RS5 - HALSA - GREMLIN Contacts

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RS5 - 30S ribosomal protein S5

UniProt:	Q9HPB4	Sequences: MSYNDTWQPKTRLGGLVQDGEVEDMSEALDTGLPLKEPEIVDQLLPGLDDEVLDINMVQRMTDSGRRVKFRCVVAIGNRDGYVGYAEGRDDQVGGAIQKAIEVAKLNIIDVSRGCGSWECGCGRPHTVALKSTGKAGSVDVELMPAPRGLGLAGGETVQHVLELAGIDDVWTRSSGKTRTTVNFAKATFNALRETSEARVPQHAREEREVIE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	212 (161)
Sequences:	927 (460)
Seq/√Len:	36.3

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
49_D	79_R	5.215	1.00
190_N	194_E	3.684	1.00
78_N	82_Y	3.488	1.00
147_P	171_W	3.228	1.00
53_L	185_A	2.989	1.00
113_R	167_I	2.760	1.00
61_M	68_V	2.649	1.00
196_S	204_A	2.637	1.00
70_F	93_V	2.593	1.00
158_V	172_T	2.504	1.00
128_V	195_T	2.481	1.00
134_G	190_N	2.426	1.00
61_M	66_R	2.358	1.00
131_K	145_P	2.237	0.99
41_V	48_L	2.199	0.99
101_I	105_K	2.193	0.99
61_M	64_S	2.191	0.99
190_N	193_R	2.191	0.99
162_L	170_V	2.177	0.99
85_Y	185_A	2.097	0.99
52_V	55_I	2.091	0.99
74_V	100_A	1.998	0.98
148_R	169_D	1.984	0.98
126_H	169_D	1.979	0.98
146_A	150_L	1.978	0.98
128_V	170_V	1.920	0.98
87_E	182_V	1.901	0.98
127_T	169_D	1.874	0.98
129_A	195_T	1.834	0.97
41_V	46_P	1.714	0.96
85_Y	186_K	1.681	0.95
132_S	194_E	1.644	0.95
182_V	186_K	1.614	0.94
103_V	107_N	1.562	0.93
131_K	144_M	1.561	0.93
75_A	161_V	1.452	0.90
48_L	82_Y	1.416	0.89
157_T	184_F	1.384	0.88
107_N	172_T	1.381	0.88
132_S	195_T	1.364	0.87
49_D	164_L	1.358	0.87
83_V	165_A	1.352	0.87
86_A	103_V	1.348	0.87
69_K	171_W	1.339	0.86
135_K	140_D	1.310	0.85
82_Y	108_I	1.296	0.84
60_R	150_L	1.265	0.83
50_D	55_I	1.237	0.81
81_G	113_R	1.215	0.80
71_R	87_E	1.200	0.79
95_G	98_Q	1.198	0.79
157_T	185_A	1.196	0.79
88_G	99_K	1.189	0.79
169_D	189_F	1.167	0.77
134_G	201_P	1.155	0.77
89_R	99_K	1.151	0.76
100_A	166_G	1.138	0.76
90_D	96_A	1.117	0.74
132_S	143_L	1.105	0.73
67_R	91_D	1.102	0.73
37_E	44_L	1.097	0.73
128_V	143_L	1.060	0.70
58_V	189_F	1.052	0.70
37_E	126_H	1.044	0.69
125_P	206_E	1.043	0.69
141_V	153_A	1.027	0.68
83_V	98_Q	1.026	0.68
88_G	96_A	1.010	0.66
150_L	171_W	1.007	0.66
40_I	48_L	1.004	0.66
111_V	164_L	1.003	0.66
52_V	74_V	1.001	0.66
51_E	164_L	0.998	0.66
154_G	172_T	0.994	0.65
56_N	71_R	0.994	0.65
150_L	155_G	0.990	0.65
197_E	200_V	0.986	0.65
174_S	184_F	0.973	0.64
140_D	177_K	0.966	0.63
92_Q	127_T	0.955	0.62
201_P	204_A	0.953	0.62
80_D	200_V	0.948	0.61
58_V	69_K	0.941	0.61
139_V	174_S	0.933	0.60
48_L	80_D	0.929	0.60
69_K	87_E	0.924	0.59
75_A	160_H	0.922	0.59
41_V	82_Y	0.907	0.58
79_R	163_E	0.906	0.58
141_V	187_A	0.905	0.58
151_G	166_G	0.897	0.57
110_D	169_D	0.894	0.57
143_L	172_T	0.882	0.56
51_E	141_V	0.873	0.55
152_L	162_L	0.861	0.54
52_V	97_I	0.857	0.54
170_V	195_T	0.856	0.54
146_A	176_G	0.853	0.53
161_V	188_T	0.839	0.52
134_G	139_V	0.837	0.52
53_L	144_M	0.832	0.52
69_K	90_D	0.826	0.51
75_A	164_L	0.823	0.51
56_N	181_T	0.821	0.51
40_I	110_D	0.818	0.50
54_D	71_R	0.816	0.50
52_V	101_I	0.812	0.50
133_T	142_E	0.807	0.49
76_I	149_G	0.805	0.49
74_V	101_I	0.793	0.48
76_I	81_G	0.792	0.48
196_S	200_V	0.790	0.48
126_H	168_D	0.785	0.47
109_I	193_R	0.782	0.47
168_D	197_E	0.780	0.47
142_E	147_P	0.779	0.47
129_A	198_A	0.774	0.46
78_N	110_D	0.774	0.46
105_K	126_H	0.764	0.46
69_K	91_D	0.756	0.45
143_L	188_T	0.754	0.45
57_M	64_S	0.752	0.45
80_D	113_R	0.748	0.44
43_Q	46_P	0.747	0.44
136_A	186_K	0.745	0.44
65_G	77_G	0.744	0.44
200_V	203_H	0.741	0.44
89_R	155_G	0.736	0.43
90_D	103_V	0.735	0.43
42_D	206_E	0.732	0.43
56_N	132_S	0.718	0.42
73_V	157_T	0.716	0.42
174_S	179_R	0.715	0.41
68_V	71_R	0.714	0.41
154_G	173_R	0.712	0.41
100_A	176_G	0.710	0.41
60_R	64_S	0.709	0.41
190_N	206_E	0.709	0.41
69_K	82_Y	0.708	0.41
57_M	61_M	0.708	0.41
57_M	68_V	0.707	0.41
163_E	177_K	0.706	0.41
74_V	96_A	0.704	0.40
177_K	184_F	0.700	0.40
114_G	126_H	0.696	0.40
136_A	180_T	0.694	0.40
114_G	198_A	0.694	0.40
62_T	67_R	0.691	0.39
143_L	170_V	0.685	0.39
113_R	126_H	0.680	0.38
189_F	193_R	0.679	0.38
77_G	84_G	0.673	0.38
109_I	189_F	0.673	0.38
71_R	85_Y	0.669	0.38
60_R	153_A	0.668	0.38
47_G	80_D	0.667	0.37
52_V	164_L	0.664	0.37
51_E	181_T	0.663	0.37
139_V	179_R	0.663	0.37
57_M	69_K	0.659	0.37
52_V	72_C	0.656	0.37
83_V	109_I	0.655	0.36
83_V	190_N	0.650	0.36
72_C	96_A	0.647	0.36
83_V	161_V	0.645	0.36
60_R	69_K	0.643	0.35
126_H	132_S	0.642	0.35
52_V	156_E	0.641	0.35
53_L	85_Y	0.635	0.35
93_V	97_I	0.634	0.35
96_A	151_G	0.631	0.35
98_Q	179_R	0.630	0.34
133_T	140_D	0.621	0.34
81_G	89_R	0.619	0.34
128_V	167_I	0.619	0.34
44_L	193_R	0.615	0.33
37_E	41_V	0.612	0.33
81_G	84_G	0.611	0.33
66_R	81_G	0.610	0.33
204_A	207_E	0.610	0.33
130_L	154_G	0.608	0.33
37_E	59_Q	0.606	0.33
39_E	45_L	0.604	0.32
64_S	68_V	0.603	0.32
76_I	161_V	0.603	0.32
150_L	154_G	0.601	0.32
100_A	172_T	0.601	0.32
40_I	114_G	0.595	0.32
97_I	189_F	0.593	0.32
66_R	71_R	0.587	0.31
37_E	40_I	0.586	0.31
84_G	149_G	0.584	0.31
40_I	160_H	0.584	0.31
110_D	165_A	0.580	0.31
89_R	173_R	0.578	0.30
81_G	166_G	0.578	0.30
71_R	79_R	0.574	0.30
62_T	98_Q	0.567	0.30
48_L	85_Y	0.564	0.29
135_K	190_N	0.558	0.29
70_F	188_T	0.558	0.29
97_I	185_A	0.554	0.29
125_P	169_D	0.552	0.29
124_R	145_P	0.552	0.29
74_V	143_L	0.550	0.28
196_S	199_R	0.549	0.28
79_R	168_D	0.548	0.28
105_K	139_V	0.548	0.28
42_D	143_L	0.547	0.28
50_D	101_I	0.547	0.28
109_I	112_S	0.546	0.28
56_N	182_V	0.543	0.28
49_D	174_S	0.542	0.28
148_R	168_D	0.542	0.28
67_R	182_V	0.541	0.28
56_N	73_V	0.541	0.28
153_A	171_W	0.540	0.28
85_Y	100_A	0.538	0.28
203_H	206_E	0.537	0.28
59_Q	67_R	0.532	0.27
66_R	144_M	0.532	0.27
46_P	127_T	0.532	0.27
92_Q	136_A	0.529	0.27
163_E	197_E	0.528	0.27
45_L	59_Q	0.526	0.27
57_M	63_D	0.525	0.27
114_G	125_P	0.523	0.27
111_V	193_R	0.521	0.26
144_M	172_T	0.519	0.26
134_G	152_L	0.517	0.26
164_L	180_T	0.517	0.26
200_V	204_A	0.516	0.26
162_L	172_T	0.516	0.26
67_R	142_E	0.515	0.26
147_P	152_L	0.515	0.26
53_L	193_R	0.515	0.26
64_S	155_G	0.514	0.26
42_D	91_D	0.511	0.26
93_V	153_A	0.507	0.25
91_D	135_K	0.502	0.25
71_R	182_V	0.502	0.25
89_R	107_N	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	0.9481	100	0.064	Contact Map
4kzyC	1	0.9906	100	0.073	Contact Map
3j80C	1	0.967	100	0.074	Contact Map
3j38C	1	0.9858	100	0.076	Contact Map
3j60C	1	0.967	100	0.076	Contact Map
4ujpD	1	0.967	100	0.077	Contact Map
4bpeE	1	0.9764	100	0.079	Contact Map
3zeyP	1	0.9764	100	0.08	Contact Map
3j7aG	1	0.9717	100	0.083	Contact Map
5a2qC	1	0.967	100	0.11	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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