OPENSEQ.org - 1496156840 - GREMLIN Submission

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5LOX_1_200_lowerEvalue

ID:	1496156840	Query Sequence MPSYTVTVATGSQWFAGTDDYIYLSLVGSAGCSEKHLLDKPFYNDFERGAVDSYDVTVDEELGEIQLVRIEKRKYWLNDDWYLKYITLKTPHGDYIEFPCYRWITGDVEVVLRDGRAKLARDDQIHILKQHRRKELETRQKQYRWMEWNPGFPLSIDAKCHKDLPRDIQFDSEKGVDFVLNYSKAMENLFINRFMHMFQSSW	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	202 (200)
Sequences:	380 (255.8)
Seq/Len:	1.900
Nf(neff/√len):	18.1

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: 1.900).

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
70_I	86_I	2.329	1.00
100_C	112_L	2.067	0.99
98_F	103_W	2.036	0.99
132_R	143_Y	1.960	0.99
4_Y	10_T	1.951	0.99
39_D	45_D	1.833	0.98
193_R	196_H	1.767	0.97
26_L	88_L	1.743	0.96
194_F	198_F	1.687	0.96
194_F	197_M	1.662	0.95
70_I	83_L	1.637	0.94
101_Y	115_G	1.635	0.94
139_R	143_Y	1.597	0.93
193_R	197_M	1.582	0.93
135_E	143_Y	1.493	0.90
136_L	143_Y	1.492	0.90
132_R	135_E	1.460	0.89
20_D	79_D	1.457	0.89
40_K	45_D	1.447	0.88
44_N	47_E	1.418	0.87
132_R	136_L	1.409	0.86
20_D	27_V	1.404	0.86
62_L	72_K	1.388	0.85
6_V	10_T	1.383	0.85
33_S	57_T	1.379	0.85
28_G	115_G	1.376	0.84
197_M	200_S	1.373	0.84
189_L	194_F	1.328	0.81
81_W	98_F	1.327	0.81
68_V	77_L	1.326	0.81
18_T	39_D	1.322	0.81
193_R	198_F	1.310	0.80
38_L	46_F	1.295	0.79
65_I	145_W	1.292	0.79
100_C	104_I	1.283	0.78
23_Y	48_R	1.283	0.78
58_V	68_V	1.278	0.78
13_Q	16_A	1.276	0.78
147_E	150_P	1.264	0.77
148_W	170_F	1.253	0.76
99_P	103_W	1.239	0.75
68_V	127_I	1.234	0.74
9_A	85_Y	1.225	0.74
187_E	191_I	1.208	0.72
123_D	135_E	1.207	0.72
16_A	48_R	1.202	0.72
46_F	54_Y	1.196	0.71
145_W	191_I	1.188	0.70
194_F	200_S	1.183	0.70
46_F	50_A	1.178	0.69
65_I	144_R	1.167	0.68
79_D	83_L	1.166	0.68
189_L	197_M	1.153	0.67
188_N	198_F	1.148	0.66
72_K	91_P	1.148	0.66
28_G	31_G	1.147	0.66
17_G	39_D	1.146	0.66
188_N	191_I	1.145	0.66
52_D	82_Y	1.145	0.66
88_L	136_L	1.135	0.65
64_E	82_Y	1.132	0.65
103_W	115_G	1.131	0.65
102_R	138_T	1.131	0.65
33_S	38_L	1.131	0.65
189_L	198_F	1.129	0.65
158_A	164_L	1.127	0.64
124_Q	142_Q	1.116	0.63
28_G	62_L	1.114	0.63
44_N	68_V	1.108	0.62
188_N	196_H	1.107	0.62
98_F	115_G	1.103	0.62
4_Y	28_G	1.102	0.62
53_S	89_K	1.094	0.61
6_V	86_I	1.091	0.61
177_D	181_N	1.083	0.60
20_D	33_S	1.062	0.58
118_K	160_C	1.060	0.57
110_V	115_G	1.055	0.57
143_Y	146_M	1.055	0.57
36_H	46_F	1.054	0.57
25_S	33_S	1.054	0.57
28_G	110_V	1.053	0.57
21_Y	54_Y	1.053	0.57
28_G	63_G	1.052	0.56
25_S	29_S	1.050	0.56
192_N	195_M	1.043	0.55
110_V	114_D	1.039	0.55
153_P	202_W	1.038	0.55
63_G	115_G	1.036	0.55
24_L	28_G	1.035	0.55
186_M	191_I	1.034	0.55
8_V	170_F	1.029	0.54
179_V	182_Y	1.024	0.53
185_A	191_I	1.024	0.53
123_D	132_R	1.022	0.53
132_R	139_R	1.022	0.53
137_E	140_Q	1.020	0.53
27_V	32_C	1.018	0.53
9_A	51_V	1.018	0.53
97_E	102_R	1.011	0.52
32_C	51_V	1.004	0.51
163_D	173_E	1.002	0.51

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
4nreA	1	0.9851	100	0.165	Contact Map
3v98A	2	0.9703	100	0.21	Contact Map
1loxA	1	0.901	100	0.215	Contact Map
3vf1A	2	0.9752	100	0.221	Contact Map
3fg1A	4	0.9653	100	0.233	Contact Map
3dy5A	2	0.9059	100	0.241	Contact Map
2wxuA	1	0.5545	100	0.434	Contact Map
1olpA	4	0.5545	100	0.465	Contact Map
3cwzB	1	0.5842	100	0.516	Contact Map
2iujA	1	0.9406	99.9	0.608	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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