OPENSEQ.org - 1506627547 - GREMLIN Submission

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

CHMP3

ID:	1506627547	Query Sequence MGLFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIVLAKEMIRSRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMRELSKEMMKAGIIEEMLEDTFESMDDQEEMEEEAEMEIDRILFEITAGALGKAPSKVTDALPEPEPPGAMAASEDEEEEEEALEAMQSRLATLRS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	222 (220)
Sequences:	1073 (619.3)
Seq/Len:	4.877
Nf(neff/√len):	41.8

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: 4.877).

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
70_S	73_A	2.930	1.00
42_E	45_K	2.683	1.00
217_L	220_L	2.621	1.00
50_D	54_K	2.613	1.00
10_K	18_E	2.543	1.00
41_E	71_R	2.460	1.00
214_Q	218_A	2.218	1.00
56_Q	59_V	1.976	1.00
71_R	171_E	1.876	1.00
23_I	84_M	1.875	1.00
41_E	45_K	1.821	1.00
119_K	122_E	1.817	1.00
46_R	50_D	1.803	1.00
11_P	14_E	1.720	1.00
125_A	129_E	1.699	0.99
133_E	136_K	1.687	0.99
144_L	147_T	1.669	0.99
40_E	43_K	1.669	0.99
129_E	132_K	1.667	0.99
57_K	61_I	1.642	0.99
38_Q	74_V	1.640	0.99
158_E	162_E	1.626	0.99
218_A	221_R	1.619	0.99
10_K	15_L	1.597	0.99
38_Q	42_E	1.513	0.99
215_S	218_A	1.506	0.98
37_I	73_A	1.501	0.98
11_P	15_L	1.489	0.98
216_R	219_T	1.446	0.98
145_E	149_E	1.436	0.98
98_L	102_G	1.432	0.98
44_V	47_S	1.384	0.97
87_V	127_M	1.379	0.97
48_V	67_M	1.368	0.97
34_I	78_Y	1.352	0.96
217_L	221_R	1.320	0.96
124_Q	128_R	1.311	0.96
113_A	116_S	1.299	0.95
206_E	209_A	1.282	0.95
94_Q	98_L	1.271	0.94
46_R	54_K	1.268	0.94
165_I	169_L	1.254	0.94
132_K	181_P	1.249	0.94
30_V	64_A	1.240	0.93
19_W	22_K	1.229	0.93
69_R	80_S	1.214	0.92
170_F	173_T	1.211	0.92
216_R	221_R	1.207	0.92
39_R	43_K	1.199	0.92
216_R	220_L	1.198	0.92
2_G	6_K	1.195	0.92
47_S	50_D	1.190	0.91
80_S	100_V	1.187	0.91
5_G	16_V	1.183	0.91
43_K	47_S	1.166	0.90
4_F	12_P	1.164	0.90
117_L	138_G	1.163	0.90
130_L	134_M	1.159	0.90
2_G	5_G	1.148	0.89
213_M	216_R	1.145	0.89
40_E	70_S	1.145	0.89
124_Q	162_E	1.134	0.89
112_K	129_E	1.134	0.89
25_K	29_V	1.134	0.89
42_E	46_R	1.132	0.89
31_D	81_K	1.121	0.88
143_M	146_D	1.119	0.88
34_I	74_V	1.118	0.88
166_D	170_F	1.114	0.87
61_I	119_K	1.111	0.87
134_M	164_E	1.103	0.87
136_K	140_I	1.101	0.87
198_A	201_E	1.099	0.86
175_G	178_G	1.096	0.86
92_K	96_A	1.093	0.86
69_R	105_Q	1.093	0.86
92_K	144_L	1.085	0.86
197_M	200_S	1.085	0.86
48_V	60_C	1.077	0.85
41_E	181_P	1.075	0.85
27_M	88_L	1.072	0.85
168_I	171_E	1.070	0.84
181_P	184_V	1.069	0.84
51_A	54_K	1.058	0.84
204_E	207_E	1.052	0.83
65_K	81_K	1.051	0.83
68_I	71_R	1.049	0.83
102_G	106_K	1.047	0.83
14_E	20_S	1.039	0.82
3_L	6_K	1.036	0.82
40_E	73_A	1.035	0.82
51_A	59_V	1.034	0.82
132_K	182_S	1.031	0.81
38_Q	148_F	1.031	0.81
213_M	220_L	1.030	0.81
51_A	163_M	1.029	0.81
187_A	197_M	1.024	0.81
205_E	209_A	1.022	0.81
61_I	163_M	1.020	0.80
1_M	5_G	1.016	0.80
104_L	131_S	1.016	0.80
26_E	134_M	1.015	0.80
206_E	210_L	1.014	0.80
205_E	208_E	1.012	0.80
97_V	107_S	1.011	0.80
87_V	111_M	1.010	0.79
15_L	18_E	1.006	0.79
111_M	127_M	1.004	0.79
174_A	213_M	1.001	0.79
41_E	67_M	1.000	0.78

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
3frtA	2	0.6396	100	0.197	Contact Map
2gd5A	4	0.7297	100	0.298	Contact Map
3eabG	6	0.1892	98.2	0.826	Contact Map
3frrA	1	0.7973	95.9	0.88	Contact Map
3um3B	1	0.0721	91.2	0.901	Contact Map
2xzeQ	2	0.1036	90.3	0.903	Contact Map
3ggyA	2	0.7523	89.1	0.905	Contact Map
2v6xB	1	0.1667	56.1	0.929	Contact Map
4abmA	4	0.3559	31	0.939	Contact Map
2luhB	1	0.2658	28.9	0.94	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 1.3995 seconds.