FLIA - ECOLI - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

FLIA - RNA polymerase sigma factor FliA

UniProt:	P0AEM6	Sequences: MNSLYTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWVPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11355
Length:	239 (223)
Sequences:	7403 (4484)
Seq/√Len:	300.3

ECOLI - FLIA RPOD RPOS RPOH
BACSU - SIGA RPSD RPSG RPSB RPSF RPSK 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
13_K	57_E	3.624	1.00
107_L	111_L	3.593	1.00
110_E	123_R	3.533	1.00
113_R	119_E	3.208	1.00
24_V	48_G	3.189	1.00
194_K	198_T	3.061	1.00
118_T	128_I	2.930	1.00
106_Q	123_R	2.852	1.00
216_V	221_V	2.631	1.00
14_H	18_Q	2.621	1.00
199_L	213_V	2.278	1.00
220_R	223_Q	2.267	1.00
103_A	123_R	2.264	1.00
188_T	235_K	2.244	1.00
117_E	132_R	2.200	1.00
200_Y	225_H	2.158	1.00
193_E	231_R	2.149	1.00
199_L	205_L	2.112	1.00
23_L	68_T	2.074	1.00
195_L	213_V	2.056	1.00
208_K	212_A	1.949	1.00
127_D	130_D	1.938	1.00
60_D	63_Q	1.932	1.00
187_E	194_K	1.911	1.00
219_S	222_S	1.884	1.00
205_L	213_V	1.856	1.00
21_V	49_G	1.819	1.00
47_A	82_E	1.815	1.00
195_L	199_L	1.802	1.00
27_E	72_V	1.789	1.00
195_L	214_L	1.776	1.00
66_A	69_T	1.755	1.00
106_Q	110_E	1.725	1.00
15_S	19_R	1.706	1.00
120_V	131_Y	1.700	1.00
196_V	224_L	1.689	1.00
103_A	106_Q	1.678	1.00
196_V	228_A	1.674	1.00
107_L	115_A	1.650	1.00
170_L	174_L	1.650	1.00
118_T	122_E	1.649	1.00
117_E	135_L	1.646	1.00
214_L	221_V	1.646	1.00
117_E	128_I	1.638	1.00
190_P	231_R	1.584	1.00
27_E	79_M	1.581	1.00
163_D	166_R	1.580	1.00
28_A	79_M	1.576	1.00
10_V	14_H	1.545	1.00
205_L	209_E	1.540	1.00
100_V	120_V	1.536	1.00
45_L	49_G	1.535	1.00
100_V	134_M	1.532	1.00
25_R	45_L	1.517	1.00
58_R	70_Y	1.510	1.00
147_D	158_E	1.487	1.00
17_W	53_L	1.475	1.00
48_G	79_M	1.438	1.00
117_E	131_Y	1.429	1.00
56_V	67_F	1.427	1.00
107_L	113_R	1.422	1.00
28_A	45_L	1.391	1.00
220_R	224_L	1.380	1.00
107_L	123_R	1.372	1.00
128_I	132_R	1.366	1.00
190_P	193_E	1.358	1.00
103_A	107_L	1.337	1.00
34_R	38_S	1.319	1.00
67_F	71_A	1.314	1.00
24_V	52_L	1.309	1.00
28_A	41_L	1.307	1.00
103_A	124_L	1.306	1.00
104_I	135_L	1.297	1.00
193_E	227_Q	1.289	1.00
121_A	131_Y	1.258	1.00
121_A	128_I	1.256	1.00
96_N	130_D	1.243	1.00
95_R	99_E	1.240	1.00
126_I	134_M	1.219	1.00
197_L	232_L	1.216	1.00
100_V	124_L	1.214	1.00
174_L	177_N	1.212	1.00
201_Y	225_H	1.203	1.00
126_I	131_Y	1.202	1.00
9_G	12_D	1.200	1.00
11_M	14_H	1.199	1.00
96_N	134_M	1.195	1.00
199_L	210_I	1.166	1.00
116_T	119_E	1.136	1.00
191_E	194_K	1.132	1.00
177_N	181_R	1.130	1.00
29_L	41_L	1.125	1.00
55_A	71_A	1.125	1.00
219_S	223_Q	1.123	1.00
192_R	224_L	1.122	1.00
115_A	119_E	1.120	1.00
168_N	171_Q	1.114	1.00
96_N	126_I	1.112	1.00
100_V	131_Y	1.110	1.00
111_L	115_A	1.096	1.00
195_L	198_T	1.091	1.00
102_Q	106_Q	1.082	1.00
224_L	228_A	1.080	1.00
51_G	55_A	1.055	1.00
208_K	218_E	1.054	1.00
207_L	211_G	1.052	1.00
39_V	82_E	1.047	1.00
17_W	56_V	1.035	1.00
33_V	38_S	1.024	1.00
87_D	94_R	1.018	1.00
176_S	180_Q	1.016	1.00
11_M	15_S	1.015	1.00
89_V	97_A	1.009	1.00
159_L	162_D	1.004	1.00
179_R	183_M	1.001	1.00
45_L	48_G	0.998	1.00
207_L	222_S	0.996	1.00
207_L	219_S	0.996	1.00
29_L	32_Q	0.992	1.00
108_E	115_A	0.978	1.00
193_E	224_L	0.974	1.00
192_R	220_R	0.957	1.00
20_Y	68_T	0.951	1.00
15_S	18_Q	0.949	1.00
54_N	58_R	0.949	1.00
104_I	120_V	0.945	1.00
207_L	218_E	0.944	1.00
54_N	78_A	0.938	1.00
70_Y	74_R	0.935	1.00
121_A	126_I	0.930	1.00
76_R	80_L	0.927	1.00
181_R	184_E	0.921	1.00
200_Y	210_I	0.908	1.00
151_E	155_D	0.896	1.00
107_L	120_V	0.892	1.00
16_L	56_V	0.891	1.00
25_R	49_G	0.889	1.00
191_E	195_L	0.886	1.00
156_S	160_V	0.876	1.00
192_R	196_V	0.873	1.00
230_K	234_T	0.873	1.00
144_F	148_E	0.873	1.00
103_A	120_V	0.872	1.00
81_D	85_S	0.872	1.00
41_L	45_L	0.866	1.00
170_L	173_L	0.865	1.00
27_E	76_R	0.862	1.00
24_V	49_G	0.862	1.00
108_E	111_L	0.858	1.00
171_Q	174_L	0.853	1.00
49_G	53_L	0.850	1.00
151_E	154_G	0.850	1.00
198_T	203_E	0.849	1.00
111_L	119_E	0.848	1.00
74_R	77_G	0.845	1.00
25_R	41_L	0.843	1.00
90_P	93_V	0.838	1.00
146_Y	158_E	0.837	1.00
82_E	86_R	0.831	1.00
32_Q	41_L	0.830	1.00
132_R	136_L	0.829	1.00
8_E	12_D	0.828	1.00
21_V	24_V	0.828	1.00
111_L	123_R	0.826	1.00
217_G	220_R	0.825	1.00
208_K	211_G	0.821	1.00
152_E	156_S	0.814	1.00
58_R	74_R	0.812	1.00
100_V	135_L	0.808	1.00
225_H	228_A	0.802	1.00
52_L	71_A	0.801	1.00
175_D	179_R	0.800	1.00
173_L	177_N	0.796	1.00
196_V	214_L	0.795	1.00
130_D	133_Q	0.790	0.99
150_R	160_V	0.782	0.99
186_I	198_T	0.779	0.99
96_N	99_E	0.778	0.99
185_A	235_K	0.772	0.99
184_E	187_E	0.770	0.99
210_I	225_H	0.770	0.99
169_P	173_L	0.768	0.99
31_L	79_M	0.764	0.99
26_H	29_L	0.762	0.99
16_L	20_Y	0.761	0.99
69_T	72_V	0.752	0.99
200_Y	207_L	0.744	0.99
108_E	114_N	0.742	0.99
217_G	223_Q	0.741	0.99
84_R	91_R	0.740	0.99
55_A	67_F	0.738	0.99
13_K	56_V	0.733	0.99
201_Y	229_I	0.732	0.99
101_A	104_I	0.732	0.99
196_V	216_V	0.731	0.99
207_L	223_Q	0.731	0.99
65_T	69_T	0.728	0.99
172_Q	176_S	0.728	0.99
192_R	223_Q	0.727	0.99
77_G	81_D	0.727	0.99
131_Y	135_L	0.727	0.99
185_A	232_L	0.722	0.99
183_M	198_T	0.707	0.99
197_L	229_I	0.704	0.99
61_A	64_G	0.698	0.99
173_L	176_S	0.697	0.99
209_E	212_A	0.697	0.99
97_A	134_M	0.689	0.99
23_L	72_V	0.688	0.99
77_G	84_R	0.682	0.99
107_L	119_E	0.678	0.98
93_V	97_A	0.678	0.98
121_A	124_L	0.675	0.98
149_W	155_D	0.674	0.98
193_E	228_A	0.669	0.98
22_P	25_R	0.668	0.98
19_R	22_P	0.667	0.98
185_A	228_A	0.664	0.98
13_K	17_W	0.664	0.98
192_R	216_V	0.662	0.98
180_Q	184_E	0.660	0.98
183_M	187_E	0.660	0.98
51_G	79_M	0.658	0.98
98_R	101_A	0.656	0.98
94_R	98_R	0.656	0.98
43_D	46_Q	0.655	0.98
71_A	75_I	0.654	0.98
133_Q	136_L	0.652	0.98
104_I	114_N	0.651	0.98
26_H	30_R	0.651	0.98
169_P	172_Q	0.647	0.98
200_Y	218_E	0.641	0.98
50_I	53_L	0.634	0.98
207_L	220_R	0.634	0.98
124_L	131_Y	0.632	0.98
211_G	218_E	0.630	0.97
39_V	83_L	0.627	0.97
59_Y	63_Q	0.627	0.97
158_E	161_T	0.625	0.97
167_E	175_D	0.622	0.97
74_R	222_S	0.620	0.97
74_R	81_D	0.620	0.97
97_A	138_T	0.616	0.97
133_Q	137_D	0.616	0.97
190_P	228_A	0.614	0.97
74_R	219_S	0.613	0.97
122_E	125_G	0.613	0.97
115_A	120_V	0.612	0.97
81_D	95_R	0.608	0.97
151_E	156_S	0.606	0.97
185_A	188_T	0.604	0.97
112_G	115_A	0.604	0.97
56_V	61_A	0.598	0.97
207_L	225_H	0.595	0.96
23_L	69_T	0.595	0.96
53_L	56_V	0.593	0.96
7_A	12_D	0.592	0.96
216_V	220_R	0.586	0.96
25_R	28_A	0.585	0.96
97_A	100_V	0.581	0.96
167_E	172_Q	0.580	0.96
150_R	159_L	0.580	0.96
185_A	236_L	0.579	0.96
59_Y	65_T	0.579	0.96
203_E	213_V	0.575	0.96
104_I	108_E	0.574	0.96
80_L	91_R	0.570	0.96
186_I	190_P	0.570	0.96
176_S	179_R	0.569	0.95
21_V	45_L	0.569	0.95
157_I	161_T	0.568	0.95
39_V	44_L	0.567	0.95
21_V	25_R	0.566	0.95
182_V	185_A	0.565	0.95
210_I	214_L	0.563	0.95
160_V	163_D	0.563	0.95
93_V	134_M	0.561	0.95
25_R	42_D	0.560	0.95
103_A	111_L	0.559	0.95
157_I	162_D	0.553	0.95
10_V	13_K	0.552	0.95
107_L	110_E	0.551	0.95
117_E	124_L	0.549	0.95
218_E	223_Q	0.549	0.95
83_L	94_R	0.549	0.95
134_M	137_D	0.549	0.95
99_E	103_A	0.548	0.94
54_N	94_R	0.548	0.94
157_I	160_V	0.545	0.94
54_N	57_E	0.544	0.94
119_E	123_R	0.544	0.94
25_R	29_L	0.542	0.94
182_V	236_L	0.540	0.94
26_H	46_Q	0.538	0.94
78_A	82_E	0.537	0.94
105_G	109_Q	0.533	0.94
145_S	148_E	0.532	0.94
70_Y	73_Q	0.531	0.94
102_Q	105_G	0.525	0.93
175_D	183_M	0.523	0.93
47_A	86_R	0.523	0.93
44_L	82_E	0.523	0.93
116_T	120_V	0.522	0.93
54_N	70_Y	0.518	0.93
131_Y	137_D	0.518	0.93
100_V	126_I	0.518	0.93
27_E	75_I	0.516	0.93
229_I	233_R	0.515	0.92
190_P	224_L	0.515	0.92
24_V	56_V	0.514	0.92
177_N	180_Q	0.514	0.92
46_Q	50_I	0.513	0.92
121_A	127_D	0.513	0.92
8_E	11_M	0.513	0.92
189_L	232_L	0.511	0.92
221_V	236_L	0.511	0.92
120_V	124_L	0.511	0.92
81_D	200_Y	0.509	0.92
117_E	121_A	0.509	0.92
48_G	75_I	0.509	0.92
227_Q	230_K	0.508	0.92
98_R	102_Q	0.508	0.92
28_A	40_E	0.507	0.92
178_L	185_A	0.505	0.92
211_G	219_S	0.505	0.92
144_F	149_W	0.503	0.92
136_L	139_N	0.502	0.92
96_N	124_L	0.502	0.92
52_L	67_F	0.501	0.91
227_Q	231_R	0.501	0.91
200_Y	206_N	0.501	0.91
144_F	147_D	0.501	0.91
150_R	156_S	0.500	0.91
218_E	222_S	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	0.9582	100	0.244	Contact Map
1l9zH	1	0.9456	100	0.244	Contact Map
4yfkF	1	0.9791	100	0.292	Contact Map
1rp3A	1	0.9749	100	0.384	Contact Map
1l0oC	1	0.2301	100	0.436	Contact Map
3ugoA	1	0.3515	99.9	0.576	Contact Map
4nqwA	1	0.6025	99.9	0.599	Contact Map
2q1zA	1	0.6987	99.9	0.633	Contact Map
4cxfA	1	0.6192	99.9	0.633	Contact Map
1or7A	2	0.7155	99.8	0.634	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.

Page generated in 0.0087 seconds.