OPENSEQ.org - 1401388686 - GREMLIN Submission

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T0798

ID:	1401388686	Query Sequence YDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNNLSFIETSALDSTNVEEAFKNILTEIYRIVSQKQIADCAAHDESPGNNVVDISVPPTTD	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	198 (197)
Sequences:	242 (154.1)
Seq/Len:	1.228
Nf(neff/√len):	11.0

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: 1.228).

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
20_L	154_V	3.439	1.00
12_D	94_N	2.805	1.00
84_Y	143_F	2.073	0.98
84_Y	125_R	2.057	0.98
89_H	131_E	2.048	0.97
8_V	102_L	1.948	0.96
1_Y	4_L	1.928	0.96
143_F	153_N	1.918	0.96
57_I	74_Y	1.671	0.90
27_N	33_S	1.658	0.89
132_A	136_A	1.629	0.88
19_N	162_L	1.603	0.87
10_I	69_I	1.602	0.87
18_S	83_V	1.592	0.87
79_G	165_I	1.580	0.86
88_K	91_T	1.499	0.82
149_L	158_F	1.493	0.81
54_K	74_Y	1.459	0.79
156_E	163_T	1.420	0.77
5_F	86_I	1.401	0.75
66_Y	72_A	1.376	0.74
8_V	43_T	1.360	0.72
80_A	102_L	1.348	0.71
132_A	143_F	1.347	0.71
54_K	70_T	1.335	0.70
19_N	149_L	1.316	0.69
40_E	55_A	1.304	0.68
40_E	139_N	1.285	0.66
70_T	74_Y	1.278	0.65
66_Y	75_R	1.278	0.65
72_A	89_H	1.272	0.65
60_T	64_E	1.252	0.63
37_I	162_L	1.236	0.62
60_T	67_R	1.234	0.61
40_E	68_A	1.229	0.61
80_A	146_T	1.225	0.61
40_E	110_I	1.223	0.60
84_Y	132_A	1.222	0.60
190_D	196_T	1.213	0.59
40_E	43_T	1.210	0.59
70_T	79_G	1.202	0.58
84_Y	117_N	1.185	0.57
84_Y	127_V	1.183	0.57
60_T	69_I	1.174	0.56
64_E	75_R	1.168	0.55
64_E	145_E	1.166	0.55
105_H	113_M	1.159	0.54
47_Q	50_G	1.147	0.53
71_S	78_V	1.144	0.53
135_F	139_N	1.143	0.53
145_E	153_N	1.140	0.52
138_K	141_L	1.133	0.52
149_L	162_L	1.123	0.51
133_R	137_E	1.111	0.50
114_L	153_N	1.110	0.49
10_I	37_I	1.105	0.49
79_G	161_I	1.104	0.49
74_Y	151_S	1.104	0.49
23_R	27_N	1.102	0.49
3_Y	21_L	1.096	0.48
57_I	76_G	1.095	0.48
42_A	71_S	1.095	0.48
102_L	110_I	1.089	0.47
37_I	63_Q	1.088	0.47
91_T	126_A	1.088	0.47
134_A	167_R	1.084	0.47
63_Q	67_R	1.081	0.47
57_I	84_Y	1.077	0.46
57_I	101_E	1.076	0.46
56_Q	67_R	1.075	0.46
37_I	54_K	1.075	0.46
86_I	117_N	1.069	0.45
13_S	54_K	1.068	0.45
8_V	71_S	1.066	0.45
43_T	80_A	1.066	0.45
61_A	64_E	1.066	0.45
44_R	103_R	1.055	0.44
88_K	97_R	1.053	0.44
87_A	122_R	1.051	0.44
61_A	75_R	1.050	0.44
14_G	69_I	1.050	0.44
5_F	146_T	1.049	0.44
6_K	76_G	1.046	0.43
99_L	106_A	1.044	0.43
67_R	145_E	1.043	0.43
189_V	193_V	1.039	0.43
44_R	97_R	1.038	0.42
134_A	138_K	1.036	0.42
19_N	102_L	1.035	0.42
134_A	137_E	1.033	0.42
21_L	25_T	1.029	0.42
39_V	70_T	1.020	0.41
60_T	75_R	1.018	0.41
4_L	37_I	1.014	0.40
109_N	133_R	1.013	0.40
20_L	116_G	1.013	0.40
60_T	145_E	1.009	0.40
10_I	68_A	1.003	0.39
42_A	68_A	1.003	0.39

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
3cpjB	1	0.8283	100	0.468	Contact Map
2g3yA	1	0.8384	100	0.47	Contact Map
4lhwA	5	0.8687	100	0.481	Contact Map
3dz8A	1	0.8535	100	0.482	Contact Map
1zbdA	1	0.8788	100	0.483	Contact Map
2cjwA	1	0.8737	100	0.485	Contact Map
2f7sA	2	0.8788	100	0.487	Contact Map
2a5jA	1	0.8535	100	0.49	Contact Map
2ew1A	1	0.8586	100	0.491	Contact Map
2yc2C	2	0.702	100	0.492	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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