OPENSEQ.org - 1400839222 - GREMLIN Submission

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ND1

ID:	1400839222	Query Sequence LVLSDLNIGVFLWIAISSIAPIGLLMSGYGSNNKYSFLGGLRAAAQSISYEIPLTLCVLSISLRAILDIVEAQSKYGFWGWNLWRQPIGFIVFLISSLAECERLPFDLPEAEEELVAGYQTEYSGIKFGLFYVASYLNLLVSSLFVTVLYLGGWDLSIPYIFVPEFFEINKAAKTYLFLFIPITTRWTLPRLRMDQLLNLGWKFLLPISLGNLLLTTSSQLLSL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	224 (209)
Sequences:	363 (237.1)
Seq/Len:	1.737
Nf(neff/√len):	16.4

HHblits Results: (2013_03)
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: 1.737).

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
111_A	115_L	2.741	1.00
63_L	217_T	2.468	1.00
86_Q	216_T	2.445	1.00
22_I	194_M	2.266	1.00
72_A	82_N	2.215	0.99
108_L	197_L	2.080	0.99
86_Q	212_N	1.984	0.98
151_L	178_F	1.956	0.98
49_S	198_L	1.947	0.98
109_P	119_Y	1.831	0.97
60_S	86_Q	1.726	0.95
5_D	65_A	1.695	0.95
30_G	183_I	1.687	0.95
57_C	60_S	1.675	0.94
97_S	142_S	1.632	0.93
43_A	111_A	1.626	0.93
33_N	36_S	1.597	0.92
27_S	30_G	1.592	0.92
10_V	58_V	1.564	0.91
94_L	98_L	1.562	0.91
147_T	151_L	1.539	0.90
93_F	206_L	1.459	0.87
53_P	201_G	1.449	0.87
22_I	55_T	1.447	0.86
93_F	134_A	1.435	0.86
88_I	212_N	1.428	0.85
29_Y	50_Y	1.416	0.85
98_L	185_T	1.412	0.85
89_G	212_N	1.368	0.82
93_F	146_V	1.351	0.81
178_F	182_P	1.340	0.80
90_F	146_V	1.330	0.79
143_S	178_F	1.326	0.79
36_S	121_T	1.322	0.79
139_L	179_L	1.320	0.79
88_I	208_I	1.320	0.79
70_V	154_W	1.318	0.78
11_F	194_M	1.316	0.78
33_N	57_C	1.311	0.78
90_F	151_L	1.305	0.78
21_P	194_M	1.303	0.77
126_I	132_Y	1.294	0.77
178_F	185_T	1.278	0.75
126_I	129_G	1.260	0.74
12_L	16_I	1.247	0.73
31_S	123_Y	1.236	0.72
132_Y	186_R	1.236	0.72
11_F	22_I	1.233	0.72
33_N	216_T	1.226	0.71
33_N	116_V	1.225	0.71
52_I	206_L	1.208	0.69
84_W	187_W	1.206	0.69
44_A	52_I	1.206	0.69
116_V	121_T	1.204	0.69
13_W	145_F	1.198	0.69
99_A	107_D	1.193	0.68
27_S	115_L	1.189	0.68
183_I	186_R	1.181	0.67
37_F	65_A	1.176	0.66
143_S	189_L	1.174	0.66
121_T	197_L	1.156	0.65
4_S	213_L	1.151	0.64
156_L	159_P	1.145	0.63
25_L	201_G	1.140	0.63
83_L	86_Q	1.139	0.63
10_V	148_V	1.134	0.62
147_T	175_T	1.131	0.62
46_Q	197_L	1.129	0.62
43_A	180_F	1.126	0.62
22_I	53_P	1.125	0.61
144_L	148_V	1.113	0.60
140_L	179_L	1.104	0.59
34_K	99_A	1.100	0.59
114_E	191_R	1.100	0.59
92_V	138_N	1.098	0.59
107_D	191_R	1.094	0.58
102_E	184_T	1.083	0.57
86_Q	89_G	1.076	0.56
16_I	130_L	1.076	0.56
102_E	198_L	1.076	0.56
9_G	34_K	1.070	0.56
23_G	55_T	1.060	0.55
95_I	180_F	1.057	0.54
94_L	214_L	1.056	0.54
18_S	66_I	1.052	0.54
83_L	88_I	1.045	0.53
186_R	195_D	1.045	0.53
54_L	201_G	1.045	0.53
119_Y	185_T	1.036	0.52
172_A	175_T	1.035	0.52
136_Y	185_T	1.033	0.52
7_N	145_F	1.032	0.52
80_G	160_Y	1.030	0.51
94_L	146_V	1.023	0.51
55_T	194_M	1.020	0.50
83_L	216_T	1.017	0.50
89_G	150_Y	1.013	0.50
93_F	197_L	1.012	0.49
94_L	178_F	1.006	0.49
124_S	215_L	1.000	0.48

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: (10May14)
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
4he8H	2	0.8839	100	0.213	Contact Map
1fftB	2	0.3036	1.9	0.978	Contact Map
1q16C	1	0.6116	1	0.981	Contact Map
4hr6A	1	0.1696	0.9	0.982	Contact Map
2kncA	1	0.2411	0.8	0.982	Contact Map
2yevB	2	0.2946	0.8	0.982	Contact Map
2rmfA	1	0.1786	0.8	0.982	Contact Map
4lx2B	1	0.0357	0.8	0.982	Contact Map
1no1A	3	0.2321	0.7	0.983	Contact Map
2l16A	1	0.125	0.7	0.983	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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