OPENSEQ.org - 1499186081 - GREMLIN Submission

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cox2realing

ID:	1499186081	Query Sequence MATWLNMSLQDGASPIMEQLVFFHDHVLMIMLMITTTVSYMMITLIRNQTITSSTNNNHMNHCTCNHPCIHRHTIPTTSLPNSRSPQPSINAKSSWTPMMKMWMLSLHKASVEDLMYNSTTIPTTSHQPNRFRLLEVTYKLTYPINRYIRVLVSAEDVLHSSSCPTLGVNNPKTGGKNSRHTFITTKPSSWYRTVSNLRSKPQIHAHYNWKSTPLKKFENW	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	221 (221)
Sequences:	4481 (1961)
Seq/Len:	20.276
Nf(neff/√len):	131.9

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: 20.276).

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
214_P	217_K	3.749	1.00
215_L	219_E	3.363	1.00
96_W	141_L	3.333	1.00
147_R	215_L	3.202	1.00
142_T	213_T	3.096	1.00
143_Y	185_T	3.070	1.00
99_M	154_S	3.062	1.00
153_V	173_K	3.014	1.00
101_K	106_S	2.949	1.00
188_P	214_P	2.944	1.00
145_I	212_S	2.716	1.00
185_T	212_S	2.565	1.00
145_I	188_P	2.532	1.00
97_T	108_H	2.445	1.00
170_N	197_N	2.268	1.00
140_K	211_K	2.201	1.00
95_S	150_R	2.153	1.00
188_P	212_S	2.121	1.00
151_V	183_F	2.010	1.00
172_P	197_N	1.972	1.00
112_V	218_F	1.969	1.00
94_S	218_F	1.897	1.00
213_T	217_K	1.880	1.00
195_V	199_R	1.841	1.00
93_K	147_R	1.812	1.00
153_V	171_N	1.804	1.00
96_W	143_Y	1.784	1.00
148_Y	184_I	1.761	1.00
145_I	215_L	1.729	1.00
122_I	131_R	1.721	1.00
171_N	181_H	1.673	1.00
101_K	156_E	1.669	1.00
98_P	151_V	1.656	1.00
18_E	186_T	1.635	1.00
199_R	203_Q	1.622	1.00
95_S	152_L	1.567	1.00
150_R	180_R	1.554	1.00
195_V	203_Q	1.553	1.00
149_I	185_T	1.530	1.00
167_L	210_W	1.517	1.00
190_S	211_K	1.484	1.00
27_V	75_I	1.467	1.00
193_R	208_Y	1.464	1.00
61_N	65_C	1.464	1.00
163_S	196_S	1.460	1.00
217_K	220_N	1.457	1.00
101_K	104_M	1.438	1.00
97_T	152_L	1.438	1.00
107_L	141_L	1.424	1.00
13_A	166_T	1.408	1.00
99_M	108_H	1.400	0.99
140_K	209_N	1.399	0.99
97_T	154_S	1.379	0.99
142_T	211_K	1.368	0.99
203_Q	206_A	1.367	0.99
161_S	196_S	1.354	0.99
93_K	148_Y	1.354	0.99
188_P	191_W	1.333	0.99
152_L	178_N	1.331	0.99
106_S	118_N	1.330	0.99
164_C	210_W	1.320	0.99
124_T	127_H	1.311	0.99
107_L	208_Y	1.306	0.99
161_S	197_N	1.301	0.99
194_T	207_H	1.299	0.99
13_A	191_W	1.279	0.99
161_S	170_N	1.275	0.99
167_L	185_T	1.259	0.99
190_S	209_N	1.253	0.99
162_S	210_W	1.253	0.99
124_T	131_R	1.246	0.98
151_V	181_H	1.240	0.98
12_G	17_M	1.220	0.98
160_H	195_V	1.208	0.98
195_V	206_A	1.201	0.98
3_T	6_N	1.194	0.98
100_M	173_K	1.190	0.98
59_H	63_C	1.174	0.98
192_Y	207_H	1.168	0.97
13_A	187_K	1.165	0.97
14_S	167_L	1.161	0.97
143_Y	183_F	1.158	0.97
66_N	70_I	1.152	0.97
1_M	4_W	1.152	0.97
29_M	33_M	1.149	0.97
164_C	167_L	1.147	0.97
128_Q	131_R	1.142	0.97
70_I	74_T	1.141	0.97
202_P	205_H	1.140	0.97
102_M	157_D	1.139	0.97
119_S	137_V	1.131	0.97
199_R	206_A	1.131	0.97
188_P	217_K	1.130	0.97
137_V	209_N	1.121	0.97
15_P	184_I	1.109	0.96
64_T	68_P	1.106	0.96
155_A	159_L	1.097	0.96
218_F	221_W	1.096	0.96
140_K	190_S	1.082	0.96
96_W	151_V	1.082	0.96
170_N	196_S	1.069	0.95
62_H	65_C	1.068	0.95
163_S	169_V	1.067	0.95
61_N	68_P	1.056	0.95
160_H	199_R	1.045	0.94
81_P	85_S	1.041	0.94
107_L	193_R	1.034	0.94
145_I	214_P	1.025	0.93
33_M	40_Y	1.024	0.93
26_H	69_C	1.023	0.93
146_N	215_L	1.022	0.93
18_E	22_F	1.017	0.93
191_W	212_S	1.008	0.93

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
1v54B	2	0.9955	100	0.047	Contact Map
3hb3B	1	0.9955	100	0.065	Contact Map
2gsmB	2	0.9955	100	0.077	Contact Map
1fftB	2	0.8778	100	0.164	Contact Map
2yevB	2	0.8914	100	0.193	Contact Map
4txvB	2	0.6018	100	0.314	Contact Map
1cyxA	1	0.4932	100	0.391	Contact Map
3s8fB	1	0.7149	100	0.441	Contact Map
2cuaA	2	0.5158	99.9	0.624	Contact Map
3sbqA	2	0.9502	99.9	0.63	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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