RS4 - ECOLI - GREMLIN Contacts

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RS4 - 30S ribosomal protein S4

UniProt:	P0A7V8	Sequences: MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIVELYSK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10903
Length:	206 (200)
Sequences:	2929 (1403)
Seq/√Len:	99.2

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
126_N	141_D	5.078	1.00
105_M	180_G	4.446	1.00
125_V	135_Y	3.493	1.00
124_M	144_S	3.314	1.00
121_K	129_V	3.224	1.00
130_V	135_Y	3.133	1.00
188_R	197_E	3.073	1.00
61_V	200_I	2.853	1.00
2_A	68_L	2.661	1.00
113_E	154_R	2.625	1.00
82_L	89_N	2.567	1.00
57_E	60_K	2.499	1.00
144_S	179_E	2.370	1.00
123_I	145_I	2.356	1.00
96_G	182_F	2.290	1.00
74_N	78_E	2.280	1.00
78_E	81_R	2.201	1.00
105_M	171_L	2.200	1.00
78_E	136_Q	2.145	1.00
89_N	92_A	2.125	1.00
109_A	113_E	2.117	1.00
121_K	131_N	2.085	1.00
184_R	190_D	2.064	1.00
172_E	181_T	2.056	1.00
15_E	63_R	2.015	1.00
73_R	77_K	1.938	1.00
105_M	173_V	1.927	1.00
174_D	177_K	1.910	1.00
36_Q	43_A	1.834	1.00
48_L	52_G	1.767	1.00
107_F	173_V	1.738	1.00
137_V	143_V	1.691	1.00
84_G	89_N	1.659	1.00
78_E	82_L	1.629	1.00
91_L	191_L	1.612	1.00
153_S	157_A	1.596	1.00
147_E	150_K	1.578	1.00
203_L	206_K	1.558	1.00
15_E	56_R	1.551	1.00
18_D	23_S	1.474	1.00
172_E	183_K	1.448	1.00
92_A	185_K	1.421	1.00
82_L	93_L	1.384	0.99
74_N	77_K	1.381	0.99
18_D	21_L	1.362	0.99
129_V	146_R	1.360	0.99
108_G	114_A	1.359	0.99
8_K	112_A	1.348	0.99
111_R	170_W	1.320	0.99
67_V	75_Y	1.308	0.99
171_L	182_F	1.307	0.99
11_L	63_R	1.307	0.99
122_A	149_A	1.301	0.99
174_D	179_E	1.300	0.99
67_V	94_L	1.298	0.99
169_T	184_R	1.263	0.99
155_V	159_L	1.255	0.99
145_I	178_M	1.253	0.99
96_G	136_Q	1.242	0.99
101_V	137_V	1.241	0.99
75_Y	136_Q	1.241	0.99
150_K	178_M	1.240	0.99
142_V	179_E	1.235	0.99
9_L	31_K	1.232	0.99
38_P	41_H	1.232	0.99
96_G	185_K	1.219	0.99
78_E	93_L	1.187	0.98
38_P	42_G	1.180	0.98
92_A	96_G	1.178	0.98
75_Y	90_L	1.177	0.98
9_L	32_C	1.176	0.98
18_D	110_T	1.171	0.98
156_K	160_E	1.161	0.98
48_L	56_R	1.148	0.98
146_R	149_A	1.147	0.98
12_S	18_D	1.147	0.98
142_V	181_T	1.144	0.98
108_G	113_E	1.143	0.98
149_A	152_Q	1.129	0.98
9_L	12_S	1.128	0.98
119_S	132_I	1.126	0.98
18_D	22_K	1.120	0.98
39_G	42_G	1.101	0.97
145_I	155_V	1.100	0.97
62_R	203_L	1.099	0.97
9_L	18_D	1.089	0.97
155_V	158_A	1.088	0.97
56_R	63_R	1.088	0.97
98_L	125_V	1.073	0.97
4_Y	7_P	1.071	0.97
11_L	15_E	1.064	0.97
169_T	190_D	1.059	0.97
21_L	31_K	1.053	0.97
17_T	194_D	1.033	0.96
9_L	23_S	1.011	0.96
9_L	22_K	1.007	0.96
91_L	188_R	1.007	0.96
68_L	72_F	1.002	0.95
15_E	19_L	0.997	0.95
153_S	156_K	0.996	0.95
86_T	201_V	0.995	0.95
117_L	123_I	0.991	0.95
3_R	6_G	0.987	0.95
69_E	204_Y	0.986	0.95
101_V	143_V	0.982	0.95
61_V	91_L	0.978	0.95
9_L	110_T	0.977	0.95
101_V	182_F	0.974	0.95
93_L	136_Q	0.969	0.94
58_K	69_E	0.966	0.94
61_V	195_I	0.960	0.94
90_L	203_L	0.959	0.94
116_Q	120_H	0.948	0.94
125_V	130_V	0.944	0.94
167_K	173_V	0.940	0.94
19_L	22_K	0.937	0.93
9_L	21_L	0.936	0.93
36_Q	42_G	0.934	0.93
91_L	197_E	0.932	0.93
85_N	201_V	0.913	0.93
147_E	151_K	0.912	0.92
12_S	19_L	0.912	0.92
101_V	180_G	0.910	0.92
123_I	155_V	0.890	0.92
143_V	180_G	0.884	0.91
34_I	37_A	0.884	0.91
82_L	92_A	0.881	0.91
21_L	32_C	0.878	0.91
100_N	111_R	0.874	0.91
156_K	178_M	0.866	0.90
34_I	39_G	0.863	0.90
88_E	200_I	0.852	0.90
12_S	23_S	0.847	0.89
171_L	180_G	0.833	0.89
159_L	175_A	0.831	0.89
64_I	195_I	0.822	0.88
15_E	20_F	0.811	0.87
139_P	182_F	0.808	0.87
87_G	91_L	0.804	0.87
95_E	104_R	0.803	0.87
119_S	131_N	0.802	0.87
108_G	117_L	0.790	0.86
88_E	187_E	0.787	0.86
102_V	118_V	0.786	0.86
89_N	93_L	0.782	0.85
9_L	30_T	0.780	0.85
68_L	203_L	0.777	0.85
4_Y	11_L	0.776	0.85
151_K	156_K	0.774	0.85
96_G	137_V	0.767	0.84
182_F	185_K	0.767	0.84
115_R	133_A	0.759	0.84
197_E	201_V	0.758	0.83
98_L	130_V	0.756	0.83
4_Y	10_K	0.755	0.83
195_I	199_L	0.749	0.83
96_G	138_S	0.747	0.83
15_E	22_K	0.742	0.82
18_D	24_G	0.738	0.82
123_I	144_S	0.737	0.82
64_I	191_L	0.736	0.82
5_L	8_K	0.734	0.81
33_K	38_P	0.733	0.81
188_R	199_L	0.733	0.81
34_I	38_P	0.732	0.81
98_L	123_I	0.731	0.81
70_R	74_N	0.731	0.81
22_K	31_K	0.726	0.81
87_G	197_E	0.725	0.81
152_Q	155_V	0.725	0.81
37_A	42_G	0.719	0.80
54_Q	206_K	0.719	0.80
17_T	64_I	0.712	0.79
76_Y	201_V	0.706	0.79
62_R	67_V	0.701	0.78
15_E	31_K	0.695	0.78
93_L	96_G	0.689	0.77
62_R	69_E	0.688	0.77
198_H	203_L	0.687	0.77
72_F	111_R	0.684	0.77
23_S	30_T	0.683	0.77
102_V	108_G	0.683	0.77
76_Y	90_L	0.682	0.77
196_N	199_L	0.682	0.77
37_A	41_H	0.681	0.76
92_A	187_E	0.677	0.76
154_R	158_A	0.676	0.76
12_S	20_F	0.675	0.76
88_E	189_S	0.675	0.76
20_F	110_T	0.674	0.76
12_S	22_K	0.674	0.76
157_A	161_L	0.674	0.76
189_S	192_S	0.672	0.75
18_D	32_C	0.665	0.75
9_L	19_L	0.663	0.74
17_T	21_L	0.662	0.74
33_K	36_Q	0.658	0.74
159_L	173_V	0.656	0.74
139_P	185_K	0.654	0.73
117_L	122_A	0.653	0.73
102_V	123_I	0.651	0.73
54_Q	203_L	0.650	0.73
152_Q	178_M	0.649	0.73
105_M	137_V	0.647	0.73
117_L	155_V	0.645	0.72
151_K	157_A	0.644	0.72
96_G	139_P	0.641	0.72
184_R	187_E	0.641	0.72
119_S	133_A	0.640	0.72
80_A	86_T	0.639	0.72
8_K	11_L	0.638	0.72
157_A	160_E	0.634	0.71
34_I	41_H	0.630	0.71
72_F	200_I	0.630	0.71
167_K	175_A	0.629	0.71
135_Y	141_D	0.628	0.70
19_L	63_R	0.628	0.70
87_G	188_R	0.628	0.70
8_K	21_L	0.624	0.70
11_L	19_L	0.624	0.70
188_R	191_L	0.622	0.70
50_D	53_V	0.620	0.69
18_D	30_T	0.615	0.69
64_I	192_S	0.614	0.69
66_G	112_A	0.612	0.68
100_N	170_W	0.605	0.68
82_L	96_G	0.605	0.68
9_L	15_E	0.604	0.67
11_L	110_T	0.595	0.66
85_N	88_E	0.595	0.66
52_G	56_R	0.595	0.66
142_V	145_I	0.592	0.66
186_P	190_D	0.590	0.66
51_Y	203_L	0.587	0.65
149_A	155_V	0.585	0.65
35_E	39_G	0.584	0.65
118_V	127_G	0.581	0.64
19_L	31_K	0.580	0.64
72_F	80_A	0.579	0.64
84_G	87_G	0.577	0.64
170_W	182_F	0.574	0.64
123_I	143_V	0.574	0.64
88_E	197_E	0.574	0.64
62_R	90_L	0.571	0.63
37_A	45_K	0.571	0.63
98_L	135_Y	0.568	0.63
15_E	21_L	0.568	0.63
103_Y	132_I	0.568	0.63
55_L	59_Q	0.565	0.62
3_R	14_R	0.559	0.62
53_V	196_N	0.557	0.61
12_S	30_T	0.557	0.61
23_S	110_T	0.556	0.61
36_Q	40_Q	0.553	0.61
122_A	152_Q	0.551	0.60
123_I	149_A	0.550	0.60
143_V	169_T	0.548	0.60
85_N	110_T	0.546	0.60
22_K	63_R	0.539	0.59
22_K	32_C	0.539	0.59
62_R	68_L	0.538	0.59
124_M	146_R	0.537	0.58
102_V	142_V	0.536	0.58
74_N	93_L	0.536	0.58
2_A	6_G	0.535	0.58
12_S	32_C	0.532	0.58
12_S	110_T	0.532	0.58
10_K	193_A	0.530	0.58
140_N	174_D	0.529	0.57
7_P	139_P	0.528	0.57
129_V	184_R	0.528	0.57
86_T	89_N	0.527	0.57
70_R	78_E	0.527	0.57
140_N	172_E	0.524	0.57
62_R	193_A	0.524	0.57
14_R	22_K	0.523	0.57
35_E	196_N	0.523	0.57
127_G	147_E	0.520	0.56
140_N	184_R	0.520	0.56
3_R	119_S	0.519	0.56
68_L	75_Y	0.518	0.56
19_L	24_G	0.515	0.55
156_K	159_L	0.513	0.55
62_R	85_N	0.512	0.55
81_R	93_L	0.512	0.55
8_K	23_S	0.511	0.55
138_S	143_V	0.509	0.55
59_Q	69_E	0.509	0.55
54_Q	61_V	0.508	0.54
9_L	20_F	0.508	0.54
30_T	36_Q	0.508	0.54
113_E	158_A	0.507	0.54
61_V	64_I	0.505	0.54
70_R	119_S	0.504	0.54
21_L	24_G	0.503	0.54
12_S	31_K	0.503	0.54
98_L	137_V	0.502	0.54
140_N	181_T	0.501	0.53
33_K	39_G	0.500	0.53
193_A	196_N	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
4tp8D	1	0.9951	100	0.246	Contact Map
3bbnD	1	0.9612	100	0.259	Contact Map
4rb5D	1	0.9903	100	0.287	Contact Map
1c05A	1	0.7718	100	0.457	Contact Map
3j20E	1	0.7136	100	0.626	Contact Map
3j38J	1	0.733	99.9	0.67	Contact Map
3kbgA	2	0.534	99.9	0.682	Contact Map
4bpeD	2	0.6505	99.8	0.701	Contact Map
3j7aE	1	0.7621	99.8	0.718	Contact Map
4ujpK	1	0.6942	99.8	0.727	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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