OPENSEQ.org - 1490238973 - GREMLIN Submission

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E4 it4

ID:	1490238973	Query Sequence LTANLVCRVALGILANLLCLVPLRLLYHNHELAAVVFILNIEFKNILTIVSALIWRDDNMEDWWAGYGLCDFASFANNFSFGLFDTCMLAIMRNLAHQANLLSAHPSAQRYLIGTLTGCTWTQYPSWPYVVFFALPPLVLSVVVSVLVPYFPVVVTIFIMNHGWIPILSAIPVIVFFGMTKEAINDYRRVLLLPGFADGSFGSSHSAANSGS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	212 (208)
Sequences:	760 (647.2)
Seq/Len:	3.654
Nf(neff/√len):	44.9

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: 3.654).

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
64_W	111_Y	3.974	1.00
127_W	131_V	3.502	1.00
155_V	159_I	2.965	1.00
60_M	116_L	2.770	1.00
174_I	178_G	2.387	1.00
61_E	65_A	2.131	1.00
68_G	72_F	1.899	1.00
110_R	118_G	1.897	1.00
9_V	12_G	1.809	0.99
9_V	13_I	1.732	0.99
109_Q	112_L	1.676	0.99
187_Y	191_L	1.661	0.99
184_I	187_Y	1.657	0.99
8_R	12_G	1.631	0.98
50_V	73_A	1.597	0.98
151_F	155_V	1.596	0.98
47_L	80_S	1.596	0.98
64_W	67_Y	1.594	0.98
25_L	28_H	1.541	0.98
177_F	187_Y	1.512	0.97
89_L	140_L	1.512	0.97
71_D	110_R	1.492	0.97
32_L	37_F	1.487	0.97
23_L	45_N	1.485	0.97
71_D	74_S	1.480	0.97
182_E	187_Y	1.474	0.97
110_R	119_C	1.456	0.96
174_I	177_F	1.455	0.96
123_Q	129_Y	1.418	0.96
75_F	79_F	1.398	0.95
10_A	14_L	1.374	0.94
89_L	93_R	1.364	0.94
83_L	87_C	1.362	0.94
35_V	39_L	1.347	0.94
8_R	59_N	1.345	0.94
69_L	73_A	1.341	0.93
101_L	104_A	1.330	0.93
177_F	182_E	1.323	0.93
22_P	45_N	1.320	0.93
152_P	178_G	1.294	0.92
35_V	90_A	1.287	0.92
29_N	37_F	1.278	0.91
10_A	13_I	1.277	0.91
202_G	206_S	1.259	0.90
19_C	52_A	1.257	0.90
18_L	48_T	1.235	0.89
111_Y	118_G	1.231	0.89
87_C	92_M	1.227	0.89
14_L	18_L	1.225	0.89
107_S	194_P	1.219	0.88
76_A	165_I	1.217	0.88
194_P	198_D	1.213	0.88
151_F	182_E	1.204	0.87
86_T	140_L	1.202	0.87
112_L	122_T	1.199	0.87
96_A	102_L	1.194	0.87
177_F	183_A	1.181	0.86
100_N	155_V	1.164	0.85
183_A	187_Y	1.163	0.85
105_H	187_Y	1.145	0.84
81_F	125_P	1.144	0.84
18_L	170_A	1.138	0.83
5_L	9_V	1.137	0.83
13_I	17_L	1.123	0.82
33_A	41_I	1.105	0.81
180_T	183_A	1.092	0.79
201_F	204_S	1.089	0.79
54_I	58_D	1.082	0.79
79_F	82_G	1.080	0.78
203_S	207_A	1.080	0.78
113_I	118_G	1.078	0.78
174_I	182_E	1.072	0.78
65_A	68_G	1.070	0.78
43_F	54_I	1.069	0.77
194_P	197_A	1.068	0.77
152_P	177_F	1.067	0.77
46_I	50_V	1.058	0.76
11_L	163_G	1.056	0.76
178_G	182_E	1.055	0.76
71_D	75_F	1.055	0.76
186_D	190_V	1.052	0.76
138_L	154_V	1.049	0.76
178_G	183_A	1.046	0.75
70_C	119_C	1.043	0.75
30_H	33_A	1.040	0.75
34_A	43_F	1.039	0.75
12_G	23_L	1.036	0.74
12_G	59_N	1.031	0.74
88_M	146_V	1.030	0.74
108_A	112_L	1.023	0.73
199_G	202_G	1.023	0.73
202_G	205_H	1.022	0.73
11_L	44_K	1.021	0.73
164_W	177_F	1.017	0.72
195_G	198_D	1.010	0.72
34_A	58_D	1.006	0.71
198_D	204_S	1.006	0.71
141_S	150_Y	1.005	0.71
26_L	31_E	1.004	0.71
68_G	71_D	1.003	0.71

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
4xesA	1	0	22.9	0.938	Contact Map
2z73A	2	0.9623	22.6	0.938	Contact Map
4pxzA	1	0.9104	21.4	0.938	Contact Map
4n6hA	1	0.9434	20.4	0.939	Contact Map
3oduA	2	0.9481	17.8	0.94	Contact Map
4grvA	1	0.9434	12.7	0.944	Contact Map
4mbsA	2	0.9623	12	0.945	Contact Map
4ea3A	2	0.9434	11.8	0.945	Contact Map
4mqsA	1	0.816	11.2	0.946	Contact Map
3emlA	1	0.9481	9.4	0.948	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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