YIHW - ECOLI - GREMLIN Contacts

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YIHW - Uncharacterized HTH-type transcriptional regulator YihW

UniProt:	P32144	Sequences: MSLTELTGNPRHDQLLMLIAERGYMNIDELANLLDVSTQTVRRDIRKLSEQGLITRHHGGAGRASSVVNTAFEQREVSQTEEKKAIAEAVADYIPDGSTIFITIGTTVEHVARALLNHNHLRIITNSLRVAHILYHNPRFEVMVPGGTLRSHNSGIIGPSAASFVADFRADYLVTSVGAIESDGALMEFDVNEANVVKTMMAHARNILLVADHTKYHASAAVEIGNVAQVTALFTDELPPAALKSRLQDSQIEIILPQEDA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11849
Length:	261 (249)
Sequences:	7677 (5666)
Seq/√Len:	359.1

ECOLI - YIHW AGAR YGBI GLPR GATR SGCR YDJF SRLR DEOR ULAR YCIT FUCR
BACSU - YULB IOLR GLCR FRUR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
98_S	172_Y	3.336	1.00
89_A	92_D	3.060	1.00
111_V	210_V	2.941	1.00
141_E	148_T	2.734	1.00
173_L	204_A	2.622	1.00
103_T	197_V	2.399	1.00
18_L	33_L	2.345	1.00
213_H	236_D	2.267	1.00
201_M	225_G	2.226	1.00
113_R	133_I	2.222	1.00
232_A	255_I	2.169	1.00
208_L	232_A	2.087	1.00
95_P	98_S	2.078	1.00
166_A	199_T	2.077	1.00
172_Y	208_L	2.045	1.00
18_L	22_R	2.036	1.00
14_Q	17_M	2.024	1.00
101_F	170_A	2.009	1.00
84_K	110_H	1.998	1.00
88_E	114_A	1.984	1.00
201_M	207_I	1.953	1.00
223_E	226_N	1.942	1.00
102_I	108_V	1.926	1.00
163_S	166_A	1.915	1.00
239_P	244_K	1.895	1.00
172_Y	206_N	1.862	1.00
101_F	200_M	1.849	1.00
244_K	248_Q	1.773	1.00
206_N	232_A	1.772	1.00
124_I	170_A	1.764	1.00
110_H	113_R	1.758	1.00
96_D	119_N	1.743	1.00
90_V	174_V	1.698	1.00
89_A	255_I	1.692	1.00
226_N	229_Q	1.660	1.00
170_A	200_M	1.652	1.00
163_S	167_D	1.646	1.00
90_V	210_V	1.593	1.00
144_V	156_I	1.583	1.00
162_A	195_N	1.579	1.00
145_P	164_F	1.577	1.00
199_T	202_A	1.567	1.00
171_D	205_R	1.548	1.00
79_Q	214_T	1.533	1.00
131_A	144_V	1.532	1.00
111_V	174_V	1.528	1.00
186_L	209_L	1.523	1.00
166_A	202_A	1.515	1.00
186_L	230_V	1.507	1.00
36_V	41_V	1.495	1.00
245_S	249_D	1.494	1.00
91_A	114_A	1.475	1.00
87_A	114_A	1.453	1.00
24_Y	62_G	1.451	1.00
30_L	41_V	1.439	1.00
12_H	51_Q	1.438	1.00
145_P	156_I	1.430	1.00
161_A	196_V	1.425	1.00
84_K	114_A	1.421	1.00
15_L	30_L	1.421	1.00
18_L	25_M	1.417	1.00
8_G	12_H	1.405	1.00
45_I	61_A	1.398	1.00
123_I	134_L	1.398	1.00
13_D	17_M	1.393	1.00
199_T	203_H	1.390	1.00
79_Q	82_E	1.389	1.00
55_T	64_A	1.382	1.00
22_R	29_E	1.382	1.00
149_L	156_I	1.380	1.00
93_Y	208_L	1.374	1.00
14_Q	18_L	1.373	1.00
104_I	155_G	1.369	1.00
20_A	63_R	1.357	1.00
240_P	243_L	1.355	1.00
98_S	171_D	1.354	1.00
213_H	238_L	1.354	1.00
82_E	236_D	1.350	1.00
209_L	230_V	1.350	1.00
96_D	118_H	1.346	1.00
93_Y	234_F	1.343	1.00
148_T	192_N	1.325	1.00
28_D	38_T	1.309	1.00
57_H	60_G	1.306	1.00
80_T	110_H	1.302	1.00
12_H	47_K	1.294	1.00
96_D	120_H	1.293	1.00
123_I	140_F	1.281	1.00
16_L	53_L	1.267	1.00
97_G	120_H	1.266	1.00
180_I	216_Y	1.253	1.00
94_I	115_L	1.251	1.00
26_N	29_E	1.251	1.00
225_G	229_Q	1.250	1.00
145_P	161_A	1.248	1.00
83_K	106_T	1.247	1.00
241_A	245_S	1.245	1.00
206_N	231_T	1.241	1.00
84_K	113_R	1.236	1.00
89_A	93_Y	1.236	1.00
93_Y	255_I	1.219	1.00
14_Q	33_L	1.209	1.00
39_Q	43_R	1.201	1.00
122_R	143_M	1.191	1.00
202_A	229_Q	1.182	1.00
101_F	203_H	1.169	1.00
245_S	248_Q	1.167	1.00
177_V	211_A	1.156	1.00
14_Q	34_L	1.152	1.00
112_A	134_L	1.141	1.00
216_Y	239_P	1.128	1.00
80_T	84_K	1.126	1.00
19_I	54_I	1.126	1.00
17_M	21_E	1.125	1.00
22_R	33_L	1.122	1.00
81_E	84_K	1.122	1.00
46_R	50_E	1.118	1.00
82_E	213_H	1.114	1.00
174_V	208_L	1.110	1.00
122_R	141_E	1.110	1.00
162_A	196_V	1.107	1.00
177_V	224_I	1.099	1.00
160_S	164_F	1.095	1.00
95_P	172_Y	1.094	1.00
16_L	19_I	1.084	1.00
55_T	62_G	1.082	1.00
232_A	253_E	1.078	1.00
179_A	187_M	1.077	1.00
19_I	63_R	1.073	1.00
207_I	230_V	1.059	1.00
208_L	234_F	1.054	1.00
54_I	61_A	1.043	1.00
143_M	148_T	1.041	1.00
8_G	47_K	1.029	1.00
27_I	45_I	1.026	1.00
91_A	94_I	1.019	1.00
47_K	51_Q	1.019	1.00
124_I	168_F	1.001	1.00
31_A	38_T	0.995	1.00
90_V	111_V	0.990	1.00
94_I	174_V	0.988	1.00
91_A	111_V	0.982	1.00
145_P	165_V	0.976	1.00
102_I	111_V	0.975	1.00
243_L	246_R	0.970	1.00
10_P	14_Q	0.965	1.00
112_A	133_I	0.965	1.00
82_E	86_I	0.965	1.00
160_S	168_F	0.956	1.00
87_A	91_A	0.946	1.00
180_I	211_A	0.944	1.00
105_G	108_V	0.942	1.00
46_R	49_S	0.939	1.00
162_A	199_T	0.939	1.00
108_V	130_V	0.939	1.00
93_Y	232_A	0.937	1.00
216_Y	233_L	0.936	1.00
195_N	198_K	0.935	1.00
178_G	188_E	0.935	1.00
72_F	106_T	0.933	1.00
181_E	184_G	0.931	1.00
173_L	200_M	0.927	1.00
18_L	21_E	0.925	1.00
84_K	88_E	0.925	1.00
107_T	212_D	0.925	1.00
177_V	209_L	0.923	1.00
228_A	250_S	0.922	1.00
244_K	254_I	0.920	1.00
194_A	222_V	0.915	1.00
111_V	114_A	0.905	1.00
181_E	219_S	0.897	1.00
167_D	198_K	0.897	1.00
29_E	33_L	0.896	1.00
47_K	50_E	0.895	1.00
31_A	41_V	0.892	1.00
108_V	111_V	0.891	1.00
86_I	107_T	0.889	1.00
83_K	215_K	0.888	1.00
129_R	154_S	0.887	1.00
169_R	205_R	0.887	1.00
79_Q	212_D	0.885	1.00
83_K	107_T	0.883	1.00
87_A	111_V	0.872	1.00
107_T	215_K	0.869	1.00
25_M	61_A	0.869	1.00
87_A	110_H	0.865	1.00
25_M	30_L	0.859	1.00
246_R	249_D	0.853	1.00
142_V	149_L	0.852	1.00
135_Y	154_S	0.849	1.00
48_L	53_L	0.845	1.00
112_A	130_V	0.834	1.00
116_L	133_I	0.834	1.00
16_L	20_A	0.829	1.00
205_R	219_S	0.828	1.00
127_S	130_V	0.827	1.00
160_S	167_D	0.825	1.00
116_L	137_N	0.817	1.00
165_V	200_M	0.816	1.00
188_E	194_A	0.814	1.00
153_N	178_G	0.812	1.00
10_P	13_D	0.811	1.00
174_V	210_V	0.806	1.00
207_I	231_T	0.800	1.00
168_F	191_V	0.799	1.00
17_M	20_A	0.796	1.00
169_R	219_S	0.787	1.00
85_A	88_E	0.786	1.00
165_V	199_T	0.779	1.00
169_R	223_E	0.779	1.00
75_R	178_G	0.777	1.00
90_V	234_F	0.777	1.00
180_I	186_L	0.774	1.00
133_I	136_H	0.771	1.00
79_Q	213_H	0.770	1.00
191_V	222_V	0.768	1.00
108_V	210_V	0.768	1.00
46_R	56_R	0.767	1.00
29_E	32_N	0.767	1.00
101_F	165_V	0.764	1.00
182_S	185_A	0.760	1.00
116_L	119_N	0.753	1.00
109_E	133_I	0.744	1.00
7_T	24_Y	0.742	1.00
132_H	154_S	0.738	1.00
102_I	112_A	0.738	1.00
167_D	223_E	0.735	1.00
23_G	63_R	0.733	1.00
102_I	123_I	0.733	1.00
184_G	219_S	0.730	1.00
169_R	184_G	0.729	1.00
187_M	219_S	0.729	1.00
177_V	186_L	0.728	1.00
120_H	139_R	0.726	1.00
81_E	85_A	0.725	1.00
106_T	215_K	0.722	0.99
239_P	243_L	0.721	0.99
150_R	193_E	0.720	0.99
10_P	24_Y	0.720	0.99
12_H	16_L	0.720	0.99
169_R	203_H	0.719	0.99
239_P	254_I	0.716	0.99
110_H	114_A	0.716	0.99
7_T	10_P	0.715	0.99
45_I	56_R	0.709	0.99
131_A	156_I	0.708	0.99
182_S	246_R	0.703	0.99
131_A	149_L	0.703	0.99
104_I	153_N	0.700	0.99
71_A	74_Q	0.700	0.99
146_G	161_A	0.698	0.99
150_R	157_I	0.693	0.99
201_M	224_I	0.691	0.99
186_L	224_I	0.691	0.99
173_L	207_I	0.688	0.99
188_E	224_I	0.687	0.99
180_I	227_V	0.679	0.99
170_A	204_A	0.676	0.99
28_D	32_N	0.675	0.99
146_G	164_F	0.674	0.99
117_N	137_N	0.669	0.99
36_V	39_Q	0.669	0.99
126_N	200_M	0.668	0.99
99_T	124_I	0.668	0.99
88_E	92_D	0.668	0.99
211_A	233_L	0.668	0.99
198_K	202_A	0.665	0.99
188_E	193_E	0.664	0.99
100_I	172_Y	0.660	0.99
49_S	56_R	0.660	0.99
212_D	215_K	0.658	0.99
100_I	123_I	0.657	0.99
16_L	48_L	0.656	0.99
137_N	140_F	0.656	0.99
166_A	203_H	0.654	0.99
85_A	89_A	0.653	0.99
208_L	231_T	0.652	0.99
246_R	250_S	0.651	0.99
241_A	244_K	0.651	0.99
76_E	109_E	0.649	0.99
163_S	195_N	0.648	0.99
136_H	154_S	0.648	0.99
27_I	41_V	0.646	0.99
158_G	161_A	0.645	0.99
30_L	45_I	0.645	0.99
57_H	62_G	0.643	0.99
9_N	12_H	0.643	0.99
125_T	131_A	0.643	0.99
39_Q	127_S	0.640	0.99
128_L	156_I	0.640	0.99
119_N	139_R	0.638	0.99
175_T	204_A	0.637	0.99
69_N	75_R	0.636	0.99
86_I	210_V	0.627	0.99
168_F	222_V	0.626	0.99
19_I	25_M	0.626	0.99
206_N	253_E	0.622	0.98
178_G	220_A	0.620	0.98
49_S	54_I	0.619	0.98
242_A	246_R	0.618	0.98
109_E	129_R	0.618	0.98
225_G	230_V	0.615	0.98
159_P	163_S	0.614	0.98
204_A	207_I	0.613	0.98
159_P	195_N	0.611	0.98
34_L	41_V	0.608	0.98
120_H	141_E	0.602	0.98
128_L	144_V	0.601	0.98
7_T	57_H	0.601	0.98
11_R	44_D	0.597	0.98
124_I	221_A	0.596	0.98
194_A	224_I	0.595	0.98
213_H	239_P	0.588	0.98
94_I	111_V	0.588	0.98
105_G	176_S	0.585	0.98
103_T	108_V	0.585	0.98
150_R	190_D	0.584	0.98
76_E	110_H	0.581	0.98
189_F	220_A	0.580	0.98
129_R	132_H	0.578	0.98
159_P	162_A	0.576	0.98
192_N	195_N	0.575	0.98
161_A	164_F	0.575	0.98
128_L	132_H	0.574	0.97
162_A	166_A	0.572	0.97
178_G	193_E	0.571	0.97
243_L	247_L	0.571	0.97
99_T	221_A	0.566	0.97
127_S	193_E	0.562	0.97
175_T	224_I	0.561	0.97
178_G	189_F	0.560	0.97
100_I	174_V	0.557	0.97
159_P	192_N	0.557	0.97
15_L	34_L	0.553	0.97
75_R	193_E	0.552	0.97
186_L	225_G	0.550	0.97
124_I	143_M	0.549	0.97
82_E	238_L	0.548	0.97
100_I	111_V	0.548	0.97
85_A	237_E	0.547	0.97
197_V	224_I	0.547	0.97
176_S	188_E	0.546	0.97
207_I	229_Q	0.541	0.96
196_V	199_T	0.541	0.96
101_F	173_L	0.541	0.96
216_Y	243_L	0.540	0.96
175_T	207_I	0.540	0.96
69_N	150_R	0.539	0.96
83_K	212_D	0.537	0.96
105_G	178_G	0.536	0.96
39_Q	178_G	0.536	0.96
32_N	35_D	0.534	0.96
73_E	76_E	0.533	0.96
43_R	180_I	0.532	0.96
163_S	198_K	0.530	0.96
181_E	187_M	0.530	0.96
155_G	193_E	0.527	0.96
216_Y	235_T	0.526	0.96
179_A	218_A	0.524	0.96
178_G	197_V	0.522	0.96
105_G	127_S	0.521	0.96
188_E	197_V	0.519	0.95
182_S	243_L	0.519	0.95
179_A	220_A	0.517	0.95
175_T	201_M	0.515	0.95
101_F	124_I	0.511	0.95
102_I	130_V	0.511	0.95
156_I	164_F	0.510	0.95
160_S	163_S	0.509	0.95
27_I	31_A	0.508	0.95
238_L	244_K	0.507	0.95
241_A	248_Q	0.502	0.95
143_M	160_S	0.502	0.95
82_E	85_A	0.500	0.94

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
1stzA	3	0.931	100	0.518	Contact Map
3rrlB	1	0.6628	100	0.536	Contact Map
2w48A	3	0.9693	100	0.585	Contact Map
3l7oA	2	0.5939	100	0.616	Contact Map
1o8bA	2	0.5824	100	0.626	Contact Map
1uj6A	2	0.6015	100	0.63	Contact Map
1lk5A	4	0.6015	100	0.631	Contact Map
1m0sA	2	0.6054	100	0.631	Contact Map
3uw1A	2	0.613	100	0.635	Contact Map
3ixqA	4	0.6169	100	0.636	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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