YLXR - BACSU - GREMLIN Contacts

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YLXR - Uncharacterized protein YlxR

UniProt:	P32728	Sequences: MNKHKKIPLRKCVVTGEMKPKKELIRVVRSKEGEISVDPTGKKNGRGAYLTLDKECILAAKKKNTLQNQFQSQIDDQIFDELLELAEKVKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	91 (84)
Sequences:	959 (693)
Seq/√Len:	75.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_S	36_S	2.841	1.00
67_Q	73_Q	2.749	1.00
15_T	56_C	2.708	1.00
11_K	16_G	2.596	1.00
64_N	67_Q	2.472	1.00
61_K	83_L	2.319	1.00
30_S	34_E	2.280	1.00
20_P	23_E	2.150	1.00
15_T	51_T	2.121	1.00
36_S	43_K	2.117	1.00
35_I	70_F	1.986	1.00
58_L	83_L	1.947	1.00
9_L	20_P	1.899	1.00
11_K	18_M	1.857	1.00
54_K	58_L	1.724	1.00
51_T	56_C	1.716	1.00
59_A	63_K	1.656	1.00
31_K	36_S	1.538	0.99
81_E	85_L	1.480	0.99
19_K	51_T	1.473	0.99
14_V	56_C	1.455	0.99
61_K	79_F	1.356	0.98
76_D	80_D	1.333	0.98
9_L	18_M	1.333	0.98
29_R	72_S	1.331	0.98
61_K	80_D	1.325	0.98
61_K	76_D	1.313	0.98
81_E	84_E	1.301	0.98
54_K	83_L	1.258	0.97
12_C	56_C	1.254	0.97
77_Q	81_E	1.252	0.97
67_Q	74_I	1.243	0.97
29_R	33_G	1.239	0.97
50_L	57_I	1.230	0.97
54_K	87_E	1.226	0.97
39_P	52_L	1.186	0.96
37_V	78_I	1.146	0.95
73_Q	76_D	1.102	0.94
25_I	82_L	1.066	0.93
19_K	23_E	1.061	0.93
55_E	58_L	1.050	0.93
57_I	61_K	1.035	0.92
58_L	62_K	1.027	0.92
35_I	72_S	0.978	0.90
65_T	69_Q	0.973	0.89
14_V	57_I	0.971	0.89
57_I	83_L	0.961	0.89
57_I	66_L	0.937	0.87
39_P	85_L	0.927	0.87
28_V	36_S	0.926	0.87
36_S	44_N	0.916	0.86
20_P	24_L	0.906	0.86
80_D	84_E	0.870	0.83
30_S	44_N	0.868	0.83
6_K	17_E	0.848	0.82
9_L	17_E	0.847	0.82
75_D	86_A	0.844	0.81
57_I	86_A	0.842	0.81
12_C	15_T	0.833	0.81
13_V	70_F	0.831	0.80
15_T	37_V	0.830	0.80
71_Q	74_I	0.828	0.80
14_V	62_K	0.812	0.79
19_K	53_D	0.804	0.78
44_N	50_L	0.804	0.78
37_V	82_L	0.796	0.77
24_L	56_C	0.787	0.77
35_I	74_I	0.773	0.75
82_L	86_A	0.763	0.74
52_L	57_I	0.763	0.74
84_E	87_E	0.759	0.74
29_R	35_I	0.754	0.74
6_K	22_K	0.737	0.72
6_K	41_G	0.737	0.72
65_T	71_Q	0.733	0.71
6_K	27_V	0.723	0.70
65_T	68_N	0.702	0.68
78_I	81_E	0.696	0.67
83_L	87_E	0.695	0.67
34_E	43_K	0.677	0.65
75_D	78_I	0.662	0.64
33_G	36_S	0.659	0.63
25_I	53_D	0.642	0.61
14_V	19_K	0.641	0.61
14_V	44_N	0.640	0.61
16_G	20_P	0.629	0.60
78_I	86_A	0.621	0.59
25_I	52_L	0.620	0.59
27_V	50_L	0.614	0.58
78_I	85_L	0.598	0.56
7_I	17_E	0.598	0.56
7_I	20_P	0.594	0.55
13_V	65_T	0.589	0.55
19_K	43_K	0.585	0.54
46_R	56_C	0.585	0.54
50_L	60_A	0.578	0.53
28_V	70_F	0.578	0.53
57_I	85_L	0.577	0.53
52_L	86_A	0.576	0.53
55_E	59_A	0.573	0.53
24_L	32_E	0.569	0.52
12_C	51_T	0.569	0.52
33_G	46_R	0.561	0.51
4_H	81_E	0.559	0.51
53_D	76_D	0.549	0.50
19_K	56_C	0.541	0.49
30_S	72_S	0.540	0.49
59_A	65_T	0.538	0.48
80_D	83_L	0.535	0.48
13_V	48_A	0.535	0.48
8_P	12_C	0.535	0.48
15_T	65_T	0.518	0.46
10_R	15_T	0.516	0.46
30_S	33_G	0.514	0.45
14_V	51_T	0.512	0.45
32_E	36_S	0.510	0.45
40_T	44_N	0.510	0.45
13_V	16_G	0.509	0.45
15_T	19_K	0.506	0.44
11_K	72_S	0.505	0.44
29_R	70_F	0.504	0.44
52_L	76_D	0.503	0.44
44_N	63_K	0.502	0.44
40_T	55_E	0.501	0.44
58_L	87_E	0.501	0.44
48_A	70_F	0.500	0.44

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
1g2rA	1	0.956	100	0.223	Contact Map
4adnA	2	0.7033	63.9	0.896	Contact Map
2yb5A	1	0.6593	50.1	0.904	Contact Map
1ovxA	2	0.4176	19.8	0.923	Contact Map
2ogfA	4	0.6044	16.2	0.926	Contact Map
2ds5A	2	0.4835	15	0.927	Contact Map
3anwA	1	0.4286	14.3	0.928	Contact Map
2i52A	5	0.5604	10.4	0.932	Contact Map
4uhqA	1	0.5055	6.9	0.937	Contact Map
1k3xA	1	0.3736	6.5	0.938	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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