSLVLHMWLRRQGLPSRLRFGVWKAEEDLRAHAWVELAGVPVNDDRRSLQGISPMTSPRRVDREAAYDL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	234 (227)
Sequences:	422 (364.5)
Seq/Len:	1.859
Nf(neff/√len):	24.2

HHblits Results: (2016_02)
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: 1.859).

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
170_L	200_V	2.987	1.00
206_P	209_D	2.681	1.00
45_R	48_E	2.304	1.00
60_D	63_T	2.126	0.99
207_V	210_D	2.038	0.99
59_V	64_V	2.026	0.99
35_R	56_E	2.004	0.99
61_R	65_E	1.938	0.98
109_I	169_V	1.777	0.97
110_D	209_D	1.663	0.95
20_H	79_E	1.628	0.94
26_Y	196_A	1.624	0.94
11_H	14_D	1.602	0.93
3_I	37_W	1.595	0.93
7_V	18_L	1.584	0.93
101_K	173_W	1.562	0.92
162_R	167_S	1.557	0.92
157_C	161_A	1.524	0.91
184_R	219_P	1.454	0.88
17_V	122_L	1.425	0.87
65_E	69_R	1.422	0.86
105_D	109_I	1.417	0.86
101_K	177_Q	1.411	0.86
106_L	153_A	1.406	0.86
170_L	208_N	1.393	0.85
16_V	34_S	1.383	0.84
37_W	185_F	1.367	0.83
167_S	209_D	1.366	0.83
23_T	27_F	1.359	0.83
160_G	166_R	1.351	0.82
51_D	61_R	1.342	0.82
105_D	169_V	1.335	0.81
201_E	204_G	1.331	0.81
46_P	50_V	1.320	0.80
136_S	142_L	1.316	0.80
145_R	178_G	1.316	0.80
185_F	220_M	1.304	0.79
105_D	172_M	1.304	0.79
168_L	171_H	1.292	0.78
208_N	223_P	1.292	0.78
33_G	49_I	1.290	0.78
27_F	99_I	1.263	0.76
162_R	165_H	1.259	0.76
44_K	49_I	1.254	0.75
15_E	57_Y	1.252	0.75
48_E	228_R	1.249	0.75
229_E	233_D	1.246	0.75
107_I	189_K	1.244	0.75
161_A	170_L	1.239	0.74
91_L	107_I	1.225	0.73
70_D	73_R	1.214	0.72
20_H	23_T	1.211	0.72
132_P	137_R	1.210	0.72
70_D	74_A	1.207	0.71
69_R	73_R	1.206	0.71
173_W	200_V	1.181	0.69
175_R	225_R	1.179	0.69
51_D	55_A	1.176	0.68
61_R	150_I	1.173	0.68
91_L	100_A	1.155	0.66
10_A	17_V	1.148	0.66
55_A	63_T	1.136	0.65
143_A	180_P	1.136	0.65
186_G	196_A	1.130	0.64
33_G	36_I	1.127	0.64
230_A	233_D	1.124	0.63
27_F	149_R	1.123	0.63
23_T	71_F	1.120	0.63
154_A	161_A	1.113	0.62
2_K	228_R	1.110	0.62
72_L	81_L	1.110	0.62
1_M	72_L	1.107	0.62
46_P	72_L	1.103	0.61
80_L	184_R	1.101	0.61
139_H	142_L	1.097	0.61
150_I	170_L	1.095	0.60
54_C	73_R	1.093	0.60
49_I	91_L	1.089	0.60
119_D	123_I	1.088	0.60
35_R	39_L	1.086	0.59
166_R	213_S	1.084	0.59
162_R	166_R	1.080	0.59
92_R	95_D	1.080	0.59
184_R	208_N	1.077	0.58
117_G	120_P	1.067	0.57
10_A	24_G	1.064	0.57
17_V	33_G	1.063	0.57
147_A	166_R	1.060	0.57
5_D	79_E	1.059	0.57
54_C	97_Q	1.053	0.56
228_R	231_A	1.053	0.56
107_I	110_D	1.053	0.56
15_E	189_K	1.048	0.55
169_V	200_V	1.046	0.55
165_H	203_A	1.045	0.55
165_H	189_K	1.043	0.55
24_G	115_H	1.042	0.55
33_G	71_F	1.034	0.54
26_Y	187_V	1.030	0.53
167_S	175_R	1.028	0.53
53_I	68_L	1.027	0.53
17_V	159_V	1.025	0.53
74_A	77_N	1.022	0.53
40_L	72_L	1.021	0.52
36_I	49_I	1.012	0.51
196_A	217_I	1.011	0.51
182_R	224_R	1.008	0.51
8_V	106_L	1.007	0.51
75_L	184_R	1.003	0.50
184_R	201_E	1.002	0.50

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: (06Aug15)
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
3g2bA	1	0.3462	99.5	0.729	Contact Map
1x3zA	1	0.7479	63.2	0.931	Contact Map
4fgqA	2	0.641	60.5	0.932	Contact Map
3deeA	1	0.3632	53.8	0.935	Contact Map
1l9mA	2	0.8803	49	0.937	Contact Map
4ktyA	2	0.8376	46.4	0.938	Contact Map
2q3zA	1	0.8333	39.9	0.94	Contact Map
2hlyA	1	0.406	39.5	0.94	Contact Map
3isrA	4	0.8718	38.2	0.941	Contact Map
2dk5A	1	0.3846	38.1	0.941	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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