OPENSEQ.org - 1424381721 - GREMLIN Submission

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CarO

ID:	1424381721	Query Sequence MKVLRVLVTTTALLAAGAAMADEAVVHDSYAFDKNQLIPVGARAEVGTTGYGGALLWQANPYVGLALGYNGGDISWSDDLSINGTKYDMDMDNKLAYLNAEIRPWGASTNPWAQGLYVAAGAAYVDNQYDLTKNVGTNASVEIDGNRFNGGANGVSIAGNLKYDNDIAPYIGFGFAPKFSKNWGVFGEVGAYYSGNPKVSLASNNDALIGSDGRTLGQTLDDQERKIANDDKYKWLPVGKVGVNFYW	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	247 (241)
Sequences:	305 (269.5)
Seq/Len:	1.266
Nf(neff/√len):	17.4

Jackhmmer Results: (2015_01_07)
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: 1.266).

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
45_E	52_G	2.545	1.00
193_Y	235_W	2.506	1.00
117_Y	188_E	2.302	0.99
148_F	219_T	2.266	0.99
66_A	101_E	1.961	0.97
186_F	242_G	1.952	0.97
146_N	219_T	1.890	0.96
43_R	54_A	1.870	0.95
183_W	243_V	1.702	0.91
123_A	192_Y	1.693	0.91
172_G	238_V	1.661	0.90
184_G	244_N	1.646	0.89
101_E	119_A	1.606	0.88
5_R	9_T	1.558	0.86
115_G	175_F	1.556	0.86
68_G	97_Y	1.525	0.84
8_V	14_L	1.523	0.84
131_L	159_G	1.491	0.82
5_R	8_V	1.464	0.80
144_D	219_T	1.442	0.79
24_A	28_D	1.433	0.78
173_F	189_V	1.428	0.78
6_V	9_T	1.414	0.77
40_V	55_L	1.407	0.77
6_V	11_T	1.406	0.77
11_T	14_L	1.403	0.76
213_G	216_L	1.395	0.76
199_V	221_D	1.392	0.76
3_V	7_L	1.387	0.75
8_V	11_T	1.386	0.75
70_N	127_N	1.377	0.74
148_F	216_L	1.361	0.73
9_T	14_L	1.355	0.73
48_T	236_L	1.341	0.72
62_Y	102_I	1.322	0.70
122_A	167_I	1.310	0.69
179_F	182_N	1.309	0.69
5_R	20_M	1.301	0.68
102_I	245_F	1.290	0.67
48_T	52_G	1.289	0.67
5_R	16_A	1.276	0.66
193_Y	233_Y	1.276	0.66
221_D	224_E	1.258	0.65
43_R	68_G	1.258	0.65
135_V	153_N	1.257	0.64
87_Y	223_Q	1.245	0.63
5_R	10_T	1.232	0.62
7_L	11_T	1.229	0.62
125_V	168_A	1.227	0.62
140_S	148_F	1.222	0.61
173_F	246_Y	1.222	0.61
3_V	6_V	1.217	0.61
24_A	27_H	1.211	0.60
63_V	100_A	1.197	0.59
10_T	16_A	1.187	0.58
6_V	14_L	1.185	0.58
143_I	191_A	1.184	0.58
116_L	178_K	1.182	0.57
5_R	11_T	1.179	0.57
78_D	233_Y	1.176	0.57
135_V	168_A	1.176	0.57
45_E	240_K	1.168	0.56
56_L	103_R	1.165	0.56
93_N	125_V	1.162	0.55
11_T	18_A	1.162	0.55
135_V	141_V	1.160	0.55
41_G	177_P	1.160	0.55
59_A	100_A	1.160	0.55
106_G	114_Q	1.155	0.55
6_V	10_T	1.145	0.54
158_A	202_A	1.144	0.54
49_T	54_A	1.141	0.53
125_V	163_Y	1.140	0.53
8_V	12_A	1.134	0.53
119_A	172_G	1.134	0.53
191_A	235_W	1.129	0.52
79_D	90_D	1.128	0.52
3_V	18_A	1.127	0.52
64_G	177_P	1.121	0.51
20_M	24_A	1.119	0.51
144_D	223_Q	1.117	0.51
97_Y	123_A	1.113	0.51
9_T	12_A	1.112	0.51
10_T	17_G	1.111	0.50
64_G	176_A	1.106	0.50
138_N	218_Q	1.105	0.50
3_V	14_L	1.097	0.49
188_E	191_A	1.092	0.49
23_E	27_H	1.090	0.48
116_L	184_G	1.086	0.48
85_T	133_K	1.082	0.48
17_G	24_A	1.076	0.47
6_V	12_A	1.074	0.47
14_L	18_A	1.073	0.47
46_V	243_V	1.068	0.46
18_A	27_H	1.065	0.46
3_V	20_M	1.063	0.46
10_T	14_L	1.061	0.45
7_L	10_T	1.060	0.45
52_G	127_N	1.059	0.45
85_T	157_I	1.058	0.45
24_A	30_Y	1.058	0.45
23_E	28_D	1.054	0.45
135_V	143_I	1.052	0.45
13_L	16_A	1.048	0.44
53_G	71_G	1.043	0.44
41_G	56_L	1.042	0.44
99_N	188_E	1.037	0.43
7_L	24_A	1.029	0.42
3_V	10_T	1.029	0.42
77_S	216_L	1.024	0.42
86_K	241_V	1.024	0.42
11_T	16_A	1.022	0.42
54_A	68_G	1.018	0.41
243_V	246_Y	1.018	0.41
5_R	14_L	1.017	0.41
3_V	9_T	1.015	0.41
6_V	29_S	1.015	0.41
63_V	122_A	1.014	0.41
4_L	7_L	1.010	0.41
153_N	157_I	1.009	0.40
41_G	55_L	1.006	0.40
133_K	200_S	1.001	0.40
138_N	148_F	1.000	0.40

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: (31Jan15)
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
4fuvA	1	0.8583	100	0.219	Contact Map
3nb3A	3	0.5263	98.8	0.84	Contact Map
2x27X	1	0.7814	97.8	0.88	Contact Map
2k0lA	1	0.7328	97.4	0.888	Contact Map
1qjpA	1	0.5385	97	0.895	Contact Map
3qraA	1	0.6032	96.3	0.904	Contact Map
2f1vA	6	0.7126	96	0.907	Contact Map
2jmmA	1	0.5547	96	0.907	Contact Map
2lhfA	1	0.6478	95.4	0.911	Contact Map
1p4tA	1	0.5789	94.2	0.916	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.

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