OPENSEQ.org - 1457815933 - GREMLIN Submission

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Av2

ID:	1457815933	Query Sequence AMRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDPKADSTRLILHSKAQNTIMEMAAEAGTVEDLELEDVLKAGYGGVKCVESGGPEPGVGCAGRGVITAINFLEEEGAYEDDLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANNISKGIVKYANSGSVRLGGLICNSRNTDREDELIIALANKLGTQMIHFVPRDNVVQRAEIRRMTVIEYDPKAKQADEYRALARKVVDNKLLVIPNPITMDELEELLMEFG	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	272 (248)
Sequences:	15151 (9122.2)
Seq/Len:	61.093
Nf(neff/√len):	579.3

HHblits Results: (2015_06)
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: 61.093).

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
84_K	119_L	4.920	1.00
212_P	239_E	4.435	1.00
19_T	123_F	4.282	1.00
6_A	144_A	3.379	1.00
18_T	240_Y	3.253	1.00
26_L	121_F	3.167	1.00
186_S	213_R	3.069	1.00
34_M	119_L	2.991	1.00
3_R	146_E	2.875	1.00
31_K	121_F	2.864	1.00
226_T	229_E	2.811	1.00
152_S	186_S	2.585	1.00
7_I	22_L	2.437	1.00
29_M	245_R	2.402	1.00
19_T	35_I	2.289	1.00
25_A	244_A	2.259	1.00
32_K	120_D	2.203	1.00
35_I	44_S	2.148	1.00
18_T	183_I	2.148	1.00
183_I	243_L	2.136	1.00
23_V	35_I	2.124	1.00
23_V	123_F	2.064	1.00
78_A	84_K	2.044	1.00
26_L	123_F	2.010	1.00
216_V	219_R	2.001	1.00
20_Q	44_S	1.942	1.00
28_E	241_R	1.924	1.00
4_Q	124_Y	1.906	1.00
188_N	213_R	1.896	1.00
25_A	228_I	1.883	1.00
209_H	246_K	1.866	1.00
184_C	196_I	1.859	1.00
197_I	201_N	1.853	1.00
7_I	148_Y	1.818	1.00
18_T	185_N	1.755	1.00
31_K	248_V	1.750	1.00
47_L	156_M	1.743	1.00
27_A	83_V	1.731	1.00
146_E	181_G	1.728	1.00
6_A	126_V	1.682	1.00
181_G	208_I	1.631	1.00
14_G	185_N	1.628	1.00
34_M	122_V	1.588	1.00
22_L	244_A	1.588	1.00
2_M	122_V	1.575	1.00
153_G	184_C	1.570	1.00
46_R	159_Y	1.561	1.00
31_K	120_D	1.552	1.00
7_I	19_T	1.527	1.00
38_C	124_Y	1.524	1.00
146_E	180_G	1.507	1.00
209_H	243_L	1.495	1.00
27_A	82_G	1.492	1.00
22_L	247_V	1.488	1.00
26_L	244_A	1.474	1.00
147_I	168_I	1.470	1.00
3_R	145_Q	1.463	1.00
214_D	236_Q	1.462	1.00
196_I	200_A	1.453	1.00
150_V	185_N	1.453	1.00
211_V	236_Q	1.437	1.00
148_Y	183_I	1.432	1.00
21_N	240_Y	1.385	0.99
25_A	241_R	1.377	0.99
23_V	83_V	1.375	0.99
187_R	210_F	1.360	0.99
214_D	234_A	1.351	0.99
23_V	44_S	1.344	0.99
219_R	223_R	1.342	0.99
21_N	24_A	1.326	0.99
17_T	217_V	1.294	0.99
245_R	249_D	1.276	0.99
198_A	202_K	1.275	0.99
217_V	236_Q	1.252	0.99
26_L	33_V	1.249	0.99
225_M	229_E	1.242	0.98
243_L	247_V	1.237	0.98
225_M	230_Y	1.228	0.98
2_M	116_E	1.219	0.98
234_A	237_A	1.212	0.98
197_I	210_F	1.207	0.98
34_M	76_L	1.198	0.98
239_E	242_A	1.197	0.98
207_M	210_F	1.195	0.98
199_L	203_L	1.194	0.98
43_D	160_A	1.193	0.98
36_V	122_V	1.189	0.98
36_V	124_Y	1.187	0.98
7_I	123_F	1.184	0.98
121_F	248_V	1.180	0.98
154_E	157_A	1.159	0.97
21_N	228_I	1.157	0.97
156_M	221_E	1.144	0.97
208_I	246_K	1.142	0.97
38_C	138_P	1.139	0.97
242_A	245_R	1.135	0.97
162_N	202_K	1.125	0.97
198_A	201_N	1.123	0.97
18_T	22_L	1.116	0.96
238_D	241_R	1.112	0.96
242_A	246_K	1.101	0.96
22_L	243_L	1.098	0.96
84_K	117_D	1.097	0.96
10_K	15_K	1.095	0.96
5_C	121_F	1.081	0.95
18_T	150_V	1.080	0.95
48_I	83_V	1.074	0.95
17_T	221_E	1.074	0.95
211_V	239_E	1.073	0.95
215_N	219_R	1.061	0.95
126_V	138_P	1.043	0.94
241_R	245_R	1.035	0.94
25_A	240_Y	1.031	0.94
20_Q	47_L	1.022	0.93
166_K	169_V	1.021	0.93
73_E	118_D	1.014	0.93
71_E	74_D	1.012	0.93
232_P	237_A	1.012	0.93
90_G	163_N	1.009	0.93
7_I	18_T	1.005	0.93
4_Q	116_E	1.004	0.93
111_E	114_A	1.000	0.92

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
1cp2A	2	0.9743	100	0.213	Contact Map
4wzaE	4	1	100	0.224	Contact Map
3fwyA	2	0.9632	100	0.253	Contact Map
2ynmA	2	0.9522	100	0.259	Contact Map
1hyqA	1	0.8456	100	0.28	Contact Map
3ea0A	2	0.8713	100	0.297	Contact Map
4rz3A	2	0.864	100	0.303	Contact Map
1g3qA	1	0.8603	100	0.307	Contact Map
4pfsA	2	0.875	100	0.325	Contact Map
1wcv1	1	0.8713	100	0.345	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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