OPENSEQ.org - 1387460539 - GREMLIN Submission

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2pw9

ID:	1387460539	Query Sequence MSKLDIPLSIMQKSVVIRPGGRQEMDEHVAIETPYAIALNDRVIGSSMVLPVDLEEFGAGFLFGQGYIKKAEEIREILVCPQGRISVYADVENEEPREVIITSGCGGTGKIPKEMLEGEFAPLADYCLPFAEIKSFIREALHSSPLGPQTHCVHGCGLWNNGRLQVYHEDVGRHNAVDKVLGSILLGRASNNSAVYTTGRLTSDMVLKCARIGIPIIMSRTSPSSLGLALAKRSGATLVAYSRPERINVFNAPERILT	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	258 (242)
Sequences:	1091 (781.3)
Seq/Len:	4.508
Nf(neff/√len):	50.2

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: 4.508).

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
29_V	228_L	3.679	1.00
210_A	236_A	3.363	1.00
218_M	242_S	3.326	1.00
56_E	186_L	3.279	1.00
39_L	62_L	3.186	1.00
59_A	74_I	2.812	1.00
68_I	74_I	2.662	1.00
56_E	168_H	2.639	1.00
53_D	56_E	2.602	1.00
63_F	185_L	2.535	1.00
181_L	212_I	2.508	1.00
160_N	163_R	2.360	1.00
166_V	183_S	2.307	1.00
222_S	241_Y	2.175	1.00
59_A	186_L	2.057	1.00
210_A	234_S	2.049	1.00
197_T	205_M	2.004	1.00
183_S	187_G	1.946	1.00
151_H	250_F	1.909	1.00
237_T	255_R	1.881	1.00
47_S	57_F	1.821	1.00
232_K	252_A	1.816	1.00
151_H	241_Y	1.801	1.00
168_H	183_S	1.783	1.00
159_W	164_L	1.723	0.99
217_I	236_A	1.719	0.99
216_I	237_T	1.680	0.99
184_I	191_N	1.677	0.99
35_Y	49_V	1.662	0.99
166_V	180_V	1.661	0.99
239_V	242_S	1.636	0.99
197_T	217_I	1.617	0.99
156_C	176_A	1.599	0.99
156_C	197_T	1.591	0.99
159_W	195_V	1.546	0.99
27_E	241_Y	1.522	0.98
241_Y	250_F	1.506	0.98
172_G	175_N	1.505	0.98
128_L	195_V	1.499	0.98
27_E	248_N	1.436	0.97
37_I	58_G	1.433	0.97
232_K	251_N	1.425	0.97
151_H	240_A	1.374	0.96
147_G	241_Y	1.370	0.96
195_V	216_I	1.366	0.96
56_E	183_S	1.364	0.96
239_V	249_V	1.359	0.96
35_Y	58_G	1.351	0.96
136_F	195_V	1.348	0.96
137_I	242_S	1.344	0.96
31_I	225_S	1.337	0.95
160_N	165_Q	1.326	0.95
201_L	241_Y	1.314	0.95
198_T	248_N	1.311	0.95
116_L	119_E	1.310	0.95
75_R	91_V	1.288	0.94
63_F	181_L	1.277	0.94
139_E	142_H	1.275	0.94
190_S	193_S	1.274	0.94
38_A	87_V	1.270	0.94
158_L	184_I	1.260	0.93
181_L	214_I	1.230	0.92
150_T	241_Y	1.229	0.92
35_Y	54_L	1.228	0.92
70_K	73_E	1.226	0.92
27_E	250_F	1.223	0.92
49_V	54_L	1.222	0.92
229_A	233_R	1.213	0.91
58_G	86_S	1.211	0.91
75_R	94_E	1.208	0.91
74_I	77_I	1.196	0.91
69_K	73_E	1.193	0.90
197_T	219_S	1.182	0.90
27_E	240_A	1.181	0.90
49_V	57_F	1.175	0.90
45_G	61_F	1.168	0.89
100_I	104_G	1.162	0.89
165_Q	183_S	1.160	0.89
61_F	66_G	1.157	0.89
11_M	14_S	1.153	0.88
198_T	241_Y	1.142	0.88
113_K	116_L	1.139	0.88
39_L	90_D	1.139	0.88
59_A	185_L	1.127	0.87
135_S	139_E	1.121	0.86
178_D	208_K	1.112	0.86
27_E	151_H	1.109	0.86
55_E	186_L	1.103	0.85
98_E	101_I	1.103	0.85
55_E	77_I	1.099	0.85
34_P	46_S	1.086	0.84
201_L	227_G	1.086	0.84
77_I	90_D	1.076	0.83
168_H	219_S	1.073	0.83
225_S	229_A	1.072	0.83
241_Y	248_N	1.072	0.83
36_A	43_V	1.071	0.83
157_G	196_Y	1.062	0.82
158_L	180_V	1.060	0.82
240_A	250_F	1.048	0.81
201_L	219_S	1.047	0.81
30_A	153_V	1.042	0.80
229_A	232_K	1.040	0.80
44_I	102_T	1.034	0.80
151_H	198_T	1.034	0.80
68_I	77_I	1.032	0.79
115_M	119_E	1.032	0.79
239_V	256_I	1.020	0.78
66_G	210_A	1.018	0.78
133_I	242_S	1.012	0.78
158_L	194_A	1.012	0.78
177_V	180_V	1.008	0.77
110_K	199_G	1.008	0.77
157_G	164_L	1.001	0.77

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: (08Feb14)
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
2pw9A	4	0.9186	100	0.048	Contact Map
1oi7A	1	0.4767	30.4	0.96	Contact Map
3g8qA	4	0.4535	29.4	0.96	Contact Map
3mtjA	1	0.5349	18.3	0.964	Contact Map
2yv1A	1	0.4806	16.5	0.965	Contact Map
2pq0A	2	0.2829	16.4	0.965	Contact Map
3tqrA	1	0.2636	15.6	0.965	Contact Map
1xviA	2	0.2946	15.1	0.965	Contact Map
2nu8A	2	0.5116	10.8	0.968	Contact Map
3fzqA	2	0.2829	10.7	0.968	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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