YOBQ - BACSU - GREMLIN Contacts

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YOBQ - Uncharacterized HTH-type transcriptional regulator YobQ

UniProt:	O34901	Sequences: MLMDSLQEIICEKRTYTRLYHSHKHAYSQFLFPLEGSIDLETEGRQVKLNPDHFLYIPPQCEHRFRSIGRNECLVLDVPLHAMKIDEYRAGSGIEAALDPFWSSIRYLLTEEAKAGTANSLHMLVQYIKEKLQSHSYASIAYIHSHLFERLTIKKLAEIEHYHPAYYSSWFKKQTGKSPQNYIADLRLEEAKRMLMERNETLTVVSEALGFQNLSSFTRWFTKSTGMPPRLYRNTLYSDKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	241 (209)
Sequences:	34713 (29590)
Seq/√Len:	2046.8

ECOLI - YIDL MELR RHAR YPDC CHBR YEAM YQHC RHAS ARAC YDIP YBCM FEAR YIJO RCLR GADX APPY ADIY EUTR ENVY GADW YDEO ROB MARA SOXS YKGA XYLR
BACSU - YOBQ YBFI YISR YDEC YFIF BTR YTDP ADAA YESS YDEE YESN YBFP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
192_K	225_T	3.130	1.00
177_K	185_D	2.972	1.00
200_E	208_A	2.918	1.00
144_H	186_L	2.723	1.00
154_K	164_P	2.685	1.00
188_L	225_T	2.658	1.00
190_E	193_R	2.577	1.00
221_F	232_Y	2.553	1.00
185_D	224_S	2.518	1.00
146_H	149_E	2.458	1.00
142_Y	146_H	2.423	1.00
194_M	208_A	2.281	1.00
191_A	217_F	2.253	1.00
171_F	182_Y	2.073	1.00
139_S	167_Y	2.061	1.00
194_M	209_L	2.004	1.00
152_T	155_K	1.997	1.00
227_M	235_T	1.909	1.00
200_E	204_V	1.851	1.00
142_Y	159_I	1.770	1.00
194_M	200_E	1.768	1.00
140_I	175_T	1.766	1.00
180_Q	184_A	1.747	1.00
214_L	218_T	1.726	1.00
147_L	186_L	1.723	1.00
39_D	48_K	1.718	1.00
39_D	46_Q	1.704	1.00
192_K	232_Y	1.696	1.00
143_I	183_I	1.664	1.00
139_S	160_E	1.662	1.00
188_L	224_S	1.644	1.00
166_Y	170_W	1.637	1.00
220_W	223_K	1.626	1.00
153_I	168_S	1.617	1.00
201_T	204_V	1.610	1.00
123_M	126_Q	1.595	1.00
126_Q	130_E	1.592	1.00
41_E	46_Q	1.571	1.00
186_L	190_E	1.552	1.00
142_Y	151_L	1.546	1.00
166_Y	169_S	1.544	1.00
193_R	197_E	1.531	1.00
190_E	194_M	1.526	1.00
156_L	179_P	1.519	1.00
34_L	74_L	1.516	1.00
37_S	48_K	1.508	1.00
177_K	181_N	1.481	1.00
35_E	72_E	1.473	1.00
164_P	168_S	1.472	1.00
167_Y	179_P	1.465	1.00
195_L	202_L	1.463	1.00
203_T	214_L	1.459	1.00
141_A	145_S	1.454	1.00
216_S	220_W	1.448	1.00
50_N	53_H	1.425	1.00
179_P	183_I	1.393	1.00
140_I	144_H	1.391	1.00
28_S	59_P	1.372	1.00
41_E	64_R	1.371	1.00
227_M	231_L	1.368	1.00
147_L	190_E	1.368	1.00
204_V	208_A	1.366	1.00
191_A	209_L	1.364	1.00
215_S	218_T	1.360	1.00
204_V	207_E	1.359	1.00
211_F	220_W	1.352	1.00
203_T	207_E	1.346	1.00
122_H	126_Q	1.344	1.00
162_Y	166_Y	1.344	1.00
190_E	209_L	1.343	1.00
230_R	234_N	1.343	1.00
144_H	182_Y	1.332	1.00
165_A	169_S	1.309	1.00
123_M	130_E	1.305	1.00
39_D	66_R	1.297	1.00
37_S	50_N	1.290	1.00
185_D	189_E	1.283	1.00
155_K	159_I	1.281	1.00
168_S	179_P	1.275	1.00
205_V	209_L	1.269	1.00
184_A	220_W	1.264	1.00
148_F	208_A	1.263	1.00
178_S	181_N	1.236	1.00
162_Y	167_Y	1.234	1.00
104_S	108_L	1.219	1.00
186_L	189_E	1.211	1.00
163_H	166_Y	1.210	1.00
43_E	61_C	1.205	1.00
139_S	156_L	1.204	1.00
154_K	158_E	1.180	1.00
149_E	155_K	1.177	1.00
130_E	134_S	1.174	1.00
218_T	228_P	1.170	1.00
192_K	196_M	1.155	1.00
123_M	127_Y	1.154	1.00
58_P	61_C	1.151	1.00
143_I	186_L	1.128	1.00
198_R	233_R	1.115	1.00
218_T	230_R	1.114	1.00
200_E	205_V	1.085	1.00
219_R	223_K	1.082	1.00
35_E	51_P	1.080	1.00
34_L	72_E	1.075	1.00
189_E	192_K	1.061	1.00
231_L	234_N	1.057	1.00
103_S	107_Y	1.038	1.00
170_W	174_Q	1.035	1.00
151_L	156_L	1.035	1.00
228_P	231_L	1.032	1.00
170_W	173_K	1.029	1.00
157_A	164_P	1.023	1.00
29_Q	63_H	1.013	1.00
104_S	107_Y	1.010	1.00
184_A	223_K	1.004	1.00
230_R	233_R	1.003	1.00
107_Y	111_E	1.001	1.00
25_H	63_H	0.998	1.00
153_I	179_P	0.988	1.00
148_F	190_E	0.976	1.00
140_I	182_Y	0.970	1.00
23_H	63_H	0.969	1.00
218_T	222_T	0.960	1.00
22_S	62_E	0.959	1.00
142_Y	160_E	0.945	1.00
38_I	71_N	0.943	1.00
213_N	219_R	0.941	1.00
150_R	212_Q	0.939	1.00
171_F	175_T	0.931	1.00
202_L	205_V	0.928	1.00
194_M	205_V	0.915	1.00
147_L	151_L	0.909	1.00
94_I	97_A	0.907	1.00
162_Y	170_W	0.906	1.00
181_N	184_A	0.904	1.00
165_A	168_S	0.902	1.00
155_K	158_E	0.897	1.00
231_L	235_T	0.894	1.00
139_S	142_Y	0.894	1.00
220_W	224_S	0.893	1.00
150_R	155_K	0.893	1.00
33_P	38_I	0.893	1.00
156_L	159_I	0.878	1.00
94_I	98_L	0.878	1.00
160_E	167_Y	0.877	1.00
225_T	232_Y	0.870	1.00
216_S	219_R	0.865	1.00
153_I	164_P	0.861	1.00
195_L	233_R	0.859	1.00
184_A	224_S	0.855	1.00
181_N	185_D	0.837	1.00
227_M	232_Y	0.836	1.00
188_L	220_W	0.835	1.00
80_L	84_K	0.826	1.00
222_T	228_P	0.823	1.00
106_R	112_E	0.822	1.00
180_Q	216_S	0.816	1.00
143_I	179_P	0.813	1.00
31_L	75_V	0.811	1.00
187_R	209_L	0.810	1.00
22_S	64_R	0.810	1.00
192_K	221_F	0.810	1.00
206_S	214_L	0.809	1.00
53_H	97_A	0.803	1.00
99_D	102_W	0.800	1.00
37_S	68_I	0.799	1.00
38_I	49_L	0.798	1.00
188_L	217_F	0.792	1.00
71_N	75_V	0.790	1.00
39_D	68_I	0.789	1.00
41_E	44_G	0.788	1.00
28_S	56_Y	0.786	1.00
147_L	183_I	0.786	1.00
195_L	205_V	0.786	1.00
112_E	116_G	0.780	1.00
181_N	224_S	0.779	1.00
41_E	66_R	0.777	1.00
142_Y	156_L	0.771	1.00
182_Y	186_L	0.769	1.00
171_F	179_P	0.768	1.00
139_S	171_F	0.767	1.00
139_S	143_I	0.763	1.00
180_Q	183_I	0.761	1.00
113_A	116_G	0.761	1.00
198_R	205_V	0.758	1.00
108_L	112_E	0.755	1.00
127_Y	130_E	0.751	1.00
125_V	131_K	0.747	1.00
168_S	172_K	0.742	1.00
95_E	98_L	0.739	1.00
207_E	212_Q	0.739	1.00
101_F	104_S	0.725	1.00
117_T	120_S	0.725	1.00
191_A	194_M	0.724	1.00
146_H	159_I	0.721	1.00
29_Q	77_D	0.720	1.00
146_H	155_K	0.717	1.00
42_T	45_R	0.714	1.00
151_L	155_K	0.714	1.00
147_L	209_L	0.711	1.00
140_I	171_F	0.705	1.00
92_S	95_E	0.703	1.00
40_L	55_L	0.702	1.00
127_Y	131_K	0.700	1.00
222_T	231_L	0.697	1.00
121_L	124_L	0.693	1.00
156_L	167_Y	0.689	1.00
109_L	112_E	0.684	1.00
38_I	48_K	0.683	1.00
124_L	127_Y	0.683	1.00
143_I	182_Y	0.680	1.00
122_H	125_V	0.678	1.00
214_L	217_F	0.675	1.00
110_T	114_K	0.673	1.00
196_M	232_Y	0.671	1.00
205_V	233_R	0.669	1.00
104_S	111_E	0.667	1.00
25_H	29_Q	0.667	1.00
108_L	111_E	0.662	1.00
168_S	180_Q	0.659	1.00
121_L	132_L	0.659	1.00
215_S	228_P	0.658	1.00
57_I	63_H	0.656	1.00
177_K	182_Y	0.656	1.00
32_F	54_F	0.653	1.00
175_T	182_Y	0.650	1.00
31_L	73_C	0.648	1.00
24_K	62_E	0.647	1.00
33_P	73_C	0.645	1.00
213_N	216_S	0.645	1.00
201_T	205_V	0.644	1.00
33_P	36_G	0.640	1.00
122_H	130_E	0.639	1.00
144_H	190_E	0.637	1.00
49_L	55_L	0.631	1.00
168_S	178_S	0.631	1.00
156_L	160_E	0.630	1.00
30_F	56_Y	0.628	1.00
172_K	178_S	0.625	1.00
217_F	221_F	0.625	1.00
169_S	173_K	0.623	1.00
28_S	31_L	0.622	1.00
212_Q	216_S	0.616	1.00
31_L	57_I	0.616	1.00
139_S	179_P	0.612	1.00
112_E	115_A	0.610	1.00
188_L	211_F	0.608	1.00
199_N	205_V	0.605	1.00
157_A	160_E	0.605	1.00
105_I	109_L	0.604	1.00
121_L	127_Y	0.603	1.00
122_H	129_K	0.600	1.00
189_E	224_S	0.597	1.00
215_S	219_R	0.594	1.00
153_I	180_Q	0.594	1.00
107_Y	110_T	0.590	1.00
30_F	54_F	0.587	1.00
184_A	216_S	0.586	1.00
121_L	131_K	0.585	1.00
80_L	83_M	0.584	1.00
27_Y	77_D	0.584	1.00
151_L	187_R	0.581	1.00
38_I	65_F	0.575	1.00
158_E	161_H	0.573	1.00
191_A	205_V	0.573	1.00
131_K	135_H	0.572	1.00
217_F	229_P	0.570	1.00
183_I	187_R	0.570	1.00
33_P	71_N	0.567	1.00
194_M	197_E	0.564	1.00
189_E	225_T	0.563	1.00
31_L	40_L	0.561	1.00
213_N	223_K	0.560	1.00
193_R	196_M	0.560	1.00
141_A	144_H	0.559	1.00
139_S	159_I	0.559	1.00
111_E	115_A	0.558	1.00
139_S	170_W	0.558	1.00
221_F	227_M	0.555	1.00
206_S	211_F	0.553	1.00
33_P	49_L	0.552	1.00
121_L	125_V	0.552	1.00
147_L	187_R	0.548	1.00
133_Q	136_S	0.547	1.00
43_E	62_E	0.546	1.00
202_L	230_R	0.546	1.00
81_H	84_K	0.545	1.00
151_L	183_I	0.542	1.00
105_I	108_L	0.538	1.00
143_I	151_L	0.536	1.00
142_Y	155_K	0.534	1.00
124_L	132_L	0.531	1.00
126_Q	136_S	0.528	1.00
106_R	110_T	0.527	1.00
121_L	126_Q	0.525	1.00
153_I	165_A	0.525	1.00
130_E	133_Q	0.523	1.00
197_E	200_E	0.517	1.00
40_L	65_F	0.515	1.00
191_A	221_F	0.514	1.00
192_K	227_M	0.511	1.00
181_N	223_K	0.511	1.00
220_W	225_T	0.510	1.00
167_Y	170_W	0.509	1.00
103_S	106_R	0.509	1.00
26_A	79_P	0.506	1.00
37_S	69_G	0.506	1.00
131_K	134_S	0.505	1.00
202_L	214_L	0.504	1.00
93_G	97_A	0.503	1.00
125_V	136_S	0.503	1.00
160_E	164_P	0.502	1.00
39_D	42_T	0.501	1.00
211_F	216_S	0.501	1.00
31_L	55_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
3gbgA	1	0.9751	100	0.226	Contact Map
1bl0A	1	0.4564	100	0.455	Contact Map
3mn2A	1	0.4398	100	0.457	Contact Map
3oouA	1	0.4357	100	0.457	Contact Map
2k9sA	1	0.4398	99.9	0.459	Contact Map
3oioA	1	0.4647	99.9	0.463	Contact Map
3w6vA	1	0.4523	99.9	0.466	Contact Map
3mklA	1	0.4606	99.9	0.469	Contact Map
3lsgA	2	0.4232	99.9	0.471	Contact Map
1d5yA	1	0.4564	99.9	0.482	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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