OPENSEQ.org - 1428460924 - GREMLIN Submission

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new-cs2

ID:	1428460924	Query Sequence MSKATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQN	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	267 (264)
Sequences:	386 (219.9)
Seq/Len:	1.462
Nf(neff/√len):	13.5

Jackhmmer Results: (2015_01_07)
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: 1.462).

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
49_E	84_Y	2.964	1.00
123_G	168_T	2.946	1.00
27_E	85_N	2.777	1.00
49_E	80_L	2.583	1.00
55_I	58_L	2.532	1.00
7_K	26_H	2.476	1.00
247_E	250_R	2.414	1.00
54_K	249_E	2.349	0.99
105_Y	145_R	2.306	0.99
253_K	257_E	2.244	0.99
54_K	252_R	2.225	0.99
41_T	69_S	2.194	0.99
249_E	252_R	2.184	0.99
40_T	66_T	2.134	0.99
62_V	73_T	2.113	0.99
36_L	48_V	2.094	0.99
22_F	198_L	2.039	0.98
48_V	58_L	2.022	0.98
53_P	84_Y	2.017	0.98
114_E	140_V	1.969	0.98
152_E	186_R	1.953	0.97
127_P	174_S	1.937	0.97
44_L	73_T	1.925	0.97
123_G	171_I	1.882	0.97
38_V	44_L	1.826	0.96
249_E	253_K	1.804	0.95
41_T	76_P	1.758	0.95
147_L	150_L	1.687	0.93
78_K	117_D	1.682	0.93
24_I	85_N	1.672	0.92
44_L	48_V	1.663	0.92
49_E	83_K	1.635	0.91
173_K	195_Y	1.616	0.91
6_Y	255_G	1.580	0.89
36_L	58_L	1.510	0.86
243_D	246_V	1.509	0.86
29_Q	260_L	1.493	0.85
231_I	255_G	1.490	0.85
30_T	56_C	1.484	0.85
102_K	135_Q	1.479	0.85
111_R	114_E	1.469	0.84
195_Y	199_I	1.457	0.83
129_I	150_L	1.451	0.83
204_V	223_V	1.416	0.81
153_L	220_V	1.400	0.80
40_T	43_E	1.384	0.79
25_M	230_I	1.383	0.79
36_L	55_I	1.382	0.79
41_T	71_E	1.381	0.79
41_T	73_T	1.370	0.78
89_F	183_I	1.353	0.77
118_I	180_I	1.342	0.76
17_V	117_D	1.337	0.75
120_N	147_L	1.303	0.73
21_L	87_L	1.302	0.73
103_L	107_A	1.279	0.71
163_E	166_K	1.274	0.70
78_K	82_A	1.272	0.70
89_F	120_N	1.270	0.70
68_F	74_V	1.251	0.68
21_L	118_I	1.249	0.68
89_F	148_L	1.231	0.66
220_V	248_G	1.227	0.66
76_P	79_A	1.210	0.64
48_V	81_S	1.206	0.64
3_K	262_R	1.205	0.64
252_R	256_W	1.204	0.64
51_L	248_G	1.204	0.64
205_G	218_R	1.197	0.63
8_E	11_A	1.196	0.63
36_L	44_L	1.195	0.63
19_A	23_N	1.188	0.62
257_E	261_R	1.187	0.62
210_G	216_Q	1.179	0.62
154_S	202_P	1.179	0.62
180_I	198_L	1.167	0.60
44_L	65_L	1.167	0.60
26_H	29_Q	1.157	0.59
47_L	244_A	1.152	0.59
17_V	57_L	1.149	0.59
13_H	196_D	1.137	0.57
205_G	209_K	1.135	0.57
221_D	261_R	1.134	0.57
48_V	55_I	1.133	0.57
101_V	129_I	1.132	0.57
79_A	82_A	1.129	0.57
87_L	249_E	1.123	0.56
25_M	33_C	1.122	0.56
220_V	237_L	1.122	0.56
202_P	233_V	1.121	0.56
222_D	225_S	1.114	0.55
148_L	182_F	1.102	0.54
62_V	110_Y	1.096	0.53
62_V	65_L	1.095	0.53
182_F	197_W	1.093	0.53
110_Y	122_H	1.089	0.52
57_L	200_M	1.088	0.52
183_I	228_S	1.075	0.51
154_S	233_V	1.074	0.51
130_V	156_K	1.071	0.51
184_A	199_I	1.071	0.51
227_G	262_R	1.069	0.50
23_N	27_E	1.063	0.50
122_H	202_P	1.048	0.48
134_K	177_D	1.048	0.48
135_Q	213_L	1.045	0.48
185_Q	228_S	1.043	0.48
238_F	252_R	1.038	0.47
125_V	133_L	1.030	0.46
31_N	255_G	1.029	0.46
130_V	147_L	1.025	0.46
207_D	250_R	1.024	0.46
232_I	255_G	1.021	0.46
55_I	81_S	1.018	0.45
34_A	144_P	1.013	0.45
87_L	117_D	1.009	0.44
46_E	50_A	1.008	0.44
6_Y	31_N	1.007	0.44
38_V	65_L	1.004	0.44
167_G	170_D	1.002	0.44
34_A	117_D	1.002	0.44

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: (31Jan15)
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
3g3dA	2	0.9588	100	0.487	Contact Map
3gdmA	2	0.9775	100	0.496	Contact Map
3ewwA	2	0.9551	100	0.564	Contact Map
2fdsA	2	0.8727	100	0.627	Contact Map
3n3mA	2	0.9101	100	0.633	Contact Map
3v75A	1	0.9064	100	0.664	Contact Map
4mjzA	2	0.8801	100	0.67	Contact Map
2yyuA	2	0.8052	100	0.672	Contact Map
3qw3A	2	0.8315	100	0.674	Contact Map
3r89A	2	0.8689	100	0.681	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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