OPENSEQ.org - 1448017083 - GREMLIN Submission

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

1GU8

ID:	1448017083	Query Sequence MVGLTTLFWLGAIGMLVGTLAFAWAGRDAGSGERRYYVTLVGISGIAAVAYVVMALGVGWVPVAERTVFAPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPGIERYALFGMGAVAFLGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVILWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAATLRAEHGESLAGVDTDAPAVAD	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	239 (223)
Sequences:	744 (538.4)
Seq/Len:	3.336
Nf(neff/√len):	36.1

HHblits Results: (2015_06)
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: 3.336).

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
46_I	78_L	4.198	1.00
70_A	74_I	2.686	1.00
80_T	105_N	2.567	1.00
75_D	205_K	2.437	1.00
9_W	55_A	2.387	1.00
14_G	202_L	2.380	1.00
22_F	209_G	2.305	1.00
170_L	203_V	2.225	1.00
16_L	48_A	2.092	1.00
75_D	79_T	2.013	1.00
53_V	126_L	1.974	1.00
19_T	44_S	1.882	0.99
44_S	209_G	1.819	0.99
111_A	130_G	1.758	0.99
80_T	205_K	1.747	0.99
8_F	194_V	1.628	0.98
40_L	86_F	1.626	0.98
79_T	205_K	1.618	0.98
107_V	133_A	1.583	0.98
115_G	178_W	1.581	0.98
18_G	22_F	1.578	0.98
108_V	112_G	1.557	0.97
111_A	204_T	1.522	0.97
73_Y	76_W	1.518	0.97
85_Y	102_I	1.508	0.97
79_T	82_L	1.495	0.96
40_L	209_G	1.491	0.96
80_T	108_V	1.469	0.96
112_G	205_K	1.458	0.96
171_W	205_K	1.454	0.96
7_L	11_G	1.442	0.95
39_T	82_L	1.442	0.95
21_A	25_A	1.422	0.95
15_M	47_A	1.421	0.95
107_V	129_M	1.404	0.94
61_V	117_M	1.391	0.94
76_W	175_P	1.381	0.94
52_V	118_V	1.342	0.92
19_T	45_G	1.340	0.92
183_P	193_D	1.325	0.92
47_A	54_M	1.322	0.92
77_I	106_T	1.313	0.91
177_I	196_L	1.311	0.91
105_N	108_V	1.309	0.91
50_A	54_M	1.304	0.91
11_G	198_V	1.288	0.90
50_A	116_A	1.280	0.90
80_T	112_G	1.275	0.90
173_I	177_I	1.272	0.89
79_T	105_N	1.271	0.89
104_L	136_G	1.267	0.89
47_A	75_D	1.267	0.89
45_G	49_V	1.252	0.88
19_T	48_A	1.246	0.88
23_A	41_V	1.228	0.87
17_V	135_L	1.225	0.87
18_G	210_F	1.220	0.87
127_F	131_A	1.216	0.86
18_G	206_V	1.215	0.86
43_I	82_L	1.211	0.86
151_Q	195_A	1.209	0.86
45_G	203_V	1.200	0.85
84_V	105_N	1.199	0.85
108_V	137_L	1.194	0.85
75_D	80_T	1.174	0.84
124_Y	179_L	1.171	0.84
84_V	112_G	1.170	0.83
47_A	108_V	1.168	0.83
155_G	223_H	1.158	0.83
76_W	81_P	1.155	0.82
202_L	214_D	1.154	0.82
23_A	140_Y	1.145	0.82
179_L	185_V	1.143	0.81
76_W	174_Y	1.137	0.81
195_A	199_Y	1.137	0.81
22_F	40_L	1.130	0.80
47_A	86_F	1.130	0.80
189_T	192_V	1.128	0.80
12_A	48_A	1.125	0.80
134_F	138_V	1.113	0.79
117_M	183_P	1.105	0.78
76_W	112_G	1.103	0.78
47_A	205_K	1.095	0.77
22_F	44_S	1.091	0.77
11_G	15_M	1.084	0.76
84_V	93_L	1.080	0.76
52_V	125_A	1.071	0.75
47_A	79_T	1.067	0.75
47_A	83_I	1.056	0.74
173_I	196_L	1.055	0.74
128_G	132_V	1.050	0.73
102_I	106_T	1.050	0.73
15_M	75_D	1.042	0.72
112_G	175_P	1.041	0.72
81_P	174_Y	1.039	0.72
166_L	170_L	1.029	0.71
63_V	119_P	1.021	0.70
43_I	208_F	1.019	0.70
19_T	23_A	1.012	0.69
139_Y	143_G	1.011	0.69
23_A	136_G	1.002	0.68
178_W	193_D	1.002	0.68
178_W	184_G	1.002	0.68

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
3qapA	1	0.9163	100	0.069	Contact Map
4qi1A	3	0	100	0.133	Contact Map
1xioA	1	0.887	100	0.134	Contact Map
1m0kA	1	0.8996	100	0.139	Contact Map
3wqjA	1	0.9121	100	0.14	Contact Map
4fbzA	1	0.9498	100	0.143	Contact Map
4l35A	1	0.9582	100	0.144	Contact Map
3wt9A	1	0.9331	100	0.171	Contact Map
3am6A	4	0.9079	100	0.172	Contact Map
3qbgA	3	0.9414	100	0.193	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 1.1759 seconds.