OPENSEQ.org - 1501768596 - GREMLIN Submission

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glubp

ID:	1501768596	Query Sequence ADKKLVVATDTAFVPFEFKQGDLYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPALQTKNVDLALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNAYMELGTNRADAVLHDTPNILYFIKTAGNGQFKAVGDSLEAQQYGIAFPKGSDELRDKVNGALKTLRENGTYNEIYKKWFGTEPK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	226 (223)
Sequences:	24260 (16534.1)
Seq/Len:	108.789
Nf(neff/√len):	1107.2

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: 108.789).

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
113_A	151_A	4.224	1.00
8_A	62_V	3.655	1.00
4_K	44_E	3.069	1.00
38_E	206_T	2.726	1.00
71_I	76_K	2.492	1.00
136_F	145_E	2.479	1.00
34_A	212_T	2.334	1.00
6_V	44_E	2.231	1.00
142_A	154_V	2.219	1.00
58_Q	78_A	2.205	1.00
56_A	62_V	2.161	1.00
36_A	43_Y	2.153	1.00
83_D	205_K	2.143	1.00
56_A	61_N	2.114	1.00
79_I	188_A	2.095	1.00
38_E	203_A	2.001	1.00
34_A	37_K	1.991	1.00
156_H	161_I	1.980	1.00
30_D	219_K	1.974	1.00
197_R	201_N	1.968	1.00
80_D	197_R	1.957	1.00
121_V	135_Q	1.952	1.00
6_V	46_K	1.902	1.00
121_V	125_K	1.878	1.00
145_E	150_R	1.875	1.00
138_N	141_N	1.866	1.00
212_T	215_E	1.854	1.00
20_Q	25_V	1.826	1.00
189_F	197_R	1.815	1.00
82_S	201_N	1.813	1.00
83_D	201_N	1.801	1.00
71_I	186_G	1.782	1.00
189_F	200_V	1.778	1.00
214_N	218_K	1.750	1.00
4_K	42_D	1.728	1.00
73_D	76_K	1.687	1.00
34_A	207_L	1.670	1.00
103_S	106_D	1.661	1.00
7_V	32_W	1.636	1.00
95_K	149_N	1.619	1.00
30_D	220_W	1.612	1.00
87_K	184_Q	1.593	1.00
93_M	161_I	1.589	1.00
34_A	38_E	1.588	1.00
205_K	209_E	1.560	1.00
190_P	193_S	1.554	1.00
35_I	203_A	1.554	1.00
203_A	207_L	1.551	1.00
91_L	158_T	1.539	1.00
29_V	33_A	1.533	1.00
203_A	206_T	1.524	1.00
7_V	64_L	1.522	1.00
112_V	153_A	1.521	1.00
111_V	134_R	1.520	1.00
136_F	142_A	1.520	1.00
55_P	59_T	1.511	1.00
39_L	203_A	1.501	1.00
111_V	152_D	1.491	1.00
18_F	25_V	1.489	1.00
48_M	56_A	1.477	1.00
53_I	65_A	1.469	1.00
102_K	106_D	1.468	1.00
94_V	153_A	1.464	1.00
110_K	152_D	1.429	1.00
123_Y	127_N	1.420	1.00
145_E	151_A	1.408	1.00
38_E	210_N	1.408	1.00
28_D	85_Y	1.406	0.99
113_A	142_A	1.389	0.99
144_M	148_T	1.382	0.99
116_S	137_P	1.369	0.99
92_V	153_A	1.343	0.99
69_I	188_A	1.336	0.99
198_D	202_G	1.316	0.99
144_M	147_G	1.313	0.99
89_G	158_T	1.312	0.99
199_K	202_G	1.305	0.99
66_L	187_I	1.302	0.99
212_T	216_I	1.297	0.99
158_T	162_L	1.293	0.99
64_L	189_F	1.284	0.99
95_K	98_N	1.270	0.99
94_V	176_V	1.268	0.99
96_A	174_K	1.264	0.99
146_L	154_V	1.261	0.99
199_K	203_A	1.250	0.99
146_L	173_F	1.238	0.98
33_A	45_L	1.232	0.98
19_K	47_P	1.228	0.98
208_R	213_Y	1.223	0.98
55_P	58_Q	1.212	0.98
111_V	132_D	1.210	0.98
194_D	198_D	1.201	0.98
49_D	52_G	1.186	0.98
81_F	188_A	1.185	0.98
147_G	172_Q	1.184	0.98
113_A	136_F	1.176	0.98
80_D	192_G	1.172	0.98
202_G	206_T	1.159	0.97
38_E	212_T	1.158	0.97
116_S	135_Q	1.140	0.97
54_I	79_I	1.136	0.97
206_T	210_N	1.117	0.96
134_R	145_E	1.114	0.96
72_T	75_R	1.108	0.96
32_W	66_L	1.095	0.96
142_A	145_E	1.094	0.96
8_A	53_I	1.092	0.96
80_D	191_K	1.091	0.96
114_V	121_V	1.080	0.95
20_Q	23_L	1.077	0.95
31_L	213_Y	1.069	0.95
80_D	194_D	1.061	0.95
137_P	141_N	1.058	0.95
90_L	120_S	1.048	0.94
94_V	174_K	1.048	0.94
27_F	217_Y	1.044	0.94
201_N	205_K	1.041	0.94
52_G	56_A	1.035	0.94
25_V	30_D	1.029	0.94
207_L	212_T	1.016	0.93
41_L	199_K	1.003	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: (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
1wdnA	1	0.9867	100	0.004	Contact Map
4powA	2	0.9912	100	0.008	Contact Map
3k4uA	6	1	100	0.023	Contact Map
3kzgA	4	0.969	100	0.026	Contact Map
4ohnA	1	0.9956	100	0.027	Contact Map
3h7mA	1	0.9956	100	0.029	Contact Map
3hv1A	2	0.9956	100	0.032	Contact Map
3kbrA	1	0.9602	100	0.036	Contact Map
4c0rA	2	0.9956	100	0.037	Contact Map
3i6vA	1	0.9469	100	0.042	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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