OPENSEQ.org - 1411595771 - GREMLIN Submission

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1ARBA

ID:	1411595771	Query Sequence GVSGSCNIDVVCPEGDGRRDIIRAVGAYSKSGTLACTGSLVNNTANDRKMYFLTAHHCGMGTASTAASIVVYWNYQNSTCRAPNTPASGANGDGSMSQTQSGSTVKATYATSDFTLLELNNAANPAFNLFWAGWDRRDQNYPGAIAIHHPNVAEKRISNSTSPTSFVAWGGGAGTTHLNVQWQPSGGVTEPGSSGSPIYSPEKRVLGQLHGGPSSCSATGTNRSDQYGRVFTSWTGGGAAASRLSDWLDPASTGAQFIDGLDS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	263 (252)
Sequences:	306 (218.1)
Seq/Len:	1.214
Nf(neff/√len):	13.7

HHblits Results: (2013_03)
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: 1.214).

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
36_C	58_C	2.338	0.99
129_L	200_S	2.320	0.99
53_L	205_V	2.262	0.99
244_L	248_L	2.181	0.98
39_S	197_P	2.129	0.98
40_L	123_A	2.118	0.98
112_S	244_L	2.050	0.97
196_S	227_Y	1.891	0.95
38_G	52_F	1.833	0.94
193_S	196_S	1.829	0.94
40_L	52_F	1.818	0.94
197_P	205_V	1.801	0.93
188_V	227_Y	1.799	0.93
55_A	216_C	1.718	0.91
132_A	199_Y	1.593	0.86
189_T	225_D	1.564	0.85
37_T	55_A	1.550	0.84
146_A	196_S	1.522	0.83
55_A	194_S	1.508	0.82
57_H	194_S	1.503	0.82
146_A	227_Y	1.496	0.81
36_C	55_A	1.491	0.81
37_T	193_S	1.484	0.81
212_G	227_Y	1.481	0.80
208_Q	233_S	1.472	0.80
24_A	27_A	1.469	0.80
131_W	209_L	1.452	0.79
28_Y	117_L	1.449	0.78
193_S	228_G	1.440	0.78
133_G	216_C	1.439	0.78
18_R	203_K	1.415	0.76
233_S	236_G	1.412	0.76
177_H	211_G	1.403	0.75
188_V	225_D	1.371	0.73
15_G	18_R	1.365	0.72
114_F	247_W	1.365	0.72
135_D	190_E	1.357	0.72
70_V	93_D	1.341	0.70
114_F	210_H	1.338	0.70
198_I	227_Y	1.329	0.69
193_S	209_L	1.327	0.69
55_A	133_G	1.325	0.69
114_F	208_Q	1.311	0.68
51_Y	177_H	1.294	0.66
207_G	216_C	1.283	0.65
178_L	217_S	1.281	0.65
54_T	115_T	1.281	0.65
57_H	216_C	1.277	0.65
30_K	117_L	1.277	0.65
115_T	197_P	1.274	0.65
193_S	208_Q	1.272	0.65
114_F	244_L	1.262	0.64
4_G	45_A	1.261	0.64
192_G	227_Y	1.256	0.63
58_C	216_C	1.254	0.63
54_T	59_G	1.250	0.63
147_I	155_K	1.234	0.61
19_R	22_I	1.218	0.60
19_R	227_Y	1.216	0.59
208_Q	228_G	1.209	0.59
179_N	190_E	1.204	0.58
54_T	156_R	1.195	0.57
182_W	225_D	1.194	0.57
199_Y	215_S	1.177	0.56
37_T	196_S	1.164	0.54
82_A	202_E	1.160	0.54
114_F	228_G	1.156	0.54
36_C	216_C	1.152	0.53
55_A	58_C	1.152	0.53
211_G	227_Y	1.150	0.53
51_Y	203_K	1.150	0.53
190_E	193_S	1.145	0.53
37_T	190_E	1.141	0.52
80_C	156_R	1.138	0.52
210_H	228_G	1.134	0.51
41_V	68_S	1.134	0.51
111_T	174_G	1.130	0.51
42_N	116_L	1.129	0.51
112_S	248_L	1.114	0.50
105_V	185_S	1.114	0.50
49_K	118_E	1.113	0.49
233_S	244_L	1.112	0.49
11_V	22_I	1.111	0.49
56_H	105_V	1.111	0.49
191_P	196_S	1.110	0.49
185_S	219_T	1.107	0.49
39_S	42_N	1.100	0.48
102_G	112_S	1.088	0.47
211_G	215_S	1.085	0.47
236_G	243_R	1.085	0.47
47_D	50_M	1.083	0.46
182_W	217_S	1.082	0.46
54_T	159_N	1.081	0.46
67_A	118_E	1.081	0.46
178_L	198_I	1.078	0.46
40_L	191_P	1.071	0.45
18_R	132_A	1.069	0.45
196_S	208_Q	1.065	0.45
49_K	179_N	1.064	0.45
191_P	217_S	1.060	0.44
230_V	247_W	1.057	0.44
23_R	48_R	1.056	0.44
173_A	177_H	1.055	0.44
54_T	61_G	1.054	0.44
177_H	210_H	1.053	0.44
189_T	209_L	1.043	0.43
58_C	133_G	1.040	0.42
178_L	249_D	1.038	0.42
72_Y	75_Y	1.037	0.42
242_S	257_F	1.037	0.42
119_L	181_Q	1.035	0.42
237_G	242_S	1.033	0.42
73_W	156_R	1.026	0.41
209_L	230_V	1.022	0.41
119_L	200_S	1.018	0.40
182_W	189_T	1.017	0.40
35_A	161_T	1.014	0.40
102_G	228_G	1.007	0.39
43_N	116_L	1.004	0.39

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: (06Sep14)
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
4nsvA	2	1	100	0.274	Contact Map
2f83A	1	0.7414	100	0.469	Contact Map
3nxpA	1	0.8327	100	0.471	Contact Map
4nzqA	1	0.8403	100	0.472	Contact Map
4igdA	1	0.8365	100	0.483	Contact Map
4kkdA	2	0.8213	100	0.484	Contact Map
2xrcA	4	0.7757	100	0.49	Contact Map
2b9lA	1	0.8631	100	0.49	Contact Map
2xxlA	2	0.8821	100	0.495	Contact Map
4durA	2	0.7985	100	0.497	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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