OPENSEQ.org - 1500057776 - GREMLIN Submission

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190

ID:	1500057776	Query Sequence MPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPDDETFIKNIIIQDCMWSGFSAAAKLVSEKLASYQAARKDSGSPNPARGHSVCSTSSLYLQDLSAAASECID	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	190 (183)
Sequences:	443 (306.9)
Seq/Len:	2.421
Nf(neff/√len):	22.7

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: 2.421).

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
66_R	69_L	1.939	0.99
28_E	32_Y	1.838	0.99
124_F	127_N	1.807	0.98
145_V	149_L	1.754	0.98
140_A	144_L	1.750	0.98
187_E	190_D	1.650	0.97
139_S	144_L	1.634	0.96
98_Q	101_M	1.619	0.96
59_P	62_S	1.617	0.96
20_Q	26_D	1.609	0.96
22_Y	46_S	1.575	0.95
100_E	105_L	1.546	0.95
127_N	130_I	1.531	0.94
19_V	22_Y	1.521	0.94
58_T	62_S	1.506	0.94
49_I	52_K	1.491	0.93
96_A	101_M	1.477	0.93
30_N	33_Q	1.426	0.91
31_F	36_Q	1.417	0.91
162_P	165_A	1.404	0.90
50_W	53_F	1.396	0.90
103_T	106_L	1.376	0.89
97_D	101_M	1.371	0.89
146_S	149_L	1.365	0.89
59_P	63_P	1.321	0.86
30_N	36_Q	1.320	0.86
45_P	52_K	1.318	0.86
30_N	35_Q	1.317	0.86
61_L	64_S	1.302	0.85
23_F	55_L	1.300	0.85
115_F	118_D	1.296	0.85
29_E	32_Y	1.293	0.85
98_Q	102_V	1.275	0.83
52_K	55_L	1.269	0.83
48_D	53_F	1.263	0.83
145_V	148_K	1.253	0.82
169_S	175_S	1.246	0.81
138_F	144_L	1.242	0.81
114_S	117_C	1.240	0.81
159_S	162_P	1.240	0.81
58_T	65_R	1.237	0.81
98_Q	103_T	1.229	0.80
29_E	34_Q	1.226	0.80
106_L	130_I	1.223	0.80
181_L	185_A	1.211	0.79
21_P	56_L	1.206	0.78
24_Y	137_G	1.195	0.78
50_W	55_L	1.189	0.77
143_K	149_L	1.175	0.76
48_D	55_L	1.169	0.75
31_F	35_Q	1.169	0.75
22_Y	44_A	1.163	0.75
30_N	34_Q	1.161	0.75
107_G	115_F	1.160	0.75
113_Q	117_C	1.160	0.75
32_Y	36_Q	1.158	0.74
101_M	104_E	1.151	0.74
31_F	34_Q	1.146	0.73
12_Y	16_Y	1.145	0.73
31_F	38_S	1.144	0.73
59_P	65_R	1.143	0.73
45_P	48_D	1.143	0.73
19_V	25_C	1.136	0.72
99_L	106_L	1.133	0.72
180_D	183_A	1.123	0.71
145_V	150_A	1.108	0.70
97_D	100_E	1.108	0.70
46_S	49_I	1.102	0.69
146_S	150_A	1.098	0.69
94_S	98_Q	1.098	0.69
47_E	52_K	1.095	0.68
18_S	24_Y	1.088	0.68
171_C	174_S	1.070	0.66
76_A	79_P	1.067	0.65
148_K	152_Y	1.063	0.65
33_Q	38_S	1.058	0.65
109_D	114_S	1.058	0.65
165_A	173_T	1.053	0.64
47_E	51_K	1.053	0.64
119_P	122_E	1.052	0.64
61_L	66_R	1.050	0.64
24_Y	54_E	1.048	0.63
153_Q	156_R	1.046	0.63
174_S	179_Q	1.037	0.62
35_Q	46_S	1.037	0.62
161_S	169_S	1.037	0.62
102_V	105_L	1.037	0.62
48_D	52_K	1.037	0.62
161_S	167_G	1.026	0.61
33_Q	36_Q	1.025	0.61
186_S	190_D	1.025	0.61
60_P	63_P	1.023	0.61
164_P	168_H	1.022	0.61
98_Q	105_L	1.021	0.60
110_M	113_Q	1.017	0.60
76_A	81_S	1.014	0.60
161_S	164_P	1.014	0.60
103_T	108_G	1.009	0.59
95_T	98_Q	1.008	0.59
152_Y	156_R	1.002	0.58

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
2yuhA	1	0.3789	2	0.971	Contact Map
2xl1A	1	0.0789	1.7	0.972	Contact Map
1h5oA	1	0.2211	1.4	0.973	Contact Map
4qhwA	1	0.3158	1.2	0.974	Contact Map
1n0uA	1	0.3158	1.1	0.975	Contact Map
3suiB	1	0.0789	1.1	0.975	Contact Map
4w224	1	0.3158	1	0.976	Contact Map
4bjoA	2	0.1316	0.9	0.976	Contact Map
1x9uA	2	0.2263	0.7	0.977	Contact Map
2eqpA	1	0.1632	0.7	0.978	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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