OPENSEQ.org - 1449144106 - GREMLIN Submission

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2LP4_Achain

ID:	1449144106	Query Sequence MSMDISDFYQTFFDEADELLADMEQHLLDLVPESPDAEQLNAIFRAAHSIKGGAGTFGFTILQETTHLMENLLDEARRGEMQLNTDIINLFLETKDIMQEQLDAYKNSEEPDAASFEYICNALRQLALEAKGETPSAVTRLSVVAKSEPQDEQSRSQSPRRIILSRLKAGEVDLLEEELGHLTTLTDVVKGADSLSAILPGDIAEDDITAVLCFVIEADQITFET	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	225 (214)
Sequences:	682 (492.6)
Seq/Len:	3.187
Nf(neff/√len):	33.7

HHblits Results: (2015_06)
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: 3.187).

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
205_E	209_T	2.593	1.00
34_S	37_A	2.524	1.00
47_A	66_T	2.408	1.00
179_L	199_L	2.145	1.00
40_L	76_A	2.130	1.00
93_E	122_A	1.992	1.00
14_D	95_K	1.986	1.00
75_E	81_M	1.892	0.99
162_I	212_L	1.731	0.99
68_L	124_R	1.681	0.98
204_A	207_D	1.638	0.98
175_L	218_A	1.624	0.98
59_F	63_Q	1.518	0.96
56_T	66_T	1.486	0.96
17_D	106_K	1.469	0.96
182_L	208_I	1.465	0.95
36_D	82_Q	1.447	0.95
121_N	125_Q	1.425	0.94
178_E	181_H	1.406	0.94
28_L	56_T	1.406	0.94
55_G	63_Q	1.403	0.94
173_D	176_E	1.399	0.94
41_N	55_G	1.391	0.93
164_L	185_L	1.389	0.93
69_M	91_F	1.389	0.93
97_I	119_I	1.368	0.93
209_T	213_C	1.368	0.93
38_E	79_G	1.364	0.93
7_D	56_T	1.364	0.93
151_D	154_S	1.345	0.92
160_R	201_G	1.337	0.92
43_I	47_A	1.307	0.90
21_A	99_Q	1.301	0.90
163_I	196_S	1.301	0.90
69_M	94_T	1.289	0.90
19_L	46_A	1.277	0.89
24_E	28_L	1.276	0.89
65_T	69_M	1.269	0.89
81_M	87_I	1.255	0.88
8_F	59_F	1.254	0.88
125_Q	129_E	1.251	0.88
199_L	208_I	1.251	0.88
63_Q	66_T	1.246	0.87
87_I	126_L	1.243	0.87
41_N	104_A	1.235	0.87
61_I	105_Y	1.231	0.86
125_Q	135_P	1.227	0.86
20_L	102_L	1.218	0.86
76_A	87_I	1.201	0.85
76_A	83_L	1.191	0.84
91_F	177_E	1.190	0.84
9_Y	73_L	1.185	0.83
206_D	210_A	1.182	0.83
207_D	210_A	1.173	0.83
53_G	57_F	1.167	0.82
104_A	111_P	1.166	0.82
203_I	207_D	1.160	0.82
56_T	63_Q	1.156	0.81
152_E	155_R	1.154	0.81
162_I	179_L	1.144	0.80
182_L	199_L	1.144	0.80
61_I	111_P	1.137	0.80
125_Q	130_A	1.128	0.79
116_F	119_I	1.127	0.79
13_F	32_P	1.121	0.79
62_L	102_L	1.119	0.78
170_G	174_L	1.115	0.78
53_G	56_T	1.106	0.77
169_A	195_L	1.100	0.77
65_T	120_C	1.099	0.77
172_V	195_L	1.099	0.77
206_D	209_T	1.098	0.76
124_R	128_L	1.098	0.76
55_G	100_E	1.097	0.76
81_M	126_L	1.092	0.76
182_L	211_V	1.087	0.75
125_Q	128_L	1.085	0.75
72_L	123_L	1.085	0.75
161_R	204_A	1.083	0.75
107_N	110_E	1.081	0.75
148_E	154_S	1.081	0.75
138_V	141_L	1.080	0.75
147_S	150_Q	1.079	0.75
161_R	196_S	1.078	0.75
12_F	73_L	1.077	0.75
182_L	189_V	1.072	0.74
7_D	17_D	1.070	0.74
103_D	107_N	1.067	0.74
44_F	77_R	1.062	0.73
69_M	98_M	1.058	0.73
184_T	200_P	1.057	0.73
27_L	88_I	1.044	0.71
145_A	149_P	1.043	0.71
45_R	67_H	1.041	0.71
23_M	93_E	1.039	0.71
151_D	156_S	1.031	0.70
108_S	111_P	1.030	0.70
62_L	103_D	1.028	0.70
31_V	34_S	1.024	0.69
146_K	149_P	1.023	0.69
49_S	53_G	1.020	0.69
16_A	92_L	1.019	0.69
132_G	135_P	1.018	0.68
141_L	144_V	1.016	0.68
143_V	150_Q	1.015	0.68
132_G	204_A	1.014	0.68
8_F	56_T	1.013	0.68
57_F	168_K	1.011	0.68
47_A	69_M	1.006	0.67
57_F	171_E	1.005	0.67
8_F	58_G	1.005	0.67
83_L	87_I	1.001	0.67
91_F	95_K	1.001	0.67

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
2lp4A	1	1	100	0.31	Contact Map
1i5nA	4	0.5822	100	0.514	Contact Map
3kyjA	1	0.5689	100	0.548	Contact Map
2ld6A	1	0.5867	100	0.569	Contact Map
2lchA	1	0.5022	99.9	0.593	Contact Map
1tqgA	1	0.4667	99.9	0.638	Contact Map
1y6dA	1	0.4267	99.2	0.801	Contact Map
1yviA	2	0.4667	99.1	0.806	Contact Map
4pacA	1	0	99.1	0.807	Contact Map
2oocA	2	0.4044	99	0.81	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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