YRAE - BACSU - GREMLIN Contacts

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YRAE - Uncharacterized protein YraE

UniProt:	O06011	Sequences: MEYALHEVLEVQEMTAFKTLCLTKSKTMKALVSDPKLKEIMQQDVDITTRQLQEFASILSNAKQE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	65 (60)
Sequences:	133 (103)
Seq/√Len:	13.3

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_F	21_C	2.745	0.95
15_T	52_L	2.659	0.94
45_V	55_F	2.423	0.90
17_F	44_D	2.054	0.80
19_T	26_K	1.952	0.77
21_C	44_D	1.902	0.75
36_K	39_E	1.800	0.71
21_C	31_L	1.747	0.68
6_H	10_E	1.714	0.67
32_V	35_P	1.638	0.63
24_K	31_L	1.632	0.63
19_T	49_T	1.616	0.62
4_A	32_V	1.559	0.59
23_T	27_T	1.553	0.59
10_E	36_K	1.420	0.52
29_K	42_Q	1.412	0.51
42_Q	46_D	1.391	0.50
17_F	25_S	1.384	0.50
19_T	34_D	1.358	0.49
12_Q	55_F	1.358	0.49
18_K	44_D	1.312	0.46
5_L	9_L	1.274	0.44
4_A	14_M	1.268	0.44
8_V	41_M	1.242	0.42
16_A	26_K	1.235	0.42
25_S	47_I	1.223	0.41
17_F	53_Q	1.201	0.40
24_K	32_V	1.192	0.40
14_M	55_F	1.137	0.37
53_Q	60_S	1.111	0.36
39_E	58_I	1.081	0.34
16_A	33_S	0.997	0.31
11_V	58_I	0.996	0.30
35_P	56_A	0.983	0.30
11_V	35_P	0.979	0.30
5_L	23_T	0.972	0.29
22_L	60_S	0.961	0.29
47_I	51_Q	0.950	0.28
51_Q	54_E	0.941	0.28
22_L	59_L	0.926	0.27
32_V	58_I	0.923	0.27
24_K	53_Q	0.869	0.25
48_T	58_I	0.861	0.25
10_E	15_T	0.820	0.23
27_T	53_Q	0.814	0.23
11_V	43_Q	0.807	0.23
48_T	61_N	0.775	0.22
18_K	21_C	0.757	0.21
30_A	56_A	0.756	0.21
30_A	33_S	0.749	0.21
5_L	8_V	0.748	0.21
3_Y	51_Q	0.740	0.20
52_L	58_I	0.735	0.20
43_Q	59_L	0.729	0.20
48_T	51_Q	0.726	0.20
28_M	37_L	0.719	0.20
34_D	55_F	0.716	0.20
14_M	51_Q	0.712	0.19
20_L	24_K	0.689	0.19
23_T	44_D	0.685	0.19
28_M	62_A	0.658	0.18
33_S	59_L	0.657	0.18
30_A	40_I	0.657	0.18
23_T	59_L	0.654	0.18
29_K	55_F	0.654	0.18
3_Y	15_T	0.652	0.17
23_T	53_Q	0.645	0.17
10_E	40_I	0.620	0.17
15_T	22_L	0.619	0.16
22_L	40_I	0.616	0.16
10_E	51_Q	0.615	0.16
33_S	62_A	0.612	0.16
26_K	59_L	0.591	0.16
26_K	43_Q	0.582	0.15
47_I	53_Q	0.575	0.15
9_L	44_D	0.574	0.15
16_A	41_M	0.567	0.15
19_T	29_K	0.558	0.15
41_M	55_F	0.551	0.15
23_T	28_M	0.549	0.15
9_L	52_L	0.543	0.14
10_E	24_K	0.537	0.14
25_S	36_K	0.531	0.14
27_T	30_A	0.529	0.14
5_L	50_R	0.514	0.14
11_V	42_Q	0.505	0.13
16_A	43_Q	0.503	0.13
29_K	34_D	0.502	0.13
25_S	56_A	0.502	0.13
6_H	9_L	0.500	0.13

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
2rbdA	4	1	98.3	0.672	Contact Map
3oghB	2	0.9692	24.8	0.893	Contact Map
2gs4A	5	0.9692	21.1	0.897	Contact Map
3hiuA	3	0.9538	18.3	0.9	Contact Map
1ysmA	1	0.3846	14.6	0.904	Contact Map
2gyqA	2	1	13.8	0.905	Contact Map
4zuzA	1	0.8308	9.9	0.911	Contact Map
1xneA	1	0.9846	8.9	0.913	Contact Map
4etrA	1	0.9538	8.8	0.913	Contact Map
5al7A	2	0.9692	7.8	0.915	Contact Map

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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