RPOS - ECOLI - GREMLIN Contacts

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RPOS - RNA polymerase sigma factor RpoS

UniProt:	P13445	Sequences: MSQNTLKVHDLNEDAEFDENGVEVFDEKALVEQEPSDNDLAEEELLSQGATQRVLDATQLYLGEIGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGLNIEALFRE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10510
Length:	330 (271)
Sequences:	4549 (2024)
Seq/√Len:	122.9

ECOLI - RPOS RPOD RPOH FLIA
BACSU - SIGA RPSK RPSB RPSG RPSF 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
271_R	275_A	4.422	1.00
75_E	93_R	3.798	1.00
196_E	206_V	3.656	1.00
297_L	302_V	3.467	1.00
82_R	87_D	3.395	1.00
102_V	123_G	3.340	1.00
185_L	189_L	3.226	1.00
191_H	197_E	3.032	1.00
223_D	233_A	2.931	1.00
272_E	295_I	2.795	1.00
101_L	143_S	2.761	1.00
92_R	96_E	2.758	1.00
78_Y	82_R	2.609	1.00
61_Y	124_N	2.586	1.00
301_R	304_Q	2.548	1.00
276_R	294_E	2.487	1.00
300_E	303_R	2.451	1.00
272_E	294_E	2.428	1.00
277_R	306_Q	2.424	1.00
247_E	251_Q	2.418	1.00
270_Q	312_R	2.333	1.00
295_I	302_V	2.306	1.00
65_I	103_V	2.270	1.00
276_R	286_A	2.268	1.00
91_R	132_E	2.149	1.00
289_E	293_R	2.126	1.00
275_A	281_L	2.080	1.00
267_N	312_R	2.038	1.00
72_T	75_E	2.001	1.00
84_L	137_E	1.991	1.00
184_E	201_Q	1.934	1.00
73_A	77_V	1.901	1.00
178_Y	202_L	1.897	1.00
178_Y	198_I	1.863	1.00
188_K	201_Q	1.862	1.00
81_R	137_E	1.819	1.00
129_R	133_K	1.815	1.00
232_K	237_I	1.805	1.00
84_L	136_P	1.780	1.00
264_F	271_R	1.775	1.00
77_V	81_R	1.773	1.00
70_L	100_R	1.735	1.00
198_I	209_V	1.725	1.00
272_E	276_R	1.675	1.00
61_Y	76_E	1.674	1.00
105_I	147_T	1.670	1.00
95_I	128_I	1.653	1.00
101_L	144_T	1.641	1.00
71_L	76_E	1.632	1.00
130_A	146_A	1.627	1.00
135_D	138_R	1.593	1.00
205_P	208_D	1.591	1.00
68_S	97_S	1.590	1.00
300_E	304_Q	1.564	1.00
185_L	191_H	1.561	1.00
301_R	305_I	1.519	1.00
286_A	294_E	1.500	1.00
178_Y	181_T	1.486	1.00
93_R	97_S	1.460	1.00
181_T	201_Q	1.448	1.00
181_T	185_L	1.437	1.00
131_V	142_F	1.433	1.00
256_K	260_V	1.432	1.00
223_D	235_L	1.427	1.00
62_L	103_V	1.414	1.00
195_A	210_S	1.408	1.00
99_L	124_N	1.407	1.00
189_L	197_E	1.405	1.00
288_L	300_E	1.386	1.00
195_A	206_V	1.376	1.00
95_I	131_V	1.338	1.00
273_V	309_G	1.337	1.00
274_L	313_L	1.330	1.00
60_L	64_E	1.324	1.00
88_V	92_R	1.322	1.00
251_Q	254_D	1.322	1.00
199_A	209_V	1.322	1.00
61_Y	65_I	1.300	1.00
58_T	120_I	1.296	1.00
62_L	65_I	1.295	1.00
130_A	142_F	1.292	1.00
250_T	254_D	1.287	1.00
265_E	318_Q	1.284	1.00
122_E	157_A	1.275	1.00
282_G	286_A	1.274	1.00
288_L	303_R	1.268	1.00
315_E	318_Q	1.267	1.00
179_L	183_R	1.267	1.00
193_P	197_E	1.254	1.00
81_R	136_P	1.248	0.99
174_E	208_D	1.248	0.99
103_V	120_I	1.246	0.99
101_L	147_T	1.215	0.99
82_R	90_S	1.213	0.99
181_T	202_L	1.204	0.99
195_A	213_L	1.202	0.99
114_L	157_A	1.190	0.99
94_M	131_V	1.187	0.99
91_R	131_V	1.179	0.99
182_A	213_L	1.178	0.99
268_A	271_R	1.177	0.99
185_L	197_E	1.175	0.99
82_R	93_R	1.173	0.99
178_Y	182_A	1.170	0.99
104_K	107_R	1.160	0.99
185_L	198_I	1.154	0.99
196_E	200_E	1.154	0.99
273_V	305_I	1.140	0.99
62_L	66_G	1.128	0.99
289_E	298_T	1.124	0.99
104_K	121_E	1.121	0.99
288_L	306_Q	1.121	0.99
76_E	80_A	1.110	0.99
270_Q	308_E	1.097	0.99
165_I	219_I	1.094	0.99
133_K	145_Y	1.091	0.99
70_L	76_E	1.089	0.99
267_N	270_Q	1.071	0.98
268_A	272_E	1.064	0.98
288_L	292_G	1.061	0.98
185_L	193_P	1.059	0.98
142_F	146_A	1.039	0.98
289_E	299_R	1.030	0.98
226_L	237_I	1.028	0.98
83_A	86_G	1.021	0.98
204_K	209_V	1.020	0.98
254_D	258_S	1.010	0.98
87_D	90_S	1.006	0.98
184_E	188_K	1.004	0.98
174_E	212_M	1.002	0.98
249_T	253_D	1.001	0.98
253_D	257_Q	0.999	0.98
288_L	301_R	0.988	0.97
288_L	304_Q	0.987	0.97
98_N	143_S	0.985	0.97
289_E	292_G	0.983	0.97
286_A	290_D	0.983	0.97
171_I	212_M	0.978	0.97
172_V	176_N	0.975	0.97
194_S	197_E	0.955	0.97
278_F	310_L	0.952	0.97
131_V	247_E	0.949	0.97
178_Y	212_M	0.949	0.97
156_R	173_K	0.948	0.97
260_V	275_A	0.947	0.97
265_E	316_I	0.943	0.97
149_W	303_R	0.936	0.96
103_V	124_N	0.935	0.96
246_P	250_T	0.935	0.96
106_A	120_I	0.927	0.96
61_Y	70_L	0.926	0.96
123_G	154_I	0.926	0.96
65_I	68_S	0.922	0.96
89_A	92_R	0.922	0.96
199_A	206_V	0.920	0.96
143_S	156_R	0.915	0.96
167_L	171_I	0.912	0.96
144_T	147_T	0.904	0.96
206_V	210_S	0.903	0.96
79_F	90_S	0.889	0.95
195_A	209_V	0.886	0.95
120_I	124_N	0.882	0.95
56_D	76_E	0.881	0.95
84_L	135_D	0.872	0.95
269_K	301_R	0.865	0.94
167_L	175_L	0.861	0.94
79_F	83_A	0.860	0.94
75_E	78_Y	0.858	0.94
68_S	96_E	0.856	0.94
83_A	142_F	0.855	0.94
89_A	93_R	0.853	0.94
149_W	300_E	0.852	0.94
308_E	311_R	0.852	0.94
51_T	54_V	0.848	0.94
69_P	75_E	0.848	0.94
70_L	98_N	0.848	0.94
288_L	299_R	0.846	0.94
76_E	141_R	0.846	0.94
81_R	84_L	0.838	0.93
110_G	116_L	0.833	0.93
190_D	193_P	0.830	0.93
208_D	211_R	0.830	0.93
287_T	298_T	0.828	0.93
140_F	144_T	0.822	0.93
104_K	108_R	0.822	0.93
171_I	175_L	0.821	0.93
115_A	157_A	0.813	0.92
122_E	161_Q	0.809	0.92
151_R	155_E	0.809	0.92
168_P	278_F	0.808	0.92
259_I	262_W	0.808	0.92
258_S	261_K	0.804	0.92
141_R	144_T	0.802	0.92
147_T	151_R	0.802	0.92
273_V	295_I	0.802	0.92
291_V	295_I	0.801	0.92
105_I	154_I	0.801	0.92
152_Q	156_R	0.796	0.92
305_I	308_E	0.792	0.91
181_T	184_E	0.791	0.91
267_N	305_I	0.789	0.91
82_R	85_R	0.786	0.91
289_E	297_L	0.780	0.91
234_L	237_I	0.780	0.91
86_G	90_S	0.779	0.91
185_L	201_Q	0.776	0.90
291_V	306_Q	0.774	0.90
222_V	235_L	0.774	0.90
173_K	177_V	0.772	0.90
91_R	95_I	0.772	0.90
61_Y	66_G	0.771	0.90
107_R	116_L	0.768	0.90
71_L	79_F	0.765	0.90
198_I	201_Q	0.765	0.90
175_L	212_M	0.764	0.90
125_L	128_I	0.763	0.90
170_H	173_K	0.763	0.90
298_T	301_R	0.760	0.90
245_G	249_T	0.760	0.90
269_K	304_Q	0.760	0.90
61_Y	99_L	0.759	0.89
111_N	114_L	0.758	0.89
50_A	53_R	0.756	0.89
56_D	59_Q	0.756	0.89
263_L	271_R	0.756	0.89
141_R	160_N	0.754	0.89
160_N	166_R	0.753	0.89
269_K	300_E	0.752	0.89
77_V	137_E	0.746	0.89
186_S	193_P	0.745	0.89
245_G	250_T	0.739	0.88
74_E	78_Y	0.738	0.88
202_L	209_V	0.728	0.87
155_E	173_K	0.723	0.87
240_D	243_E	0.722	0.87
263_L	275_A	0.721	0.87
152_Q	170_H	0.721	0.87
259_I	278_F	0.710	0.86
262_W	265_E	0.707	0.86
189_L	193_P	0.704	0.86
121_E	298_T	0.702	0.85
169_I	298_T	0.700	0.85
80_A	136_P	0.699	0.85
83_A	131_V	0.699	0.85
80_A	94_M	0.698	0.85
61_Y	80_A	0.697	0.85
143_S	147_T	0.697	0.85
99_L	103_V	0.695	0.85
174_E	177_V	0.693	0.85
292_G	303_R	0.693	0.85
198_I	203_D	0.692	0.85
157_A	161_Q	0.689	0.84
226_L	232_K	0.688	0.84
260_V	281_L	0.687	0.84
209_V	212_M	0.683	0.84
226_L	236_D	0.683	0.84
197_E	201_Q	0.682	0.84
241_E	249_T	0.680	0.84
225_P	231_E	0.677	0.83
149_W	152_Q	0.675	0.83
61_Y	71_L	0.673	0.83
58_T	66_G	0.672	0.83
148_W	151_R	0.671	0.83
108_R	142_F	0.670	0.83
121_E	153_T	0.669	0.83
114_L	158_I	0.668	0.83
284_E	294_E	0.665	0.82
102_V	154_I	0.664	0.82
107_R	110_G	0.664	0.82
162_T	172_V	0.662	0.82
107_R	142_F	0.662	0.82
79_F	93_R	0.661	0.82
103_V	117_L	0.657	0.82
272_E	275_A	0.655	0.81
159_M	169_I	0.655	0.81
292_G	298_T	0.651	0.81
81_R	85_R	0.650	0.81
113_G	162_T	0.649	0.81
135_D	139_G	0.648	0.81
156_R	170_H	0.645	0.80
156_R	160_N	0.644	0.80
56_D	61_Y	0.644	0.80
148_W	153_T	0.641	0.80
129_R	153_T	0.641	0.80
182_A	185_L	0.640	0.80
155_E	169_I	0.639	0.80
133_K	173_K	0.638	0.80
220_T	223_D	0.638	0.80
141_R	159_M	0.637	0.80
159_M	173_K	0.633	0.79
63_G	68_S	0.631	0.79
109_Y	154_I	0.630	0.79
135_D	221_S	0.628	0.79
109_Y	151_R	0.626	0.78
136_P	139_G	0.623	0.78
277_R	291_V	0.622	0.78
71_L	97_S	0.622	0.78
58_T	116_L	0.620	0.78
178_Y	213_L	0.619	0.78
254_D	257_Q	0.617	0.77
102_V	150_I	0.616	0.77
100_R	103_V	0.614	0.77
152_Q	168_P	0.609	0.76
289_E	302_V	0.608	0.76
215_L	291_V	0.606	0.76
171_I	178_Y	0.605	0.76
284_E	290_D	0.603	0.76
80_A	83_A	0.602	0.76
288_L	298_T	0.600	0.75
58_T	117_L	0.600	0.75
147_T	298_T	0.599	0.75
280_L	283_Y	0.599	0.75
156_R	287_T	0.598	0.75
261_K	264_F	0.596	0.75
156_R	169_I	0.594	0.75
292_G	300_E	0.593	0.75
50_A	198_I	0.592	0.74
275_A	280_L	0.591	0.74
57_A	60_L	0.590	0.74
108_R	170_H	0.587	0.74
94_M	169_I	0.585	0.74
129_R	132_E	0.582	0.73
199_A	204_K	0.582	0.73
101_L	156_R	0.579	0.73
78_Y	81_R	0.578	0.73
187_H	190_D	0.577	0.73
177_V	180_R	0.576	0.72
245_G	248_D	0.576	0.72
155_E	170_H	0.575	0.72
298_T	304_Q	0.574	0.72
277_R	288_L	0.573	0.72
125_L	153_T	0.572	0.72
83_A	136_P	0.570	0.72
103_V	116_L	0.569	0.71
287_T	299_R	0.565	0.71
225_P	236_D	0.565	0.71
259_I	280_L	0.563	0.71
65_I	87_D	0.562	0.71
274_L	309_G	0.561	0.70
157_A	279_G	0.560	0.70
114_L	122_E	0.559	0.70
99_L	115_A	0.556	0.70
315_E	319_T	0.555	0.70
178_Y	209_V	0.553	0.69
144_T	156_R	0.551	0.69
166_R	170_H	0.551	0.69
179_L	185_L	0.551	0.69
220_T	224_T	0.550	0.69
115_A	259_I	0.547	0.68
178_Y	185_L	0.543	0.68
100_R	104_K	0.542	0.68
155_E	158_I	0.539	0.67
233_A	236_D	0.538	0.67
292_G	301_R	0.538	0.67
80_A	131_V	0.537	0.67
112_R	163_R	0.537	0.67
125_L	129_R	0.536	0.67
109_Y	113_G	0.534	0.67
108_R	314_R	0.534	0.67
77_V	139_G	0.533	0.67
168_P	279_G	0.532	0.66
78_Y	85_R	0.531	0.66
73_A	80_A	0.531	0.66
73_A	76_E	0.529	0.66
276_R	295_I	0.529	0.66
185_L	194_S	0.525	0.65
69_P	320_Q	0.525	0.65
106_A	122_E	0.524	0.65
122_E	163_R	0.524	0.65
314_R	318_Q	0.524	0.65
156_R	299_R	0.521	0.65
110_G	115_A	0.520	0.65
263_L	269_K	0.519	0.64
307_V	311_R	0.519	0.64
238_L	252_D	0.519	0.64
142_F	168_P	0.518	0.64
112_R	176_N	0.517	0.64
204_K	212_M	0.517	0.64
293_R	296_G	0.516	0.64
64_E	67_Y	0.515	0.64
292_G	304_Q	0.515	0.64
182_A	193_P	0.515	0.64
224_T	234_L	0.515	0.64
54_V	57_A	0.514	0.64
302_V	317_L	0.514	0.64
56_D	60_L	0.513	0.64
70_L	80_A	0.513	0.64
260_V	264_F	0.513	0.64
99_L	122_E	0.512	0.63
172_V	211_R	0.512	0.63
56_D	117_L	0.511	0.63
95_I	125_L	0.511	0.63
232_K	252_D	0.510	0.63
229_D	233_A	0.509	0.63
172_V	175_L	0.509	0.63
263_L	267_N	0.507	0.63
61_Y	64_E	0.506	0.63
266_L	274_L	0.505	0.62
143_S	170_H	0.504	0.62
94_M	147_T	0.504	0.62
65_I	99_L	0.503	0.62
186_S	206_V	0.503	0.62
79_F	198_I	0.502	0.62
148_W	155_E	0.501	0.62
65_I	124_N	0.500	0.62
179_L	182_A	0.500	0.62

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	0.8242	100	0.306	Contact Map
1l9zH	1	0.8	100	0.306	Contact Map
4yfkF	1	0.8333	100	0.365	Contact Map
3ugoA	1	0.3333	100	0.592	Contact Map
1l0oC	1	0.1727	100	0.592	Contact Map
1rp3A	1	0.6939	100	0.622	Contact Map
4nqwA	1	0.4485	99.9	0.736	Contact Map
1sigA	1	0.4879	99.9	0.743	Contact Map
4x8kA	1	0.2758	99.9	0.755	Contact Map
1or7A	2	0.5576	99.8	0.77	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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