OPENSEQ.org - 1508531819 - GREMLIN Submission

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Sigmar1

ID:	1508531819	Query Sequence MQWAVGRRWAWAALLLAVAAVLTQVVWLWLGTQSFVFQREEIAQLARQYAGLDHELAFSRLIVELRRLHPGHVLPDEELQWVFVNAGGWMGAMCLLHASLSEYVLLFGTALGSRGHSGRYWAEISDTIISGTFHQWREGTTKSEVFYPGETVVHGPGEATAVEWGPNTWMVEYGRGVIPSTLAFALADTVFSTQDFLTLFYTLRSYARGLRLELTTYLFGQDP	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	223 (205)
Sequences:	293 (192.7)
Seq/Len:	1.429
Nf(neff/√len):	13.5

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: 1.429).

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
190_V	199_L	2.866	1.00
95_L	206_Y	2.792	1.00
80_Q	208_R	1.924	0.97
92_A	136_W	1.880	0.96
127_T	151_T	1.875	0.96
92_A	169_W	1.804	0.95
201_Y	204_R	1.802	0.95
43_A	151_T	1.762	0.94
164_W	168_T	1.687	0.93
152_V	160_T	1.679	0.92
147_Y	150_E	1.654	0.92
86_A	107_F	1.652	0.91
186_L	203_L	1.623	0.90
88_G	188_D	1.617	0.90
211_R	215_T	1.614	0.90
130_S	148_P	1.582	0.89
14_L	18_V	1.581	0.89
144_E	160_T	1.573	0.89
124_I	174_G	1.541	0.87
58_F	106_L	1.533	0.87
135_Q	152_V	1.524	0.86
117_S	152_V	1.519	0.86
12_A	22_L	1.512	0.86
96_L	150_E	1.478	0.84
48_Q	64_E	1.455	0.83
189_T	199_L	1.448	0.82
61_L	96_L	1.420	0.81
121_W	180_S	1.394	0.79
92_A	138_E	1.375	0.78
103_Y	108_G	1.344	0.75
57_A	130_S	1.319	0.73
119_R	197_L	1.317	0.73
62_I	106_L	1.315	0.73
135_Q	160_T	1.313	0.73
119_R	159_A	1.311	0.73
44_Q	67_R	1.303	0.72
44_Q	48_Q	1.278	0.70
13_A	18_V	1.271	0.69
155_G	158_E	1.256	0.68
16_L	22_L	1.244	0.67
104_V	120_Y	1.235	0.66
186_L	189_T	1.234	0.66
52_L	60_R	1.225	0.65
82_V	182_L	1.224	0.65
62_I	96_L	1.224	0.65
82_V	205_S	1.212	0.64
53_D	191_F	1.206	0.63
134_H	143_S	1.193	0.62
121_W	168_T	1.192	0.62
181_T	185_A	1.192	0.62
117_S	153_V	1.187	0.62
76_D	140_T	1.164	0.59
144_E	152_V	1.161	0.59
16_L	26_V	1.159	0.59
17_A	27_W	1.141	0.57
174_G	185_A	1.141	0.57
15_L	43_A	1.141	0.57
189_T	203_L	1.124	0.55
45_L	216_T	1.124	0.55
57_A	127_T	1.109	0.54
205_S	208_R	1.103	0.53
41_E	68_L	1.102	0.53
85_N	193_T	1.102	0.53
137_R	158_E	1.096	0.53
44_Q	47_R	1.091	0.52
89_W	162_V	1.086	0.51
40_E	191_F	1.084	0.51
45_L	60_R	1.079	0.51
177_V	206_Y	1.078	0.51
48_Q	60_R	1.078	0.51
126_D	170_M	1.074	0.50
90_M	193_T	1.074	0.50
186_L	190_V	1.072	0.50
45_L	61_L	1.072	0.50
117_S	154_H	1.070	0.50
107_F	133_F	1.062	0.49
70_P	212_L	1.061	0.49
34_S	101_S	1.060	0.49
156_P	159_A	1.058	0.49
95_L	177_V	1.056	0.48
85_N	90_M	1.054	0.48
72_H	76_D	1.051	0.48
84_V	185_A	1.051	0.48
137_R	140_T	1.049	0.48
18_V	211_R	1.048	0.48
12_A	15_L	1.048	0.48
45_L	48_Q	1.044	0.47
57_A	148_P	1.044	0.47
15_L	22_L	1.043	0.47
150_E	180_S	1.043	0.47
69_H	148_P	1.041	0.47
163_E	173_Y	1.038	0.47
12_A	19_A	1.036	0.46
120_Y	129_I	1.036	0.46
111_L	132_T	1.033	0.46
86_A	133_F	1.032	0.46
59_S	205_S	1.025	0.45
124_I	170_M	1.024	0.45
174_G	181_T	1.023	0.45
43_A	47_R	1.022	0.45
85_N	116_H	1.019	0.45
153_V	157_G	1.015	0.44
58_F	163_E	1.012	0.44
38_Q	215_T	1.012	0.44
126_D	133_F	1.010	0.44
11_W	25_V	1.009	0.44
126_D	181_T	1.008	0.44
53_D	57_A	1.006	0.43
45_L	63_V	1.006	0.43
126_D	174_G	1.005	0.43
160_T	213_E	1.004	0.43
200_F	204_R	1.003	0.43
15_L	18_V	1.002	0.43
65_L	83_F	1.001	0.43
135_Q	144_E	1.001	0.43

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
3balA	4	0.6323	89.3	0.947	Contact Map
2o1qA	2	0.6099	76.7	0.955	Contact Map
3cjxA	8	0.6726	62.9	0.959	Contact Map
5bpxA	1	0	53.4	0.961	Contact Map
1yhfA	1	0.5112	43.6	0.963	Contact Map
1fi2A	1	0.7354	38.1	0.965	Contact Map
2q30A	8	0.4439	33.9	0.965	Contact Map
2ozjA	2	0.4888	33.2	0.966	Contact Map
1v70A	1	0.4484	27.2	0.967	Contact Map
1sfnA	2	0.722	20.8	0.969	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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