OPENSEQ.org - 1488572320 - GREMLIN Submission

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

3

ID:	1488572320	Query Sequence MGSSHHHHHHSSGLVPRGSHMVANAISEFWRDIRPIESPFKPDALPEAYIPNAATEDERYYVPFTETVASRPLWISPQQNRWCDILLAREAGLVNRHYHPHEVFAYTISGKWGYLEHDWTATRGDFVYETPGEGHTLVAFEHEEPMRVFFIVQGPLIWLDEAGNSIGHFDVHDYIAMCREHYEKVGLGADLVVTLFR	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	197 (170)
Sequences:	171 (94.5)
Seq/Len:	1.006
Nf(neff/√len):	7.2

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: 1.006).

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
37_E	162_A	1.935	0.94
179_R	193_V	1.931	0.94
83_C	151_I	1.821	0.92
113_G	140_F	1.750	0.89
83_C	149_F	1.731	0.89
64_F	174_Y	1.710	0.88
182_Y	193_V	1.707	0.88
117_H	133_E	1.646	0.85
111_K	122_T	1.615	0.84
40_F	44_A	1.611	0.83
55_T	178_C	1.572	0.81
104_F	126_F	1.556	0.80
111_K	140_F	1.553	0.80
41_K	134_G	1.490	0.76
130_T	174_Y	1.469	0.75
65_T	69_A	1.460	0.74
71_R	188_G	1.446	0.73
47_E	105_A	1.442	0.73
77_P	175_I	1.433	0.72
93_L	113_G	1.429	0.72
130_T	169_F	1.403	0.70
84_D	174_Y	1.390	0.69
47_E	82_W	1.383	0.68
85_I	147_R	1.368	0.67
175_I	192_V	1.366	0.67
58_E	193_V	1.359	0.66
67_T	101_H	1.340	0.65
68_V	95_N	1.331	0.64
47_E	100_P	1.325	0.63
82_W	100_P	1.324	0.63
183_E	189_A	1.294	0.61
176_A	180_E	1.284	0.60
46_P	102_E	1.275	0.59
53_A	149_F	1.266	0.58
87_L	111_K	1.266	0.58
178_C	182_Y	1.246	0.56
151_I	178_C	1.242	0.56
168_H	173_D	1.228	0.55
102_E	126_F	1.227	0.55
191_L	195_L	1.212	0.53
109_S	149_F	1.203	0.52
105_A	150_F	1.192	0.51
107_T	113_G	1.189	0.51
59_R	71_R	1.178	0.50
34_R	37_E	1.175	0.50
105_A	127_V	1.175	0.50
169_F	174_Y	1.168	0.49
49_Y	125_D	1.162	0.49
89_R	143_E	1.148	0.47
107_T	125_D	1.148	0.47
40_F	155_P	1.134	0.46
49_Y	134_G	1.132	0.46
59_R	188_G	1.129	0.46
92_G	146_M	1.127	0.45
115_L	138_V	1.125	0.45
107_T	148_V	1.119	0.45
133_E	173_D	1.119	0.45
41_K	138_V	1.113	0.44
40_F	163_G	1.111	0.44
57_D	71_R	1.103	0.43
93_L	134_G	1.101	0.43
79_Q	126_F	1.101	0.43
93_L	138_V	1.094	0.42
44_A	101_H	1.092	0.42
86_L	127_V	1.092	0.42
181_H	187_L	1.084	0.41
93_L	147_R	1.083	0.41
71_R	155_P	1.082	0.41
55_T	60_Y	1.080	0.41
86_L	172_H	1.079	0.41
157_I	165_S	1.078	0.41
71_R	175_I	1.071	0.40
52_N	55_T	1.069	0.40
81_R	104_F	1.067	0.40
58_E	89_R	1.060	0.39
48_A	127_V	1.058	0.39
188_G	192_V	1.050	0.38
180_E	184_K	1.050	0.38
95_N	148_V	1.046	0.38
76_S	177_M	1.044	0.38
175_I	196_F	1.042	0.38
87_L	125_D	1.038	0.37
37_E	161_E	1.037	0.37
47_E	101_H	1.036	0.37
40_F	43_D	1.034	0.37
182_Y	194_T	1.033	0.37
39_P	193_V	1.029	0.37
47_E	96_R	1.024	0.36
82_W	156_L	1.021	0.36
94_V	126_F	1.020	0.36
58_E	71_R	1.020	0.36
44_A	52_N	1.007	0.35
94_V	123_R	1.000	0.34

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
4p9gA	1	0.7614	100	0.611	Contact Map
5bpxA	1	0	100	0.661	Contact Map
3cjxA	8	0.7766	99.9	0.681	Contact Map
3balA	4	0.7107	99.9	0.709	Contact Map
3ebrA	1	0.7766	99.8	0.763	Contact Map
2o1qA	2	0.6853	99.6	0.798	Contact Map
2q1zB	2	0.6853	98.8	0.864	Contact Map
3o14A	2	0.7208	98.6	0.874	Contact Map
4e2gA	8	0.6294	98.3	0.884	Contact Map
2pfwA	2	0.5431	98	0.892	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 1.1224 seconds.