OPENSEQ.org - 1496155512 - GREMLIN Submission

May 4, 2021 - We are working on upgrading the webserver, some pages may not work.

5LOX_1_200

ID:	1496155512	Query Sequence MPSYTVTVATGSQWFAGTDDYIYLSLVGSAGCSEKHLLDKPFYNDFERGAVDSYDVTVDEELGEIQLVRIEKRKYWLNDDWYLKYITLKTPHGDYIEFPCYRWITGDVEVVLRDGRAKLARDDQIHILKQHRRKELETRQKQYRWMEWNPGFPLSIDAKCHKDLPRDIQFDSEKGVDFVLNYSKAMENLFINRFMHMFQSSW	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	202 (201)
Sequences:	295 (198.3)
Seq/Len:	1.468
Nf(neff/√len):	14.0

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: 1.468).

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
100_C	112_L	2.549	1.00
70_I	86_I	2.255	0.99
101_Y	115_G	2.137	0.99
26_L	88_L	2.086	0.99
39_D	45_D	2.002	0.98
98_F	103_W	1.965	0.98
132_R	135_E	1.814	0.96
81_W	98_F	1.707	0.93
193_R	196_H	1.603	0.90
16_A	148_W	1.603	0.90
18_T	39_D	1.580	0.89
99_P	103_W	1.546	0.88
194_F	198_F	1.542	0.88
194_F	197_M	1.540	0.88
72_K	91_P	1.515	0.86
4_Y	10_T	1.510	0.86
62_L	72_K	1.489	0.85
135_E	143_Y	1.468	0.84
132_R	143_Y	1.466	0.84
177_D	181_N	1.465	0.84
40_K	45_D	1.452	0.83
132_R	136_L	1.451	0.83
193_R	197_M	1.437	0.82
44_N	47_E	1.398	0.80
17_G	49_G	1.369	0.78
145_W	191_I	1.351	0.77
103_W	115_G	1.351	0.77
68_V	86_I	1.325	0.75
23_Y	48_R	1.314	0.74
68_V	77_L	1.313	0.74
188_N	191_I	1.310	0.73
46_F	49_G	1.298	0.72
123_D	136_L	1.293	0.72
8_V	69_R	1.284	0.71
100_C	104_I	1.274	0.70
64_E	82_Y	1.273	0.70
65_I	145_W	1.250	0.68
102_R	138_T	1.250	0.68
45_D	54_Y	1.240	0.67
55_D	61_E	1.225	0.66
153_P	202_W	1.220	0.66
28_G	110_V	1.220	0.66
38_L	45_D	1.219	0.65
33_S	36_H	1.210	0.65
197_M	200_S	1.205	0.64
18_T	46_F	1.201	0.64
124_Q	142_Q	1.200	0.64
38_L	46_F	1.191	0.63
6_V	10_T	1.187	0.62
70_I	83_L	1.182	0.62
158_A	164_L	1.177	0.61
28_G	62_L	1.176	0.61
13_Q	16_A	1.170	0.61
123_D	132_R	1.168	0.61
123_D	135_E	1.159	0.60
97_E	102_R	1.156	0.59
86_I	98_F	1.156	0.59
27_V	32_C	1.143	0.58
23_Y	71_E	1.140	0.58
20_D	33_S	1.131	0.57
123_D	128_L	1.127	0.56
135_E	139_R	1.121	0.56
33_S	38_L	1.120	0.56
189_L	194_F	1.117	0.55
69_R	156_I	1.116	0.55
159_K	163_D	1.114	0.55
193_R	198_F	1.103	0.54
63_G	72_K	1.098	0.54
33_S	57_T	1.089	0.53
58_V	68_V	1.084	0.52
187_E	191_I	1.083	0.52
136_L	142_Q	1.083	0.52
119_L	126_H	1.080	0.52
20_D	27_V	1.076	0.51
119_L	132_R	1.075	0.51
64_E	80_D	1.074	0.51
28_G	49_G	1.071	0.51
53_S	89_K	1.071	0.51
22_I	54_Y	1.067	0.50
186_M	190_F	1.056	0.49
187_E	190_F	1.055	0.49
82_Y	99_P	1.054	0.49
161_H	169_Q	1.049	0.48
23_Y	33_S	1.047	0.48
18_T	33_S	1.034	0.47
39_D	44_N	1.033	0.47
42_F	45_D	1.032	0.47
62_L	88_L	1.032	0.47
31_G	38_L	1.031	0.47
194_F	200_S	1.029	0.46
19_D	47_E	1.028	0.46
82_Y	176_V	1.026	0.46
39_D	46_F	1.024	0.46
4_Y	28_G	1.020	0.46
179_V	182_Y	1.019	0.45
178_F	185_A	1.016	0.45
185_A	191_I	1.013	0.45
175_G	179_V	1.012	0.45
117_A	139_R	1.010	0.44
10_T	26_L	1.010	0.44
110_V	114_D	1.007	0.44
132_R	139_R	1.007	0.44

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
4nreA	1	0.9851	100	0.176	Contact Map
3v98A	2	0.9703	100	0.22	Contact Map
1loxA	1	0.901	100	0.224	Contact Map
3vf1A	2	0.9752	100	0.23	Contact Map
3fg1A	4	0.9653	100	0.238	Contact Map
3dy5A	2	0.9059	100	0.247	Contact Map
2wxuA	1	0.5545	100	0.46	Contact Map
1olpA	4	0.5545	100	0.499	Contact Map
3cwzB	1	0.5842	99.9	0.554	Contact Map
2iujA	1	0.9406	99.9	0.571	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.

Page generated in 1.4231 seconds.