RPPH - ECOLI - GREMLIN Contacts

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RPPH - RNA pyrophosphohydrolase

UniProt:	P0A776	Sequences: MIDDDGYRPNVGIVICNRQGQVMWARRFGQHSWQFPQGGINPGESAEQAMYRELFEEVGLSRKDVRILASTRNWLRYKLPKRLVRWDTKPVCIGQKQKWFLLQLVSGDAEINMQTSSTPEFDGWRWVSYWYPVRQVVSFKRDVYRRVMKEFASVVMSLQENTPKPQNASAYRRKRG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13091
Length:	176 (150)
Sequences:	1114 (615)
Seq/√Len:	50.2

ECOLI - RPPH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
66_R	105_V	4.299	1.00
70_S	98_K	3.911	1.00
64_D	110_E	3.662	1.00
72_R	150_E	3.622	1.00
45_S	48_Q	3.242	1.00
26_R	122_D	2.839	1.00
7_Y	78_K	2.826	1.00
67_I	102_L	2.772	1.00
47_E	70_S	2.655	1.00
40_I	46_A	2.620	1.00
142_D	145_R	2.554	1.00
76_R	96_K	2.503	1.00
66_R	103_Q	2.491	1.00
15_I	60_L	2.318	1.00
55_F	61_S	2.266	1.00
21_Q	128_S	2.259	1.00
74_W	98_K	2.197	1.00
47_E	67_I	2.109	1.00
14_V	35_F	2.047	1.00
14_V	129_Y	2.033	1.00
17_N	21_Q	2.019	1.00
106_S	110_E	2.006	1.00
129_Y	148_M	1.999	1.00
71_T	75_L	1.957	0.99
54_L	65_V	1.854	0.99
6_G	93_I	1.774	0.99
46_A	74_W	1.770	0.99
147_V	151_F	1.679	0.98
130_W	152_A	1.650	0.98
127_V	131_Y	1.648	0.98
23_M	58_V	1.639	0.98
10_N	143_V	1.639	0.98
79_L	90_P	1.546	0.97
50_M	102_L	1.534	0.97
47_E	102_L	1.530	0.97
26_R	123_G	1.501	0.97
47_E	51_Y	1.481	0.96
20_G	103_Q	1.481	0.96
128_S	131_Y	1.435	0.96
74_W	96_K	1.359	0.94
16_C	20_G	1.311	0.93
71_T	151_F	1.305	0.93
58_V	61_S	1.257	0.91
78_K	93_I	1.253	0.91
104_L	111_I	1.215	0.90
60_L	64_D	1.211	0.90
40_I	49_A	1.206	0.89
23_M	113_M	1.195	0.89
71_T	150_E	1.194	0.89
23_M	88_T	1.178	0.88
130_W	133_V	1.173	0.88
16_C	101_L	1.172	0.88
51_Y	65_V	1.161	0.88
32_S	50_M	1.159	0.88
5_D	93_I	1.154	0.87
24_W	127_V	1.142	0.87
26_R	31_H	1.124	0.86
24_W	132_P	1.111	0.85
12_G	99_W	1.096	0.84
69_A	151_F	1.093	0.84
143_V	147_V	1.092	0.84
13_I	50_M	1.039	0.81
113_M	116_S	1.032	0.81
125_R	135_Q	1.027	0.80
99_W	137_V	1.022	0.80
68_L	153_S	1.020	0.80
10_N	25_A	1.017	0.80
33_W	36_P	1.008	0.79
16_C	129_Y	1.005	0.79
5_D	84_V	0.997	0.78
112_N	115_T	0.972	0.77
79_L	85_R	0.958	0.75
128_S	133_V	0.953	0.75
24_W	125_R	0.948	0.75
59_G	113_M	0.945	0.74
61_S	64_D	0.914	0.72
75_L	143_V	0.910	0.72
107_G	110_E	0.908	0.71
23_M	119_P	0.881	0.69
15_I	65_V	0.870	0.68
10_N	97_Q	0.868	0.68
75_L	147_V	0.859	0.67
79_L	89_K	0.857	0.67
131_Y	145_R	0.855	0.67
127_V	135_Q	0.850	0.66
69_A	154_V	0.850	0.66
55_F	115_T	0.846	0.66
104_L	124_W	0.838	0.65
79_L	83_L	0.832	0.65
51_Y	102_L	0.821	0.64
16_C	148_M	0.819	0.63
14_V	132_P	0.808	0.62
88_T	91_V	0.799	0.62
36_P	144_Y	0.798	0.61
108_D	111_I	0.792	0.61
131_Y	135_Q	0.791	0.61
35_F	132_P	0.788	0.60
15_I	58_V	0.784	0.60
5_D	85_R	0.783	0.60
18_R	107_G	0.779	0.60
55_F	116_S	0.774	0.59
11_V	143_V	0.773	0.59
10_N	100_F	0.773	0.59
113_M	152_A	0.763	0.58
58_V	154_V	0.757	0.57
46_A	100_F	0.753	0.57
105_V	108_D	0.753	0.57
22_V	35_F	0.752	0.57
51_Y	55_F	0.750	0.57
48_Q	125_R	0.749	0.57
9_P	96_K	0.749	0.57
73_N	98_K	0.747	0.56
68_L	101_L	0.743	0.56
104_L	110_E	0.742	0.56
8_R	11_V	0.738	0.55
80_P	97_Q	0.732	0.55
111_I	124_W	0.731	0.55
81_K	84_V	0.730	0.55
129_Y	132_P	0.730	0.55
134_R	149_K	0.724	0.54
145_R	149_K	0.719	0.54
122_D	141_R	0.716	0.53
35_F	136_V	0.699	0.51
85_R	132_P	0.694	0.51
84_V	89_K	0.691	0.51
99_W	124_W	0.686	0.50
10_N	35_F	0.680	0.50
49_A	143_V	0.676	0.49
79_L	87_D	0.674	0.49
29_G	32_S	0.671	0.49
16_C	68_L	0.670	0.48
73_N	96_K	0.669	0.48
13_I	23_M	0.664	0.48
146_R	150_E	0.659	0.47
87_D	91_V	0.656	0.47
80_P	139_F	0.656	0.47
123_G	142_D	0.656	0.47
101_L	129_Y	0.655	0.47
22_V	132_P	0.652	0.47
129_Y	133_V	0.649	0.46
65_V	105_V	0.646	0.46
28_F	131_Y	0.645	0.46
42_P	116_S	0.645	0.46
6_G	84_V	0.643	0.46
87_D	125_R	0.643	0.46
6_G	85_R	0.639	0.45
48_Q	118_T	0.637	0.45
12_G	137_V	0.631	0.44
71_T	98_K	0.631	0.44
33_W	144_Y	0.631	0.44
128_S	149_K	0.629	0.44
128_S	146_R	0.629	0.44
36_P	99_W	0.627	0.44
75_L	150_E	0.625	0.44
101_L	155_V	0.621	0.43
64_D	106_S	0.617	0.43
16_C	155_V	0.615	0.43
80_P	151_F	0.610	0.42
74_W	97_Q	0.606	0.42
30_Q	142_D	0.605	0.42
51_Y	67_I	0.604	0.42
135_Q	155_V	0.602	0.42
25_A	111_I	0.601	0.41
19_Q	146_R	0.601	0.41
80_P	99_W	0.599	0.41
128_S	135_Q	0.598	0.41
99_W	126_W	0.595	0.41
64_D	104_L	0.591	0.40
78_K	111_I	0.589	0.40
19_Q	141_R	0.589	0.40
50_M	60_L	0.588	0.40
23_M	86_W	0.585	0.40
55_F	60_L	0.584	0.40
28_F	119_P	0.581	0.39
60_L	65_V	0.580	0.39
119_P	123_G	0.579	0.39
70_S	74_W	0.576	0.39
65_V	102_L	0.574	0.39
11_V	74_W	0.574	0.39
138_S	155_V	0.573	0.39
108_D	124_W	0.567	0.38
46_A	107_G	0.566	0.38
133_V	148_M	0.557	0.37
19_Q	107_G	0.557	0.37
99_W	144_Y	0.557	0.37
20_G	112_N	0.556	0.37
135_Q	138_S	0.555	0.37
27_R	34_Q	0.554	0.37
128_S	138_S	0.554	0.37
30_Q	122_D	0.553	0.37
15_I	23_M	0.552	0.37
61_S	67_I	0.551	0.37
16_C	134_R	0.550	0.36
71_T	96_K	0.547	0.36
25_A	124_W	0.546	0.36
54_L	80_P	0.544	0.36
111_I	155_V	0.542	0.36
36_P	139_F	0.542	0.36
11_V	49_A	0.538	0.35
84_V	92_C	0.536	0.35
35_F	147_V	0.528	0.34
69_A	101_L	0.527	0.34
82_R	85_R	0.525	0.34
32_S	115_T	0.523	0.34
50_M	100_F	0.523	0.34
99_W	139_F	0.520	0.34
46_A	98_K	0.520	0.34
35_F	138_S	0.519	0.34
32_S	40_I	0.518	0.33
148_M	155_V	0.517	0.33
108_D	114_Q	0.517	0.33
91_V	105_V	0.516	0.33
55_F	58_V	0.513	0.33
134_R	138_S	0.511	0.33
86_W	111_I	0.510	0.33
142_D	146_R	0.507	0.32
78_K	92_C	0.506	0.32
113_M	140_K	0.505	0.32
136_V	141_R	0.502	0.32
17_N	72_R	0.502	0.32
12_G	36_P	0.502	0.32
73_N	146_R	0.502	0.32
65_V	136_V	0.502	0.32
42_P	55_F	0.501	0.32
30_Q	83_L	0.500	0.32

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
4s2xA	1	0.892	100	0.584	Contact Map
1f3yA	1	0.8693	100	0.595	Contact Map
4ickA	1	0.7841	99.8	0.713	Contact Map
3fcmA	2	0.8068	99.8	0.717	Contact Map
2qjtB	2	0.8011	99.8	0.72	Contact Map
2o1cA	1	0.8011	99.8	0.725	Contact Map
4mpoA	4	0.7955	99.8	0.726	Contact Map
3f6aA	2	0.8125	99.7	0.728	Contact Map
3grnA	2	0.7557	99.7	0.728	Contact Map
3smdA	2	0.6875	99.7	0.729	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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