RHMR - ECOLI - GREMLIN Contacts

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RHMR - Uncharacterized HTH-type transcriptional regulator RhmR

UniProt:	P77732	Sequences: MLESSKVPALTRAIDILNLIARIGPCSAATIIDTLGIPKSTAYLLLNELRRQRFLSLDHQENFCLWTRLVELSGHALSKMDLRELARPRLTQLMDTTGLLCHLGIIDNGSAYYILKVESSATISVRSHEGKSLSLYRSGIGKCLLAWQPAAVQQSIIEGLVWEQATPTTITHPQQLHEELARIRRQGWSYDNGEDYADVRCVAAPVFNANNELTAAISVVGTRLQINEEYRDYLAGKAIACARDISRLLGWKSPFDLQAS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14086
Length:	260 (243)
Sequences:	12759 (9376)
Seq/√Len:	601.5

ECOLI - RHMR YJHI YIAJ ALLR KDGR MHPR ICLR YAGI
BACSU - KIPR
HALSA - Q9HHM8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_L	13_A	3.214	1.00
96_T	237_K	3.053	1.00
11_T	52_Q	2.792	1.00
104_G	140_I	2.791	1.00
89_R	241_C	2.788	1.00
182_R	186_Q	2.551	1.00
18_N	68_R	2.550	1.00
87_R	115_L	2.394	1.00
142_K	179_E	2.373	1.00
14_I	54_F	2.371	1.00
154_Q	177_H	2.336	1.00
110_S	132_S	2.220	1.00
142_K	194_E	2.193	1.00
99_L	225_Q	2.154	1.00
89_R	244_D	2.096	1.00
20_I	55_L	2.094	1.00
15_D	52_Q	2.039	1.00
148_Q	152_V	2.012	1.00
91_T	117_V	1.972	1.00
147_W	207_F	1.924	1.00
106_I	135_L	1.901	1.00
191_D	201_C	1.895	1.00
204_A	238_A	1.887	1.00
192_N	200_R	1.833	1.00
89_R	248_L	1.809	1.00
92_Q	244_D	1.788	1.00
230_Y	233_Y	1.778	1.00
16_I	31_I	1.774	1.00
200_R	223_R	1.768	1.00
204_A	242_A	1.765	1.00
56_S	64_C	1.760	1.00
18_N	52_Q	1.719	1.00
235_A	239_I	1.710	1.00
92_Q	96_T	1.678	1.00
86_A	245_I	1.676	1.00
46_L	55_L	1.674	1.00
19_L	35_L	1.662	1.00
172_H	175_Q	1.661	1.00
173_P	177_H	1.648	1.00
94_M	101_C	1.646	1.00
19_L	26_C	1.634	1.00
19_L	31_I	1.633	1.00
204_A	239_I	1.622	1.00
193_G	223_R	1.606	1.00
19_L	34_T	1.601	1.00
219_V	234_L	1.572	1.00
26_C	34_T	1.566	1.00
46_L	63_F	1.551	1.00
221_G	226_I	1.548	1.00
27_S	30_T	1.536	1.00
166_T	169_T	1.528	1.00
179_E	182_R	1.524	1.00
188_W	235_A	1.512	1.00
31_I	42_A	1.508	1.00
193_G	198_D	1.504	1.00
153_Q	177_H	1.499	1.00
89_R	92_Q	1.498	1.00
118_E	124_S	1.479	1.00
97_T	237_K	1.468	1.00
25_P	64_C	1.460	1.00
37_I	42_A	1.454	1.00
25_P	62_N	1.451	1.00
149_P	152_V	1.442	1.00
237_K	240_A	1.438	1.00
183_I	189_S	1.435	1.00
111_A	144_L	1.415	1.00
207_F	246_S	1.410	1.00
68_R	71_E	1.402	1.00
154_Q	173_P	1.389	1.00
50_R	57_L	1.372	1.00
111_A	135_L	1.365	1.00
50_R	55_L	1.355	1.00
83_R	115_L	1.353	1.00
93_L	237_K	1.351	1.00
14_I	52_Q	1.348	1.00
18_N	54_F	1.347	1.00
94_M	117_V	1.343	1.00
20_I	26_C	1.337	1.00
20_I	25_P	1.323	1.00
109_G	159_G	1.321	1.00
86_A	103_L	1.321	1.00
23_I	26_C	1.294	1.00
90_L	103_L	1.291	1.00
242_A	246_S	1.289	1.00
58_D	64_C	1.283	1.00
180_L	183_I	1.249	1.00
93_L	241_C	1.247	1.00
38_P	41_T	1.240	1.00
240_A	244_D	1.239	1.00
87_R	91_T	1.229	1.00
43_Y	47_N	1.229	1.00
31_I	46_L	1.221	1.00
32_I	42_A	1.212	1.00
23_I	34_T	1.200	1.00
137_R	169_T	1.197	1.00
150_A	177_H	1.192	1.00
158_E	173_P	1.192	1.00
170_I	179_E	1.185	1.00
207_F	213_L	1.173	1.00
147_W	205_P	1.173	1.00
146_A	183_I	1.163	1.00
150_A	154_Q	1.148	1.00
137_R	165_A	1.142	1.00
153_Q	184_R	1.133	1.00
28_A	43_Y	1.125	1.00
104_G	111_A	1.124	1.00
29_A	33_D	1.124	1.00
97_T	234_L	1.116	1.00
106_I	148_Q	1.104	1.00
204_A	235_A	1.101	1.00
7_V	48_E	1.100	1.00
239_I	243_R	1.098	1.00
106_I	109_G	1.093	1.00
168_T	193_G	1.089	1.00
90_L	101_C	1.088	1.00
147_W	213_L	1.083	1.00
27_S	62_N	1.075	1.00
107_D	132_S	1.074	1.00
150_A	153_Q	1.074	1.00
105_I	215_A	1.072	1.00
103_L	215_A	1.065	1.00
11_T	48_E	1.062	1.00
103_L	206_V	1.058	1.00
69_L	76_A	1.056	1.00
11_T	51_R	1.052	1.00
138_S	141_G	1.042	1.00
140_I	216_A	1.041	1.00
136_Y	169_T	1.041	1.00
150_A	181_A	1.033	1.00
91_T	95_D	1.032	1.00
157_I	173_P	1.030	1.00
244_D	248_L	1.029	1.00
232_D	236_G	1.024	1.00
97_T	219_V	1.016	1.00
217_I	245_I	1.013	1.00
236_G	240_A	1.005	1.00
30_T	33_D	0.999	1.00
208_N	212_E	0.992	1.00
28_A	32_I	0.992	1.00
96_T	240_A	0.982	1.00
8_P	12_R	0.981	1.00
92_Q	241_C	0.979	1.00
54_F	72_L	0.977	1.00
154_Q	158_E	0.967	1.00
164_Q	171_T	0.964	1.00
183_I	186_Q	0.961	1.00
104_G	113_Y	0.961	1.00
139_G	201_C	0.960	1.00
29_A	39_K	0.959	1.00
243_R	247_R	0.958	1.00
227_N	230_Y	0.939	1.00
205_P	213_L	0.936	1.00
82_L	215_A	0.935	1.00
112_Y	132_S	0.913	1.00
16_I	35_L	0.911	1.00
25_P	58_D	0.911	1.00
143_C	147_W	0.910	1.00
152_V	155_S	0.909	1.00
87_R	117_V	0.901	1.00
202_V	235_A	0.901	1.00
165_A	169_T	0.898	1.00
143_C	213_L	0.886	1.00
167_P	197_A	0.885	1.00
20_I	24_G	0.885	1.00
85_L	248_L	0.885	1.00
178_E	182_R	0.884	1.00
30_T	34_T	0.881	1.00
178_E	181_A	0.880	1.00
145_L	176_L	0.878	1.00
90_L	115_L	0.873	1.00
22_R	34_T	0.866	1.00
181_A	185_R	0.866	1.00
155_S	159_G	0.862	1.00
90_L	217_I	0.860	1.00
175_Q	179_E	0.860	1.00
153_Q	180_L	0.859	1.00
17_L	69_L	0.855	1.00
102_H	220_V	0.853	1.00
165_A	195_D	0.844	1.00
40_S	43_Y	0.844	1.00
238_A	242_A	0.843	1.00
186_Q	235_A	0.842	1.00
101_C	219_V	0.840	1.00
99_L	121_A	0.840	1.00
16_I	45_L	0.836	1.00
152_V	156_I	0.834	1.00
193_G	197_A	0.830	1.00
20_I	23_I	0.827	1.00
143_C	183_I	0.827	1.00
208_N	214_T	0.826	1.00
83_R	87_R	0.826	1.00
139_G	203_A	0.825	1.00
177_H	181_A	0.821	1.00
203_A	218_S	0.818	1.00
50_R	63_F	0.814	1.00
140_I	218_S	0.814	1.00
175_Q	178_E	0.811	1.00
12_R	41_T	0.805	1.00
222_T	225_Q	0.797	1.00
192_N	223_R	0.794	1.00
179_E	183_I	0.789	1.00
89_R	245_I	0.785	1.00
146_A	180_L	0.781	1.00
107_D	112_Y	0.778	1.00
37_I	41_T	0.774	1.00
241_C	244_D	0.773	1.00
182_R	185_R	0.772	1.00
179_E	186_Q	0.771	1.00
170_I	175_Q	0.768	1.00
106_I	152_V	0.764	1.00
231_R	235_A	0.758	1.00
144_L	216_A	0.756	1.00
35_L	42_A	0.754	1.00
17_L	54_F	0.754	1.00
9_A	13_A	0.754	1.00
233_Y	237_K	0.751	1.00
231_R	236_G	0.747	1.00
190_Y	231_R	0.746	1.00
201_C	220_V	0.742	1.00
102_H	116_K	0.741	1.00
201_C	218_S	0.739	1.00
69_L	73_S	0.738	1.00
47_N	50_R	0.734	1.00
32_I	35_L	0.734	1.00
28_A	46_L	0.729	1.00
102_H	127_S	0.727	1.00
69_L	72_L	0.722	1.00
57_L	61_E	0.721	1.00
170_I	176_L	0.721	1.00
28_A	42_A	0.719	1.00
137_R	195_D	0.718	1.00
90_L	117_V	0.717	1.00
156_I	160_L	0.717	1.00
65_L	69_L	0.716	1.00
82_L	86_A	0.716	1.00
28_A	39_K	0.715	1.00
148_Q	153_Q	0.714	1.00
153_Q	156_I	0.710	1.00
47_N	51_R	0.703	1.00
56_S	66_W	0.700	1.00
153_Q	181_A	0.697	1.00
236_G	239_I	0.696	1.00
26_C	31_I	0.694	1.00
202_V	231_R	0.685	1.00
150_A	184_R	0.685	1.00
109_G	156_I	0.681	1.00
121_A	225_Q	0.679	1.00
142_K	183_I	0.679	1.00
10_L	45_L	0.674	1.00
81_D	84_E	0.671	1.00
207_F	214_T	0.670	1.00
28_A	63_F	0.668	1.00
192_N	231_R	0.663	1.00
92_Q	95_D	0.659	1.00
181_A	184_R	0.659	1.00
106_I	144_L	0.659	1.00
93_L	219_V	0.659	1.00
233_Y	236_G	0.656	1.00
105_I	114_I	0.653	1.00
217_I	242_A	0.653	1.00
16_I	42_A	0.652	1.00
241_C	245_I	0.649	1.00
56_S	67_T	0.648	1.00
153_Q	157_I	0.648	1.00
243_R	246_S	0.647	1.00
239_I	242_A	0.646	1.00
94_M	119_S	0.645	1.00
10_L	14_I	0.645	1.00
73_S	76_A	0.643	1.00
230_Y	234_L	0.641	1.00
204_A	246_S	0.641	1.00
144_L	148_Q	0.633	1.00
240_A	243_R	0.633	1.00
166_T	170_I	0.632	1.00
54_F	68_R	0.631	1.00
171_T	175_Q	0.630	1.00
99_L	221_G	0.628	1.00
30_T	62_N	0.625	1.00
102_H	201_C	0.623	1.00
85_L	88_P	0.622	1.00
12_R	37_I	0.622	1.00
145_L	180_L	0.620	1.00
58_D	62_N	0.618	1.00
57_L	63_F	0.612	1.00
93_L	101_C	0.610	1.00
217_I	241_C	0.608	1.00
244_D	247_R	0.608	1.00
136_Y	162_W	0.605	1.00
93_L	97_T	0.603	1.00
18_N	71_E	0.602	1.00
88_P	248_L	0.595	1.00
9_A	45_L	0.593	1.00
91_T	115_L	0.593	1.00
95_D	120_S	0.590	1.00
193_G	200_R	0.589	1.00
168_T	197_A	0.588	1.00
116_K	129_E	0.587	1.00
47_N	57_L	0.586	1.00
128_H	131_K	0.585	1.00
187_G	207_F	0.585	1.00
7_V	45_L	0.582	1.00
134_S	137_R	0.581	1.00
118_E	128_H	0.579	1.00
138_S	201_C	0.578	1.00
144_L	215_A	0.578	1.00
32_I	39_K	0.574	1.00
145_L	153_Q	0.572	1.00
21_A	72_L	0.570	1.00
53_R	68_R	0.569	1.00
192_N	228_E	0.569	1.00
98_G	120_S	0.567	1.00
15_D	18_N	0.566	1.00
116_K	127_S	0.565	1.00
99_L	219_V	0.564	1.00
113_Y	138_S	0.562	1.00
101_C	117_V	0.561	1.00
86_A	90_L	0.559	1.00
123_I	224_L	0.558	1.00
174_Q	177_H	0.557	1.00
188_W	239_I	0.555	0.99
164_Q	167_P	0.554	0.99
15_D	19_L	0.554	0.99
237_K	241_C	0.554	0.99
204_A	217_I	0.552	0.99
10_L	48_E	0.549	0.99
113_Y	140_I	0.549	0.99
111_A	140_I	0.548	0.99
176_L	180_L	0.545	0.99
18_N	72_L	0.542	0.99
143_C	203_A	0.542	0.99
111_A	133_L	0.541	0.99
206_V	246_S	0.540	0.99
43_Y	57_L	0.538	0.99
17_L	72_L	0.538	0.99
113_Y	127_S	0.538	0.99
27_S	39_K	0.537	0.99
140_I	201_C	0.536	0.99
143_C	205_P	0.536	0.99
85_L	245_I	0.536	0.99
19_L	23_I	0.535	0.99
21_A	65_L	0.535	0.99
111_A	138_S	0.534	0.99
13_A	45_L	0.534	0.99
234_L	237_K	0.532	0.99
70_V	77_L	0.529	0.99
135_L	156_I	0.528	0.99
143_C	189_S	0.525	0.99
104_G	138_S	0.524	0.99
198_D	223_R	0.519	0.99
206_V	215_A	0.519	0.99
174_Q	178_E	0.513	0.99
12_R	45_L	0.512	0.99
142_K	191_D	0.512	0.99
168_T	192_N	0.512	0.99
7_V	10_L	0.510	0.99
127_S	131_K	0.510	0.99
113_Y	116_K	0.509	0.99
100_L	116_K	0.509	0.99
14_I	48_E	0.508	0.99
74_G	77_L	0.508	0.99
217_I	238_A	0.507	0.99
207_F	215_A	0.503	0.99
164_Q	169_T	0.501	0.99
169_T	172_H	0.500	0.99

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
3mq0A	2	0.9538	100	0.095	Contact Map
2ia2A	4	0.9538	100	0.098	Contact Map
2g7uA	6	0.9615	100	0.101	Contact Map
1mkmA	4	0.9462	100	0.107	Contact Map
3r4kA	2	0.9731	100	0.11	Contact Map
2xrnA	3	0.9192	100	0.133	Contact Map
2o0yA	4	0.95	100	0.149	Contact Map
1ysqA	1	0.6769	100	0.402	Contact Map
1tf1A	1	0.7077	100	0.403	Contact Map
3obfA	1	0.6769	100	0.412	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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