PSPF - ECOLI - GREMLIN Contacts

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PSPF - Psp operon transcriptional activator

UniProt:	P37344	Sequences: MAEYKDNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPMMVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLDRLAFDVVQLPPLRERESDIMLMAEYFAIQMCREIKLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYRHGTSDYPLDDIIIDPFKRRPPEDAIAVSETTSLPTLPLDLREFQMQQEKELLQLSLQQGKYNQKRAAELLGLTYHQFRALLKKHQI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12344
Length:	325 (304)
Sequences:	26857 (17620)
Seq/√Len:	1010.6

ECOLI - NTRC PSPF NORR DHAR ATOC YGEV GLRR HYFR RTCR PRPR FHLA TYRR ZRAR
BACSU - ROCR ACOR YQIR LEVR YPLP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
298_G	308_L	3.982	1.00
155_M	160_T	3.517	1.00
81_E	91_R	2.854	1.00
95_R	130_E	2.705	1.00
150_A	155_M	2.701	1.00
70_E	115_M	2.686	1.00
37_E	180_R	2.606	1.00
154_A	158_E	2.557	1.00
24_H	241_G	2.522	1.00
129_L	140_V	2.482	1.00
128_E	137_P	2.443	1.00
288_K	292_Q	2.365	1.00
128_E	139_Q	2.275	1.00
297_Q	308_L	2.248	1.00
130_E	137_P	2.239	1.00
96_F	123_V	2.189	1.00
81_E	134_G	2.159	1.00
196_Q	230_K	2.141	1.00
105_F	147_A	2.137	1.00
97_E	131_R	2.107	1.00
22_V	45_I	2.098	1.00
187_M	214_R	2.042	1.00
298_G	305_A	2.024	1.00
66_A	118_E	1.904	1.00
187_M	218_L	1.862	1.00
74_D	119_K	1.857	1.00
287_E	319_L	1.854	1.00
290_L	294_S	1.817	1.00
304_R	307_E	1.809	1.00
191_E	214_R	1.799	1.00
314_H	318_A	1.787	1.00
190_A	233_V	1.786	1.00
210_T	246_P	1.783	1.00
23_S	52_L	1.777	1.00
155_M	158_E	1.777	1.00
154_A	157_N	1.752	1.00
101_G	141_N	1.737	1.00
35_I	175_Q	1.736	1.00
82_A	91_R	1.735	1.00
82_A	89_Q	1.730	1.00
222_W	232_V	1.724	1.00
111_T	150_A	1.711	1.00
11_E	188_L	1.695	1.00
151_D	154_A	1.688	1.00
183_E	187_M	1.671	1.00
301_N	304_R	1.665	1.00
35_I	173_V	1.661	1.00
208_G	244_D	1.658	1.00
45_I	176_L	1.651	1.00
192_Y	196_Q	1.644	1.00
220_Y	223_P	1.597	1.00
93_P	97_E	1.579	1.00
82_A	90_K	1.571	1.00
80_H	85_F	1.568	1.00
292_Q	296_Q	1.544	1.00
73_L	116_V	1.541	1.00
284_M	322_K	1.518	1.00
25_L	172_D	1.509	1.00
286_Q	290_L	1.493	1.00
293_L	297_Q	1.492	1.00
212_R	247_L	1.484	1.00
134_G	138_L	1.481	1.00
303_K	307_E	1.474	1.00
12_A	184_S	1.471	1.00
55_R	141_N	1.459	1.00
295_L	305_A	1.459	1.00
294_S	298_G	1.451	1.00
153_P	157_N	1.439	1.00
314_H	317_R	1.437	1.00
97_E	138_L	1.435	1.00
304_R	308_L	1.416	1.00
43_E	122_R	1.412	1.00
30_K	234_E	1.408	1.00
210_T	213_A	1.402	1.00
48_R	52_L	1.398	1.00
205_L	208_G	1.394	1.00
70_E	113_P	1.385	1.00
10_G	15_F	1.385	1.00
302_Q	317_R	1.362	1.00
246_P	249_D	1.360	1.00
7_N	51_Y	1.355	1.00
125_E	230_K	1.350	1.00
183_E	186_I	1.342	1.00
47_S	62_S	1.338	1.00
303_K	313_Y	1.327	1.00
58_G	101_G	1.326	1.00
213_A	245_Y	1.293	1.00
190_A	209_F	1.289	1.00
216_T	247_L	1.279	1.00
294_S	305_A	1.277	1.00
312_T	315_Q	1.276	1.00
10_G	19_L	1.263	1.00
213_A	217_L	1.261	1.00
96_F	104_L	1.256	1.00
220_Y	228_E	1.256	1.00
8_L	15_F	1.253	1.00
213_A	247_L	1.244	1.00
193_F	230_K	1.243	1.00
318_A	322_K	1.242	1.00
215_E	219_N	1.234	1.00
18_V	45_I	1.232	1.00
100_D	140_V	1.231	1.00
15_F	19_L	1.230	1.00
81_E	131_R	1.229	1.00
9_L	192_Y	1.224	1.00
209_F	233_V	1.219	1.00
183_E	221_R	1.217	1.00
282_F	286_Q	1.206	1.00
131_R	134_G	1.206	1.00
240_H	249_D	1.202	1.00
207_P	243_S	1.202	1.00
289_E	293_L	1.202	1.00
29_D	55_R	1.192	1.00
251_I	254_P	1.189	1.00
312_T	318_A	1.189	1.00
289_E	292_Q	1.186	1.00
278_D	281_E	1.177	1.00
315_Q	319_L	1.175	1.00
210_T	244_D	1.170	1.00
313_Y	317_R	1.168	1.00
17_E	20_E	1.160	1.00
189_M	193_F	1.159	1.00
27_P	54_S	1.157	1.00
251_I	255_F	1.156	1.00
112_A	116_V	1.153	1.00
100_D	141_N	1.149	1.00
35_I	153_P	1.149	1.00
20_E	23_S	1.148	1.00
40_T	176_L	1.147	1.00
18_V	174_V	1.146	1.00
14_S	17_E	1.146	1.00
92_H	135_S	1.146	1.00
198_C	204_P	1.143	1.00
17_E	21_Q	1.141	1.00
187_M	190_A	1.126	1.00
197_M	237_V	1.125	1.00
283_Q	286_Q	1.120	1.00
152_L	161_F	1.110	1.00
29_D	200_E	1.109	1.00
284_M	288_K	1.107	1.00
98_R	135_S	1.103	1.00
93_P	98_R	1.083	1.00
146_C	169_L	1.081	1.00
302_Q	313_Y	1.080	1.00
317_R	321_K	1.075	1.00
183_E	218_L	1.066	1.00
230_K	234_E	1.062	1.00
279_L	282_F	1.060	1.00
200_E	234_E	1.058	1.00
76_E	92_H	1.054	1.00
43_E	62_S	1.051	1.00
30_K	171_F	1.051	1.00
100_D	142_V	1.043	1.00
187_M	191_E	1.041	1.00
294_S	309_L	1.040	1.00
110_A	148_T	1.039	1.00
123_V	129_L	1.038	1.00
184_S	218_L	1.038	1.00
30_K	238_Y	1.036	1.00
194_A	209_F	1.035	1.00
124_I	144_L	1.030	1.00
153_P	253_D	1.029	1.00
14_S	181_E	1.029	1.00
29_D	54_S	1.026	1.00
80_H	84_A	1.026	1.00
198_C	205_L	1.020	1.00
282_F	290_L	1.019	1.00
214_R	218_L	1.019	1.00
66_A	111_T	1.014	1.00
47_S	51_Y	1.013	1.00
285_Q	289_E	1.008	1.00
279_L	283_Q	1.008	1.00
157_N	163_A	1.006	1.00
195_I	199_R	1.006	1.00
97_E	129_L	1.005	1.00
95_R	98_R	1.004	1.00
93_P	135_S	1.003	1.00
30_K	201_I	0.996	1.00
294_S	308_L	0.994	1.00
198_C	207_P	0.994	1.00
283_Q	290_L	0.994	1.00
75_S	80_H	0.993	1.00
129_L	139_Q	0.992	1.00
32_V	49_L	0.991	1.00
175_Q	181_E	0.987	1.00
298_G	304_R	0.977	1.00
235_R	239_R	0.976	1.00
281_E	285_Q	0.974	1.00
60_F	102_G	0.968	1.00
282_F	285_Q	0.967	1.00
19_L	22_V	0.967	1.00
31_P	127_G	0.965	1.00
170_A	173_V	0.960	1.00
215_E	218_L	0.959	1.00
295_L	300_Y	0.958	1.00
197_M	233_V	0.953	1.00
211_E	215_E	0.953	1.00
50_H	103_T	0.951	1.00
21_Q	239_R	0.950	1.00
73_L	77_L	0.948	1.00
278_D	310_G	0.944	1.00
211_E	214_R	0.943	1.00
13_N	17_E	0.939	1.00
150_A	160_T	0.936	1.00
197_M	201_I	0.936	1.00
33_L	146_C	0.935	1.00
37_E	40_T	0.934	1.00
22_V	48_R	0.931	1.00
193_F	197_M	0.929	1.00
18_V	22_V	0.929	1.00
191_E	195_I	0.924	1.00
232_V	236_S	0.923	1.00
197_M	230_K	0.919	1.00
34_I	46_A	0.911	1.00
315_Q	318_A	0.909	1.00
296_Q	300_Y	0.908	1.00
302_Q	320_L	0.904	1.00
66_A	119_K	0.903	1.00
62_S	122_R	0.903	1.00
11_E	16_L	0.888	1.00
212_R	246_P	0.885	1.00
16_L	19_L	0.884	1.00
236_S	240_H	0.883	1.00
302_Q	314_H	0.880	1.00
22_V	174_V	0.879	1.00
311_L	316_F	0.878	1.00
302_Q	316_F	0.877	1.00
301_N	313_Y	0.877	1.00
85_F	88_A	0.876	1.00
186_I	190_A	0.875	1.00
127_G	139_Q	0.875	1.00
131_R	138_L	0.873	1.00
198_C	203_L	0.872	1.00
188_L	191_E	0.869	1.00
8_L	45_I	0.869	1.00
209_F	213_A	0.866	1.00
293_L	296_Q	0.865	1.00
48_R	51_Y	0.860	1.00
291_L	319_L	0.859	1.00
279_L	286_Q	0.858	1.00
305_A	308_L	0.858	1.00
209_F	214_R	0.857	1.00
317_R	320_L	0.854	1.00
37_E	178_P	0.848	1.00
305_A	316_F	0.846	1.00
197_M	234_E	0.845	1.00
316_F	320_L	0.844	1.00
166_L	170_A	0.837	1.00
198_C	237_V	0.832	1.00
8_L	44_L	0.830	1.00
153_P	156_V	0.820	1.00
178_P	181_E	0.819	1.00
196_Q	200_E	0.818	1.00
19_L	23_S	0.812	1.00
153_P	173_V	0.811	1.00
295_L	302_Q	0.810	1.00
103_T	145_V	0.804	1.00
10_G	188_L	0.800	1.00
311_L	315_Q	0.799	1.00
15_F	18_V	0.796	1.00
92_H	98_R	0.795	1.00
16_L	20_E	0.794	1.00
203_L	207_P	0.792	1.00
201_I	238_Y	0.792	1.00
13_N	16_L	0.790	1.00
171_F	231_N	0.789	1.00
46_A	60_F	0.789	1.00
312_T	317_R	0.786	1.00
34_I	45_I	0.783	1.00
290_L	293_L	0.783	1.00
96_F	142_V	0.778	1.00
84_A	88_A	0.773	1.00
318_A	321_K	0.770	1.00
76_E	95_R	0.769	1.00
194_A	237_V	0.769	1.00
47_S	126_Y	0.769	1.00
110_A	152_L	0.764	1.00
61_I	99_A	0.763	1.00
245_Y	250_I	0.763	1.00
89_Q	92_H	0.763	1.00
19_L	45_I	0.762	1.00
55_R	58_G	0.761	1.00
183_E	188_L	0.759	1.00
303_K	317_R	0.758	1.00
110_A	150_A	0.756	1.00
287_E	290_L	0.753	1.00
30_K	172_D	0.753	1.00
8_L	19_L	0.753	1.00
291_L	316_F	0.751	1.00
285_Q	288_K	0.750	1.00
94_G	97_E	0.740	1.00
295_L	320_L	0.739	1.00
190_A	194_A	0.736	1.00
197_M	200_E	0.729	1.00
9_L	188_L	0.725	1.00
236_S	245_Y	0.725	1.00
280_R	284_M	0.722	1.00
98_R	134_G	0.720	1.00
20_E	24_H	0.720	1.00
28_L	238_Y	0.719	1.00
63_L	95_R	0.718	1.00
192_Y	195_I	0.714	1.00
129_L	138_L	0.710	1.00
18_V	176_L	0.703	1.00
156_V	166_L	0.699	1.00
96_F	140_V	0.699	1.00
281_E	289_E	0.697	1.00
122_R	126_Y	0.695	1.00
22_V	49_L	0.690	1.00
302_Q	309_L	0.690	1.00
283_Q	287_E	0.682	1.00
110_A	149_N	0.680	1.00
92_H	95_R	0.679	1.00
201_I	237_V	0.677	1.00
20_E	241_G	0.677	1.00
123_V	142_V	0.676	1.00
235_R	238_Y	0.676	1.00
64_N	111_T	0.673	1.00
65_C	106_L	0.673	1.00
245_Y	249_D	0.669	1.00
301_N	305_A	0.666	1.00
190_A	214_R	0.664	1.00
73_L	112_A	0.664	1.00
313_Y	318_A	0.662	1.00
300_Y	320_L	0.662	1.00
314_H	321_K	0.660	1.00
290_L	309_L	0.656	1.00
80_H	92_H	0.656	1.00
204_P	207_P	0.655	1.00
31_P	146_C	0.654	1.00
94_G	98_R	0.654	1.00
186_I	217_L	0.650	1.00
24_H	239_R	0.644	1.00
25_L	32_V	0.643	1.00
68_L	77_L	0.643	1.00
252_I	255_F	0.639	1.00
194_A	198_C	0.637	1.00
277_L	282_F	0.632	1.00
183_E	219_N	0.631	1.00
277_L	281_E	0.630	1.00
213_A	216_T	0.630	1.00
291_L	305_A	0.623	1.00
22_V	52_L	0.622	1.00
153_P	163_A	0.622	1.00
104_L	144_L	0.621	1.00
191_E	208_G	0.621	1.00
188_L	192_Y	0.618	1.00
209_F	245_Y	0.617	1.00
84_A	132_V	0.615	1.00
26_A	52_L	0.615	1.00
71_N	74_D	0.611	1.00
21_Q	172_D	0.610	1.00
19_L	48_R	0.610	1.00
279_L	290_L	0.608	1.00
111_T	149_N	0.606	1.00
232_V	235_R	0.606	1.00
193_F	233_V	0.605	1.00
90_K	135_S	0.603	1.00
207_P	237_V	0.603	1.00
21_Q	24_H	0.602	1.00
234_E	237_V	0.602	1.00
250_I	253_D	0.602	1.00
34_I	145_V	0.601	1.00
80_H	89_Q	0.601	1.00
91_R	136_Q	0.600	1.00
252_I	256_K	0.598	1.00
11_E	184_S	0.597	1.00
235_R	251_I	0.594	1.00
216_T	219_N	0.594	1.00
14_S	18_V	0.594	1.00
250_I	254_P	0.586	1.00
242_T	249_D	0.585	1.00
295_L	299_K	0.584	1.00
114_M	118_E	0.583	1.00
29_D	201_I	0.579	1.00
33_L	109_L	0.579	1.00
216_T	254_P	0.579	1.00
10_G	16_L	0.579	1.00
247_L	251_I	0.579	1.00
172_D	239_R	0.577	1.00
59_P	98_R	0.577	1.00
203_L	237_V	0.577	1.00
173_V	235_R	0.575	1.00
93_P	131_R	0.574	1.00
300_Y	305_A	0.573	1.00
277_L	285_Q	0.571	1.00
233_V	236_S	0.570	1.00
15_F	45_I	0.570	1.00
190_A	236_S	0.566	1.00
175_Q	178_P	0.565	1.00
73_L	119_K	0.565	1.00
170_A	235_R	0.565	1.00
29_D	141_N	0.559	1.00
291_L	294_S	0.559	1.00
38_R	163_A	0.558	1.00
281_E	284_M	0.557	1.00
69_N	132_V	0.557	1.00
294_S	297_Q	0.555	1.00
276_P	279_L	0.555	1.00
306_A	316_F	0.555	1.00
313_Y	316_F	0.553	1.00
216_T	220_Y	0.553	1.00
34_I	176_L	0.553	1.00
303_K	314_H	0.553	1.00
287_E	291_L	0.553	1.00
104_L	123_V	0.551	1.00
69_N	72_L	0.549	1.00
319_L	322_K	0.549	1.00
80_H	88_A	0.549	1.00
216_T	251_I	0.549	1.00
24_H	203_L	0.548	1.00
236_S	250_I	0.546	1.00
100_D	138_L	0.543	1.00
305_A	309_L	0.542	1.00
237_V	240_H	0.542	1.00
186_I	218_L	0.538	1.00
71_N	115_M	0.536	1.00
242_T	246_P	0.536	1.00
275_L	279_L	0.536	1.00
96_F	129_L	0.535	1.00
225_N	228_E	0.535	1.00
274_T	277_L	0.534	1.00
161_F	165_L	0.530	1.00
23_S	48_R	0.528	1.00
8_L	48_R	0.528	1.00
213_A	236_S	0.525	1.00
28_L	201_I	0.522	1.00
284_M	287_E	0.522	1.00
75_S	85_F	0.522	1.00
68_L	73_L	0.522	1.00
207_P	240_H	0.520	1.00
53_S	56_W	0.519	1.00
286_Q	289_E	0.518	1.00
281_E	286_Q	0.516	1.00
127_G	140_V	0.514	1.00
14_S	184_S	0.514	1.00
19_L	52_L	0.514	1.00
40_T	44_L	0.513	1.00
83_G	86_T	0.512	1.00
240_H	243_S	0.512	1.00
204_P	243_S	0.511	1.00
244_D	247_L	0.510	1.00
222_W	228_E	0.510	1.00
205_L	237_V	0.510	1.00
312_T	322_K	0.509	1.00
224_G	228_E	0.509	1.00
116_V	119_K	0.508	1.00
129_L	137_P	0.505	1.00
31_P	171_F	0.505	1.00
153_P	166_L	0.505	1.00
217_L	232_V	0.504	1.00
7_N	47_S	0.503	1.00
43_E	126_Y	0.502	1.00
65_C	112_A	0.502	1.00
179_L	229_L	0.502	1.00
189_M	192_Y	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
4l4uA	2	0.7662	100	0.069	Contact Map
1ojlA	3	0.9262	100	0.202	Contact Map
3dzdA	2	0.7538	100	0.317	Contact Map
4qosA	1	0.7415	100	0.443	Contact Map
4qhsA	3	0.7508	100	0.448	Contact Map
1r6bX	1	0.8123	100	0.474	Contact Map
1qvrA	3	0.7877	100	0.497	Contact Map
1hqcA	1	0.8246	100	0.504	Contact Map
1in4A	1	0.7938	100	0.509	Contact Map
3vkgA	2	0.9662	100	0.517	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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