OPENSEQ.org - 1497028789 - GREMLIN Submission

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ID:	1497028789	Query Sequence MAEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSEL	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	150 (145)
Sequences:	197 (106.8)
Seq/Len:	1.359
Nf(neff/√len):	8.9

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: 1.359).

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 > 50% 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
54_Q	67_R	2.038	0.98
18_H	21_A	1.995	0.97
7_D	10_L	1.959	0.97
42_M	74_F	1.847	0.96
122_P	130_F	1.824	0.95
35_F	83_G	1.767	0.94
96_V	111_P	1.756	0.94
47_L	117_T	1.696	0.92
73_L	76_P	1.652	0.91
84_R	97_Y	1.632	0.90
73_L	110_W	1.631	0.90
60_Q	71_I	1.613	0.89
44_G	97_Y	1.578	0.88
48_N	93_H	1.569	0.87
131_S	135_G	1.519	0.85
44_G	84_R	1.515	0.85
117_T	120_F	1.460	0.82
46_I	93_H	1.458	0.82
116_N	121_R	1.442	0.81
7_D	18_H	1.413	0.79
6_N	109_N	1.396	0.78
122_P	131_S	1.374	0.76
139_N	147_Y	1.350	0.74
132_D	135_G	1.347	0.74
24_T	44_G	1.341	0.74
36_I	80_H	1.268	0.68
46_I	97_Y	1.245	0.65
8_P	13_Y	1.233	0.64
10_L	13_Y	1.188	0.60
24_T	97_Y	1.179	0.59
72_L	107_W	1.173	0.59
42_M	103_Y	1.172	0.59
7_D	13_Y	1.169	0.58
46_I	80_H	1.169	0.58
18_H	23_L	1.159	0.57
124_E	132_D	1.154	0.57
101_R	107_W	1.142	0.56
44_G	48_N	1.136	0.55
44_G	93_H	1.133	0.55
30_G	33_D	1.123	0.54
72_L	84_R	1.119	0.53
84_R	93_H	1.119	0.53
9_L	26_I	1.118	0.53
93_H	97_Y	1.114	0.53
136_Q	139_N	1.109	0.52
12_G	94_Q	1.107	0.52
49_L	84_R	1.093	0.51
140_A	145_G	1.093	0.51
26_I	36_I	1.090	0.50
122_P	128_P	1.086	0.50
39_P	46_I	1.063	0.48
6_N	117_T	1.060	0.47
133_L	136_Q	1.054	0.47
45_Y	118_G	1.051	0.46
101_R	104_W	1.045	0.46
14_S	17_A	1.041	0.45
128_P	132_D	1.038	0.45
13_Y	99_R	1.034	0.45
56_V	67_R	1.032	0.45
12_G	69_G	1.027	0.44
33_D	97_Y	1.024	0.44
138_I	142_Q	1.020	0.43
123_D	147_Y	1.018	0.43
146_R	149_E	1.017	0.43
94_Q	122_P	1.016	0.43
71_I	78_E	1.016	0.43
9_L	25_P	1.014	0.43
56_V	63_E	1.013	0.43
48_N	97_Y	1.013	0.43
121_R	124_E	1.011	0.43
16_N	35_F	1.010	0.42
34_F	40_L	1.004	0.42
24_T	84_R	1.001	0.42
44_G	98_F	1.001	0.42

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
2arcA	2	0.96	99.8	0.656	Contact Map
3gbgA	1	0.82	97.9	0.858	Contact Map
4mv2A	2	0.7133	97.7	0.863	Contact Map
4rd7A	1	0.6933	97.1	0.876	Contact Map
4qglA	1	0.7	97.1	0.877	Contact Map
2pfwA	2	0.64	97	0.878	Contact Map
2opkA	4	0.6467	96.9	0.881	Contact Map
4e2gA	8	0.6933	96.8	0.882	Contact Map
3h8uA	2	0.7067	96.8	0.882	Contact Map
1yhfA	1	0.6	96.7	0.884	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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