OPENSEQ.org - 1469716672 - GREMLIN Submission

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BAF47_homo

ID:	1469716672	Query Sequence SSHHLDAVPCSTTINRNRMGRDKKRTFPLCFDDHDPAVIHENASQPEVLVPIRLDMEIDGQKLRDAFTWNMNEKLMTPEMFSEILCDDLDLNPLTFVPAIASAIRQQIESYPTDSILEDQSDQRVIIKLNIHVGNISLVDQFEWDMSEKENSPEKFALKLCSELGLGGEFVTTIAYSIRGQLSWHQKTYAFSENPLPTVEIAIRNTGDADQWCPLLETLTDAEMEKKIRD	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	230 (190)
Sequences:	470 (268.6)
Seq/Len:	2.474
Nf(neff/√len):	19.5

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: 2.474).

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
69_W	81_F	2.779	1.00
176_Y	180_G	2.381	1.00
128_K	141_Q	2.288	1.00
63_L	85_L	2.025	0.99
52_I	108_I	2.018	0.99
66_A	173_T	1.769	0.98
220_T	227_K	1.729	0.98
79_E	105_R	1.720	0.98
78_P	82_S	1.713	0.98
130_N	137_S	1.691	0.97
47_E	70_N	1.597	0.96
149_K	175_A	1.584	0.96
38_V	225_E	1.575	0.96
50_V	108_I	1.497	0.94
178_I	181_Q	1.478	0.93
138_L	160_L	1.469	0.93
71_M	108_I	1.455	0.92
59_D	100_I	1.440	0.92
86_C	165_G	1.394	0.90
158_L	171_V	1.383	0.90
101_A	105_R	1.355	0.88
90_D	163_E	1.331	0.87
54_L	57_E	1.324	0.87
124_R	178_I	1.323	0.87
79_E	101_A	1.307	0.86
55_D	64_R	1.306	0.86
99_A	163_E	1.303	0.86
203_I	209_A	1.296	0.85
146_M	151_N	1.291	0.85
66_A	172_T	1.277	0.84
57_E	84_I	1.271	0.84
154_E	179_R	1.266	0.83
110_S	180_G	1.261	0.83
170_F	181_Q	1.258	0.83
131_I	172_T	1.257	0.83
170_F	173_T	1.253	0.82
122_D	147_S	1.252	0.82
157_A	173_T	1.248	0.82
78_P	104_I	1.247	0.82
86_C	123_Q	1.243	0.82
145_D	148_E	1.237	0.81
182_L	193_E	1.225	0.80
44_S	72_N	1.216	0.80
104_I	111_Y	1.216	0.80
154_E	224_M	1.212	0.80
124_R	176_Y	1.212	0.80
99_A	102_S	1.196	0.78
53_R	143_E	1.191	0.78
200_E	218_T	1.190	0.78
50_V	187_K	1.188	0.78
154_E	175_A	1.179	0.77
55_D	58_I	1.166	0.76
130_N	176_Y	1.164	0.76
99_A	106_Q	1.157	0.75
126_I	167_G	1.155	0.75
68_T	175_A	1.148	0.74
62_K	67_F	1.145	0.74
71_M	211_Q	1.145	0.74
50_V	100_I	1.144	0.74
57_E	90_D	1.141	0.73
66_A	216_L	1.137	0.73
40_H	43_A	1.135	0.73
110_S	176_Y	1.131	0.73
45_Q	220_T	1.127	0.72
134_G	224_M	1.114	0.71
175_A	179_R	1.105	0.70
47_E	121_S	1.103	0.70
156_F	178_I	1.103	0.70
82_S	92_N	1.101	0.70
90_D	160_L	1.095	0.69
76_M	88_D	1.092	0.69
222_A	225_E	1.089	0.68
54_L	103_A	1.085	0.68
85_L	211_Q	1.084	0.68
42_N	218_T	1.082	0.68
67_F	154_E	1.078	0.67
199_V	202_A	1.071	0.67
52_I	116_I	1.071	0.67
122_D	224_M	1.059	0.65
53_R	59_D	1.056	0.65
56_M	127_I	1.040	0.63
93_P	150_E	1.039	0.63
108_I	117_L	1.037	0.63
161_C	216_L	1.029	0.62
122_D	175_A	1.028	0.62
222_A	226_K	1.022	0.61
73_E	222_A	1.019	0.61
73_E	77_T	1.018	0.61
153_P	175_A	1.013	0.60
60_G	160_L	1.012	0.60
44_S	94_L	1.010	0.60
39_I	182_L	1.008	0.60
82_S	86_C	1.004	0.59
193_E	223_E	1.002	0.59
74_K	90_D	1.000	0.59

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
2lruA	1	0.387	72.4	0.949	Contact Map
4bjtA	3	0.4957	27.4	0.961	Contact Map
3cuqA	1	0.4304	21.5	0.963	Contact Map
2d6fC	2	0.5913	13.4	0.966	Contact Map
2dplA	2	0.5435	12.1	0.967	Contact Map
3cuqB	1	0.4348	11.6	0.967	Contact Map
2wpnA	1	0.2	8.3	0.969	Contact Map
2k89A	1	0.3478	7.4	0.97	Contact Map
2v3sA	2	0.3913	7.3	0.97	Contact Map
1u5tA	1	0.4522	6	0.972	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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