OPENSEQ.org - 1496311211 - GREMLIN Submission

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3dfl_test

ID:	1496311211	Query Sequence ITGGSSAVAGQWPWQVSITYEGVHVCGGSLVSEQWVLSAAHCFPSEHHKEAYEVKLGAHQLDSYSEDAKVSTLKDIIPHPSYLQEGSQGDIALLQLSRPITFSRYIRPISLPAANASFPNGLHCTVTGWGHVAPSVSLLTPKPLQQLEVPLISRETCNALYNIDAKPEEPHFVQEDMVCAGYVEGGKDACQGDSGGPLSCPVEGLWYLTGIVSWGDACGARNRPGVYTLASSYASWIQSKVTELQLVPRGSGSGSLEHHHHHH	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	263 (242)
Sequences:	12320 (8959.5)
Seq/Len:	50.909
Nf(neff/√len):	575.9

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: 50.909).

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
124_C	200_C	4.195	1.00
26_C	42_C	3.573	1.00
74_K	95_Q	3.088	1.00
11_Q	146_Q	3.037	1.00
35_W	93_L	2.866	1.00
28_G	36_V	2.809	1.00
35_W	95_Q	2.785	1.00
6_S	145_Q	2.678	1.00
72_T	97_S	2.630	1.00
30_L	100_I	2.544	1.00
15_Q	127_T	2.527	1.00
43_F	92_A	2.483	1.00
29_S	208_L	2.441	1.00
17_S	24_H	2.419	1.00
12_W	146_Q	2.406	1.00
37_L	208_L	2.358	1.00
89_G	233_Y	2.314	1.00
56_L	100_I	2.283	1.00
190_C	218_C	2.273	1.00
75_D	95_Q	2.226	1.00
34_Q	99_P	2.207	1.00
147_L	187_K	2.198	1.00
34_Q	95_Q	2.181	1.00
16_V	28_G	2.111	1.00
6_S	143_P	2.103	1.00
96_L	100_I	2.086	1.00
157_C	179_C	2.067	1.00
16_V	56_L	2.062	1.00
41_H	194_S	2.046	1.00
33_E	99_P	2.036	1.00
32_S	35_W	2.033	1.00
126_V	189_A	2.014	1.00
214_W	226_V	2.012	1.00
77_I	240_K	1.986	1.00
12_W	127_T	1.951	1.00
73_L	94_L	1.949	1.00
55_K	70_V	1.916	1.00
80_P	240_K	1.910	1.00
91_I	233_Y	1.857	1.00
1_I	4_G	1.850	1.00
176_D	232_S	1.849	1.00
71_S	100_I	1.822	1.00
74_K	97_S	1.806	1.00
234_A	238_Q	1.762	1.00
71_S	97_S	1.754	1.00
88_Q	176_D	1.713	1.00
124_C	151_L	1.693	1.00
127_T	199_S	1.652	1.00
102_F	108_P	1.644	1.00
81_S	89_G	1.633	1.00
14_W	199_S	1.598	1.00
16_V	36_V	1.575	1.00
19_T	24_H	1.548	1.00
38_S	43_F	1.548	1.00
126_V	147_L	1.527	1.00
229_L	232_S	1.517	1.00
109_I	208_L	1.484	1.00
228_T	233_Y	1.477	1.00
53_E	70_V	1.468	1.00
7_A	12_W	1.445	1.00
198_L	227_Y	1.437	1.00
188_D	225_G	1.434	1.00
60_Q	142_K	1.417	1.00
39_A	211_I	1.416	1.00
134_P	220_A	1.399	0.99
79_H	89_G	1.395	0.99
189_A	212_V	1.385	0.99
152_I	224_P	1.384	0.99
58_A	68_A	1.368	0.99
10_G	59_H	1.365	0.99
123_H	148_E	1.358	0.99
29_S	109_I	1.344	0.99
91_I	228_T	1.342	0.99
132_V	145_Q	1.341	0.99
9_A	59_H	1.338	0.99
71_S	98_R	1.324	0.99
14_W	110_S	1.320	0.99
55_K	58_A	1.312	0.99
125_T	148_E	1.310	0.99
109_I	199_S	1.305	0.99
41_H	90_D	1.303	0.99
77_I	95_Q	1.298	0.99
178_V	198_L	1.297	0.99
29_S	211_I	1.297	0.99
212_V	215_G	1.295	0.99
78_P	92_A	1.272	0.99
43_F	78_P	1.269	0.99
30_L	56_L	1.242	0.98
126_V	149_V	1.242	0.98
177_M	214_W	1.230	0.98
15_Q	144_L	1.218	0.98
15_Q	27_G	1.213	0.98
141_P	145_Q	1.210	0.98
216_D	223_R	1.197	0.98
153_S	156_T	1.190	0.98
8_V	11_Q	1.185	0.98
62_D	142_K	1.175	0.98
89_G	176_D	1.173	0.98
15_Q	129_W	1.173	0.98
200_C	209_T	1.168	0.97
60_Q	143_P	1.167	0.97
36_V	54_V	1.160	0.97
14_W	206_W	1.155	0.97
201_P	206_W	1.145	0.97
18_I	54_V	1.143	0.97
236_W	240_K	1.133	0.97
195_G	198_L	1.133	0.97
76_I	94_L	1.115	0.96
124_C	198_L	1.108	0.96
124_C	209_T	1.106	0.96
10_G	105_Y	1.083	0.96
35_W	240_K	1.080	0.95
43_F	76_I	1.072	0.95
12_W	125_T	1.064	0.95
83_L	86_G	1.059	0.95
30_L	36_V	1.059	0.95
5_S	146_Q	1.055	0.95
12_W	206_W	1.053	0.95
126_V	212_V	1.045	0.94
19_T	55_K	1.042	0.94
29_S	37_L	1.042	0.94
88_Q	174_Q	1.039	0.94
6_S	59_H	1.015	0.93
7_A	146_Q	1.015	0.93
69_K	106_I	1.015	0.93
199_S	206_W	1.011	0.93
79_H	82_Y	1.001	0.92

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
2f83A	1	0.8061	100	-0.004	Contact Map
3gylB	1	0.9392	100	0.011	Contact Map
4nzqA	1	0.9049	100	0.034	Contact Map
4kkdA	2	0.8973	100	0.036	Contact Map
2xxlA	2	0.8973	100	0.037	Contact Map
2b9lA	1	0.9506	100	0.038	Contact Map
2anyA	1	0.8935	100	0.039	Contact Map
4durA	2	0.8593	100	0.041	Contact Map
4crgA	1	0.8783	100	0.041	Contact Map
3nxpA	1	0.8935	100	0.042	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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