OPENSEQ.org - 1402694783 - GREMLIN Submission

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solo_1wdn

ID:	1402694783	Query Sequence LVVATDTAFVPFEFKQGDLYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKWFGTEP	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	221 (214)
Sequences:	714 (579.7)
Seq/Len:	3.336
Nf(neff/√len):	39.6

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: 3.336).

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
201_K	205_E	4.191	1.00
142_L	147_A	3.713	1.00
109_A	147_A	3.054	1.00
132_F	141_E	2.364	1.00
142_L	150_V	2.230	1.00
68_T	71_R	2.039	1.00
69_D	72_K	1.951	1.00
195_K	198_G	1.912	1.00
185_F	196_V	1.894	1.00
11_P	14_F	1.890	1.00
52_A	58_V	1.844	0.99
203_L	206_N	1.697	0.99
66_T	71_R	1.696	0.99
71_R	77_F	1.680	0.99
61_A	65_I	1.651	0.98
16_Q	19_L	1.640	0.98
202_T	206_N	1.624	0.98
197_N	201_K	1.604	0.98
9_F	13_E	1.588	0.98
102_D	105_G	1.587	0.98
111_K	114_T	1.528	0.97
30_A	34_E	1.521	0.97
130_R	147_A	1.508	0.97
34_E	202_T	1.462	0.96
210_N	214_K	1.461	0.96
193_R	197_N	1.453	0.96
186_P	190_D	1.418	0.95
67_I	71_R	1.416	0.95
118_D	122_A	1.408	0.94
98_K	102_D	1.401	0.94
209_Y	213_Y	1.397	0.94
141_E	147_A	1.397	0.94
208_T	211_E	1.369	0.93
153_D	181_Y	1.359	0.93
105_G	113_G	1.358	0.93
213_Y	216_W	1.355	0.93
197_N	204_R	1.339	0.92
185_F	193_R	1.334	0.92
147_A	150_V	1.333	0.92
32_A	39_Y	1.316	0.91
153_D	156_N	1.306	0.91
85_G	90_V	1.287	0.90
97_V	102_D	1.285	0.90
99_S	102_D	1.277	0.90
67_I	72_K	1.275	0.90
9_F	12_F	1.275	0.90
100_V	103_L	1.269	0.89
134_N	137_N	1.266	0.89
186_P	189_S	1.264	0.89
206_N	211_E	1.232	0.87
161_I	169_F	1.232	0.87
197_N	213_Y	1.228	0.87
65_I	71_R	1.223	0.87
42_K	46_F	1.223	0.87
34_E	206_N	1.219	0.87
105_G	108_V	1.217	0.87
67_I	79_D	1.217	0.87
42_K	45_D	1.199	0.85
175_S	178_A	1.198	0.85
94_N	97_V	1.196	0.85
93_N	97_V	1.160	0.83
203_L	208_T	1.158	0.83
40_E	46_F	1.156	0.82
190_D	194_D	1.155	0.82
160_F	164_A	1.152	0.82
152_H	155_P	1.141	0.81
124_I	127_K	1.122	0.80
51_P	54_Q	1.121	0.80
53_L	61_A	1.119	0.80
40_E	45_D	1.116	0.79
40_E	47_S	1.112	0.79
4_A	20_Y	1.108	0.79
67_I	80_G	1.105	0.78
84_S	92_A	1.104	0.78
194_D	198_G	1.104	0.78
195_K	204_R	1.104	0.78
43_P	46_F	1.099	0.78
109_A	142_L	1.099	0.78
109_A	138_A	1.094	0.77
45_D	48_G	1.093	0.77
119_Y	123_N	1.089	0.77
189_S	192_L	1.072	0.75
213_Y	217_F	1.067	0.75
159_Y	163_T	1.059	0.74
76_D	79_D	1.058	0.74
56_K	61_A	1.056	0.74
87_L	90_V	1.055	0.74
11_P	15_K	1.049	0.73
206_N	212_I	1.046	0.73
208_T	212_I	1.044	0.73
201_K	204_R	1.043	0.72
46_F	50_I	1.041	0.72
125_K	128_D	1.035	0.72
63_A	81_Y	1.033	0.71
165_G	168_Q	1.028	0.71
25_V	64_G	1.023	0.70
119_Y	127_K	1.022	0.70
46_F	53_L	1.017	0.70
86_L	89_M	1.016	0.70
108_V	113_G	1.011	0.69
28_W	62_L	1.006	0.69
157_I	177_E	1.006	0.69
71_R	76_D	1.005	0.68

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: (07Jun14)
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
1wdnA	1	1	100	0.262	Contact Map
4oenA	2	0.9729	100	0.33	Contact Map
1pb7A	1	0.9457	100	0.383	Contact Map
1yaeA	6	0.9683	100	0.383	Contact Map
2rc8A	2	0.9729	100	0.383	Contact Map
2ylnA	1	0.9864	100	0.387	Contact Map
4f3pA	2	0.9955	100	0.398	Contact Map
3kzgA	4	0.9774	100	0.403	Contact Map
3vv5A	2	0.9819	100	0.407	Contact Map
4io2A	2	0.9638	100	0.408	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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