OPENSEQ.org - 1438496268 - GREMLIN Submission

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370-624

ID:	1438496268	Query Sequence HDVTEQQKIDNDRKQFVSNVSHELRTPLTSLRSYIEALSDGAWKDPEVAPGFLKVTQEETDRMIRMINELLSLSRMDSGTTRVDMELVNINEMFNYVLDRFDMILKKDDNPAKYYTIKREFTKROLWVEIDTDKFTQVLDNIMNNAIKYSPDGGVVTCRLLETHNQVIISISDQGLGIPRADLGHVFDRFFRVDKARSRAQGGTGLGLAISKEVVQMLGGRIWVDSVEGKGSTFYISLPYEPYEEEDLWDDDSQA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	255 (235)
Sequences:	52741 (42968.9)
Seq/Len:	224.430
Nf(neff/√len):	2803.0

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: 224.430).

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
172_S	233_T	2.948	1.00
88_V	130_I	2.905	1.00
223_W	235_Y	2.796	1.00
166_Q	237_S	2.572	1.00
173_D	177_G	2.571	1.00
170_S	233_T	2.558	1.00
212_K	216_Q	2.543	1.00
35_I	56_T	2.435	1.00
170_S	235_Y	2.392	1.00
159_R	170_S	2.257	1.00
168_I	237_S	2.182	1.00
168_I	235_Y	2.172	1.00
130_I	218_L	2.163	1.00
179_P	182_D	2.117	1.00
150_S	174_Q	2.117	1.00
118_K	157_T	2.103	1.00
87_L	129_E	2.036	1.00
32_R	60_T	1.972	1.00
183_L	226_S	1.966	1.00
120_E	159_R	1.963	1.00
32_R	61_D	1.946	1.00
224_V	234_F	1.932	1.00
118_K	155_V	1.930	1.00
39_S	57_Q	1.925	1.00
227_V	230_K	1.922	1.00
155_V	174_Q	1.911	1.00
162_E	240_Y	1.897	1.00
157_T	172_S	1.873	1.00
211_S	222_I	1.869	1.00
225_D	235_Y	1.829	1.00
138_V	215_V	1.822	1.00
161_L	168_I	1.822	1.00
183_L	224_V	1.788	1.00
185_H	191_F	1.778	1.00
96_Y	136_T	1.775	1.00
159_R	172_S	1.753	1.00
87_L	127_W	1.747	1.00
225_D	233_T	1.735	1.00
187_F	222_I	1.727	1.00
89_N	92_E	1.711	1.00
180_R	183_L	1.704	1.00
215_V	220_G	1.676	1.00
86_E	132_T	1.668	1.00
161_L	170_S	1.661	1.00
221_R	237_S	1.656	1.00
182_D	185_H	1.655	1.00
178_I	186_V	1.644	1.00
101_F	140_D	1.629	1.00
64_I	68_N	1.620	1.00
120_E	157_T	1.597	1.00
144_N	148_K	1.595	1.00
138_V	211_S	1.570	1.00
39_S	54_K	1.534	1.00
185_H	188_D	1.534	1.00
116_T	155_V	1.513	1.00
32_R	64_I	1.501	1.00
215_V	236_I	1.500	1.00
31_L	60_T	1.493	1.00
163_T	168_I	1.490	1.00
138_V	214_V	1.486	1.00
226_S	232_S	1.474	1.00
178_I	182_D	1.472	1.00
223_W	237_S	1.471	1.00
85_M	129_E	1.442	1.00
182_D	191_F	1.426	1.00
36_E	57_Q	1.415	1.00
57_Q	61_D	1.400	0.99
130_I	135_F	1.388	0.99
178_I	232_S	1.384	0.99
154_G	174_Q	1.381	0.99
105_L	147_I	1.379	0.99
182_D	193_V	1.336	0.99
32_R	57_Q	1.334	0.99
150_S	154_G	1.312	0.99
35_I	57_Q	1.294	0.99
179_P	228_E	1.279	0.99
139_L	169_I	1.277	0.99
34_Y	52_F	1.253	0.99
188_D	191_F	1.237	0.98
25_R	68_N	1.228	0.98
23_E	137_Q	1.224	0.98
187_F	224_V	1.214	0.98
131_D	134_K	1.212	0.98
134_K	217_M	1.208	0.98
91_N	95_N	1.205	0.98
214_V	218_L	1.205	0.98
216_Q	221_R	1.198	0.98
100_R	136_T	1.178	0.98
59_E	62_R	1.165	0.97
91_N	160_L	1.164	0.97
34_Y	55_V	1.163	0.97
15_Q	19_N	1.144	0.97
95_N	119_R	1.129	0.97
132_T	136_T	1.124	0.97
89_N	127_W	1.110	0.96
102_D	106_K	1.109	0.96
141_N	211_S	1.107	0.96
169_I	236_I	1.098	0.96
157_T	174_Q	1.086	0.96
134_K	137_Q	1.082	0.96
186_V	224_V	1.077	0.95
30_S	34_Y	1.075	0.95
65_R	133_D	1.074	0.95
150_S	156_V	1.071	0.95
19_N	189_R	1.048	0.94
30_S	59_E	1.044	0.94
35_I	60_T	1.039	0.94
226_S	230_K	1.039	0.94
38_L	53_L	1.025	0.93
39_S	50_P	1.025	0.93
100_R	140_D	1.025	0.93
96_Y	132_T	1.023	0.93
215_V	222_I	1.021	0.93
177_G	232_S	1.017	0.93
220_G	238_L	1.011	0.93
31_L	56_T	1.007	0.93
104_I	107_K	1.006	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: (31Jan15)
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
3a0rA	1	0.8706	100	0.084	Contact Map
4i5sA	2	0.898	100	0.195	Contact Map
4gczA	2	0.9176	100	0.256	Contact Map
2c2aA	1	0.8941	100	0.27	Contact Map
3jz3A	2	0.6353	100	0.272	Contact Map
4q20A	2	0.8941	100	0.273	Contact Map
4mpcA	1	0.9216	100	0.274	Contact Map
4e01A	1	0.8941	100	0.279	Contact Map
3d36A	2	0.8627	100	0.286	Contact Map
4bixA	2	0.8706	100	0.293	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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