OPENSEQ.org - 1494533929 - GREMLIN Submission

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

Tau_RDs_mafft

ID:	1494533929	Query Sequence QTAPVPMPDLKNVKSKIGSTENLKHQPGGGKVQIINKKLDLSNVQSKCGSKDNIKHVPGGGSVQIVYKPVDLSKVTSKCGSLGNIHHKPGGGQVEVKSEKLDFKDRVQSKIGSLDNITHVPGGGNKK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	127 (123)
Sequences:	226 (88.7)
Seq/Len:	1.837
Nf(neff/√len):	8.0

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: 1.837).

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
82_L	85_I	2.073	0.99
119_H	123_G	1.920	0.98
11_K	17_I	1.752	0.96
14_K	17_I	1.741	0.96
9_D	20_T	1.735	0.96
20_T	26_Q	1.486	0.89
56_H	60_G	1.484	0.89
18_G	30_G	1.436	0.87
9_D	24_K	1.403	0.85
9_D	23_L	1.396	0.85
25_H	29_G	1.392	0.85
11_K	14_K	1.387	0.84
51_K	54_I	1.387	0.84
73_S	79_C	1.359	0.83
44_V	48_C	1.352	0.82
103_F	107_V	1.341	0.81
19_S	29_G	1.333	0.81
113_S	116_N	1.321	0.80
53_N	56_H	1.294	0.78
6_P	25_H	1.286	0.78
64_Q	85_I	1.276	0.77
11_K	16_K	1.274	0.77
19_S	22_N	1.244	0.74
51_K	55_K	1.230	0.73
75_V	79_C	1.225	0.73
64_Q	79_C	1.221	0.72
19_S	30_G	1.213	0.72
33_Q	64_Q	1.209	0.71
78_K	89_P	1.190	0.69
56_H	59_G	1.189	0.69
116_N	119_H	1.188	0.69
107_V	111_I	1.185	0.69
70_V	93_Q	1.177	0.68
104_K	114_L	1.170	0.68
11_K	20_T	1.166	0.67
68_K	75_V	1.162	0.67
11_K	26_Q	1.161	0.67
49_G	56_H	1.153	0.66
14_K	20_T	1.142	0.65
33_Q	55_K	1.137	0.64
114_L	118_T	1.123	0.63
10_L	13_V	1.110	0.62
71_D	85_I	1.108	0.61
18_G	29_G	1.106	0.61
10_L	20_T	1.099	0.60
57_V	79_C	1.098	0.60
97_K	104_K	1.093	0.60
20_T	23_L	1.088	0.59
34_I	62_S	1.085	0.59
7_M	25_H	1.082	0.59
88_K	110_K	1.079	0.58
69_P	96_V	1.077	0.58
28_G	31_K	1.068	0.57
43_N	57_V	1.066	0.57
68_K	79_C	1.062	0.57
82_L	86_H	1.061	0.56
50_S	53_N	1.059	0.56
25_H	28_G	1.054	0.56
45_Q	48_C	1.052	0.55
19_S	28_G	1.051	0.55
99_E	117_I	1.048	0.55
97_K	111_I	1.048	0.55
59_G	89_P	1.042	0.54
78_K	81_S	1.040	0.54
71_D	82_L	1.037	0.54
70_V	95_E	1.026	0.53
116_N	124_G	1.021	0.52
78_K	101_L	1.015	0.51
22_N	29_G	1.010	0.51
79_C	86_H	1.005	0.50
50_S	56_H	1.003	0.50
9_D	63_V	1.002	0.50

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
2mz7A	1	0	99.8	0.673	Contact Map
3qr8A	1	0.4803	6.9	0.961	Contact Map
1lq7A	1	0.4016	2.5	0.968	Contact Map
3nngA	2	0.2835	1.8	0.971	Contact Map
2nnzA	1	0.7559	1.5	0.972	Contact Map
5bxvB	2	0	1.4	0.973	Contact Map
4r29A	4	0.3386	1.4	0.973	Contact Map
4heiA	2	0.4488	1.3	0.973	Contact Map
2lmkA	1	0.189	1.3	0.973	Contact Map
3v2cY	1	0.4409	1.2	0.974	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 0.5321 seconds.