OPENSEQ.org - 1490274220 - GREMLIN Submission

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E6 1it

ID:	1490274220	Query Sequence LTANLVCRVALGILANLLCLVPLRLLYHNHELAAVVFILNIEFKNILTIVSALIWRDDNMEDWWAGYGLCDFASFANNFSFGLFDTCMLAIMRNLAHQANLLSAHPSAQRYLIGTLTGCTWTQYPSWPYVVFFALPPLVLSVVVSVLVPYFPVVVTIFIMNHGWIPILSAIPVIVFFGMTKEAINDYRRVLLLPGFADGSFGSSHSAANSGS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	212 (197)
Sequences:	220 (186.4)
Seq/Len:	1.117
Nf(neff/√len):	13.3

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: 1.117).

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
128_P	136_P	2.363	0.99
127_W	131_V	1.993	0.96
15_A	170_A	1.896	0.95
62_D	111_Y	1.888	0.94
57_D	116_L	1.802	0.93
16_N	21_V	1.658	0.88
68_G	72_F	1.619	0.86
87_C	113_I	1.602	0.85
54_I	139_V	1.587	0.84
64_W	82_G	1.573	0.84
58_D	63_W	1.561	0.83
142_V	151_F	1.559	0.83
131_V	142_V	1.511	0.80
69_L	73_A	1.489	0.79
47_L	73_A	1.486	0.79
89_L	93_R	1.459	0.77
5_L	9_V	1.418	0.74
18_L	23_L	1.417	0.74
86_T	167_I	1.415	0.74
138_L	142_V	1.410	0.73
26_L	187_Y	1.398	0.73
148_V	155_V	1.382	0.71
135_L	155_V	1.373	0.71
20_L	140_L	1.356	0.69
123_Q	133_F	1.349	0.69
148_V	162_H	1.332	0.67
33_A	153_V	1.328	0.67
13_I	49_I	1.326	0.67
138_L	141_S	1.267	0.62
135_L	175_V	1.256	0.61
53_L	58_D	1.254	0.60
15_A	58_D	1.252	0.60
86_T	133_F	1.247	0.60
6_V	74_S	1.228	0.58
54_I	148_V	1.218	0.57
26_L	98_Q	1.213	0.57
128_P	135_L	1.211	0.56
26_L	31_E	1.208	0.56
45_N	108_A	1.180	0.53
153_V	194_P	1.173	0.53
39_L	157_I	1.170	0.52
122_T	175_V	1.169	0.52
75_F	107_S	1.169	0.52
136_P	142_V	1.168	0.52
111_Y	153_V	1.160	0.51
35_V	38_I	1.159	0.51
58_D	115_T	1.153	0.51
59_N	62_D	1.151	0.51
23_L	111_Y	1.150	0.51
92_M	176_F	1.150	0.51
141_S	150_Y	1.144	0.50
13_I	191_L	1.142	0.50
52_A	91_I	1.141	0.50
52_A	146_V	1.139	0.49
149_P	170_A	1.136	0.49
13_I	131_V	1.131	0.49
10_A	18_L	1.122	0.48
155_V	184_I	1.117	0.47
46_I	51_S	1.115	0.47
124_Y	164_W	1.102	0.46
87_C	132_F	1.100	0.46
79_F	113_I	1.100	0.46
190_V	193_L	1.096	0.45
23_L	35_V	1.095	0.45
10_A	13_I	1.094	0.45
75_F	79_F	1.093	0.45
85_D	90_A	1.092	0.45
30_H	143_V	1.087	0.45
20_L	192_L	1.085	0.44
14_L	39_L	1.083	0.44
68_G	189_R	1.082	0.44
50_V	129_Y	1.081	0.44
86_T	117_T	1.081	0.44
33_A	53_L	1.077	0.44
107_S	164_W	1.071	0.43
76_A	165_I	1.069	0.43
14_L	17_L	1.065	0.42
145_S	175_V	1.054	0.41
183_A	187_Y	1.051	0.41
152_P	178_G	1.051	0.41
71_D	110_R	1.042	0.40
176_F	181_K	1.042	0.40
190_V	194_P	1.039	0.40
10_A	192_L	1.035	0.40
70_C	119_C	1.034	0.40
53_L	56_R	1.034	0.40
11_L	63_W	1.032	0.39
74_S	81_F	1.030	0.39
128_P	181_K	1.027	0.39
132_F	151_F	1.026	0.39
50_V	194_P	1.023	0.39
33_A	182_E	1.023	0.39
1_L	8_R	1.021	0.38
128_P	134_A	1.015	0.38
35_V	116_L	1.011	0.38
128_P	189_R	1.010	0.37
139_V	148_V	1.009	0.37
55_W	63_W	1.009	0.37
39_L	168_L	1.008	0.37
126_S	143_V	1.007	0.37
135_L	138_L	1.006	0.37
39_L	73_A	1.004	0.37
67_Y	196_F	1.001	0.37
56_R	73_A	1.000	0.37

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
4l6rA	1	0.9151	80.9	0.938	Contact Map
4eiyA	1	0.9387	56.9	0.948	Contact Map
4pxzA	1	0.9198	54.8	0.949	Contact Map
4xt1A	1	0.8868	50	0.95	Contact Map
3oduA	2	0.9434	49.2	0.951	Contact Map
4xesA	1	0	46.6	0.951	Contact Map
3emlA	1	0.9528	46.3	0.951	Contact Map
4mbsA	2	0.934	36.9	0.954	Contact Map
4phuA	1	0.9245	34.8	0.955	Contact Map
3pblA	2	0.9528	34.3	0.955	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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