OPENSEQ.org - 1402625476 - GREMLIN Submission

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

Welcome: casp11@openseq.org

T0794 - roll 300-470

ID:	1402625476	Query Sequence SSIEALSSGNKEFKGTVFFDEFTFVKLTGVAGNYTVCQKDLCCHLSYKMSENIPNEVYALGAFDGLHTVEGRYYLQICTLLKCKTTNLNTCGDSAETASTRFEMFSLSGTFGTQYVFPEVLLSENQLAPGEFQVSTDGRLFSLKPTSGPVLTVTLFGRLYEKDWASNASSG	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	171 (164)
Sequences:	180 (83.3)
Seq/Len:	1.098
Nf(neff/√len):	6.5

Jackhmmer Results: (2014_04_16)
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: 1.098).

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
58_Y	98_A	2.530	0.99
15_G	59_A	1.947	0.95
158_R	163_D	1.829	0.93
60_L	107_L	1.776	0.92
20_D	63_F	1.679	0.88
20_D	67_H	1.628	0.86
150_V	153_V	1.618	0.86
82_K	117_F	1.603	0.85
54_P	68_T	1.504	0.79
68_T	71_G	1.496	0.79
160_Y	163_D	1.483	0.78
19_F	69_V	1.437	0.75
120_V	131_E	1.417	0.73
96_E	104_M	1.395	0.72
26_K	156_F	1.394	0.72
82_K	155_L	1.388	0.71
18_F	70_E	1.377	0.70
25_V	115_Y	1.359	0.69
140_L	149_P	1.357	0.69
5_A	10_N	1.342	0.68
37_C	42_C	1.341	0.67
33_N	45_L	1.337	0.67
63_F	67_H	1.315	0.65
109_G	121_L	1.308	0.65
23_T	36_V	1.305	0.64
59_A	90_T	1.304	0.64
147_S	160_Y	1.303	0.64
66_L	74_Y	1.297	0.64
5_A	9_G	1.296	0.64
63_F	107_L	1.283	0.62
17_V	81_L	1.264	0.61
70_E	75_L	1.263	0.61
25_V	54_P	1.233	0.58
41_L	161_E	1.229	0.57
20_D	109_G	1.202	0.55
109_G	157_G	1.188	0.54
102_F	149_P	1.181	0.53
71_G	127_L	1.162	0.51
23_T	73_Y	1.155	0.51
60_L	108_S	1.141	0.49
38_Q	64_D	1.117	0.47
63_F	74_Y	1.116	0.47
97_T	125_N	1.115	0.47
20_D	61_G	1.105	0.46
60_L	105_F	1.102	0.45
82_K	108_S	1.093	0.45
37_C	79_T	1.089	0.44
27_L	100_T	1.086	0.44
41_L	162_K	1.079	0.43
79_T	82_K	1.079	0.43
98_A	157_G	1.078	0.43
111_F	155_L	1.075	0.43
39_K	47_Y	1.075	0.43
148_G	151_L	1.074	0.43
41_L	80_L	1.067	0.42
25_V	59_A	1.065	0.42
90_T	117_F	1.063	0.42
22_F	112_G	1.061	0.42
100_T	128_A	1.061	0.42
20_D	92_G	1.060	0.42
68_T	85_T	1.060	0.42
20_D	66_L	1.054	0.41
121_L	129_P	1.051	0.41
68_T	75_L	1.050	0.41
52_N	87_N	1.049	0.41
69_V	72_R	1.043	0.40
15_G	87_N	1.042	0.40
4_E	18_F	1.042	0.40
71_G	75_L	1.041	0.40
121_L	152_T	1.041	0.40
20_D	98_A	1.038	0.40
117_F	124_E	1.033	0.39
97_T	119_E	1.024	0.38
67_H	98_A	1.014	0.37
102_F	137_D	1.013	0.37
100_T	132_F	1.010	0.37
74_Y	82_K	1.008	0.37
112_G	134_V	1.007	0.37
24_F	27_L	1.007	0.37
64_D	131_E	1.004	0.36
50_S	64_D	1.003	0.36

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: (07Jun14)
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
3elbA	1	0.6842	20.9	0.959	Contact Map
1scfA	4	0.4211	3.5	0.972	Contact Map
3aqyA	2	0.3216	2.9	0.973	Contact Map
2dyuA	2	0.4152	2.9	0.973	Contact Map
3do8A	2	0.6199	2.5	0.973	Contact Map
4mvcA	2	0.8772	2.3	0.974	Contact Map
2ljbA	4	0.1111	2.1	0.975	Contact Map
3hl4A	2	0.8655	1.8	0.976	Contact Map
3ie4A	2	0.3275	1.7	0.976	Contact Map
2kaoA	1	0.5088	1.6	0.976	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 0.5535 seconds.