RPSE - BACSU - GREMLIN Contacts

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RPSE - RNA polymerase sigma-E factor

UniProt:	P06222	Sequences: MKKLKLRLTHLWYKLLMKLGLKSDEVYYIGGSEALPPPLSKDEEQVLLMKLPNGDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKIRSEVSFDEPLNIDWDGNELLLSDVLGTDDDIITKDIEANVDKKLLKKALEQLNEREKQIMELRFGLVGEEEKTQKDVADMMGISQSYISRLEKRIIKRLRKEFNKMV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	239 (194)
Sequences:	6653 (4010)
Seq/√Len:	287.9

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
50_K	55_D	3.468	1.00
59_R	100_N	3.356	1.00
189_K	193_E	3.147	1.00
70_V	91_G	3.044	1.00
194_L	212_M	2.835	1.00
153_L	157_L	2.692	1.00
46_V	50_K	2.645	1.00
60_A	64_E	2.564	1.00
43_E	61_I	2.519	1.00
195_R	224_E	2.518	1.00
194_L	204_K	2.485	1.00
215_I	220_I	2.395	1.00
159_T	165_T	2.363	1.00
173_D	176_L	2.318	1.00
219_Y	222_R	2.122	1.00
156_V	169_E	2.104	1.00
204_K	212_M	2.077	1.00
61_I	65_R	2.074	1.00
69_L	111_A	2.056	1.00
188_E	230_R	2.001	1.00
185_N	230_R	1.882	1.00
190_Q	213_M	1.873	1.00
190_Q	212_M	1.857	1.00
190_Q	194_L	1.847	1.00
207_K	211_D	1.813	1.00
218_S	221_S	1.811	1.00
152_L	169_E	1.807	1.00
98_A	114_A	1.745	1.00
45_Q	49_M	1.741	1.00
183_Q	234_E	1.726	1.00
173_D	177_L	1.721	1.00
63_I	96_I	1.711	1.00
103_N	106_K	1.690	1.00
73_I	115_S	1.648	1.00
182_E	189_K	1.630	1.00
52_P	104_P	1.616	1.00
149_N	169_E	1.601	1.00
41_K	45_Q	1.593	1.00
56_Q	60_A	1.592	1.00
90_I	125_Y	1.569	1.00
185_N	188_E	1.544	1.00
174_K	178_K	1.529	1.00
40_S	43_E	1.518	1.00
67_L	92_T	1.512	1.00
213_M	220_I	1.478	1.00
192_M	231_L	1.471	1.00
74_A	122_I	1.449	1.00
57_A	60_A	1.436	1.00
191_I	227_I	1.429	1.00
175_K	178_K	1.419	1.00
204_K	208_D	1.396	1.00
88_I	92_T	1.379	1.00
191_I	223_L	1.376	1.00
50_K	53_N	1.369	1.00
152_L	156_V	1.364	1.00
74_A	88_I	1.356	1.00
48_L	51_L	1.339	1.00
149_N	153_L	1.307	1.00
164_I	174_K	1.290	1.00
47_L	61_I	1.269	1.00
52_P	105_E	1.256	1.00
71_V	88_I	1.251	1.00
109_K	112_T	1.248	1.00
188_E	226_R	1.239	1.00
74_A	84_I	1.238	1.00
101_T	113_Y	1.235	1.00
52_P	103_N	1.229	1.00
194_L	209_V	1.226	1.00
218_S	222_R	1.210	1.00
158_G	161_D	1.200	1.00
43_E	46_V	1.191	1.00
164_I	168_I	1.188	1.00
55_D	58_A	1.155	1.00
223_L	227_I	1.153	1.00
153_L	159_T	1.152	1.00
219_Y	223_L	1.148	1.00
149_N	152_L	1.147	1.00
78_E	84_I	1.135	1.00
140_E	144_I	1.132	1.00
73_I	122_I	1.110	1.00
190_Q	193_E	1.109	1.00
174_K	177_L	1.107	1.00
176_L	179_K	1.090	1.00
49_M	105_E	1.087	1.00
99_V	110_L	1.075	1.00
175_K	179_K	1.074	1.00
50_K	58_A	1.061	1.00
153_L	169_E	1.053	1.00
72_Y	75_R	1.050	1.00
46_V	49_M	1.050	1.00
70_V	95_L	1.042	1.00
50_K	61_I	1.031	1.00
125_Y	129_N	1.030	1.00
49_M	53_N	1.029	1.00
48_L	52_P	1.023	1.00
97_K	121_E	1.019	1.00
59_R	99_V	1.015	1.00
51_L	62_L	1.014	1.00
135_E	138_F	1.006	1.00
206_Q	221_S	1.002	1.00
98_A	110_L	1.000	1.00
166_K	170_A	0.994	1.00
145_D	170_A	0.993	1.00
54_G	58_A	0.990	1.00
187_R	191_I	0.971	1.00
110_L	114_A	0.969	1.00
173_D	178_K	0.967	1.00
95_L	114_A	0.965	1.00
186_E	190_Q	0.953	1.00
51_L	54_G	0.951	1.00
145_D	166_K	0.951	1.00
141_P	172_V	0.941	1.00
132_I	135_E	0.939	1.00
167_D	170_A	0.929	1.00
57_A	61_I	0.924	1.00
130_N	139_D	0.916	1.00
206_Q	218_S	0.916	1.00
153_L	161_D	0.914	1.00
167_D	172_V	0.908	1.00
191_I	213_M	0.902	1.00
97_K	101_T	0.895	1.00
75_R	84_I	0.893	1.00
142_L	145_D	0.890	1.00
49_M	104_P	0.889	1.00
47_L	58_A	0.887	1.00
51_L	58_A	0.885	1.00
163_I	166_K	0.883	1.00
206_Q	222_R	0.881	1.00
206_Q	210_A	0.874	1.00
161_D	165_T	0.869	1.00
117_C	120_N	0.869	1.00
91_G	122_I	0.864	1.00
42_D	46_V	0.862	1.00
187_R	223_L	0.861	1.00
92_T	96_I	0.857	1.00
180_A	183_Q	0.848	1.00
162_D	165_T	0.845	1.00
195_R	209_V	0.842	1.00
73_I	119_E	0.841	1.00
186_E	189_K	0.840	1.00
63_I	99_V	0.839	1.00
39_L	44_E	0.831	1.00
119_E	123_L	0.826	1.00
75_R	78_E	0.816	1.00
67_L	71_V	0.815	1.00
149_N	170_A	0.814	1.00
161_D	166_K	0.810	1.00
101_T	117_C	0.804	0.99
154_S	157_L	0.801	0.99
168_I	171_N	0.799	0.99
82_I	125_Y	0.794	0.99
229_K	233_K	0.793	0.99
167_D	171_N	0.792	0.99
61_I	64_E	0.792	0.99
71_V	92_T	0.792	0.99
166_K	171_N	0.792	0.99
207_K	217_Q	0.790	0.99
209_V	224_E	0.785	0.99
180_A	231_L	0.782	0.99
168_I	172_V	0.780	0.99
38_P	68_R	0.775	0.99
196_F	228_I	0.763	0.99
48_L	104_P	0.761	0.99
71_V	84_I	0.759	0.99
39_L	65_R	0.754	0.99
94_G	122_I	0.752	0.99
207_K	210_A	0.750	0.99
224_E	227_I	0.744	0.99
71_V	74_A	0.735	0.99
53_N	58_A	0.735	0.99
144_I	147_D	0.735	0.99
69_L	112_T	0.735	0.99
149_N	166_K	0.726	0.99
108_I	112_T	0.725	0.99
153_L	156_V	0.717	0.99
180_A	235_F	0.717	0.99
141_P	144_I	0.710	0.99
137_S	141_P	0.707	0.99
66_N	111_A	0.705	0.99
172_V	176_L	0.704	0.99
56_Q	59_R	0.704	0.99
196_F	224_E	0.702	0.99
52_P	55_D	0.694	0.98
165_T	169_E	0.693	0.98
143_N	146_W	0.688	0.98
47_L	51_L	0.687	0.98
90_I	121_E	0.685	0.98
88_I	91_G	0.684	0.98
216_S	219_Y	0.680	0.98
113_Y	117_C	0.680	0.98
139_D	143_N	0.680	0.98
67_L	70_V	0.678	0.98
147_D	152_L	0.667	0.98
69_L	115_S	0.667	0.98
70_V	92_T	0.666	0.98
59_R	63_I	0.666	0.98
77_F	122_I	0.662	0.98
210_A	217_Q	0.660	0.98
93_I	96_I	0.659	0.98
45_Q	107_K	0.658	0.98
184_L	227_I	0.657	0.98
44_E	65_R	0.653	0.98
157_L	169_E	0.648	0.98
159_T	166_K	0.648	0.98
181_L	193_E	0.647	0.98
206_Q	217_Q	0.646	0.98
48_L	99_V	0.642	0.97
94_G	117_C	0.641	0.97
195_R	206_Q	0.635	0.97
150_E	154_S	0.635	0.97
104_P	107_K	0.632	0.97
209_V	220_I	0.631	0.97
206_Q	224_E	0.631	0.97
157_L	165_T	0.631	0.97
62_L	99_V	0.629	0.97
187_R	215_I	0.623	0.97
138_F	145_D	0.620	0.97
163_I	167_D	0.618	0.97
121_E	125_Y	0.617	0.97
143_N	147_D	0.617	0.97
154_S	160_D	0.616	0.97
67_L	88_I	0.612	0.97
139_D	145_D	0.609	0.97
180_A	234_E	0.608	0.96
72_Y	76_K	0.608	0.96
66_N	197_G	0.605	0.96
94_G	98_A	0.601	0.96
137_S	140_E	0.601	0.96
164_I	167_D	0.600	0.96
149_N	157_L	0.600	0.96
206_Q	219_Y	0.594	0.96
157_L	161_D	0.594	0.96
209_V	213_M	0.591	0.96
159_T	167_D	0.588	0.96
152_L	155_D	0.586	0.96
174_K	179_K	0.581	0.95
117_C	124_M	0.580	0.95
159_T	162_D	0.580	0.95
185_N	223_L	0.579	0.95
44_E	48_L	0.578	0.95
166_K	177_L	0.577	0.95
48_L	62_L	0.577	0.95
124_M	128_R	0.573	0.95
44_E	109_K	0.572	0.95
181_L	189_K	0.571	0.95
51_L	110_L	0.570	0.95
120_N	124_M	0.569	0.95
141_P	145_D	0.561	0.95
41_K	44_E	0.560	0.94
82_I	126_L	0.560	0.94
39_L	47_L	0.560	0.94
114_A	118_I	0.557	0.94
124_M	195_R	0.555	0.94
163_I	170_A	0.554	0.94
117_C	218_S	0.553	0.94
150_E	153_L	0.553	0.94
226_R	229_K	0.552	0.94
187_R	219_Y	0.552	0.94
170_A	173_D	0.549	0.94
65_R	68_R	0.549	0.94
117_C	221_S	0.545	0.94
120_N	216_S	0.539	0.93
162_D	166_K	0.538	0.93
173_D	179_K	0.538	0.93
37_P	40_S	0.537	0.93
86_D	89_S	0.537	0.93
68_R	71_V	0.534	0.93
82_I	129_N	0.530	0.93
192_M	228_I	0.528	0.93
161_D	170_A	0.528	0.93
69_L	118_I	0.527	0.93
134_S	138_F	0.526	0.92
164_I	171_N	0.526	0.92
191_I	209_V	0.526	0.92
170_A	177_L	0.525	0.92
181_L	185_N	0.524	0.92
153_L	165_T	0.524	0.92
205_T	208_D	0.521	0.92
53_N	56_Q	0.519	0.92
133_R	137_S	0.519	0.92
58_A	62_L	0.519	0.92
129_N	132_I	0.518	0.92
136_V	140_E	0.515	0.92
89_S	121_E	0.508	0.91
164_I	170_A	0.507	0.91
127_R	136_V	0.506	0.91
138_F	144_I	0.506	0.91
90_I	221_S	0.504	0.91
54_G	100_N	0.502	0.91
120_N	136_V	0.501	0.91
116_R	119_E	0.500	0.90

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	0.9038	100	0.256	Contact Map
2a6hF	1	0.8996	100	0.26	Contact Map
4yfkF	1	0.9958	100	0.366	Contact Map
1l0oC	1	0.1632	100	0.464	Contact Map
3ugoA	1	0.4561	100	0.482	Contact Map
1rp3A	1	0.7615	100	0.533	Contact Map
4nqwA	1	0.6192	99.9	0.577	Contact Map
1or7A	2	0.7657	99.9	0.601	Contact Map
4cxfA	1	0.6444	99.9	0.614	Contact Map
2q1zA	1	0.7322	99.9	0.619	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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