OPENSEQ.org - 1502383441 - GREMLIN Submission

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dcp2

ID:	1502383441	Query Sequence MSFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIPVRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIEWHNLMDLPTFKKNKPQTMKNKFYMVIPFLAPLKKWIKKRNIANNTTKEKNISVDVDADASSQLLSLLKSSTAPSDLATPQPSTFPQPPVESHSSFDIKQKILH	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	300 (250)
Sequences:	289 (177.8)
Seq/Len:	1.156
Nf(neff/√len):	11.2

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: 1.156).

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
110_Q	181_L	3.073	1.00
99_R	136_D	2.807	1.00
101_A	144_V	2.645	1.00
48_F	190_R	2.279	0.99
124_G	127_K	2.249	0.99
105_D	109_Q	2.125	0.98
136_D	187_S	2.083	0.97
101_A	152_C	2.030	0.97
168_G	206_T	1.956	0.96
13_D	71_H	1.903	0.95
132_K	199_H	1.876	0.95
40_Q	99_R	1.866	0.94
32_E	89_F	1.695	0.90
17_A	99_R	1.624	0.87
203_D	230_K	1.581	0.85
103_M	112_V	1.549	0.83
161_F	172_R	1.533	0.82
96_I	131_D	1.531	0.82
96_I	169_Q	1.526	0.82
69_F	75_L	1.520	0.82
183_T	209_K	1.505	0.81
155_R	179_I	1.498	0.80
115_K	194_S	1.498	0.80
98_V	127_K	1.492	0.80
21_L	174_Y	1.473	0.79
117_W	191_K	1.464	0.78
127_K	136_D	1.453	0.77
56_L	232_W	1.448	0.77
141_I	150_F	1.438	0.76
104_L	175_I	1.435	0.76
163_D	172_R	1.432	0.76
30_S	89_F	1.415	0.75
199_H	219_F	1.395	0.73
46_E	191_K	1.385	0.72
105_D	181_L	1.372	0.71
106_M	178_G	1.369	0.71
113_L	199_H	1.356	0.70
105_D	110_Q	1.341	0.69
21_L	172_R	1.325	0.68
175_I	236_R	1.312	0.67
27_E	131_D	1.311	0.66
102_I	173_L	1.306	0.66
189_T	224_P	1.301	0.66
51_A	191_K	1.291	0.65
42_H	127_K	1.290	0.65
15_L	39_E	1.289	0.65
99_R	187_S	1.274	0.63
15_L	22_N	1.264	0.62
33_R	39_E	1.255	0.61
26_E	54_D	1.250	0.61
124_G	152_C	1.248	0.61
99_R	130_I	1.207	0.57
84_E	88_D	1.199	0.56
17_A	40_Q	1.195	0.56
79_S	82_H	1.182	0.55
20_I	152_C	1.181	0.55
12_L	222_V	1.181	0.55
133_D	159_N	1.179	0.54
98_V	136_D	1.177	0.54
39_E	44_F	1.176	0.54
103_M	152_C	1.175	0.54
62_R	176_I	1.174	0.54
110_Q	178_G	1.154	0.52
13_D	38_I	1.154	0.52
59_L	91_R	1.152	0.52
27_E	96_I	1.151	0.52
15_L	44_F	1.140	0.51
39_E	93_K	1.140	0.51
105_D	135_S	1.140	0.51
46_E	58_S	1.137	0.50
62_R	157_N	1.135	0.50
50_R	61_L	1.133	0.50
127_K	208_K	1.130	0.50
174_Y	217_N	1.126	0.49
22_N	33_R	1.124	0.49
248_I	252_V	1.117	0.48
150_F	155_R	1.105	0.47
203_D	220_Y	1.104	0.47
99_R	170_N	1.092	0.46
81_V	211_K	1.090	0.46
105_D	196_I	1.088	0.46
40_Q	136_D	1.087	0.45
22_N	39_E	1.086	0.45
48_F	105_D	1.078	0.45
136_D	172_R	1.071	0.44
150_F	185_F	1.067	0.44
89_F	115_K	1.066	0.43
117_W	194_S	1.062	0.43
6_A	111_C	1.057	0.43
154_S	178_G	1.057	0.43
157_N	186_E	1.049	0.42
114_V	193_I	1.043	0.41
199_H	235_K	1.042	0.41
50_R	57_P	1.042	0.41
75_L	191_K	1.041	0.41
103_M	178_G	1.040	0.41
72_C	232_W	1.039	0.41
113_L	124_G	1.038	0.41
61_L	86_F	1.038	0.41
66_A	233_I	1.035	0.41
28_Q	127_K	1.033	0.40
14_D	36_F	1.032	0.40
96_I	135_S	1.028	0.40
72_C	136_D	1.027	0.40
161_F	174_Y	1.026	0.40
17_A	132_K	1.023	0.39
65_S	83_E	1.020	0.39
243_T	248_I	1.019	0.39
127_K	132_K	1.018	0.39
102_I	162_I	1.016	0.39
37_Q	48_F	1.015	0.39
28_Q	98_V	1.014	0.39
246_K	249_S	1.012	0.38
14_D	18_R	1.005	0.38
91_R	150_F	1.002	0.38
4_T	112_V	1.000	0.37
126_P	193_I	1.000	0.37

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
2a6tA	2	0.7667	100	0.532	Contact Map
2qklB	1	0.3	100	0.699	Contact Map
4kg3A	3	0.4833	99.9	0.807	Contact Map
3o8sA	1	0.4267	99.7	0.851	Contact Map
4hfqA	2	0.6533	99.7	0.86	Contact Map
3q1pA	2	0.64	99.7	0.861	Contact Map
4ickA	2	0.45	99.6	0.868	Contact Map
1vk6A	1	0.7	99.6	0.868	Contact Map
1f3yA	1	0.48	99.6	0.869	Contact Map
1sjyA	1	0.5	99.6	0.87	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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