OPENSEQ.org - 1486797218 - GREMLIN Submission

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1a_48_380 1-190

ID:	1486797218	Query Sequence VRNKLSIEEADAFRDRYGGAFDLNLTQQYHAPHSLAGALRVAEHYDCLDSFPPEDPVIDFGGSWWHHFSRRDKRVHSCCPVLGVRDAARHEERMCRMRKILQESDDFDEVPNFCLNRAQDCDVQADWAICIHGGYDMGFQGLCDAMHSHGVRVLRGTVMFDGAMLFDREGFLPLLKCHWQRDGSGADEVI	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	190 (183)
Sequences:	207 (157.7)
Seq/Len:	1.131
Nf(neff/√len):	11.7

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: 1.131).

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_A	151_V	2.690	1.00
59_D	62_G	2.189	0.98
58_I	149_H	2.109	0.98
161_D	164_M	2.104	0.98
119_Q	141_G	2.029	0.97
40_R	62_G	1.909	0.95
114_C	121_C	1.809	0.93
59_D	67_H	1.613	0.86
59_D	83_G	1.606	0.86
158_V	161_D	1.551	0.83
91_E	153_V	1.499	0.80
164_M	179_W	1.493	0.79
12_A	15_D	1.491	0.79
23_L	42_A	1.466	0.78
171_F	178_H	1.453	0.77
62_G	67_H	1.435	0.76
44_H	131_I	1.427	0.75
8_E	158_V	1.425	0.75
17_Y	74_R	1.421	0.75
10_A	25_L	1.397	0.73
131_I	134_G	1.374	0.71
36_A	93_R	1.361	0.70
9_E	23_L	1.341	0.68
5_L	23_L	1.325	0.67
36_A	43_E	1.322	0.67
38_A	59_D	1.275	0.63
39_L	132_H	1.266	0.62
7_I	88_A	1.265	0.62
23_L	175_L	1.254	0.61
78_C	136_D	1.244	0.60
19_G	28_Q	1.241	0.60
38_A	80_P	1.236	0.59
134_G	156_G	1.229	0.58
79_C	93_R	1.229	0.58
33_H	89_R	1.226	0.58
23_L	137_M	1.217	0.57
37_G	93_R	1.208	0.56
159_M	177_C	1.205	0.56
40_R	59_D	1.201	0.56
130_C	133_G	1.192	0.55
32_P	157_T	1.191	0.55
39_L	160_F	1.190	0.55
44_H	85_R	1.184	0.54
52_P	99_K	1.162	0.52
117_R	149_H	1.161	0.52
34_S	158_V	1.160	0.52
130_C	142_L	1.160	0.52
130_C	134_G	1.157	0.52
116_N	122_D	1.154	0.51
58_I	125_A	1.141	0.50
74_R	95_C	1.140	0.50
47_C	158_V	1.127	0.49
59_D	77_S	1.125	0.49
159_M	162_G	1.119	0.48
19_G	59_D	1.119	0.48
175_L	179_W	1.116	0.48
124_Q	150_G	1.112	0.47
43_E	88_A	1.111	0.47
33_H	61_G	1.104	0.47
116_N	129_I	1.100	0.46
83_G	98_R	1.095	0.46
11_D	19_G	1.094	0.46
44_H	179_W	1.094	0.46
43_E	93_R	1.092	0.45
73_K	144_D	1.085	0.45
85_R	134_G	1.078	0.44
61_G	89_R	1.073	0.44
23_L	165_L	1.072	0.43
33_H	121_C	1.067	0.43
26_T	71_R	1.061	0.42
99_K	109_E	1.059	0.42
47_C	57_V	1.059	0.42
117_R	120_D	1.056	0.42
119_Q	142_L	1.053	0.42
161_D	179_W	1.053	0.42
31_A	163_A	1.049	0.41
23_L	96_R	1.047	0.41
89_R	121_C	1.041	0.41
135_Y	160_F	1.037	0.40
62_G	78_C	1.029	0.39
64_W	79_C	1.028	0.39
5_L	35_L	1.027	0.39
33_H	114_C	1.023	0.39
118_A	145_A	1.021	0.39
98_R	126_D	1.018	0.38
28_Q	31_A	1.011	0.38
60_F	128_A	1.008	0.38
14_R	115_L	1.005	0.37
13_F	28_Q	1.003	0.37
63_S	159_M	1.003	0.37
170_G	179_W	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
3i33A	1	0.9526	15.2	0.953	Contact Map
4czgA	1	0.8579	9.7	0.957	Contact Map
4gniA	2	0.9105	9.4	0.957	Contact Map
1b6aA	1	0.4421	7.7	0.959	Contact Map
4fl9A	1	0.9421	7.6	0.959	Contact Map
3qhqA	2	0.2789	6.7	0.96	Contact Map
3u0kA	1	0.7053	6.3	0.96	Contact Map
1jceA	1	0.9	5.1	0.962	Contact Map
2v7yA	1	0.9368	4.8	0.963	Contact Map
4j8fA	1	0.9421	4.8	0.963	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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