OPENSEQ.org - 1492620957 - GREMLIN Submission

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Chmp7_NTD

ID:	1492620957	Query Sequence MWSPEREAEAPAGGDPAGLLPPEWEEDEERMSFLFSAFKRSREVNSTDWDSKMGFWAPLVLSHSRRQGVVRLRLRDLQEAFQRKGSVPLGLATVLQDLLRRGELQRESDFMASVDSSWISWGVGVFLLKPLKWTLSNMLGDNKVPAEEVLVAVELLKEKAEEVYRLYQNSPLSSHPVVALSELSTLCANSCPDERTFYLVLLQLQKEKRVTVLEQNGEKIVKFARGPR	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	228 (207)
Sequences:	414 (323.2)
Seq/Len:	2.000
Nf(neff/√len):	22.5

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: 2.000).

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
30_R	34_L	2.579	1.00
42_R	203_Q	2.193	1.00
65_R	158_E	1.939	0.99
172_L	221_V	1.851	0.98
106_R	109_D	1.813	0.98
24_W	31_M	1.756	0.97
184_S	194_E	1.651	0.95
71_R	195_R	1.644	0.95
127_L	130_P	1.611	0.94
39_K	90_G	1.575	0.93
73_R	149_V	1.548	0.93
163_V	187_C	1.482	0.90
48_D	51_S	1.463	0.90
87_V	223_F	1.456	0.89
77_L	81_F	1.444	0.89
126_F	130_P	1.421	0.88
55_F	85_G	1.400	0.87
42_R	120_S	1.398	0.87
79_E	82_Q	1.395	0.86
47_T	155_L	1.380	0.86
57_A	103_E	1.363	0.85
75_R	87_V	1.352	0.84
37_A	110_F	1.341	0.83
60_V	81_F	1.315	0.82
30_R	52_K	1.313	0.82
211_T	221_V	1.307	0.81
183_L	187_C	1.295	0.80
132_K	219_K	1.267	0.78
104_L	214_E	1.260	0.78
157_K	187_C	1.258	0.78
17_A	20_L	1.254	0.77
38_F	52_K	1.253	0.77
177_V	211_T	1.243	0.76
59_L	95_L	1.239	0.76
21_P	24_W	1.234	0.76
50_D	53_M	1.233	0.76
219_K	225_R	1.216	0.74
37_A	86_S	1.210	0.74
32_S	76_D	1.208	0.74
219_K	223_F	1.206	0.73
30_R	45_N	1.197	0.73
19_L	22_P	1.195	0.72
42_R	50_D	1.186	0.72
131_L	223_F	1.180	0.71
35_F	49_W	1.180	0.71
101_R	108_S	1.178	0.71
174_S	177_V	1.177	0.71
49_W	85_G	1.170	0.70
16_P	26_E	1.169	0.70
24_W	35_F	1.165	0.70
57_A	165_R	1.159	0.69
71_R	199_L	1.151	0.68
161_E	185_T	1.145	0.68
55_F	59_L	1.143	0.67
19_L	26_E	1.136	0.67
109_D	156_L	1.130	0.66
38_F	187_C	1.126	0.66
193_D	196_T	1.123	0.66
150_L	183_L	1.121	0.65
36_S	90_G	1.114	0.65
42_R	132_K	1.108	0.64
34_L	49_W	1.106	0.64
28_E	31_M	1.104	0.64
73_R	108_S	1.103	0.63
134_T	223_F	1.096	0.63
16_P	19_L	1.094	0.63
19_L	23_E	1.085	0.62
156_L	164_Y	1.083	0.61
20_L	119_I	1.083	0.61
66_R	73_R	1.078	0.61
180_L	198_Y	1.078	0.61
134_T	179_A	1.074	0.60
29_E	201_L	1.073	0.60
57_A	63_H	1.072	0.60
65_R	80_A	1.069	0.60
48_D	52_K	1.066	0.60
50_D	87_V	1.061	0.59
152_A	199_L	1.054	0.58
45_N	52_K	1.052	0.58
30_R	38_F	1.052	0.58
19_L	35_F	1.050	0.58
164_Y	210_V	1.045	0.57
69_V	115_D	1.044	0.57
71_R	102_G	1.044	0.57
77_L	133_W	1.041	0.57
122_G	211_T	1.039	0.57
95_L	211_T	1.039	0.57
55_F	81_F	1.037	0.56
62_S	66_R	1.037	0.56
104_L	220_I	1.036	0.56
219_K	224_A	1.035	0.56
133_W	208_K	1.032	0.56
36_S	177_V	1.032	0.56
196_T	206_K	1.029	0.56
52_K	55_F	1.029	0.56
181_S	198_Y	1.028	0.55
199_L	215_Q	1.024	0.55
58_P	62_S	1.018	0.54
30_R	133_W	1.017	0.54
135_L	157_K	1.017	0.54
220_I	225_R	1.016	0.54
96_Q	151_V	1.013	0.54
96_Q	197_F	1.010	0.53
33_F	89_L	1.007	0.53
24_W	27_D	1.005	0.53
17_A	26_E	1.004	0.53
49_W	149_V	1.004	0.53
198_Y	221_V	1.003	0.53
59_L	83_R	1.002	0.53
36_S	207_E	1.001	0.52

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
3cuqC	2	0.7061	98.7	0.831	Contact Map
1xb4A	4	0.7368	98.6	0.838	Contact Map
3htuA	4	0.307	77.1	0.931	Contact Map
2l02A	2	0.307	61.8	0.938	Contact Map
2l01A	2	0.3158	33.1	0.948	Contact Map
3edyA	1	0.4737	32.9	0.948	Contact Map
3dptA	2	0.307	29.6	0.95	Contact Map
4y66A	3	0.307	11.1	0.959	Contact Map
1u5tB	1	0.3465	10.8	0.959	Contact Map
1lvaA	1	0.5658	10.8	0.959	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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