RL13 - BACSU - GREMLIN Contacts

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RL13 - 50S ribosomal protein L13

UniProt:	P70974	Sequences: MRTTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGDHVIIINAEKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKMLELAIKGMLPKGSLGRQMFKKLNVYRGSEHPHEAQKPEVYELRG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	145 (140)
Sequences:	2716 (1397)
Seq/√Len:	118.1

ECOLI - RL13
BACSU - RL13
SULSO - RL13

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_K	139_E	3.092	1.00
71_T	91_L	2.796	1.00
97_Y	100_K	2.689	1.00
33_V	57_I	2.545	1.00
65_L	90_A	2.544	1.00
26_L	65_L	2.532	1.00
76_Y	87_S	2.408	1.00
54_H	124_N	2.188	1.00
22_A	62_K	2.184	1.00
8_N	11_T	2.164	1.00
74_I	87_S	2.145	1.00
76_Y	85_L	2.040	1.00
70_L	90_A	1.966	1.00
70_L	94_R	1.917	1.00
30_S	105_A	1.812	1.00
100_K	103_E	1.811	1.00
42_K	53_D	1.756	1.00
126_Y	132_P	1.682	1.00
23_G	64_E	1.651	1.00
19_V	33_V	1.645	1.00
32_E	35_A	1.608	1.00
92_E	96_N	1.603	1.00
12_I	49_V	1.592	1.00
36_I	141_Y	1.586	1.00
68_K	72_D	1.582	1.00
31_S	35_A	1.572	1.00
88_R	93_M	1.568	1.00
126_Y	133_H	1.566	1.00
118_Q	121_K	1.531	1.00
36_I	55_V	1.530	1.00
89_T	92_E	1.519	1.00
36_I	41_H	1.472	1.00
38_R	45_Y	1.472	1.00
88_R	96_N	1.455	1.00
74_I	89_T	1.454	1.00
61_E	127_R	1.452	1.00
90_A	101_M	1.439	1.00
102_L	106_I	1.419	1.00
14_R	122_K	1.405	1.00
33_V	106_I	1.401	1.00
90_A	94_R	1.400	1.00
60_A	125_V	1.393	1.00
107_K	120_F	1.383	1.00
58_I	129_S	1.377	1.00
103_E	120_F	1.369	1.00
94_R	101_M	1.368	1.00
70_L	101_M	1.352	1.00
77_R	88_R	1.351	1.00
75_Y	90_A	1.350	1.00
61_E	128_G	1.343	1.00
24_K	32_E	1.329	1.00
24_K	142_E	1.328	1.00
68_K	71_T	1.304	1.00
88_R	92_E	1.296	1.00
50_D	122_K	1.289	1.00
18_V	58_I	1.281	1.00
21_A	29_L	1.263	0.99
6_M	48_H	1.239	0.99
7_A	46_T	1.205	0.99
110_L	119_M	1.198	0.99
22_A	25_T	1.187	0.99
22_A	129_S	1.172	0.99
26_L	63_I	1.146	0.99
44_T	51_T	1.142	0.99
18_V	56_I	1.120	0.99
100_K	104_L	1.117	0.99
17_L	141_Y	1.114	0.99
98_P	127_R	1.096	0.98
104_L	107_K	1.085	0.98
110_L	116_G	1.075	0.98
70_L	91_L	1.061	0.98
110_L	120_F	1.044	0.98
60_A	98_P	1.036	0.98
120_F	125_V	1.033	0.98
79_T	86_K	1.029	0.98
32_E	141_Y	1.014	0.97
104_L	108_G	1.012	0.97
25_T	64_E	0.997	0.97
99_E	127_R	0.997	0.97
51_T	122_K	0.987	0.97
77_R	104_L	0.970	0.97
8_N	49_V	0.952	0.96
102_L	125_V	0.949	0.96
29_L	33_V	0.943	0.96
41_H	53_D	0.942	0.96
5_P	44_T	0.941	0.96
14_R	50_D	0.925	0.96
63_I	102_L	0.923	0.96
106_I	123_L	0.921	0.96
124_N	132_P	0.910	0.95
37_L	123_L	0.909	0.95
74_I	85_L	0.904	0.95
103_E	125_V	0.897	0.95
79_T	84_G	0.888	0.95
35_A	41_H	0.885	0.94
19_V	29_L	0.884	0.94
29_L	102_L	0.879	0.94
93_M	97_Y	0.868	0.94
92_E	95_T	0.868	0.94
118_Q	122_K	0.865	0.94
7_A	51_T	0.861	0.94
99_E	103_E	0.853	0.93
77_R	86_K	0.851	0.93
26_L	90_A	0.840	0.93
116_G	119_M	0.838	0.93
103_E	121_K	0.829	0.92
38_R	108_G	0.814	0.92
17_L	55_V	0.812	0.91
93_M	104_L	0.810	0.91
54_H	122_K	0.801	0.91
33_V	102_L	0.797	0.91
33_V	55_V	0.797	0.91
133_H	136_Q	0.786	0.90
29_L	63_I	0.775	0.89
60_A	102_L	0.772	0.89
8_N	12_I	0.767	0.89
28_R	31_S	0.764	0.89
114_S	117_R	0.756	0.88
21_A	57_I	0.756	0.88
112_K	119_M	0.753	0.88
14_R	54_H	0.750	0.88
4_T	7_A	0.743	0.87
91_L	95_T	0.741	0.87
112_K	116_G	0.735	0.87
61_E	98_P	0.711	0.85
108_G	112_K	0.709	0.85
73_K	105_A	0.706	0.85
5_P	11_T	0.705	0.85
20_D	59_N	0.702	0.84
9_A	12_I	0.701	0.84
119_M	122_K	0.700	0.84
60_A	99_E	0.697	0.84
7_A	49_V	0.694	0.84
113_G	117_R	0.691	0.83
66_T	69_K	0.687	0.83
62_K	128_G	0.686	0.83
65_L	70_L	0.673	0.82
6_M	9_A	0.665	0.81
17_L	41_H	0.660	0.80
7_A	12_I	0.653	0.80
60_A	127_R	0.653	0.80
5_P	49_V	0.653	0.80
55_V	141_Y	0.650	0.79
19_V	57_I	0.650	0.79
26_L	102_L	0.639	0.78
116_G	120_F	0.637	0.78
14_R	42_K	0.634	0.78
17_L	36_I	0.632	0.78
78_H	85_L	0.629	0.77
27_G	109_M	0.627	0.77
41_H	141_Y	0.626	0.77
34_A	38_R	0.623	0.77
81_H	84_G	0.622	0.76
90_A	93_M	0.620	0.76
93_M	100_K	0.618	0.76
45_Y	48_H	0.608	0.75
35_A	110_L	0.606	0.75
67_G	73_K	0.605	0.74
25_T	66_T	0.603	0.74
99_E	124_N	0.601	0.74
73_K	101_M	0.601	0.74
26_L	101_M	0.599	0.74
113_G	116_G	0.599	0.74
97_Y	104_L	0.594	0.73
120_F	124_N	0.594	0.73
19_V	141_Y	0.594	0.73
10_S	44_T	0.590	0.73
52_G	55_V	0.587	0.72
65_L	101_M	0.586	0.72
42_K	52_G	0.586	0.72
57_I	106_I	0.579	0.71
130_E	134_E	0.576	0.71
33_V	36_I	0.576	0.71
88_R	95_T	0.576	0.71
137_K	140_V	0.575	0.71
58_I	61_E	0.575	0.71
38_R	119_M	0.574	0.71
61_E	129_S	0.573	0.70
24_K	29_L	0.573	0.70
72_D	90_A	0.565	0.69
72_D	89_T	0.563	0.69
56_I	132_P	0.558	0.68
32_E	36_I	0.557	0.68
17_L	24_K	0.550	0.67
97_Y	103_E	0.548	0.67
18_V	129_S	0.547	0.67
81_H	97_Y	0.544	0.66
82_P	114_S	0.542	0.66
17_L	139_E	0.542	0.66
113_G	119_M	0.541	0.66
42_K	54_H	0.539	0.66
110_L	113_G	0.537	0.65
103_E	107_K	0.532	0.65
78_H	83_G	0.531	0.65
88_R	97_Y	0.530	0.64
54_H	132_P	0.528	0.64
107_K	112_K	0.526	0.64
65_L	73_K	0.525	0.64
18_V	22_A	0.521	0.63
135_A	138_P	0.521	0.63
30_S	102_L	0.517	0.63
3_T	90_A	0.513	0.62
75_Y	110_L	0.512	0.62
57_I	123_L	0.510	0.62
68_K	91_L	0.510	0.62
78_H	84_G	0.506	0.61
14_R	37_L	0.505	0.61
8_N	25_T	0.501	0.60
3_T	79_T	0.501	0.60
94_R	99_E	0.500	0.60

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
3j3wJ	1	0.9862	100	0.083	Contact Map
3bboL	1	0.8621	100	0.094	Contact Map
4tp9J	1	0.0138	100	0.099	Contact Map
2zjrG	1	0.9724	100	0.103	Contact Map
4rb6N	1	0.9655	100	0.105	Contact Map
3f1fN	1	0.9448	100	0.106	Contact Map
1vw4H	1	0.9517	100	0.124	Contact Map
3j7yK	1	0.9931	100	0.13	Contact Map
3zf7O	1	0.8276	100	0.326	Contact Map
1j3aA	1	0.7241	100	0.353	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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