RPSD - BACSU - GREMLIN Contacts

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RPSD - RNA polymerase sigma-D factor

UniProt:	P10726	Sequences: MQSLNYEDQVLWTRWKEWKDPKAGDDLMRRYMPLVTYHVGRISVGLPKSVHKDDLMSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDWLPRTSREKTKKVEAAIEKLEQRYLRNVSPAEIAEELGMTVQDVVSTMNEGFFANLLSIDEKLHDQDDGENIQVMIRDDKNVPPEEKIMKDELIAQLAEKIHELSEKEQLVVSLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLKNLLEKVIQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	254 (228)
Sequences:	7555 (4531)
Seq/√Len:	300.1

ECOLI - RPOD RPOS FLIA RPOH
BACSU - RPSD SIGA RPSB RPSG RPSF RPSK RPSE RPSH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
118_L	122_Y	3.499	1.00
24_G	68_E	3.465	1.00
121_R	134_E	3.354	1.00
124_R	130_E	3.170	1.00
35_V	59_G	2.965	1.00
207_Q	211_S	2.928	1.00
129_A	139_V	2.882	1.00
117_K	134_E	2.752	1.00
14_R	20_D	2.703	1.00
25_D	29_R	2.647	1.00
229_L	234_I	2.632	1.00
212_L	226_V	2.251	1.00
114_A	134_E	2.235	1.00
233_R	236_Q	2.159	1.00
201_E	248_L	2.153	1.00
206_E	244_K	2.101	1.00
128_P	143_V	2.075	1.00
212_L	218_L	2.065	1.00
213_F	238_H	2.047	1.00
208_L	226_V	2.015	1.00
34_L	79_D	1.950	1.00
158_D	169_N	1.949	1.00
221_T	225_Q	1.919	1.00
200_H	207_Q	1.901	1.00
71_D	74_R	1.900	1.00
138_T	141_D	1.882	1.00
38_H	83_S	1.799	1.00
232_S	235_S	1.785	1.00
32_M	60_M	1.757	1.00
208_L	212_L	1.747	1.00
118_L	126_V	1.744	1.00
208_L	227_L	1.736	1.00
218_L	226_V	1.735	1.00
58_L	93_G	1.724	1.00
26_D	30_R	1.691	1.00
131_I	142_V	1.683	1.00
117_K	121_R	1.677	1.00
209_V	237_I	1.660	1.00
77_K	80_T	1.636	1.00
209_V	241_A	1.633	1.00
114_A	117_K	1.626	1.00
128_P	139_V	1.625	1.00
227_L	234_I	1.621	1.00
183_E	187_M	1.616	1.00
128_P	146_M	1.609	1.00
111_V	131_I	1.602	1.00
203_S	244_K	1.597	1.00
129_A	133_E	1.595	1.00
176_D	179_N	1.559	1.00
39_V	90_I	1.545	1.00
38_H	90_I	1.544	1.00
28_M	64_Y	1.527	1.00
218_L	222_E	1.523	1.00
158_D	171_Q	1.520	1.00
21_P	25_D	1.515	1.00
111_V	145_T	1.492	1.00
69_K	81_Y	1.486	1.00
56_M	60_M	1.480	1.00
36_T	56_M	1.479	1.00
59_G	90_I	1.436	1.00
203_S	206_E	1.399	1.00
128_P	142_V	1.392	1.00
39_V	56_M	1.382	1.00
118_L	134_E	1.377	1.00
168_E	173_M	1.370	1.00
233_R	237_I	1.350	1.00
139_V	143_V	1.342	1.00
45_G	49_S	1.335	1.00
114_A	118_L	1.315	1.00
67_L	78_F	1.309	1.00
118_L	124_R	1.304	1.00
114_A	135_L	1.303	1.00
78_F	82_A	1.295	1.00
115_I	146_M	1.294	1.00
132_A	142_V	1.264	1.00
206_E	240_K	1.246	1.00
16_K	73_S	1.244	1.00
107_K	141_D	1.243	1.00
35_V	63_L	1.234	1.00
137_M	145_T	1.223	1.00
39_V	52_K	1.218	1.00
210_V	245_L	1.197	1.00
204_E	207_Q	1.191	1.00
137_M	142_V	1.191	1.00
106_E	110_K	1.185	1.00
132_A	139_V	1.183	1.00
127_S	130_E	1.174	1.00
187_M	190_E	1.168	1.00
111_V	135_L	1.162	1.00
22_K	25_D	1.160	1.00
214_Y	238_H	1.146	1.00
107_K	145_T	1.139	1.00
208_L	211_S	1.123	1.00
40_G	52_K	1.123	1.00
126_V	130_E	1.122	1.00
66_A	82_A	1.119	1.00
14_R	18_W	1.119	1.00
190_E	194_Q	1.098	1.00
111_V	142_V	1.094	1.00
28_M	67_L	1.086	1.00
113_A	117_K	1.078	1.00
107_K	137_M	1.077	1.00
205_K	237_I	1.075	1.00
212_L	223_I	1.070	1.00
237_I	241_A	1.067	1.00
15_W	19_K	1.057	1.00
221_T	231_T	1.042	1.00
62_G	66_A	1.040	1.00
232_S	236_Q	1.040	1.00
192_I	196_A	1.037	1.00
220_L	224_G	1.030	1.00
50_V	93_G	1.030	1.00
132_A	137_M	1.007	1.00
119_E	126_V	1.001	1.00
122_Y	126_V	0.998	1.00
22_K	26_D	0.988	1.00
220_L	235_S	0.987	1.00
220_L	231_T	0.983	1.00
186_I	190_E	0.977	1.00
44_V	49_S	0.977	1.00
100_L	108_T	0.976	1.00
40_G	43_S	0.973	1.00
98_D	105_R	0.967	1.00
169_N	172_V	0.966	1.00
205_K	233_R	0.964	1.00
26_D	29_R	0.962	1.00
220_L	232_S	0.959	1.00
189_D	193_A	0.949	1.00
206_E	237_I	0.945	1.00
56_M	59_G	0.943	1.00
16_K	72_P	0.941	1.00
31_Y	79_D	0.929	1.00
194_Q	197_E	0.929	1.00
182_P	186_I	0.928	1.00
119_E	122_Y	0.928	1.00
155_L	159_E	0.926	1.00
20_D	23_A	0.922	1.00
65_D	69_K	0.922	1.00
181_P	184_E	0.915	1.00
188_K	192_I	0.910	1.00
118_L	131_I	0.906	1.00
27_L	67_L	0.905	1.00
115_I	131_I	0.904	1.00
16_K	19_K	0.896	1.00
122_Y	130_E	0.894	1.00
65_D	89_A	0.894	1.00
81_Y	85_R	0.892	1.00
87_R	91_I	0.888	1.00
183_E	186_I	0.887	1.00
101_P	104_S	0.882	1.00
243_F	247_N	0.881	1.00
204_E	208_L	0.878	1.00
114_A	131_I	0.877	1.00
209_V	229_L	0.872	1.00
43_S	52_K	0.868	1.00
19_K	23_A	0.868	1.00
157_I	171_Q	0.864	1.00
38_H	87_R	0.864	1.00
16_K	20_D	0.862	1.00
52_K	56_M	0.860	1.00
36_T	52_K	0.855	1.00
205_K	209_V	0.851	1.00
213_F	223_I	0.847	1.00
35_V	60_M	0.844	1.00
93_G	97_E	0.833	1.00
36_T	60_M	0.833	1.00
14_R	23_A	0.833	1.00
230_S	233_R	0.832	1.00
32_M	35_V	0.830	1.00
107_K	110_K	0.829	1.00
122_Y	134_E	0.824	1.00
143_V	147_N	0.819	1.00
211_S	216_E	0.818	1.00
221_T	224_G	0.814	1.00
85_R	88_G	0.813	1.00
60_M	64_Y	0.811	1.00
69_K	85_R	0.810	1.00
15_W	18_W	0.807	1.00
209_V	227_L	0.806	1.00
63_L	82_A	0.806	1.00
184_E	187_M	0.799	1.00
92_D	96_K	0.797	1.00
223_I	238_H	0.795	1.00
238_H	241_A	0.792	0.99
111_V	146_M	0.785	0.99
199_I	211_S	0.781	0.99
170_I	174_I	0.773	0.99
214_Y	242_L	0.772	0.99
213_F	220_L	0.763	0.99
80_T	83_S	0.763	0.99
172_V	175_R	0.760	0.99
42_I	90_I	0.760	0.99
66_A	78_F	0.757	0.99
141_D	144_S	0.752	0.99
197_E	200_H	0.739	0.99
37_Y	40_G	0.737	0.99
193_A	197_E	0.731	0.99
230_S	236_Q	0.728	0.99
119_E	125_N	0.728	0.99
205_K	236_Q	0.725	0.99
142_V	146_M	0.724	0.99
24_G	67_L	0.721	0.99
220_L	236_Q	0.720	0.99
198_K	248_L	0.719	0.99
61_L	64_Y	0.718	0.99
112_E	115_I	0.718	0.99
118_L	130_E	0.717	0.99
144_S	147_N	0.716	0.99
27_L	31_Y	0.715	0.99
88_G	95_R	0.715	0.99
34_L	83_S	0.712	0.99
76_L	80_T	0.712	0.99
206_E	241_A	0.710	0.99
62_G	90_I	0.710	0.99
185_K	189_D	0.708	0.99
95_R	102_R	0.707	0.99
210_V	242_L	0.707	0.99
196_A	211_S	0.704	0.99
108_T	145_T	0.699	0.99
186_I	189_D	0.697	0.99
220_L	233_R	0.694	0.99
187_M	191_L	0.690	0.99
198_K	245_L	0.688	0.99
161_L	169_N	0.686	0.99
37_Y	41_R	0.682	0.98
104_S	108_T	0.677	0.98
170_I	173_M	0.674	0.98
196_A	200_H	0.673	0.98
72_P	75_D	0.672	0.98
88_G	92_D	0.670	0.98
162_H	165_D	0.664	0.98
105_R	109_K	0.662	0.98
123_L	126_V	0.662	0.98
30_R	33_P	0.656	0.98
82_A	86_I	0.656	0.98
70_F	74_R	0.655	0.98
189_D	192_I	0.653	0.98
222_E	225_Q	0.653	0.98
224_G	231_T	0.650	0.98
198_K	241_A	0.642	0.98
182_P	185_K	0.642	0.98
24_G	28_M	0.642	0.98
92_D	106_E	0.641	0.98
213_F	231_T	0.635	0.98
169_N	173_M	0.634	0.98
14_R	26_D	0.634	0.98
33_P	36_T	0.633	0.98
85_R	235_S	0.633	0.98
70_F	76_L	0.631	0.98
109_K	112_E	0.630	0.97
220_L	238_H	0.629	0.97
135_L	142_V	0.627	0.97
205_K	229_L	0.627	0.97
18_W	23_A	0.623	0.97
203_S	241_A	0.620	0.97
132_A	135_L	0.620	0.97
32_M	36_T	0.619	0.97
161_L	173_M	0.618	0.97
229_L	233_R	0.618	0.97
188_K	196_A	0.615	0.97
216_E	226_V	0.614	0.97
161_L	172_V	0.613	0.97
14_R	19_K	0.610	0.97
54_D	57_S	0.610	0.97
50_V	55_L	0.606	0.97
108_T	149_G	0.605	0.97
65_D	68_E	0.604	0.97
115_I	125_N	0.603	0.97
133_E	136_G	0.603	0.97
85_R	232_S	0.601	0.97
32_M	56_M	0.599	0.97
50_V	94_L	0.598	0.97
198_K	201_E	0.598	0.97
231_T	236_Q	0.597	0.97
94_L	105_R	0.594	0.96
195_L	198_K	0.593	0.96
85_R	92_D	0.590	0.96
64_Y	67_L	0.589	0.96
16_K	71_D	0.586	0.96
198_K	249_L	0.586	0.96
34_L	80_T	0.586	0.96
67_L	72_P	0.582	0.96
36_T	53_D	0.581	0.96
223_I	227_L	0.578	0.96
115_I	119_E	0.576	0.96
144_S	148_E	0.576	0.96
36_T	39_V	0.576	0.96
130_E	134_E	0.574	0.96
213_F	219_T	0.572	0.96
199_I	203_S	0.571	0.96
36_T	40_G	0.567	0.95
180_V	185_K	0.566	0.95
114_A	122_Y	0.566	0.95
18_W	21_P	0.562	0.95
91_I	102_R	0.561	0.95
55_L	93_G	0.558	0.95
160_K	167_G	0.551	0.95
242_L	246_K	0.550	0.95
88_G	235_S	0.549	0.95
35_V	90_I	0.546	0.94
203_S	237_I	0.543	0.94
89_A	93_G	0.541	0.94
57_S	61_L	0.541	0.94
18_W	22_K	0.541	0.94
118_L	121_R	0.539	0.94
132_A	138_T	0.538	0.94
62_G	82_A	0.536	0.94
111_V	137_M	0.535	0.94
127_S	131_I	0.535	0.94
15_W	23_A	0.533	0.94
59_G	86_I	0.531	0.94
104_S	145_T	0.530	0.93
128_P	135_L	0.529	0.93
126_V	131_I	0.529	0.93
108_T	111_V	0.528	0.93
21_P	24_G	0.526	0.93
107_K	135_L	0.526	0.93
231_T	235_S	0.524	0.93
58_L	97_E	0.522	0.93
62_G	86_I	0.522	0.93
130_E	133_E	0.522	0.93
156_S	161_L	0.519	0.93
191_L	198_K	0.517	0.93
99_W	105_R	0.516	0.93
223_I	234_I	0.516	0.93
155_L	158_D	0.515	0.92
37_Y	57_S	0.514	0.92
65_D	81_Y	0.512	0.92
142_V	148_E	0.512	0.92
92_D	213_F	0.510	0.92
219_T	224_G	0.510	0.92
168_E	172_V	0.507	0.92
110_K	114_A	0.506	0.92
145_T	148_E	0.506	0.92
103_T	106_E	0.503	0.92
202_L	245_L	0.502	0.91
162_H	173_M	0.502	0.91
183_E	191_L	0.501	0.91
38_H	86_I	0.501	0.91
81_Y	84_F	0.501	0.91
171_Q	174_I	0.500	0.91
225_Q	228_N	0.500	0.91

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
2a6hF	1	0.9528	100	0.231	Contact Map
1l9zH	1	0.937	100	0.231	Contact Map
4yfkF	1	0.9724	100	0.284	Contact Map
1rp3A	1	0.9213	100	0.42	Contact Map
1l0oC	1	0.2165	100	0.422	Contact Map
3ugoA	1	0.374	99.9	0.562	Contact Map
4nqwA	1	0.5827	99.9	0.589	Contact Map
1or7A	2	0.7205	99.9	0.627	Contact Map
4cxfA	1	0.6063	99.9	0.627	Contact Map
2q1zA	1	0.689	99.9	0.634	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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