OPENSEQ.org - 1512502837 - GREMLIN Submission

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AC1_rep

ID:	1512502837	Query Sequence MPPKRNGFYSKNYFITYPKCSLTKEEALSQLLNIQTPTSKKYIRICRELHEDGTPHLHVLIQFEGKFKCQNMRFFDLVSPSRSAHFHPNIQGAKSSSDVKSYIEKDGDILDWGQFQIDGRSARGGQQTANDAYATALNAGSKSEALRVIKELAPKDFVLQFHNLNANLDRIFQEPPAPYISPFSSSSFDQVPEELEEWVSENVVDAAARPHRPQSIVIEGDSRTGKTMW	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	229 (229)
Sequences:	696 (268.2)
Seq/Len:	3.039
Nf(neff/√len):	17.7

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: 3.039).

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
135_T	152_L	2.477	1.00
161_F	165_N	2.102	1.00
142_K	169_D	2.061	1.00
142_K	165_N	1.990	1.00
153_A	159_L	1.936	1.00
104_E	111_D	1.842	0.99
7_G	68_K	1.837	0.99
44_R	109_I	1.780	0.99
104_E	109_I	1.750	0.99
141_S	144_E	1.738	0.99
174_E	177_A	1.708	0.98
220_G	226_K	1.698	0.98
226_K	229_W	1.693	0.98
221_D	228_M	1.671	0.98
133_Y	159_L	1.664	0.98
82_R	85_H	1.660	0.98
153_A	156_D	1.656	0.98
44_R	104_E	1.649	0.98
223_R	226_K	1.605	0.97
45_I	109_I	1.601	0.97
93_A	99_V	1.595	0.97
44_R	111_D	1.570	0.97
102_Y	105_K	1.539	0.96
79_S	82_R	1.514	0.96
152_L	158_V	1.483	0.95
192_P	199_V	1.471	0.95
222_S	226_K	1.452	0.95
76_D	87_H	1.414	0.94
220_G	225_G	1.410	0.94
224_T	228_M	1.404	0.93
109_I	112_W	1.385	0.93
50_H	56_H	1.365	0.92
134_A	137_L	1.357	0.92
133_Y	153_A	1.357	0.92
73_R	76_D	1.342	0.91
225_G	229_W	1.341	0.91
36_T	74_F	1.307	0.90
174_E	178_P	1.303	0.89
158_V	168_L	1.302	0.89
223_R	229_W	1.300	0.89
19_K	54_T	1.293	0.89
193_E	196_E	1.275	0.88
165_N	168_L	1.275	0.88
196_E	200_S	1.273	0.88
60_L	103_I	1.271	0.88
27_A	30_Q	1.264	0.87
196_E	201_E	1.263	0.87
13_Y	69_C	1.261	0.87
26_E	29_S	1.256	0.87
211_H	214_Q	1.253	0.87
91_Q	99_V	1.253	0.87
220_G	227_T	1.252	0.87
203_V	217_V	1.252	0.87
185_S	190_Q	1.250	0.87
101_S	112_W	1.247	0.86
81_S	84_A	1.230	0.85
133_Y	155_K	1.227	0.85
212_R	215_S	1.220	0.85
81_S	85_H	1.219	0.85
154_P	198_W	1.213	0.84
67_F	74_F	1.213	0.84
160_Q	163_N	1.210	0.84
149_I	153_A	1.205	0.84
38_T	74_F	1.193	0.83
15_I	31_L	1.183	0.82
155_K	158_V	1.181	0.82
222_S	227_T	1.177	0.82
78_V	81_S	1.169	0.81
185_S	201_E	1.167	0.81
24_K	28_L	1.166	0.81
145_A	167_N	1.159	0.80
153_A	161_F	1.158	0.80
156_D	159_L	1.158	0.80
185_S	196_E	1.155	0.80
176_P	200_S	1.152	0.80
87_H	90_I	1.149	0.80
212_R	217_V	1.149	0.80
132_A	135_T	1.133	0.78
69_C	74_F	1.132	0.78
148_V	152_L	1.131	0.78
7_G	70_Q	1.128	0.78
189_D	196_E	1.125	0.78
79_S	85_H	1.124	0.78
27_A	57_L	1.123	0.77
42_Y	111_D	1.122	0.77
100_K	104_E	1.122	0.77
49_L	55_P	1.121	0.77
200_S	217_V	1.120	0.77
109_I	114_Q	1.119	0.77
224_T	229_W	1.110	0.76
216_I	226_K	1.105	0.76
220_G	223_R	1.102	0.76
62_Q	65_G	1.100	0.75
103_I	112_W	1.099	0.75
190_Q	196_E	1.093	0.75
52_D	56_H	1.086	0.74
220_G	224_T	1.084	0.74
212_R	226_K	1.083	0.74
7_G	31_L	1.081	0.74
188_F	192_P	1.079	0.73
34_I	38_T	1.077	0.73
144_E	147_R	1.077	0.73
195_L	204_V	1.074	0.73
52_D	58_H	1.072	0.73
161_F	169_D	1.068	0.72
133_Y	136_A	1.064	0.72
17_Y	20_C	1.059	0.71
132_A	153_A	1.057	0.71
140_G	158_V	1.056	0.71
155_K	163_N	1.049	0.70
216_I	219_E	1.048	0.70
162_H	167_N	1.048	0.70
189_D	195_L	1.036	0.69
181_S	200_S	1.036	0.69
140_G	168_L	1.035	0.69
9_Y	68_K	1.024	0.68
13_Y	36_T	1.022	0.67
195_L	202_N	1.020	0.67
18_P	55_P	1.015	0.67
87_H	105_K	1.014	0.67
165_N	169_D	1.007	0.66
217_V	222_S	1.006	0.66
179_Y	221_D	1.006	0.66
179_Y	202_N	1.003	0.65
212_R	219_E	1.003	0.65
213_P	223_R	1.000	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: (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
1l2mA	1	0.5153	100	0.443	Contact Map
2hwtA	1	0.3843	99.7	0.758	Contact Map
2hw0A	1	0.4629	99.6	0.783	Contact Map
2qbyA	1	0.2314	93.2	0.926	Contact Map
2v1uA	1	0.2489	92.2	0.929	Contact Map
3te6A	2	0.2445	91.1	0.931	Contact Map
1tueA	6	0.2882	89.4	0.933	Contact Map
3b9pA	1	0.2795	89.2	0.933	Contact Map
2w58A	2	0.2882	88.1	0.935	Contact Map
1fnnA	2	0.2445	88	0.935	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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