OPENSEQ.org - 1504789307 - GREMLIN Submission

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

2wvoA

ID:	1504789307	Query Sequence MSEPFEIVAGALGVAGLFNNCVACFEYVQLGRHFGRDYERCQLRLDIAKVRLSRWGEAVQINDDPRFHSSAPIDKSVQLAKSIVEEILLLFESAQKTSKRYELVADQQDLVVFEDKDMKPIGRALHRRLKDLVSRRQKQTSLAKKTAWALYDGKSLEKIVDQVAGFVDELEKAFPIEAVCHKLAENEIEEVEDEASLTILKDAAGGIDAAMSDAAAQKIDAIVGRNSHHHHHH	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	233 (223)
Sequences:	374 (316.8)
Seq/Len:	1.677
Nf(neff/√len):	21.2

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: 1.677).

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
25_F	167_V	2.230	0.99
5_F	10_G	2.219	0.99
48_A	167_V	2.203	0.99
19_N	23_A	2.055	0.99
51_R	168_D	2.049	0.99
3_E	6_E	1.997	0.98
52_L	56_G	1.956	0.98
47_I	83_I	1.944	0.98
25_F	163_V	1.838	0.97
35_G	133_V	1.803	0.96
26_E	154_K	1.778	0.96
45_L	74_D	1.776	0.96
80_A	174_F	1.636	0.93
4_P	8_V	1.583	0.91
91_F	174_F	1.574	0.91
123_R	200_L	1.558	0.91
55_W	170_L	1.554	0.90
37_D	80_A	1.547	0.90
97_T	103_L	1.523	0.89
155_S	215_A	1.497	0.88
98_S	103_L	1.490	0.88
28_V	142_L	1.444	0.86
101_Y	152_D	1.440	0.85
18_F	56_G	1.440	0.85
21_C	101_Y	1.432	0.85
37_D	153_G	1.429	0.85
93_S	201_K	1.374	0.81
100_R	147_A	1.372	0.81
6_E	10_G	1.368	0.81
52_L	204_A	1.367	0.81
25_F	45_L	1.357	0.80
51_R	171_E	1.350	0.80
31_G	213_D	1.347	0.80
14_V	17_L	1.329	0.78
3_E	10_G	1.328	0.78
37_D	148_W	1.326	0.78
153_G	220_D	1.310	0.77
138_K	144_K	1.306	0.77
45_L	163_V	1.302	0.76
101_Y	173_A	1.302	0.76
28_V	73_I	1.299	0.76
141_S	145_K	1.291	0.76
56_G	60_Q	1.281	0.75
4_P	7_I	1.280	0.75
35_G	137_Q	1.256	0.73
158_K	162_Q	1.247	0.72
97_T	155_S	1.243	0.72
7_I	174_F	1.241	0.71
44_R	165_G	1.238	0.71
20_N	130_K	1.238	0.71
34_F	37_D	1.234	0.71
12_L	146_T	1.227	0.70
5_F	8_V	1.227	0.70
154_K	200_L	1.221	0.70
159_I	162_Q	1.220	0.70
15_A	141_S	1.216	0.69
2_S	6_E	1.195	0.67
187_E	208_D	1.194	0.67
54_R	208_D	1.192	0.67
51_R	91_F	1.185	0.66
41_C	102_E	1.180	0.66
29_Q	32_R	1.179	0.66
60_Q	170_L	1.170	0.65
160_V	200_L	1.170	0.65
52_L	61_I	1.170	0.65
56_G	61_I	1.165	0.64
215_A	218_K	1.164	0.64
193_D	197_L	1.156	0.63
153_G	157_E	1.154	0.63
51_R	56_G	1.146	0.62
140_T	145_K	1.146	0.62
28_V	38_Y	1.142	0.62
133_V	137_Q	1.142	0.62
80_A	169_E	1.142	0.62
163_V	167_V	1.138	0.62
14_V	203_A	1.125	0.60
184_A	205_G	1.121	0.60
4_P	154_K	1.113	0.59
55_W	60_Q	1.113	0.59
188_I	192_E	1.109	0.59
43_L	52_L	1.108	0.59
41_C	152_D	1.107	0.58
93_S	102_E	1.098	0.58
24_C	48_A	1.087	0.56
64_D	160_V	1.086	0.56
22_V	143_A	1.083	0.56
40_R	86_E	1.077	0.55
131_D	160_V	1.076	0.55
21_C	50_V	1.074	0.55
43_L	54_R	1.069	0.55
20_N	45_L	1.065	0.54
44_R	162_Q	1.064	0.54
35_G	140_T	1.061	0.54
97_T	102_E	1.061	0.54
59_V	83_I	1.059	0.53
21_C	168_D	1.058	0.53
44_R	97_T	1.057	0.53
51_R	197_L	1.052	0.53
52_L	55_W	1.048	0.52
17_L	20_N	1.035	0.51
9_A	156_L	1.030	0.50
160_V	186_N	1.030	0.50
26_E	32_R	1.028	0.50
30_L	48_A	1.028	0.50
97_T	156_L	1.024	0.50
145_K	159_I	1.020	0.49
82_S	140_T	1.014	0.49
13_G	16_G	1.010	0.48
80_A	125_L	1.009	0.48
122_G	126_H	1.006	0.48

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
2wvqA	2	0.9142	100	0.134	Contact Map
2msvA	1	0.6052	25	0.931	Contact Map
4btfA	1	0.6309	9.9	0.943	Contact Map
3he4A	4	0.1931	7.5	0.946	Contact Map
2uytA	1	0.2103	5.5	0.949	Contact Map
3pltA	3	0.7811	5	0.95	Contact Map
4abxA	4	0.5021	4.6	0.951	Contact Map
2k9jB	1	0.1459	3.2	0.954	Contact Map
1hy5A	2	0.3906	2.8	0.956	Contact Map
2fywA	3	0.3176	2.5	0.957	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 1.4127 seconds.