RS5 - SULSO - GREMLIN Contacts

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RS5 - 30S ribosomal protein S5

UniProt:	Q9UX87	Sequences: MAEEVPSLNIEEWKPRTSIGSLVKEGKISSIKELFDRNLPITEPEIVDVLLPKLKYEVVDIKVVQKQTDAGEISRYKVLVIMGNMDGYVSIGTGKAKQLRVAIQKAIRDAKMNIIPVRRGCGSWQCTCGEPHSLPFKVVGKAGSVEVDLLPAPKGTGLVVGSVLKTLLTYAGIKDAWSTTKGETRTTENFVRAGYSALYNTYKFVTLQDWVRKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	214 (170)
Sequences:	959 (463)
Seq/√Len:	35.5

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
55_K	85_M	3.580	1.00
59_V	191_V	3.558	1.00
84_N	88_Y	3.446	1.00
76_Y	99_L	3.404	1.00
119_R	173_I	3.325	1.00
164_L	178_S	2.776	1.00
196_S	200_N	2.748	1.00
154_K	175_D	2.689	1.00
153_P	177_W	2.600	1.00
80_V	106_A	2.568	1.00
58_V	61_I	2.562	1.00
134_L	201_T	2.522	1.00
137_K	151_P	2.495	1.00
67_Q	72_E	2.475	1.00
67_Q	74_S	2.355	0.99
81_I	167_L	2.335	0.99
55_K	170_Y	2.252	0.99
91_I	192_R	2.176	0.99
67_Q	70_A	2.090	0.99
152_A	156_T	2.060	0.99
202_Y	210_W	2.048	0.99
196_S	199_Y	2.007	0.98
93_T	188_E	2.003	0.98
62_K	77_K	1.866	0.97
149_L	197_A	1.861	0.97
135_P	201_T	1.736	0.96
158_L	168_L	1.706	0.95
43_E	46_I	1.703	0.95
58_V	80_V	1.703	0.95
81_I	166_T	1.703	0.95
168_L	176_A	1.655	0.95
137_K	150_L	1.642	0.94
63_V	74_S	1.606	0.94
113_N	178_S	1.550	0.92
132_H	175_D	1.524	0.92
43_E	50_L	1.504	0.91
94_G	105_K	1.480	0.91
163_V	190_F	1.476	0.91
208_Q	212_R	1.473	0.90
107_I	111_K	1.461	0.90
53_K	86_D	1.395	0.88
101_V	104_Q	1.381	0.87
87_G	95_K	1.375	0.87
106_A	172_G	1.371	0.87
91_I	191_V	1.354	0.86
140_G	196_S	1.294	0.84
43_E	132_H	1.285	0.83
90_S	155_G	1.276	0.83
86_D	119_R	1.249	0.81
138_V	201_T	1.249	0.81
119_R	195_Y	1.248	0.81
116_P	176_A	1.236	0.81
139_V	146_E	1.232	0.80
66_K	156_T	1.201	0.79
87_G	119_R	1.183	0.78
160_V	178_S	1.180	0.77
156_T	161_G	1.170	0.77
187_T	191_V	1.163	0.76
133_S	175_D	1.156	0.76
33_E	36_D	1.156	0.76
62_K	187_T	1.148	0.75
42_T	45_E	1.139	0.75
109_D	113_N	1.137	0.75
47_V	54_L	1.132	0.74
98_Q	133_S	1.120	0.74
202_Y	206_T	1.096	0.72
42_T	46_I	1.095	0.72
207_L	210_W	1.088	0.71
77_K	91_I	1.068	0.70
119_R	175_D	1.067	0.70
94_G	102_A	1.065	0.70
74_S	77_K	1.062	0.70
41_I	46_I	1.061	0.69
77_K	93_T	1.058	0.69
156_T	163_V	1.056	0.69
95_K	105_K	1.042	0.68
34_L	37_R	1.041	0.68
147_V	193_A	1.035	0.68
192_R	199_Y	1.033	0.67
41_I	45_E	1.029	0.67
41_I	47_V	1.026	0.67
36_D	147_V	1.021	0.66
62_K	108_R	0.995	0.64
72_E	150_L	0.981	0.63
71_G	83_G	0.973	0.63
80_V	102_A	0.968	0.62
81_I	170_Y	0.967	0.62
142_A	192_R	0.964	0.62
134_L	149_L	0.958	0.61
188_E	192_R	0.957	0.61
92_G	109_D	0.949	0.61
82_M	155_G	0.937	0.60
85_M	169_T	0.937	0.60
64_V	75_R	0.935	0.60
145_V	175_D	0.935	0.60
132_H	174_K	0.925	0.59
93_T	192_R	0.921	0.58
203_K	206_T	0.905	0.57
87_G	92_G	0.902	0.57
75_R	93_T	0.895	0.56
115_I	195_Y	0.892	0.56
54_L	114_I	0.875	0.54
134_L	176_A	0.865	0.54
139_V	148_D	0.863	0.53
181_K	184_T	0.862	0.53
191_V	205_V	0.862	0.53
40_P	50_L	0.859	0.53
56_Y	104_Q	0.855	0.53
141_K	146_E	0.849	0.52
151_P	171_A	0.846	0.52
138_V	200_N	0.843	0.52
167_L	194_G	0.839	0.51
43_E	195_Y	0.838	0.51
142_A	196_S	0.832	0.51
120_G	205_V	0.832	0.51
72_E	77_K	0.829	0.50
82_M	167_L	0.828	0.50
197_A	210_W	0.815	0.49
87_G	90_S	0.810	0.49
95_K	161_G	0.806	0.48
42_T	154_K	0.799	0.48
66_K	70_A	0.796	0.48
115_I	202_Y	0.794	0.47
62_K	188_E	0.794	0.47
63_V	76_Y	0.787	0.47
86_D	206_T	0.780	0.46
110_A	175_D	0.772	0.46
206_T	209_D	0.770	0.45
160_V	179_T	0.761	0.45
109_D	114_I	0.759	0.44
92_G	135_P	0.754	0.44
83_G	90_S	0.752	0.44
169_T	183_E	0.752	0.44
43_E	138_V	0.744	0.43
114_I	209_D	0.738	0.43
63_V	70_A	0.734	0.42
71_G	157_G	0.733	0.42
52_P	200_N	0.732	0.42
131_P	212_R	0.731	0.42
89_V	167_L	0.726	0.42
38_N	43_E	0.723	0.41
42_T	200_N	0.722	0.41
60_D	77_K	0.719	0.41
87_G	172_G	0.716	0.41
139_V	174_K	0.716	0.41
75_R	98_Q	0.714	0.41
103_I	192_R	0.708	0.40
50_L	154_K	0.707	0.40
42_T	48_D	0.706	0.40
58_V	78_V	0.703	0.40
83_G	193_A	0.701	0.40
135_P	164_L	0.697	0.39
163_V	191_V	0.696	0.39
58_V	103_I	0.693	0.39
136_F	160_V	0.692	0.39
73_I	99_L	0.691	0.39
185_R	198_L	0.689	0.39
138_V	197_A	0.682	0.38
46_I	116_P	0.681	0.38
174_K	198_L	0.678	0.38
120_G	151_P	0.672	0.37
54_L	84_N	0.668	0.37
140_G	143_G	0.666	0.37
206_T	210_W	0.665	0.37
43_E	206_T	0.665	0.37
59_V	136_F	0.665	0.37
137_K	168_L	0.664	0.37
164_L	201_T	0.664	0.37
99_L	103_I	0.661	0.36
149_L	194_G	0.661	0.36
189_N	192_R	0.660	0.36
43_E	47_V	0.660	0.36
58_V	97_K	0.659	0.36
140_G	145_V	0.655	0.36
89_V	115_I	0.654	0.36
84_N	116_P	0.649	0.35
156_T	177_W	0.644	0.35
88_Y	114_I	0.642	0.35
151_P	197_A	0.641	0.35
39_L	146_E	0.640	0.35
90_S	172_G	0.639	0.35
120_G	184_T	0.638	0.35
64_V	76_Y	0.636	0.34
92_G	138_V	0.634	0.34
96_A	102_A	0.633	0.34
136_F	158_L	0.632	0.34
56_Y	61_I	0.631	0.34
85_M	114_I	0.617	0.33
86_D	196_S	0.613	0.33
109_D	115_I	0.613	0.33
56_Y	73_I	0.611	0.32
135_P	171_A	0.606	0.32
82_M	110_A	0.603	0.32
98_Q	142_A	0.602	0.32
174_K	203_K	0.601	0.32
175_D	201_T	0.598	0.31
132_H	201_T	0.597	0.31
135_P	151_P	0.596	0.31
43_E	51_L	0.595	0.31
34_L	41_I	0.593	0.31
79_L	91_I	0.587	0.31
113_N	184_T	0.583	0.30
157_G	172_G	0.580	0.30
91_I	195_Y	0.580	0.30
34_L	39_L	0.579	0.30
79_L	163_V	0.576	0.30
158_L	173_I	0.576	0.30
62_K	79_L	0.575	0.30
66_K	168_L	0.575	0.30
78_V	103_I	0.575	0.30
62_K	99_L	0.570	0.29
109_D	206_T	0.568	0.29
54_L	82_M	0.567	0.29
79_L	209_D	0.565	0.29
145_V	180_T	0.563	0.29
139_V	181_K	0.563	0.29
183_E	198_L	0.560	0.29
72_E	189_N	0.558	0.29
152_A	182_G	0.555	0.28
33_E	50_L	0.555	0.28
161_G	211_V	0.553	0.28
106_A	203_K	0.553	0.28
53_K	61_I	0.553	0.28
85_M	170_Y	0.549	0.28
97_K	166_T	0.548	0.28
69_D	98_Q	0.545	0.28
52_P	133_S	0.545	0.28
40_P	46_I	0.543	0.28
61_I	167_L	0.543	0.28
45_E	139_V	0.541	0.27
75_R	96_A	0.541	0.27
145_V	184_T	0.540	0.27
140_G	193_A	0.537	0.27
118_R	201_T	0.536	0.27
173_I	212_R	0.534	0.27
80_V	107_I	0.534	0.27
202_Y	205_V	0.532	0.27
44_P	139_V	0.531	0.27
83_G	141_K	0.530	0.27
64_V	167_L	0.528	0.26
184_T	210_W	0.527	0.26
141_K	198_L	0.526	0.26
106_A	113_N	0.523	0.26
160_V	180_T	0.517	0.26
81_I	169_T	0.516	0.26
69_D	183_E	0.514	0.26
132_H	145_V	0.513	0.25
142_A	204_F	0.513	0.25
108_R	134_L	0.511	0.25
149_L	178_S	0.511	0.25
33_E	38_N	0.508	0.25
66_K	75_R	0.503	0.25
46_I	51_L	0.503	0.25
154_K	174_K	0.500	0.25
69_D	105_K	0.500	0.25

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
3j20F	1	0.9813	100	0.056	Contact Map
3j80C	1	0.9393	100	0.088	Contact Map
4kzyC	1	0.9673	100	0.089	Contact Map
3j60C	1	0.9393	100	0.091	Contact Map
3j7aG	1	0.9439	100	0.092	Contact Map
3j38C	1	0.9579	100	0.092	Contact Map
4ujpD	1	0.9393	100	0.092	Contact Map
3zeyP	1	0.9486	100	0.094	Contact Map
4bpeE	1	0.9486	100	0.094	Contact Map
5a2qC	1	0.9393	100	0.122	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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