OPENSEQ.org - 1428411705 - GREMLIN Submission

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HET-S1-227

ID:	1428411705	Query Sequence MSEPFEIVAGALGVAGLFNNCVACFEYVQLGRHFGRDYERCQLRLDIAKVRLSRWGEAVQINDDPRFHSSAPIDKSVQLAKSIVEEILLLFESAQKTSKRYELVADQQDLVVFEDKDMKPIGRALHRRLKDLVSRRQKQTSLAKKTAWALYDGKSLEKIVDQVAGFVDELEKAFPIEAVCHKLAENEIEEVEDEASLTILKDAAGGIDAAMSDAAAQKIDAIVGRNSAKDIRTEK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	235 (231)
Sequences:	367 (324.8)
Seq/Len:	1.589
Nf(neff/√len):	21.4

Jackhmmer Results: (2015_01_07)
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: 1.589).

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
13_G	16_G	2.203	0.99
51_R	168_D	2.129	0.99
4_P	8_V	2.119	0.99
37_D	153_G	2.098	0.99
5_F	10_G	2.046	0.99
101_Y	152_D	2.018	0.98
47_I	83_I	1.860	0.97
25_F	167_V	1.853	0.97
72_P	77_V	1.800	0.96
80_A	174_F	1.743	0.95
18_F	56_G	1.674	0.93
35_G	133_V	1.663	0.93
3_E	6_E	1.604	0.91
220_D	223_V	1.509	0.88
20_N	24_C	1.473	0.86
227_S	231_I	1.469	0.86
51_R	171_E	1.466	0.86
98_S	103_L	1.459	0.85
5_F	8_V	1.448	0.85
18_F	43_L	1.411	0.83
30_L	48_A	1.375	0.80
228_A	231_I	1.363	0.79
7_I	10_G	1.350	0.79
48_A	167_V	1.334	0.77
28_V	178_A	1.330	0.77
97_T	163_V	1.326	0.77
9_A	212_S	1.323	0.77
5_F	9_A	1.320	0.76
31_G	174_F	1.315	0.76
218_K	222_I	1.300	0.75
52_L	56_G	1.300	0.75
122_G	126_H	1.297	0.75
103_L	155_S	1.292	0.74
51_R	56_G	1.291	0.74
43_L	54_R	1.281	0.73
54_R	174_F	1.277	0.73
25_F	45_L	1.272	0.72
19_N	23_A	1.259	0.71
4_P	7_I	1.253	0.71
15_A	204_A	1.252	0.71
54_R	59_V	1.252	0.71
24_C	29_Q	1.248	0.70
21_C	101_Y	1.244	0.70
3_E	12_L	1.240	0.70
108_Q	111_V	1.236	0.69
3_E	15_A	1.235	0.69
63_D	160_V	1.234	0.69
24_C	31_G	1.226	0.68
102_E	150_L	1.221	0.68
136_R	174_F	1.214	0.67
34_F	175_P	1.210	0.67
28_V	38_Y	1.202	0.66
54_R	208_D	1.199	0.66
51_R	54_R	1.185	0.65
34_F	38_Y	1.181	0.64
93_S	102_E	1.181	0.64
48_A	164_A	1.180	0.64
97_T	101_Y	1.174	0.64
84_V	101_Y	1.170	0.63
9_A	25_F	1.165	0.63
15_A	141_S	1.162	0.62
197_L	209_A	1.159	0.62
167_V	189_E	1.159	0.62
156_L	166_F	1.159	0.62
221_A	225_R	1.156	0.62
11_A	173_A	1.154	0.62
90_L	159_I	1.153	0.61
22_V	45_L	1.145	0.61
24_C	187_E	1.143	0.60
48_A	59_V	1.141	0.60
126_H	132_L	1.134	0.60
45_L	163_V	1.130	0.59
141_S	145_K	1.125	0.59
29_Q	32_R	1.119	0.58
218_K	221_A	1.117	0.58
34_F	53_S	1.115	0.58
37_D	144_K	1.112	0.57
95_Q	149_A	1.108	0.57
182_K	185_E	1.107	0.57
3_E	10_G	1.105	0.57
90_L	166_F	1.102	0.56
12_L	22_V	1.098	0.56
106_D	160_V	1.095	0.56
156_L	159_I	1.093	0.55
44_R	162_Q	1.092	0.55
25_F	163_V	1.091	0.55
159_I	197_L	1.090	0.55
25_F	28_V	1.088	0.55
153_G	157_E	1.081	0.54
22_V	25_F	1.079	0.54
23_A	94_A	1.073	0.53
80_A	156_L	1.070	0.53
221_A	229_K	1.068	0.53
21_C	167_V	1.066	0.53
13_G	113_F	1.063	0.52
154_K	188_I	1.058	0.52
52_L	61_I	1.050	0.51
4_P	152_D	1.046	0.50
7_I	130_K	1.035	0.49
18_F	25_F	1.033	0.49
20_N	149_A	1.029	0.49
44_R	165_G	1.029	0.49
215_A	218_K	1.028	0.49
84_V	160_V	1.027	0.48
211_M	217_Q	1.025	0.48
94_A	160_V	1.023	0.48
21_C	197_L	1.022	0.48
33_H	105_A	1.022	0.48
31_G	200_L	1.019	0.48
212_S	216_A	1.017	0.47
41_C	48_A	1.017	0.47
37_D	115_D	1.015	0.47
27_Y	136_R	1.012	0.47
89_L	219_I	1.011	0.47
203_A	218_K	1.011	0.47
112_V	116_K	1.010	0.47
25_F	188_I	1.010	0.47
60_Q	204_A	1.009	0.47
101_Y	144_K	1.009	0.47
152_D	188_I	1.003	0.46
223_V	228_A	1.000	0.46

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
2wvqA	2	0.9064	100	0.189	Contact Map
4btfA	1	0.617	13.2	0.945	Contact Map
4ogqG	1	0.1404	8.2	0.95	Contact Map
1q90G	1	0.1106	7.7	0.951	Contact Map
3he4A	4	0.1915	5.8	0.953	Contact Map
2msvA	1	0.5702	4	0.957	Contact Map
5rubA	2	0.2553	4	0.957	Contact Map
3lfjA	2	0.4766	3.9	0.957	Contact Map
4wbdA	1	0.8681	3.8	0.957	Contact Map
3wgcA	4	0.6553	3.8	0.957	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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