RPSF - BACSU - GREMLIN Contacts

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RPSF - RNA polymerase sigma-F factor

UniProt:	P07860	Sequences: MDVEVKKNGKNAQLKDHEVKELIKQSQNGDQQARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLTYDVRFSTYAVPMIIGEIQRFIRDDGTVKVSRSLKELGNKIRRAKDELSKTLGRVPTVQEIADHLEIEAEDVVLAQEAVRAPSSIHETVYENDGDPITLLDQIADNSEEKWFDKIALKEAISDLEEREKLIVYLRYYKDQTQSEVAERLGISQVQVSRLEKKILKQIKVQMDHTDG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	255 (227)
Sequences:	7365 (4386)
Seq/√Len:	291.1

ECOLI - RPOS RPOD RPOH FLIA
BACSU - RPSF SIGA RPSG 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
127_L	131_L	3.752	1.00
34_R	75_D	3.616	1.00
133_R	139_E	3.342	1.00
130_T	143_H	3.249	1.00
45_V	66_G	3.132	1.00
208_K	212_Y	3.000	1.00
126_E	143_H	2.896	1.00
230_I	235_V	2.825	1.00
138_Q	148_A	2.818	1.00
25_Q	30_D	2.798	1.00
35_D	39_E	2.633	1.00
123_A	143_H	2.429	1.00
213_L	227_R	2.261	1.00
207_E	245_Q	2.247	1.00
234_Q	237_R	2.210	1.00
202_D	249_Q	2.135	1.00
213_L	219_Q	2.111	1.00
214_R	239_E	2.103	1.00
137_V	152_V	2.091	1.00
209_L	227_R	2.021	1.00
222_S	226_E	1.995	1.00
44_L	86_S	1.957	1.00
201_S	208_K	1.957	1.00
147_E	150_D	1.956	1.00
127_L	135_P	1.826	1.00
78_D	81_Y	1.821	1.00
219_Q	227_R	1.818	1.00
48_V	90_V	1.813	1.00
209_L	213_L	1.775	1.00
210_I	238_L	1.766	1.00
126_E	130_T	1.758	1.00
210_I	242_I	1.749	1.00
42_M	67_C	1.745	1.00
65_I	100_F	1.745	1.00
209_L	228_L	1.722	1.00
233_V	236_S	1.714	1.00
204_E	245_Q	1.710	1.00
36_L	40_K	1.684	1.00
165_H	177_T	1.652	1.00
140_I	151_V	1.640	1.00
84_R	87_T	1.626	1.00
228_L	235_V	1.620	1.00
120_I	140_I	1.611	1.00
48_V	97_I	1.595	1.00
137_V	148_A	1.584	1.00
138_Q	142_D	1.577	1.00
76_K	88_Y	1.568	1.00
137_V	155_Q	1.568	1.00
123_A	127_L	1.548	1.00
63_F	67_C	1.546	1.00
123_A	126_E	1.539	1.00
46_W	63_F	1.522	1.00
31_Q	35_D	1.521	1.00
38_I	71_L	1.509	1.00
49_V	97_I	1.494	1.00
120_I	154_A	1.485	1.00
66_G	97_I	1.478	1.00
219_Q	223_E	1.473	1.00
137_V	151_V	1.428	1.00
27_Q	80_T	1.414	1.00
124_K	155_Q	1.406	1.00
74_V	85_F	1.406	1.00
204_E	207_E	1.399	1.00
127_L	143_H	1.392	1.00
148_A	152_V	1.376	1.00
165_H	179_L	1.372	1.00
234_Q	238_L	1.371	1.00
127_L	133_R	1.354	1.00
49_V	63_F	1.354	1.00
116_L	146_I	1.336	1.00
85_F	89_A	1.336	1.00
49_V	59_P	1.313	1.00
115_E	119_K	1.310	1.00
123_A	144_L	1.290	1.00
141_A	151_V	1.280	1.00
207_E	241_K	1.277	1.00
45_V	70_L	1.260	1.00
146_I	151_V	1.254	1.00
141_A	148_A	1.235	1.00
211_V	246_I	1.235	1.00
23_I	26_S	1.228	1.00
146_I	154_A	1.226	1.00
32_Q	35_D	1.206	1.00
116_L	154_A	1.181	1.00
215_Y	239_E	1.177	1.00
191_F	195_A	1.168	1.00
120_I	144_L	1.167	1.00
136_T	139_E	1.161	1.00
50_Q	59_P	1.150	1.00
23_I	27_Q	1.143	1.00
188_E	191_F	1.143	1.00
27_Q	79_L	1.121	1.00
193_K	197_K	1.101	1.00
205_E	208_K	1.100	1.00
238_L	242_I	1.081	1.00
57_Y	100_F	1.078	1.00
135_P	139_E	1.077	1.00
120_I	151_V	1.072	1.00
38_I	74_V	1.070	1.00
24_K	80_T	1.068	1.00
73_S	89_A	1.068	1.00
25_Q	28_N	1.060	1.00
209_L	212_Y	1.056	1.00
221_Q	225_A	1.055	1.00
213_L	224_V	1.052	1.00
206_R	238_L	1.043	1.00
141_A	146_I	1.038	1.00
24_K	28_N	1.035	1.00
116_L	150_D	1.029	1.00
233_V	237_R	1.024	1.00
50_Q	53_L	1.017	1.00
105_G	114_K	1.011	1.00
128_S	135_P	1.010	1.00
69_G	73_S	1.009	1.00
222_S	232_Q	0.999	1.00
183_A	186_S	0.985	1.00
244_K	248_V	0.978	1.00
122_R	126_E	0.973	1.00
221_Q	233_V	0.972	1.00
123_A	140_I	0.971	1.00
124_K	140_I	0.958	1.00
26_S	29_G	0.952	1.00
221_Q	232_Q	0.948	1.00
32_Q	36_L	0.945	1.00
63_F	66_G	0.944	1.00
221_Q	236_S	0.941	1.00
206_R	234_Q	0.938	1.00
94_I	98_Q	0.934	1.00
189_K	193_K	0.930	1.00
25_Q	36_L	0.930	1.00
164_I	179_L	0.929	1.00
195_A	198_E	0.925	1.00
53_L	59_P	0.920	1.00
184_D	187_E	0.916	1.00
128_S	134_V	0.915	1.00
72_K	76_K	0.913	1.00
37_L	74_V	0.913	1.00
222_S	225_A	0.905	1.00
25_Q	33_A	0.904	1.00
174_D	181_Q	0.903	1.00
131_L	135_P	0.901	1.00
190_W	194_I	0.900	1.00
207_E	238_L	0.899	1.00
127_L	140_I	0.893	1.00
48_V	94_I	0.888	1.00
214_R	224_V	0.888	1.00
45_V	67_C	0.880	1.00
41_N	86_S	0.875	1.00
59_P	63_F	0.873	1.00
210_I	230_I	0.873	1.00
88_Y	92_M	0.869	1.00
131_L	139_E	0.868	1.00
30_D	33_A	0.862	1.00
72_K	96_E	0.856	1.00
24_K	79_L	0.856	1.00
152_V	156_E	0.848	1.00
36_L	39_E	0.847	1.00
109_V	117_G	0.847	1.00
70_L	89_A	0.843	1.00
212_Y	217_K	0.838	1.00
67_C	71_L	0.835	1.00
162_S	166_E	0.832	1.00
46_W	59_P	0.831	1.00
76_K	92_M	0.830	1.00
46_W	67_C	0.830	1.00
200_I	212_Y	0.827	1.00
92_M	95_G	0.826	1.00
205_E	209_L	0.820	1.00
210_I	228_L	0.820	1.00
206_R	210_I	0.818	1.00
110_S	113_L	0.815	1.00
128_S	131_L	0.810	1.00
47_S	50_Q	0.794	0.99
99_R	103_D	0.784	0.99
120_I	155_Q	0.782	0.99
100_F	104_D	0.780	0.99
42_M	45_V	0.779	0.99
231_S	234_Q	0.775	0.99
29_G	33_A	0.767	0.99
150_D	153_L	0.766	0.99
224_V	239_E	0.759	0.99
22_L	26_S	0.759	0.99
117_G	154_A	0.756	0.99
26_S	37_L	0.755	0.99
102_R	111_R	0.755	0.99
37_L	41_N	0.752	0.99
27_Q	30_D	0.749	0.99
22_L	36_L	0.749	0.99
73_S	85_F	0.738	0.99
214_R	221_Q	0.737	0.99
83_V	87_T	0.732	0.99
211_V	243_L	0.732	0.99
239_E	242_I	0.729	0.99
34_R	74_V	0.727	0.99
22_L	33_A	0.727	0.99
119_K	122_R	0.726	0.99
131_L	143_H	0.725	0.99
113_L	117_G	0.725	0.99
199_A	249_Q	0.719	0.99
116_L	119_K	0.718	0.99
52_F	97_I	0.717	0.99
198_E	201_S	0.713	0.99
89_A	93_I	0.709	0.99
168_V	181_Q	0.708	0.99
207_E	242_I	0.703	0.99
116_L	144_L	0.698	0.99
151_V	155_Q	0.697	0.99
221_Q	237_R	0.693	0.99
87_T	90_V	0.689	0.98
114_K	118_N	0.687	0.98
197_K	212_Y	0.687	0.98
197_K	201_S	0.684	0.98
44_L	90_V	0.681	0.98
47_S	51_R	0.681	0.98
117_G	158_V	0.680	0.98
221_Q	234_Q	0.679	0.98
199_A	246_I	0.676	0.98
95_G	99_R	0.675	0.98
231_S	237_R	0.674	0.98
68_I	71_L	0.673	0.98
177_T	180_D	0.666	0.98
118_N	121_R	0.665	0.98
106_T	161_P	0.664	0.98
95_G	102_R	0.664	0.98
69_G	97_I	0.663	0.98
154_A	157_A	0.658	0.98
215_Y	243_L	0.655	0.98
24_K	27_Q	0.654	0.98
44_L	87_T	0.651	0.98
79_L	82_D	0.647	0.98
27_Q	78_D	0.645	0.98
141_A	144_L	0.643	0.98
77_F	81_Y	0.642	0.98
223_E	226_E	0.641	0.98
163_S	167_T	0.639	0.97
178_L	181_Q	0.638	0.97
121_R	124_K	0.636	0.97
177_T	181_Q	0.634	0.97
206_R	230_I	0.633	0.97
132_G	135_P	0.632	0.97
194_I	198_E	0.630	0.97
190_W	193_K	0.628	0.97
103_D	108_K	0.626	0.97
217_K	227_R	0.626	0.97
23_I	79_L	0.623	0.97
40_K	43_R	0.622	0.97
43_R	46_W	0.622	0.97
92_M	233_V	0.621	0.97
153_L	156_E	0.621	0.97
127_L	139_E	0.621	0.97
153_L	157_A	0.618	0.97
199_A	242_I	0.618	0.97
214_R	220_T	0.612	0.97
230_I	234_Q	0.611	0.97
206_R	237_R	0.611	0.97
124_K	134_V	0.610	0.97
77_F	83_V	0.609	0.97
61_D	64_Q	0.608	0.97
92_M	236_S	0.608	0.97
199_A	202_D	0.607	0.97
112_S	115_E	0.605	0.96
120_I	146_I	0.604	0.96
72_K	88_Y	0.603	0.96
144_L	151_V	0.603	0.96
225_A	232_Q	0.601	0.96
46_W	60_D	0.601	0.96
57_Y	101_I	0.600	0.96
28_N	33_A	0.600	0.96
243_L	247_K	0.599	0.96
119_K	123_A	0.596	0.96
62_L	100_F	0.593	0.96
221_Q	239_E	0.593	0.96
99_R	214_R	0.592	0.96
204_E	242_I	0.592	0.96
47_S	64_Q	0.591	0.96
46_W	49_V	0.590	0.96
42_M	46_W	0.590	0.96
72_K	75_D	0.590	0.96
214_R	232_Q	0.589	0.96
224_V	228_L	0.586	0.96
169_Y	181_Q	0.585	0.96
42_M	63_F	0.580	0.96
71_L	74_V	0.578	0.95
139_E	143_H	0.577	0.95
203_L	246_I	0.574	0.95
135_P	140_I	0.571	0.95
113_L	154_A	0.565	0.95
191_F	194_I	0.564	0.95
151_V	154_A	0.562	0.95
142_D	145_E	0.562	0.95
26_S	33_A	0.561	0.95
225_A	233_V	0.560	0.95
66_G	93_I	0.559	0.95
196_L	250_M	0.559	0.95
168_V	174_D	0.558	0.95
65_I	104_D	0.557	0.94
34_R	38_I	0.557	0.94
169_Y	172_D	0.555	0.94
226_E	229_G	0.554	0.94
22_L	25_Q	0.552	0.94
45_V	97_I	0.550	0.94
232_Q	237_R	0.550	0.94
92_M	99_R	0.549	0.94
64_Q	68_I	0.549	0.94
124_K	135_P	0.543	0.94
141_A	147_E	0.543	0.94
192_D	199_A	0.542	0.94
95_G	236_S	0.542	0.94
183_A	187_E	0.541	0.94
163_S	166_E	0.536	0.93
204_E	238_L	0.536	0.93
179_L	182_I	0.534	0.93
169_Y	173_G	0.533	0.93
161_P	165_H	0.532	0.93
188_E	192_D	0.532	0.93
162_S	165_H	0.532	0.93
160_A	165_H	0.526	0.93
117_G	120_I	0.525	0.93
46_W	50_Q	0.524	0.93
57_Y	62_L	0.524	0.93
168_V	177_T	0.523	0.92
136_T	140_I	0.521	0.92
49_V	62_L	0.520	0.92
137_V	144_L	0.520	0.92
69_G	93_I	0.519	0.92
200_I	204_E	0.519	0.92
98_Q	111_R	0.513	0.92
101_I	114_K	0.513	0.92
69_G	89_A	0.512	0.92
104_D	110_S	0.511	0.92
124_K	128_S	0.510	0.91
74_V	79_L	0.510	0.91
31_Q	34_R	0.509	0.91
196_L	199_A	0.508	0.91
41_N	44_L	0.506	0.91
186_S	189_K	0.505	0.91
60_D	67_C	0.505	0.91
232_Q	236_S	0.502	0.91
156_E	159_R	0.501	0.91
241_K	244_K	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	0.9725	100	0.224	Contact Map
1l9zH	1	0.9569	100	0.224	Contact Map
4yfkF	1	0.9922	100	0.305	Contact Map
1l0oC	1	0.2235	100	0.4	Contact Map
1rp3A	1	0.8784	100	0.488	Contact Map
3ugoA	1	0.4118	100	0.526	Contact Map
4nqwA	1	0.5804	99.9	0.608	Contact Map
4cxfA	1	0.6039	99.9	0.653	Contact Map
1or7A	2	0.7216	99.9	0.654	Contact Map
2q1zA	1	0.6863	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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