YBDO - ECOLI - GREMLIN Contacts

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YBDO - Uncharacterized HTH-type transcriptional regulator YbdO

UniProt:	P77746	Sequences: MANLYDLKKFDLNLLVIFECIYQHLSISKAAESLYITPSAVSQSLQRLRAQFNDPLFIRSGKGIAPTTTGLNLHHHLEKNLRGLEQTINIVNKSELKKNFIIYGPQLISCSNNSMLIRCLRQDSSVEIECHDILMSAENAEELLVHRKADLVITQMPVISRSVICMPLHTIRNTLICSNRHPRITDNSTYEQIMAEEFTQLISKSAGVDDIQMEIDERFMNRKISFRGSSLLTIINSIAVTDLLGIVPYELYNSYRDFLNLKEIKLEHPLPSIKLYISYNKSSLNNLVFSRFIDRLNESF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13534
Length:	300 (283)
Sequences:	79181 (57618)
Seq/√Len:	3425.1

ECOLI - YBDO YBEF YDCI LEUO OXYR PGRR YEIE TDCA LYSR DSDC YBHD NAC CYSB XAPR NHAR YIDZ TTDR YFIE AAER CYNR ICIA YAFC YHJC YNEJ CBL YFER ABGR DMLR METR ILVY YNFL HCAR YHAJ YCAN YIAU YEEY YDHB ALLS YAHB GCVA YGFI PERR LRHA YJIE HDFR
BACSU - CYSL YWBI YCGK GLTR YWQM GLTC ALSR YYBE BSDA YUST YVBU YTLI CITR YOFA CZCR YKUM YXJO 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
79_K	83_G	3.589	1.00
24_H	33_S	3.389	1.00
166_M	297_N	2.602	1.00
103_Y	149_A	2.508	1.00
76_H	90_I	2.398	1.00
238_I	245_G	2.330	1.00
172_R	249_Y	2.250	1.00
181_H	196_E	2.221	1.00
20_C	33_S	2.189	1.00
167_P	170_T	2.187	1.00
170_T	274_K	2.185	1.00
99_N	131_H	2.170	1.00
29_K	32_E	2.145	1.00
23_Q	78_E	2.138	1.00
99_N	129_E	2.127	1.00
189_T	192_Q	2.077	1.00
167_P	274_K	2.069	1.00
54_D	69_T	2.015	1.00
19_E	74_H	2.010	1.00
17_I	44_S	2.005	1.00
235_I	255_Y	1.987	1.00
170_T	272_S	1.978	1.00
101_I	131_H	1.978	1.00
239_A	260_N	1.972	1.00
76_H	83_G	1.955	1.00
119_C	295_R	1.940	1.00
177_C	264_I	1.912	1.00
199_T	243_L	1.905	1.00
20_C	23_Q	1.902	1.00
19_E	78_E	1.900	1.00
80_N	84_L	1.886	1.00
17_I	41_V	1.884	1.00
20_C	24_H	1.867	1.00
27_I	45_L	1.862	1.00
22_Y	66_P	1.854	1.00
19_E	23_Q	1.852	1.00
74_H	78_E	1.812	1.00
174_T	249_Y	1.812	1.00
140_A	152_V	1.802	1.00
58_I	65_A	1.743	1.00
239_A	255_Y	1.729	1.00
73_L	87_T	1.697	1.00
197_E	225_S	1.697	1.00
72_N	90_I	1.660	1.00
165_C	276_Y	1.653	1.00
174_T	263_E	1.648	1.00
143_L	148_K	1.624	1.00
23_Q	33_S	1.614	1.00
120_L	292_F	1.612	1.00
18_F	74_H	1.590	1.00
164_I	281_K	1.579	1.00
22_Y	74_H	1.578	1.00
19_E	77_L	1.564	1.00
17_I	36_I	1.557	1.00
24_H	29_K	1.553	1.00
120_L	128_I	1.526	1.00
28_S	38_P	1.517	1.00
68_T	71_L	1.511	1.00
142_E	146_H	1.504	1.00
14_L	44_S	1.474	1.00
55_P	58_I	1.452	1.00
11_D	14_L	1.452	1.00
14_L	51_Q	1.452	1.00
166_M	279_Y	1.446	1.00
37_T	40_A	1.442	1.00
19_E	81_L	1.438	1.00
26_S	29_K	1.417	1.00
20_C	34_L	1.413	1.00
14_L	47_R	1.409	1.00
285_N	289_F	1.408	1.00
208_V	212_Q	1.406	1.00
76_H	79_K	1.405	1.00
179_N	260_N	1.389	1.00
164_I	279_Y	1.384	1.00
154_T	278_S	1.380	1.00
76_H	86_Q	1.375	1.00
80_N	87_T	1.365	1.00
156_M	276_Y	1.362	1.00
12_L	84_L	1.347	1.00
151_L	289_F	1.344	1.00
110_C	232_L	1.338	1.00
97_K	127_E	1.323	1.00
277_I	293_I	1.319	1.00
145_V	162_S	1.318	1.00
101_I	133_I	1.309	1.00
279_Y	293_I	1.286	1.00
51_Q	88_I	1.286	1.00
119_C	124_S	1.281	1.00
143_L	149_A	1.278	1.00
144_L	152_V	1.278	1.00
177_C	244_L	1.270	1.00
73_L	88_I	1.265	1.00
171_I	250_E	1.261	1.00
196_E	244_L	1.259	1.00
121_R	225_S	1.257	1.00
293_I	297_N	1.254	1.00
151_L	277_I	1.254	1.00
234_I	245_G	1.248	1.00
60_S	65_A	1.247	1.00
291_R	294_D	1.238	1.00
46_Q	50_A	1.229	1.00
249_Y	253_N	1.227	1.00
253_N	257_D	1.225	1.00
71_L	75_H	1.222	1.00
215_I	220_M	1.221	1.00
83_G	86_Q	1.219	1.00
236_N	239_A	1.212	1.00
249_Y	263_E	1.200	1.00
75_H	79_K	1.198	1.00
121_R	197_E	1.192	1.00
186_D	262_K	1.192	1.00
72_N	75_H	1.189	1.00
255_Y	260_N	1.187	1.00
76_H	87_T	1.182	1.00
179_N	262_K	1.177	1.00
119_C	122_Q	1.173	1.00
18_F	57_F	1.172	1.00
118_R	122_Q	1.164	1.00
167_P	276_Y	1.161	1.00
182_P	196_E	1.156	1.00
165_C	278_S	1.143	1.00
199_T	234_I	1.143	1.00
100_F	292_F	1.139	1.00
124_S	295_R	1.134	1.00
18_F	22_Y	1.124	1.00
36_I	40_A	1.119	1.00
16_V	85_E	1.114	1.00
18_F	56_L	1.113	1.00
43_Q	46_Q	1.113	1.00
197_E	223_K	1.106	1.00
43_Q	47_R	1.101	1.00
131_H	227_R	1.099	1.00
42_S	46_Q	1.095	1.00
125_S	291_R	1.088	1.00
79_K	86_Q	1.083	1.00
228_G	234_I	1.082	1.00
176_I	263_E	1.081	1.00
27_I	64_I	1.081	1.00
120_L	295_R	1.078	1.00
118_R	240_V	1.077	1.00
15_L	77_L	1.076	1.00
21_I	30_A	1.068	1.00
187_N	267_E	1.065	1.00
13_N	16_V	1.062	1.00
80_N	83_G	1.059	1.00
20_C	30_A	1.050	1.00
109_S	134_L	1.049	1.00
290_S	294_D	1.043	1.00
44_S	47_R	1.040	1.00
66_P	70_G	1.029	1.00
145_V	160_S	1.025	1.00
178_S	241_T	1.024	1.00
188_S	192_Q	1.023	1.00
235_I	239_A	1.023	1.00
175_L	244_L	1.020	1.00
263_E	266_L	1.018	1.00
72_N	76_H	1.017	1.00
190_Y	268_H	1.015	1.00
115_M	240_V	1.012	1.00
236_N	240_V	1.001	1.00
103_Y	140_A	1.001	1.00
85_E	89_N	0.991	1.00
85_E	88_I	0.989	1.00
294_D	297_N	0.988	1.00
88_I	92_N	0.983	1.00
176_I	252_Y	0.981	1.00
17_I	34_L	0.980	1.00
166_M	293_I	0.979	1.00
36_I	41_V	0.975	1.00
172_R	272_S	0.974	1.00
116_L	296_L	0.966	1.00
120_L	125_S	0.966	1.00
22_Y	57_F	0.963	1.00
254_S	258_F	0.954	1.00
18_F	66_P	0.949	1.00
177_C	181_H	0.946	1.00
181_H	184_I	0.946	1.00
143_L	146_H	0.942	1.00
82_R	86_Q	0.941	1.00
116_L	295_R	0.940	1.00
73_L	77_L	0.937	1.00
21_I	27_I	0.936	1.00
286_N	289_F	0.932	1.00
181_H	197_E	0.931	1.00
209_D	212_Q	0.927	1.00
162_S	281_K	0.926	1.00
228_G	237_S	0.919	1.00
18_F	48_L	0.919	1.00
252_Y	255_Y	0.918	1.00
133_I	143_L	0.917	1.00
54_D	91_V	0.913	1.00
200_Q	224_I	0.912	1.00
129_E	223_K	0.910	1.00
22_Y	70_G	0.909	1.00
57_F	64_I	0.905	1.00
30_A	41_V	0.900	1.00
47_R	50_A	0.890	1.00
149_A	152_V	0.889	1.00
72_N	94_S	0.885	1.00
75_H	78_E	0.878	1.00
280_N	283_S	0.878	1.00
128_I	288_V	0.877	1.00
198_F	222_R	0.873	1.00
181_H	185_T	0.866	1.00
29_K	33_S	0.866	1.00
103_Y	154_T	0.863	1.00
106_Q	230_S	0.863	1.00
28_S	32_E	0.855	1.00
163_V	278_S	0.854	1.00
177_C	182_P	0.851	1.00
25_L	65_A	0.849	1.00
176_I	245_G	0.843	1.00
182_P	186_D	0.842	1.00
156_M	274_K	0.841	1.00
185_T	197_E	0.838	1.00
69_T	94_S	0.834	1.00
285_N	290_S	0.831	1.00
13_N	44_S	0.827	1.00
102_I	151_L	0.827	1.00
12_L	81_L	0.825	1.00
79_K	82_R	0.822	1.00
34_L	41_V	0.819	1.00
183_R	196_E	0.816	1.00
214_E	218_R	0.816	1.00
141_E	145_V	0.816	1.00
197_E	224_I	0.814	1.00
256_R	259_L	0.813	1.00
192_Q	195_A	0.813	1.00
60_S	63_G	0.809	1.00
164_I	167_P	0.804	1.00
21_I	45_L	0.801	1.00
98_K	128_I	0.800	1.00
103_Y	152_V	0.799	1.00
255_Y	258_F	0.799	1.00
69_T	91_V	0.799	1.00
46_Q	55_P	0.798	1.00
180_R	184_I	0.798	1.00
18_F	73_L	0.796	1.00
98_K	288_V	0.795	1.00
133_I	149_A	0.795	1.00
25_L	71_L	0.792	1.00
92_N	95_E	0.785	1.00
96_L	125_S	0.782	1.00
118_R	242_D	0.782	1.00
23_Q	74_H	0.779	1.00
139_N	142_E	0.778	1.00
22_Y	25_L	0.773	1.00
191_E	194_M	0.773	1.00
38_P	42_S	0.768	1.00
21_I	57_F	0.768	1.00
178_S	242_D	0.765	1.00
83_G	87_T	0.765	1.00
172_R	265_K	0.758	1.00
237_S	242_D	0.754	1.00
84_L	87_T	0.747	1.00
153_I	296_L	0.747	1.00
208_V	227_R	0.746	1.00
211_I	215_I	0.746	1.00
209_D	213_M	0.745	1.00
151_L	292_F	0.744	1.00
24_H	30_A	0.742	1.00
66_P	71_L	0.738	1.00
145_V	163_V	0.738	1.00
121_R	242_D	0.737	1.00
86_Q	90_I	0.736	1.00
189_T	267_E	0.735	1.00
25_L	63_G	0.733	1.00
287_L	291_R	0.728	1.00
184_I	262_K	0.727	1.00
252_Y	256_R	0.727	1.00
177_C	183_R	0.726	1.00
65_A	71_L	0.726	1.00
176_I	247_V	0.726	1.00
69_T	72_N	0.724	1.00
256_R	263_E	0.722	1.00
14_L	17_I	0.721	1.00
77_L	80_N	0.718	1.00
101_I	149_A	0.717	1.00
248_P	251_L	0.716	1.00
177_C	262_K	0.714	1.00
176_I	256_R	0.712	1.00
120_L	291_R	0.710	1.00
84_L	88_I	0.709	1.00
194_M	220_M	0.709	1.00
172_R	270_L	0.705	1.00
40_A	44_S	0.705	1.00
104_G	109_S	0.698	1.00
16_V	20_C	0.697	1.00
27_I	41_V	0.695	1.00
58_I	67_T	0.695	1.00
195_A	223_K	0.695	1.00
178_S	181_H	0.694	1.00
191_E	218_R	0.686	1.00
214_E	217_E	0.684	1.00
209_D	214_E	0.684	1.00
87_T	91_V	0.681	1.00
21_I	41_V	0.680	1.00
124_S	291_R	0.680	1.00
187_N	265_K	0.679	1.00
58_I	63_G	0.677	1.00
230_S	233_T	0.677	1.00
226_F	237_S	0.675	1.00
69_T	73_L	0.674	1.00
49_R	54_D	0.672	1.00
239_A	258_F	0.669	1.00
104_G	113_N	0.669	1.00
82_R	85_E	0.669	1.00
213_M	217_E	0.668	1.00
101_I	150_D	0.667	1.00
77_L	81_L	0.665	1.00
211_I	214_E	0.664	1.00
78_E	82_R	0.663	1.00
201_L	234_I	0.663	1.00
254_S	257_D	0.662	1.00
212_Q	216_D	0.661	1.00
100_F	288_V	0.661	1.00
86_Q	89_N	0.657	1.00
202_I	227_R	0.653	1.00
213_M	216_D	0.653	1.00
175_L	193_I	0.652	1.00
73_L	91_V	0.651	1.00
129_E	227_R	0.650	1.00
68_T	72_N	0.648	1.00
150_D	289_F	0.646	1.00
144_L	278_S	0.646	1.00
71_L	74_H	0.645	1.00
180_R	262_K	0.644	1.00
180_R	183_R	0.644	1.00
27_I	63_G	0.640	1.00
45_L	49_R	0.638	1.00
49_R	59_R	0.636	1.00
30_A	34_L	0.635	1.00
32_E	35_Y	0.632	1.00
147_R	280_N	0.628	1.00
97_K	129_E	0.628	1.00
13_N	47_R	0.626	1.00
189_T	268_H	0.617	1.00
169_H	275_L	0.612	1.00
215_I	222_R	0.611	1.00
180_R	241_T	0.611	1.00
21_I	26_S	0.609	1.00
76_H	80_N	0.608	1.00
134_L	229_S	0.607	1.00
164_I	282_S	0.607	1.00
16_V	19_E	0.607	1.00
110_C	236_N	0.605	1.00
198_F	244_L	0.605	1.00
179_N	259_L	0.605	1.00
113_N	116_L	0.601	1.00
283_S	286_N	0.600	1.00
291_R	295_R	0.599	1.00
212_Q	215_I	0.595	1.00
292_F	296_L	0.593	1.00
182_P	185_T	0.592	1.00
187_N	192_Q	0.592	1.00
134_L	230_S	0.591	1.00
183_R	188_S	0.590	1.00
66_P	74_H	0.590	1.00
72_N	91_V	0.589	1.00
98_K	125_S	0.588	1.00
89_N	93_K	0.587	1.00
144_L	163_V	0.587	1.00
175_L	198_F	0.586	1.00
210_D	214_E	0.586	1.00
234_I	238_I	0.586	1.00
287_L	290_S	0.586	1.00
100_F	151_L	0.584	1.00
237_S	243_L	0.580	1.00
52_F	91_V	0.579	1.00
151_L	293_I	0.576	1.00
173_N	246_I	0.575	1.00
98_K	127_E	0.574	1.00
208_V	214_E	0.573	1.00
171_I	273_I	0.571	1.00
175_L	246_I	0.570	1.00
210_D	213_M	0.570	1.00
54_D	58_I	0.569	1.00
117_I	130_C	0.567	1.00
39_S	43_Q	0.566	1.00
139_N	143_L	0.563	1.00
57_F	66_P	0.559	1.00
52_F	73_L	0.558	1.00
202_I	229_S	0.556	1.00
13_N	17_I	0.553	1.00
75_H	90_I	0.552	1.00
140_A	147_R	0.551	1.00
40_A	43_Q	0.551	1.00
155_Q	273_I	0.549	1.00
16_V	81_L	0.549	1.00
37_T	43_Q	0.549	1.00
228_G	233_T	0.549	1.00
108_I	112_N	0.543	1.00
81_L	84_L	0.542	1.00
45_L	57_F	0.540	1.00
181_H	244_L	0.539	1.00
279_Y	290_S	0.539	1.00
115_M	118_R	0.536	1.00
247_V	252_Y	0.536	1.00
194_M	221_N	0.535	1.00
266_L	269_P	0.535	1.00
115_M	119_C	0.535	1.00
52_F	55_P	0.533	1.00
125_S	128_I	0.531	1.00
203_S	227_R	0.531	1.00
77_L	84_L	0.530	1.00
81_L	85_E	0.530	1.00
11_D	51_Q	0.529	1.00
177_C	184_I	0.526	1.00
153_I	277_I	0.525	1.00
17_I	45_L	0.522	1.00
142_E	148_K	0.522	1.00
103_Y	133_I	0.520	1.00
289_F	293_I	0.518	1.00
168_L	277_I	0.518	1.00
76_H	91_V	0.518	1.00
231_L	248_P	0.514	1.00
156_M	165_C	0.511	1.00
110_C	230_S	0.510	1.00
93_K	96_L	0.510	1.00
122_Q	184_I	0.510	1.00
80_N	88_I	0.505	1.00
91_V	94_S	0.504	1.00
27_I	38_P	0.504	1.00
27_I	59_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
2esnA	3	0.9833	100	0.083	Contact Map
1uthA	2	0.73	100	0.087	Contact Map
3fxqA	3	0.9667	100	0.103	Contact Map
3fzvA	4	0.9467	100	0.109	Contact Map
2h98A	2	0.6667	100	0.119	Contact Map
1al3A	1	0.68	100	0.12	Contact Map
1ixcA	4	0.9567	100	0.12	Contact Map
4x6gA	4	0.98	100	0.122	Contact Map
2h9bA	2	0.6667	100	0.123	Contact Map
3szpA	3	0.9533	100	0.128	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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