OPENSEQ.org - 1401218044 - GREMLIN Submission

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T0794 - roll 300-470

ID:	1401218044	Query Sequence SSIEALSSGNKEFKGTVFFDEFTFVKLTGVAGNYTVCQKDLCCHLSYKMSENIPNEVYALGAFDGLHTVEGRYYLQICTLLKCKTTNLNTCGDSAETASTRFEMFSLSGTFGTQYVFPEVLLSENQLAPGEFQVSTDGRLFSLKPTSGPVLTVTLFGRLYEKDWASNASSG	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	171 (167)
Sequences:	270 (163)
Seq/Len:	1.617
Nf(neff/√len):	12.6

Jackhmmer Results: (2014_04_16)
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: 1.617).

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
37_C	42_C	2.750	1.00
158_R	163_D	1.949	0.98
41_L	157_G	1.877	0.97
68_T	71_G	1.729	0.95
58_Y	98_A	1.684	0.94
45_L	153_V	1.609	0.92
76_Q	149_P	1.584	0.91
45_L	59_A	1.555	0.90
74_Y	160_Y	1.536	0.89
120_V	153_V	1.458	0.86
61_G	81_L	1.450	0.85
150_V	153_V	1.409	0.83
60_L	105_F	1.383	0.81
103_E	140_L	1.373	0.81
66_L	74_Y	1.370	0.80
15_G	59_A	1.339	0.78
5_A	9_G	1.324	0.77
142_S	162_K	1.311	0.76
98_A	157_G	1.293	0.75
45_L	107_L	1.289	0.74
5_A	10_N	1.285	0.74
49_M	61_G	1.284	0.74
24_F	27_L	1.270	0.73
137_D	140_L	1.269	0.73
88_L	132_F	1.263	0.72
85_T	90_T	1.261	0.72
37_C	79_T	1.249	0.71
61_G	74_Y	1.247	0.71
121_L	152_T	1.241	0.70
81_L	158_R	1.238	0.70
16_T	19_F	1.234	0.70
80_L	109_G	1.216	0.68
47_Y	82_K	1.213	0.68
8_S	12_E	1.197	0.66
67_H	119_E	1.188	0.65
62_A	139_R	1.180	0.65
40_D	140_L	1.178	0.64
90_T	148_G	1.178	0.64
17_V	67_H	1.177	0.64
33_N	60_L	1.173	0.64
20_D	68_T	1.172	0.64
3_I	10_N	1.169	0.64
20_D	67_H	1.168	0.64
74_Y	163_D	1.168	0.64
49_M	77_I	1.161	0.63
59_A	115_Y	1.161	0.63
45_L	82_K	1.158	0.63
143_L	146_T	1.157	0.62
48_K	150_V	1.156	0.62
38_Q	102_F	1.142	0.61
20_D	27_L	1.138	0.61
149_P	156_F	1.126	0.59
59_A	153_V	1.112	0.58
53_I	80_L	1.106	0.57
41_L	161_E	1.105	0.57
19_F	80_L	1.104	0.57
141_F	152_T	1.101	0.57
11_K	14_K	1.101	0.57
134_V	158_R	1.101	0.57
61_G	73_Y	1.093	0.56
152_T	156_F	1.089	0.55
80_L	136_T	1.089	0.55
149_P	153_V	1.087	0.55
86_T	154_T	1.085	0.55
126_Q	149_P	1.083	0.55
56_E	82_K	1.081	0.55
94_S	158_R	1.077	0.54
98_A	109_G	1.075	0.54
34_Y	88_L	1.060	0.52
102_F	151_L	1.060	0.52
58_Y	121_L	1.059	0.52
15_G	18_F	1.056	0.52
92_G	121_L	1.055	0.52
59_A	92_G	1.055	0.52
36_V	56_E	1.049	0.51
51_E	64_D	1.049	0.51
81_L	102_F	1.043	0.51
5_A	14_K	1.035	0.50
18_F	69_V	1.031	0.49
17_V	81_L	1.024	0.49
25_V	115_Y	1.023	0.49
63_F	92_G	1.023	0.49
64_D	74_Y	1.020	0.48
35_T	44_H	1.019	0.48
69_V	133_Q	1.017	0.48
70_E	75_L	1.017	0.48
7_S	12_E	1.017	0.48
61_G	92_G	1.016	0.48
98_A	149_P	1.014	0.48
42_C	152_T	1.013	0.48
37_C	152_T	1.008	0.47
61_G	66_L	1.006	0.47
8_S	14_K	1.006	0.47
20_D	116_V	1.005	0.47
147_S	160_Y	1.000	0.46

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: (24May14)
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
3l15A	2	0.345	7.4	0.954	Contact Map
3kysA	2	0.3509	2.9	0.962	Contact Map
3g46A	2	0.3041	2.3	0.964	Contact Map
2l1uA	1	0.6433	2	0.965	Contact Map
2kaoA	1	0.5146	1.8	0.966	Contact Map
1hznA	1	0.1228	1.4	0.968	Contact Map
2ed6A	12	0.3801	1.4	0.968	Contact Map
2qv3A	1	0.7135	1.3	0.969	Contact Map
1rh5C	1	0.0585	1.3	0.969	Contact Map
1s1dA	2	0.3333	1.2	0.969	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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