YYBE - BACSU - GREMLIN Contacts

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YYBE - Uncharacterized HTH-type transcriptional regulator YybE

UniProt:	P37499	Sequences: MEWEQLEYFQTLARMQHVTKAAKSLSITQPALSRSIARLENHLGVPLFDRQGRSISLNQYGHIFLRRVQAMMKEYTEGKEEIQALLKPDQGVVSLGFLHTLGTTLVPDLIGSFQQEYPNISFQLKQNHSYWLLERLKSGDLDLCLLASIKPENPIQWIKLWSEELFVFVPNDHPLASRESITLNEIAGERFILLKKGYALRMTVDELFEKANIQPNIMFEGEEATTAAGFVAAGLGISILPDLKGLDQSKITKIRVSWPECQRVIGIAWIKGRFLSPVAETFKQYVISHFSE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	292 (283)
Sequences:	79635 (58064)
Seq/√Len:	3451.5

ECOLI - CYNR OXYR CYSB LYSR YBHD AAER CBL YNFL NAC HCAR TDCA YFER PGRR ABGR LEUO YEIE YAFC YHJC ILVY TTDR YFIE YDCI YCAN DMLR XAPR DSDC METR NHAR YBDO YDHB YEEY YNEJ YAHB ALLS ICIA YIDZ YBEF GCVA YIAU YGFI YHAJ YJIE HDFR LRHA PERR
BACSU - YYBE CYSL YWBI YCGK GLTC YTLI ALSR BSDA CITR YVBU GLTR YWQM YUST YOFA YXJO 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
70_A	74_E	3.608	1.00
15_M	24_S	3.394	1.00
158_I	287_I	2.682	1.00
96_G	141_L	2.563	1.00
67_R	81_E	2.439	1.00
11_T	24_S	2.291	1.00
231_V	238_S	2.255	1.00
159_K	162_S	2.234	1.00
162_S	264_V	2.223	1.00
92_V	123_Q	2.205	1.00
173_H	189_E	2.192	1.00
164_E	242_D	2.176	1.00
159_K	264_V	2.133	1.00
92_V	121_S	2.110	1.00
20_K	23_K	2.096	1.00
45_V	60_Y	2.072	1.00
182_T	185_E	2.060	1.00
8_Y	35_S	2.054	1.00
162_S	262_Q	2.034	1.00
14_R	69_Q	2.031	1.00
232_A	250_K	2.016	1.00
112_S	285_Y	2.012	1.00
10_Q	65_L	1.974	1.00
67_R	74_E	1.973	1.00
10_Q	69_Q	1.965	1.00
94_S	123_Q	1.960	1.00
10_Q	14_R	1.915	1.00
11_T	14_R	1.907	1.00
11_T	15_M	1.886	1.00
192_I	236_G	1.883	1.00
166_F	242_D	1.876	1.00
8_Y	32_L	1.864	1.00
169_V	254_I	1.863	1.00
71_M	75_Y	1.862	1.00
228_A	245_G	1.853	1.00
13_A	57_L	1.846	1.00
65_L	69_Q	1.832	1.00
18_V	36_I	1.748	1.00
49_D	56_S	1.742	1.00
190_R	218_M	1.733	1.00
64_F	78_G	1.704	1.00
166_F	253_K	1.694	1.00
63_I	81_E	1.676	1.00
157_W	266_G	1.670	1.00
135_R	140_D	1.644	1.00
232_A	245_G	1.629	1.00
13_A	65_L	1.608	1.00
15_M	20_K	1.589	1.00
14_R	24_S	1.581	1.00
113_F	282_F	1.580	1.00
156_Q	271_K	1.578	1.00
10_Q	68_V	1.567	1.00
178_R	185_E	1.564	1.00
9_F	65_L	1.544	1.00
88_P	119_N	1.539	1.00
8_Y	27_I	1.528	1.00
134_E	138_S	1.517	1.00
19_T	29_Q	1.483	1.00
5_Q	35_S	1.482	1.00
5_Q	42_H	1.474	1.00
158_I	269_W	1.474	1.00
113_F	120_I	1.472	1.00
201_R	205_D	1.470	1.00
59_Q	62_H	1.465	1.00
67_R	70_A	1.462	1.00
17_H	20_K	1.456	1.00
46_P	49_D	1.454	1.00
28_T	31_A	1.447	1.00
5_Q	38_R	1.446	1.00
11_T	25_L	1.440	1.00
156_Q	269_W	1.407	1.00
146_L	268_A	1.395	1.00
10_Q	72_M	1.391	1.00
67_R	77_E	1.388	1.00
283_K	287_I	1.388	1.00
103_T	225_T	1.378	1.00
148_S	266_G	1.375	1.00
275_L	279_A	1.372	1.00
171_N	250_K	1.368	1.00
90_Q	119_N	1.349	1.00
71_M	78_G	1.347	1.00
269_W	283_K	1.345	1.00
137_K	154_P	1.340	1.00
94_S	125_K	1.336	1.00
136_L	144_C	1.318	1.00
51_Q	56_S	1.316	1.00
135_R	141_L	1.313	1.00
281_T	284_Q	1.312	1.00
267_I	283_K	1.309	1.00
143_L	279_A	1.302	1.00
112_S	116_E	1.299	1.00
64_F	79_K	1.298	1.00
143_L	267_I	1.278	1.00
42_H	79_K	1.278	1.00
169_V	237_I	1.269	1.00
74_E	77_E	1.268	1.00
189_E	237_I	1.253	1.00
3_W	75_Y	1.251	1.00
114_Q	218_M	1.250	1.00
227_A	238_S	1.242	1.00
66_R	70_A	1.241	1.00
116_E	285_Y	1.238	1.00
229_G	232_A	1.232	1.00
114_Q	190_R	1.214	1.00
67_R	78_G	1.213	1.00
63_I	66_R	1.205	1.00
159_K	266_G	1.199	1.00
37_A	41_N	1.197	1.00
171_N	252_T	1.196	1.00
111_G	115_Q	1.189	1.00
62_H	66_R	1.188	1.00
9_F	48_F	1.178	1.00
242_D	253_K	1.172	1.00
245_G	250_K	1.164	1.00
157_W	268_A	1.160	1.00
27_I	31_A	1.159	1.00
179_E	252_T	1.153	1.00
174_P	189_E	1.145	1.00
111_G	233_A	1.141	1.00
123_Q	220_E	1.134	1.00
34_R	38_R	1.128	1.00
9_F	13_A	1.126	1.00
112_S	115_Q	1.124	1.00
127_N	135_R	1.108	1.00
190_R	216_N	1.106	1.00
180_S	257_S	1.105	1.00
34_R	37_A	1.100	1.00
9_F	47_L	1.097	1.00
192_I	227_A	1.093	1.00
208_F	213_I	1.090	1.00
33_S	37_A	1.090	1.00
284_Q	287_I	1.090	1.00
117_Y	281_T	1.089	1.00
93_V	282_F	1.089	1.00
102_G	126_Q	1.083	1.00
113_F	285_Y	1.078	1.00
70_A	77_E	1.077	1.00
221_G	227_A	1.076	1.00
168_F	253_K	1.073	1.00
18_V	55_I	1.068	1.00
6_L	68_V	1.063	1.00
108_D	233_A	1.060	1.00
71_M	74_E	1.059	1.00
12_L	21_A	1.057	1.00
63_I	67_R	1.055	1.00
246_L	249_S	1.055	1.00
11_T	21_A	1.055	1.00
270_I	273_R	1.053	1.00
280_E	284_Q	1.049	1.00
137_K	152_E	1.045	1.00
7_E	76_T	1.042	1.00
181_I	185_E	1.041	1.00
253_K	256_V	1.038	1.00
35_S	38_R	1.028	1.00
229_G	233_A	1.027	1.00
158_I	283_K	1.027	1.00
228_A	232_A	1.026	1.00
170_P	234_G	1.025	1.00
4_E	7_E	1.018	1.00
79_K	83_Q	1.012	1.00
183_L	258_W	1.009	1.00
57_L	61_G	1.007	1.00
109_L	286_V	1.007	1.00
202_M	205_D	1.001	1.00
244_K	248_Q	0.999	1.00
167_V	237_I	0.999	1.00
163_E	243_L	0.986	1.00
164_E	262_Q	0.980	1.00
76_T	80_E	0.980	1.00
76_T	79_K	0.975	1.00
27_I	32_L	0.970	1.00
13_A	48_F	0.965	1.00
64_F	68_V	0.965	1.00
8_Y	25_L	0.964	1.00
73_K	77_E	0.962	1.00
12_L	18_V	0.958	1.00
202_M	206_E	0.954	1.00
193_L	217_I	0.951	1.00
135_R	138_S	0.938	1.00
169_V	173_H	0.938	1.00
125_K	135_R	0.938	1.00
113_F	117_Y	0.937	1.00
9_F	57_L	0.935	1.00
173_H	176_A	0.931	1.00
109_L	285_Y	0.927	1.00
116_E	288_S	0.922	1.00
21_A	32_L	0.922	1.00
221_G	230_F	0.920	1.00
38_R	41_N	0.919	1.00
276_S	279_A	0.918	1.00
9_F	39_L	0.912	1.00
96_G	144_C	0.907	1.00
48_F	55_I	0.904	1.00
20_K	24_S	0.901	1.00
63_I	85_L	0.899	1.00
177_S	190_R	0.897	1.00
45_V	82_I	0.894	1.00
121_S	216_N	0.891	1.00
285_Y	288_S	0.886	1.00
173_H	190_R	0.885	1.00
141_L	144_C	0.879	1.00
66_R	69_Q	0.874	1.00
13_A	61_G	0.865	1.00
120_I	278_V	0.863	1.00
70_A	73_K	0.863	1.00
154_P	271_K	0.861	1.00
16_Q	56_S	0.860	1.00
99_H	223_E	0.855	1.00
96_G	146_L	0.853	1.00
174_P	179_E	0.851	1.00
169_V	174_P	0.848	1.00
133_L	137_K	0.848	1.00
19_T	23_K	0.847	1.00
190_R	217_I	0.843	1.00
51_Q	54_S	0.842	1.00
155_I	268_A	0.837	1.00
25_L	32_L	0.834	1.00
185_E	188_G	0.833	1.00
148_S	264_V	0.832	1.00
95_L	143_L	0.826	1.00
245_G	248_Q	0.820	1.00
168_F	238_S	0.820	1.00
60_Y	85_L	0.819	1.00
125_K	141_L	0.818	1.00
156_Q	159_K	0.815	1.00
284_Q	288_S	0.812	1.00
9_F	64_F	0.809	1.00
91_G	278_V	0.807	1.00
207_L	211_A	0.807	1.00
275_L	280_E	0.806	1.00
191_F	215_P	0.806	1.00
184_N	187_A	0.803	1.00
60_Y	82_I	0.802	1.00
111_G	235_L	0.793	1.00
16_Q	62_H	0.793	1.00
13_A	16_Q	0.791	1.00
204_V	208_F	0.789	1.00
4_E	35_S	0.787	1.00
172_D	176_A	0.785	1.00
175_L	189_E	0.785	1.00
37_A	46_P	0.783	1.00
29_Q	33_S	0.780	1.00
75_Y	79_K	0.778	1.00
14_R	65_L	0.776	1.00
164_E	260_E	0.773	1.00
60_Y	63_I	0.771	1.00
74_E	78_G	0.771	1.00
75_Y	78_G	0.769	1.00
3_W	72_M	0.769	1.00
77_E	81_E	0.769	1.00
114_Q	235_L	0.769	1.00
16_Q	54_S	0.762	1.00
182_T	257_S	0.761	1.00
277_P	281_T	0.761	1.00
164_E	255_R	0.758	1.00
12_L	36_I	0.755	1.00
15_M	21_A	0.755	1.00
12_L	48_F	0.755	1.00
170_P	235_L	0.754	1.00
89_D	117_Y	0.753	1.00
91_G	120_I	0.752	1.00
143_L	282_F	0.751	1.00
232_A	248_Q	0.748	1.00
230_F	235_L	0.745	1.00
116_E	281_T	0.743	1.00
5_Q	8_Y	0.736	1.00
207_L	210_K	0.735	1.00
7_E	11_T	0.733	1.00
83_Q	86_L	0.732	1.00
206_E	210_K	0.730	1.00
68_V	71_M	0.726	1.00
137_K	155_I	0.724	1.00
113_F	281_T	0.719	1.00
56_S	62_H	0.717	1.00
170_P	173_H	0.716	1.00
168_F	240_L	0.716	1.00
78_G	82_I	0.715	1.00
18_V	32_L	0.713	1.00
49_D	58_N	0.713	1.00
173_H	177_S	0.712	1.00
31_A	35_S	0.711	1.00
244_K	247_D	0.709	1.00
57_L	62_H	0.709	1.00
97_F	102_G	0.708	1.00
69_Q	73_K	0.708	1.00
223_E	226_T	0.707	1.00
94_S	141_L	0.705	1.00
12_L	32_L	0.700	1.00
184_N	211_A	0.696	1.00
273_R	276_S	0.696	1.00
60_Y	64_F	0.694	1.00
176_A	252_T	0.694	1.00
203_T	207_L	0.692	1.00
187_A	213_I	0.691	1.00
169_V	252_T	0.689	1.00
139_G	270_I	0.681	1.00
62_H	65_L	0.681	1.00
195_K	220_E	0.678	1.00
94_S	142_D	0.678	1.00
188_G	216_N	0.670	1.00
59_Q	63_I	0.669	1.00
49_D	54_S	0.667	1.00
206_E	209_E	0.667	1.00
281_T	285_Y	0.666	1.00
40_E	45_V	0.665	1.00
205_D	209_E	0.665	1.00
180_S	255_R	0.663	1.00
172_D	175_L	0.663	1.00
112_S	288_S	0.660	1.00
168_F	246_L	0.659	1.00
64_F	82_I	0.657	1.00
142_D	279_A	0.656	1.00
73_K	76_T	0.656	1.00
201_R	220_E	0.656	1.00
219_F	230_F	0.655	1.00
145_L	286_V	0.653	1.00
246_L	253_K	0.651	1.00
169_V	175_L	0.650	1.00
77_E	80_E	0.647	1.00
97_F	106_V	0.645	1.00
204_V	207_L	0.643	1.00
172_D	234_G	0.643	1.00
7_E	10_Q	0.642	1.00
194_L	227_A	0.640	1.00
172_D	252_T	0.638	1.00
93_V	278_V	0.638	1.00
68_V	72_M	0.637	1.00
191_F	237_I	0.636	1.00
40_E	50_R	0.634	1.00
23_K	26_S	0.633	1.00
103_T	229_G	0.631	1.00
182_T	258_W	0.628	1.00
67_R	71_M	0.626	1.00
121_S	220_E	0.626	1.00
36_I	40_E	0.625	1.00
99_H	128_H	0.622	1.00
167_V	186_I	0.620	1.00
171_N	249_S	0.619	1.00
126_Q	222_E	0.617	1.00
161_W	265_I	0.614	1.00
21_A	25_L	0.613	1.00
136_L	268_A	0.611	1.00
18_V	54_S	0.610	1.00
90_Q	121_S	0.610	1.00
277_P	280_E	0.609	1.00
4_E	38_R	0.604	1.00
208_F	215_P	0.602	1.00
202_M	207_L	0.601	1.00
12_L	17_H	0.601	1.00
245_G	249_S	0.600	1.00
106_V	109_L	0.599	1.00
80_E	84_A	0.595	1.00
93_V	143_L	0.594	1.00
282_F	286_V	0.590	1.00
195_K	222_E	0.589	1.00
63_I	82_I	0.589	1.00
108_D	111_G	0.584	1.00
203_T	206_E	0.583	1.00
143_L	283_K	0.582	1.00
156_Q	272_G	0.581	1.00
7_E	72_M	0.580	1.00
147_A	263_R	0.579	1.00
31_A	34_R	0.579	1.00
200_L	204_V	0.579	1.00
96_G	127_N	0.576	1.00
48_F	57_L	0.572	1.00
221_G	226_T	0.570	1.00
167_V	239_I	0.568	1.00
269_W	280_E	0.568	1.00
57_L	65_L	0.568	1.00
30_P	34_R	0.568	1.00
230_F	236_G	0.567	1.00
43_L	64_F	0.567	1.00
4_E	8_Y	0.567	1.00
108_D	112_S	0.564	1.00
167_V	191_F	0.564	1.00
45_V	49_D	0.564	1.00
43_L	82_I	0.563	1.00
136_L	155_I	0.563	1.00
227_A	231_V	0.562	1.00
165_L	239_I	0.561	1.00
126_Q	223_E	0.561	1.00
163_E	263_R	0.558	1.00
175_L	181_I	0.555	1.00
110_I	122_F	0.554	1.00
28_T	34_R	0.549	1.00
175_L	178_R	0.546	1.00
101_L	105_L	0.546	1.00
96_G	125_K	0.546	1.00
174_P	178_R	0.545	1.00
205_D	208_F	0.545	1.00
117_Y	120_I	0.543	1.00
9_F	61_G	0.543	1.00
201_R	207_L	0.541	1.00
72_M	76_T	0.540	1.00
173_H	237_I	0.536	1.00
196_K	220_E	0.536	1.00
160_L	267_I	0.534	1.00
43_L	46_P	0.532	1.00
8_Y	36_I	0.530	1.00
201_R	204_V	0.529	1.00
66_R	81_E	0.528	1.00
18_V	29_Q	0.527	1.00
180_S	185_E	0.525	1.00
91_G	119_N	0.525	1.00
115_Q	176_A	0.522	1.00
84_A	89_D	0.522	1.00
72_M	75_Y	0.522	1.00
224_A	241_P	0.520	1.00
103_T	223_E	0.520	1.00
184_N	213_I	0.517	1.00
46_P	60_Y	0.515	1.00
244_K	249_S	0.515	1.00
169_V	176_A	0.515	1.00
27_I	35_S	0.513	1.00
8_Y	21_A	0.511	1.00
105_L	109_L	0.510	1.00
279_A	283_K	0.509	1.00
16_Q	55_I	0.508	1.00
145_L	267_I	0.507	1.00
148_S	157_W	0.505	1.00
67_R	82_I	0.504	1.00
13_A	62_H	0.501	1.00
80_E	83_Q	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
1ixcA	4	0.9966	100	0.074	Contact Map
2h98A	2	0.6918	100	0.075	Contact Map
1al3A	1	0.7089	100	0.075	Contact Map
2esnA	3	0.9932	100	0.076	Contact Map
1uthA	2	0.7534	100	0.079	Contact Map
2h9bA	2	0.6918	100	0.08	Contact Map
3fxqA	3	0.9897	100	0.081	Contact Map
4x6gA	4	1	100	0.081	Contact Map
3fzvA	4	0.9726	100	0.083	Contact Map
3szpA	3	0.9829	100	0.103	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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