YDHB - ECOLI - GREMLIN Contacts

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YDHB - Uncharacterized HTH-type transcriptional regulator YdhB

UniProt:	P0ACR2	Sequences: MWSEYSLEVVDAVARNGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTAAGAWFLKEGRSVVKKMQITRQQCQQIANGWRGQLAIAVDNIVRPERTRQMIVDFYRHFDDVELLVFQEVFNGVWDALSDGRVELAIGATRAIPVGGRYAFRDMGMLSWSCVVASHHPLALMDGPFSDDTLRNWPSLVREDTSRTLPKRITWLLDNQKRVVVPDWESSATCISAGLCIGMVPTHFAKPWLNEGKWVALELENPFPDSACCLTWQQNDMSPALTWLLEYLGDSETLNKEWLREPEETPATGD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12140
Length:	310 (281)
Sequences:	79753 (57657)
Seq/√Len:	3439.5

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
71_S	75_K	3.520	1.00
16_N	25_E	3.293	1.00
161_R	289_G	2.582	1.00
97_A	142_V	2.423	1.00
68_E	82_Q	2.402	1.00
12_A	25_E	2.308	1.00
176_H	193_W	2.184	1.00
231_I	238_G	2.169	1.00
165_M	267_A	2.167	1.00
93_Q	124_L	2.153	1.00
162_D	165_M	2.148	1.00
113_D	291_S	2.146	1.00
162_D	267_A	2.132	1.00
167_S	242_T	2.069	1.00
46_V	61_A	2.062	1.00
9_V	36_T	2.038	1.00
93_Q	122_E	2.033	1.00
165_M	265_D	1.998	1.00
21_A	24_Q	1.991	1.00
11_D	70_R	1.984	1.00
186_S	189_T	1.964	1.00
68_E	75_K	1.959	1.00
232_S	253_K	1.954	1.00
113_D	287_Y	1.942	1.00
11_D	15_R	1.920	1.00
15_R	70_R	1.915	1.00
95_A	124_L	1.915	1.00
169_S	242_T	1.896	1.00
12_A	15_R	1.888	1.00
11_D	66_L	1.887	1.00
12_A	16_N	1.884	1.00
228_A	248_W	1.854	1.00
14_A	58_L	1.836	1.00
9_V	33_V	1.831	1.00
72_V	76_M	1.823	1.00
172_V	257_L	1.816	1.00
196_L	236_C	1.814	1.00
66_L	70_R	1.782	1.00
232_S	248_W	1.708	1.00
169_S	256_A	1.693	1.00
50_E	57_E	1.686	1.00
194_P	218_R	1.675	1.00
19_F	37_V	1.663	1.00
160_F	269_C	1.661	1.00
65_F	79_T	1.658	1.00
64_W	82_Q	1.649	1.00
133_V	145_A	1.632	1.00
136_A	141_R	1.624	1.00
14_A	66_L	1.614	1.00
16_N	21_A	1.577	1.00
11_D	69_G	1.538	1.00
159_A	274_Q	1.523	1.00
15_R	25_E	1.523	1.00
114_F	284_L	1.498	1.00
68_E	71_S	1.490	1.00
6_S	36_T	1.488	1.00
135_D	139_D	1.487	1.00
6_S	43_W	1.473	1.00
161_R	272_W	1.471	1.00
10_V	66_L	1.466	1.00
205_L	208_R	1.466	1.00
9_V	28_R	1.459	1.00
18_S	21_A	1.457	1.00
6_S	39_Q	1.444	1.00
89_G	120_D	1.435	1.00
47_P	50_E	1.426	1.00
114_F	121_V	1.424	1.00
285_L	289_G	1.424	1.00
20_S	30_P	1.416	1.00
29_V	32_A	1.411	1.00
181_M	189_T	1.396	1.00
159_A	272_W	1.394	1.00
277_M	281_L	1.392	1.00
12_A	26_L	1.391	1.00
272_W	285_L	1.389	1.00
147_G	271_T	1.384	1.00
60_A	63_A	1.377	1.00
68_E	78_I	1.376	1.00
149_T	269_C	1.376	1.00
104_P	225_E	1.362	1.00
52_R	57_E	1.340	1.00
72_V	79_T	1.339	1.00
11_D	73_V	1.337	1.00
95_A	126_F	1.325	1.00
136_A	142_V	1.322	1.00
91_R	120_D	1.322	1.00
283_W	286_E	1.317	1.00
75_K	78_I	1.312	1.00
137_L	145_A	1.308	1.00
270_L	285_L	1.298	1.00
117_H	287_Y	1.297	1.00
113_D	117_H	1.294	1.00
138_S	157_R	1.289	1.00
65_F	80_R	1.285	1.00
166_L	243_H	1.283	1.00
174_S	253_K	1.281	1.00
3_S	6_S	1.276	1.00
144_L	270_L	1.271	1.00
4_E	76_M	1.262	1.00
193_W	237_I	1.259	1.00
172_V	237_I	1.255	1.00
67_K	71_S	1.250	1.00
227_S	238_G	1.240	1.00
144_L	281_L	1.228	1.00
229_T	232_S	1.218	1.00
115_Y	218_R	1.217	1.00
43_W	80_R	1.213	1.00
68_E	79_T	1.211	1.00
174_S	255_V	1.197	1.00
162_D	269_C	1.194	1.00
64_W	67_K	1.187	1.00
242_T	246_K	1.186	1.00
10_V	49_F	1.186	1.00
28_R	32_A	1.182	1.00
112_V	116_R	1.179	1.00
242_T	256_A	1.177	1.00
115_Y	194_P	1.168	1.00
248_W	253_K	1.151	1.00
176_H	179_A	1.149	1.00
112_V	233_A	1.142	1.00
160_F	271_T	1.139	1.00
10_V	14_A	1.136	1.00
35_Y	39_Q	1.134	1.00
38_R	42_E	1.131	1.00
63_A	67_K	1.127	1.00
183_G	255_V	1.125	1.00
172_V	176_H	1.116	1.00
246_K	250_N	1.115	1.00
35_Y	38_R	1.104	1.00
124_L	220_V	1.098	1.00
64_W	68_E	1.093	1.00
113_D	116_R	1.091	1.00
204_T	207_K	1.087	1.00
184_P	260_E	1.084	1.00
71_S	78_I	1.083	1.00
194_P	216_Q	1.080	1.00
118_F	283_W	1.079	1.00
273_Q	276_D	1.075	1.00
138_S	155_G	1.075	1.00
171_V	256_A	1.072	1.00
10_V	48_L	1.070	1.00
109_Q	233_A	1.068	1.00
7_L	69_G	1.064	1.00
5_Y	8_E	1.061	1.00
287_Y	291_S	1.061	1.00
286_E	289_G	1.060	1.00
19_F	56_V	1.058	1.00
12_A	22_A	1.057	1.00
256_A	259_L	1.052	1.00
161_R	285_L	1.051	1.00
36_T	39_Q	1.050	1.00
34_S	38_R	1.050	1.00
204_T	208_R	1.048	1.00
110_M	288_L	1.044	1.00
72_V	75_K	1.042	1.00
185_F	189_T	1.039	1.00
94_L	284_L	1.038	1.00
282_T	286_E	1.033	1.00
13_V	22_A	1.030	1.00
228_A	232_S	1.030	1.00
229_T	233_A	1.026	1.00
114_F	287_Y	1.025	1.00
221_V	227_S	1.025	1.00
196_L	227_S	1.006	1.00
80_R	84_Q	1.003	1.00
167_S	265_D	1.000	1.00
8_E	77_Q	0.995	1.00
173_A	234_G	0.993	1.00
247_P	251_E	0.983	1.00
187_D	261_N	0.979	1.00
74_K	78_I	0.978	1.00
126_F	136_A	0.974	1.00
287_Y	290_D	0.972	1.00
28_R	33_V	0.963	1.00
58_L	62_G	0.962	1.00
197_V	217_K	0.956	1.00
77_Q	80_R	0.954	1.00
13_V	19_F	0.951	1.00
171_V	245_A	0.950	1.00
114_F	118_F	0.946	1.00
9_V	26_L	0.945	1.00
14_A	49_F	0.942	1.00
65_F	69_G	0.939	1.00
39_Q	42_E	0.939	1.00
170_C	237_I	0.932	1.00
77_Q	81_Q	0.925	1.00
10_V	58_L	0.922	1.00
10_V	40_L	0.921	1.00
22_A	33_V	0.920	1.00
172_V	178_L	0.918	1.00
136_A	139_D	0.913	1.00
221_V	230_C	0.913	1.00
97_A	133_V	0.909	1.00
117_H	290_D	0.908	1.00
278_S	281_L	0.905	1.00
100_N	223_D	0.901	1.00
21_A	25_E	0.900	1.00
64_W	86_I	0.896	1.00
49_F	56_V	0.891	1.00
110_M	287_Y	0.882	1.00
142_V	145_A	0.875	1.00
5_Y	36_T	0.874	1.00
46_V	83_C	0.874	1.00
71_S	74_K	0.872	1.00
149_T	267_A	0.870	1.00
97_A	147_G	0.867	1.00
67_K	70_R	0.864	1.00
17_G	57_E	0.861	1.00
159_A	162_D	0.858	1.00
122_E	216_Q	0.854	1.00
14_A	62_G	0.851	1.00
20_S	24_Q	0.847	1.00
189_T	192_N	0.837	1.00
194_P	217_K	0.833	1.00
96_I	144_L	0.832	1.00
121_V	280_A	0.827	1.00
134_W	138_S	0.827	1.00
61_A	86_I	0.826	1.00
76_M	80_R	0.820	1.00
52_R	55_D	0.820	1.00
112_V	235_L	0.816	1.00
26_L	33_V	0.814	1.00
171_V	238_G	0.813	1.00
158_Y	271_T	0.811	1.00
126_F	142_V	0.811	1.00
157_R	274_Q	0.811	1.00
175_H	179_A	0.809	1.00
61_A	83_C	0.803	1.00
179_A	255_V	0.801	1.00
10_V	65_F	0.800	1.00
277_M	282_T	0.799	1.00
245_A	248_W	0.798	1.00
92_G	280_A	0.798	1.00
61_A	64_W	0.796	1.00
97_A	145_A	0.796	1.00
30_P	34_S	0.794	1.00
14_A	17_G	0.793	1.00
38_R	47_P	0.791	1.00
248_W	251_E	0.791	1.00
15_R	66_L	0.790	1.00
78_I	82_Q	0.789	1.00
286_E	290_D	0.787	1.00
17_G	63_A	0.786	1.00
75_K	79_T	0.785	1.00
4_E	73_V	0.784	1.00
16_N	22_A	0.783	1.00
173_A	176_H	0.783	1.00
208_R	213_L	0.783	1.00
188_D	191_R	0.782	1.00
17_G	55_D	0.781	1.00
173_A	235_L	0.781	1.00
110_M	291_S	0.777	1.00
76_M	79_T	0.776	1.00
115_Y	235_L	0.772	1.00
176_H	194_P	0.770	1.00
13_V	49_F	0.765	1.00
6_S	9_V	0.765	1.00
167_S	258_E	0.757	1.00
132_G	135_D	0.756	1.00
8_E	12_A	0.756	1.00
249_L	252_G	0.750	1.00
230_C	235_L	0.749	1.00
279_P	283_W	0.749	1.00
186_S	260_E	0.745	1.00
144_L	284_L	0.745	1.00
13_V	37_V	0.744	1.00
178_L	183_G	0.743	1.00
92_G	121_V	0.742	1.00
70_R	74_K	0.740	1.00
245_A	249_L	0.738	1.00
19_F	33_V	0.735	1.00
79_T	83_C	0.733	1.00
178_L	193_W	0.733	1.00
138_S	158_Y	0.729	1.00
171_V	240_V	0.728	1.00
50_E	59_T	0.724	1.00
13_V	33_V	0.723	1.00
117_H	283_W	0.723	1.00
98_V	103_R	0.720	1.00
114_F	283_W	0.717	1.00
203_R	206_P	0.716	1.00
69_G	72_V	0.714	1.00
113_D	290_D	0.713	1.00
90_W	118_F	0.711	1.00
172_V	255_V	0.709	1.00
140_G	273_Q	0.708	1.00
63_A	66_L	0.708	1.00
84_Q	87_A	0.707	1.00
171_V	249_L	0.705	1.00
241_P	244_F	0.704	1.00
232_S	251_E	0.703	1.00
283_W	287_Y	0.700	1.00
143_E	281_L	0.699	1.00
184_P	258_E	0.688	1.00
188_D	211_W	0.686	1.00
57_E	63_A	0.686	1.00
60_A	64_W	0.685	1.00
61_A	65_F	0.684	1.00
223_D	226_S	0.683	1.00
58_L	63_A	0.681	1.00
186_S	261_N	0.679	1.00
8_E	11_D	0.679	1.00
95_A	142_V	0.676	1.00
50_E	55_D	0.673	1.00
175_H	234_G	0.670	1.00
191_R	213_L	0.668	1.00
249_L	256_A	0.668	1.00
198_R	227_S	0.666	1.00
32_A	36_T	0.666	1.00
181_M	194_P	0.664	1.00
199_E	220_V	0.659	1.00
176_H	181_M	0.658	1.00
167_S	263_F	0.657	1.00
195_S	237_I	0.654	1.00
5_Y	39_Q	0.653	1.00
65_F	83_C	0.653	1.00
95_A	143_E	0.652	1.00
74_K	77_Q	0.649	1.00
41_E	46_V	0.648	1.00
104_P	229_T	0.648	1.00
24_Q	27_H	0.645	1.00
78_I	81_Q	0.644	1.00
68_E	72_V	0.642	1.00
219_V	230_C	0.642	1.00
122_E	220_V	0.639	1.00
41_E	51_R	0.637	1.00
247_P	250_N	0.635	1.00
170_C	239_M	0.634	1.00
192_N	216_Q	0.631	1.00
103_R	130_F	0.631	1.00
98_V	107_T	0.629	1.00
175_H	255_V	0.625	1.00
170_C	190_L	0.622	1.00
94_L	280_A	0.622	1.00
69_G	73_V	0.617	1.00
37_V	41_E	0.616	1.00
279_P	282_T	0.616	1.00
148_A	266_S	0.615	1.00
109_Q	112_V	0.609	1.00
132_G	136_A	0.609	1.00
109_Q	113_D	0.606	1.00
13_V	18_S	0.603	1.00
181_M	184_P	0.600	1.00
22_A	26_L	0.598	1.00
81_Q	85_Q	0.598	1.00
199_E	222_P	0.597	1.00
8_E	73_V	0.597	1.00
10_V	62_G	0.592	1.00
107_T	110_M	0.591	1.00
5_Y	9_V	0.591	1.00
174_S	252_G	0.590	1.00
178_L	181_M	0.588	1.00
64_W	83_C	0.587	1.00
44_L	83_C	0.587	1.00
144_L	285_L	0.587	1.00
137_L	271_T	0.587	1.00
94_L	144_L	0.586	1.00
195_S	215_N	0.586	1.00
44_L	65_F	0.581	1.00
172_V	179_A	0.578	1.00
272_W	282_T	0.578	1.00
227_S	231_I	0.574	1.00
32_A	35_Y	0.572	1.00
284_L	288_L	0.572	1.00
166_L	266_S	0.571	1.00
3_S	39_Q	0.570	1.00
91_R	122_E	0.570	1.00
102_V	106_R	0.570	1.00
146_I	288_L	0.570	1.00
164_G	268_C	0.570	1.00
170_C	195_S	0.566	1.00
200_D	220_V	0.565	1.00
19_F	55_D	0.565	1.00
31_S	35_Y	0.564	1.00
168_W	239_M	0.564	1.00
221_V	226_S	0.560	1.00
137_L	158_Y	0.560	1.00
73_V	77_Q	0.560	1.00
46_V	50_E	0.560	1.00
58_L	66_L	0.559	1.00
49_F	58_L	0.557	1.00
230_C	236_C	0.555	1.00
29_V	35_Y	0.551	1.00
118_F	121_V	0.550	1.00
149_T	160_F	0.550	1.00
85_Q	90_W	0.550	1.00
163_M	270_L	0.547	1.00
159_A	275_N	0.546	1.00
19_F	30_P	0.544	1.00
44_L	47_P	0.543	1.00
176_H	237_I	0.542	1.00
240_V	245_A	0.539	1.00
111_I	123_L	0.538	1.00
14_A	63_A	0.538	1.00
224_W	241_P	0.538	1.00
97_A	126_F	0.538	1.00
259_L	262_P	0.535	1.00
135_D	141_R	0.533	1.00
92_G	120_D	0.533	1.00
9_V	37_V	0.532	1.00
104_P	223_D	0.528	1.00
180_L	183_G	0.526	1.00
81_Q	84_Q	0.526	1.00
133_V	140_G	0.523	1.00
67_K	82_Q	0.521	1.00
28_R	36_T	0.521	1.00
73_V	76_M	0.519	1.00
272_W	277_M	0.515	1.00
184_P	189_T	0.515	1.00
99_D	102_V	0.514	1.00
19_F	51_R	0.512	1.00
17_G	56_V	0.511	1.00
109_Q	229_T	0.511	1.00
106_R	110_M	0.511	1.00
9_V	22_A	0.511	1.00
47_P	61_A	0.510	1.00
281_L	285_L	0.505	1.00
138_S	141_R	0.504	1.00
82_Q	85_Q	0.504	1.00
68_E	83_C	0.503	1.00
98_V	125_V	0.501	1.00
72_V	80_R	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
3fxqA	3	0.9355	100	0.129	Contact Map
3fzvA	4	0.9161	100	0.135	Contact Map
2esnA	3	0.9355	100	0.136	Contact Map
1ixcA	4	0.929	100	0.137	Contact Map
1uthA	2	0.7161	100	0.145	Contact Map
2h9bA	2	0.6613	100	0.15	Contact Map
2h98A	2	0.6742	100	0.15	Contact Map
1al3A	1	0.7129	100	0.153	Contact Map
4x6gA	4	0.9613	100	0.155	Contact Map
3szpA	3	0.9226	100	0.162	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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