OPENSEQ.org - 1512415027 - GREMLIN Submission

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AC1_rep

ID:	1512415027	Query Sequence MPPKRNGFYSKNYFITYPKCSLTKEEALSQLLNIQTPTSKKYIRICRELHEDGTPHLHVLIQFEGKFKCQNMRFFDLVSPSRSAHFHPNIQGAKSSSDVKSYIEKDGDILDWGQFQIDGRSARGGQQTANDAYATALNAGSKSEALRVIKELAPKDFVLQFHNLNANLDRIFQEPPAPYISPFSSSSFDQVPEELEEWVSENVVDAAARPHRPQSIVIEGDSRTGKTMW	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	229 (227)
Sequences:	679 (255.9)
Seq/Len:	2.991
Nf(neff/√len):	17.0

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: 2.991).

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 > 50% 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	2.517	1.00
161_F	165_N	2.056	1.00
142_K	165_N	1.967	1.00
142_K	169_D	1.965	1.00
153_A	159_L	1.960	1.00
104_E	111_D	1.923	0.99
7_G	68_K	1.824	0.99
44_R	109_I	1.822	0.99
220_G	226_K	1.789	0.99
104_E	109_I	1.760	0.99
141_S	144_E	1.709	0.98
226_K	229_W	1.709	0.98
44_R	104_E	1.685	0.98
133_Y	159_L	1.682	0.98
174_E	177_A	1.680	0.98
221_D	228_M	1.672	0.98
223_R	226_K	1.620	0.98
44_R	111_D	1.618	0.98
93_A	99_V	1.612	0.97
45_I	109_I	1.609	0.97
79_S	82_R	1.594	0.97
82_R	85_H	1.549	0.97
153_A	156_D	1.533	0.96
152_L	158_V	1.525	0.96
222_S	226_K	1.500	0.96
102_Y	105_K	1.494	0.96
220_G	225_G	1.488	0.95
224_T	228_M	1.462	0.95
76_D	87_H	1.458	0.95
50_H	56_H	1.436	0.94
134_A	137_L	1.382	0.92
192_P	199_V	1.381	0.92
133_Y	153_A	1.369	0.92
109_I	112_W	1.369	0.92
225_G	229_W	1.361	0.92
36_T	74_F	1.360	0.92
19_K	54_T	1.351	0.91
220_G	227_T	1.333	0.91
223_R	229_W	1.320	0.90
158_V	168_L	1.311	0.90
60_L	103_I	1.304	0.89
212_R	215_S	1.299	0.89
196_E	200_S	1.291	0.89
165_N	168_L	1.287	0.88
193_E	196_E	1.275	0.88
133_Y	155_K	1.269	0.87
174_E	178_P	1.268	0.87
196_E	201_E	1.266	0.87
13_Y	69_C	1.261	0.87
203_V	217_V	1.261	0.87
101_S	112_W	1.246	0.86
73_R	76_D	1.245	0.86
91_Q	99_V	1.244	0.86
67_F	74_F	1.231	0.85
7_G	31_L	1.225	0.85
81_S	85_H	1.225	0.85
27_A	30_Q	1.223	0.85
26_E	29_S	1.215	0.84
154_P	198_W	1.212	0.84
38_T	74_F	1.211	0.84
222_S	227_T	1.208	0.84
185_S	190_Q	1.206	0.84
15_I	31_L	1.202	0.83
81_S	84_A	1.199	0.83
211_H	214_Q	1.199	0.83
27_A	57_L	1.195	0.83
49_L	55_P	1.185	0.82
160_Q	163_N	1.181	0.82
24_K	28_L	1.175	0.81
185_S	201_E	1.172	0.81
145_A	167_N	1.171	0.81
220_G	223_R	1.169	0.81
155_K	158_V	1.168	0.81
185_S	196_E	1.162	0.80
79_S	85_H	1.158	0.80
149_I	153_A	1.156	0.80
156_D	159_L	1.147	0.79
212_R	217_V	1.146	0.79
224_T	229_W	1.134	0.78
188_F	192_P	1.131	0.78
78_V	81_S	1.128	0.77
153_A	161_F	1.128	0.77
176_P	200_S	1.127	0.77
69_C	74_F	1.124	0.77
215_S	220_G	1.122	0.77
216_I	226_K	1.118	0.77
132_A	135_T	1.117	0.77
103_I	112_W	1.112	0.76
189_D	196_E	1.111	0.76
190_Q	196_E	1.099	0.75
212_R	226_K	1.097	0.75
109_I	114_Q	1.097	0.75
17_Y	20_C	1.095	0.74
162_H	167_N	1.086	0.74
42_Y	111_D	1.082	0.73
140_G	158_V	1.070	0.72
181_S	200_S	1.066	0.72
62_Q	65_G	1.066	0.72
132_A	153_A	1.065	0.72
195_L	204_V	1.065	0.72
216_I	219_E	1.061	0.71
220_G	229_W	1.052	0.70
200_S	217_V	1.048	0.70
7_G	70_Q	1.046	0.70
100_K	104_E	1.046	0.70
161_F	169_D	1.045	0.69
87_H	90_I	1.027	0.68
34_I	38_T	1.024	0.67
18_P	55_P	1.023	0.67
217_V	222_S	1.023	0.67
48_E	56_H	1.018	0.67
27_A	77_L	1.017	0.66
148_V	152_L	1.015	0.66
188_F	191_V	1.013	0.66
173_Q	178_P	1.010	0.66
212_R	219_E	1.009	0.66
213_P	223_R	1.007	0.65
220_G	224_T	1.004	0.65
152_L	159_L	1.001	0.65
144_E	147_R	1.001	0.65
212_R	216_I	1.001	0.65
216_I	220_G	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

See coupling matrix (for protein design or mutagenesis)
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	0.445	Contact Map
2hwtA	1	0.3843	99.7	0.759	Contact Map
2hw0A	1	0.4629	99.6	0.783	Contact Map
2qbyA	1	0.2314	93.3	0.926	Contact Map
2v1uA	1	0.2489	92.2	0.928	Contact Map
3te6A	2	0.2445	91.1	0.93	Contact Map
3pvsA	4	0.2227	89.8	0.932	Contact Map
3b9pA	1	0.2795	89.6	0.933	Contact Map
1tueA	6	0.2882	89.4	0.933	Contact Map
2w58A	2	0.2882	88.1	0.934	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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