RRAA - ECOLI - GREMLIN Contacts

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RRAA - Regulator of ribonuclease activity A

UniProt:	P0A8R0	Sequences: MKYDTSELCDIYQEDVNVVEPLFSNFGGRASFGGQIITVKCFEDNGLLYDLLEQNGRGRVLVVDGGGSVRRALVDAELARLAVQNEWEGLVIYGAVRQVDDLEELDIGIQAMAAIPVGAAGEGIGESDVRVNFGGVTFFSGDHLYADNTGIILSEDPLDIE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11879
Length:	161 (153)
Sequences:	3617 (2217)
Seq/√Len:	179.2

ECOLI - RRAA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
76_A	101_D	3.409	1.00
100_D	148_N	3.086	1.00
37_I	128_D	3.021	1.00
65_G	73_L	2.664	1.00
55_N	87_W	2.651	1.00
144_L	153_L	2.601	1.00
74_V	79_A	2.560	1.00
128_D	140_S	2.521	1.00
126_E	129_V	2.442	1.00
56_G	59_R	2.409	1.00
36_I	144_L	2.382	1.00
90_L	107_I	2.179	1.00
40_K	126_E	2.111	1.00
37_I	59_R	2.100	1.00
8_L	145_Y	2.083	1.00
95_A	113_A	1.996	1.00
103_E	148_N	1.971	1.00
36_I	138_F	1.948	1.00
40_K	64_D	1.932	1.00
130_R	139_F	1.899	1.00
79_A	102_L	1.863	1.00
32_F	89_G	1.858	1.00
29_R	106_D	1.797	1.00
19_V	133_F	1.779	1.00
110_Q	146_A	1.740	1.00
74_V	90_L	1.739	1.00
29_R	148_N	1.737	1.00
57_R	86_E	1.708	1.00
102_L	109_I	1.671	1.00
35_Q	59_R	1.655	1.00
139_F	157_P	1.638	1.00
25_N	110_Q	1.623	1.00
32_F	60_V	1.593	1.00
83_V	105_L	1.587	1.00
26_F	111_A	1.583	1.00
99_V	114_A	1.551	1.00
146_A	151_I	1.535	1.00
22_L	112_M	1.503	1.00
80_R	84_Q	1.501	1.00
96_V	102_L	1.498	1.00
32_F	146_A	1.470	1.00
54_Q	127_S	1.447	1.00
99_V	149_T	1.395	1.00
91_V	144_L	1.380	1.00
45_N	121_G	1.299	1.00
60_V	88_E	1.277	1.00
129_V	140_S	1.269	1.00
32_F	110_Q	1.253	1.00
74_V	82_A	1.249	1.00
36_I	142_D	1.249	1.00
6_S	149_T	1.247	1.00
83_V	106_D	1.214	1.00
35_Q	58_G	1.200	1.00
132_N	137_T	1.164	1.00
19_V	138_F	1.161	1.00
28_G	103_E	1.150	1.00
7_E	10_D	1.125	1.00
30_A	106_D	1.125	1.00
71_R	119_A	1.120	1.00
69_V	95_A	1.106	1.00
145_Y	154_S	1.103	1.00
99_V	103_E	1.097	1.00
93_Y	112_M	1.078	1.00
47_L	50_D	1.068	1.00
91_V	151_I	1.065	1.00
53_E	81_L	1.059	1.00
62_V	144_L	1.047	1.00
80_R	105_L	1.036	1.00
74_V	78_L	1.035	1.00
55_N	61_L	1.032	1.00
77_E	81_L	1.028	0.99
101_D	104_E	1.011	0.99
83_V	107_I	0.999	0.99
40_K	66_G	0.998	0.99
35_Q	143_H	0.998	0.99
52_L	78_L	0.997	0.99
22_L	134_G	0.986	0.99
19_V	134_G	0.980	0.99
73_L	92_I	0.964	0.99
23_F	133_F	0.963	0.99
20_E	134_G	0.958	0.99
37_I	127_S	0.958	0.99
27_G	106_D	0.955	0.99
91_V	146_A	0.953	0.99
44_D	123_G	0.952	0.99
64_D	93_Y	0.951	0.99
36_I	153_L	0.951	0.99
96_V	111_A	0.951	0.99
27_G	30_A	0.947	0.99
4_D	7_E	0.945	0.99
25_N	28_G	0.934	0.99
24_S	114_A	0.926	0.99
33_G	145_Y	0.924	0.99
142_D	155_E	0.916	0.99
133_F	138_F	0.916	0.99
82_A	87_W	0.913	0.99
17_N	142_D	0.911	0.99
9_C	13_Q	0.902	0.99
61_L	87_W	0.898	0.99
93_Y	133_F	0.887	0.98
52_L	81_L	0.886	0.98
77_E	80_R	0.883	0.98
31_S	100_D	0.878	0.98
138_F	153_L	0.869	0.98
96_V	109_I	0.868	0.98
69_V	112_M	0.867	0.98
38_T	128_D	0.865	0.98
37_I	51_L	0.862	0.98
61_L	82_A	0.861	0.98
51_L	61_L	0.848	0.98
130_R	137_T	0.844	0.98
41_C	73_L	0.842	0.98
76_A	80_R	0.834	0.98
35_Q	156_D	0.834	0.98
31_S	148_N	0.833	0.98
56_G	85_N	0.831	0.98
22_L	69_V	0.814	0.97
71_R	115_I	0.811	0.97
50_D	54_Q	0.808	0.97
50_D	127_S	0.801	0.97
20_E	133_F	0.800	0.97
52_L	82_A	0.797	0.97
77_E	118_G	0.791	0.97
43_E	70_R	0.785	0.97
20_E	135_G	0.783	0.97
61_L	90_L	0.780	0.97
7_E	13_Q	0.780	0.97
138_F	144_L	0.779	0.97
21_P	95_A	0.769	0.96
19_V	23_F	0.767	0.96
132_N	135_G	0.764	0.96
50_D	53_E	0.748	0.96
48_L	63_V	0.744	0.96
37_I	56_G	0.742	0.95
9_C	12_Y	0.735	0.95
26_F	99_V	0.731	0.95
139_F	142_D	0.729	0.95
46_G	124_I	0.728	0.95
35_Q	88_E	0.721	0.95
19_V	153_L	0.717	0.95
18_V	117_V	0.713	0.94
76_A	105_L	0.694	0.94
33_G	143_H	0.689	0.93
23_F	134_G	0.678	0.93
74_V	92_I	0.676	0.93
13_Q	122_E	0.673	0.93
44_D	125_G	0.669	0.92
37_I	54_Q	0.657	0.92
12_Y	155_E	0.657	0.92
27_G	103_E	0.656	0.92
37_I	55_N	0.654	0.91
110_Q	151_I	0.653	0.91
100_D	104_E	0.652	0.91
39_V	63_V	0.652	0.91
24_S	99_V	0.650	0.91
64_D	132_N	0.650	0.91
139_F	155_E	0.648	0.91
53_E	78_L	0.648	0.91
59_R	128_D	0.647	0.91
56_G	87_W	0.644	0.91
49_Y	121_G	0.643	0.91
100_D	149_T	0.641	0.91
79_A	105_L	0.635	0.90
41_C	48_L	0.634	0.90
136_V	153_L	0.634	0.90
122_E	126_E	0.631	0.90
41_C	63_V	0.629	0.90
59_R	88_E	0.624	0.89
38_T	131_V	0.621	0.89
9_C	116_P	0.621	0.89
42_F	125_G	0.617	0.89
35_Q	56_G	0.617	0.89
23_F	151_I	0.616	0.89
19_V	144_L	0.613	0.89
92_I	96_V	0.606	0.88
55_N	59_R	0.603	0.88
55_N	85_N	0.603	0.88
51_L	127_S	0.601	0.88
97_R	118_G	0.601	0.88
71_R	117_V	0.594	0.87
46_G	119_A	0.593	0.87
63_V	92_I	0.589	0.87
49_Y	78_L	0.586	0.86
60_V	91_V	0.584	0.86
100_D	103_E	0.583	0.86
64_D	67_G	0.581	0.86
72_A	119_A	0.577	0.85
53_E	77_E	0.576	0.85
72_A	149_T	0.573	0.85
13_Q	16_V	0.571	0.85
45_N	125_G	0.570	0.85
67_G	93_Y	0.569	0.85
12_Y	154_S	0.569	0.85
5_T	8_L	0.565	0.84
55_N	82_A	0.560	0.84
79_A	107_I	0.554	0.83
8_L	154_S	0.551	0.83
49_Y	53_E	0.550	0.83
46_G	50_D	0.549	0.83
25_N	30_A	0.549	0.83
99_V	148_N	0.545	0.82
17_N	155_E	0.544	0.82
73_L	94_G	0.539	0.81
52_L	61_L	0.536	0.81
81_L	84_Q	0.535	0.81
116_P	150_G	0.534	0.81
72_A	78_L	0.534	0.81
40_K	131_V	0.531	0.80
4_D	143_H	0.525	0.80
52_L	83_V	0.525	0.80
21_P	69_V	0.524	0.80
57_R	88_E	0.524	0.80
4_D	101_D	0.521	0.79
45_N	118_G	0.520	0.79
138_F	142_D	0.519	0.79
53_E	85_N	0.519	0.79
23_F	26_F	0.519	0.79
83_V	86_E	0.519	0.79
93_Y	138_F	0.518	0.79
9_C	18_V	0.517	0.79
130_R	142_D	0.515	0.78
9_C	117_V	0.511	0.78
134_G	138_F	0.511	0.78
43_E	71_R	0.508	0.77
64_D	131_V	0.507	0.77
96_V	99_V	0.507	0.77
73_L	119_A	0.507	0.77
65_G	92_I	0.504	0.77
5_T	9_C	0.501	0.76
40_K	129_V	0.500	0.76

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
1vi4A	1	0.9938	100	0.078	Contact Map
3c8oA	4	1	100	0.081	Contact Map
1q5xA	3	0.9938	100	0.085	Contact Map
1j3lA	3	0.9938	100	0.103	Contact Map
3nojA	5	0.9938	100	0.106	Contact Map
2pcnA	3	0.9876	100	0.114	Contact Map
3k4iA	3	0.9814	100	0.12	Contact Map
2c5qA	3	1	100	0.131	Contact Map
1nxjA	3	0.9441	100	0.133	Contact Map
1kblA	2	0.8509	47	0.925	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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