OPENSEQ.org - 1414276041 - GREMLIN Submission

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

VP3

ID:	1414276041	Query Sequence GLPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEIDTMIPFDLSATKKNTMEMYRVRLSDKPHTAASILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTFLFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNSTYRQTIDDSFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQKALAQ	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	238 (235)
Sequences:	542 (234.2)
Seq/Len:	2.306
Nf(neff/√len):	15.3

HHblits Results: (2013_03)
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: 2.306).

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 > 50% 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
116_F	168_V	2.773	1.00
113_S	219_D	2.426	1.00
117_T	163_S	2.271	1.00
159_G	177_R	1.987	0.99
104_L	222_V	1.963	0.99
5_M	19_F	1.957	0.99
113_S	217_C	1.885	0.99
51_T	99_M	1.785	0.98
41_K	45_E	1.695	0.97
120_F	156_W	1.638	0.96
109_H	121_C	1.625	0.96
162_S	172_S	1.617	0.96
46_L	51_T	1.617	0.96
116_F	190_I	1.609	0.96
133_S	153_H	1.609	0.96
130_L	192_V	1.601	0.95
134_Y	188_G	1.563	0.95
147_E	168_V	1.519	0.94
122_G	137_P	1.473	0.92
137_P	142_P	1.416	0.90
215_S	223_R	1.413	0.90
107_Y	111_A	1.405	0.90
152_T	205_P	1.392	0.89
115_K	215_S	1.382	0.88
144_K	147_E	1.368	0.88
114_L	214_V	1.359	0.87
118_F	212_G	1.327	0.86
167_V	205_P	1.323	0.85
123_S	126_A	1.294	0.84
159_G	162_S	1.283	0.83
129_K	227_D	1.281	0.83
170_W	177_R	1.280	0.83
40_V	45_E	1.263	0.82
123_S	204_T	1.247	0.80
151_G	159_G	1.232	0.79
132_V	190_I	1.230	0.79
162_S	169_P	1.229	0.79
19_F	22_P	1.227	0.79
17_D	22_P	1.225	0.79
152_T	177_R	1.223	0.79
156_W	223_R	1.217	0.78
107_Y	135_A	1.214	0.78
219_D	224_L	1.211	0.78
7_T	10_S	1.205	0.77
5_M	33_P	1.205	0.77
155_I	190_I	1.192	0.76
127_T	159_G	1.191	0.76
172_S	177_R	1.189	0.76
210_I	222_V	1.187	0.76
118_F	156_W	1.185	0.75
5_M	22_P	1.180	0.75
22_P	30_V	1.176	0.75
20_Q	23_C	1.174	0.75
159_G	163_S	1.168	0.74
216_A	220_F	1.157	0.73
124_M	158_I	1.154	0.73
134_Y	138_G	1.151	0.72
5_M	17_D	1.146	0.72
148_A	162_S	1.144	0.72
128_G	158_I	1.139	0.71
134_Y	137_P	1.137	0.71
151_G	193_F	1.135	0.71
120_F	208_M	1.129	0.70
103_I	114_L	1.128	0.70
122_G	125_M	1.126	0.70
156_W	160_L	1.125	0.70
83_L	192_V	1.122	0.70
169_P	172_S	1.119	0.69
168_V	190_I	1.112	0.69
52_M	213_F	1.109	0.68
46_L	99_M	1.104	0.68
142_P	148_A	1.099	0.67
172_S	223_R	1.097	0.67
85_L	94_R	1.094	0.67
98_T	188_G	1.093	0.67
117_T	128_G	1.089	0.66
125_M	201_P	1.089	0.66
151_G	172_S	1.088	0.66
156_W	159_G	1.083	0.66
196_T	227_D	1.082	0.66
125_M	128_G	1.082	0.66
156_W	162_S	1.077	0.65
17_D	21_S	1.076	0.65
120_F	123_S	1.074	0.65
7_T	23_C	1.073	0.65
151_G	156_W	1.072	0.65
5_M	28_F	1.071	0.64
164_C	217_C	1.069	0.64
44_M	48_E	1.068	0.64
190_I	195_Q	1.066	0.64
5_M	20_Q	1.051	0.62
160_L	215_S	1.048	0.62
30_V	33_P	1.046	0.62
53_I	212_G	1.040	0.61
98_T	114_L	1.040	0.61
4_V	236_L	1.039	0.61
5_M	14_L	1.037	0.61
113_S	164_C	1.037	0.61
68_Y	72_L	1.035	0.61
109_H	122_G	1.034	0.60
135_A	193_F	1.032	0.60
159_G	213_F	1.027	0.60
123_S	220_F	1.026	0.60
51_T	221_S	1.022	0.59
81_S	84_C	1.021	0.59
98_T	170_W	1.019	0.59
5_M	11_N	1.018	0.59
152_T	172_S	1.018	0.59
137_P	153_H	1.017	0.59
145_R	149_M	1.014	0.58
166_M	216_A	1.014	0.58
129_K	137_P	1.009	0.58
58_S	61_K	1.007	0.57
29_D	44_M	1.006	0.57
113_S	118_F	1.005	0.57
98_T	172_S	1.005	0.57
197_R	220_F	1.005	0.57
162_S	216_A	1.005	0.57
109_H	208_M	1.004	0.57
4_V	63_N	1.001	0.57
10_S	22_P	1.001	0.57
185_T	219_D	1.001	0.57
33_P	39_E	1.000	0.57

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: (06Sep14)
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
1m113	1	1	100	0.047	Contact Map
4gb33	1	1	100	0.047	Contact Map
3vbhC	1	0.9916	100	0.047	Contact Map
1hxs3	1	0.979	100	0.048	Contact Map
1aym3	1	0.9958	100	0.056	Contact Map
1bev3	1	0.9874	100	0.057	Contact Map
1ncqC	1	0.979	100	0.066	Contact Map
3cjiB	1	0.9664	100	0.105	Contact Map
1tme3	1	0.958	100	0.123	Contact Map
2mev3	1	0.9496	100	0.136	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 0.43 seconds.