RPSG - BACSU - GREMLIN Contacts

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RPSG - RNA polymerase sigma-G factor

UniProt:	P19940	Sequences: MSRNKVEICGVDTSKLPVLKNEEMRKLFRQLQDEGDDSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVRERLISETSKEPTAEDIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDERNTDSQWIEELALKEGMRRLNDREKMILRKRFFQGKTQMEVAEEIGISQAQVSRLEKAAIKQMNKNIHQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	260 (231)
Sequences:	7453 (4464)
Seq/√Len:	293.7

ECOLI - RPOS RPOD RPOH FLIA
BACSU - RPSG SIGA RPSF RPSB RPSK RPSD 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
133_L	137_T	3.696	1.00
40_R	81_D	3.511	1.00
139_K	145_D	3.212	1.00
136_E	149_V	3.182	1.00
51_V	72_G	3.001	1.00
216_K	220_R	2.947	1.00
132_R	149_V	2.922	1.00
144_E	154_H	2.833	1.00
30_Q	36_D	2.720	1.00
238_I	243_V	2.670	1.00
41_E	45_N	2.576	1.00
195_D	199_I	2.507	1.00
129_V	149_V	2.374	1.00
26_K	30_Q	2.227	1.00
221_K	235_E	2.227	1.00
242_Q	245_R	2.163	1.00
143_A	158_V	2.155	1.00
215_E	253_Q	2.130	1.00
210_R	257_N	2.126	1.00
221_K	227_K	2.113	1.00
222_R	247_E	2.043	1.00
217_M	235_E	1.989	1.00
50_L	92_S	1.963	1.00
153_P	156_E	1.958	1.00
230_M	234_E	1.924	1.00
209_R	216_K	1.916	1.00
84_D	87_H	1.878	1.00
171_F	183_Y	1.810	1.00
54_V	96_V	1.782	1.00
227_K	235_E	1.774	1.00
133_L	141_P	1.771	1.00
48_L	73_C	1.766	1.00
217_M	221_K	1.743	1.00
132_R	136_E	1.727	1.00
217_M	236_I	1.719	1.00
71_V	106_Y	1.688	1.00
218_I	246_L	1.687	1.00
241_A	244_S	1.680	1.00
143_A	161_L	1.672	1.00
42_K	46_G	1.662	1.00
212_N	253_Q	1.661	1.00
218_I	250_A	1.644	1.00
90_K	93_T	1.615	1.00
236_I	243_V	1.602	1.00
37_D	41_E	1.600	1.00
144_E	148_K	1.596	1.00
54_V	103_I	1.595	1.00
146_I	157_I	1.592	1.00
55_I	103_I	1.562	1.00
129_V	132_R	1.543	1.00
143_A	154_H	1.539	1.00
129_V	133_L	1.538	1.00
69_F	73_C	1.535	1.00
126_A	146_I	1.531	1.00
82_N	94_Y	1.510	1.00
195_D	200_E	1.501	1.00
52_L	69_F	1.478	1.00
143_A	157_I	1.467	1.00
227_K	231_E	1.453	1.00
126_A	160_A	1.451	1.00
72_G	103_I	1.444	1.00
25_R	29_R	1.430	1.00
44_V	77_M	1.430	1.00
122_I	152_V	1.429	1.00
154_H	158_V	1.394	1.00
130_R	161_L	1.387	1.00
212_N	215_E	1.372	1.00
242_Q	246_L	1.367	1.00
32_Q	86_S	1.355	1.00
133_L	139_K	1.325	1.00
133_L	149_V	1.322	1.00
171_F	185_M	1.318	1.00
80_I	91_F	1.316	1.00
91_F	95_A	1.306	1.00
55_I	69_F	1.294	1.00
111_N	120_R	1.277	1.00
121_D	125_K	1.269	1.00
147_A	154_H	1.265	1.00
129_V	150_L	1.260	1.00
215_E	249_A	1.253	1.00
147_A	157_I	1.253	1.00
32_Q	85_L	1.235	1.00
55_I	65_V	1.227	1.00
219_L	254_M	1.214	1.00
152_V	157_I	1.201	1.00
51_V	76_L	1.190	1.00
196_S	200_E	1.190	1.00
122_I	160_A	1.188	1.00
152_V	160_A	1.187	1.00
126_A	150_L	1.156	1.00
223_F	247_E	1.145	1.00
38_S	41_E	1.144	1.00
142_T	145_D	1.127	1.00
221_K	232_V	1.115	1.00
122_I	156_E	1.096	1.00
246_L	250_A	1.095	1.00
56_Q	65_V	1.095	1.00
141_P	145_D	1.094	1.00
213_D	216_K	1.081	1.00
229_Q	233_A	1.079	1.00
147_A	152_V	1.076	1.00
28_F	31_L	1.068	1.00
44_V	80_I	1.061	1.00
180_D	187_Q	1.059	1.00
134_I	141_P	1.054	1.00
29_R	86_S	1.051	1.00
56_Q	59_N	1.046	1.00
79_S	95_A	1.045	1.00
241_A	245_R	1.032	1.00
217_M	220_R	1.031	1.00
214_R	246_L	1.023	1.00
38_S	42_K	1.023	1.00
28_F	32_Q	1.022	1.00
63_E	106_Y	1.021	1.00
126_A	157_I	1.020	1.00
75_G	79_S	1.010	1.00
30_Q	39_A	0.997	1.00
230_M	240_Q	0.984	1.00
43_L	80_I	0.973	1.00
30_Q	34_E	0.970	1.00
229_Q	241_A	0.969	1.00
229_Q	244_S	0.967	1.00
26_K	29_R	0.962	1.00
196_S	199_I	0.960	1.00
30_Q	42_K	0.948	1.00
130_R	146_I	0.932	1.00
229_Q	240_Q	0.929	1.00
31_L	35_G	0.925	1.00
133_L	146_I	0.920	1.00
51_V	73_C	0.910	1.00
128_Q	132_R	0.909	1.00
78_K	82_N	0.905	1.00
215_E	246_L	0.903	1.00
195_D	198_W	0.902	1.00
252_K	256_K	0.900	1.00
59_N	65_V	0.899	1.00
222_R	232_V	0.898	1.00
69_F	72_G	0.893	1.00
115_V	123_A	0.888	1.00
214_R	242_Q	0.886	1.00
201_E	205_K	0.886	1.00
27_L	42_K	0.884	1.00
100_I	104_R	0.883	1.00
170_L	185_M	0.881	1.00
78_K	102_E	0.878	1.00
29_R	85_L	0.873	1.00
214_R	218_I	0.871	1.00
54_V	100_I	0.871	1.00
134_I	140_E	0.870	1.00
183_Y	186_D	0.869	1.00
129_V	146_I	0.863	1.00
189_S	192_R	0.862	1.00
230_M	233_A	0.859	1.00
47_N	92_S	0.859	1.00
42_K	45_N	0.857	1.00
137_T	141_P	0.855	1.00
213_D	217_M	0.851	1.00
194_T	197_Q	0.849	1.00
31_L	43_L	0.848	1.00
197_Q	200_E	0.845	1.00
208_M	220_R	0.838	1.00
218_I	238_I	0.837	1.00
29_R	34_E	0.836	1.00
52_L	73_C	0.836	1.00
73_C	77_M	0.831	1.00
65_V	69_F	0.830	1.00
98_M	101_G	0.830	1.00
137_T	145_D	0.829	1.00
94_Y	98_M	0.827	1.00
168_V	172_E	0.819	1.00
158_V	162_D	0.818	1.00
239_S	242_Q	0.804	1.00
82_N	98_M	0.803	1.00
35_G	39_A	0.801	0.99
106_Y	110_N	0.800	0.99
52_L	65_V	0.798	0.99
116_S	119_L	0.796	0.99
53_S	56_Q	0.795	0.99
220_R	225_Q	0.791	0.99
156_E	159_F	0.783	0.99
134_I	137_T	0.781	0.99
40_R	80_I	0.775	0.99
218_I	236_I	0.774	0.99
27_L	39_A	0.773	0.99
232_V	247_E	0.773	0.99
126_A	161_L	0.772	0.99
76_L	95_A	0.770	0.99
48_L	51_V	0.770	0.99
105_R	109_D	0.759	0.99
222_R	229_Q	0.749	0.99
25_R	88_N	0.749	0.99
123_A	160_A	0.746	0.99
190_D	193_N	0.737	0.99
223_F	251_I	0.736	0.99
79_S	91_F	0.736	0.99
108_R	117_R	0.732	0.99
247_E	250_A	0.732	0.99
203_A	206_E	0.732	0.99
43_L	47_N	0.729	0.99
58_F	103_I	0.728	0.99
167_P	171_F	0.727	0.99
32_Q	84_D	0.724	0.99
32_Q	35_G	0.722	0.99
219_L	251_I	0.718	0.99
125_K	128_Q	0.718	0.99
89_V	93_T	0.715	0.99
109_D	114_R	0.713	0.99
138_S	141_P	0.712	0.99
137_T	149_V	0.712	0.99
31_L	34_E	0.711	0.99
50_L	96_V	0.708	0.99
231_E	234_E	0.703	0.99
169_S	173_P	0.702	0.99
133_L	145_D	0.701	0.99
36_D	39_A	0.699	0.99
53_S	57_R	0.699	0.99
157_I	161_L	0.699	0.99
207_G	254_M	0.694	0.99
95_A	99_I	0.693	0.99
123_A	164_I	0.693	0.99
93_T	96_V	0.688	0.98
239_S	245_R	0.687	0.98
122_I	125_K	0.686	0.98
120_R	124_Y	0.684	0.98
206_E	209_R	0.681	0.98
229_Q	245_R	0.681	0.98
215_E	250_A	0.680	0.98
183_Y	187_Q	0.679	0.98
122_I	150_L	0.678	0.98
207_G	257_N	0.672	0.98
124_Y	127_L	0.672	0.98
118_S	121_D	0.671	0.98
29_R	32_Q	0.668	0.98
207_G	250_A	0.667	0.98
83_F	87_H	0.661	0.98
67_D	70_Q	0.657	0.98
101_G	108_R	0.656	0.98
229_Q	242_Q	0.656	0.98
119_L	123_A	0.655	0.98
214_R	245_R	0.653	0.98
27_L	31_L	0.651	0.98
74_I	77_M	0.650	0.98
229_Q	247_E	0.642	0.98
63_E	107_L	0.641	0.98
214_R	238_I	0.637	0.97
205_K	220_R	0.636	0.97
83_F	89_V	0.636	0.97
204_L	207_G	0.634	0.97
159_F	163_A	0.633	0.97
101_G	105_R	0.633	0.97
169_S	172_E	0.632	0.97
34_E	39_A	0.631	0.97
205_K	209_R	0.631	0.97
25_R	32_Q	0.630	0.97
126_A	152_V	0.629	0.97
159_F	162_D	0.627	0.97
46_G	49_R	0.622	0.97
145_D	149_V	0.620	0.97
148_K	151_E	0.619	0.97
85_L	88_N	0.618	0.97
125_K	129_V	0.618	0.97
40_R	44_V	0.614	0.97
222_R	240_Q	0.611	0.97
49_R	52_L	0.610	0.97
48_L	69_F	0.608	0.97
147_A	150_L	0.608	0.97
233_A	240_Q	0.605	0.97
75_G	103_I	0.603	0.97
130_R	140_E	0.603	0.97
77_M	80_I	0.602	0.96
225_Q	235_E	0.599	0.96
238_I	242_Q	0.595	0.96
37_D	40_R	0.595	0.96
166_D	171_F	0.594	0.96
207_G	210_R	0.594	0.96
98_M	244_S	0.593	0.96
52_L	55_I	0.588	0.96
141_P	146_I	0.587	0.96
98_M	241_A	0.586	0.96
68_L	106_Y	0.583	0.96
104_R	117_R	0.581	0.96
78_K	81_D	0.580	0.96
174_I	180_D	0.580	0.96
50_L	93_T	0.580	0.96
232_V	236_I	0.579	0.96
184_V	188_I	0.578	0.96
127_L	130_R	0.577	0.96
147_A	153_P	0.576	0.95
175_Y	187_Q	0.576	0.95
160_A	163_A	0.575	0.95
48_L	52_L	0.574	0.95
191_E	197_Q	0.573	0.95
212_N	250_A	0.573	0.95
142_T	146_I	0.572	0.95
70_Q	74_I	0.571	0.95
150_L	157_I	0.570	0.95
222_R	228_T	0.570	0.95
173_P	179_G	0.568	0.95
211_L	254_M	0.562	0.95
53_S	70_Q	0.560	0.95
119_L	160_A	0.559	0.95
232_V	243_V	0.557	0.95
32_Q	36_D	0.556	0.95
174_I	187_Q	0.555	0.95
52_L	66_D	0.552	0.94
240_Q	245_R	0.552	0.94
78_K	94_Y	0.552	0.94
130_R	141_P	0.549	0.94
28_F	85_L	0.547	0.94
105_R	222_R	0.547	0.94
168_V	171_F	0.546	0.94
51_V	103_I	0.544	0.94
110_N	116_S	0.543	0.94
98_M	105_R	0.538	0.94
251_I	255_N	0.538	0.94
71_V	110_N	0.537	0.94
175_Y	178_G	0.535	0.93
105_R	117_R	0.533	0.93
31_L	36_D	0.532	0.93
72_G	99_I	0.529	0.93
28_F	80_I	0.526	0.93
52_L	56_Q	0.526	0.93
63_E	68_L	0.525	0.93
47_N	50_L	0.522	0.93
107_L	120_R	0.522	0.93
192_R	195_D	0.522	0.93
234_E	237_G	0.522	0.93
174_I	183_Y	0.521	0.92
233_A	241_A	0.520	0.92
101_G	244_S	0.519	0.92
249_A	252_K	0.517	0.92
51_V	99_I	0.516	0.92
202_L	206_E	0.514	0.92
211_L	250_A	0.513	0.92
123_A	126_A	0.512	0.92
84_D	88_N	0.512	0.92
80_I	85_L	0.510	0.92
184_V	187_Q	0.510	0.92
212_N	246_L	0.506	0.91
185_M	188_I	0.506	0.91
228_T	233_A	0.505	0.91
75_G	95_A	0.505	0.91
208_M	212_N	0.503	0.91
157_I	160_A	0.501	0.91
113_I	167_P	0.501	0.91
162_D	165_Q	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
1l9zH	1	0.9462	100	0.225	Contact Map
2a6hF	1	0.9692	100	0.227	Contact Map
4yfkF	1	0.9885	100	0.32	Contact Map
1l0oC	1	0.2192	100	0.41	Contact Map
1rp3A	1	0.8577	100	0.48	Contact Map
3ugoA	1	0.4192	100	0.519	Contact Map
4nqwA	1	0.5692	99.9	0.615	Contact Map
1or7A	2	0.6962	99.9	0.654	Contact Map
4cxfA	1	0.5846	99.9	0.655	Contact Map
2q1zA	1	0.6731	99.9	0.658	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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