OPENSEQ.org - 1393318664 - GREMLIN Submission

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FrhB

ID:	1393318664	Query Sequence MVLGTYKEIVSARSTDREIQKLAQDGGIVTGLLAYALDEGIIEGAVVAGPGEEFWKPQPMVAMSSDELKAAAGTKYTFSPNVMMLKKAVRQYGIEKLGTVAIPCQTMGIRKMQTYPFGVRFLADKIKLLVGIYCMENFPYTSLQTFICEKLGVSMELVEKMDIGKGKFWVYTQDDVLTLPLKETHGYEQAGCKICKDYVAELADVSTGSVGSPDGWSTVITRTDAGDSIFKQAVEAGLFETKPIEEVKPGLGLLEKLAAQKKEKAEKNIAARKEMGLPTPF	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	281 (264)
Sequences:	614 (482.6)
Seq/Len:	2.326
Nf(neff/√len):	29.7

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: 2.326).

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
221_T	230_F	2.792	1.00
14_S	31_G	2.668	1.00
64_S	67_E	2.663	1.00
61_V	88_A	2.380	1.00
208_G	218_T	2.375	1.00
131_G	200_A	2.175	1.00
99_T	106_T	2.104	1.00
8_E	227_D	2.052	0.99
47_V	61_V	2.045	0.99
49_G	57_P	2.030	0.99
13_R	240_E	1.935	0.99
33_L	98_G	1.930	0.99
101_A	106_T	1.911	0.99
47_V	88_A	1.908	0.99
44_G	94_I	1.896	0.99
62_A	71_A	1.893	0.99
133_Y	206_S	1.854	0.99
36_A	128_L	1.832	0.98
12_A	219_V	1.813	0.98
227_D	231_K	1.801	0.98
106_T	129_L	1.762	0.98
110_R	129_L	1.761	0.98
205_V	226_G	1.736	0.98
230_F	241_T	1.716	0.97
157_L	173_Q	1.704	0.97
33_L	100_V	1.701	0.97
42_I	45_A	1.638	0.96
29_V	100_V	1.609	0.96
104_C	195_C	1.608	0.96
133_Y	208_G	1.595	0.95
38_D	65_S	1.589	0.95
28_I	219_V	1.586	0.95
36_A	98_G	1.552	0.94
25_D	209_S	1.545	0.94
67_E	70_A	1.541	0.94
197_D	222_R	1.540	0.94
62_A	67_E	1.518	0.94
102_I	105_Q	1.518	0.94
28_I	207_T	1.515	0.94
128_L	229_I	1.512	0.93
231_K	234_V	1.496	0.93
228_S	231_K	1.493	0.93
166_G	211_G	1.488	0.93
28_I	68_L	1.472	0.92
47_V	62_A	1.472	0.92
34_A	68_L	1.410	0.90
185_H	188_E	1.403	0.90
219_V	230_F	1.388	0.89
31_G	233_A	1.379	0.88
59_P	79_S	1.370	0.88
30_T	72_A	1.356	0.87
60_M	71_A	1.355	0.87
52_E	56_K	1.349	0.87
138_F	164_G	1.349	0.87
14_S	23_A	1.345	0.87
132_I	219_V	1.327	0.86
9_I	220_I	1.321	0.85
164_G	209_S	1.319	0.85
13_R	20_Q	1.306	0.85
224_D	227_D	1.305	0.84
35_Y	232_Q	1.291	0.84
260_Q	263_E	1.287	0.83
104_C	192_C	1.273	0.82
30_T	34_A	1.268	0.82
36_A	229_I	1.266	0.82
192_C	195_C	1.260	0.82
113_Q	117_F	1.252	0.81
63_M	95_E	1.249	0.81
19_I	30_T	1.247	0.81
46_V	99_T	1.246	0.81
12_A	239_F	1.238	0.80
145_T	149_E	1.234	0.80
15_T	240_E	1.233	0.80
37_L	42_I	1.214	0.78
12_A	20_Q	1.202	0.77
249_P	253_L	1.184	0.76
50_P	60_M	1.184	0.76
25_D	138_F	1.183	0.76
223_T	226_G	1.182	0.75
47_V	71_A	1.180	0.75
205_V	230_F	1.173	0.75
136_E	188_E	1.173	0.75
211_G	215_G	1.169	0.74
130_V	207_T	1.161	0.74
39_E	232_Q	1.160	0.73
135_M	138_F	1.160	0.73
143_L	146_F	1.156	0.73
138_F	209_S	1.139	0.72
87_K	229_I	1.135	0.71
139_P	215_G	1.134	0.71
28_I	31_G	1.134	0.71
41_I	229_I	1.126	0.70
263_E	266_E	1.122	0.70
13_R	216_W	1.119	0.70
35_Y	38_D	1.118	0.70
252_G	255_E	1.118	0.70
110_R	202_L	1.114	0.69
136_E	209_S	1.110	0.69
250_G	253_L	1.109	0.69
249_P	252_G	1.108	0.69
234_V	241_T	1.107	0.68
29_V	217_S	1.100	0.68
24_Q	73_G	1.098	0.68
110_R	113_Q	1.094	0.67
136_E	189_Q	1.092	0.67
62_A	70_A	1.086	0.66
24_Q	135_M	1.078	0.65
75_K	105_Q	1.070	0.65
64_S	70_A	1.068	0.64
47_V	84_M	1.062	0.64
135_M	210_V	1.056	0.63
12_A	205_V	1.048	0.62
128_L	228_S	1.042	0.62
143_L	163_I	1.042	0.62
158_V	223_T	1.041	0.61
76_Y	209_S	1.036	0.61
19_I	223_T	1.032	0.60
163_I	209_S	1.014	0.58
63_M	67_E	1.014	0.58
32_L	66_D	1.010	0.58
40_G	223_T	1.006	0.58

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
3zfsC	1	0.9858	100	0.109	Contact Map
3i2wA	2	0.242	13	0.966	Contact Map
4dylA	1	0.1993	7.3	0.97	Contact Map
2v0oA	3	0.242	6.3	0.97	Contact Map
2hgoA	1	0.0925	6.1	0.971	Contact Map
3q6zA	1	0.4875	6	0.971	Contact Map
4g6vB	4	0.3274	6	0.971	Contact Map
1vk9A	1	0.2491	5.9	0.971	Contact Map
4khbA	4	0.1495	5.8	0.971	Contact Map
3kh6A	1	0.4591	5.6	0.971	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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