YOAU - BACSU - GREMLIN Contacts

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YOAU - Uncharacterized HTH-type transcriptional regulator YoaU

UniProt:	O34701	Sequences: MVMNMNHLHIFVKVGEKLNITEAAKELFISQPAVSKAIKNLESSLQLKLLIRDKHHGLMLTDIGKEILLLARQMKGIESKIYQVANRENKLLNGKVKIGSFPAVSTNIMPQAIAAFRSNYPLIRIELIEGTSDQIKGWVEDRTVDIGIAASPFEPFENQLLCNDYMVAVIPPQRDELKLEKHVDLETYQDDLIFCKGGHEIAMSNAFSQYNIELKENLTVQNAETLINMVKNNLGIGIISNFTLSSVPHQLIKKDIFPRVTRDIGVIAHSFEEITPAAHEFVKVLKAVVI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	290 (278)
Sequences:	79351 (57706)
Seq/√Len:	3460.9

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
73_Q	77_I	3.743	1.00
17_K	26_E	3.419	1.00
13_K	26_E	2.690	1.00
70_L	84_V	2.587	1.00
159_Q	286_K	2.580	1.00
160_L	263_D	2.412	1.00
99_G	144_V	2.376	1.00
47_L	63_I	2.338	1.00
12_V	72_R	2.305	1.00
95_K	126_E	2.251	1.00
160_L	163_N	2.216	1.00
163_N	263_D	2.212	1.00
12_V	16_E	2.196	1.00
167_V	241_N	2.189	1.00
10_I	37_A	2.161	1.00
70_L	77_I	2.159	1.00
13_K	17_K	2.122	1.00
95_K	124_R	2.092	1.00
97_K	126_E	2.031	1.00
165_Y	241_N	2.005	1.00
230_V	237_G	2.005	1.00
115_A	284_V	1.989	1.00
163_N	261_T	1.982	1.00
15_G	60_L	1.969	1.00
74_M	78_E	1.936	1.00
227_I	247_V	1.924	1.00
10_I	34_V	1.880	1.00
68_L	72_R	1.879	1.00
13_K	16_E	1.878	1.00
184_D	187_T	1.872	1.00
16_E	72_R	1.855	1.00
15_G	68_L	1.845	1.00
22_E	25_K	1.829	1.00
12_V	68_L	1.816	1.00
231_K	247_V	1.738	1.00
66_E	84_V	1.729	1.00
70_L	73_Q	1.718	1.00
158_N	265_G	1.712	1.00
191_D	217_N	1.701	1.00
17_K	22_E	1.689	1.00
193_I	235_G	1.679	1.00
51_I	59_M	1.660	1.00
19_N	22_E	1.637	1.00
138_W	143_T	1.636	1.00
67_I	81_I	1.595	1.00
159_Q	268_A	1.561	1.00
7_H	44_S	1.526	1.00
12_V	71_A	1.518	1.00
7_H	40_N	1.507	1.00
77_I	80_K	1.501	1.00
70_L	80_K	1.499	1.00
106_T	224_E	1.498	1.00
53_D	59_M	1.498	1.00
157_E	270_S	1.495	1.00
20_I	38_I	1.490	1.00
30_S	33_A	1.482	1.00
7_H	37_A	1.481	1.00
16_E	26_E	1.480	1.00
138_W	144_V	1.442	1.00
13_K	27_L	1.438	1.00
268_A	282_V	1.438	1.00
97_K	128_I	1.431	1.00
157_E	268_A	1.414	1.00
200_E	204_S	1.410	1.00
149_A	267_I	1.403	1.00
137_G	141_D	1.398	1.00
119_N	284_V	1.392	1.00
69_L	73_Q	1.383	1.00
167_V	255_D	1.382	1.00
116_F	123_I	1.380	1.00
48_K	51_I	1.378	1.00
74_M	81_I	1.376	1.00
282_V	286_K	1.370	1.00
116_F	281_F	1.366	1.00
274_I	278_A	1.357	1.00
139_V	147_G	1.354	1.00
11_F	68_L	1.351	1.00
91_L	122_L	1.342	1.00
266_V	282_V	1.341	1.00
5_M	78_E	1.333	1.00
70_L	81_I	1.321	1.00
160_L	265_G	1.319	1.00
21_T	31_Q	1.314	1.00
226_L	237_G	1.312	1.00
164_D	242_F	1.308	1.00
62_D	65_K	1.307	1.00
93_N	122_L	1.306	1.00
12_V	75_K	1.305	1.00
67_I	82_Y	1.298	1.00
280_E	283_K	1.294	1.00
228_N	231_K	1.288	1.00
4_N	7_H	1.284	1.00
29_I	33_A	1.279	1.00
66_E	70_L	1.273	1.00
54_K	57_G	1.273	1.00
10_I	29_I	1.267	1.00
146_I	266_V	1.264	1.00
114_A	232_N	1.261	1.00
180_E	187_T	1.260	1.00
36_K	40_N	1.257	1.00
170_I	236_I	1.253	1.00
115_A	119_N	1.231	1.00
146_I	278_A	1.230	1.00
117_R	217_N	1.222	1.00
170_I	254_K	1.211	1.00
201_I	205_N	1.207	1.00
66_E	69_L	1.207	1.00
130_G	138_W	1.201	1.00
114_A	118_S	1.197	1.00
111_Q	232_N	1.182	1.00
73_Q	80_K	1.175	1.00
172_P	252_I	1.169	1.00
11_F	15_G	1.165	1.00
8_L	71_A	1.160	1.00
44_S	82_Y	1.159	1.00
36_K	39_K	1.154	1.00
11_F	50_L	1.148	1.00
182_H	257_F	1.148	1.00
65_K	69_L	1.146	1.00
117_R	191_D	1.139	1.00
241_N	245_S	1.134	1.00
228_N	232_N	1.134	1.00
158_N	267_I	1.132	1.00
140_E	155_P	1.129	1.00
120_Y	280_E	1.113	1.00
181_K	254_K	1.111	1.00
183_V	187_T	1.111	1.00
151_S	265_G	1.107	1.00
13_K	23_A	1.107	1.00
251_L	255_D	1.102	1.00
159_Q	282_V	1.101	1.00
74_M	77_I	1.098	1.00
128_I	138_W	1.093	1.00
191_D	215_K	1.090	1.00
39_K	43_S	1.086	1.00
231_K	252_I	1.082	1.00
37_A	40_N	1.082	1.00
227_I	231_K	1.067	1.00
96_V	281_F	1.054	1.00
165_Y	261_T	1.049	1.00
78_E	82_Y	1.044	1.00
126_E	219_T	1.039	1.00
172_P	250_Q	1.033	1.00
171_P	233_N	1.032	1.00
35_S	39_K	1.026	1.00
105_S	129_E	1.025	1.00
279_H	283_K	1.024	1.00
82_Y	86_N	1.023	1.00
20_I	58_L	1.022	1.00
6_N	9_H	1.015	1.00
76_G	80_K	1.013	1.00
63_I	66_E	0.997	1.00
14_V	23_A	0.993	1.00
116_F	120_Y	0.989	1.00
116_F	284_V	0.983	1.00
115_A	118_S	0.975	1.00
170_I	174_R	0.975	1.00
67_I	71_A	0.970	1.00
9_H	79_S	0.966	1.00
241_N	255_D	0.959	1.00
73_Q	76_G	0.957	1.00
23_A	34_V	0.949	1.00
40_N	43_S	0.948	1.00
201_I	204_S	0.948	1.00
114_A	234_L	0.946	1.00
112_A	285_L	0.946	1.00
60_L	64_G	0.945	1.00
11_F	49_L	0.941	1.00
193_I	226_L	0.940	1.00
194_F	216_E	0.937	1.00
14_V	20_I	0.936	1.00
283_K	286_K	0.932	1.00
157_E	160_L	0.932	1.00
169_V	244_L	0.931	1.00
66_E	88_E	0.929	1.00
174_R	177_L	0.927	1.00
15_G	50_L	0.921	1.00
18_L	59_M	0.920	1.00
231_K	250_Q	0.917	1.00
29_I	34_V	0.913	1.00
220_V	226_L	0.912	1.00
11_F	41_L	0.910	1.00
22_E	26_E	0.909	1.00
200_E	206_A	0.907	1.00
168_A	236_I	0.902	1.00
206_A	210_Y	0.902	1.00
79_S	82_Y	0.900	1.00
78_E	81_I	0.898	1.00
275_T	278_A	0.895	1.00
80_K	84_V	0.894	1.00
10_I	27_L	0.891	1.00
138_W	141_D	0.891	1.00
207_F	212_I	0.889	1.00
69_L	72_R	0.886	1.00
220_V	229_M	0.884	1.00
6_N	37_A	0.882	1.00
53_D	57_G	0.881	1.00
102_P	222_N	0.881	1.00
247_V	250_Q	0.879	1.00
11_F	60_L	0.875	1.00
276_P	280_E	0.870	1.00
112_A	284_V	0.869	1.00
21_T	25_K	0.867	1.00
17_K	23_A	0.866	1.00
245_S	249_H	0.864	1.00
47_L	85_A	0.861	1.00
9_H	13_K	0.860	1.00
94_G	277_A	0.857	1.00
77_I	81_I	0.855	1.00
176_E	181_K	0.855	1.00
167_V	253_K	0.853	1.00
63_I	88_E	0.852	1.00
247_V	252_I	0.852	1.00
117_R	234_L	0.844	1.00
79_S	83_Q	0.842	1.00
18_L	57_G	0.842	1.00
9_H	12_V	0.840	1.00
15_G	18_L	0.838	1.00
98_I	146_I	0.837	1.00
136_K	140_E	0.836	1.00
16_E	68_L	0.831	1.00
174_R	178_K	0.830	1.00
14_V	50_L	0.829	1.00
99_G	147_G	0.829	1.00
65_K	68_L	0.824	1.00
248_P	251_L	0.822	1.00
269_H	272_E	0.816	1.00
151_S	263_D	0.816	1.00
174_R	191_D	0.814	1.00
165_Y	255_D	0.814	1.00
128_I	144_V	0.813	1.00
50_L	58_L	0.812	1.00
186_E	189_Q	0.812	1.00
81_I	85_A	0.811	1.00
173_Q	233_N	0.807	1.00
229_M	234_L	0.806	1.00
31_Q	35_S	0.803	1.00
63_I	85_A	0.802	1.00
14_V	38_I	0.801	1.00
274_I	279_H	0.800	1.00
171_P	174_R	0.798	1.00
27_L	34_V	0.797	1.00
171_P	234_L	0.795	1.00
14_V	34_V	0.793	1.00
165_Y	259_R	0.791	1.00
144_V	147_G	0.790	1.00
206_A	209_Q	0.789	1.00
99_G	149_A	0.788	1.00
202_A	205_N	0.784	1.00
222_N	225_T	0.783	1.00
246_S	250_Q	0.777	1.00
71_A	74_M	0.775	1.00
280_E	284_V	0.771	1.00
72_R	76_G	0.770	1.00
100_S	105_S	0.762	1.00
191_D	216_E	0.762	1.00
184_D	257_F	0.761	1.00
5_M	75_K	0.761	1.00
116_F	280_E	0.757	1.00
252_I	255_D	0.753	1.00
20_I	34_V	0.753	1.00
39_K	48_K	0.749	1.00
202_A	206_A	0.746	1.00
62_D	66_E	0.746	1.00
169_V	253_K	0.744	1.00
244_L	247_V	0.743	1.00
123_I	277_A	0.741	1.00
187_T	190_D	0.740	1.00
124_R	215_K	0.740	1.00
156_F	267_I	0.739	1.00
106_T	228_N	0.737	1.00
11_F	67_I	0.737	1.00
51_I	61_T	0.737	1.00
140_E	156_F	0.737	1.00
7_H	10_I	0.736	1.00
196_K	219_T	0.733	1.00
142_R	269_H	0.733	1.00
205_N	209_Q	0.732	1.00
145_D	278_A	0.731	1.00
203_M	206_A	0.730	1.00
9_H	75_K	0.730	1.00
111_Q	114_A	0.729	1.00
169_V	239_I	0.724	1.00
18_L	65_K	0.722	1.00
15_G	64_G	0.721	1.00
11_F	64_G	0.721	1.00
168_A	238_I	0.718	1.00
60_L	65_K	0.717	1.00
192_L	214_L	0.713	1.00
203_M	207_F	0.713	1.00
155_P	270_S	0.711	1.00
70_L	74_M	0.706	1.00
6_N	40_N	0.705	1.00
201_I	207_F	0.701	1.00
92_L	120_Y	0.698	1.00
204_S	208_S	0.696	1.00
146_I	281_F	0.692	1.00
179_L	191_D	0.692	1.00
86_N	89_N	0.691	1.00
97_K	145_D	0.689	1.00
176_E	180_E	0.689	1.00
15_G	65_K	0.687	1.00
174_R	236_I	0.687	1.00
94_G	123_I	0.685	1.00
169_V	237_G	0.682	1.00
174_R	179_L	0.682	1.00
25_K	28_F	0.681	1.00
33_A	37_A	0.670	1.00
244_L	248_P	0.666	1.00
272_E	275_T	0.665	1.00
53_D	56_H	0.665	1.00
51_I	57_G	0.664	1.00
170_I	176_E	0.663	1.00
189_Q	212_I	0.663	1.00
251_L	254_K	0.659	1.00
173_Q	178_K	0.655	1.00
63_I	67_I	0.655	1.00
59_M	65_K	0.652	1.00
169_V	248_P	0.645	1.00
67_I	85_A	0.644	1.00
201_I	206_A	0.642	1.00
75_K	79_S	0.641	1.00
276_P	279_H	0.641	1.00
119_N	280_E	0.639	1.00
124_R	219_T	0.636	1.00
218_L	229_M	0.635	1.00
109_M	112_A	0.634	1.00
80_K	83_Q	0.628	1.00
97_K	144_V	0.626	1.00
129_E	221_Q	0.625	1.00
42_E	52_R	0.624	1.00
205_N	208_S	0.623	1.00
192_L	236_I	0.621	1.00
150_A	262_R	0.620	1.00
45_L	67_I	0.613	1.00
281_F	285_L	0.609	1.00
139_V	156_F	0.609	1.00
177_L	180_E	0.609	1.00
195_C	226_L	0.608	1.00
240_S	243_T	0.606	1.00
146_I	282_V	0.606	1.00
196_K	221_Q	0.599	1.00
102_P	131_T	0.596	1.00
200_E	205_N	0.592	1.00
220_V	225_T	0.586	1.00
96_V	146_I	0.585	1.00
176_E	179_L	0.583	1.00
6_N	10_I	0.581	1.00
84_V	87_R	0.580	1.00
140_E	143_T	0.579	1.00
14_V	19_N	0.578	1.00
114_A	117_R	0.577	1.00
66_E	85_A	0.575	1.00
110_P	114_A	0.575	1.00
120_Y	123_I	0.573	1.00
108_I	112_A	0.571	1.00
111_Q	115_A	0.570	1.00
45_L	48_K	0.570	1.00
76_G	79_S	0.569	1.00
99_G	130_G	0.569	1.00
277_A	280_E	0.568	1.00
99_G	128_I	0.568	1.00
170_I	177_L	0.568	1.00
20_I	31_Q	0.567	1.00
93_N	124_R	0.564	1.00
23_A	27_L	0.563	1.00
166_M	238_I	0.563	1.00
83_Q	87_R	0.562	1.00
200_E	219_T	0.560	1.00
139_V	267_I	0.559	1.00
186_E	210_Y	0.556	1.00
100_S	109_M	0.554	1.00
173_Q	177_L	0.547	1.00
47_L	51_I	0.542	1.00
168_A	188_Y	0.541	1.00
100_S	127_L	0.540	1.00
45_L	85_A	0.538	1.00
50_L	60_L	0.537	1.00
168_A	192_L	0.535	1.00
268_A	279_H	0.535	1.00
278_A	282_V	0.534	1.00
48_K	63_I	0.533	1.00
224_E	228_N	0.531	1.00
192_L	195_C	0.530	1.00
279_H	282_V	0.530	1.00
8_L	67_I	0.530	1.00
94_G	122_L	0.530	1.00
111_Q	228_N	0.529	1.00
81_I	84_V	0.528	1.00
251_L	256_I	0.528	1.00
18_L	58_L	0.525	1.00
226_L	230_V	0.525	1.00
71_A	75_K	0.524	1.00
246_S	249_H	0.522	1.00
40_N	44_S	0.522	1.00
268_A	274_I	0.521	1.00
33_A	36_K	0.521	1.00
12_V	79_S	0.520	1.00
38_I	42_E	0.518	1.00
164_D	262_R	0.518	1.00
204_S	207_F	0.516	1.00
101_F	104_V	0.516	1.00
45_L	82_Y	0.515	1.00
83_Q	86_N	0.515	1.00
32_P	35_S	0.515	1.00
148_I	285_L	0.514	1.00
32_P	36_K	0.514	1.00
106_T	222_N	0.513	1.00
99_G	138_W	0.512	1.00
4_N	40_N	0.507	1.00
47_L	89_N	0.507	1.00
92_L	122_L	0.504	1.00
87_R	92_L	0.503	1.00
74_M	82_Y	0.501	1.00
207_F	210_Y	0.500	1.00
207_F	214_L	0.500	1.00
239_I	244_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
2esnA	3	0.9862	100	0.12	Contact Map
1ixcA	4	0.9828	100	0.122	Contact Map
2h98A	2	0.6759	100	0.128	Contact Map
2h9bA	2	0.6759	100	0.129	Contact Map
3fzvA	4	0.969	100	0.129	Contact Map
1uthA	2	0.7379	100	0.137	Contact Map
3fxqA	3	0.9828	100	0.138	Contact Map
1al3A	1	0.6931	100	0.138	Contact Map
4x6gA	4	0.9862	100	0.151	Contact Map
3hhgA	3	0.9828	100	0.152	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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