RPOE - BACSU - GREMLIN Contacts

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RPOE - DNA-directed RNA polymerase subunit delta

UniProt:	P12464	Sequences: MGIKQYSQEELKEMALVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYTDLNIDGRFLALSDQTWGLRSWYPYDQLDEETQPTVKAKKKKAKKAVEEDLDLDEFEEIDEDDLDLDEVEEELDLEADDFDEEDLDEDDDDLEIEEDIIDEDDEDYDDEEEEIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	173 (168)
Sequences:	408 (326)
Seq/√Len:	25.2

BACSU - RPOE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
124_D	130_E	3.797	1.00
47_K	50_E	3.240	1.00
16_L	85_D	3.197	1.00
102_A	105_A	2.801	0.99
37_L	55_I	2.681	0.99
160_E	168_E	2.406	0.98
58_F	87_L	2.392	0.98
152_E	155_E	2.372	0.98
7_S	10_E	2.327	0.98
27_H	39_E	2.266	0.98
44_L	79_R	2.228	0.97
118_I	121_D	2.220	0.97
133_D	152_E	2.152	0.97
99_K	102_A	2.114	0.96
71_L	82_Y	2.058	0.96
40_I	58_F	2.013	0.95
96_K	99_K	1.883	0.93
110_L	134_L	1.746	0.90
125_L	128_V	1.728	0.90
31_V	36_L	1.700	0.89
75_T	90_E	1.696	0.89
31_V	35_E	1.695	0.89
146_E	154_E	1.693	0.89
14_M	19_I	1.635	0.87
97_A	102_A	1.627	0.87
112_L	115_F	1.623	0.86
127_E	137_D	1.617	0.86
163_E	166_D	1.612	0.86
107_E	110_L	1.610	0.86
135_E	169_E	1.592	0.85
101_K	104_K	1.572	0.85
113_D	119_D	1.555	0.84
54_R	79_R	1.526	0.83
49_E	53_D	1.505	0.82
26_E	29_K	1.501	0.82
127_E	130_E	1.494	0.81
115_F	120_E	1.487	0.81
41_A	48_K	1.468	0.80
149_D	156_D	1.421	0.78
145_D	149_D	1.419	0.78
86_Q	90_E	1.410	0.77
123_L	132_L	1.408	0.77
19_I	44_L	1.405	0.77
44_L	58_F	1.399	0.77
31_V	58_F	1.376	0.76
137_D	140_D	1.352	0.74
13_E	36_L	1.338	0.73
50_E	89_E	1.337	0.73
30_P	86_Q	1.334	0.73
77_G	82_Y	1.325	0.73
8_Q	88_D	1.309	0.72
64_I	77_G	1.303	0.71
15_A	18_E	1.295	0.71
58_F	61_D	1.288	0.71
46_V	51_L	1.286	0.70
27_H	73_D	1.271	0.69
122_D	147_D	1.264	0.69
69_L	79_R	1.258	0.69
132_L	144_L	1.255	0.68
21_H	25_E	1.238	0.67
52_G	91_T	1.235	0.67
25_E	90_E	1.234	0.67
149_D	155_E	1.231	0.67
24_F	84_Y	1.222	0.66
111_D	135_E	1.211	0.66
118_I	123_L	1.211	0.66
120_E	123_L	1.205	0.65
11_L	86_Q	1.177	0.63
73_D	79_R	1.172	0.63
157_I	160_E	1.164	0.63
19_I	73_D	1.152	0.62
32_P	35_E	1.139	0.61
152_E	157_I	1.136	0.61
100_K	103_K	1.133	0.60
36_L	45_G	1.127	0.60
120_E	130_E	1.125	0.60
39_E	42_S	1.120	0.59
37_L	40_I	1.109	0.59
37_L	79_R	1.106	0.58
50_E	55_I	1.087	0.57
49_E	125_L	1.069	0.56
99_K	103_K	1.062	0.55
118_I	141_E	1.059	0.55
29_K	75_T	1.056	0.55
127_E	132_L	1.049	0.54
40_I	128_V	1.047	0.54
145_D	148_D	1.036	0.53
19_I	43_L	1.025	0.53
21_H	28_K	1.023	0.53
11_L	14_M	1.008	0.51
38_N	42_S	1.003	0.51
35_E	52_G	1.001	0.51
45_G	55_I	1.000	0.51
135_E	164_D	0.994	0.50
109_D	117_E	0.976	0.49
97_A	104_K	0.970	0.49
6_Y	73_D	0.969	0.49
156_D	165_Y	0.959	0.48
37_L	94_T	0.957	0.48
54_R	84_Y	0.948	0.47
122_D	125_L	0.946	0.47
27_H	51_L	0.944	0.47
117_E	122_D	0.934	0.46
9_E	89_E	0.930	0.46
71_L	77_G	0.926	0.45
97_A	101_K	0.924	0.45
113_D	124_D	0.922	0.45
141_E	144_L	0.921	0.45
57_Q	61_D	0.914	0.45
133_D	136_A	0.901	0.44
109_D	112_L	0.897	0.43
37_L	51_L	0.889	0.43
42_S	153_I	0.888	0.43
27_H	42_S	0.887	0.43
163_E	169_E	0.887	0.43
35_E	108_E	0.887	0.43
110_L	144_L	0.886	0.43
44_L	88_D	0.885	0.43
11_L	43_L	0.880	0.42
113_D	116_E	0.880	0.42
3_I	97_A	0.869	0.41
24_F	56_A	0.869	0.41
138_D	143_D	0.869	0.41
92_Q	98_K	0.858	0.41
164_D	168_E	0.857	0.41
86_Q	102_A	0.855	0.40
6_Y	118_I	0.852	0.40
9_E	117_E	0.851	0.40
37_L	44_L	0.838	0.39
115_F	118_I	0.831	0.39
132_L	142_E	0.826	0.38
87_L	93_P	0.826	0.38
71_L	75_T	0.816	0.38
61_D	69_L	0.815	0.38
126_D	129_E	0.813	0.38
33_F	69_L	0.800	0.37
111_D	121_D	0.800	0.37
122_D	132_L	0.797	0.36
70_A	91_T	0.796	0.36
110_L	117_E	0.789	0.36
38_N	51_L	0.782	0.35
33_F	41_A	0.781	0.35
7_S	93_P	0.780	0.35
6_Y	9_E	0.778	0.35
71_L	89_E	0.775	0.35
98_K	101_K	0.772	0.35
43_L	67_R	0.761	0.34
153_I	158_I	0.758	0.34
87_L	91_T	0.748	0.33
16_L	80_S	0.744	0.33
2_G	28_K	0.741	0.33
27_H	79_R	0.740	0.33
41_A	79_R	0.735	0.32
129_E	147_D	0.731	0.32
150_D	154_E	0.730	0.32
145_D	166_D	0.724	0.32
130_E	151_L	0.722	0.32
138_D	144_L	0.716	0.31
157_I	167_D	0.702	0.30
133_D	144_L	0.698	0.30
127_E	139_F	0.697	0.30
117_E	142_E	0.693	0.30
18_E	80_S	0.690	0.30
80_S	98_K	0.689	0.30
64_I	93_P	0.685	0.29
3_I	23_L	0.684	0.29
32_P	97_A	0.681	0.29
131_E	167_D	0.680	0.29
57_Q	94_T	0.675	0.29
149_D	152_E	0.673	0.29
10_E	86_Q	0.670	0.28
6_Y	43_L	0.668	0.28
117_E	127_E	0.663	0.28
48_K	103_K	0.655	0.27
34_Q	54_R	0.653	0.27
57_Q	60_T	0.651	0.27
37_L	73_D	0.646	0.27
24_F	57_Q	0.642	0.27
143_D	147_D	0.636	0.26
18_E	115_F	0.634	0.26
142_E	164_D	0.629	0.26
33_F	58_F	0.628	0.26
5_Q	77_G	0.628	0.26
16_L	30_P	0.627	0.26
124_D	129_E	0.620	0.26
140_D	169_E	0.619	0.25
126_D	167_D	0.615	0.25
10_E	90_E	0.613	0.25
134_L	145_D	0.611	0.25
135_E	163_E	0.610	0.25
164_D	167_D	0.599	0.24
36_L	62_L	0.599	0.24
35_E	93_P	0.595	0.24
136_A	148_D	0.593	0.24
148_D	157_I	0.593	0.24
147_D	152_E	0.590	0.24
150_D	167_D	0.589	0.24
97_A	112_L	0.589	0.24
23_L	153_I	0.586	0.24
16_L	84_Y	0.585	0.24
59_Y	66_G	0.583	0.24
123_L	126_D	0.582	0.23
147_D	159_D	0.582	0.23
30_P	77_G	0.580	0.23
17_V	70_A	0.572	0.23
10_E	93_P	0.570	0.23
128_V	168_E	0.567	0.23
155_E	159_D	0.566	0.23
61_D	93_P	0.566	0.23
75_T	87_L	0.566	0.23
33_F	40_I	0.563	0.22
109_D	148_D	0.560	0.22
28_K	79_R	0.560	0.22
70_A	86_Q	0.560	0.22
130_E	149_D	0.559	0.22
96_K	100_K	0.559	0.22
4_K	7_S	0.554	0.22
39_E	64_I	0.552	0.22
69_L	87_L	0.552	0.22
137_D	156_D	0.549	0.22
141_E	159_D	0.547	0.22
159_D	167_D	0.547	0.22
106_V	160_E	0.545	0.22
153_I	160_E	0.545	0.22
19_I	70_A	0.542	0.21
50_E	110_L	0.541	0.21
22_E	92_Q	0.540	0.21
42_S	116_E	0.539	0.21
108_E	138_D	0.539	0.21
48_K	155_E	0.539	0.21
2_G	5_Q	0.537	0.21
11_L	88_D	0.536	0.21
3_I	59_Y	0.536	0.21
23_L	71_L	0.535	0.21
30_P	87_L	0.534	0.21
56_A	80_S	0.534	0.21
39_E	82_Y	0.531	0.21
24_F	81_W	0.529	0.21
31_V	62_L	0.526	0.21
14_M	33_F	0.526	0.21
19_I	40_I	0.525	0.21
53_D	129_E	0.522	0.20
62_L	67_R	0.519	0.20
133_D	168_E	0.519	0.20
8_Q	11_L	0.518	0.20
153_I	157_I	0.516	0.20
131_E	137_D	0.512	0.20
11_L	67_R	0.511	0.20
140_D	168_E	0.511	0.20
33_F	72_S	0.509	0.20
21_H	73_D	0.500	0.19
73_D	95_V	0.500	0.19

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
2krcA	1	0.5723	100	0.397	Contact Map
4u7aA	1	0	97.4	0.869	Contact Map
4fp9B	2	0.6185	89	0.914	Contact Map
4fdgB	1	0.0116	53.5	0.937	Contact Map
3q9sA	1	0.3931	36.9	0.943	Contact Map
1wj7A	1	0.5376	36.6	0.943	Contact Map
3go5A	1	0.3815	29.7	0.946	Contact Map
4bjqA	2	0.422	28.3	0.946	Contact Map
2ma3A	1	0.4277	28.1	0.946	Contact Map
3h93A	1	0.6012	24.9	0.948	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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