OPENSEQ.org - 1500058671 - GREMLIN Submission

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190

ID:	1500058671	Query Sequence MPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPDDETFIKNIIIQDCMWSGFSAAAKLVSEKLASYQAARKDSGSPNPARGHSVCSTSSLYLQDLSAAASECID	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	190 (190)
Sequences:	452 (312.9)
Seq/Len:	2.379
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: 2.379).

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
66_R	69_L	1.846	0.99
28_E	32_Y	1.800	0.98
124_F	127_N	1.755	0.98
145_V	149_L	1.705	0.97
58_T	62_S	1.647	0.97
20_Q	26_D	1.642	0.96
140_A	144_L	1.636	0.96
187_E	190_D	1.625	0.96
100_E	105_L	1.595	0.96
98_Q	101_M	1.590	0.96
59_P	62_S	1.581	0.95
139_S	144_L	1.559	0.95
127_N	130_I	1.550	0.95
22_Y	46_S	1.540	0.94
49_I	52_K	1.527	0.94
181_L	185_A	1.524	0.94
96_A	101_M	1.498	0.93
19_V	22_Y	1.488	0.93
50_W	53_F	1.473	0.93
50_W	55_L	1.398	0.90
103_T	106_L	1.389	0.89
23_F	55_L	1.388	0.89
115_F	118_D	1.387	0.89
59_P	63_P	1.354	0.88
52_K	55_L	1.331	0.86
30_N	33_Q	1.327	0.86
31_F	36_Q	1.320	0.86
30_N	36_Q	1.319	0.86
162_P	165_A	1.313	0.85
45_P	52_K	1.307	0.85
146_S	149_L	1.302	0.85
29_E	32_Y	1.300	0.85
159_S	162_P	1.298	0.85
30_N	35_Q	1.279	0.83
98_Q	102_V	1.265	0.82
48_D	53_F	1.259	0.82
61_L	64_S	1.254	0.82
145_V	148_K	1.250	0.81
97_D	101_M	1.236	0.80
21_P	56_L	1.236	0.80
99_L	106_L	1.233	0.80
106_L	130_I	1.227	0.80
138_F	144_L	1.225	0.80
145_V	150_A	1.214	0.79
48_D	55_L	1.196	0.77
24_Y	137_G	1.196	0.77
58_T	65_R	1.194	0.77
57_P	62_S	1.192	0.77
98_Q	103_T	1.178	0.76
169_S	175_S	1.175	0.75
114_S	117_C	1.173	0.75
31_F	34_Q	1.154	0.74
97_D	100_E	1.152	0.73
12_Y	16_Y	1.150	0.73
107_G	115_F	1.149	0.73
113_Q	117_C	1.149	0.73
50_W	134_M	1.149	0.73
45_P	48_D	1.131	0.71
180_D	183_A	1.130	0.71
29_E	34_Q	1.127	0.71
19_V	25_C	1.125	0.71
143_K	149_L	1.120	0.70
101_M	104_E	1.114	0.70
34_Q	37_Q	1.105	0.69
30_N	34_Q	1.103	0.69
18_S	24_Y	1.100	0.68
94_S	98_Q	1.099	0.68
171_C	174_S	1.098	0.68
22_Y	44_A	1.097	0.68
59_P	65_R	1.089	0.67
47_E	52_K	1.088	0.67
36_Q	39_E	1.075	0.66
161_S	167_G	1.072	0.65
46_S	49_I	1.070	0.65
153_Q	156_R	1.069	0.65
61_L	66_R	1.066	0.65
95_T	98_Q	1.061	0.64
164_P	168_H	1.055	0.64
174_S	179_Q	1.047	0.63
146_S	150_A	1.046	0.63
186_S	190_D	1.045	0.63
32_Y	36_Q	1.042	0.62
99_L	102_V	1.041	0.62
48_D	52_K	1.040	0.62
110_M	113_Q	1.040	0.62
47_E	51_K	1.038	0.62
169_S	174_S	1.037	0.62
31_F	38_S	1.037	0.62
102_V	105_L	1.036	0.62
24_Y	54_E	1.019	0.60
129_I	140_A	1.019	0.60
103_T	108_G	1.014	0.59
76_A	81_S	1.011	0.59
31_F	35_Q	1.009	0.59
13_D	21_P	1.008	0.58
60_P	63_P	1.007	0.58
157_K	163_N	1.004	0.58
166_R	169_S	1.003	0.58
99_L	103_T	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
2xl1A	1	0.0789	2.1	0.969	Contact Map
2yuhA	1	0.3789	1.2	0.973	Contact Map
4okvE	2	0.3316	0.9	0.975	Contact Map
1x9uA	2	0.2316	0.9	0.975	Contact Map
4bjoA	2	0.1316	0.9	0.976	Contact Map
1n0uA	1	0.3158	0.8	0.976	Contact Map
2mcmA	1	0.2	0.8	0.977	Contact Map
1noaA	1	0.2053	0.8	0.977	Contact Map
4qhwA	1	0.3158	0.7	0.977	Contact Map
1akpA	1	0.2053	0.7	0.977	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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