OPENSEQ.org - 1504851107 - GREMLIN Submission

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

scEMC4

ID:	1504851107	Query Sequence MSEQEPYEWAKHLLDTKYIEKYNIQNSNTLPSPPGFEGNSSKGNVTRKQQDATSQTTSLAQKNQITVLQVQKAWQIALQPAKSIPMNIFMSYMSGTSLQIIPIMTALMLLSGPIKAIFSTRSAFKPVLGNKATQSQVQTAMFMYIVFQGVLMYIGYRKLNSMGLIPNAKGDWLPWERIAHYNNGLQWFSD	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	190 (177)
Sequences:	358 (251.5)
Seq/Len:	2.023
Nf(neff/√len):	18.9

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: 2.023).

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
87_N	109_L	2.419	1.00
72_K	75_Q	2.081	0.99
89_F	93_M	1.998	0.99
142_F	146_V	1.942	0.99
101_I	165_I	1.936	0.99
94_S	108_M	1.903	0.98
84_I	151_L	1.789	0.97
90_M	148_Q	1.760	0.97
121_R	141_M	1.737	0.97
104_M	108_M	1.734	0.97
99_Q	155_G	1.646	0.95
20_E	23_N	1.600	0.94
123_A	144_Y	1.575	0.94
85_P	109_L	1.543	0.93
163_G	166_P	1.540	0.93
165_I	170_G	1.531	0.92
32_S	72_K	1.520	0.92
109_L	151_L	1.495	0.91
71_Q	105_T	1.488	0.91
85_P	173_L	1.474	0.90
85_P	92_Y	1.471	0.90
91_S	101_I	1.452	0.89
157_R	160_N	1.447	0.89
87_N	112_G	1.429	0.88
87_N	115_K	1.414	0.88
119_S	144_Y	1.404	0.87
85_P	162_M	1.349	0.84
106_A	140_A	1.325	0.83
98_L	159_L	1.282	0.80
112_G	115_K	1.262	0.78
136_Q	150_V	1.255	0.78
87_N	108_M	1.252	0.77
143_M	146_V	1.249	0.77
76_I	79_Q	1.239	0.76
85_P	99_Q	1.236	0.76
166_P	171_D	1.231	0.76
149_G	153_Y	1.211	0.74
164_L	170_G	1.209	0.74
158_K	172_W	1.207	0.74
124_F	141_M	1.199	0.73
93_M	103_I	1.197	0.73
99_Q	102_P	1.193	0.73
75_Q	175_W	1.192	0.72
81_A	109_L	1.185	0.72
109_L	155_G	1.183	0.72
81_A	87_N	1.181	0.71
174_P	183_N	1.180	0.71
96_T	161_S	1.161	0.70
85_P	108_M	1.156	0.69
73_A	127_V	1.152	0.69
160_N	170_G	1.150	0.69
137_V	140_A	1.148	0.68
27_S	40_S	1.146	0.68
106_A	152_M	1.144	0.68
142_F	145_I	1.141	0.68
110_L	156_Y	1.138	0.67
91_S	117_I	1.133	0.67
55_Q	154_I	1.123	0.66
64_Q	72_K	1.116	0.65
94_S	144_Y	1.115	0.65
148_Q	151_L	1.113	0.65
169_K	176_E	1.099	0.63
101_I	167_N	1.092	0.63
103_I	181_Y	1.090	0.62
13_L	103_I	1.087	0.62
108_M	112_G	1.087	0.62
91_S	104_M	1.081	0.61
7_Y	92_Y	1.066	0.60
154_I	158_K	1.065	0.60
164_L	174_P	1.061	0.59
92_Y	109_L	1.059	0.59
87_N	127_V	1.058	0.59
99_Q	148_Q	1.049	0.58
102_P	127_V	1.048	0.58
168_A	179_A	1.045	0.58
106_A	159_L	1.043	0.57
98_L	156_Y	1.042	0.57
155_G	158_K	1.041	0.57
87_N	102_P	1.032	0.56
162_M	172_W	1.029	0.56
114_I	119_S	1.022	0.55
108_M	113_P	1.021	0.55
98_L	175_W	1.019	0.55
68_L	85_P	1.014	0.54
163_G	171_D	1.011	0.54
63_N	142_F	1.008	0.54
69_Q	99_Q	1.005	0.53
113_P	173_L	1.004	0.53
94_S	99_Q	1.001	0.53

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
4ardA	2	0.3053	2.8	0.97	Contact Map
2v4xA	1	0.3526	2.6	0.971	Contact Map
1em9A	2	0.3526	2.6	0.971	Contact Map
2mc7A	1	0.1579	1.5	0.974	Contact Map
3tirA	1	0.3316	1.5	0.974	Contact Map
2kgfA	1	0.3579	1.4	0.975	Contact Map
1jb0K	1	0.1211	1.4	0.975	Contact Map
1g92A	1	0.1211	1.3	0.975	Contact Map
2fq3A	1	0.1105	1.2	0.976	Contact Map
4rsxA	1	0.3421	1	0.977	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 0.5257 seconds.