RPOE - ECOLI - GREMLIN Contacts

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RPOE - ECF RNA polymerase sigma-E factor

UniProt:	P0AGB6	Sequences: MSEQLTDQVLVERVQKGDQKAFNLLVVRYQHKVASLVSRYVPSGDVPDVVQEAFIKAYRALDSFRGDSAFYTWLYRIAVNTAKNYLVAQGRRPPSSDVDAIEAENFESGGALKEISNPENLMLSEELRQIVFRTIESLPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIFRAREAIDNKVQPLIRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11897
Length:	191 (159)
Sequences:	43365 (31654)
Seq/√Len:	2510.3

ECOLI - RPOE FECI RPOH FLIA RPOS
BACSU - SIGW SIGY YLAC SIGX SIGV SIGZ SIGM RPSD RPSE RPSH RPSG RPSK RPSB RPSF SIGA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_K	81_T	3.185	1.00
149_R	159_I	2.679	1.00
32_K	71_Y	2.467	1.00
142_L	180_A	2.312	1.00
157_E	167_V	2.276	1.00
137_S	184_K	2.231	1.00
79_V	83_K	2.201	1.00
134_T	184_K	2.195	1.00
37_V	78_A	2.038	1.00
53_A	78_A	1.993	1.00
141_D	173_R	1.981	1.00
154_L	162_I	1.980	1.00
168_G	171_R	1.918	1.00
148_L	162_I	1.889	1.00
165_C	173_R	1.707	1.00
69_A	72_T	1.705	1.00
148_L	154_L	1.688	1.00
139_P	142_L	1.672	1.00
23_N	27_V	1.654	1.00
142_L	173_R	1.646	1.00
166_P	169_T	1.646	1.00
36_L	75_Y	1.609	1.00
81_T	84_N	1.607	1.00
60_A	63_S	1.603	1.00
84_N	87_V	1.602	1.00
156_Y	167_V	1.600	1.00
24_L	28_R	1.584	1.00
150_E	178_R	1.576	1.00
44_G	47_P	1.554	1.00
57_A	74_L	1.551	1.00
40_Y	82_A	1.550	1.00
169_T	173_R	1.536	1.00
45_D	85_Y	1.529	1.00
155_S	158_E	1.515	1.00
32_K	75_Y	1.515	1.00
156_Y	174_I	1.489	1.00
175_F	179_E	1.489	1.00
156_Y	171_R	1.468	1.00
56_K	84_N	1.457	1.00
169_T	172_S	1.453	1.00
143_R	147_T	1.449	1.00
49_V	85_Y	1.417	1.00
180_A	184_K	1.411	1.00
52_E	81_T	1.410	1.00
33_V	78_A	1.400	1.00
29_Y	71_Y	1.379	1.00
165_C	170_V	1.348	1.00
76_R	79_V	1.343	1.00
149_R	174_I	1.335	1.00
37_V	82_A	1.334	1.00
80_N	83_K	1.308	1.00
71_Y	75_Y	1.308	1.00
167_V	171_R	1.287	1.00
56_K	60_A	1.286	1.00
145_A	177_A	1.282	1.00
145_A	173_R	1.258	1.00
145_A	174_I	1.238	1.00
172_S	175_F	1.216	1.00
76_R	80_N	1.210	1.00
55_I	59_R	1.203	1.00
26_V	30_Q	1.202	1.00
142_L	177_A	1.164	1.00
26_V	54_F	1.162	1.00
157_E	161_A	1.160	1.00
33_V	50_V	1.147	1.00
41_V	82_A	1.146	1.00
53_A	77_I	1.142	1.00
36_L	79_V	1.142	1.00
123_L	126_E	1.141	1.00
149_R	156_Y	1.133	1.00
41_V	49_V	1.131	1.00
154_L	158_E	1.129	1.00
64_F	67_D	1.129	1.00
37_V	49_V	1.122	1.00
136_E	143_R	1.114	1.00
150_E	174_I	1.111	1.00
29_Y	54_F	1.093	1.00
172_S	176_R	1.091	1.00
174_I	178_R	1.089	1.00
81_T	85_Y	1.078	1.00
22_F	58_Y	1.069	1.00
34_A	38_S	1.067	1.00
37_V	50_V	1.065	1.00
84_N	88_A	1.061	1.00
85_Y	89_Q	1.061	1.00
168_G	172_S	1.055	1.00
53_A	81_T	1.051	1.00
147_T	152_D	1.046	1.00
134_T	137_S	1.044	1.00
30_Q	34_A	1.043	1.00
38_S	46_V	1.042	1.00
148_L	159_I	1.035	1.00
45_D	89_Q	1.033	1.00
29_Y	74_L	1.031	1.00
159_I	170_V	1.029	1.00
82_A	86_L	1.021	1.00
142_L	176_R	1.017	1.00
49_V	81_T	1.016	1.00
18_D	21_A	1.009	1.00
68_S	72_T	1.005	1.00
156_Y	170_V	1.000	1.00
33_V	53_A	0.973	1.00
83_K	86_L	0.969	1.00
34_A	47_P	0.967	1.00
34_A	50_V	0.956	1.00
144_M	147_T	0.950	1.00
141_D	165_C	0.944	1.00
128_R	132_F	0.942	1.00
29_Y	32_K	0.942	1.00
140_E	144_M	0.937	1.00
147_T	151_L	0.936	1.00
33_V	74_L	0.933	1.00
37_V	46_V	0.928	1.00
34_A	46_V	0.927	1.00
49_V	82_A	0.920	1.00
19_Q	23_N	0.919	1.00
142_L	145_A	0.917	1.00
56_K	59_R	0.916	1.00
25_L	70_F	0.904	1.00
30_Q	50_V	0.902	1.00
119_E	123_L	0.885	1.00
168_G	175_F	0.883	1.00
35_S	39_R	0.882	1.00
88_A	91_R	0.880	1.00
134_T	181_I	0.873	1.00
22_F	62_D	0.872	1.00
145_A	165_C	0.871	1.00
165_C	169_T	0.862	1.00
179_E	183_N	0.851	1.00
144_M	148_L	0.845	1.00
146_I	150_E	0.841	1.00
57_A	73_W	0.839	1.00
31_H	35_S	0.835	1.00
52_E	85_Y	0.835	1.00
144_M	163_M	0.826	1.00
73_W	77_I	0.815	1.00
160_A	167_V	0.809	1.00
146_I	177_A	0.805	1.00
76_R	83_K	0.802	1.00
134_T	185_V	0.794	1.00
50_V	54_F	0.782	1.00
20_K	23_N	0.777	1.00
89_Q	92_R	0.762	1.00
52_E	55_I	0.755	1.00
148_L	152_D	0.753	1.00
24_L	27_V	0.753	1.00
157_E	171_R	0.752	1.00
32_K	36_L	0.750	1.00
46_V	50_V	0.745	1.00
51_Q	55_I	0.743	1.00
65_R	68_S	0.738	1.00
36_L	40_Y	0.725	1.00
88_A	92_R	0.720	1.00
30_Q	54_F	0.719	1.00
145_A	163_M	0.715	1.00
159_I	163_M	0.714	1.00
38_S	42_P	0.706	1.00
97_D	101_I	0.703	1.00
148_L	163_M	0.702	1.00
155_S	159_I	0.701	1.00
75_Y	79_V	0.699	1.00
126_E	130_I	0.689	1.00
129_Q	133_R	0.684	1.00
158_E	161_A	0.683	1.00
127_L	130_I	0.682	1.00
130_I	133_R	0.680	1.00
132_F	136_E	0.676	1.00
83_K	87_V	0.675	1.00
97_D	100_A	0.669	1.00
27_V	30_Q	0.659	1.00
141_D	144_M	0.656	1.00
122_M	126_E	0.650	1.00
176_R	179_E	0.648	1.00
40_Y	83_K	0.644	1.00
41_V	46_V	0.642	1.00
40_Y	79_V	0.636	1.00
118_P	121_L	0.636	1.00
86_L	90_G	0.633	1.00
176_R	180_A	0.631	1.00
85_Y	88_A	0.631	1.00
32_K	35_S	0.626	1.00
48_D	51_Q	0.624	1.00
126_E	129_Q	0.620	1.00
58_Y	61_L	0.620	1.00
67_D	70_F	0.615	1.00
178_R	182_D	0.613	1.00
36_L	82_A	0.613	1.00
99_D	102_E	0.612	1.00
64_F	68_S	0.605	1.00
78_A	82_A	0.601	1.00
173_R	177_A	0.597	1.00
82_A	85_Y	0.592	1.00
53_A	57_A	0.587	1.00
122_M	125_E	0.584	1.00
125_E	128_R	0.583	1.00
121_L	125_E	0.581	1.00
90_G	94_P	0.579	1.00
57_A	77_I	0.573	1.00
61_L	70_F	0.571	1.00
66_G	69_A	0.568	1.00
160_A	163_M	0.567	1.00
146_I	181_I	0.562	1.00
140_E	143_R	0.560	1.00
138_L	177_A	0.560	1.00
144_M	162_I	0.558	1.00
20_K	24_L	0.556	1.00
86_L	89_Q	0.555	1.00
139_P	180_A	0.552	1.00
180_A	183_N	0.552	1.00
171_R	175_F	0.551	1.00
160_A	170_V	0.550	1.00
156_Y	159_I	0.550	1.00
120_N	124_S	0.547	1.00
57_A	70_F	0.546	1.00
43_S	47_P	0.541	1.00
33_V	54_F	0.536	1.00
124_S	127_L	0.534	1.00
41_V	85_Y	0.533	1.00
72_T	75_Y	0.531	1.00
117_N	120_N	0.529	1.00
159_I	174_I	0.529	1.00
132_F	151_L	0.528	1.00
98_V	101_I	0.526	1.00
49_V	78_A	0.525	1.00
64_F	72_T	0.524	1.00
41_V	45_D	0.521	1.00
130_I	134_T	0.519	1.00
112_L	115_I	0.518	1.00
89_Q	93_P	0.516	1.00
37_V	40_Y	0.515	1.00
54_F	58_Y	0.512	1.00
135_I	146_I	0.511	1.00
22_F	26_V	0.508	1.00
133_R	137_S	0.506	1.00
173_R	176_R	0.503	1.00
123_L	127_L	0.502	1.00
135_I	147_T	0.500	1.00
163_M	170_V	0.500	1.00

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
1or7A	2	0.9529	100	0.141	Contact Map
4cxfA	1	0.801	100	0.165	Contact Map
4nqwA	1	0.7644	100	0.224	Contact Map
4yfkF	1	1	100	0.226	Contact Map
2q1zA	1	0.9005	100	0.226	Contact Map
1rp3A	1	0.9215	100	0.268	Contact Map
1l0oC	1	0.0785	100	0.269	Contact Map
2a6hF	1	0.9686	100	0.283	Contact Map
1l9zH	1	0.9529	100	0.288	Contact Map
2lfwA	1	0.7644	100	0.315	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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