OPENSEQ.org - 1504072724 - GREMLIN Submission

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RB1600-2100

ID:	1504072724	Query Sequence QHDKSFQDIMKCYRTQPQASSHVSLTFLNRYLNHKHSIDNQHFSRMYLQQELCISSAPPTPTRLAGLGATVDGDERGDLIQFYNTIFVTKLKSYVRKFSPTGDQKVGLEQKNLSPIPLPRTHMQSPRRVSVRHPIYISPHKNGRPLTPTSAMLYCFGKSPAKNLQDITSMIKSGEQPTKKRALNYDTNENPAKRLCSAGGADRTLFQKLKDIDTVRQAANANQ	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	223 (201)
Sequences:	310 (199.2)
Seq/Len:	1.542
Nf(neff/√len):	14.1

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: 1.542).

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
164_L	168_T	2.934	1.00
138_S	141_K	2.087	0.99
164_L	167_I	2.067	0.99
56_S	62_T	1.925	0.97
56_S	60_T	1.835	0.96
35_K	38_I	1.803	0.96
113_L	117_P	1.760	0.95
97_K	156_F	1.665	0.93
25_L	78_D	1.631	0.92
60_T	63_R	1.606	0.91
77_G	94_Y	1.597	0.91
59_P	63_R	1.590	0.90
59_P	64_L	1.581	0.90
58_P	63_R	1.579	0.90
6_F	13_Y	1.531	0.88
130_S	133_H	1.524	0.88
55_S	59_P	1.517	0.88
57_A	60_T	1.501	0.87
55_S	58_P	1.495	0.86
57_A	63_R	1.454	0.84
16_Q	27_F	1.442	0.84
56_S	59_P	1.427	0.83
60_T	64_L	1.411	0.82
214_T	217_Q	1.397	0.81
78_D	84_N	1.394	0.81
55_S	60_T	1.392	0.81
13_Y	17_P	1.350	0.78
34_H	37_S	1.336	0.77
56_S	63_R	1.329	0.76
115_P	159_S	1.324	0.76
19_A	79_L	1.322	0.76
13_Y	16_Q	1.318	0.75
58_P	64_L	1.307	0.74
58_P	62_T	1.294	0.73
24_S	27_F	1.275	0.72
38_I	41_Q	1.269	0.71
35_K	39_D	1.269	0.71
39_D	55_S	1.252	0.70
9_I	13_Y	1.247	0.69
59_P	62_T	1.238	0.69
14_R	78_D	1.238	0.69
213_D	217_Q	1.226	0.68
29_N	77_G	1.224	0.67
11_K	14_R	1.220	0.67
16_Q	25_L	1.210	0.66
55_S	62_T	1.201	0.65
18_Q	78_D	1.192	0.64
168_T	171_I	1.190	0.64
9_I	19_A	1.189	0.64
9_I	25_L	1.186	0.64
9_I	16_Q	1.174	0.63
114_S	159_S	1.168	0.62
37_S	41_Q	1.166	0.62
207_Q	210_K	1.164	0.62
27_F	78_D	1.163	0.62
55_S	63_R	1.161	0.61
17_P	27_F	1.158	0.61
6_F	9_I	1.154	0.61
86_I	167_I	1.146	0.60
36_H	39_D	1.143	0.60
56_S	64_L	1.118	0.57
215_V	218_A	1.112	0.56
151_A	156_F	1.112	0.56
164_L	171_I	1.103	0.56
167_I	170_M	1.103	0.56
41_Q	66_G	1.103	0.56
58_P	66_G	1.094	0.55
167_I	171_I	1.093	0.54
14_R	17_P	1.086	0.54
190_N	194_R	1.079	0.53
171_I	174_G	1.075	0.53
207_Q	215_V	1.074	0.53
14_R	24_S	1.073	0.52
163_N	168_T	1.072	0.52
204_T	213_D	1.071	0.52
203_R	206_F	1.071	0.52
83_Y	87_F	1.066	0.52
34_H	38_I	1.065	0.52
147_T	151_A	1.064	0.51
205_L	209_L	1.063	0.51
41_Q	57_A	1.060	0.51
55_S	64_L	1.060	0.51
25_L	80_I	1.059	0.51
37_S	62_T	1.057	0.51
206_F	210_K	1.057	0.51
158_K	163_N	1.055	0.51
39_D	66_G	1.054	0.50
147_T	150_S	1.054	0.50
66_G	70_T	1.052	0.50
80_I	83_Y	1.048	0.50
21_S	24_S	1.045	0.49
41_Q	55_S	1.044	0.49
63_R	66_G	1.043	0.49
86_I	97_K	1.043	0.49
208_K	212_I	1.040	0.49
39_D	63_R	1.037	0.49
195_L	202_D	1.033	0.48
67_L	71_V	1.032	0.48
87_F	95_V	1.032	0.48
10_M	14_R	1.028	0.48
204_T	214_T	1.019	0.47
39_D	57_A	1.017	0.47
57_A	62_T	1.015	0.46
78_D	94_Y	1.013	0.46
39_D	64_L	1.012	0.46
77_G	82_F	1.005	0.45
35_K	41_Q	1.003	0.45
29_N	157_G	1.001	0.45
7_Q	10_M	1.001	0.45
198_A	208_K	1.000	0.45

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
4yozA	1	0	99.9	0.482	Contact Map
4ellA	2	0.3184	99.9	0.497	Contact Map
4eljA	1	0.2511	99.9	0.515	Contact Map
2r7gA	2	0.3139	99.9	0.517	Contact Map
1g1eB	1	0.2152	20.2	0.935	Contact Map
2czyA	1	0.2466	12.5	0.941	Contact Map
1e91A	1	0.2242	12.3	0.941	Contact Map
2azeC	1	0.1883	12.3	0.941	Contact Map
4nawC	4	0.1525	12	0.942	Contact Map
2cr7A	1	0.2332	10.2	0.943	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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