RS5 - BACSU - GREMLIN Contacts

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RS5 - 30S ribosomal protein S5

UniProt:	P21467	Sequences: MRRIDPSKLELEERLVTVNRVAKVVKGGRRFRFAALVVVGDKNGHVGFGTGKAQEVPEAIRKAVEDAKKNLIEVPMVGTTIPHEIIGRFGAGNILLKPASEGTGVIAGGPVRAVLELAGVADILSKSLGSNTPINMIRATLQGLSELKRAEDVAKLRGKSVEELLG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	166 (155)
Sequences:	2374 (1053)
Seq/√Len:	84.6

ECOLI - RS5
BACSU - RS5
HALSA - RS5
SULSO - RS5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
12_E	42_K	3.686	1.00
142_Q	146_E	3.201	1.00
41_D	45_H	2.917	1.00
100_S	124_L	2.839	1.00
37_V	63_A	2.834	1.00
87_G	142_Q	2.709	1.00
24_V	31_F	2.616	1.00
148_K	156_L	2.548	1.00
79_T	122_D	2.396	1.00
142_Q	145_S	2.155	1.00
12_E	117_L	2.142	1.00
48_F	137_I	2.137	1.00
115_L	120_V	2.016	1.00
58_E	61_R	2.007	1.00
34_A	50_T	1.992	1.00
24_V	29_R	1.956	1.00
48_F	141_L	1.920	1.00
76_M	120_V	1.903	1.00
81_I	96_L	1.874	1.00
81_I	123_I	1.862	1.00
81_I	147_L	1.844	1.00
84_E	98_P	1.840	1.00
48_F	138_R	1.799	1.00
101_E	122_D	1.797	1.00
45_H	71_L	1.789	1.00
64_V	68_K	1.738	1.00
16_V	137_I	1.736	1.00
19_N	34_A	1.714	1.00
115_L	123_I	1.689	1.00
11_L	45_H	1.681	1.00
103_T	124_L	1.647	1.00
33_F	56_V	1.620	1.00
50_T	134_I	1.606	1.00
111_V	125_S	1.593	1.00
79_T	121_A	1.582	1.00
25_V	30_R	1.566	1.00
86_I	93_N	1.566	1.00
149_R	152_D	1.543	1.00
45_H	73_E	1.519	1.00
9_L	45_H	1.510	0.99
84_E	97_K	1.477	0.99
85_I	146_E	1.471	0.99
35_A	59_A	1.457	0.99
66_D	70_N	1.370	0.99
95_L	128_L	1.366	0.99
111_V	115_L	1.346	0.99
82_P	147_L	1.338	0.99
20_R	31_F	1.335	0.99
127_S	136_M	1.329	0.99
99_A	103_T	1.316	0.99
88_R	93_N	1.305	0.99
15_L	18_V	1.286	0.98
92_G	127_S	1.283	0.98
72_I	145_S	1.278	0.98
21_V	32_R	1.273	0.98
61_R	65_E	1.272	0.98
85_I	96_L	1.268	0.98
43_N	76_M	1.238	0.98
76_M	79_T	1.222	0.98
22_A	31_F	1.193	0.97
49_G	66_D	1.189	0.97
13_E	64_V	1.178	0.97
15_L	37_V	1.160	0.97
86_I	95_L	1.149	0.97
72_I	141_L	1.144	0.97
96_L	143_G	1.130	0.96
152_D	155_K	1.125	0.96
150_A	161_V	1.114	0.96
80_T	122_D	1.108	0.96
134_I	138_R	1.068	0.95
15_L	35_A	1.064	0.95
38_V	114_V	1.060	0.95
11_L	71_L	1.056	0.95
17_T	34_A	1.038	0.94
127_S	131_N	1.008	0.93
87_G	92_G	0.970	0.92
32_R	54_Q	0.961	0.91
114_V	137_I	0.955	0.91
74_V	118_A	0.951	0.91
85_I	147_L	0.942	0.90
77_V	150_A	0.924	0.90
96_L	140_T	0.919	0.89
50_T	132_T	0.914	0.89
30_R	54_Q	0.908	0.89
89_F	138_R	0.905	0.89
156_L	159_K	0.900	0.88
8_K	11_L	0.893	0.88
46_V	141_L	0.893	0.88
77_V	80_T	0.884	0.87
75_P	82_P	0.880	0.87
50_T	63_A	0.874	0.87
11_L	39_V	0.870	0.87
110_P	137_I	0.867	0.86
18_V	57_P	0.864	0.86
152_D	156_L	0.861	0.86
38_V	117_L	0.854	0.86
46_V	118_A	0.851	0.85
82_P	150_A	0.848	0.85
56_V	60_I	0.826	0.84
151_E	155_K	0.821	0.83
114_V	140_T	0.819	0.83
32_R	124_L	0.817	0.83
16_V	38_V	0.817	0.83
92_G	130_S	0.815	0.83
92_G	128_L	0.815	0.83
11_L	43_N	0.812	0.83
110_P	136_M	0.808	0.82
14_R	133_P	0.804	0.82
105_V	115_L	0.801	0.82
15_L	60_I	0.801	0.82
38_V	137_I	0.801	0.82
18_V	55_E	0.800	0.82
103_T	106_I	0.796	0.81
135_N	138_R	0.792	0.81
44_G	76_M	0.791	0.81
35_A	56_V	0.791	0.81
37_V	64_V	0.787	0.81
52_K	62_K	0.787	0.81
76_M	122_D	0.786	0.81
140_T	144_L	0.779	0.80
154_A	161_V	0.775	0.80
89_F	142_Q	0.771	0.79
39_V	67_A	0.769	0.79
51_G	66_D	0.767	0.79
46_V	72_I	0.762	0.78
18_V	56_V	0.762	0.78
22_A	30_R	0.761	0.78
107_A	126_K	0.760	0.78
94_I	139_A	0.755	0.78
96_L	125_S	0.747	0.77
92_G	131_N	0.733	0.76
18_V	35_A	0.732	0.76
14_R	117_L	0.732	0.76
42_K	116_E	0.726	0.75
28_G	40_G	0.721	0.75
87_G	139_A	0.718	0.74
110_P	114_V	0.718	0.74
74_V	120_V	0.716	0.74
36_L	134_I	0.709	0.73
73_E	76_M	0.707	0.73
29_R	135_N	0.706	0.73
35_A	60_I	0.698	0.72
92_G	136_M	0.698	0.72
20_R	27_G	0.696	0.72
49_G	70_N	0.696	0.72
24_V	27_G	0.689	0.71
9_L	68_K	0.688	0.71
154_A	159_K	0.686	0.71
42_K	117_L	0.681	0.70
93_N	129_G	0.679	0.70
104_G	119_G	0.676	0.70
10_E	18_V	0.675	0.70
106_I	132_T	0.673	0.69
20_R	33_F	0.669	0.69
107_A	125_S	0.667	0.69
148_K	152_D	0.667	0.69
53_A	103_T	0.665	0.68
72_I	75_P	0.663	0.68
79_T	101_E	0.662	0.68
105_V	137_I	0.660	0.68
51_G	62_K	0.660	0.68
31_F	34_A	0.659	0.68
78_G	122_D	0.658	0.68
16_V	130_S	0.658	0.68
28_G	104_G	0.655	0.67
10_E	43_N	0.652	0.67
76_M	118_A	0.647	0.66
46_V	73_E	0.642	0.66
17_T	133_P	0.642	0.66
103_T	108_G	0.639	0.65
154_A	158_G	0.639	0.65
19_N	134_I	0.633	0.65
42_K	121_A	0.633	0.65
85_I	143_G	0.627	0.64
91_A	130_S	0.627	0.64
86_I	146_E	0.620	0.63
107_A	123_I	0.614	0.62
46_V	114_V	0.609	0.62
32_R	50_T	0.608	0.62
115_L	125_S	0.607	0.61
22_A	29_R	0.601	0.61
21_V	51_G	0.600	0.61
9_L	71_L	0.596	0.60
113_A	116_E	0.587	0.59
88_R	155_K	0.583	0.58
41_D	71_L	0.580	0.58
115_L	118_A	0.577	0.58
9_L	43_N	0.575	0.57
16_V	49_G	0.573	0.57
12_E	71_L	0.573	0.57
120_V	123_I	0.569	0.57
138_R	145_S	0.568	0.56
93_N	128_L	0.568	0.56
35_A	48_F	0.568	0.56
12_E	66_D	0.565	0.56
111_V	136_M	0.561	0.55
50_T	138_R	0.561	0.55
29_R	65_E	0.560	0.55
22_A	25_V	0.557	0.55
8_K	158_G	0.556	0.55
51_G	59_A	0.555	0.55
50_T	58_E	0.555	0.55
55_E	80_T	0.545	0.53
151_E	158_G	0.542	0.53
19_N	50_T	0.541	0.53
68_K	147_L	0.541	0.53
73_E	78_G	0.540	0.53
129_G	156_L	0.540	0.53
44_G	119_G	0.538	0.52
14_R	113_A	0.538	0.52
114_V	141_L	0.537	0.52
30_R	56_V	0.535	0.52
52_K	126_K	0.533	0.52
28_G	102_G	0.531	0.52
94_I	111_V	0.530	0.51
16_V	48_F	0.528	0.51
15_L	63_A	0.527	0.51
150_A	154_A	0.525	0.51
17_T	134_I	0.525	0.51
31_F	54_Q	0.524	0.51
69_K	132_T	0.524	0.51
59_A	121_A	0.522	0.50
51_G	63_A	0.521	0.50
71_L	141_L	0.520	0.50
44_G	115_L	0.518	0.50
53_A	59_A	0.517	0.50
87_G	94_I	0.517	0.50
116_E	126_K	0.514	0.49
88_R	142_Q	0.511	0.49
106_I	124_L	0.508	0.48
106_I	116_E	0.500	0.47
48_F	89_F	0.500	0.47

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
4kiyE	1	0.9036	100	0.038	Contact Map
4rb5E	1	0.8916	100	0.048	Contact Map
3bbnE	1	0.9458	100	0.055	Contact Map
5aj3E	1	1	100	0.062	Contact Map
4tp8E	1	0.9036	100	0.089	Contact Map
1pkpA	2	0.8735	100	0.115	Contact Map
3j20F	1	0.9217	100	0.119	Contact Map
4kzyC	1	1	100	0.16	Contact Map
3j80C	1	1	100	0.16	Contact Map
3zeyP	1	1	100	0.16	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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