OPENSEQ.org - 1516177936 - GREMLIN Submission

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

1a0l

ID:	1516177936	Query Sequence IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPKK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	244 (236)
Sequences:	11503 (8035.2)
Seq/Len:	48.742
Nf(neff/√len):	523.0

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: 48.742).

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
125_C	200_C	4.021	1.00
11_K	147_Q	3.112	1.00
29_C	45_C	2.962	1.00
31_G	39_V	2.953	1.00
75_S	96_E	2.902	1.00
6_E	146_K	2.818	1.00
38_W	94_L	2.775	1.00
17_S	27_H	2.745	1.00
15_Q	128_T	2.745	1.00
12_W	147_Q	2.636	1.00
73_P	98_E	2.615	1.00
38_W	96_E	2.602	1.00
46_V	93_A	2.497	1.00
40_L	208_Q	2.394	1.00
32_S	208_Q	2.340	1.00
90_A	233_Y	2.338	1.00
33_L	101_V	2.335	1.00
60_L	101_V	2.288	1.00
148_V	187_R	2.240	1.00
214_W	226_I	2.171	1.00
81_P	240_Y	2.133	1.00
37_Q	100_P	2.094	1.00
6_E	144_P	2.094	1.00
76_R	96_E	2.078	1.00
127_V	189_S	2.059	1.00
37_Q	96_E	2.029	1.00
16_V	31_G	2.028	1.00
44_H	194_S	2.017	1.00
97_L	101_V	2.005	1.00
16_V	60_L	2.004	1.00
59_Q	71_L	1.938	1.00
78_I	240_Y	1.891	1.00
36_P	100_P	1.876	1.00
1_I	4_G	1.876	1.00
12_W	128_T	1.871	1.00
74_V	95_L	1.852	1.00
178_D	232_Y	1.841	1.00
89_G	178_D	1.828	1.00
103_V	109_T	1.808	1.00
92_I	233_Y	1.749	1.00
234_L	238_H	1.742	1.00
72_L	101_V	1.734	1.00
72_L	98_E	1.724	1.00
75_S	98_E	1.704	1.00
127_V	148_V	1.682	1.00
35_H	38_W	1.666	1.00
125_C	152_I	1.646	1.00
188_D	225_G	1.623	1.00
32_S	110_V	1.590	1.00
82_Q	90_A	1.581	1.00
7_A	12_W	1.578	1.00
41_T	46_V	1.576	1.00
190_C	218_C	1.576	1.00
128_T	199_V	1.575	1.00
16_V	39_V	1.549	1.00
19_R	27_H	1.547	1.00
158_C	181_C	1.544	1.00
62_E	69_D	1.509	1.00
110_V	208_Q	1.466	1.00
64_H	143_F	1.450	1.00
133_V	146_K	1.444	1.00
10_S	63_Q	1.438	1.00
137_E	220_Q	1.434	1.00
110_V	199_V	1.401	0.99
15_Q	145_L	1.400	0.99
212_V	215_G	1.397	0.99
180_L	198_L	1.395	0.99
14_W	199_V	1.385	0.99
228_T	233_Y	1.382	0.99
80_H	90_A	1.367	0.99
57_R	71_L	1.364	0.99
9_R	63_Q	1.361	0.99
32_S	211_V	1.353	0.99
153_M	224_P	1.343	0.99
59_Q	62_E	1.337	0.99
90_A	178_D	1.319	0.99
124_P	149_K	1.318	0.99
229_R	232_Y	1.315	0.99
92_I	228_T	1.314	0.99
126_W	149_K	1.305	0.99
189_S	212_V	1.305	0.99
79_V	93_A	1.303	0.99
46_V	79_V	1.303	0.99
195_G	198_L	1.299	0.99
66_Y	143_F	1.278	0.99
200_C	209_A	1.273	0.99
72_L	99_E	1.267	0.99
14_W	111_T	1.254	0.99
33_L	60_L	1.243	0.98
6_E	63_Q	1.236	0.98
154_E	157_I	1.233	0.98
64_H	144_P	1.191	0.98
142_P	146_K	1.190	0.98
179_M	214_W	1.187	0.98
127_V	150_V	1.182	0.98
216_E	223_R	1.176	0.98
5_Q	147_Q	1.171	0.98
77_I	95_L	1.162	0.97
155_N	229_R	1.161	0.97
78_I	96_E	1.161	0.97
127_V	212_V	1.157	0.97
151_P	183_G	1.157	0.97
18_L	58_V	1.156	0.97
10_S	106_H	1.153	0.97
58_V	61_R	1.131	0.97
8_P	11_K	1.129	0.97
38_W	240_Y	1.127	0.97
42_A	211_V	1.125	0.97
70_Q	107_V	1.121	0.97
32_S	40_L	1.120	0.96
14_W	206_W	1.109	0.96
44_H	91_D	1.106	0.96
89_G	176_R	1.100	0.96
46_V	77_I	1.097	0.96
15_Q	130_W	1.082	0.96
80_H	83_F	1.078	0.95
7_A	147_Q	1.050	0.94
178_D	233_Y	1.047	0.94
84_Y	87_Q	1.033	0.94
41_T	93_A	1.032	0.94
182_A	198_L	1.019	0.93
198_L	227_Y	1.014	0.93
132_D	136_D	1.014	0.93
63_Q	144_P	1.012	0.93
33_L	39_V	1.004	0.93
112_L	234_L	1.002	0.92

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	0.8689	100	-0.021	Contact Map
4nzqA	1	0.9467	100	-0.009	Contact Map
2xxlA	2	0.9426	100	-0.001	Contact Map
3nxpA	1	0.9385	100	0.001	Contact Map
4kkdA	2	0.9631	100	0.007	Contact Map
2b9lA	1	0.9713	100	0.016	Contact Map
1z8gA	1	0.9467	100	0.023	Contact Map
2f9nA	4	0.9836	100	0.025	Contact Map
4crgA	1	0.9385	100	0.03	Contact Map
2anyA	1	0.9549	100	0.031	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 0.9007 seconds.