OPENSEQ.org - 1490700831 - GREMLIN Submission

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

comb

ID:	1490700831	Query Sequence ASSVNELENWSKWMQPIPDSIPLARISIPGTHDSGTFKLQNPIKQVWGMTQEYDFRYQMDHGARIFDIRGRLTDDNTIVLHHGPLYLYVTLHEFINEAKQFLKDNPSETIIMSLKKEYEDMKGAEDSFSSTFEKKYFVDPIFLKTEGNIKLGDARGKIVLLKRYSGSNEPGGYNNFYWPDNETFTTTVNQNANVTVQDKYKVSYDEKVKSIKDTMDETMNNSEDLNHLYINFTSLSSGGTAWNSPYYYASYINPEIANYIKQKNPARVGWVIQDYINEKWSPLLYQEVIRANKSLIKE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	298 (291)
Sequences:	1181 (843.9)
Seq/Len:	4.058
Nf(neff/√len):	49.5

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: 4.058).

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
66_F	98_A	3.927	1.00
19_D	152_G	3.789	1.00
197_Q	231_N	3.361	1.00
33_D	50_T	2.633	1.00
63_A	276_I	2.546	1.00
69_R	82_H	2.532	1.00
65_I	272_I	2.490	1.00
31_T	34_S	2.414	1.00
68_I	112_M	2.406	1.00
22_P	25_R	2.364	1.00
56_R	60_D	2.351	1.00
98_A	110_I	2.294	1.00
112_M	158_I	2.227	1.00
12_K	105_N	2.220	1.00
56_R	97_E	2.175	1.00
33_D	69_R	2.120	1.00
54_D	57_Y	2.106	1.00
245_P	249_A	2.084	1.00
55_F	66_F	2.054	1.00
150_K	153_D	2.017	1.00
113_S	163_R	1.984	1.00
28_I	65_I	1.968	1.00
14_M	151_L	1.934	1.00
98_A	112_M	1.892	1.00
59_M	101_F	1.885	1.00
35_G	55_F	1.853	1.00
288_V	292_N	1.849	1.00
109_T	151_L	1.760	0.99
52_E	277_N	1.758	0.99
11_S	105_N	1.673	0.99
27_S	288_V	1.653	0.99
65_I	270_W	1.641	0.99
70_G	128_F	1.641	0.99
56_R	100_Q	1.624	0.99
68_I	94_F	1.623	0.99
15_Q	107_S	1.591	0.99
13_W	29_P	1.549	0.98
69_R	198_D	1.546	0.98
59_M	66_F	1.544	0.98
289_I	292_N	1.531	0.98
19_D	155_R	1.519	0.98
69_R	274_D	1.496	0.98
68_I	270_W	1.482	0.97
63_A	273_Q	1.458	0.97
12_K	16_P	1.453	0.97
117_E	198_D	1.451	0.97
233_T	273_Q	1.417	0.96
79_V	90_T	1.390	0.96
12_K	15_Q	1.385	0.96
125_E	163_R	1.382	0.96
57_Y	63_A	1.381	0.96
80_L	94_F	1.379	0.96
28_I	111_I	1.373	0.95
50_T	69_R	1.365	0.95
32_H	274_D	1.344	0.95
36_T	87_L	1.335	0.94
154_A	159_V	1.331	0.94
33_D	61_H	1.327	0.94
30_G	34_S	1.305	0.94
33_D	82_H	1.288	0.93
196_V	200_Y	1.287	0.93
115_K	198_D	1.282	0.93
276_I	285_Y	1.277	0.93
20_S	152_G	1.267	0.92
111_I	159_V	1.266	0.92
55_F	270_W	1.264	0.92
17_I	21_I	1.263	0.92
73_T	79_V	1.261	0.92
7_L	10_W	1.255	0.92
9_N	12_K	1.249	0.91
117_E	163_R	1.248	0.91
31_T	58_Q	1.244	0.91
147_G	153_D	1.243	0.91
58_Q	64_R	1.236	0.91
27_S	268_V	1.218	0.90
113_S	117_E	1.216	0.90
212_K	216_D	1.214	0.90
150_K	154_A	1.209	0.90
113_S	232_F	1.208	0.90
81_H	118_Y	1.205	0.89
21_I	25_R	1.196	0.89
31_T	276_I	1.195	0.89
59_M	64_R	1.191	0.89
68_I	80_L	1.183	0.88
10_W	289_I	1.179	0.88
71_R	81_H	1.171	0.87
37_F	87_L	1.167	0.87
207_K	234_S	1.161	0.87
65_I	232_F	1.155	0.87
286_Q	290_R	1.137	0.85
26_I	30_G	1.137	0.85
53_Y	61_H	1.136	0.85
126_D	131_T	1.106	0.83
18_P	21_I	1.103	0.83
14_M	109_T	1.102	0.83
48_G	85_L	1.101	0.83
59_M	110_I	1.099	0.83
72_L	131_T	1.098	0.83
230_I	272_I	1.095	0.82
60_D	100_Q	1.093	0.82
55_F	89_V	1.093	0.82
10_W	286_Q	1.092	0.82
273_Q	276_I	1.091	0.82
90_T	93_E	1.089	0.82
115_K	200_Y	1.089	0.82
102_L	158_I	1.086	0.82
130_S	160_L	1.082	0.81
260_I	291_A	1.081	0.81
38_K	87_L	1.080	0.81
113_S	162_K	1.080	0.81
21_I	271_V	1.078	0.81
113_S	276_I	1.068	0.80
36_T	39_L	1.058	0.79
109_T	155_R	1.057	0.79
182_E	188_V	1.055	0.79
30_G	270_W	1.046	0.78
59_M	108_E	1.044	0.78
66_F	137_F	1.042	0.78
26_I	29_P	1.039	0.77
53_Y	276_I	1.037	0.77
182_E	185_T	1.037	0.77
32_H	69_R	1.028	0.76
68_I	278_E	1.021	0.76
107_S	155_R	1.019	0.75
68_I	101_F	1.009	0.74
252_I	255_E	1.009	0.74
67_D	108_E	1.006	0.74
185_T	188_V	1.006	0.74
58_Q	292_N	1.005	0.74

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
3ea1A	2	0.9899	100	0.153	Contact Map
4i90A	1	0.9698	100	0.228	Contact Map
2plcA	1	0.8893	100	0.257	Contact Map
3h4xA	1	0.8322	99.9	0.613	Contact Map
2zkmX	1	0.8456	95.4	0.908	Contact Map
3qr0A	1	0.8859	95.4	0.908	Contact Map
1djxA	2	0.8087	95.3	0.908	Contact Map
3ohmB	1	0.8054	93.9	0.915	Contact Map
4gnkB	2	0.8154	92.6	0.918	Contact Map
4iqyA	2	0.4362	24.3	0.954	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 0.4607 seconds.