OPENSEQ.org - 1493332112 - GREMLIN Submission

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nanC

ID:	1493332112	Query Sequence ALDVRGGYRSGSHAYETRLKVSEGWQNGWWASMESNTWNTINDVQVEVNYAIKLDDQWTVRPGMLTHFSSNGTRYGPYVKLSWDATKDLNFGIRYRYDWKAYRQQDLSGDMSRDNVHRWDGYVTYHINSDFTFAWQTTLYSKQNDYRYANHKKWATENAFVLQYHMTPDITPYIEYDYLDRQGVYNGRDNLSENSYRIGVSFKL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	204 (203)
Sequences:	228 (144.5)
Seq/Len:	1.123
Nf(neff/√len):	10.1

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: 1.123).

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
159_A	177_D	3.104	1.00
159_A	175_E	2.795	1.00
135_W	158_N	2.294	0.99
6_G	17_T	2.163	0.98
118_R	157_E	2.059	0.97
98_D	118_R	2.013	0.97
63_G	78_Y	1.953	0.96
120_D	138_T	1.725	0.90
5_R	197_R	1.695	0.89
30_W	49_N	1.609	0.86
90_N	124_T	1.605	0.85
5_R	18_R	1.586	0.85
120_D	136_Q	1.578	0.84
18_R	197_R	1.558	0.83
63_G	77_P	1.555	0.83
178_Y	194_N	1.534	0.82
25_W	30_W	1.525	0.81
178_Y	192_S	1.505	0.80
5_R	45_Q	1.493	0.79
86_T	89_L	1.481	0.79
6_G	15_Y	1.445	0.76
133_F	196_Y	1.362	0.70
116_V	120_D	1.359	0.70
60_V	81_L	1.359	0.70
3_D	173_Y	1.355	0.69
118_R	138_T	1.321	0.66
67_H	118_R	1.319	0.66
10_S	194_N	1.304	0.65
95_Y	117_H	1.289	0.64
94_R	172_P	1.287	0.63
59_T	82_S	1.283	0.63
18_R	94_R	1.272	0.62
81_L	93_I	1.269	0.62
53_K	56_D	1.268	0.62
119_W	198_I	1.268	0.62
86_T	115_N	1.253	0.60
151_H	192_S	1.242	0.59
53_K	150_N	1.241	0.59
57_Q	86_T	1.239	0.59
120_D	157_E	1.238	0.59
11_G	160_F	1.228	0.58
55_D	89_L	1.220	0.57
56_D	70_S	1.200	0.55
45_Q	195_S	1.197	0.55
10_S	178_Y	1.193	0.55
52_I	60_V	1.190	0.55
64_M	68_F	1.185	0.54
158_N	178_Y	1.180	0.54
122_Y	134_A	1.177	0.53
108_S	191_L	1.176	0.53
77_P	95_Y	1.174	0.53
177_D	195_S	1.171	0.53
4_V	135_W	1.157	0.51
70_S	198_I	1.155	0.51
98_D	139_L	1.144	0.50
33_M	41_I	1.144	0.50
36_N	43_D	1.141	0.50
72_G	100_K	1.140	0.50
16_E	20_K	1.138	0.50
45_Q	76_G	1.137	0.49
5_R	94_R	1.137	0.49
79_V	154_W	1.133	0.49
43_D	67_H	1.133	0.49
141_S	153_K	1.131	0.49
42_N	151_H	1.124	0.48
67_H	157_E	1.099	0.46
5_R	177_D	1.097	0.46
45_Q	63_G	1.092	0.45
19_L	162_L	1.084	0.44
73_T	84_D	1.081	0.44
5_R	195_S	1.075	0.44
63_G	94_R	1.075	0.44
155_A	180_D	1.071	0.43
38_W	131_F	1.068	0.43
5_R	8_Y	1.067	0.43
2_L	95_Y	1.066	0.43
20_K	32_S	1.061	0.42
19_L	54_L	1.060	0.42
75_Y	192_S	1.058	0.42
19_L	31_A	1.058	0.42
43_D	68_F	1.058	0.42
31_A	191_L	1.051	0.41
178_Y	193_E	1.045	0.41
34_E	76_G	1.043	0.41
79_V	83_W	1.040	0.40
90_N	137_T	1.039	0.40
188_R	191_L	1.032	0.40
161_V	173_Y	1.030	0.39
71_N	105_Q	1.026	0.39
161_V	203_K	1.016	0.38
85_A	89_L	1.015	0.38
85_A	90_N	1.015	0.38
83_W	152_K	1.007	0.37
98_D	157_E	1.004	0.37

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
2wjrA	1	0.9902	100	0.084	Contact Map
4fqeA	1	0.8137	100	0.109	Contact Map
2x9kA	1	0.9559	97.8	0.863	Contact Map
3qraA	1	0.7157	96.2	0.892	Contact Map
3dwoX	1	0.9951	96.1	0.893	Contact Map
1ormA	1	0.6618	96.1	0.893	Contact Map
1xkwA	1	0.9559	95.9	0.895	Contact Map
3qlbA	2	0.9951	95.8	0.895	Contact Map
3efmA	1	0.9755	95.8	0.895	Contact Map
3bs0A	2	0.9608	95.5	0.897	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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