PERR - ECOLI - GREMLIN Contacts

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PERR - HTH-type transcriptional regulator PerR

UniProt:	Q57083	Sequences: MKLLAKAPLNLLRAFEAAGRTGAFALAASELELSPSAISHAIRKLENLLDVRLFQRSTREITLTKEGEILLEHIQRGFNELQQGLALVTADESRPLRLHTAPSFAHQWLLPRLGKFIRENPSIDLRLSASTEYARFEQDDFDLDIVYGEPRPSPYEKIPLAVEELTPLCSPQLAERLKKPEDLYALTLIQCDVQLYQWKGWFEANKMTPPNNYGLRFDRSFMAIAAAVDGLGVVLESKLLAEREIASGKLVCPLVNSTSEIHYIGHYLVFPQHQHMHSALDVFKTWLLNELNLGKIR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13340
Length:	297 (276)
Sequences:	79640 (57886)
Seq/√Len:	3484.3

ECOLI - PERR DSDC TDCA LYSR NHAR TTDR NAC YBDO XAPR YHAJ PGRR LEUO YDCI OXYR AAER YFER DMLR YAHB YBEF YIDZ YIAU YFIE GCVA CYSB CYNR YAFC YCAN CBL YBHD ABGR YEIE HCAR YEEY YNEJ YDHB ILVY METR YNFL YHJC ICIA YGFI LRHA ALLS YJIE HDFR
BACSU - CYSL YCGK GLTC YWBI ALSR YVBU GLTR YOFA CITR YWQM YTLI YYBE BSDA YXJO YUST CZCR YOAU YRAN YKUM

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
76_R	80_E	3.713	1.00
21_T	30_E	3.438	1.00
158_I	288_L	2.697	1.00
73_H	87_L	2.550	1.00
99_H	141_F	2.509	1.00
17_A	30_E	2.500	1.00
173_L	186_L	2.283	1.00
159_P	265_G	2.283	1.00
162_V	265_G	2.261	1.00
159_P	162_V	2.234	1.00
227_A	234_V	2.222	1.00
51_V	66_E	2.214	1.00
95_P	126_R	2.214	1.00
14_A	41_A	2.152	1.00
16_E	75_Q	2.120	1.00
95_P	124_D	2.095	1.00
16_E	20_R	2.072	1.00
164_E	238_K	2.065	1.00
73_H	80_E	2.065	1.00
162_V	263_Y	2.056	1.00
115_K	286_W	2.046	1.00
166_T	238_K	2.040	1.00
179_K	182_D	2.015	1.00
17_A	21_T	2.011	1.00
26_L	29_S	2.006	1.00
224_I	244_E	1.957	1.00
17_A	20_R	1.937	1.00
97_R	126_R	1.935	1.00
16_E	71_L	1.913	1.00
19_G	63_L	1.907	1.00
20_R	75_Q	1.901	1.00
14_A	38_I	1.875	1.00
77_G	81_L	1.855	1.00
71_L	75_Q	1.845	1.00
228_V	244_E	1.830	1.00
189_I	232_G	1.816	1.00
187_T	214_G	1.761	1.00
157_K	267_Y	1.748	1.00
55_Q	62_T	1.719	1.00
19_G	71_L	1.710	1.00
69_I	87_L	1.701	1.00
70_L	84_G	1.675	1.00
228_V	249_K	1.667	1.00
21_T	26_L	1.655	1.00
135_R	140_D	1.653	1.00
24_F	42_I	1.614	1.00
73_H	76_R	1.585	1.00
16_E	74_I	1.572	1.00
156_E	272_Q	1.559	1.00
158_I	270_F	1.548	1.00
11_L	41_A	1.537	1.00
23_A	26_L	1.533	1.00
11_L	48_L	1.517	1.00
20_R	30_E	1.516	1.00
134_A	138_Q	1.505	1.00
116_F	283_F	1.491	1.00
11_L	44_K	1.485	1.00
15_F	71_L	1.457	1.00
34_S	37_A	1.452	1.00
14_A	33_L	1.452	1.00
17_A	31_L	1.450	1.00
73_H	83_Q	1.447	1.00
146_V	269_V	1.445	1.00
284_K	288_L	1.441	1.00
52_R	55_Q	1.440	1.00
270_F	284_K	1.429	1.00
8_P	11_L	1.425	1.00
25_A	35_P	1.423	1.00
156_E	270_F	1.423	1.00
106_H	221_F	1.420	1.00
57_S	62_T	1.411	1.00
116_F	123_I	1.397	1.00
135_R	141_F	1.394	1.00
195_L	199_K	1.388	1.00
80_E	83_Q	1.384	1.00
136_F	144_D	1.383	1.00
148_G	267_Y	1.379	1.00
119_E	286_W	1.379	1.00
282_V	285_T	1.373	1.00
77_G	84_G	1.370	1.00
65_K	68_E	1.356	1.00
276_M	280_L	1.353	1.00
16_E	78_F	1.348	1.00
196_Y	200_G	1.339	1.00
93_S	122_S	1.338	1.00
70_L	85_L	1.337	1.00
268_L	284_K	1.327	1.00
163_E	239_L	1.323	1.00
97_R	128_S	1.316	1.00
72_E	76_R	1.309	1.00
9_L	81_L	1.304	1.00
143_L	268_L	1.297	1.00
73_H	84_G	1.291	1.00
137_E	154_P	1.285	1.00
223_A	234_V	1.279	1.00
225_A	228_V	1.275	1.00
115_K	119_E	1.261	1.00
169_C	233_V	1.258	1.00
186_L	233_V	1.251	1.00
143_L	280_L	1.247	1.00
159_P	267_Y	1.243	1.00
33_L	37_A	1.233	1.00
69_I	72_E	1.232	1.00
117_I	214_G	1.221	1.00
169_C	173_L	1.216	1.00
48_L	85_L	1.214	1.00
15_F	54_F	1.207	1.00
40_H	44_K	1.202	1.00
117_I	187_T	1.201	1.00
114_G	118_R	1.201	1.00
114_G	229_D	1.196	1.00
69_I	73_H	1.177	1.00
15_F	19_G	1.167	1.00
157_K	269_V	1.144	1.00
40_H	43_R	1.141	1.00
238_K	242_E	1.136	1.00
244_E	249_K	1.136	1.00
111_P	229_D	1.132	1.00
120_N	282_V	1.120	1.00
130_S	135_R	1.116	1.00
76_R	83_Q	1.112	1.00
12_L	74_I	1.108	1.00
68_E	72_E	1.107	1.00
126_R	216_R	1.097	1.00
43_R	47_N	1.095	1.00
158_I	284_K	1.095	1.00
178_K	182_D	1.091	1.00
224_I	228_V	1.090	1.00
225_A	229_D	1.083	1.00
285_T	288_L	1.078	1.00
169_C	252_C	1.077	1.00
17_A	27_A	1.075	1.00
105_A	129_A	1.063	1.00
252_C	255_V	1.059	1.00
137_E	152_P	1.056	1.00
77_G	80_E	1.055	1.00
41_A	44_K	1.055	1.00
24_F	61_I	1.054	1.00
242_E	246_A	1.053	1.00
15_F	53_L	1.050	1.00
39_S	43_R	1.050	1.00
166_T	252_C	1.048	1.00
10_N	13_R	1.040	1.00
85_L	89_T	1.040	1.00
170_S	230_G	1.034	1.00
271_P	274_Q	1.032	1.00
112_R	287_L	1.029	1.00
115_K	118_R	1.029	1.00
281_D	285_T	1.022	1.00
217_F	223_A	1.009	1.00
79_N	83_Q	1.008	1.00
202_F	207_M	1.007	1.00
18_A	27_A	1.005	1.00
164_E	263_Y	1.005	1.00
190_Q	213_Y	1.003	1.00
116_F	286_W	0.988	1.00
128_S	135_R	0.986	1.00
196_Y	199_K	0.983	1.00
286_W	289_N	0.981	1.00
96_L	283_F	0.980	1.00
44_K	47_N	0.970	1.00
70_L	74_I	0.966	1.00
63_L	67_G	0.965	1.00
116_F	120_N	0.965	1.00
243_R	247_S	0.964	1.00
168_L	241_A	0.964	1.00
27_A	38_I	0.963	1.00
18_A	24_F	0.961	1.00
33_L	38_I	0.961	1.00
189_I	223_A	0.955	1.00
177_L	255_V	0.949	1.00
180_P	257_S	0.949	1.00
19_G	54_F	0.948	1.00
135_R	138_Q	0.946	1.00
82_Q	85_L	0.941	1.00
198_W	202_F	0.939	1.00
167_P	233_V	0.935	1.00
26_L	30_E	0.934	1.00
13_R	82_Q	0.934	1.00
14_A	31_L	0.931	1.00
15_F	63_L	0.926	1.00
76_R	79_N	0.918	1.00
112_R	286_W	0.910	1.00
15_F	45_L	0.905	1.00
200_G	204_A	0.904	1.00
277_H	280_L	0.903	1.00
82_Q	86_A	0.903	1.00
10_N	41_A	0.900	1.00
94_R	279_A	0.899	1.00
217_F	226_A	0.899	1.00
102_P	219_R	0.895	1.00
51_V	88_V	0.890	1.00
81_L	85_L	0.884	1.00
210_P	213_Y	0.880	1.00
22_G	62_T	0.878	1.00
148_G	265_G	0.877	1.00
99_H	144_D	0.874	1.00
119_E	289_N	0.874	1.00
114_G	231_L	0.862	1.00
91_D	122_S	0.861	1.00
72_E	75_Q	0.860	1.00
54_F	61_I	0.859	1.00
92_E	122_S	0.859	1.00
66_E	88_V	0.855	1.00
187_T	213_Y	0.853	1.00
169_C	174_A	0.851	1.00
156_E	159_P	0.850	1.00
141_F	144_D	0.846	1.00
25_A	29_S	0.844	1.00
57_S	60_E	0.839	1.00
99_H	146_V	0.838	1.00
83_Q	87_L	0.835	1.00
31_L	38_I	0.830	1.00
200_G	203_E	0.828	1.00
170_S	173_L	0.826	1.00
9_L	78_F	0.824	1.00
187_T	210_P	0.822	1.00
81_L	84_G	0.822	1.00
117_I	231_L	0.821	1.00
66_E	69_I	0.813	1.00
123_I	279_A	0.811	1.00
35_P	39_S	0.809	1.00
197_Q	201_W	0.806	1.00
98_L	143_L	0.805	1.00
80_E	84_G	0.804	1.00
278_S	282_V	0.804	1.00
19_G	22_G	0.804	1.00
15_F	70_L	0.796	1.00
21_T	27_A	0.796	1.00
20_R	71_L	0.795	1.00
22_G	60_E	0.794	1.00
19_G	67_G	0.793	1.00
13_R	17_A	0.792	1.00
199_K	203_E	0.789	1.00
173_L	187_T	0.789	1.00
170_S	231_L	0.788	1.00
155_Y	269_V	0.788	1.00
22_G	68_E	0.786	1.00
171_P	249_K	0.783	1.00
276_M	281_D	0.781	1.00
168_L	234_V	0.781	1.00
285_T	289_N	0.779	1.00
181_E	184_Y	0.778	1.00
249_K	253_P	0.778	1.00
43_R	52_R	0.771	1.00
100_T	105_A	0.768	1.00
171_P	248_G	0.767	1.00
128_S	141_F	0.766	1.00
11_L	14_A	0.760	1.00
68_E	71_L	0.760	1.00
18_A	54_F	0.756	1.00
75_Q	79_N	0.755	1.00
94_R	123_I	0.754	1.00
226_A	231_L	0.752	1.00
245_I	248_G	0.751	1.00
197_Q	200_G	0.750	1.00
84_G	88_V	0.746	1.00
244_E	247_S	0.744	1.00
198_W	201_W	0.741	1.00
119_E	282_V	0.739	1.00
55_Q	64_T	0.738	1.00
74_I	77_G	0.738	1.00
24_F	38_I	0.736	1.00
18_A	38_I	0.732	1.00
195_L	201_W	0.729	1.00
116_F	282_V	0.724	1.00
282_V	286_W	0.724	1.00
13_R	16_E	0.723	1.00
274_Q	277_H	0.723	1.00
201_W	205_N	0.721	1.00
209_P	213_Y	0.717	1.00
139_D	271_P	0.716	1.00
168_L	236_E	0.716	1.00
143_L	283_F	0.715	1.00
238_K	252_C	0.714	1.00
18_A	42_I	0.713	1.00
192_D	216_R	0.711	1.00
182_D	185_A	0.709	1.00
137_E	155_Y	0.709	1.00
66_E	70_L	0.707	1.00
237_S	240_L	0.707	1.00
154_P	272_Q	0.706	1.00
168_L	245_I	0.702	1.00
172_Q	230_G	0.702	1.00
219_R	222_M	0.701	1.00
252_C	256_N	0.701	1.00
142_D	280_L	0.693	1.00
65_K	69_I	0.692	1.00
241_A	244_E	0.689	1.00
172_Q	175_E	0.686	1.00
70_L	88_V	0.684	1.00
241_A	245_I	0.678	1.00
201_W	204_A	0.674	1.00
106_H	225_A	0.674	1.00
10_N	44_K	0.663	1.00
171_P	250_L	0.662	1.00
62_T	68_E	0.662	1.00
73_H	77_G	0.661	1.00
97_R	142_D	0.661	1.00
188_L	233_V	0.661	1.00
191_C	223_A	0.661	1.00
63_L	68_E	0.660	1.00
147_Y	264_I	0.655	1.00
37_A	41_A	0.652	1.00
97_R	141_F	0.648	1.00
46_E	51_V	0.647	1.00
55_Q	60_E	0.646	1.00
29_S	32_E	0.644	1.00
195_L	216_R	0.643	1.00
228_V	248_G	0.640	1.00
167_P	235_L	0.639	1.00
111_P	114_G	0.636	1.00
13_R	78_F	0.634	1.00
83_Q	86_A	0.633	1.00
46_E	56_R	0.632	1.00
8_P	48_L	0.628	1.00
42_I	46_E	0.628	1.00
254_L	257_S	0.627	1.00
124_D	216_R	0.623	1.00
192_D	218_D	0.621	1.00
115_K	289_N	0.620	1.00
79_N	82_Q	0.613	1.00
15_F	67_G	0.611	1.00
109_L	112_R	0.610	1.00
179_K	255_V	0.608	1.00
278_S	281_D	0.607	1.00
171_P	251_V	0.606	1.00
18_A	23_A	0.606	1.00
196_Y	201_W	0.604	1.00
163_E	264_I	0.599	1.00
102_P	131_T	0.599	1.00
270_F	281_D	0.599	1.00
215_L	226_A	0.596	1.00
10_N	14_A	0.596	1.00
199_K	202_F	0.594	1.00
243_R	246_A	0.593	1.00
86_A	90_A	0.593	1.00
100_T	109_L	0.589	1.00
51_V	55_Q	0.588	1.00
167_P	183_L	0.588	1.00
202_F	209_P	0.586	1.00
27_A	31_L	0.585	1.00
143_L	284_K	0.585	1.00
164_E	253_P	0.584	1.00
74_I	78_F	0.583	1.00
196_Y	202_F	0.582	1.00
69_I	88_V	0.579	1.00
78_F	82_Q	0.578	1.00
184_Y	207_M	0.577	1.00
49_L	88_V	0.576	1.00
96_L	143_L	0.576	1.00
217_F	222_M	0.573	1.00
205_N	209_P	0.572	1.00
210_P	214_G	0.571	1.00
49_L	70_L	0.570	1.00
96_L	279_A	0.569	1.00
173_L	233_V	0.568	1.00
111_P	115_K	0.565	1.00
54_F	63_L	0.563	1.00
19_G	68_E	0.559	1.00
129_A	218_D	0.558	1.00
120_N	123_I	0.557	1.00
283_F	287_L	0.556	1.00
195_L	202_F	0.556	1.00
136_F	155_Y	0.550	1.00
165_L	235_L	0.549	1.00
37_A	40_H	0.549	1.00
169_C	175_E	0.548	1.00
24_F	35_P	0.546	1.00
167_P	188_L	0.543	1.00
195_L	200_G	0.543	1.00
160_L	268_L	0.541	1.00
193_V	216_R	0.540	1.00
202_F	205_N	0.539	1.00
236_E	241_A	0.535	1.00
49_L	52_R	0.534	1.00
108_W	112_R	0.533	1.00
148_G	157_K	0.531	1.00
223_A	227_A	0.531	1.00
34_S	40_H	0.530	1.00
93_S	124_D	0.529	1.00
129_A	219_R	0.528	1.00
36_S	40_H	0.528	1.00
174_A	186_L	0.526	1.00
169_C	253_P	0.525	1.00
63_L	71_L	0.524	1.00
161_A	266_H	0.523	1.00
87_L	90_A	0.522	1.00
33_L	41_A	0.522	1.00
177_L	182_D	0.520	1.00
134_A	140_D	0.519	1.00
199_K	209_P	0.519	1.00
52_R	66_E	0.519	1.00
104_F	108_W	0.516	1.00
110_L	114_G	0.515	1.00
111_P	225_A	0.515	1.00
136_F	269_V	0.513	1.00
14_A	42_I	0.512	1.00
24_F	60_E	0.511	1.00
106_H	219_R	0.510	1.00
22_G	61_I	0.510	1.00
99_H	130_S	0.509	1.00
99_H	128_S	0.509	1.00
84_G	87_L	0.506	1.00
94_R	122_S	0.506	1.00
156_E	273_H	0.506	1.00
137_E	140_D	0.506	1.00
226_A	232_G	0.505	1.00
101_A	104_F	0.505	1.00
181_E	207_M	0.504	1.00
248_G	252_C	0.504	1.00
114_G	117_I	0.501	1.00
250_L	253_P	0.501	1.00
72_E	87_L	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
3szpA	3	0.9461	100	0.141	Contact Map
1uthA	2	0.7239	100	0.146	Contact Map
2esnA	3	0.963	100	0.146	Contact Map
3hhgA	3	0.963	100	0.153	Contact Map
1ixcA	4	0.9428	100	0.156	Contact Map
3fzvA	4	0.9394	100	0.157	Contact Map
3fxqA	3	0.9495	100	0.16	Contact Map
2h98A	2	0.6667	100	0.161	Contact Map
2h9bA	2	0.6667	100	0.164	Contact Map
1al3A	1	0.6768	100	0.164	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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