OPENSEQ.org - 1512536462 - GREMLIN Submission

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AC1_rep

ID:	1512536462	Query Sequence MPPKRNGFYSKNYFITYPKCSLTKEEALSQLLNIQTPTSKKYIRICRELHEDGTPHLHVLIQFEGKFKCQNMRFFDLVSPSRSAHFHPNIQGAKSSSDVKSYIEKDGDILDWGQFQIDGRSARGGQQTANDAYATALNAGSKSEALRVIKELAPKDFVLQFHNLNANLDRIFQEPPAPYISPFSSSSFDQVPEELEEWVSENVVDAAARPHRPQSIVIEGDSRTGKTMW	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	229 (228)
Sequences:	481 (163.1)
Seq/Len:	2.110
Nf(neff/√len):	10.8

Jackhmmer Results: (2016_04)
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: 2.110).

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	2.884	1.00
44_R	109_I	2.165	1.00
142_K	165_N	2.146	1.00
133_Y	159_L	2.076	0.99
158_V	168_L	2.060	0.99
153_A	159_L	2.021	0.99
221_D	228_M	1.920	0.99
161_F	165_N	1.837	0.98
174_E	177_A	1.809	0.98
104_E	111_D	1.774	0.97
44_R	111_D	1.766	0.97
203_V	217_V	1.759	0.97
133_Y	153_A	1.748	0.97
174_E	178_P	1.724	0.97
142_K	169_D	1.719	0.97
44_R	104_E	1.698	0.97
152_L	158_V	1.637	0.95
7_G	68_K	1.619	0.95
132_A	153_A	1.605	0.95
104_E	109_I	1.598	0.95
79_S	82_R	1.581	0.94
13_Y	69_C	1.573	0.94
148_V	152_L	1.556	0.94
196_E	203_V	1.517	0.92
36_T	74_F	1.507	0.92
109_I	112_W	1.490	0.92
189_D	196_E	1.470	0.91
156_D	168_L	1.470	0.91
196_E	200_S	1.465	0.91
200_S	203_V	1.454	0.90
133_Y	155_K	1.431	0.89
101_S	112_W	1.422	0.89
140_G	168_L	1.416	0.89
79_S	85_H	1.406	0.88
192_P	199_V	1.404	0.88
181_S	200_S	1.391	0.87
153_A	161_F	1.381	0.87
181_S	203_V	1.373	0.86
185_S	196_E	1.364	0.86
200_S	217_V	1.363	0.86
149_I	156_D	1.362	0.86
189_D	202_N	1.357	0.85
155_K	158_V	1.349	0.85
45_I	109_I	1.343	0.85
165_N	168_L	1.339	0.84
82_R	85_H	1.323	0.83
153_A	156_D	1.308	0.83
210_P	213_P	1.307	0.82
152_L	159_L	1.296	0.82
190_Q	196_E	1.267	0.80
89_N	99_V	1.256	0.79
162_H	167_N	1.235	0.77
179_Y	202_N	1.228	0.77
13_Y	36_T	1.227	0.77
179_Y	195_L	1.221	0.76
141_S	144_E	1.221	0.76
139_A	148_V	1.220	0.76
211_H	214_Q	1.213	0.75
132_A	168_L	1.204	0.75
93_A	99_V	1.203	0.75
132_A	152_L	1.201	0.74
140_G	158_V	1.199	0.74
58_H	62_Q	1.191	0.74
163_N	167_N	1.183	0.73
69_C	74_F	1.174	0.72
196_E	201_E	1.165	0.71
27_A	30_Q	1.159	0.71
38_T	74_F	1.149	0.70
13_Y	38_T	1.149	0.70
212_R	215_S	1.146	0.69
7_G	31_L	1.145	0.69
195_L	204_V	1.145	0.69
139_A	147_R	1.142	0.69
179_Y	203_V	1.141	0.69
196_E	202_N	1.140	0.69
181_S	217_V	1.131	0.68
188_F	192_P	1.118	0.67
223_R	226_K	1.116	0.66
51_E	59_V	1.109	0.66
26_E	29_S	1.108	0.66
174_E	179_Y	1.106	0.65
188_F	191_V	1.098	0.65
217_V	222_S	1.097	0.64
94_K	99_V	1.097	0.64
144_E	147_R	1.096	0.64
109_I	114_Q	1.096	0.64
220_G	225_G	1.092	0.64
149_I	153_A	1.091	0.64
40_K	51_E	1.090	0.64
204_V	217_V	1.089	0.64
224_T	228_M	1.089	0.64
185_S	190_Q	1.087	0.63
91_Q	99_V	1.086	0.63
16_T	20_C	1.081	0.63
50_H	56_H	1.080	0.63
9_Y	68_K	1.076	0.62
156_D	165_N	1.076	0.62
34_I	74_F	1.070	0.62
103_I	112_W	1.067	0.61
120_R	123_R	1.064	0.61
135_T	153_A	1.063	0.61
160_Q	171_I	1.062	0.61
17_Y	20_C	1.060	0.61
173_Q	176_P	1.058	0.60
158_V	165_N	1.055	0.60
76_D	87_H	1.055	0.60
193_E	196_E	1.052	0.60
126_Q	130_N	1.039	0.58
132_A	142_K	1.039	0.58
179_Y	221_D	1.036	0.58
146_L	161_F	1.033	0.58
220_G	226_K	1.031	0.57
160_Q	163_N	1.027	0.57
133_Y	158_V	1.022	0.56
42_Y	111_D	1.018	0.56
179_Y	204_V	1.015	0.56
27_A	77_L	1.015	0.56

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	0.499	Contact Map
2hwtA	1	0.3843	99.9	0.8	Contact Map
2hw0A	1	0.4629	99.8	0.821	Contact Map
2qbyA	1	0.2314	95.2	0.946	Contact Map
3b9pA	1	0.2576	94.5	0.948	Contact Map
2v1uA	1	0.2489	94.4	0.948	Contact Map
3d8bA	2	0.31	94.3	0.948	Contact Map
3pfiA	2	0.2052	94.3	0.948	Contact Map
1sxjA	1	0.2358	94.2	0.949	Contact Map
4lcbA	1	0.2096	94.1	0.949	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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