OPENSEQ.org - 1399653758 - GREMLIN Submission

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T0772 -force run

ID:	1399653758	Query Sequence MNKRLLTVAAFALAGCVTVVAQDKKKEFKMPTGYAGITHEMSEFYEPVPPVVTPGTDLKGGGFTAPSDAIVLFDGKDLSAWESVKGGAAEWDVHDGVFTVNKKKGDIQTKQKFNDFQMHIEWQVPTNITGESQSRGNSGIFLQGMYEVQVLDCYNNPTYVNGQTGSIYKQSIPLANAMRKPGEWNVYDIIYTAPTFKEDGSYRTHPTVTVIQNGVVLQNHTTILGTTEWIGFPQVKKHGAGPIILQSHGDPSEPISFRNIWIREL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	265 (247)
Sequences:	97 (85.3)
Seq/Len:	0.393
Nf(neff/√len):	5.4

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: 0.393).

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
207_T	220_H	2.879	0.98
190_I	211_I	2.212	0.88
143_Q	191_Y	2.061	0.83
99_T	256_S	2.014	0.81
177_A	212_Q	2.002	0.80
90_E	104_K	1.988	0.80
120_I	150_V	1.932	0.77
114_N	240_A	1.871	0.74
39_H	229_W	1.827	0.71
202_Y	235_V	1.798	0.70
43_E	161_N	1.779	0.68
43_E	169_K	1.778	0.68
78_L	89_A	1.766	0.68
153_C	164_T	1.750	0.66
148_V	189_I	1.738	0.66
191_Y	223_I	1.737	0.66
171_S	221_T	1.686	0.62
186_V	212_Q	1.670	0.61
150_V	257_F	1.668	0.61
140_I	189_I	1.629	0.58
130_G	134_S	1.623	0.58
165_G	186_V	1.581	0.55
42_S	169_K	1.573	0.54
161_N	231_G	1.553	0.53
42_S	161_N	1.511	0.50
178_M	211_I	1.498	0.49
167_I	208_V	1.485	0.48
43_E	231_G	1.481	0.48
165_G	217_L	1.479	0.48
143_Q	223_I	1.450	0.45
170_Q	233_P	1.449	0.45
115_D	195_T	1.421	0.43
161_N	169_K	1.408	0.42
165_G	212_Q	1.406	0.42
39_H	42_S	1.405	0.42
126_T	150_V	1.389	0.41
192_T	219_N	1.352	0.39
51_V	181_P	1.345	0.38
205_H	235_V	1.345	0.38
122_W	164_T	1.342	0.38
128_I	250_D	1.337	0.38
39_H	43_E	1.331	0.37
111_Q	264_E	1.328	0.37
74_D	98_F	1.327	0.37
11_F	27_E	1.319	0.36
176_N	181_P	1.303	0.35
43_E	230_I	1.302	0.35
247_S	255_I	1.300	0.35
206_P	235_V	1.299	0.35
240_A	264_E	1.294	0.35
103_K	177_A	1.290	0.34
226_T	234_Q	1.286	0.34
123_Q	256_S	1.277	0.34
46_E	169_K	1.265	0.33
54_P	167_I	1.262	0.33
106_D	244_I	1.245	0.32
116_F	262_I	1.243	0.31
132_S	142_L	1.240	0.31
144_G	241_G	1.236	0.31
116_F	255_I	1.223	0.30
122_W	212_Q	1.215	0.30
169_K	233_P	1.212	0.30
43_E	46_E	1.206	0.29
134_S	250_D	1.203	0.29
65_A	130_G	1.202	0.29
50_P	175_A	1.195	0.28
163_Q	212_Q	1.188	0.28
77_D	183_E	1.185	0.28
154_Y	176_N	1.183	0.28
133_Q	158_T	1.178	0.28
118_M	245_L	1.165	0.27
150_V	243_I	1.150	0.26
131_E	264_E	1.139	0.25
45_Y	231_G	1.138	0.25
77_D	93_V	1.138	0.25
185_N	222_T	1.135	0.25
124_V	164_T	1.119	0.24
235_V	241_G	1.117	0.24
81_W	95_D	1.113	0.24
191_Y	226_T	1.110	0.24
195_T	204_T	1.110	0.24
192_T	207_T	1.099	0.23
187_Y	247_S	1.094	0.23
165_G	223_I	1.091	0.23
143_Q	172_I	1.091	0.23
44_F	172_I	1.087	0.23
148_V	216_V	1.078	0.22
7_T	10_A	1.078	0.22
144_G	167_I	1.076	0.22
117_Q	263_R	1.071	0.22
54_P	114_N	1.070	0.22
223_I	235_V	1.068	0.22
161_N	230_I	1.067	0.22
42_S	231_G	1.063	0.21
45_Y	161_N	1.062	0.21
103_K	185_N	1.061	0.21
51_V	155_N	1.061	0.21
195_T	235_V	1.043	0.20
24_K	28_F	1.042	0.20
42_S	46_E	1.040	0.20
39_H	169_K	1.039	0.20
95_D	234_Q	1.039	0.20
243_I	262_I	1.037	0.20
10_A	21_A	1.033	0.20
206_P	243_I	1.031	0.20
144_G	244_I	1.030	0.20
42_S	45_Y	1.029	0.20
193_A	204_T	1.025	0.20
94_H	148_V	1.023	0.20
72_L	156_N	1.022	0.19
7_T	27_E	1.021	0.19
95_D	208_V	1.021	0.19
15_G	22_Q	1.018	0.19
81_W	156_N	1.016	0.19
11_F	21_A	1.014	0.19
80_A	140_I	1.007	0.19
76_K	262_I	1.004	0.19
197_K	222_T	1.004	0.19
169_K	231_G	1.003	0.19
148_V	155_N	1.002	0.19
102_K	251_P	1.002	0.19

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
4qhzA	4	0.8528	100	0.377	Contact Map
3u1xA	2	0.7019	100	0.588	Contact Map
3hbkA	1	0.717	100	0.593	Contact Map
3osdA	1	0.7811	100	0.593	Contact Map
3h3lA	3	0.7094	100	0.593	Contact Map
4jqtA	2	0.8604	100	0.595	Contact Map
3immA	3	0.6415	100	0.605	Contact Map
3s5qA	1	0.7019	100	0.62	Contact Map
4b1mA	3	0.5962	100	0.759	Contact Map
4w65A	1	0.6491	91	0.954	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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