OPENSEQ.org - 1505648334 - GREMLIN Submission

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NTER

ID:	1505648334	Query Sequence MAQWNQLQQLDTRYLEQLHQLYSDSFPMELRQFLAPWIESQDWAYAASKESHATLVFHNLLGEIDQQYSRFLQESNVLYQHNLRRIKQFLQSRYLEKPMEIARIVARCLWEESRLLQTAATAAQQGGQANHPTAAVVTEKQQMLEQHLQDVRKR	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	154 (153)
Sequences:	207 (134.2)
Seq/Len:	1.353
Nf(neff/√len):	10.8

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: 1.353).

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
109_L	112_E	2.545	1.00
3_Q	116_L	1.739	0.93
1_M	37_W	1.735	0.93
35_A	117_Q	1.671	0.91
124_Q	127_G	1.638	0.90
29_E	68_Y	1.619	0.89
8_Q	15_L	1.605	0.89
34_L	64_I	1.524	0.85
105_V	112_E	1.482	0.83
13_R	116_L	1.481	0.83
132_P	135_A	1.467	0.82
10_L	15_L	1.455	0.81
98_P	109_L	1.430	0.80
61_L	67_Q	1.408	0.78
15_L	26_F	1.364	0.75
65_D	71_F	1.351	0.74
105_V	109_L	1.331	0.73
61_L	65_D	1.328	0.72
19_H	102_A	1.319	0.72
55_L	81_H	1.310	0.71
41_Q	56_V	1.300	0.70
1_M	10_L	1.292	0.70
16_E	19_H	1.289	0.69
47_A	103_R	1.286	0.69
23_S	83_L	1.280	0.68
16_E	76_N	1.279	0.68
124_Q	129_A	1.273	0.68
53_A	57_F	1.260	0.67
118_T	144_L	1.245	0.65
67_Q	87_K	1.228	0.64
101_I	112_E	1.221	0.63
139_E	148_L	1.213	0.62
93_R	104_I	1.198	0.61
60_L	90_L	1.197	0.61
31_R	39_E	1.177	0.59
124_Q	128_Q	1.174	0.59
28_M	32_Q	1.166	0.58
111_E	114_R	1.152	0.56
62_G	113_S	1.151	0.56
3_Q	10_L	1.145	0.56
105_V	115_L	1.141	0.55
98_P	112_E	1.131	0.54
28_M	87_K	1.127	0.54
102_A	113_S	1.122	0.53
32_Q	101_I	1.121	0.53
29_E	36_P	1.117	0.53
80_Q	84_R	1.117	0.53
102_A	112_E	1.117	0.53
31_R	112_E	1.114	0.53
39_E	43_W	1.114	0.53
48_S	114_R	1.113	0.53
102_A	115_L	1.110	0.52
133_T	141_Q	1.108	0.52
55_L	91_Q	1.108	0.52
6_Q	120_A	1.107	0.52
47_A	102_A	1.106	0.52
41_Q	93_R	1.102	0.51
71_F	74_E	1.101	0.51
109_L	115_L	1.097	0.51
17_Q	81_H	1.093	0.51
23_S	101_I	1.090	0.50
8_Q	79_Y	1.087	0.50
92_S	100_E	1.081	0.49
56_V	89_F	1.072	0.48
109_L	119_A	1.068	0.48
7_L	15_L	1.058	0.47
11_D	57_F	1.056	0.47
126_G	129_A	1.056	0.47
63_E	66_Q	1.056	0.47
67_Q	78_L	1.048	0.46
21_L	49_K	1.048	0.46
57_F	65_D	1.043	0.46
83_L	125_Q	1.039	0.45
6_Q	90_L	1.035	0.45
48_S	120_A	1.030	0.44
115_L	119_A	1.029	0.44
101_I	109_L	1.027	0.44
107_R	116_L	1.023	0.44
113_S	150_D	1.019	0.43
125_Q	131_H	1.016	0.43
23_S	32_Q	1.002	0.42
28_M	81_H	1.001	0.41
14_Y	71_F	1.001	0.41
27_P	31_R	1.001	0.41

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
1yvlA	2	0.9416	100	0.027	Contact Map
4ziaA	5	0	100	0.12	Contact Map
3wwtA	1	0	100	0.13	Contact Map
1bgfA	1	0.7987	100	0.144	Contact Map
3r6nA	2	0.6104	6.6	0.948	Contact Map
3zkvA	1	0.526	5.1	0.951	Contact Map
3o2tA	1	0.6948	3.5	0.954	Contact Map
4imiA	2	0.7013	3.1	0.956	Contact Map
1yviA	2	0.6818	2.9	0.956	Contact Map
3j94A	6	0.3896	2.6	0.957	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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