OPENSEQ.org - 1518105022 - GREMLIN Submission

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ID:	1518105022	Query Sequence MVKKLVMAQKRGETRALCLGVTMVVCAVITYYILVTTVLPLYQKSVWTQESKCHLIETNIRDQEELKGKKVPQYPCLWVNVSAAGRWAVLYHTEDTRDQNQQCSYIPGSVDNYQTARADVEKVRAKFQEQQVFYCFSAPRGNETSVLFQRLYGPQALLFSLFWPTFLLTGGLLIIAMVKSNQYLSILAAQK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	191 (187)
Sequences:	312 (191.4)
Seq/Len:	1.668
Nf(neff/√len):	14.0

Jackhmmer Results: (2016_04)
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: 1.668).

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
76_C	81_V	2.554	1.00
158_L	162_F	2.472	1.00
103_C	107_P	2.375	1.00
76_C	103_C	1.867	0.97
5_L	9_Q	1.758	0.96
59_N	146_V	1.672	0.94
66_L	76_C	1.667	0.94
75_P	81_V	1.653	0.93
103_C	109_S	1.622	0.93
12_G	16_A	1.580	0.91
90_L	93_T	1.564	0.91
76_C	164_P	1.534	0.90
90_L	163_W	1.525	0.89
17_L	68_G	1.513	0.89
90_L	94_E	1.482	0.87
137_S	146_V	1.460	0.86
109_S	112_N	1.453	0.86
106_I	120_V	1.414	0.84
128_Q	136_F	1.374	0.81
178_V	182_Q	1.370	0.81
179_K	182_Q	1.369	0.81
138_A	145_S	1.365	0.81
159_F	163_W	1.355	0.80
153_G	173_L	1.348	0.80
4_K	10_K	1.342	0.79
38_V	173_L	1.338	0.79
30_T	146_V	1.316	0.77
29_I	136_F	1.311	0.77
68_G	72_P	1.303	0.76
75_P	90_L	1.297	0.76
76_C	90_L	1.290	0.75
41_L	116_A	1.271	0.74
23_M	167_L	1.267	0.73
168_L	175_I	1.264	0.73
165_T	168_L	1.262	0.73
53_C	135_C	1.255	0.72
126_K	129_E	1.243	0.71
59_N	136_F	1.230	0.70
90_L	96_T	1.226	0.70
88_A	173_L	1.224	0.70
49_Q	95_D	1.219	0.69
171_G	175_I	1.191	0.67
65_E	69_K	1.191	0.67
26_C	147_L	1.188	0.66
27_A	171_G	1.186	0.66
23_M	182_Q	1.184	0.66
35_V	77_L	1.181	0.66
50_E	136_F	1.174	0.65
163_W	171_G	1.166	0.64
76_C	94_E	1.165	0.64
76_C	79_V	1.161	0.64
103_C	163_W	1.159	0.64
150_R	158_L	1.159	0.64
177_M	185_S	1.154	0.63
19_L	23_M	1.153	0.63
17_L	72_P	1.142	0.62
53_C	76_C	1.140	0.62
66_L	164_P	1.130	0.61
54_H	68_G	1.124	0.60
27_A	49_Q	1.124	0.60
72_P	109_S	1.124	0.60
157_L	168_L	1.121	0.60
133_F	136_F	1.120	0.60
87_W	146_V	1.115	0.59
74_Y	81_V	1.111	0.59
123_V	148_F	1.109	0.59
76_C	107_P	1.101	0.58
11_R	14_T	1.089	0.56
39_L	42_Y	1.088	0.56
60_I	170_G	1.087	0.56
138_A	165_T	1.081	0.56
81_V	107_P	1.079	0.55
17_L	33_I	1.079	0.55
53_C	81_V	1.054	0.53
90_L	103_C	1.050	0.52
27_A	147_L	1.050	0.52
70_K	76_C	1.048	0.52
6_V	136_F	1.048	0.52
5_L	11_R	1.046	0.52
9_Q	18_C	1.045	0.52
73_Q	120_V	1.040	0.51
20_G	171_G	1.039	0.51
183_Y	186_I	1.038	0.51
156_A	167_L	1.036	0.51
57_E	166_F	1.034	0.51
17_L	102_Q	1.033	0.51
19_L	177_M	1.032	0.50
56_I	87_W	1.032	0.50
68_G	109_S	1.015	0.49
80_N	147_L	1.015	0.49
170_G	181_N	1.013	0.48
5_L	188_A	1.010	0.48
134_Y	140_R	1.008	0.48
158_L	177_M	1.005	0.48
68_G	171_G	1.005	0.48
75_P	150_R	1.005	0.48
169_T	173_L	1.004	0.47

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

See coupling matrix (for protein design or mutagenesis)
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
2m8rA	1	0.199	24	0.941	Contact Map
3wu2F	2	0.1728	14.5	0.947	Contact Map
1rh5B	1	0.2356	4.8	0.957	Contact Map
2zxeG	1	0.2042	4.7	0.957	Contact Map
4w252	1	0.2461	4.2	0.958	Contact Map
3uh0A	1	0.3141	3.7	0.959	Contact Map
2m20A	2	0.2042	3.7	0.96	Contact Map
2ww9B	1	0.2356	3.7	0.96	Contact Map
3mp7B	1	0.2251	3.2	0.961	Contact Map
2jo1A	1	0.267	2.7	0.962	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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