RPOD - SULSO - GREMLIN Contacts

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RPOD - DNA-directed RNA polymerase subunit D

UniProt:	P95989	Sequences: MSINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHRLALIPFMSEEALDTYRWPEECIECTENCEKCYTKIYIEAEAPNEPRMIYSKDIKSEDPSVVPISGDIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVSLSVVRYYPKVEILANCEKAVNVCPEGVFELKDGKLSVKNELSCTLCEECLRYCNGSIRISFVEDKYILEIESVGSLKPERILLEAGKSIIRKIEELEKKLVEVVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	265 (255)
Sequences:	810 (559)
Seq/√Len:	35.0

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
65_I	130_I	6.771	1.00
32_S	241_I	5.967	1.00
101_E	138_K	4.580	1.00
203_C	206_C	3.888	1.00
230_I	242_L	3.741	1.00
108_M	129_P	3.733	1.00
67_F	145_L	3.465	1.00
89_C	92_C	3.399	1.00
99_E	140_S	3.371	1.00
183_C	203_C	3.274	1.00
114_I	143_A	3.181	1.00
152_E	156_F	3.069	1.00
51_S	133_L	3.024	1.00
82_C	92_C	3.020	1.00
183_C	206_C	2.951	1.00
47_I	140_S	2.890	1.00
53_L	131_V	2.823	1.00
199_N	202_S	2.815	1.00
206_C	209_C	2.765	1.00
99_E	138_K	2.680	1.00
244_E	247_K	2.611	1.00
82_C	89_C	2.576	1.00
41_V	62_L	2.505	1.00
116_S	120_S	2.422	1.00
97_Y	115_K	2.335	0.99
183_C	209_C	2.265	0.99
15_L	25_V	2.236	0.99
48_E	138_K	2.121	0.99
32_S	230_I	2.099	0.99
232_S	241_I	2.083	0.99
203_C	209_C	1.990	0.98
5_L	13_I	1.966	0.98
39_M	74_D	1.963	0.98
44_V	62_L	1.956	0.98
28_I	242_L	1.952	0.98
117_E	120_S	1.926	0.98
26_N	29_R	1.834	0.97
51_S	131_V	1.816	0.97
46_F	141_L	1.752	0.96
45_Y	144_R	1.749	0.96
39_M	76_Y	1.717	0.95
95_K	142_E	1.702	0.95
46_F	59_A	1.691	0.95
176_C	195_L	1.675	0.95
16_V	201_L	1.650	0.94
180_V	188_F	1.645	0.94
189_E	198_K	1.638	0.94
173_L	218_R	1.610	0.94
183_C	188_F	1.605	0.93
184_P	209_C	1.581	0.93
48_E	140_S	1.572	0.93
177_E	193_G	1.572	0.93
35_Y	252_K	1.571	0.93
17_F	20_Y	1.534	0.92
98_I	141_L	1.523	0.92
111_S	128_I	1.519	0.91
189_E	192_D	1.489	0.91
20_Y	24_F	1.486	0.90
8_K	239_E	1.446	0.89
72_A	244_E	1.385	0.87
69_S	94_T	1.378	0.87
131_V	139_I	1.376	0.87
7_H	14_D	1.344	0.85
102_A	134_G	1.336	0.85
18_E	225_K	1.320	0.84
88_N	93_Y	1.298	0.83
189_E	199_N	1.296	0.83
8_K	13_I	1.294	0.83
70_E	248_S	1.292	0.83
96_I	111_S	1.285	0.83
174_A	216_S	1.266	0.82
206_C	210_L	1.263	0.82
188_F	203_C	1.261	0.81
186_G	206_C	1.252	0.81
21_P	226_Y	1.246	0.81
78_W	82_C	1.225	0.80
41_V	44_V	1.220	0.79
189_E	196_S	1.212	0.79
148_G	152_E	1.198	0.78
38_I	233_V	1.194	0.78
180_V	184_P	1.187	0.77
33_M	157_I	1.175	0.77
42_D	146_R	1.169	0.76
184_P	188_F	1.147	0.75
122_V	126_G	1.146	0.75
184_P	203_C	1.145	0.75
35_Y	248_S	1.139	0.74
150_G	158_P	1.136	0.74
5_L	238_P	1.129	0.74
22_L	164_V	1.117	0.73
102_A	226_Y	1.109	0.72
184_P	187_V	1.094	0.71
26_N	30_R	1.074	0.70
54_Y	57_I	1.065	0.69
19_G	224_D	1.062	0.69
124_I	145_L	1.059	0.69
25_V	32_S	1.059	0.69
35_Y	149_Y	1.058	0.69
191_K	196_S	1.048	0.68
184_P	206_C	1.047	0.68
17_F	25_V	1.045	0.68
116_S	119_P	1.034	0.67
171_E	218_R	1.027	0.66
39_M	69_S	1.018	0.66
251_R	255_E	1.012	0.65
53_L	236_L	1.000	0.64
208_E	211_R	0.998	0.64
53_L	58_L	0.990	0.63
210_L	219_I	0.983	0.63
108_M	172_I	0.983	0.63
112_K	127_D	0.979	0.63
21_P	31_A	0.979	0.63
183_C	186_G	0.976	0.62
58_L	232_S	0.966	0.61
39_M	236_L	0.957	0.61
88_N	95_K	0.954	0.61
248_S	252_K	0.949	0.60
206_C	212_Y	0.943	0.60
65_I	227_I	0.940	0.59
204_T	207_E	0.940	0.59
103_P	134_G	0.922	0.58
4_N	17_F	0.921	0.58
5_L	8_K	0.919	0.58
177_E	180_V	0.915	0.57
10_D	238_P	0.915	0.57
114_I	238_P	0.905	0.56
100_A	107_R	0.899	0.56
169_K	220_S	0.897	0.56
31_A	35_Y	0.896	0.56
77_R	81_E	0.894	0.55
195_L	200_E	0.891	0.55
2_S	94_T	0.886	0.55
43_D	144_R	0.882	0.54
52_P	99_E	0.880	0.54
180_V	195_L	0.873	0.54
180_V	190_L	0.872	0.54
110_Y	113_D	0.870	0.53
229_E	242_L	0.869	0.53
51_S	139_I	0.868	0.53
90_E	95_K	0.868	0.53
238_P	252_K	0.865	0.53
15_L	228_L	0.864	0.53
188_F	197_V	0.859	0.53
183_C	187_V	0.855	0.52
203_C	207_E	0.854	0.52
118_D	122_V	0.853	0.52
99_E	256_L	0.841	0.51
97_Y	140_S	0.841	0.51
178_K	214_N	0.840	0.51
178_K	208_E	0.840	0.51
163_V	229_E	0.830	0.50
47_I	114_I	0.824	0.50
33_M	75_T	0.821	0.49
201_L	209_C	0.821	0.49
143_A	182_V	0.819	0.49
53_L	57_I	0.817	0.49
132_L	156_F	0.802	0.48
114_I	137_Q	0.799	0.47
73_L	244_E	0.794	0.47
166_Y	170_V	0.790	0.47
242_L	245_A	0.789	0.47
172_I	179_A	0.789	0.47
167_Y	222_V	0.787	0.46
187_V	203_C	0.783	0.46
67_F	95_K	0.778	0.46
76_Y	150_G	0.778	0.46
20_Y	28_I	0.776	0.45
229_E	241_I	0.775	0.45
112_K	126_G	0.772	0.45
188_F	206_C	0.769	0.45
38_I	64_L	0.766	0.45
41_V	147_L	0.763	0.44
9_D	236_L	0.763	0.44
48_E	58_L	0.762	0.44
203_C	210_L	0.756	0.44
150_G	157_I	0.747	0.43
72_A	240_R	0.741	0.42
231_E	234_G	0.739	0.42
34_L	38_I	0.737	0.42
4_N	230_I	0.735	0.42
78_W	81_E	0.731	0.42
130_I	245_A	0.727	0.41
174_A	218_R	0.726	0.41
32_S	159_V	0.726	0.41
58_L	94_T	0.724	0.41
246_G	250_I	0.714	0.40
167_Y	225_K	0.713	0.40
39_M	240_R	0.713	0.40
79_P	246_G	0.712	0.40
12_R	229_E	0.711	0.40
67_F	94_T	0.707	0.40
75_T	91_K	0.706	0.40
198_K	201_L	0.703	0.39
117_E	122_V	0.702	0.39
252_K	260_L	0.702	0.39
114_I	123_P	0.700	0.39
16_V	225_K	0.694	0.39
6_L	256_L	0.689	0.38
169_K	222_V	0.687	0.38
23_E	39_M	0.687	0.38
67_F	146_R	0.686	0.38
9_D	12_R	0.686	0.38
178_K	212_Y	0.684	0.38
41_V	145_L	0.683	0.38
170_V	180_V	0.682	0.38
28_I	93_Y	0.680	0.37
49_N	55_D	0.678	0.37
127_D	230_I	0.673	0.37
93_Y	144_R	0.672	0.37
22_L	241_I	0.670	0.37
67_F	82_C	0.668	0.36
185_E	206_C	0.668	0.36
31_A	249_I	0.667	0.36
250_I	254_E	0.667	0.36
20_Y	255_E	0.663	0.36
39_M	126_G	0.663	0.36
24_F	249_I	0.662	0.36
13_I	60_H	0.662	0.36
114_I	141_L	0.660	0.36
191_K	194_K	0.657	0.36
27_A	57_I	0.657	0.36
94_T	138_K	0.656	0.36
96_I	114_I	0.654	0.35
6_L	16_V	0.654	0.35
119_P	147_L	0.652	0.35
100_A	112_K	0.651	0.35
156_F	159_V	0.650	0.35
31_A	248_S	0.648	0.35
165_R	170_V	0.644	0.35
240_R	244_E	0.643	0.35
52_P	249_I	0.643	0.35
117_E	121_V	0.639	0.34
198_K	202_S	0.639	0.34
254_E	257_E	0.639	0.34
116_S	122_V	0.639	0.34
62_L	130_I	0.636	0.34
111_S	126_G	0.636	0.34
35_Y	133_L	0.636	0.34
67_F	254_E	0.634	0.34
96_I	116_S	0.631	0.34
216_S	220_S	0.631	0.34
140_S	229_E	0.631	0.34
177_E	190_L	0.630	0.34
195_L	253_I	0.622	0.33
7_H	11_T	0.622	0.33
36_V	64_L	0.621	0.33
34_L	50_N	0.621	0.33
38_I	190_L	0.621	0.33
58_L	209_C	0.619	0.33
20_Y	57_I	0.616	0.32
41_V	57_I	0.615	0.32
39_M	62_L	0.614	0.32
25_V	29_R	0.614	0.32
67_F	213_C	0.614	0.32
38_I	49_N	0.613	0.32
24_F	33_M	0.611	0.32
38_I	147_L	0.611	0.32
237_K	241_I	0.610	0.32
159_V	233_V	0.610	0.32
34_L	222_V	0.610	0.32
230_I	248_S	0.609	0.32
25_V	147_L	0.608	0.32
168_P	252_K	0.607	0.32
77_R	80_E	0.606	0.32
193_G	196_S	0.605	0.32
186_G	203_C	0.604	0.32
19_G	123_P	0.603	0.31
148_G	156_F	0.603	0.31
13_I	238_P	0.602	0.31
12_R	18_E	0.600	0.31
165_R	221_F	0.598	0.31
109_I	133_L	0.597	0.31
118_D	123_P	0.596	0.31
182_V	188_F	0.596	0.31
121_V	141_L	0.593	0.31
69_S	235_S	0.586	0.30
186_G	189_E	0.585	0.30
99_E	143_A	0.584	0.30
66_P	128_I	0.583	0.30
96_I	143_A	0.582	0.30
57_I	156_F	0.581	0.30
113_D	133_L	0.580	0.30
173_L	191_K	0.580	0.30
43_D	146_R	0.579	0.30
52_P	194_K	0.579	0.30
39_M	160_S	0.579	0.30
14_D	201_L	0.578	0.30
65_I	123_P	0.577	0.30
11_T	241_I	0.576	0.30
68_M	181_N	0.573	0.29
24_F	233_V	0.572	0.29
119_P	122_V	0.572	0.29
228_L	231_E	0.571	0.29
133_L	181_N	0.571	0.29
110_Y	129_P	0.570	0.29
111_S	241_I	0.568	0.29
118_D	121_V	0.567	0.29
95_K	116_S	0.567	0.29
90_E	163_V	0.563	0.29
189_E	195_L	0.562	0.29
58_L	141_L	0.561	0.28
127_D	135_T	0.558	0.28
184_P	204_T	0.558	0.28
36_V	194_K	0.558	0.28
17_F	28_I	0.558	0.28
180_V	183_C	0.557	0.28
91_K	124_I	0.555	0.28
17_F	94_T	0.555	0.28
9_D	91_K	0.555	0.28
163_V	166_Y	0.554	0.28
203_C	212_Y	0.553	0.28
4_N	127_D	0.553	0.28
69_S	238_P	0.552	0.28
243_L	247_K	0.550	0.28
68_M	122_V	0.549	0.28
104_N	107_R	0.549	0.28
212_Y	215_G	0.548	0.28
159_V	241_I	0.548	0.28
21_P	65_I	0.548	0.28
36_V	112_K	0.546	0.27
98_I	123_P	0.546	0.27
159_V	162_S	0.545	0.27
61_R	153_H	0.543	0.27
236_L	244_E	0.542	0.27
41_V	160_S	0.542	0.27
169_K	237_K	0.542	0.27
185_E	204_T	0.541	0.27
130_I	169_K	0.539	0.27
204_T	209_C	0.538	0.27
182_V	203_C	0.538	0.27
194_K	214_N	0.538	0.27
179_A	217_I	0.536	0.27
32_S	154_A	0.536	0.27
122_V	145_L	0.536	0.27
51_S	140_S	0.535	0.27
15_L	208_E	0.534	0.27
102_A	107_R	0.531	0.26
162_S	166_Y	0.529	0.26
239_E	243_L	0.528	0.26
105_E	113_D	0.527	0.26
28_I	246_G	0.527	0.26
179_A	195_L	0.526	0.26
147_L	244_E	0.526	0.26
176_C	179_A	0.525	0.26
187_V	207_E	0.524	0.26
101_E	105_E	0.524	0.26
8_K	110_Y	0.524	0.26
61_R	155_K	0.523	0.26
256_L	259_K	0.522	0.26
185_E	188_F	0.522	0.26
185_E	209_C	0.521	0.26
119_P	123_P	0.521	0.26
9_D	257_E	0.520	0.26
13_I	245_A	0.519	0.26
133_L	246_G	0.518	0.26
50_N	168_P	0.518	0.26
97_Y	142_E	0.517	0.25
152_E	167_Y	0.517	0.25
115_K	141_L	0.516	0.25
47_I	88_N	0.514	0.25
19_G	128_I	0.514	0.25
82_C	88_N	0.513	0.25
24_F	106_P	0.512	0.25
148_G	215_G	0.511	0.25
7_H	12_R	0.510	0.25
13_I	239_E	0.510	0.25
45_Y	142_E	0.510	0.25
179_A	208_E	0.509	0.25
208_E	212_Y	0.509	0.25
23_E	214_N	0.509	0.25
242_L	246_G	0.509	0.25
23_E	152_E	0.508	0.25
185_E	210_L	0.508	0.25
171_E	220_S	0.507	0.25
205_L	208_E	0.507	0.25
173_L	195_L	0.507	0.25
76_Y	191_K	0.506	0.25
70_E	190_L	0.504	0.25
42_D	144_R	0.503	0.25
47_I	132_L	0.503	0.25
205_L	210_L	0.501	0.24
51_S	95_K	0.500	0.24

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
2pa8D	1	0.9962	100	0.246	Contact Map
4c2mC	1	0.9849	100	0.256	Contact Map
4qjvA	1	0.9547	100	0.316	Contact Map
3h0gC	1	0.9245	100	0.358	Contact Map
1twfC	1	0.9472	100	0.359	Contact Map
4noiA	2	0.8113	100	0.518	Contact Map
2a6hA	2	0.7962	100	0.524	Contact Map
1bdfA	4	0.8075	100	0.533	Contact Map
4yfkA	2	0.8453	100	0.537	Contact Map
1xerA	2	0.3283	93.5	0.939	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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