RS3 - ECOLI - GREMLIN Contacts

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RS3 - 30S ribosomal protein S3

UniProt:	P0A7V3	Sequences: MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10902
Length:	233 (210)
Sequences:	2528 (1162)
Seq/√Len:	80.2

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
53_S	112_D	5.515	1.00
116_V	202_I	4.584	1.00
190_H	195_V	3.992	1.00
188_E	195_V	3.891	1.00
46_E	90_V	3.575	1.00
111_L	146_A	3.343	1.00
83_D	86_K	2.969	1.00
44_T	114_K	2.828	1.00
67_T	102_N	2.823	1.00
141_A	149_I	2.712	1.00
125_E	189_A	2.612	1.00
136_R	140_N	2.595	1.00
128_V	133_A	2.414	1.00
203_F	206_E	2.390	1.00
152_E	165_T	2.258	1.00
113_A	183_D	2.186	1.00
70_T	76_V	2.147	1.00
114_K	118_D	2.042	1.00
172_R	203_F	1.991	1.00
16_K	19_N	1.917	1.00
120_I	151_V	1.910	1.00
47_L	76_V	1.890	1.00
19_N	54_R	1.862	1.00
124_L	130_F	1.850	1.00
118_D	187_S	1.813	1.00
8_N	19_N	1.764	1.00
21_T	56_V	1.736	1.00
28_E	31_D	1.735	1.00
54_R	69_H	1.701	1.00
180_A	203_F	1.695	1.00
8_N	16_K	1.668	1.00
69_H	104_A	1.647	1.00
44_T	118_D	1.617	1.00
120_I	133_A	1.610	1.00
10_I	14_I	1.596	1.00
16_K	181_D	1.588	1.00
114_K	186_T	1.587	1.00
114_K	187_S	1.586	1.00
34_D	38_K	1.582	1.00
29_F	33_L	1.581	1.00
114_K	185_N	1.581	1.00
35_S	97_V	1.561	1.00
147_K	172_R	1.545	0.99
152_E	167_W	1.536	0.99
38_K	94_I	1.523	0.99
181_D	204_K	1.478	0.99
17_P	21_T	1.429	0.99
117_A	187_S	1.422	0.99
169_R	173_V	1.420	0.99
134_M	168_Y	1.398	0.99
111_L	141_A	1.384	0.99
34_D	37_F	1.382	0.99
21_T	58_E	1.378	0.99
47_L	87_L	1.376	0.99
42_Y	90_V	1.374	0.99
120_I	137_A	1.371	0.99
86_K	89_K	1.361	0.99
169_R	172_R	1.356	0.99
15_V	207_I	1.352	0.99
130_F	157_L	1.323	0.98
154_S	165_T	1.315	0.98
85_E	89_K	1.314	0.98
10_I	178_L	1.304	0.98
124_L	196_I	1.282	0.98
153_V	196_I	1.253	0.98
18_W	21_T	1.240	0.97
50_A	75_I	1.233	0.97
25_N	28_E	1.221	0.97
29_F	34_D	1.220	0.97
117_A	200_V	1.214	0.97
138_V	151_V	1.213	0.97
119_S	122_S	1.200	0.97
64_I	97_V	1.195	0.97
117_A	198_V	1.195	0.97
43_L	52_V	1.193	0.97
167_W	172_R	1.185	0.97
51_S	70_T	1.183	0.97
135_K	158_G	1.183	0.97
86_K	90_V	1.178	0.97
74_G	105_E	1.174	0.97
78_G	81_G	1.172	0.96
138_V	149_I	1.171	0.96
58_E	65_R	1.164	0.96
89_K	92_A	1.157	0.96
63_S	98_P	1.157	0.96
33_L	37_F	1.147	0.96
150_K	175_L	1.140	0.96
67_T	104_A	1.129	0.96
10_I	15_V	1.129	0.96
80_K	136_R	1.125	0.96
30_A	34_D	1.106	0.95
89_K	93_D	1.102	0.95
116_V	137_A	1.102	0.95
38_K	41_Q	1.101	0.95
14_I	178_L	1.098	0.95
8_N	12_L	1.095	0.95
6_H	10_I	1.095	0.95
134_M	153_V	1.067	0.94
46_E	86_K	1.065	0.94
174_P	180_A	1.062	0.94
92_A	98_P	1.057	0.94
37_F	41_Q	1.044	0.93
44_T	48_A	1.043	0.93
91_V	99_A	1.040	0.93
118_D	122_S	1.021	0.93
73_P	77_I	1.020	0.93
5_V	102_N	1.013	0.92
121_T	187_S	1.006	0.92
43_L	55_I	0.989	0.91
122_S	126_R	0.984	0.91
154_S	162_I	0.983	0.91
95_A	99_A	0.980	0.91
54_R	112_D	0.979	0.91
43_L	47_L	0.975	0.91
121_T	198_V	0.974	0.91
15_V	19_N	0.964	0.90
116_V	141_A	0.963	0.90
9_G	13_G	0.956	0.90
108_K	144_L	0.952	0.90
151_V	168_Y	0.948	0.90
139_Q	170_E	0.928	0.89
129_M	158_G	0.925	0.88
130_F	166_E	0.922	0.88
157_L	196_I	0.920	0.88
84_V	95_A	0.920	0.88
52_V	68_I	0.918	0.88
76_V	103_I	0.915	0.88
16_K	204_K	0.910	0.88
66_V	101_I	0.900	0.87
82_E	86_K	0.881	0.86
124_L	166_E	0.874	0.85
63_S	100_Q	0.867	0.85
77_I	81_G	0.865	0.85
157_L	193_Y	0.861	0.84
7_P	11_R	0.859	0.84
5_V	10_I	0.857	0.84
50_A	70_T	0.851	0.84
141_A	202_I	0.850	0.84
47_L	52_V	0.847	0.84
36_D	40_R	0.836	0.83
80_K	140_N	0.834	0.83
181_D	207_I	0.831	0.82
119_S	123_Q	0.824	0.82
174_P	203_F	0.819	0.81
173_V	203_F	0.799	0.80
56_V	69_H	0.798	0.80
42_Y	91_V	0.794	0.79
74_G	77_I	0.784	0.78
111_L	202_I	0.781	0.78
51_S	71_A	0.780	0.78
36_D	57_I	0.779	0.78
84_V	103_I	0.778	0.78
59_R	113_A	0.777	0.78
48_A	125_E	0.774	0.78
134_M	185_N	0.771	0.77
183_D	204_K	0.762	0.77
92_A	100_Q	0.758	0.76
4_K	191_T	0.754	0.76
24_A	32_N	0.748	0.75
41_Q	45_K	0.746	0.75
140_N	143_R	0.746	0.75
43_L	66_V	0.742	0.75
184_Y	201_W	0.742	0.75
74_G	78_G	0.742	0.75
180_A	205_G	0.741	0.74
74_G	81_G	0.739	0.74
35_S	38_K	0.738	0.74
111_L	204_K	0.737	0.74
73_P	78_G	0.737	0.74
22_W	36_D	0.734	0.74
130_F	192_T	0.731	0.73
119_S	173_V	0.729	0.73
74_G	79_K	0.729	0.73
151_V	167_W	0.724	0.73
45_K	48_A	0.723	0.73
194_G	197_G	0.721	0.72
36_D	127_R	0.718	0.72
40_R	57_I	0.713	0.72
81_G	105_E	0.711	0.71
156_R	193_Y	0.709	0.71
72_R	91_V	0.704	0.71
138_V	168_Y	0.699	0.70
147_K	205_G	0.690	0.69
12_L	17_P	0.690	0.69
42_Y	46_E	0.685	0.69
28_E	32_N	0.682	0.68
40_R	55_I	0.682	0.68
138_V	170_E	0.681	0.68
142_M	146_A	0.681	0.68
108_K	111_L	0.676	0.68
139_Q	143_R	0.674	0.67
176_H	203_F	0.673	0.67
17_P	202_I	0.673	0.67
47_L	68_I	0.673	0.67
130_F	158_G	0.670	0.67
162_I	166_E	0.668	0.67
134_M	151_V	0.664	0.66
35_S	95_A	0.662	0.66
56_V	67_T	0.659	0.66
110_E	140_N	0.654	0.65
106_V	115_L	0.654	0.65
147_K	203_F	0.653	0.65
64_I	136_R	0.648	0.64
167_W	173_V	0.639	0.63
109_P	145_G	0.638	0.63
138_V	203_F	0.637	0.63
164_R	179_R	0.634	0.63
60_P	136_R	0.630	0.62
19_N	56_V	0.625	0.62
3_Q	143_R	0.623	0.61
28_E	80_K	0.619	0.61
146_A	157_L	0.618	0.61
162_I	165_T	0.617	0.61
124_L	137_A	0.616	0.60
65_R	126_R	0.616	0.60
156_R	161_E	0.616	0.60
6_H	172_R	0.612	0.60
25_N	101_I	0.612	0.60
135_K	163_A	0.611	0.60
31_D	34_D	0.611	0.60
48_A	55_I	0.610	0.60
65_R	207_I	0.608	0.59
136_R	139_Q	0.608	0.59
110_E	144_L	0.608	0.59
45_K	94_I	0.607	0.59
1_M	4_K	0.606	0.59
79_K	83_D	0.604	0.59
127_R	189_A	0.603	0.59
126_R	162_I	0.601	0.59
151_V	198_V	0.601	0.59
45_K	93_D	0.601	0.59
25_N	98_P	0.600	0.58
175_L	201_W	0.599	0.58
124_L	131_R	0.599	0.58
12_L	169_R	0.597	0.58
131_R	166_E	0.595	0.58
72_R	209_G	0.594	0.58
72_R	110_E	0.594	0.58
193_Y	196_I	0.593	0.58
70_T	157_L	0.593	0.58
121_T	125_E	0.593	0.58
128_V	132_R	0.593	0.58
30_A	37_F	0.592	0.57
27_K	89_K	0.590	0.57
32_N	35_S	0.589	0.57
72_R	78_G	0.589	0.57
1_M	7_P	0.588	0.57
134_M	182_I	0.588	0.57
25_N	173_V	0.586	0.57
141_A	146_A	0.584	0.56
110_E	119_S	0.583	0.56
153_V	158_G	0.579	0.56
148_G	155_G	0.578	0.56
56_V	83_D	0.578	0.56
33_L	40_R	0.575	0.55
90_V	198_V	0.573	0.55
1_M	11_R	0.571	0.55
127_R	164_R	0.571	0.55
58_E	67_T	0.569	0.54
175_L	191_T	0.569	0.54
154_S	199_K	0.568	0.54
176_H	180_A	0.568	0.54
60_P	88_R	0.564	0.54
161_E	200_V	0.563	0.54
174_P	199_K	0.563	0.54
47_L	50_A	0.561	0.53
184_Y	199_K	0.561	0.53
66_V	96_G	0.559	0.53
135_K	175_L	0.559	0.53
110_E	116_V	0.559	0.53
4_K	11_R	0.554	0.53
17_P	210_G	0.550	0.52
40_R	180_A	0.550	0.52
179_R	205_G	0.546	0.51
49_K	108_K	0.545	0.51
47_L	150_K	0.545	0.51
57_I	117_A	0.543	0.51
52_V	70_T	0.542	0.51
162_I	167_W	0.542	0.51
64_I	95_A	0.539	0.51
152_E	169_R	0.538	0.50
39_V	100_Q	0.534	0.50
12_L	15_V	0.533	0.50
23_F	37_F	0.533	0.50
120_I	200_V	0.529	0.49
62_K	210_G	0.528	0.49
65_R	102_N	0.528	0.49
4_K	7_P	0.527	0.49
51_S	106_V	0.527	0.49
111_L	116_V	0.525	0.49
82_E	88_R	0.522	0.48
141_A	204_K	0.521	0.48
49_K	83_D	0.520	0.48
146_A	168_Y	0.520	0.48
156_R	201_W	0.520	0.48
29_F	37_F	0.520	0.48
60_P	63_S	0.519	0.48
43_L	68_I	0.517	0.48
18_W	107_R	0.517	0.48
150_K	156_R	0.516	0.48
61_A	100_Q	0.515	0.47
163_A	196_I	0.514	0.47
43_L	132_R	0.511	0.47
32_N	211_M	0.507	0.46
129_M	132_R	0.506	0.46
121_T	189_A	0.506	0.46
83_D	136_R	0.505	0.46
139_Q	209_G	0.504	0.46
70_T	105_E	0.503	0.46
177_T	180_A	0.502	0.46
112_D	183_D	0.502	0.46
111_L	144_L	0.502	0.46
61_A	80_K	0.501	0.46
161_E	164_R	0.500	0.46
98_P	104_A	0.500	0.46

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	0.8841	100	0.033	Contact Map
4kiyC	1	0.8841	100	0.033	Contact Map
3bbnC	1	0.8841	100	0.067	Contact Map
4tp8C	1	0.8841	100	0.072	Contact Map
3j20C	1	0.7854	100	0.259	Contact Map
4ujpE	1	0.897	100	0.287	Contact Map
3zeyX	1	0.8326	100	0.299	Contact Map
4w23D	1	0.9013	100	0.299	Contact Map
3j7aD	1	0.6438	100	0.305	Contact Map
4bpeC	1	0.8927	100	0.318	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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