RPOD - HALSA - GREMLIN Contacts

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RPOD - DNA-directed RNA polymerase subunit D

UniProt:	Q9HQJ4	Sequences: MSSQDFDVEFVDRDDREARFVVRNITPAFANGIRRAILVDVPTLSIDTVRFVENSSVMFDEQLGLRLGLVPLTTPEDYAAGEAVTLALDVEGPGTAYSGDLVSNDPEVEAADENIPIIELKDDQRLELEADAVMGHGRDHAKHQGGVAVGYRHLQRVHVVGDSPEYADDDPQMLRGVIEEDDELVPTDDFDNDLTTRYPGKEVEIEDVDGAFVFHVESDGSMPVEELVLRAVDTLVDRADELEQAVQL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	248 (240)
Sequences:	814 (556)
Seq/√Len:	35.9

HALSA - RPOD
SULSO - RPOD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
70_V	117_I	6.620	1.00
37_I	227_L	5.646	1.00
91_E	125_R	4.353	1.00
216_V	228_V	3.830	1.00
95_T	116_P	3.332	1.00
79_A	82_E	3.316	1.00
192_N	195_T	3.289	1.00
101_L	130_A	3.205	1.00
89_D	127_E	3.197	1.00
56_S	120_L	3.134	1.00
195_T	198_Y	3.133	1.00
72_L	132_A	3.092	1.00
52_V	127_E	2.938	1.00
139_D	143_H	2.928	1.00
58_M	118_I	2.759	1.00
89_D	125_R	2.474	1.00
78_Y	82_E	2.467	1.00
103_S	107_E	2.438	1.00
230_R	233_D	2.437	1.00
76_E	79_A	2.423	1.00
46_I	67_L	2.409	1.00
173_M	178_I	2.253	0.99
37_I	216_V	2.232	0.99
173_M	195_T	2.201	0.99
174_L	178_I	2.198	0.99
170_D	174_L	2.180	0.99
20_F	30_A	2.145	0.99
170_D	173_M	2.138	0.99
33_I	228_V	2.136	0.99
192_N	198_Y	2.100	0.99
53_E	125_R	2.050	0.99
188_D	191_D	2.029	0.99
49_V	67_L	2.009	0.98
173_M	192_N	1.972	0.98
218_S	227_L	1.885	0.98
76_E	82_E	1.869	0.97
50_R	131_D	1.865	0.97
85_T	129_E	1.842	0.97
10_F	18_A	1.812	0.97
31_N	34_R	1.779	0.97
51_F	128_L	1.738	0.96
174_L	192_N	1.616	0.94
13_R	18_A	1.608	0.94
13_R	225_E	1.599	0.94
51_F	64_G	1.588	0.94
56_S	118_I	1.588	0.94
166_Y	173_M	1.576	0.93
21_V	190_F	1.537	0.92
53_E	127_E	1.536	0.92
160_V	204_E	1.501	0.91
104_N	107_E	1.487	0.91
12_D	19_R	1.480	0.91
23_R	211_A	1.454	0.90
166_Y	169_D	1.422	0.89
6_F	22_V	1.402	0.88
22_V	25_I	1.401	0.88
176_G	187_T	1.400	0.88
169_D	174_L	1.386	0.88
74_T	84_V	1.380	0.88
171_P	174_L	1.375	0.87
98_S	115_I	1.353	0.87
86_L	98_S	1.351	0.86
25_I	29_F	1.342	0.86
118_I	126_L	1.331	0.86
197_R	200_G	1.328	0.85
92_G	121_K	1.322	0.85
26_T	212_F	1.284	0.83
195_T	199_P	1.265	0.83
135_G	139_D	1.260	0.82
166_Y	174_L	1.253	0.82
165_E	197_R	1.249	0.82
44_L	74_T	1.244	0.81
40_D	238_R	1.235	0.81
27_P	151_Y	1.226	0.80
22_V	30_A	1.223	0.80
101_L	224_V	1.204	0.79
137_G	145_G	1.198	0.79
92_G	212_F	1.188	0.78
173_M	198_Y	1.183	0.78
43_T	219_D	1.180	0.78
9_E	22_V	1.169	0.77
40_D	136_H	1.154	0.76
10_F	224_V	1.146	0.76
75_P	234_T	1.139	0.75
38_L	144_Q	1.138	0.75
101_L	124_Q	1.138	0.75
44_L	222_M	1.134	0.75
173_M	177_V	1.120	0.74
192_N	199_P	1.119	0.74
88_L	128_L	1.094	0.72
26_T	36_A	1.085	0.72
86_L	103_S	1.079	0.71
58_M	63_L	1.079	0.71
24_N	210_G	1.069	0.71
170_D	192_N	1.057	0.70
58_M	222_M	1.038	0.68
31_N	35_R	1.032	0.68
99_G	114_N	1.031	0.68
102_V	105_D	1.030	0.68
40_D	234_T	1.025	0.67
199_P	205_I	1.025	0.67
174_L	177_V	1.021	0.67
36_A	40_D	1.009	0.66
95_T	159_V	1.003	0.66
111_A	132_A	1.003	0.66
170_D	178_I	1.001	0.65
48_T	131_D	0.984	0.64
174_L	195_T	0.975	0.63
217_E	220_G	0.972	0.63
77_D	96_A	0.971	0.63
117_I	231_A	0.969	0.63
168_D	172_Q	0.940	0.60
47_D	133_V	0.929	0.60
193_D	196_T	0.922	0.59
175_R	178_I	0.921	0.59
166_Y	170_D	0.920	0.59
174_L	198_Y	0.920	0.59
156_R	206_E	0.920	0.59
170_D	201_K	0.915	0.58
46_I	49_V	0.912	0.58
11_V	21_V	0.910	0.58
234_T	238_R	0.904	0.57
30_A	37_I	0.901	0.57
15_D	224_V	0.898	0.57
8_V	104_N	0.896	0.57
80_A	85_T	0.895	0.57
158_H	204_E	0.891	0.56
59_F	62_Q	0.886	0.56
17_E	215_H	0.883	0.56
237_D	241_E	0.882	0.56
20_F	214_F	0.875	0.55
170_D	195_T	0.874	0.55
159_V	165_E	0.867	0.54
165_E	173_M	0.866	0.54
18_A	181_D	0.865	0.54
16_R	246_V	0.856	0.53
232_V	236_V	0.851	0.53
72_L	84_V	0.850	0.53
6_F	25_I	0.841	0.52
160_V	163_S	0.841	0.52
58_M	77_D	0.834	0.51
109_E	113_E	0.826	0.51
176_G	188_D	0.826	0.51
224_V	238_R	0.824	0.50
166_Y	195_T	0.821	0.50
100_D	120_L	0.812	0.49
58_M	62_Q	0.809	0.49
97_Y	100_D	0.809	0.49
101_L	181_D	0.806	0.49
53_E	63_L	0.803	0.49
21_V	211_A	0.800	0.48
171_P	176_G	0.792	0.48
57_V	89_D	0.790	0.48
163_S	184_L	0.789	0.47
86_L	101_L	0.787	0.47
72_L	85_T	0.787	0.47
87_A	127_E	0.786	0.47
37_I	146_G	0.785	0.47
150_G	215_H	0.780	0.47
46_I	132_A	0.770	0.46
46_I	62_Q	0.766	0.45
44_L	67_L	0.765	0.45
10_F	76_E	0.764	0.45
170_D	175_R	0.761	0.45
108_V	128_L	0.755	0.45
36_A	235_L	0.754	0.44
184_L	239_A	0.748	0.44
28_A	181_D	0.746	0.44
22_V	33_I	0.742	0.43
10_F	24_N	0.742	0.43
89_D	242_L	0.742	0.43
215_H	228_V	0.740	0.43
127_E	215_H	0.739	0.43
164_P	182_D	0.736	0.43
44_L	226_E	0.736	0.43
10_F	13_R	0.732	0.43
119_E	143_H	0.730	0.42
228_V	231_A	0.723	0.42
104_N	109_E	0.721	0.42
166_Y	194_L	0.719	0.41
103_S	106_P	0.714	0.41
93_P	121_K	0.711	0.41
157_V	170_D	0.711	0.41
171_P	175_R	0.710	0.41
46_I	134_M	0.709	0.41
81_G	242_L	0.707	0.40
24_N	63_L	0.706	0.40
193_D	198_Y	0.699	0.40
63_L	218_S	0.697	0.40
52_V	101_L	0.695	0.39
195_T	201_K	0.694	0.39
41_V	183_E	0.694	0.39
173_M	201_K	0.692	0.39
215_H	218_S	0.690	0.39
12_D	16_R	0.689	0.39
139_D	154_L	0.689	0.39
63_L	84_V	0.688	0.39
20_F	228_V	0.688	0.39
173_M	176_G	0.687	0.39
161_G	204_E	0.687	0.39
43_T	54_N	0.684	0.39
154_L	211_A	0.683	0.38
72_L	133_V	0.683	0.38
56_S	126_L	0.677	0.38
27_P	227_L	0.675	0.38
8_V	123_D	0.675	0.38
44_L	113_E	0.674	0.38
39_V	43_T	0.674	0.38
116_P	119_E	0.673	0.38
156_R	223_P	0.665	0.37
57_V	235_L	0.664	0.37
114_N	216_V	0.660	0.37
90_V	94_G	0.660	0.37
222_M	230_R	0.660	0.37
18_A	225_E	0.657	0.36
70_V	213_V	0.656	0.36
236_V	240_D	0.656	0.36
72_L	97_Y	0.655	0.36
169_D	173_M	0.653	0.36
89_D	130_A	0.650	0.36
101_L	110_A	0.648	0.36
190_F	194_L	0.648	0.36
40_D	56_S	0.647	0.36
29_F	219_D	0.643	0.35
25_I	33_I	0.641	0.35
67_L	77_D	0.641	0.35
135_G	143_H	0.640	0.35
71_P	115_I	0.638	0.35
99_G	113_E	0.637	0.35
98_S	113_E	0.635	0.35
153_H	157_V	0.635	0.35
178_I	192_N	0.634	0.35
81_G	111_A	0.631	0.34
18_A	224_V	0.628	0.34
142_K	145_G	0.624	0.34
154_L	208_V	0.623	0.34
40_D	120_L	0.623	0.34
214_F	217_E	0.622	0.34
14_D	18_A	0.620	0.33
157_V	196_T	0.618	0.33
9_E	114_N	0.615	0.33
152_R	207_D	0.615	0.33
134_M	230_R	0.614	0.33
114_N	122_D	0.614	0.33
74_T	108_V	0.613	0.33
9_E	216_V	0.611	0.33
72_L	240_D	0.610	0.33
215_H	227_L	0.608	0.33
165_E	201_K	0.608	0.33
5_D	24_N	0.607	0.32
159_V	163_S	0.606	0.32
191_D	198_Y	0.605	0.32
152_R	157_V	0.604	0.32
156_R	208_V	0.604	0.32
226_E	230_R	0.603	0.32
74_T	151_Y	0.603	0.32
223_P	227_L	0.602	0.32
25_I	62_Q	0.601	0.32
18_A	231_A	0.598	0.32
67_L	76_E	0.595	0.32
106_P	176_G	0.592	0.31
120_L	168_D	0.592	0.31
20_F	216_V	0.592	0.31
7_D	24_N	0.592	0.31
127_E	130_A	0.591	0.31
43_T	124_Q	0.590	0.31
47_D	131_D	0.589	0.31
14_D	222_M	0.589	0.31
46_I	147_V	0.588	0.31
36_A	234_T	0.585	0.31
167_A	171_P	0.585	0.31
196_T	200_G	0.584	0.31
57_V	132_A	0.583	0.31
193_D	199_P	0.582	0.31
106_P	134_M	0.576	0.30
61_E	66_R	0.575	0.30
67_L	117_I	0.575	0.30
32_G	62_Q	0.575	0.30
25_I	241_E	0.574	0.30
146_G	219_D	0.573	0.30
50_R	129_E	0.573	0.30
146_G	149_V	0.572	0.30
182_D	185_V	0.571	0.30
194_L	197_R	0.571	0.30
225_E	229_L	0.571	0.30
12_D	102_V	0.570	0.30
103_S	110_A	0.570	0.30
62_Q	122_D	0.570	0.30
33_I	232_V	0.568	0.30
146_G	227_L	0.568	0.30
117_I	156_R	0.567	0.29
176_G	185_V	0.566	0.29
28_A	139_D	0.566	0.29
30_A	34_R	0.565	0.29
149_V	153_H	0.562	0.29
54_N	88_L	0.562	0.29
77_D	97_Y	0.561	0.29
87_A	129_E	0.559	0.29
154_L	213_V	0.558	0.29
14_D	17_E	0.558	0.29
97_Y	116_P	0.558	0.29
83_A	131_D	0.557	0.29
56_S	127_E	0.557	0.29
137_G	144_Q	0.557	0.29
151_Y	214_F	0.557	0.29
64_G	85_T	0.556	0.29
41_V	59_F	0.556	0.29
196_T	199_P	0.555	0.29
43_T	134_M	0.555	0.29
47_D	142_K	0.555	0.29
37_I	147_V	0.552	0.28
43_T	69_L	0.552	0.28
8_V	20_F	0.552	0.28
167_A	175_R	0.550	0.28
32_G	147_V	0.547	0.28
9_E	21_V	0.546	0.28
172_Q	237_D	0.546	0.28
75_P	223_P	0.545	0.28
101_L	242_L	0.545	0.28
77_D	113_E	0.545	0.28
167_A	170_D	0.543	0.28
37_I	141_A	0.542	0.28
197_R	201_K	0.542	0.28
69_L	102_V	0.539	0.27
155_Q	238_R	0.538	0.27
130_A	169_D	0.538	0.27
82_E	85_T	0.537	0.27
47_D	151_Y	0.534	0.27
33_I	240_D	0.534	0.27
169_D	192_N	0.533	0.27
169_D	175_R	0.532	0.27
74_T	224_V	0.531	0.27
119_E	212_F	0.530	0.27
51_F	214_F	0.530	0.27
166_Y	192_N	0.530	0.27
43_T	62_Q	0.528	0.27
44_L	80_A	0.528	0.27
160_V	206_E	0.527	0.27
73_T	109_E	0.526	0.27
229_L	233_D	0.525	0.27
44_L	48_T	0.525	0.27
90_V	184_L	0.524	0.26
19_R	191_D	0.523	0.26
130_A	158_H	0.521	0.26
158_H	206_E	0.519	0.26
80_A	150_G	0.517	0.26
140_H	145_G	0.515	0.26
98_S	227_L	0.514	0.26
171_P	191_D	0.513	0.26
113_E	164_P	0.513	0.26
171_P	192_N	0.509	0.25
89_D	126_L	0.509	0.25
190_F	198_Y	0.509	0.25
20_F	25_I	0.507	0.25
109_E	132_A	0.506	0.25
30_A	185_V	0.504	0.25
243_E	246_V	0.503	0.25
222_M	227_L	0.501	0.25
88_L	117_I	0.500	0.25
56_S	157_V	0.500	0.25

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
4c2mC	1	1	100	0.253	Contact Map
2pa8D	1	0.9637	100	0.289	Contact Map
4qjvA	1	0.9798	100	0.308	Contact Map
3h0gC	1	0.9315	100	0.346	Contact Map
1twfC	1	0.9395	100	0.348	Contact Map
2a6hA	2	0.8347	100	0.507	Contact Map
4noiA	2	0.8306	100	0.51	Contact Map
1bdfA	4	0.8387	100	0.523	Contact Map
4yfkA	2	0.8589	100	0.524	Contact Map
2pa8L	1	0.3589	95	0.931	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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