YKVZ - BACSU - GREMLIN Contacts

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YKVZ - Uncharacterized HTH-type transcriptional regulator YkvZ

UniProt:	O31690	Sequences: MANIKDIAEKAGVSVTTVSRVINNHPYVSEDKRKRVFEAMESLEYTRNIHAVHLSKGFSNMIGVVLPTVNLPYFAELIAGIADAAAESGVHLSLFQTNYEVQKEIFALSQLKQRQVDGLIFCSKALADEKLMEWEGPILLCQNSDNARFPTISIPHQEAFRNGLDYLIAKGHKKIAICLARKKGMNSHFRIKAYKEALEEIGEAFREDWVIEKAITINDGKALFHKWNTWKEKPTAIFVANDQVSAGLFLEAKNQRVSVPDELAILSVDNHEISQALGITTIDIQTREMGKQAFAILEKRIQGQPIERKVLDYRLIERSTV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	321 (316)
Sequences:	36516 (26315)
Seq/√Len:	1480.3

ECOLI - GALS GALR PURR ASCG RBSR LACI CYTR MALI GNTR CRA IDNR YCJW EBGR TRER TORT ALSB YTFQ RBSB XYLF LSRB YPHF ARAF DGAL XYLR
BACSU - YKVZ RBSR KDGR CCPA NTDR EXUR DEGA MSMR GANR YVDE ARAR CCPB RBSB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
157_Q	196_E	3.390	1.00
172_H	235_T	3.202	1.00
10_K	42_S	3.146	1.00
258_S	261_D	3.081	1.00
163_G	266_L	2.617	1.00
118_G	297_L	2.565	1.00
191_I	195_K	2.540	1.00
172_H	264_A	2.514	1.00
270_N	283_D	2.502	1.00
150_P	300_R	2.446	1.00
161_R	200_E	2.343	1.00
221_K	254_N	2.256	1.00
30_E	34_K	2.236	1.00
38_E	42_S	2.204	1.00
84_A	87_E	2.196	1.00
34_K	38_E	2.181	1.00
84_A	295_A	2.148	1.00
225_H	255_Q	2.094	1.00
168_I	201_I	2.063	1.00
161_R	196_E	2.055	1.00
292_Q	295_A	2.045	1.00
165_D	197_A	2.017	1.00
161_R	197_A	2.005	1.00
158_E	162_N	1.991	1.00
85_A	294_F	1.960	1.00
21_V	36_V	1.937	1.00
225_H	251_E	1.931	1.00
80_G	290_G	1.917	1.00
33_R	37_F	1.893	1.00
157_Q	192_K	1.880	1.00
165_D	169_A	1.880	1.00
160_F	164_L	1.876	1.00
159_A	268_V	1.874	1.00
22_I	40_M	1.845	1.00
229_T	255_Q	1.838	1.00
252_A	263_L	1.834	1.00
167_L	236_A	1.825	1.00
84_A	291_K	1.824	1.00
299_K	304_Q	1.823	1.00
5_K	15_V	1.814	1.00
220_G	247_G	1.811	1.00
160_F	238_F	1.766	1.00
283_D	314_R	1.766	1.00
83_D	287_R	1.745	1.00
165_D	201_I	1.739	1.00
278_G	319_S	1.725	1.00
164_L	194_Y	1.725	1.00
161_R	165_D	1.673	1.00
11_A	39_A	1.668	1.00
221_K	251_E	1.652	1.00
174_K	206_R	1.647	1.00
10_K	39_A	1.640	1.00
257_V	262_E	1.639	1.00
285_Q	288_E	1.639	1.00
224_F	248_L	1.614	1.00
63_G	116_V	1.613	1.00
177_I	240_A	1.607	1.00
176_A	234_P	1.605	1.00
292_Q	309_K	1.598	1.00
80_G	287_R	1.595	1.00
258_S	262_E	1.591	1.00
166_Y	170_K	1.590	1.00
239_V	248_L	1.580	1.00
162_N	313_Y	1.569	1.00
84_A	88_S	1.559	1.00
251_E	255_Q	1.536	1.00
174_K	233_K	1.516	1.00
141_C	293_A	1.516	1.00
37_F	41_E	1.515	1.00
192_K	196_E	1.501	1.00
158_E	161_R	1.491	1.00
155_P	158_E	1.473	1.00
88_S	298_E	1.471	1.00
168_I	197_A	1.469	1.00
211_I	226_K	1.459	1.00
21_V	40_M	1.452	1.00
166_Y	169_A	1.442	1.00
288_E	292_Q	1.441	1.00
7_I	39_A	1.438	1.00
251_E	254_N	1.432	1.00
37_F	40_M	1.421	1.00
270_N	318_R	1.397	1.00
189_F	192_K	1.389	1.00
288_E	291_K	1.386	1.00
84_A	294_F	1.370	1.00
60_N	117_D	1.368	1.00
195_K	199_E	1.366	1.00
129_E	133_E	1.357	1.00
224_F	237_I	1.351	1.00
164_L	168_I	1.345	1.00
166_Y	317_E	1.336	1.00
225_H	254_N	1.331	1.00
176_A	227_W	1.319	1.00
252_A	257_V	1.319	1.00
197_A	200_E	1.311	1.00
159_A	313_Y	1.300	1.00
221_K	225_H	1.300	1.00
164_L	193_A	1.289	1.00
10_K	43_L	1.287	1.00
160_F	193_A	1.287	1.00
221_K	250_L	1.281	1.00
174_K	235_T	1.278	1.00
298_E	302_Q	1.267	1.00
5_K	9_E	1.265	1.00
295_A	299_K	1.263	1.00
164_L	197_A	1.262	1.00
206_R	209_W	1.258	1.00
60_N	90_V	1.257	1.00
29_S	32_K	1.248	1.00
30_E	33_R	1.247	1.00
214_A	219_D	1.245	1.00
172_H	236_A	1.244	1.00
62_I	85_A	1.242	1.00
6_D	9_E	1.232	1.00
193_A	197_A	1.232	1.00
224_F	252_A	1.227	1.00
63_G	111_L	1.227	1.00
20_R	25_H	1.222	1.00
225_H	229_T	1.215	1.00
7_I	11_A	1.215	1.00
35_R	39_A	1.215	1.00
249_F	265_I	1.215	1.00
162_N	165_D	1.204	1.00
95_F	107_A	1.198	1.00
120_I	293_A	1.195	1.00
226_K	230_W	1.194	1.00
157_Q	161_R	1.194	1.00
95_F	111_L	1.187	1.00
165_D	200_E	1.184	1.00
39_A	42_S	1.180	1.00
85_A	92_L	1.176	1.00
39_A	43_L	1.176	1.00
81_I	294_F	1.174	1.00
64_V	81_I	1.164	1.00
266_L	280_T	1.163	1.00
231_K	234_P	1.158	1.00
81_I	120_I	1.156	1.00
173_K	235_T	1.154	1.00
157_Q	189_F	1.152	1.00
7_I	43_L	1.144	1.00
32_K	35_R	1.136	1.00
287_R	291_K	1.133	1.00
4_I	15_V	1.128	1.00
218_N	222_A	1.124	1.00
194_Y	198_L	1.119	1.00
247_G	251_E	1.108	1.00
175_I	198_L	1.105	1.00
88_S	295_A	1.102	1.00
178_C	248_L	1.097	1.00
157_Q	193_A	1.084	1.00
48_N	54_L	1.082	1.00
196_E	200_E	1.082	1.00
64_V	92_L	1.081	1.00
170_K	317_E	1.078	1.00
237_I	248_L	1.076	1.00
38_E	41_E	1.075	1.00
4_I	18_V	1.075	1.00
109_S	130_K	1.069	1.00
61_M	91_H	1.066	1.00
163_G	238_F	1.064	1.00
177_I	191_I	1.061	1.00
290_G	294_F	1.060	1.00
21_V	28_V	1.059	1.00
198_L	203_E	1.055	1.00
292_Q	296_I	1.054	1.00
197_A	201_I	1.051	1.00
34_K	37_F	1.050	1.00
296_I	309_K	1.045	1.00
82_A	86_A	1.042	1.00
61_M	93_S	1.040	1.00
168_I	203_E	1.033	1.00
242_D	281_T	1.032	1.00
216_T	219_D	1.031	1.00
223_L	226_K	1.027	1.00
242_D	267_S	1.026	1.00
169_A	201_I	1.022	1.00
24_N	33_R	1.018	1.00
192_K	195_K	1.011	1.00
222_A	226_K	1.004	1.00
50_H	53_H	1.001	1.00
220_G	224_F	0.998	1.00
174_K	232_E	0.997	1.00
194_Y	238_F	0.994	1.00
105_I	109_S	0.994	1.00
239_V	244_V	0.989	1.00
239_V	245_S	0.985	1.00
291_K	295_A	0.980	1.00
88_S	302_Q	0.980	1.00
217_I	250_L	0.978	1.00
40_M	43_L	0.978	1.00
48_N	51_A	0.964	1.00
86_A	103_K	0.964	1.00
211_I	223_L	0.962	1.00
182_K	212_E	0.961	1.00
90_V	298_E	0.960	1.00
297_L	301_I	0.958	1.00
219_D	222_A	0.954	1.00
51_A	54_L	0.951	1.00
292_Q	311_L	0.948	1.00
249_F	277_L	0.947	1.00
188_H	192_K	0.936	1.00
224_F	228_N	0.935	1.00
158_E	312_D	0.932	1.00
163_G	282_I	0.931	1.00
175_I	236_A	0.930	1.00
150_P	296_I	0.930	1.00
170_K	264_A	0.928	1.00
87_E	291_K	0.927	1.00
11_A	18_V	0.922	1.00
249_F	259_V	0.917	1.00
314_R	317_E	0.899	1.00
285_Q	311_L	0.896	1.00
120_I	297_L	0.895	1.00
79_A	83_D	0.893	1.00
83_D	291_K	0.892	1.00
185_M	189_F	0.886	1.00
154_I	285_Q	0.881	1.00
164_L	198_L	0.880	1.00
47_R	52_V	0.876	1.00
168_I	173_K	0.876	1.00
24_N	37_F	0.871	1.00
183_K	188_H	0.862	1.00
242_D	270_N	0.860	1.00
81_I	290_G	0.859	1.00
257_V	263_L	0.857	1.00
180_A	215_I	0.854	1.00
174_K	209_W	0.853	1.00
151_T	308_R	0.853	1.00
62_I	120_I	0.852	1.00
176_A	237_I	0.851	1.00
64_V	78_I	0.849	1.00
155_P	310_V	0.848	1.00
228_N	251_E	0.846	1.00
152_I	296_I	0.845	1.00
103_K	106_F	0.844	1.00
78_I	82_A	0.843	1.00
252_A	265_I	0.843	1.00
267_S	281_T	0.837	1.00
222_A	225_H	0.835	1.00
158_E	313_Y	0.835	1.00
283_D	316_I	0.833	1.00
109_S	113_Q	0.833	1.00
195_K	205_F	0.831	1.00
21_V	37_F	0.824	1.00
237_I	263_L	0.821	1.00
81_I	92_L	0.817	1.00
73_Y	286_T	0.815	1.00
154_I	313_Y	0.811	1.00
118_G	301_I	0.809	1.00
155_P	312_D	0.808	1.00
296_I	299_K	0.807	1.00
112_K	134_W	0.806	1.00
31_D	34_K	0.802	1.00
213_K	244_V	0.801	1.00
233_K	257_V	0.799	1.00
130_K	133_E	0.797	1.00
167_L	266_L	0.797	1.00
209_W	230_W	0.794	1.00
59_S	117_D	0.793	1.00
196_E	199_E	0.793	1.00
173_K	203_E	0.792	1.00
166_Y	280_T	0.790	1.00
77_L	141_C	0.789	1.00
153_S	310_V	0.786	1.00
83_D	87_E	0.786	1.00
76_E	287_R	0.785	1.00
191_I	210_V	0.783	1.00
154_I	284_I	0.781	1.00
246_A	277_L	0.781	1.00
285_Q	314_R	0.781	1.00
253_K	278_G	0.780	1.00
156_H	190_R	0.776	1.00
13_V	36_V	0.776	1.00
17_T	20_R	0.774	1.00
294_F	298_E	0.773	1.00
198_L	205_F	0.772	1.00
80_G	291_K	0.770	1.00
153_S	308_R	0.770	1.00
129_E	132_M	0.768	1.00
219_D	223_L	0.764	1.00
49_I	52_V	0.763	1.00
61_M	114_R	0.761	1.00
270_N	316_I	0.758	1.00
224_F	227_W	0.758	1.00
80_G	84_A	0.756	1.00
178_C	239_V	0.755	1.00
67_P	74_F	0.753	1.00
100_E	103_K	0.753	1.00
16_T	20_R	0.742	1.00
31_D	35_R	0.741	1.00
235_T	264_A	0.740	1.00
166_Y	315_L	0.740	1.00
131_L	138_I	0.737	1.00
177_I	238_F	0.735	1.00
106_F	109_S	0.730	1.00
78_I	94_L	0.730	1.00
269_D	284_I	0.730	1.00
224_F	251_E	0.730	1.00
58_F	117_D	0.729	1.00
228_N	255_Q	0.728	1.00
179_L	191_I	0.724	1.00
20_R	26_P	0.722	1.00
93_S	116_V	0.719	1.00
20_R	27_Y	0.718	1.00
189_F	193_A	0.717	1.00
63_G	119_L	0.717	1.00
211_I	227_W	0.716	1.00
46_T	113_Q	0.716	1.00
238_F	266_L	0.714	1.00
242_D	245_S	0.713	1.00
79_A	82_A	0.711	1.00
245_S	267_S	0.707	1.00
162_N	282_I	0.705	1.00
270_N	274_S	0.705	1.00
62_I	294_F	0.703	1.00
230_W	234_P	0.703	1.00
102_Q	106_F	0.698	1.00
82_A	92_L	0.698	1.00
65_V	107_A	0.696	1.00
118_G	139_L	0.694	1.00
252_A	259_V	0.693	1.00
299_K	303_G	0.684	1.00
226_K	229_T	0.683	1.00
230_W	233_K	0.679	1.00
250_L	278_G	0.679	1.00
98_N	103_K	0.678	1.00
168_I	198_L	0.676	1.00
132_M	148_R	0.674	1.00
250_L	253_K	0.674	1.00
161_R	193_A	0.671	1.00
82_A	96_Q	0.670	1.00
278_G	318_R	0.666	1.00
103_K	107_A	0.665	1.00
211_I	230_W	0.662	1.00
34_K	41_E	0.662	1.00
58_F	302_Q	0.661	1.00
224_F	247_G	0.660	1.00
175_I	235_T	0.658	1.00
205_F	208_D	0.656	1.00
112_K	136_G	0.656	1.00
21_V	33_R	0.655	1.00
213_K	219_D	0.651	1.00
140_L	149_F	0.650	1.00
5_K	55_S	0.649	1.00
220_G	223_L	0.649	1.00
46_T	109_S	0.644	1.00
132_M	138_I	0.644	1.00
187_S	215_I	0.642	1.00
120_I	141_C	0.638	1.00
138_I	149_F	0.635	1.00
118_G	293_A	0.635	1.00
177_I	194_Y	0.633	1.00
274_S	281_T	0.632	1.00
132_M	149_F	0.631	1.00
27_Y	32_K	0.630	1.00
246_A	273_I	0.628	1.00
108_L	119_L	0.625	1.00
35_R	38_E	0.624	1.00
41_E	44_E	0.624	1.00
241_N	269_D	0.622	1.00
162_N	166_Y	0.622	1.00
176_A	209_W	0.621	1.00
252_A	255_Q	0.620	1.00
215_I	240_A	0.620	1.00
250_L	254_N	0.619	1.00
77_L	286_T	0.619	1.00
71_L	243_Q	0.618	1.00
18_V	21_V	0.613	1.00
175_I	194_Y	0.607	1.00
7_I	18_V	0.606	1.00
161_R	164_L	0.606	1.00
142_Q	156_H	0.604	1.00
76_E	286_T	0.604	1.00
79_A	287_R	0.602	1.00
18_V	40_M	0.599	1.00
287_R	290_G	0.599	1.00
167_L	238_F	0.599	1.00
215_I	244_V	0.598	1.00
280_T	315_L	0.597	1.00
180_A	187_S	0.596	1.00
205_F	210_V	0.595	1.00
90_V	301_I	0.593	1.00
80_G	286_T	0.593	1.00
93_S	114_R	0.592	1.00
13_V	32_K	0.591	1.00
156_H	189_F	0.589	1.00
300_R	303_G	0.589	1.00
139_L	300_R	0.588	1.00
249_F	253_K	0.587	1.00
217_I	273_I	0.586	1.00
241_N	244_V	0.582	1.00
142_Q	186_N	0.582	1.00
217_I	247_G	0.581	1.00
163_G	236_A	0.580	1.00
246_A	271_H	0.579	1.00
139_L	152_I	0.579	1.00
90_V	117_D	0.578	1.00
20_R	28_V	0.578	1.00
73_Y	77_L	0.578	1.00
218_N	221_K	0.576	1.00
195_K	210_V	0.575	1.00
238_F	268_V	0.573	1.00
195_K	207_E	0.571	1.00
194_Y	205_F	0.566	1.00
62_I	90_V	0.561	1.00
191_I	212_E	0.561	1.00
85_A	90_V	0.560	1.00
268_V	284_I	0.559	1.00
139_L	297_L	0.558	1.00
253_K	258_S	0.558	1.00
46_T	50_H	0.557	1.00
221_K	247_G	0.556	1.00
62_I	118_G	0.554	1.00
101_V	105_I	0.553	1.00
97_T	104_E	0.552	1.00
221_K	224_F	0.552	1.00
239_V	267_S	0.551	1.00
25_H	28_V	0.547	1.00
228_N	252_A	0.547	1.00
59_S	91_H	0.545	1.00
139_L	293_A	0.545	1.00
270_N	275_Q	0.545	1.00
296_I	300_R	0.544	1.00
18_V	36_V	0.544	1.00
242_D	271_H	0.544	1.00
111_L	116_V	0.543	1.00
166_Y	266_L	0.542	1.00
72_P	243_Q	0.541	1.00
119_L	136_G	0.541	1.00
112_K	115_Q	0.540	1.00
130_K	134_W	0.540	1.00
250_L	275_Q	0.539	1.00
52_V	56_K	0.538	1.00
62_I	301_I	0.534	1.00
95_F	110_Q	0.533	1.00
140_L	151_T	0.532	1.00
13_V	18_V	0.527	1.00
152_I	292_Q	0.525	1.00
234_P	257_V	0.525	1.00
259_V	262_E	0.524	1.00
85_A	298_E	0.524	1.00
61_M	117_D	0.524	1.00
223_L	227_W	0.522	1.00
280_T	317_E	0.522	1.00
84_A	298_E	0.521	1.00
76_E	272_E	0.521	1.00
129_E	134_W	0.521	1.00
187_S	240_A	0.520	1.00
139_L	296_I	0.519	1.00
53_H	56_K	0.518	1.00
154_I	159_A	0.518	1.00
184_G	187_S	0.518	1.00
11_A	21_V	0.515	1.00
178_C	223_L	0.515	1.00
16_T	25_H	0.515	1.00
275_Q	278_G	0.514	1.00
289_M	311_L	0.514	1.00
116_V	119_L	0.513	1.00
179_L	182_K	0.511	1.00
274_S	279_I	0.509	1.00
170_K	235_T	0.509	1.00
137_P	301_I	0.509	1.00
174_K	234_P	0.508	1.00
140_L	144_S	0.507	1.00
174_K	231_K	0.507	1.00
191_I	205_F	0.504	1.00
154_I	268_V	0.502	1.00
121_F	140_L	0.502	1.00
179_L	212_E	0.502	1.00
199_E	202_G	0.501	1.00
174_K	204_A	0.501	1.00
213_K	220_G	0.501	1.00
11_A	36_V	0.500	1.00
248_L	252_A	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
3dbiA	2	0.8255	100	0.081	Contact Map
3ctpA	2	0.8069	100	0.085	Contact Map
2hsgA	1	0.9907	100	0.091	Contact Map
3kjxA	2	1	100	0.096	Contact Map
1qpzA	2	0.9969	100	0.097	Contact Map
2o20A	2	0.8287	100	0.098	Contact Map
3e3mA	2	0.8069	100	0.105	Contact Map
4o5aA	2	0.8037	100	0.105	Contact Map
3h5oA	2	0.8131	100	0.106	Contact Map
1jyeA	2	0.81	100	0.106	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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