OPENSEQ.org - 1507881720 - GREMLIN Submission

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test1M40

ID:	1507881720	Query Sequence HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	263 (261)
Sequences:	8382 (5245)
Seq/Len:	32.115
Nf(neff/√len):	324.7

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: 32.115).

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
34_S	37_P	3.845	1.00
68_R	116_T	3.376	1.00
38_E	159_A	3.353	1.00
57_S	126_F	3.059	1.00
69_R	91_G	2.850	1.00
21_Y	33_E	2.670	1.00
126_F	129_N	2.647	1.00
20_G	41_F	2.577	1.00
55_V	113_L	2.534	1.00
58_R	63_Q	2.491	1.00
94_V	113_L	2.447	1.00
71_H	91_G	2.427	1.00
165_L	208_D	2.427	1.00
36_R	39_E	2.412	1.00
132_D	164_T	2.249	1.00
52_C	102_I	2.172	1.00
162_A	235_V	2.172	1.00
20_G	158_P	2.139	1.00
40_R	155_T	2.131	1.00
93_T	96_E	2.127	1.00
206_I	231_S	2.107	1.00
23_E	234_V	2.082	1.00
135_T	156_T	2.070	1.00
159_A	163_T	2.051	1.00
22_I	162_A	2.027	1.00
100_A	106_D	2.023	1.00
101_A	110_A	1.991	1.00
51_L	110_A	1.981	1.00
65_Q	68_R	1.933	1.00
23_E	232_R	1.932	1.00
158_P	237_Y	1.908	1.00
50_L	127_L	1.887	1.00
74_Q	88_L	1.883	1.00
76_D	115_T	1.879	1.00
72_Y	112_L	1.872	1.00
53_G	167_K	1.859	1.00
46_T	161_M	1.839	1.00
206_I	223_A	1.827	1.00
43_M	156_T	1.814	1.00
118_G	122_E	1.799	1.00
73_S	115_T	1.779	1.00
67_G	95_R	1.775	1.00
70_I	112_L	1.753	1.00
46_T	237_Y	1.751	1.00
99_S	103_T	1.738	1.00
26_L	233_I	1.734	1.00
24_L	166_R	1.726	1.00
25_D	230_P	1.725	1.00
69_R	93_T	1.716	1.00
73_S	76_D	1.679	1.00
101_A	113_L	1.676	1.00
58_R	122_E	1.658	1.00
95_R	99_S	1.657	1.00
52_C	101_A	1.654	1.00
49_V	221_I	1.647	1.00
66_L	98_C	1.639	1.00
165_L	221_I	1.610	1.00
100_A	109_A	1.601	1.00
57_S	61_A	1.597	1.00
161_M	237_Y	1.597	1.00
38_E	134_V	1.572	1.00
25_D	28_S	1.570	1.00
37_P	159_A	1.556	1.00
105_S	209_K	1.547	1.00
22_I	159_A	1.533	1.00
46_T	221_I	1.507	1.00
70_I	116_T	1.439	1.00
40_R	134_V	1.439	1.00
97_L	109_A	1.429	1.00
45_S	48_K	1.415	1.00
54_A	126_F	1.403	0.99
232_R	256_G	1.395	0.99
24_L	162_A	1.385	0.99
45_S	105_S	1.368	0.99
122_E	125_A	1.359	0.99
53_G	126_F	1.359	0.99
50_L	164_T	1.355	0.99
221_I	235_V	1.354	0.99
225_G	231_S	1.319	0.99
27_N	231_S	1.319	0.99
59_V	66_L	1.311	0.99
50_L	135_T	1.310	0.99
162_A	233_I	1.307	0.99
55_V	98_C	1.306	0.99
54_A	58_R	1.304	0.99
22_I	31_I	1.288	0.99
55_V	94_V	1.276	0.99
52_C	98_C	1.257	0.99
96_E	99_S	1.254	0.99
161_M	221_I	1.245	0.98
130_M	167_K	1.229	0.98
48_K	107_N	1.227	0.98
45_S	209_K	1.222	0.98
134_V	160_A	1.213	0.98
216_G	219_G	1.212	0.98
49_V	165_L	1.187	0.98
175_T	178_S	1.185	0.98
22_I	37_P	1.177	0.98
54_A	117_I	1.171	0.98
254_E	257_A	1.157	0.97
124_T	128_H	1.157	0.97
64_E	116_T	1.155	0.97
54_A	57_S	1.148	0.97
166_R	233_I	1.131	0.97
163_T	167_K	1.130	0.97
213_G	216_G	1.114	0.96
126_F	130_M	1.114	0.96
60_D	175_T	1.107	0.96
166_R	170_T	1.103	0.96
121_K	140_W	1.099	0.96
132_D	160_A	1.097	0.96
135_T	160_A	1.093	0.96
132_D	163_T	1.092	0.96
250_R	254_E	1.088	0.96
18_R	39_E	1.078	0.95
257_A	261_K	1.074	0.95
125_A	129_N	1.068	0.95
66_L	95_R	1.061	0.95
200_L	224_L	1.047	0.94
163_T	166_R	1.042	0.94
54_A	123_L	1.028	0.94
127_L	132_D	1.017	0.93
194_P	197_R	1.015	0.93
47_F	154_D	1.013	0.93
87_H	90_D	1.009	0.93
195_L	212_A	1.008	0.93
223_A	231_S	1.006	0.93
42_P	150_N	1.002	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

See coupling matrix (for protein design or mutagenesis)
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
1o7eA	2	0.9962	100	0.292	Contact Map
1hzoA	2	0.9924	100	0.292	Contact Map
3p09A	2	0.9696	100	0.293	Contact Map
4ua6A	2	0	100	0.296	Contact Map
1n9bA	1	1	100	0.299	Contact Map
3c5aA	1	0.9924	100	0.3	Contact Map
1g6aA	1	0.9962	100	0.301	Contact Map
3dw0A	2	0.9772	100	0.301	Contact Map
1bsgA	1	0.9924	100	0.301	Contact Map
1bueA	1	0.9886	100	0.304	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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