OPENSEQ.org - 1496306108 - GREMLIN Submission

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

1dst_test

ID:	1496306108	Query Sequence ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDYQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVSWGSRVCGNRKKPGIYTRVASYAAWIDSVLA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	228 (228)
Sequences:	15396 (11151.8)
Seq/Len:	67.526
Nf(neff/√len):	738.5

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: 67.526).

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
123_C	189_C	4.530	1.00
26_C	42_C	3.794	1.00
35_W	94_Q	3.066	1.00
73_L	94_Q	2.955	1.00
28_G	36_V	2.812	1.00
35_W	92_L	2.807	1.00
11_A	143_H	2.758	1.00
6_E	142_Q	2.736	1.00
43_L	91_L	2.599	1.00
15_M	126_A	2.536	1.00
17_S	24_H	2.520	1.00
12_R	143_H	2.517	1.00
71_D	96_S	2.503	1.00
29_V	193_L	2.498	1.00
179_C	204_C	2.363	1.00
88_H	219_Y	2.346	1.00
55_L	99_A	2.278	1.00
74_R	94_Q	2.245	1.00
34_Q	94_Q	2.221	1.00
34_Q	98_K	2.210	1.00
41_H	183_S	2.188	1.00
95_L	99_A	2.148	1.00
154_C	170_C	2.138	1.00
30_L	99_A	2.131	1.00
12_R	126_A	2.125	1.00
199_W	212_I	2.124	1.00
6_E	140_S	2.103	1.00
144_V	176_R	2.087	1.00
16_A	28_G	2.080	1.00
125_V	178_S	2.036	1.00
37_L	193_L	2.013	1.00
76_V	226_V	1.960	1.00
32_A	35_W	1.960	1.00
16_A	55_L	1.934	1.00
54_L	69_L	1.929	1.00
79_P	226_V	1.908	1.00
33_E	98_K	1.902	1.00
87_D	167_R	1.876	1.00
126_A	188_V	1.848	1.00
1_I	4_G	1.841	1.00
90_L	219_Y	1.798	1.00
14_Y	109_P	1.766	1.00
220_A	224_D	1.761	1.00
70_Y	96_S	1.759	1.00
101_L	107_P	1.755	1.00
72_V	93_L	1.754	1.00
70_Y	99_A	1.753	1.00
80_D	88_H	1.732	1.00
73_L	96_S	1.731	1.00
167_R	218_S	1.702	1.00
16_A	36_V	1.607	1.00
123_C	148_V	1.578	1.00
14_Y	188_V	1.555	1.00
19_Q	24_H	1.543	1.00
125_V	144_V	1.509	1.00
187_L	213_Y	1.456	1.00
214_T	219_Y	1.449	1.00
7_A	12_R	1.437	1.00
177_D	211_G	1.410	1.00
133_H	206_N	1.404	0.99
57_A	67_K	1.389	0.99
43_L	77_P	1.383	0.99
78_H	88_H	1.376	0.99
189_C	194_E	1.364	0.99
178_S	197_V	1.363	0.99
76_V	94_Q	1.363	0.99
15_M	141_L	1.362	0.99
215_R	218_S	1.361	0.99
124_D	145_L	1.352	0.99
169_M	187_L	1.343	0.99
10_H	58_H	1.342	0.99
197_V	200_G	1.336	0.99
52_Q	69_L	1.324	0.99
122_L	145_L	1.321	0.99
38_S	43_L	1.313	0.99
59_S	139_D	1.309	0.99
8_E	11_A	1.299	0.99
77_P	91_L	1.297	0.99
108_L	193_L	1.288	0.99
131_V	142_Q	1.276	0.99
39_A	196_V	1.276	0.99
9_A	58_H	1.273	0.99
54_L	57_A	1.271	0.99
88_H	167_R	1.234	0.98
70_Y	97_E	1.232	0.98
29_V	196_V	1.229	0.98
18_V	53_V	1.225	0.98
75_A	93_L	1.210	0.98
149_L	210_P	1.210	0.98
15_M	128_W	1.205	0.98
41_H	89_D	1.204	0.98
168_L	199_W	1.190	0.98
35_W	226_V	1.180	0.98
15_M	27_G	1.177	0.98
125_V	146_L	1.176	0.98
29_V	108_L	1.170	0.97
182_D	185_G	1.153	0.97
122_L	147_P	1.139	0.97
108_L	188_V	1.139	0.97
5_R	143_H	1.131	0.97
138_P	142_Q	1.123	0.97
61_S	139_D	1.120	0.96
29_V	37_L	1.120	0.96
150_D	153_T	1.119	0.96
59_S	140_S	1.109	0.96
30_L	55_L	1.097	0.96
6_E	58_H	1.095	0.96
181_G	184_G	1.093	0.96
90_L	214_T	1.084	0.96
109_P	192_V	1.070	0.95
78_H	81_Y	1.051	0.94
10_H	104_A	1.045	0.94
126_A	143_H	1.044	0.94
12_R	124_D	1.043	0.94
222_W	226_V	1.038	0.94
201_S	209_K	1.037	0.94
123_C	187_L	1.037	0.94
36_V	53_V	1.030	0.94
82_Q	85_T	1.016	0.93

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
2f83A	1	0.9079	100	-0.045	Contact Map
2xxlA	2	0.9868	100	-0.036	Contact Map
2xw9A	1	0.9912	100	-0.035	Contact Map
4nzqA	1	0.9868	100	-0.028	Contact Map
2b9lA	1	0.9912	100	-0.027	Contact Map
3nxpA	1	0.9781	100	-0.02	Contact Map
1z8gA	1	0.9868	100	-0.02	Contact Map
4kkdA	2	0.9825	100	-0.019	Contact Map
4q7zA	1	0.9912	100	-0.018	Contact Map
3w94A	2	0.9912	100	-0.009	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 1.1073 seconds.