RPSH - BACSU - GREMLIN Contacts

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RPSH - RNA polymerase sigma-H factor

UniProt:	P17869	Sequences: MNLQNNKGKFNKEQFCQLEDEQVIEKVHVGDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFKEDKLTSFKAFAELCITRQIITAIKTATRQKHIPLNSYASLDKPIFDEESDRTLLDVISGAKTLNPEEMIINQEEFDDIEMKMGELLSDLERKVLVLYLDGRSYQEISDELNRHVKSIDNALQRVKRKLEKYLEIREISL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	218 (191)
Sequences:	8606 (5179)
Seq/√Len:	374.8

ECOLI - RPOS RPOD RPOH FLIA
BACSU - RPSH SIGA RPSK RPSB RPSE RPSG RPSF 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
35_L	76_R	3.749	1.00
46_V	67_G	3.029	1.00
170_R	174_V	2.961	1.00
175_L	188_E	2.911	1.00
26_K	31_D	2.831	1.00
36_D	40_T	2.636	1.00
175_L	180_R	2.544	1.00
22_Q	26_K	2.452	1.00
164_L	210_Y	2.402	1.00
191_R	196_I	2.330	1.00
176_Y	200_L	2.317	1.00
180_R	188_E	2.220	1.00
169_E	206_K	2.214	1.00
37_Y	41_K	2.211	1.00
195_S	198_N	2.166	1.00
19_E	37_Y	2.061	1.00
171_K	175_L	2.045	1.00
66_E	101_A	1.990	1.00
43_R	68_M	1.918	1.00
49_K	91_E	1.894	1.00
25_E	29_V	1.887	1.00
130_R	135_V	1.883	1.00
171_K	188_E	1.879	1.00
183_Q	187_D	1.821	1.00
79_K	82_K	1.819	1.00
85_S	88_A	1.812	1.00
45_F	87_K	1.787	1.00
171_K	189_L	1.782	1.00
64_V	68_M	1.771	1.00
194_K	197_D	1.751	1.00
166_S	206_K	1.683	1.00
145_E	149_I	1.675	1.00
172_V	203_V	1.635	1.00
21_E	25_E	1.623	1.00
32_S	36_D	1.612	1.00
172_V	199_A	1.589	1.00
50_A	98_I	1.565	1.00
49_K	98_I	1.563	1.00
180_R	184_E	1.557	1.00
74_S	90_A	1.543	1.00
169_E	202_R	1.492	1.00
39_I	72_Y	1.487	1.00
50_A	60_R	1.482	1.00
166_S	169_E	1.465	1.00
195_S	199_A	1.465	1.00
47_R	64_V	1.461	1.00
163_E	170_R	1.450	1.00
175_L	185_I	1.420	1.00
131_T	135_V	1.414	1.00
173_L	207_L	1.407	1.00
189_L	196_I	1.368	1.00
50_A	64_V	1.362	1.00
86_F	90_A	1.361	1.00
138_G	141_T	1.360	1.00
24_I	27_V	1.347	1.00
77_D	89_F	1.329	1.00
130_R	134_D	1.329	1.00
131_T	134_D	1.315	1.00
28_H	80_E	1.270	1.00
75_I	86_F	1.253	1.00
67_G	98_I	1.239	1.00
109_K	112_P	1.238	1.00
28_H	81_D	1.233	1.00
33_D	36_D	1.229	1.00
171_K	174_V	1.228	1.00
177_L	200_L	1.197	1.00
19_E	22_Q	1.193	1.00
23_V	37_Y	1.192	1.00
51_R	60_R	1.175	1.00
26_K	29_V	1.171	1.00
132_L	135_V	1.168	1.00
46_V	71_L	1.154	1.00
168_L	199_A	1.153	1.00
151_Q	155_D	1.152	1.00
49_K	95_T	1.150	1.00
199_A	203_V	1.135	1.00
28_H	79_K	1.112	1.00
194_K	198_N	1.100	1.00
152_E	156_D	1.096	1.00
183_Q	193_V	1.094	1.00
129_D	135_V	1.094	1.00
73_K	97_Q	1.090	1.00
31_D	34_A	1.086	1.00
93_C	96_R	1.079	1.00
122_P	126_E	1.071	1.00
182_Y	186_S	1.068	1.00
58_A	101_A	1.067	1.00
89_F	93_C	1.050	1.00
162_G	170_R	1.045	1.00
51_R	54_F	1.039	1.00
176_Y	185_I	1.035	1.00
24_I	28_H	1.034	1.00
168_L	172_V	1.032	1.00
84_T	88_A	1.023	1.00
154_F	158_E	1.021	1.00
95_T	99_I	1.017	1.00
182_Y	197_D	1.016	1.00
122_P	125_D	1.011	1.00
70_G	98_I	0.996	1.00
149_I	152_E	0.986	1.00
64_V	67_G	0.972	1.00
22_Q	25_E	0.968	1.00
177_L	204_K	0.968	1.00
71_L	90_A	0.965	1.00
73_K	77_D	0.955	1.00
77_D	93_C	0.951	1.00
39_I	75_I	0.950	1.00
47_R	60_R	0.948	1.00
205_R	209_K	0.947	1.00
70_G	74_S	0.947	1.00
167_D	171_K	0.944	1.00
37_Y	40_T	0.944	1.00
129_D	132_L	0.939	1.00
185_I	200_L	0.932	1.00
182_Y	194_K	0.930	1.00
167_D	170_R	0.922	1.00
147_M	151_Q	0.921	1.00
200_L	203_V	0.919	1.00
172_V	189_L	0.915	1.00
26_K	34_A	0.907	1.00
54_F	60_R	0.906	1.00
25_E	81_D	0.897	1.00
160_K	163_E	0.896	1.00
123_I	126_E	0.895	1.00
68_M	72_Y	0.891	1.00
47_R	68_M	0.889	1.00
48_A	51_R	0.887	1.00
38_L	75_I	0.887	1.00
116_Y	120_D	0.885	1.00
169_E	199_A	0.877	1.00
33_D	37_Y	0.874	1.00
143_N	146_E	0.870	1.00
152_E	155_D	0.868	1.00
74_S	86_F	0.866	1.00
121_K	125_D	0.864	1.00
142_L	147_M	0.862	1.00
27_V	30_G	0.861	1.00
25_E	80_E	0.861	1.00
161_M	207_L	0.855	1.00
53_Y	98_I	0.847	1.00
101_A	105_A	0.844	1.00
23_V	34_A	0.838	1.00
142_L	150_N	0.828	1.00
146_E	149_I	0.814	1.00
119_L	122_P	0.813	1.00
182_Y	193_V	0.811	1.00
90_A	94_I	0.809	1.00
168_L	191_R	0.804	1.00
114_N	118_S	0.801	1.00
30_G	34_A	0.793	1.00
174_V	178_D	0.790	1.00
144_P	147_M	0.789	1.00
125_D	128_S	0.788	1.00
46_V	68_M	0.787	1.00
144_P	148_I	0.784	1.00
173_L	204_K	0.783	1.00
27_V	38_L	0.781	1.00
43_R	47_R	0.779	1.00
69_I	72_Y	0.778	1.00
176_Y	182_Y	0.774	1.00
45_F	91_E	0.772	1.00
27_V	34_A	0.772	1.00
151_Q	154_F	0.767	1.00
162_G	174_V	0.767	1.00
168_L	195_S	0.765	1.00
80_E	83_L	0.759	1.00
117_A	121_K	0.756	1.00
20_D	41_K	0.752	1.00
26_K	37_Y	0.750	1.00
148_I	151_Q	0.749	1.00
153_E	157_I	0.748	1.00
192_H	195_S	0.744	1.00
121_K	124_F	0.743	1.00
182_Y	198_N	0.739	1.00
142_L	146_E	0.737	1.00
183_Q	186_S	0.736	1.00
35_L	75_I	0.732	1.00
162_G	166_S	0.731	1.00
133_L	136_I	0.730	1.00
186_S	193_V	0.730	1.00
169_E	203_V	0.727	1.00
149_I	153_E	0.724	1.00
47_R	50_A	0.721	1.00
20_D	24_I	0.721	1.00
123_I	127_E	0.716	1.00
144_P	149_I	0.713	1.00
132_L	136_I	0.713	1.00
23_V	27_V	0.710	1.00
44_N	47_R	0.707	0.99
118_S	121_K	0.703	0.99
161_M	164_L	0.699	0.99
114_N	117_A	0.697	0.99
118_S	122_P	0.694	0.99
154_F	157_I	0.693	0.99
24_I	80_E	0.692	0.99
66_E	97_Q	0.692	0.99
146_E	150_N	0.680	0.99
38_L	42_Y	0.676	0.99
147_M	150_N	0.671	0.99
28_H	31_D	0.666	0.99
106_T	113_L	0.663	0.99
131_T	136_I	0.662	0.99
161_M	211_L	0.662	0.99
141_T	150_N	0.659	0.99
42_Y	87_K	0.654	0.99
27_V	31_D	0.653	0.99
48_A	52_S	0.651	0.99
140_K	150_N	0.649	0.99
132_L	137_S	0.648	0.99
166_S	203_V	0.645	0.99
45_F	94_I	0.645	0.99
43_R	46_V	0.643	0.99
60_R	64_V	0.642	0.99
62_D	65_Q	0.640	0.99
192_H	198_N	0.639	0.99
148_I	152_E	0.634	0.99
78_F	82_K	0.624	0.99
150_N	154_F	0.621	0.99
172_V	191_R	0.619	0.99
100_T	104_T	0.618	0.99
134_D	137_S	0.613	0.99
58_A	105_A	0.611	0.99
96_R	100_T	0.610	0.99
93_C	100_T	0.609	0.99
25_E	28_H	0.608	0.98
182_Y	200_L	0.607	0.98
185_I	188_E	0.606	0.98
129_D	133_L	0.603	0.98
97_Q	101_A	0.602	0.98
185_I	196_I	0.598	0.98
35_L	39_I	0.597	0.98
58_A	102_I	0.596	0.98
19_E	41_K	0.596	0.98
102_I	113_L	0.595	0.98
156_D	160_K	0.595	0.98
143_N	147_M	0.593	0.98
78_F	84_T	0.592	0.98
131_T	137_S	0.591	0.98
137_S	140_K	0.589	0.98
161_M	210_Y	0.582	0.98
46_V	50_A	0.581	0.98
72_Y	75_I	0.579	0.98
124_F	128_S	0.576	0.98
142_L	145_E	0.575	0.98
46_V	94_I	0.575	0.98
115_S	118_S	0.564	0.98
204_K	208_E	0.562	0.97
23_V	26_K	0.559	0.97
21_E	24_I	0.558	0.97
58_A	63_I	0.557	0.97
61_E	68_M	0.555	0.97
88_A	91_E	0.555	0.97
141_T	147_M	0.554	0.97
43_R	64_V	0.551	0.97
47_R	51_R	0.551	0.97
176_Y	181_S	0.551	0.97
153_E	156_D	0.550	0.97
160_K	164_L	0.545	0.97
176_Y	193_V	0.544	0.97
145_E	150_N	0.541	0.97
70_G	97_Q	0.540	0.97
21_E	83_L	0.539	0.97
70_G	93_C	0.536	0.97
46_V	75_I	0.535	0.97
158_E	174_V	0.530	0.96
92_L	95_T	0.519	0.96
186_S	194_K	0.519	0.96
70_G	94_I	0.518	0.96
134_D	138_G	0.516	0.96
120_D	123_I	0.513	0.96
20_D	27_V	0.512	0.96
199_A	202_R	0.512	0.96
130_R	133_L	0.511	0.96
116_Y	119_L	0.511	0.96
117_A	125_D	0.511	0.96
165_L	203_V	0.509	0.96
95_T	98_I	0.508	0.95
42_Y	71_L	0.508	0.95
103_K	113_L	0.507	0.95
140_K	147_M	0.506	0.95
181_S	184_E	0.505	0.95
202_R	206_K	0.505	0.95
143_N	148_I	0.502	0.95
22_Q	33_D	0.502	0.95
107_R	116_Y	0.500	0.95
50_A	63_I	0.500	0.95

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	0.9679	100	0.223	Contact Map
2a6hF	1	0.9725	100	0.224	Contact Map
4yfkF	1	0.9954	100	0.303	Contact Map
3ugoA	1	0.4908	100	0.449	Contact Map
1l0oC	1	0.1055	100	0.455	Contact Map
1rp3A	1	0.8394	99.9	0.506	Contact Map
4nqwA	1	0.6743	99.9	0.53	Contact Map
4cxfA	1	0.7018	99.9	0.57	Contact Map
1or7A	2	0.8394	99.9	0.57	Contact Map
2q1zA	1	0.7982	99.9	0.578	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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