RS4 - BACSU - GREMLIN Contacts

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RS4 - 30S ribosomal protein S4

UniProt:	P21466	Sequences: MARYTGPSWKLSRRLGISLSGTGKELEKRPYAPGPHGPGQRKKLSEYGLQLQEKQKLRHMYGVNERQFRTLFDKAGKLAGKHGENFMILLDSRLDNVVYKLGLARTRRQARQLVNHGHILVDGSRVDIPSYLVKPGQTIGVREKSRNLSIIKESVEVNNFVPEYLTFDAEKLEGTFTRLPERSELAPEINEALIVEFYSR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	200 (199)
Sequences:	2920 (1408)
Seq/√Len:	99.8

ECOLI - RS4
BACSU - RS4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
122_D	137_Q	4.979	1.00
101_L	174_G	4.345	1.00
121_V	131_Y	3.362	1.00
120_L	140_G	3.329	1.00
117_G	125_R	3.120	1.00
182_R	191_E	3.088	1.00
126_V	131_Y	3.067	1.00
57_L	194_I	2.861	1.00
2_A	64_N	2.608	1.00
109_Q	150_I	2.531	1.00
78_L	85_N	2.514	1.00
53_E	56_K	2.372	1.00
119_I	141_V	2.351	1.00
140_G	173_E	2.307	1.00
92_S	176_F	2.246	1.00
101_L	165_L	2.218	1.00
70_T	74_K	2.207	1.00
105_R	109_Q	2.149	1.00
85_N	88_I	2.108	1.00
74_K	77_K	2.106	1.00
166_T	175_T	2.073	1.00
74_K	132_L	2.069	1.00
31_Y	38_P	2.016	1.00
69_R	73_D	2.000	1.00
15_L	59_H	1.965	1.00
117_G	127_D	1.952	1.00
101_L	167_F	1.935	1.00
178_R	184_E	1.901	1.00
168_D	171_K	1.846	1.00
103_L	167_F	1.801	1.00
44_L	48_G	1.762	1.00
87_M	185_L	1.740	1.00
133_V	139_I	1.634	1.00
15_L	52_Q	1.593	1.00
149_S	153_E	1.587	1.00
80_G	85_N	1.569	1.00
143_E	146_R	1.531	1.00
74_K	78_L	1.529	1.00
197_F	200_R	1.521	1.00
166_T	177_T	1.466	1.00
78_L	89_L	1.423	1.00
18_S	23_G	1.422	1.00
70_T	73_D	1.412	1.00
165_L	176_F	1.392	1.00
88_I	179_L	1.388	0.99
168_D	173_E	1.374	0.99
125_R	142_R	1.351	0.99
118_H	145_S	1.339	0.99
8_S	108_R	1.317	0.99
71_L	132_L	1.302	0.99
11_L	59_H	1.301	0.99
22_T	25_E	1.297	0.99
92_S	132_L	1.294	0.99
63_V	71_L	1.293	0.99
107_R	164_Y	1.281	0.99
146_R	172_L	1.278	0.99
18_S	21_G	1.271	0.99
63_V	90_L	1.268	0.99
152_K	156_E	1.266	0.99
104_A	110_A	1.263	0.99
138_T	173_E	1.258	0.99
92_S	179_L	1.253	0.99
141_V	172_L	1.242	0.99
163_E	178_R	1.240	0.99
151_I	155_V	1.219	0.99
138_T	175_T	1.206	0.99
9_W	12_S	1.192	0.98
74_K	89_L	1.188	0.98
26_L	30_P	1.166	0.98
9_W	18_S	1.160	0.98
44_L	52_Q	1.158	0.98
142_R	145_S	1.150	0.98
12_S	18_S	1.145	0.98
58_R	197_F	1.144	0.98
97_V	133_V	1.132	0.98
71_L	86_F	1.128	0.98
115_N	128_I	1.126	0.98
88_I	92_S	1.123	0.98
18_S	22_T	1.114	0.98
18_S	106_T	1.112	0.98
9_W	21_G	1.110	0.98
33_P	36_H	1.107	0.97
104_A	109_Q	1.083	0.97
87_M	182_R	1.062	0.97
21_G	25_E	1.060	0.97
52_Q	59_H	1.059	0.97
11_L	15_L	1.056	0.97
113_L	119_I	1.054	0.97
26_L	29_R	1.052	0.97
141_V	151_I	1.037	0.96
9_W	23_G	1.032	0.96
17_I	188_E	1.032	0.96
87_M	191_E	1.019	0.96
54_K	65_E	1.011	0.96
15_L	19_L	1.009	0.96
57_L	87_M	1.006	0.96
163_E	184_E	1.000	0.95
64_N	68_F	0.999	0.95
161_V	167_F	0.994	0.95
57_L	189_I	0.993	0.95
4_Y	7_P	0.993	0.95
82_H	195_V	0.993	0.95
31_Y	37_G	0.992	0.95
94_L	121_V	0.988	0.95
89_L	132_L	0.973	0.95
121_V	126_V	0.968	0.95
149_S	152_K	0.964	0.94
86_F	197_F	0.959	0.94
155_V	169_A	0.958	0.94
9_W	106_T	0.957	0.94
9_W	22_T	0.951	0.94
97_V	176_F	0.945	0.94
145_S	148_L	0.943	0.94
65_E	198_Y	0.943	0.94
81_K	195_V	0.935	0.93
19_L	22_T	0.932	0.93
97_V	139_I	0.932	0.93
96_N	107_R	0.925	0.93
9_W	26_L	0.924	0.93
152_K	172_L	0.922	0.93
143_E	147_N	0.915	0.93
139_I	174_G	0.914	0.93
27_E	30_P	0.914	0.93
3_R	6_G	0.910	0.93
97_V	174_G	0.908	0.92
12_S	19_L	0.898	0.92
29_R	32_A	0.886	0.91
151_I	154_S	0.875	0.91
84_E	194_I	0.874	0.91
147_N	152_K	0.873	0.91
33_P	37_G	0.866	0.91
165_L	174_G	0.849	0.90
25_E	106_T	0.841	0.89
12_S	23_G	0.827	0.88
78_L	88_I	0.819	0.88
115_N	127_D	0.818	0.88
15_L	20_S	0.818	0.88
12_S	25_E	0.818	0.88
91_D	100_K	0.817	0.88
60_M	189_I	0.810	0.87
111_R	129_P	0.809	0.87
112_Q	116_H	0.807	0.87
9_W	25_E	0.803	0.87
83_G	87_M	0.798	0.87
191_E	195_V	0.794	0.86
119_I	151_I	0.792	0.86
161_V	169_A	0.779	0.85
150_I	154_S	0.778	0.85
104_A	113_L	0.773	0.85
85_N	89_L	0.772	0.85
50_Q	200_R	0.771	0.85
148_L	172_L	0.765	0.84
84_E	181_E	0.756	0.84
135_P	176_F	0.755	0.83
176_F	179_L	0.749	0.83
26_L	31_Y	0.747	0.83
64_N	197_F	0.745	0.83
4_Y	11_L	0.743	0.82
89_L	92_S	0.738	0.82
190_N	193_L	0.736	0.82
66_R	70_T	0.734	0.82
83_G	191_E	0.734	0.82
94_L	126_V	0.733	0.82
58_R	63_V	0.732	0.82
147_N	153_E	0.731	0.81
72_F	195_V	0.731	0.81
98_V	104_A	0.728	0.81
18_S	24_K	0.728	0.81
18_S	25_E	0.722	0.81
58_R	65_E	0.721	0.81
84_E	183_S	0.720	0.80
94_L	119_I	0.718	0.80
5_T	8_S	0.716	0.80
88_I	181_E	0.714	0.80
92_S	134_K	0.712	0.80
113_L	151_I	0.708	0.79
92_S	133_V	0.705	0.79
20_S	106_T	0.703	0.79
17_I	60_M	0.702	0.79
148_L	151_I	0.696	0.78
83_G	182_R	0.691	0.78
20_S	25_E	0.691	0.78
76_G	82_H	0.690	0.78
19_L	25_E	0.687	0.77
92_S	135_P	0.683	0.77
182_R	193_L	0.683	0.77
155_V	167_F	0.682	0.77
98_V	114_V	0.682	0.77
148_L	153_E	0.682	0.77
50_Q	197_F	0.679	0.76
192_A	197_F	0.678	0.76
119_I	140_G	0.678	0.76
135_P	179_L	0.676	0.76
8_S	21_G	0.675	0.76
72_F	86_F	0.675	0.76
27_E	32_A	0.673	0.76
189_I	193_L	0.669	0.75
153_E	157_V	0.668	0.75
4_Y	10_K	0.667	0.75
113_L	118_H	0.664	0.75
94_L	133_V	0.663	0.75
17_I	26_L	0.659	0.74
153_E	156_E	0.652	0.73
48_G	52_Q	0.652	0.73
15_L	22_T	0.649	0.73
148_L	154_S	0.648	0.73
68_F	194_I	0.644	0.73
68_F	107_R	0.643	0.72
115_N	129_P	0.642	0.72
178_R	181_E	0.642	0.72
34_G	37_G	0.641	0.72
9_W	15_L	0.638	0.72
11_L	19_L	0.636	0.72
17_I	21_G	0.636	0.72
84_E	191_E	0.636	0.72
12_S	20_S	0.635	0.72
164_Y	176_F	0.634	0.71
152_K	155_V	0.629	0.71
131_Y	137_Q	0.629	0.71
19_L	59_H	0.627	0.71
13_R	34_G	0.626	0.70
29_R	33_P	0.624	0.70
9_W	19_L	0.624	0.70
12_S	22_T	0.619	0.70
51_L	55_Q	0.618	0.69
15_L	21_G	0.615	0.69
180_P	184_E	0.615	0.69
68_F	76_G	0.614	0.69
46_E	49_L	0.611	0.69
96_N	164_Y	0.611	0.69
101_L	133_V	0.609	0.68
98_V	138_T	0.603	0.68
11_L	106_T	0.603	0.68
8_S	11_L	0.601	0.67
60_M	185_L	0.601	0.67
98_V	119_I	0.597	0.67
49_L	193_L	0.594	0.66
114_V	123_G	0.593	0.66
125_R	178_R	0.593	0.66
22_T	59_H	0.588	0.66
62_G	108_R	0.587	0.66
182_R	185_L	0.586	0.65
9_W	20_S	0.584	0.65
31_Y	35_P	0.579	0.64
80_G	83_G	0.577	0.64
66_R	74_K	0.576	0.64
82_H	85_N	0.575	0.64
11_L	22_T	0.568	0.63
120_L	142_R	0.568	0.63
133_V	137_Q	0.565	0.63
81_K	84_E	0.562	0.62
99_Y	128_I	0.562	0.62
138_T	141_V	0.562	0.62
145_S	151_I	0.560	0.62
47_Y	197_F	0.558	0.62
136_G	175_T	0.555	0.61
32_A	36_H	0.555	0.61
141_V	145_S	0.555	0.61
9_W	59_H	0.552	0.61
134_K	139_I	0.550	0.61
183_S	186_A	0.549	0.60
49_L	190_N	0.548	0.60
32_A	41_R	0.548	0.60
136_G	166_T	0.545	0.60
136_G	178_R	0.544	0.60
58_R	86_F	0.541	0.59
28_K	33_P	0.540	0.59
119_I	145_S	0.538	0.59
161_V	165_L	0.537	0.59
118_H	148_L	0.536	0.59
57_L	60_M	0.534	0.58
83_G	195_V	0.534	0.58
92_S	97_V	0.532	0.58
59_H	164_Y	0.531	0.58
2_A	6_G	0.525	0.57
3_R	14_R	0.523	0.57
77_K	89_L	0.521	0.56
123_G	140_G	0.517	0.56
70_T	89_L	0.517	0.56
94_L	131_Y	0.517	0.56
140_G	146_R	0.516	0.56
18_S	26_L	0.515	0.56
57_L	187_P	0.514	0.55
123_G	143_E	0.514	0.55
58_R	81_K	0.514	0.55
15_L	18_S	0.514	0.55
29_R	36_H	0.514	0.55
21_G	24_K	0.512	0.55
19_L	27_E	0.509	0.55
109_Q	154_S	0.507	0.54
55_Q	65_E	0.505	0.54
10_K	34_G	0.505	0.54
32_A	37_G	0.504	0.54
120_L	124_S	0.503	0.54
12_S	106_T	0.503	0.54
49_L	52_Q	0.502	0.54
78_L	92_S	0.500	0.53
19_L	24_K	0.500	0.53

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
3bbnD	1	0.98	100	0.254	Contact Map
4tp8D	1	0.98	100	0.258	Contact Map
4rb5D	1	0.995	100	0.287	Contact Map
1c05A	1	0.795	100	0.455	Contact Map
3j20E	1	0.73	99.9	0.627	Contact Map
3j38J	1	0.755	99.9	0.675	Contact Map
3kbgA	2	0.535	99.9	0.68	Contact Map
4bpeD	2	0.675	99.9	0.69	Contact Map
3j80J	1	0.705	99.8	0.718	Contact Map
4ujpK	1	0.715	99.8	0.72	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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