YAAA - BACSU - GREMLIN Contacts

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YAAA - Uncharacterized protein YaaA

UniProt:	P05650	Sequences: MANPISIDTEMITLGQFLKLADVIQSGGMAKWFLSEHEVLVNDEPDNRRGRKLYVGDVVEIEGFGSFQVVN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	71 (66)
Sequences:	781 (562)
Seq/√Len:	69.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
42_N	57_D	3.131	1.00
17_F	67_F	2.661	1.00
4_P	68_Q	2.556	1.00
60_E	66_S	2.499	1.00
24_I	33_F	2.208	1.00
41_V	46_D	2.129	1.00
41_V	51_R	2.107	1.00
48_R	51_R	2.093	1.00
11_M	54_Y	2.038	1.00
40_L	60_E	2.003	1.00
24_I	30_A	1.953	1.00
22_D	25_Q	1.788	1.00
11_M	52_K	1.780	1.00
58_V	68_Q	1.766	1.00
13_T	52_K	1.549	0.99
17_F	53_L	1.547	0.99
25_Q	29_M	1.532	0.99
29_M	32_W	1.520	0.99
33_F	61_I	1.519	0.99
37_H	47_N	1.423	0.98
22_D	26_S	1.391	0.98
58_V	66_S	1.347	0.98
5_I	21_A	1.303	0.97
7_I	20_L	1.291	0.97
46_D	51_R	1.274	0.97
59_V	69_V	1.199	0.95
16_Q	46_D	1.158	0.94
33_F	38_E	1.076	0.92
10_E	54_Y	1.056	0.91
34_L	37_H	1.049	0.91
7_I	69_V	1.027	0.90
40_L	45_P	0.976	0.87
17_F	59_V	0.966	0.87
15_G	46_D	0.955	0.86
40_L	62_E	0.942	0.85
53_L	69_V	0.926	0.84
7_I	55_V	0.916	0.84
61_I	64_F	0.909	0.83
43_D	54_Y	0.891	0.82
17_F	20_L	0.858	0.79
23_V	35_S	0.851	0.79
23_V	61_I	0.820	0.76
32_W	62_E	0.809	0.75
17_F	28_G	0.800	0.74
43_D	66_S	0.785	0.73
23_V	67_F	0.775	0.72
34_L	45_P	0.771	0.72
18_L	24_I	0.763	0.71
43_D	51_R	0.747	0.69
8_D	56_G	0.741	0.69
16_Q	48_R	0.738	0.68
43_D	58_V	0.737	0.68
13_T	25_Q	0.726	0.67
34_L	47_N	0.725	0.67
44_E	48_R	0.715	0.66
29_M	36_E	0.715	0.66
10_E	43_D	0.710	0.65
26_S	29_M	0.705	0.65
30_A	34_L	0.699	0.64
7_I	17_F	0.686	0.63
40_L	58_V	0.673	0.61
13_T	28_G	0.672	0.61
35_S	56_G	0.669	0.61
51_R	55_V	0.666	0.60
13_T	50_G	0.661	0.60
38_E	45_P	0.655	0.59
21_A	41_V	0.655	0.59
24_I	32_W	0.652	0.59
33_F	37_H	0.650	0.59
3_N	22_D	0.630	0.56
18_L	59_V	0.622	0.55
48_R	54_Y	0.620	0.55
39_V	58_V	0.619	0.55
12_I	17_F	0.619	0.55
20_L	69_V	0.618	0.55
8_D	38_E	0.599	0.53
23_V	33_F	0.596	0.52
16_Q	26_S	0.586	0.51
32_W	36_E	0.582	0.50
12_I	51_R	0.573	0.49
47_N	61_I	0.567	0.49
19_K	55_V	0.563	0.48
33_F	64_F	0.562	0.48
9_T	12_I	0.561	0.48
18_L	28_G	0.553	0.47
6_S	66_S	0.549	0.46
9_T	20_L	0.546	0.46
31_K	36_E	0.536	0.45
24_I	38_E	0.531	0.44
12_I	69_V	0.529	0.44
21_A	67_F	0.522	0.43
3_N	64_F	0.512	0.42
4_P	58_V	0.510	0.42
21_A	69_V	0.503	0.41
7_I	39_V	0.503	0.41
28_G	36_E	0.502	0.41
6_S	63_G	0.501	0.41
60_E	63_G	0.500	0.41
63_G	67_F	0.500	0.41

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
1p9kA	1	0.9718	98.1	0.717	Contact Map
1v9fA	1	0.0986	98	0.726	Contact Map
2k6pA	1	0.831	97.8	0.737	Contact Map
1dm9A	1	0.9014	97.8	0.74	Contact Map
4tp8D	1	1	97.7	0.744	Contact Map
1kskA	1	0.8732	97.7	0.745	Contact Map
3dh3A	1	0.8732	97.7	0.745	Contact Map
4rb5D	1	1	97.7	0.747	Contact Map
1vioA	2	0.8451	97.6	0.748	Contact Map
3bbnD	1	1	97.6	0.75	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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