RL28 - ECOLI - GREMLIN Contacts

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RL28 - 50S ribosomal protein L28

UniProt:	P0A7M2	Sequences: MSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKKGIDTVLAELRARGEKY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10886
Length:	78 (73)
Sequences:	1054 (369)
Seq/√Len:	43.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_N	26_K	3.991	1.00
62_K	70_E	3.572	1.00
35_S	48_T	2.703	1.00
7_V	55_G	2.399	1.00
37_R	46_F	2.332	1.00
42_S	65_D	2.248	1.00
18_R	24_A	2.166	1.00
17_N	25_T	2.142	1.00
12_P	28_R	2.030	0.99
39_W	44_K	2.003	0.99
40_V	43_E	1.929	0.99
38_F	56_M	1.887	0.99
7_V	67_V	1.708	0.98
40_V	65_D	1.628	0.97
34_H	53_A	1.563	0.96
18_R	22_L	1.537	0.95
4_V	11_R	1.528	0.95
62_K	67_V	1.496	0.95
14_T	26_K	1.440	0.93
66_T	70_E	1.433	0.93
55_G	58_V	1.414	0.93
7_V	59_I	1.346	0.91
12_P	31_P	1.329	0.90
33_L	50_R	1.326	0.90
40_V	64_I	1.280	0.89
19_S	23_N	1.278	0.89
40_V	68_L	1.266	0.88
52_S	55_G	1.244	0.87
39_W	46_F	1.204	0.85
20_H	23_N	1.163	0.83
43_E	72_R	1.124	0.81
62_K	66_T	1.095	0.79
30_L	33_L	1.093	0.79
43_E	65_D	1.055	0.77
8_T	55_G	1.045	0.76
43_E	46_F	1.039	0.76
12_P	60_D	1.013	0.74
51_V	55_G	0.973	0.71
41_E	64_I	0.972	0.71
48_T	66_T	0.932	0.67
3_R	33_L	0.915	0.66
51_V	56_M	0.910	0.65
26_K	29_F	0.904	0.65
14_T	28_R	0.885	0.63
13_V	29_F	0.876	0.62
35_S	50_R	0.859	0.61
6_Q	49_L	0.843	0.59
14_T	30_L	0.835	0.59
54_K	58_V	0.834	0.59
42_S	69_A	0.828	0.58
54_K	57_R	0.797	0.55
43_E	67_V	0.774	0.53
10_K	54_K	0.767	0.52
18_R	46_F	0.767	0.52
3_R	31_P	0.764	0.52
38_F	64_I	0.741	0.50
19_S	22_L	0.729	0.49
36_H	46_F	0.728	0.49
67_V	71_L	0.718	0.48
42_S	64_I	0.718	0.48
38_F	59_I	0.714	0.47
15_G	29_F	0.713	0.47
39_W	60_D	0.699	0.46
24_A	35_S	0.693	0.45
16_N	24_A	0.693	0.45
17_N	26_K	0.690	0.45
17_N	23_N	0.687	0.45
12_P	30_L	0.682	0.44
1_M	5_C	0.646	0.41
59_I	67_V	0.640	0.40
68_L	72_R	0.636	0.40
40_V	47_V	0.635	0.40
12_P	26_K	0.629	0.39
53_A	56_M	0.625	0.39
10_K	21_A	0.599	0.37
10_K	52_S	0.597	0.37
29_F	38_F	0.590	0.36
67_V	70_E	0.590	0.36
14_T	33_L	0.588	0.36
7_V	71_L	0.587	0.36
2_S	12_P	0.582	0.35
39_W	45_R	0.581	0.35
36_H	56_M	0.571	0.34
19_S	31_P	0.568	0.34
49_L	64_I	0.566	0.34
16_N	23_N	0.552	0.33
47_V	66_T	0.547	0.32
17_N	27_R	0.547	0.32
64_I	67_V	0.541	0.32
55_G	71_L	0.540	0.32
30_L	50_R	0.530	0.31
7_V	48_T	0.529	0.31
38_F	51_V	0.528	0.31
20_H	25_T	0.527	0.31
41_E	65_D	0.527	0.31
39_W	59_I	0.526	0.30
28_R	31_P	0.526	0.30
37_R	50_R	0.525	0.30
45_R	64_I	0.525	0.30
7_V	70_E	0.525	0.30
4_V	31_P	0.522	0.30
11_R	61_K	0.519	0.30
3_R	11_R	0.516	0.30
45_R	56_M	0.509	0.29
7_V	52_S	0.508	0.29
36_H	59_I	0.506	0.29
53_A	73_A	0.505	0.29
45_R	57_R	0.504	0.29
37_R	45_R	0.502	0.29
68_L	71_L	0.500	0.28

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
4tp9X	1	0.9872	100	0.199	Contact Map
3bboY	1	0.9744	100	0.212	Contact Map
1vw4S	1	1	99.9	0.304	Contact Map
3j7yX	1	0.9872	99.9	0.325	Contact Map
2zjrU	1	0.7179	99.9	0.328	Contact Map
2jz6A	1	0.9231	99.9	0.33	Contact Map
4rb61	1	0.9615	99.9	0.353	Contact Map
4ehiA	2	0.5256	9.2	0.928	Contact Map
2qneA	2	0.5641	8.7	0.929	Contact Map
4yfuA	1	0.9615	4.6	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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