RS3 - BACSU - GREMLIN Contacts

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RS3 - 30S ribosomal protein S3

UniProt:	P21465	Sequences: MGQKVNPVGLRIGVIRDWESKWYAGKDYADFLHEDLKIREYISKRLSDASVSKVEIERAANRVNITIHTAKPGMVIGKGGSEVEALRKALNSLTGKRVHINILEIKRADLDAQLVADNIARQLENRVSFRRAQKQQIQRTMRAGAQGVKTMVSGRLGGADIARSEYYSEGTVPLHTLRADIDYATSEADTTYGKLGVKVWIYRGEVLPTKKKNEEGGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	218 (208)
Sequences:	2445 (1148)
Seq/√Len:	79.6

ECOLI - RS3
BACSU - RS3
HALSA - RS3
SULSO - RS3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
52_S	111_D	5.570	1.00
115_V	201_I	4.476	1.00
189_D	194_K	4.101	1.00
187_E	194_K	3.962	1.00
45_R	89_A	3.476	1.00
110_L	145_A	3.264	1.00
82_E	85_A	2.981	1.00
66_T	101_N	2.892	1.00
43_S	113_Q	2.715	1.00
140_T	148_V	2.685	1.00
135_Q	139_R	2.664	1.00
124_E	188_A	2.490	1.00
202_Y	205_E	2.417	1.00
127_V	132_A	2.256	1.00
151_M	164_S	2.193	1.00
113_Q	117_D	2.121	1.00
112_A	182_D	2.087	1.00
69_T	75_V	1.973	1.00
16_R	19_E	1.953	1.00
171_T	202_Y	1.945	1.00
119_I	150_T	1.906	1.00
117_D	186_S	1.836	1.00
27_D	30_D	1.817	1.00
46_L	75_V	1.795	1.00
123_L	129_F	1.743	1.00
8_V	19_E	1.740	1.00
21_K	55_E	1.729	1.00
19_E	53_K	1.726	1.00
179_A	202_Y	1.711	1.00
53_K	68_H	1.704	1.00
119_I	132_A	1.699	1.00
8_V	16_R	1.672	1.00
28_Y	32_L	1.664	1.00
68_H	103_L	1.629	1.00
113_Q	185_T	1.621	1.00
16_R	180_D	1.579	1.00
43_S	117_D	1.573	1.00
46_L	86_L	1.571	1.00
113_Q	186_S	1.551	0.99
151_M	166_Y	1.551	0.99
146_Q	171_T	1.542	0.99
113_Q	184_A	1.537	0.99
10_L	14_V	1.521	0.99
33_H	37_K	1.515	0.99
180_D	203_R	1.503	0.99
17_D	21_K	1.487	0.99
153_S	164_S	1.468	0.99
37_K	93_L	1.455	0.99
133_Q	167_Y	1.436	0.99
116_A	186_S	1.433	0.99
119_I	136_Q	1.432	0.99
15_I	206_V	1.429	0.99
34_E	96_K	1.414	0.99
41_Y	89_A	1.401	0.99
21_K	57_E	1.348	0.99
168_S	171_T	1.328	0.98
110_L	140_T	1.322	0.98
84_E	88_K	1.322	0.98
10_L	177_L	1.316	0.98
168_S	172_V	1.311	0.98
33_H	36_L	1.307	0.98
152_V	195_L	1.304	0.98
85_A	88_K	1.298	0.98
50_S	69_T	1.295	0.98
18_W	21_K	1.276	0.98
28_Y	33_H	1.272	0.98
91_N	97_R	1.263	0.98
166_Y	171_T	1.261	0.98
129_F	156_L	1.259	0.98
32_L	36_L	1.258	0.98
63_V	96_K	1.254	0.98
85_A	89_A	1.226	0.97
137_I	150_T	1.225	0.97
44_K	47_S	1.210	0.97
134_K	157_G	1.204	0.97
10_L	15_I	1.203	0.97
42_I	51_V	1.195	0.97
62_R	97_R	1.194	0.97
118_N	121_R	1.193	0.97
79_G	135_Q	1.187	0.97
49_A	69_T	1.175	0.96
137_I	148_V	1.161	0.96
149_K	174_L	1.145	0.96
42_I	54_V	1.138	0.96
123_L	195_L	1.133	0.96
73_G	104_E	1.131	0.96
14_V	177_L	1.117	0.95
57_E	64_N	1.112	0.95
115_V	136_Q	1.108	0.95
173_P	179_A	1.102	0.95
88_K	92_S	1.101	0.95
37_K	40_E	1.100	0.95
121_R	125_N	1.096	0.95
6_N	10_L	1.094	0.95
88_K	91_N	1.092	0.95
66_T	103_L	1.083	0.94
116_A	199_V	1.077	0.94
8_V	12_I	1.074	0.94
116_A	197_V	1.067	0.94
45_R	85_A	1.064	0.94
133_Q	152_V	1.058	0.94
43_S	47_S	1.024	0.93
49_A	74_M	1.022	0.92
29_A	33_H	1.011	0.92
53_K	111_D	1.006	0.92
117_D	121_R	0.990	0.91
128_S	157_G	0.976	0.91
36_L	40_E	0.971	0.90
65_I	100_I	0.971	0.90
77_G	80_G	0.970	0.90
115_V	140_T	0.963	0.90
120_A	186_S	0.957	0.90
138_Q	169_E	0.948	0.89
9_G	13_G	0.943	0.89
120_A	197_V	0.942	0.89
72_P	76_I	0.937	0.89
42_I	46_L	0.929	0.88
41_Y	90_L	0.913	0.88
15_I	19_E	0.907	0.87
7_P	11_R	0.900	0.87
73_G	77_G	0.899	0.87
123_L	165_E	0.898	0.87
62_R	99_H	0.898	0.87
90_L	98_V	0.897	0.87
5_V	10_L	0.893	0.86
81_S	85_A	0.891	0.86
5_V	101_N	0.884	0.86
153_S	161_I	0.883	0.86
129_F	165_E	0.868	0.85
180_D	206_V	0.863	0.84
94_T	98_V	0.849	0.83
182_D	203_R	0.847	0.83
72_P	77_G	0.842	0.83
173_P	202_Y	0.842	0.83
83_V	94_T	0.841	0.83
73_G	80_G	0.837	0.83
16_R	203_R	0.836	0.82
73_G	76_I	0.832	0.82
150_T	167_Y	0.830	0.82
46_L	51_V	0.824	0.82
44_K	93_L	0.821	0.81
140_T	201_I	0.816	0.81
27_D	31_F	0.806	0.80
139_R	142_R	0.795	0.79
118_N	122_Q	0.792	0.79
110_L	201_I	0.791	0.79
183_Y	200_W	0.789	0.79
127_V	131_R	0.789	0.79
73_G	78_K	0.786	0.78
51_V	67_I	0.786	0.78
172_V	202_Y	0.784	0.78
80_G	104_E	0.783	0.78
156_L	192_Y	0.782	0.78
137_I	167_Y	0.781	0.78
30_D	33_H	0.777	0.78
156_L	195_L	0.775	0.77
12_I	17_D	0.774	0.77
133_Q	184_A	0.770	0.77
179_A	204_G	0.768	0.77
35_D	39_R	0.765	0.77
138_Q	142_R	0.751	0.75
34_E	37_K	0.748	0.75
35_D	56_I	0.747	0.75
193_G	196_G	0.746	0.75
75_V	102_I	0.740	0.74
24_A	31_F	0.739	0.74
109_D	139_R	0.736	0.74
118_N	172_V	0.732	0.73
91_N	99_H	0.728	0.73
76_I	80_G	0.727	0.73
35_D	126_R	0.723	0.72
155_R	192_Y	0.723	0.72
55_E	68_H	0.719	0.72
110_L	203_R	0.717	0.72
79_G	139_R	0.714	0.71
130_R	165_E	0.709	0.71
146_Q	202_Y	0.702	0.70
27_D	79_G	0.701	0.70
19_E	55_E	0.699	0.70
146_Q	204_G	0.692	0.69
107_R	143_A	0.691	0.69
150_T	166_Y	0.690	0.69
71_K	90_L	0.685	0.68
42_I	65_I	0.684	0.68
6_N	171_T	0.681	0.68
4_K	190_T	0.681	0.68
1_M	11_R	0.678	0.67
39_R	56_I	0.676	0.67
135_Q	138_Q	0.674	0.67
129_F	191_T	0.666	0.66
44_K	92_S	0.664	0.66
25_G	100_I	0.662	0.66
129_F	157_G	0.661	0.66
175_H	202_Y	0.661	0.66
55_E	66_T	0.661	0.66
123_L	130_R	0.660	0.65
58_R	112_A	0.659	0.65
25_G	172_V	0.658	0.65
175_H	179_A	0.658	0.65
109_D	143_A	0.655	0.65
3_Q	142_R	0.654	0.65
123_L	136_Q	0.653	0.65
93_L	98_V	0.653	0.65
166_Y	172_V	0.653	0.65
105_I	114_L	0.651	0.64
150_T	197_V	0.650	0.64
110_L	143_A	0.646	0.64
161_I	165_E	0.643	0.63
141_M	145_A	0.641	0.63
71_K	208_P	0.641	0.63
39_R	54_V	0.637	0.63
174_L	200_W	0.636	0.63
41_Y	45_R	0.630	0.62
151_M	168_S	0.630	0.62
174_L	190_T	0.626	0.61
173_P	198_K	0.625	0.61
49_A	72_P	0.625	0.61
183_Y	198_K	0.624	0.61
149_K	155_R	0.624	0.61
12_I	168_S	0.620	0.61
120_A	124_E	0.618	0.60
30_D	96_K	0.617	0.60
1_M	7_P	0.614	0.60
47_S	54_V	0.614	0.60
83_V	102_I	0.612	0.60
55_E	82_E	0.607	0.59
44_K	67_I	0.605	0.59
89_A	197_V	0.605	0.59
140_T	145_A	0.605	0.59
152_V	157_G	0.605	0.59
125_N	161_I	0.605	0.59
163_R	178_R	0.602	0.58
140_T	203_R	0.601	0.58
65_I	95_G	0.600	0.58
40_E	43_S	0.598	0.58
138_Q	208_P	0.598	0.58
145_A	156_L	0.596	0.58
192_Y	195_L	0.595	0.57
1_M	4_K	0.594	0.57
116_A	184_A	0.590	0.57
22_W	35_D	0.588	0.57
137_I	202_Y	0.588	0.57
161_I	164_S	0.587	0.56
155_R	160_D	0.587	0.56
29_A	36_L	0.587	0.56
12_I	15_I	0.586	0.56
57_E	66_T	0.586	0.56
50_S	70_A	0.585	0.56
42_I	67_I	0.583	0.56
134_K	162_A	0.580	0.56
134_K	174_L	0.577	0.55
69_T	156_L	0.577	0.55
109_D	115_V	0.577	0.55
4_K	11_R	0.576	0.55
137_I	169_E	0.574	0.55
133_Q	150_T	0.572	0.55
23_Y	36_L	0.571	0.54
109_D	118_N	0.569	0.54
17_D	201_I	0.569	0.54
71_K	77_G	0.568	0.54
132_A	152_V	0.568	0.54
48_D	107_R	0.567	0.54
15_I	208_P	0.567	0.54
31_F	65_I	0.566	0.54
47_S	124_E	0.565	0.54
40_E	44_K	0.563	0.53
64_N	125_N	0.563	0.53
15_I	18_W	0.563	0.53
151_M	200_W	0.561	0.53
176_T	179_A	0.560	0.53
119_I	199_V	0.557	0.53
126_R	188_A	0.554	0.52
140_T	143_A	0.552	0.52
126_R	163_R	0.551	0.52
51_V	69_T	0.549	0.52
64_N	101_N	0.548	0.51
28_Y	168_S	0.546	0.51
32_L	39_R	0.543	0.51
90_L	93_L	0.543	0.51
129_F	161_I	0.543	0.51
63_V	94_T	0.542	0.51
161_I	166_Y	0.536	0.50
39_R	159_A	0.534	0.50
147_G	154_G	0.534	0.50
107_R	110_L	0.533	0.50
64_N	85_A	0.532	0.49
83_V	101_N	0.530	0.49
4_K	7_P	0.530	0.49
131_R	135_Q	0.528	0.49
12_I	171_T	0.527	0.49
65_I	99_H	0.526	0.49
35_D	58_R	0.526	0.49
84_E	87_R	0.524	0.48
133_Q	181_I	0.522	0.48
110_L	115_V	0.521	0.48
108_A	144_G	0.520	0.48
128_S	161_I	0.519	0.48
59_A	87_R	0.517	0.47
188_A	195_L	0.516	0.47
31_F	96_K	0.516	0.47
38_I	99_H	0.514	0.47
39_R	179_A	0.513	0.47
38_I	41_Y	0.511	0.47
111_D	182_D	0.508	0.46
174_L	181_I	0.508	0.46
134_K	141_M	0.507	0.46
36_L	46_L	0.503	0.46
45_R	60_A	0.503	0.46
111_D	203_R	0.503	0.46
178_R	204_G	0.501	0.45
59_A	62_R	0.500	0.45
90_L	94_T	0.500	0.45

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
4rb5C	1	0.9404	100	0.025	Contact Map
4kiyC	1	0.9404	100	0.032	Contact Map
3bbnC	1	0.9404	100	0.052	Contact Map
4tp8C	1	0.9404	100	0.057	Contact Map
3j20C	1	0.8394	100	0.269	Contact Map
4ujpE	1	0.9083	100	0.289	Contact Map
4w23D	1	0.8991	100	0.293	Contact Map
3j7aD	1	0.6651	100	0.297	Contact Map
3zeyX	1	0.8761	100	0.306	Contact Map
4bpeC	1	0.9128	100	0.307	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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