RSUA - ECOLI - GREMLIN Contacts

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RSUA - Ribosomal small subunit pseudouridine synthase A

UniProt:	P0AA43	Sequences: MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVITPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEIASVV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12044
Length:	231 (207)
Sequences:	15173 (10113)
Seq/√Len:	702.9

ECOLI - RSUA RLUB RLUF RLUD RLUC RLUE RLUA TRUC
BACSU - YTZG RLUB YHCT YLYB YJBO

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_D	45_H	3.906	1.00
131_T	175_R	3.859	1.00
162_K	179_S	3.273	1.00
133_L	173_Q	3.015	1.00
28_T	48_A	2.940	1.00
26_R	50_D	2.793	1.00
34_V	39_F	2.755	1.00
129_E	177_T	2.661	1.00
58_H	113_D	2.605	1.00
164_A	175_R	2.570	1.00
61_R	114_D	2.463	1.00
131_T	177_T	2.363	1.00
176_L	190_F	2.161	1.00
133_L	175_R	2.052	1.00
135_T	173_Q	2.050	1.00
6_F	41_L	2.045	1.00
114_D	117_W	1.966	1.00
20_R	24_G	1.949	1.00
134_V	176_L	1.941	1.00
83_V	109_V	1.852	1.00
146_E	150_K	1.850	1.00
65_L	86_F	1.829	1.00
13_V	18_A	1.824	1.00
69_Q	106_T	1.818	1.00
17_I	20_R	1.796	1.00
106_T	199_E	1.776	1.00
71_Y	86_F	1.773	1.00
6_F	10_Q	1.762	1.00
73_C	109_V	1.707	1.00
29_V	39_F	1.701	1.00
146_E	149_A	1.697	1.00
140_V	172_T	1.695	1.00
7_I	18_A	1.687	1.00
3_L	34_V	1.671	1.00
131_T	204_R	1.645	1.00
160_L	179_S	1.568	1.00
101_L	109_V	1.558	1.00
174_V	190_F	1.543	1.00
136_L	174_V	1.528	1.00
166_L	175_R	1.518	1.00
28_T	33_I	1.507	1.00
136_L	190_F	1.491	1.00
56_Q	59_G	1.489	1.00
96_H	118_S	1.482	1.00
138_S	172_T	1.477	1.00
165_V	172_T	1.474	1.00
118_S	122_T	1.471	1.00
64_M	108_L	1.451	1.00
185_Q	189_M	1.443	1.00
176_L	186_V	1.433	1.00
106_T	201_H	1.414	1.00
4_D	19_G	1.372	1.00
21_E	49_Y	1.354	1.00
29_V	34_V	1.351	1.00
184_H	187_K	1.349	1.00
144_T	195_N	1.346	1.00
23_R	37_A	1.344	1.00
134_V	174_V	1.316	1.00
137_E	196_H	1.309	1.00
139_P	168_V	1.308	1.00
134_V	197_V	1.306	1.00
64_M	110_L	1.290	1.00
162_K	177_T	1.289	1.00
81_P	86_F	1.288	1.00
161_T	176_L	1.257	1.00
17_I	21_E	1.245	1.00
87_L	111_M	1.245	1.00
31_G	48_A	1.222	1.00
75_T	84_L	1.221	1.00
29_V	47_V	1.216	1.00
143_D	168_V	1.213	1.00
138_S	195_N	1.207	1.00
73_C	97_A	1.193	1.00
80_H	103_I	1.186	1.00
165_V	168_V	1.183	1.00
116_Q	120_R	1.183	1.00
139_P	172_T	1.182	1.00
84_L	97_A	1.168	1.00
140_V	195_N	1.165	1.00
135_T	199_E	1.165	1.00
68_P	71_Y	1.160	1.00
8_A	15_R	1.154	1.00
82_T	85_Y	1.152	1.00
42_L	45_H	1.144	1.00
144_T	164_A	1.141	1.00
119_H	123_S	1.140	1.00
21_E	26_R	1.134	1.00
13_V	21_E	1.133	1.00
59_G	62_Y	1.133	1.00
19_G	23_R	1.129	1.00
46_D	53_P	1.115	1.00
112_T	118_S	1.108	1.00
62_Y	117_W	1.102	1.00
145_A	149_A	1.084	1.00
136_L	195_N	1.082	1.00
27_V	49_Y	1.081	1.00
130_K	178_I	1.073	1.00
135_T	171_P	1.070	1.00
129_E	179_S	1.068	1.00
136_L	172_T	1.063	1.00
204_R	209_T	1.060	1.00
70_G	103_I	1.051	1.00
65_L	87_L	1.043	1.00
35_R	39_F	1.040	1.00
147_Q	150_K	1.037	1.00
154_L	188_R	1.030	1.00
141_A	144_T	1.029	1.00
63_F	91_V	1.027	1.00
140_V	174_V	1.025	1.00
60_P	113_D	1.014	1.00
149_A	152_V	1.011	1.00
133_L	203_E	1.005	1.00
137_E	198_V	1.000	1.00
25_N	33_I	0.999	1.00
69_Q	199_E	0.990	1.00
72_V	79_D	0.984	1.00
168_V	172_T	0.980	1.00
191_A	196_H	0.975	1.00
157_E	182_R	0.975	1.00
161_T	189_M	0.956	1.00
148_F	152_V	0.955	1.00
129_E	204_R	0.949	1.00
22_I	37_A	0.947	1.00
142_D	168_V	0.945	1.00
98_A	112_T	0.943	1.00
75_T	97_A	0.941	1.00
88_D	91_V	0.937	1.00
83_V	111_M	0.928	1.00
64_M	208_I	0.922	1.00
137_E	205_I	0.920	1.00
48_A	53_P	0.918	1.00
63_F	87_L	0.918	1.00
120_R	123_S	0.915	1.00
147_Q	151_G	0.913	1.00
22_I	27_V	0.909	1.00
63_F	111_M	0.908	1.00
75_T	82_T	0.906	1.00
152_V	192_A	0.900	1.00
104_D	187_K	0.887	1.00
163_P	190_F	0.885	1.00
133_L	166_L	0.877	1.00
61_R	117_W	0.873	1.00
112_T	117_W	0.873	1.00
95_L	111_M	0.872	1.00
178_I	186_V	0.871	1.00
16_A	19_G	0.865	1.00
20_R	23_R	0.862	1.00
137_E	195_N	0.860	1.00
119_H	122_T	0.859	1.00
41_L	47_V	0.856	1.00
152_V	156_N	0.852	1.00
32_E	39_F	0.850	1.00
188_R	191_A	0.849	1.00
178_I	185_Q	0.848	1.00
15_R	19_G	0.844	1.00
104_D	201_H	0.839	1.00
7_I	13_V	0.835	1.00
170_T	173_Q	0.833	1.00
136_L	140_V	0.832	1.00
39_F	42_L	0.823	1.00
105_T	134_V	0.821	1.00
161_T	166_L	0.818	1.00
175_R	203_E	0.818	1.00
115_G	118_S	0.816	1.00
39_F	45_H	0.816	1.00
19_G	37_A	0.812	1.00
76_D	79_D	0.806	1.00
65_L	83_V	0.803	1.00
117_W	121_I	0.803	1.00
144_T	193_V	0.801	1.00
159_D	163_P	0.796	1.00
141_A	195_N	0.795	1.00
171_P	198_V	0.787	1.00
148_F	151_G	0.784	1.00
190_F	197_V	0.781	1.00
161_T	164_A	0.776	1.00
98_A	121_I	0.760	1.00
147_Q	193_V	0.759	1.00
105_T	187_K	0.757	1.00
115_G	119_H	0.751	1.00
7_I	27_V	0.746	1.00
153_Q	156_N	0.745	1.00
6_F	47_V	0.737	1.00
85_Y	88_D	0.735	1.00
73_C	101_L	0.732	1.00
31_G	46_D	0.731	1.00
28_T	51_G	0.730	1.00
84_L	111_M	0.728	1.00
13_V	17_I	0.726	1.00
25_N	35_R	0.723	1.00
97_A	111_M	0.721	1.00
35_R	38_A	0.720	1.00
140_V	144_T	0.720	1.00
148_F	202_R	0.719	1.00
86_F	89_E	0.719	1.00
88_D	92_A	0.718	1.00
130_K	185_Q	0.715	1.00
205_I	208_I	0.714	1.00
136_L	197_V	0.713	1.00
28_T	50_D	0.713	1.00
121_I	205_I	0.704	1.00
186_V	197_V	0.703	1.00
161_T	178_I	0.698	1.00
169_I	173_Q	0.696	1.00
74_S	82_T	0.695	1.00
167_E	173_Q	0.694	1.00
2_R	40_K	0.689	1.00
142_D	165_V	0.689	1.00
100_R	181_G	0.682	1.00
162_K	165_V	0.677	1.00
120_R	126_H	0.675	1.00
5_K	9_Q	0.675	1.00
130_K	179_S	0.667	1.00
3_L	22_I	0.664	1.00
135_T	198_V	0.663	1.00
122_T	205_I	0.662	1.00
11_L	18_A	0.662	1.00
65_L	71_Y	0.660	1.00
154_L	157_E	0.657	1.00
14_S	17_I	0.656	1.00
145_A	148_F	0.653	1.00
29_V	45_H	0.652	1.00
139_P	170_T	0.648	1.00
18_A	21_E	0.648	1.00
160_L	163_P	0.643	1.00
161_T	165_V	0.631	1.00
80_H	85_Y	0.630	1.00
140_V	165_V	0.630	1.00
146_E	151_G	0.628	1.00
51_G	54_L	0.627	1.00
140_V	168_V	0.627	1.00
145_A	151_G	0.625	1.00
189_M	193_V	0.617	1.00
117_W	120_R	0.611	1.00
133_L	199_E	0.605	1.00
4_D	38_A	0.602	1.00
105_T	186_V	0.601	1.00
137_E	171_P	0.597	1.00
85_Y	89_E	0.596	1.00
73_C	84_L	0.595	1.00
150_K	153_Q	0.592	1.00
161_T	185_Q	0.591	1.00
140_V	190_F	0.589	1.00
72_V	78_P	0.584	1.00
71_Y	83_V	0.581	1.00
98_A	118_S	0.579	1.00
29_V	41_L	0.579	1.00
163_P	176_L	0.577	1.00
72_V	76_D	0.577	1.00
99_G	109_V	0.576	1.00
84_L	95_L	0.573	1.00
180_E	185_Q	0.573	1.00
83_V	86_F	0.571	1.00
205_I	209_T	0.569	1.00
72_V	103_I	0.568	1.00
144_T	163_P	0.562	1.00
159_D	182_R	0.562	1.00
137_E	208_I	0.561	1.00
119_H	125_R	0.560	1.00
156_N	188_R	0.558	1.00
7_I	54_L	0.556	1.00
84_L	88_D	0.555	1.00
62_Y	114_D	0.555	1.00
173_Q	199_E	0.553	1.00
70_G	106_T	0.552	1.00
167_E	175_R	0.551	1.00
135_T	169_I	0.549	1.00
116_Q	119_H	0.548	1.00
132_Y	181_G	0.547	1.00
3_L	47_V	0.546	1.00
81_P	85_Y	0.544	1.00
73_C	83_V	0.544	1.00
71_Y	81_P	0.540	1.00
139_P	143_D	0.540	1.00
40_K	43_P	0.539	1.00
19_G	38_A	0.538	1.00
163_P	168_V	0.537	1.00
130_K	181_G	0.535	1.00
153_Q	160_L	0.534	1.00
72_V	77_D	0.534	1.00
163_P	167_E	0.533	1.00
66_N	106_T	0.532	1.00
98_A	110_L	0.530	1.00
7_I	11_L	0.529	1.00
182_R	185_Q	0.528	1.00
164_A	168_V	0.527	1.00
164_A	177_T	0.525	1.00
30_D	47_V	0.525	1.00
58_H	91_V	0.525	1.00
155_H	188_R	0.523	1.00
69_Q	104_D	0.523	1.00
146_E	152_V	0.520	1.00
7_I	10_Q	0.517	1.00
12_G	21_E	0.515	1.00
74_S	78_P	0.514	1.00
112_T	121_I	0.512	0.99
3_L	39_F	0.512	0.99
91_V	113_D	0.511	0.99
161_T	169_I	0.511	0.99
148_F	189_M	0.508	0.99
63_F	90_P	0.505	0.99
70_G	104_D	0.504	0.99
56_Q	108_L	0.503	0.99
10_Q	13_V	0.503	0.99
172_T	195_N	0.503	0.99
12_G	49_Y	0.502	0.99
58_H	93_W	0.501	0.99
75_T	83_V	0.500	0.99
8_A	18_A	0.500	0.99
145_A	150_K	0.500	0.99

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
1vioA	2	0.9913	100	0.095	Contact Map
1kskA	1	1	100	0.136	Contact Map
3dh3A	1	0.9697	100	0.152	Contact Map
4lgtA	1	0.974	100	0.166	Contact Map
1v9fA	1	0.7619	100	0.184	Contact Map
2gmlA	1	0.7229	100	0.301	Contact Map
2omlA	1	0.71	100	0.306	Contact Map
2olwA	1	0.7056	100	0.314	Contact Map
1v9kA	1	0.7749	100	0.357	Contact Map
2i82A	1	0.8182	100	0.364	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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