YBEF - ECOLI - GREMLIN Contacts

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YBEF - Uncharacterized HTH-type transcriptional regulator YbeF

UniProt:	P30979	Sequences: MDSNNQIEPCLSRKSSEGKPQIFTTLRNIDLNLLTIFEAVYVHKGIVNAAKVLNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAFAMHLHEYISQGLESILGALDIEGSYDKQRTITIATTPSVGALVLPVIYRAIKTHYPQLLLRNPPISDAENQLSQFQTDLIIDNMFCTNRTVQHHVLFTDNMVLICREGNPLLSLEDDRETIDNAAHVLLLPEEQNFSGLRQRVQEMFPDRQINFTSYNILTIAALVANSDMLAIIPSRFYNLFSRCWPLEKLPFPSLNEEQIDFSIHYNKFSLRDPILHGVIDVIRNAF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11594
Length:	317 (285)
Sequences:	78787 (57555)
Seq/√Len:	3409.3

ECOLI - YBEF YBDO LEUO YDCI PGRR DSDC OXYR YEIE LYSR YBHD CYSB YIDZ CYNR DMLR TDCA YAFC TTDR AAER NAC NHAR YFIE ABGR YHJC CBL YFER XAPR YCAN ICIA ILVY YNEJ GCVA HCAR METR YIAU YNFL YAHB YDHB YEEY YHAJ ALLS YGFI PERR YJIE LRHA HDFR
BACSU - CYSL YWBI YWQM YCGK GLTR GLTC BSDA YYBE CITR YVBU ALSR YTLI YUST YOFA CZCR YKUM YRAN YXJO 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
98_Q	102_S	3.745	1.00
43_H	52_V	3.418	1.00
39_A	52_V	2.636	1.00
95_Y	109_I	2.572	1.00
182_H	314_R	2.555	1.00
183_V	291_D	2.426	1.00
122_A	165_T	2.385	1.00
73_D	88_F	2.274	1.00
38_E	97_S	2.242	1.00
186_T	291_D	2.233	1.00
183_V	186_T	2.218	1.00
118_T	149_R	2.203	1.00
190_V	265_S	2.161	1.00
197_N	212_A	2.152	1.00
38_E	42_V	2.149	1.00
36_I	63_S	2.146	1.00
95_Y	102_S	2.132	1.00
39_A	43_H	2.083	1.00
118_T	147_L	2.080	1.00
254_V	261_A	2.079	1.00
188_N	265_S	2.030	1.00
186_T	289_Q	2.013	1.00
255_A	276_P	1.993	1.00
120_T	149_R	1.982	1.00
138_A	312_V	1.958	1.00
190_V	279_K	1.947	1.00
41_Y	85_P	1.937	1.00
205_D	208_T	1.925	1.00
39_A	42_V	1.917	1.00
99_G	103_I	1.913	1.00
251_A	271_F	1.898	1.00
36_I	60_I	1.890	1.00
48_N	51_K	1.885	1.00
42_V	97_S	1.879	1.00
93_H	97_S	1.866	1.00
38_E	93_H	1.852	1.00
255_A	271_F	1.827	1.00
215_V	259_M	1.813	1.00
41_Y	93_H	1.807	1.00
181_H	293_S	1.759	1.00
213_A	241_N	1.753	1.00
159_Q	164_Q	1.742	1.00
193_C	280_L	1.726	1.00
91_H	109_I	1.721	1.00
95_Y	98_Q	1.685	1.00
43_H	48_N	1.666	1.00
77_I	84_T	1.663	1.00
92_L	106_A	1.603	1.00
45_G	48_N	1.601	1.00
180_Q	298_K	1.579	1.00
182_H	296_Y	1.553	1.00
33_L	70_I	1.544	1.00
38_E	96_I	1.541	1.00
46_I	64_I	1.539	1.00
156_A	168_I	1.531	1.00
42_V	52_V	1.516	1.00
33_L	63_S	1.500	1.00
129_A	248_L	1.495	1.00
158_N	162_Q	1.493	1.00
33_L	66_K	1.493	1.00
56_T	59_A	1.473	1.00
79_K	84_T	1.469	1.00
296_Y	310_I	1.467	1.00
95_Y	105_G	1.464	1.00
102_S	105_G	1.454	1.00
180_Q	296_Y	1.443	1.00
39_A	53_L	1.431	1.00
170_D	295_H	1.413	1.00
172_M	293_S	1.411	1.00
159_Q	165_T	1.407	1.00
74_P	77_I	1.407	1.00
139_I	309_V	1.407	1.00
30_D	33_L	1.396	1.00
99_G	106_A	1.378	1.00
37_F	93_H	1.374	1.00
47_V	57_P	1.367	1.00
302_R	306_L	1.364	1.00
120_T	151_P	1.361	1.00
224_F	228_R	1.358	1.00
94_E	98_Q	1.358	1.00
294_I	310_I	1.350	1.00
139_I	146_L	1.343	1.00
142_H	312_V	1.335	1.00
36_I	55_L	1.333	1.00
250_I	261_A	1.329	1.00
183_V	293_S	1.326	1.00
271_F	276_P	1.321	1.00
310_I	314_R	1.320	1.00
38_E	100_L	1.318	1.00
92_L	107_L	1.317	1.00
95_Y	106_A	1.309	1.00
87_A	90_M	1.306	1.00
252_A	255_A	1.304	1.00
31_L	103_I	1.299	1.00
187_D	266_R	1.296	1.00
55_L	59_A	1.289	1.00
195_E	278_E	1.287	1.00
167_L	294_I	1.278	1.00
308_G	311_D	1.263	1.00
62_Q	66_K	1.259	1.00
212_A	260_L	1.250	1.00
140_K	241_N	1.245	1.00
167_L	306_L	1.245	1.00
137_R	256_N	1.245	1.00
193_C	260_L	1.242	1.00
116_Q	145_Q	1.242	1.00
195_E	276_P	1.226	1.00
138_A	142_H	1.225	1.00
161_S	178_T	1.219	1.00
91_H	94_E	1.215	1.00
91_H	95_Y	1.212	1.00
137_R	141_T	1.200	1.00
203_E	283_P	1.192	1.00
265_S	279_K	1.190	1.00
140_K	213_A	1.180	1.00
198_P	212_A	1.176	1.00
37_F	41_Y	1.175	1.00
134_V	256_N	1.169	1.00
98_Q	105_G	1.164	1.00
265_S	269_N	1.162	1.00
37_F	76_F	1.157	1.00
90_M	94_E	1.157	1.00
62_Q	65_Q	1.151	1.00
279_K	282_F	1.150	1.00
181_H	295_H	1.149	1.00
34_L	96_I	1.122	1.00
143_Y	308_G	1.101	1.00
252_A	256_N	1.099	1.00
204_D	208_T	1.095	1.00
153_I	159_Q	1.095	1.00
202_L	278_E	1.092	1.00
213_A	239_Q	1.092	1.00
63_S	66_K	1.087	1.00
182_H	310_I	1.087	1.00
65_Q	69_V	1.082	1.00
39_A	49_A	1.082	1.00
99_G	102_S	1.077	1.00
70_I	107_L	1.076	1.00
251_A	255_A	1.069	1.00
151_P	159_Q	1.066	1.00
192_I	279_K	1.064	1.00
46_I	83_V	1.050	1.00
188_N	289_Q	1.044	1.00
269_N	273_R	1.043	1.00
107_L	111_G	1.040	1.00
149_R	243_T	1.030	1.00
194_R	257_S	1.027	1.00
270_L	274_C	1.027	1.00
61_S	65_Q	1.024	1.00
119_I	309_V	1.022	1.00
101_E	105_G	1.011	1.00
307_H	311_D	1.005	1.00
128_G	152_P	1.003	1.00
215_V	250_I	1.000	1.00
216_L	240_I	0.999	1.00
32_N	35_T	0.991	1.00
40_V	49_A	0.989	1.00
138_A	141_T	0.988	1.00
37_F	75_L	0.984	1.00
103_I	107_L	0.980	1.00
139_I	143_Y	0.980	1.00
139_I	312_V	0.979	1.00
225_S	228_R	0.978	1.00
92_L	96_I	0.972	1.00
91_H	113_Y	0.971	1.00
135_I	313_I	0.969	1.00
35_T	104_L	0.967	1.00
66_K	69_V	0.954	1.00
85_P	89_A	0.953	1.00
49_A	60_I	0.953	1.00
40_V	46_I	0.951	1.00
98_Q	101_E	0.945	1.00
161_S	176_N	0.945	1.00
244_S	250_I	0.941	1.00
55_L	60_I	0.930	1.00
48_N	52_V	0.929	1.00
41_Y	76_F	0.924	1.00
44_K	84_T	0.922	1.00
88_F	91_H	0.922	1.00
104_L	107_L	0.921	1.00
191_L	260_L	0.920	1.00
192_I	268_Y	0.920	1.00
37_F	67_L	0.919	1.00
311_D	314_R	0.919	1.00
160_L	168_I	0.918	1.00
225_S	229_Q	0.915	1.00
137_R	258_D	0.908	1.00
231_V	236_P	0.907	1.00
193_C	197_N	0.904	1.00
159_Q	162_Q	0.901	1.00
36_I	53_L	0.901	1.00
135_I	312_V	0.897	1.00
303_D	306_L	0.892	1.00
125_P	246_N	0.889	1.00
180_Q	183_V	0.887	1.00
122_A	170_D	0.882	1.00
37_F	85_P	0.881	1.00
172_M	291_D	0.878	1.00
244_S	253_L	0.878	1.00
32_N	63_S	0.877	1.00
94_E	97_S	0.869	1.00
206_R	284_S	0.868	1.00
88_F	113_Y	0.868	1.00
103_I	106_A	0.866	1.00
197_N	200_L	0.866	1.00
73_D	110_E	0.865	1.00
47_V	51_K	0.864	1.00
105_G	109_I	0.863	1.00
104_L	108_D	0.853	1.00
304_P	308_G	0.850	1.00
140_K	258_D	0.848	1.00
29_I	70_I	0.848	1.00
271_F	274_C	0.846	1.00
102_S	106_A	0.846	1.00
35_T	39_A	0.844	1.00
117_R	305_I	0.843	1.00
76_F	83_V	0.840	1.00
42_V	93_H	0.840	1.00
197_N	201_S	0.834	1.00
43_H	49_A	0.831	1.00
88_F	110_E	0.830	1.00
155_D	158_N	0.826	1.00
40_V	76_F	0.824	1.00
199_L	212_A	0.823	1.00
302_R	307_H	0.821	1.00
79_K	82_G	0.821	1.00
44_K	82_G	0.820	1.00
41_Y	44_K	0.820	1.00
297_N	300_S	0.814	1.00
200_L	278_E	0.810	1.00
213_A	240_I	0.809	1.00
146_L	305_I	0.809	1.00
122_A	168_I	0.804	1.00
227_L	231_V	0.802	1.00
53_L	60_I	0.801	1.00
90_M	93_H	0.801	1.00
230_R	234_M	0.800	1.00
121_I	167_L	0.799	1.00
253_L	258_D	0.798	1.00
57_P	61_S	0.798	1.00
163_F	297_N	0.795	1.00
165_T	168_I	0.791	1.00
35_T	38_E	0.789	1.00
157_E	161_S	0.789	1.00
207_E	210_D	0.788	1.00
205_D	283_P	0.788	1.00
40_V	60_I	0.785	1.00
193_C	198_P	0.779	1.00
106_A	110_E	0.779	1.00
196_G	257_S	0.778	1.00
246_N	249_T	0.776	1.00
151_P	165_T	0.773	1.00
268_Y	271_F	0.773	1.00
188_N	287_E	0.772	1.00
147_L	239_Q	0.771	1.00
97_S	101_E	0.771	1.00
31_L	100_L	0.769	1.00
40_V	64_I	0.767	1.00
155_D	159_Q	0.766	1.00
194_R	258_D	0.764	1.00
96_I	99_G	0.762	1.00
179_V	295_H	0.761	1.00
41_Y	89_A	0.759	1.00
201_S	213_A	0.753	1.00
46_I	60_I	0.751	1.00
37_F	92_L	0.751	1.00
123_T	128_G	0.750	1.00
198_P	202_L	0.749	1.00
44_K	90_M	0.745	1.00
33_L	36_I	0.743	1.00
65_Q	74_P	0.741	1.00
194_R	197_N	0.740	1.00
77_I	86_T	0.736	1.00
268_Y	272_S	0.734	1.00
139_I	308_G	0.734	1.00
192_I	263_I	0.732	1.00
230_R	233_E	0.732	1.00
166_D	306_L	0.728	1.00
192_I	261_A	0.726	1.00
87_A	91_H	0.725	1.00
210_D	236_P	0.724	1.00
188_N	281_P	0.722	1.00
214_H	238_R	0.721	1.00
218_L	243_T	0.721	1.00
161_S	179_V	0.718	1.00
115_K	143_Y	0.711	1.00
208_T	211_N	0.708	1.00
129_A	252_A	0.704	1.00
193_C	278_E	0.704	1.00
308_G	312_V	0.702	1.00
226_G	230_R	0.702	1.00
111_G	114_D	0.701	1.00
192_I	272_S	0.701	1.00
35_T	100_L	0.701	1.00
85_P	90_M	0.700	1.00
196_G	200_L	0.698	1.00
95_Y	99_G	0.696	1.00
226_G	229_Q	0.696	1.00
228_R	232_Q	0.695	1.00
227_L	230_R	0.694	1.00
167_L	309_V	0.690	1.00
120_T	166_D	0.686	1.00
191_L	262_I	0.682	1.00
37_F	89_A	0.682	1.00
117_R	146_L	0.675	1.00
32_N	66_K	0.675	1.00
205_D	284_S	0.674	1.00
203_E	281_P	0.672	1.00
134_V	137_R	0.672	1.00
92_L	110_E	0.668	1.00
147_L	243_T	0.665	1.00
264_P	267_F	0.664	1.00
59_A	63_S	0.664	1.00
229_Q	233_E	0.664	1.00
122_A	156_A	0.664	1.00
77_I	82_G	0.663	1.00
300_S	303_D	0.663	1.00
88_F	92_L	0.662	1.00
272_S	275_W	0.662	1.00
178_T	298_K	0.660	1.00
255_A	274_C	0.658	1.00
51_K	54_N	0.656	1.00
272_S	279_K	0.652	1.00
193_C	199_L	0.651	1.00
225_S	230_R	0.650	1.00
41_Y	90_M	0.647	1.00
217_L	250_I	0.647	1.00
84_T	90_M	0.645	1.00
304_P	307_H	0.643	1.00
214_H	260_L	0.641	1.00
224_F	230_R	0.638	1.00
142_H	308_G	0.635	1.00
105_G	108_D	0.631	1.00
120_T	165_T	0.630	1.00
242_F	253_L	0.628	1.00
197_N	213_A	0.625	1.00
71_F	92_L	0.625	1.00
171_N	290_I	0.619	1.00
132_L	135_I	0.617	1.00
100_L	104_L	0.615	1.00
207_E	234_M	0.615	1.00
167_L	310_I	0.609	1.00
68_R	78_R	0.606	1.00
218_L	245_Y	0.604	1.00
244_S	249_T	0.601	1.00
158_N	161_S	0.600	1.00
196_G	199_L	0.600	1.00
228_R	231_V	0.600	1.00
152_P	245_Y	0.597	1.00
224_F	243_T	0.596	1.00
101_E	104_L	0.594	1.00
191_L	209_I	0.585	1.00
153_I	156_A	0.583	1.00
40_V	45_G	0.582	1.00
229_Q	232_Q	0.582	1.00
29_I	107_L	0.581	1.00
32_N	36_I	0.579	1.00
195_E	275_W	0.577	1.00
123_T	132_L	0.577	1.00
270_L	273_R	0.574	1.00
49_A	53_L	0.574	1.00
91_H	110_E	0.573	1.00
134_V	138_A	0.572	1.00
119_I	167_L	0.569	1.00
133_P	137_R	0.569	1.00
117_R	145_Q	0.568	1.00
73_D	77_I	0.567	1.00
71_F	74_P	0.565	1.00
309_V	313_I	0.565	1.00
197_N	260_L	0.565	1.00
189_M	262_I	0.563	1.00
161_S	164_Q	0.560	1.00
305_I	308_G	0.554	1.00
172_M	181_H	0.554	1.00
211_N	239_Q	0.554	1.00
108_D	112_S	0.554	1.00
184_L	294_I	0.553	1.00
116_Q	147_L	0.551	1.00
109_I	112_S	0.550	1.00
296_Y	307_H	0.550	1.00
30_D	70_I	0.548	1.00
76_F	85_P	0.545	1.00
64_I	68_R	0.544	1.00
71_F	110_E	0.542	1.00
96_I	100_L	0.542	1.00
131_V	135_I	0.542	1.00
46_I	57_P	0.541	1.00
160_L	179_V	0.539	1.00
187_D	290_I	0.537	1.00
143_Y	146_L	0.536	1.00
196_G	278_E	0.536	1.00
158_N	164_Q	0.534	1.00
137_R	140_K	0.533	1.00
231_V	238_R	0.531	1.00
122_A	151_P	0.531	1.00
44_K	83_V	0.530	1.00
250_I	254_V	0.528	1.00
191_L	214_H	0.527	1.00
74_P	88_F	0.526	1.00
296_Y	302_R	0.525	1.00
129_A	246_N	0.523	1.00
199_L	204_D	0.523	1.00
263_I	268_Y	0.523	1.00
198_P	201_S	0.522	1.00
30_D	66_K	0.520	1.00
58_S	62_Q	0.520	1.00
108_D	111_G	0.520	1.00
59_A	62_Q	0.519	1.00
281_P	284_S	0.518	1.00
127_V	131_V	0.518	1.00
99_G	107_L	0.516	1.00
187_D	264_P	0.515	1.00
306_L	310_I	0.515	1.00
106_A	109_I	0.514	1.00
207_E	236_P	0.510	1.00
85_P	93_H	0.510	1.00
56_T	62_Q	0.509	1.00
38_E	104_L	0.508	1.00
247_I	264_P	0.507	1.00
36_I	64_I	0.507	1.00
34_L	92_L	0.506	1.00
66_K	70_I	0.505	1.00
248_L	252_A	0.505	1.00
134_V	252_A	0.505	1.00
58_S	61_S	0.503	1.00
276_P	279_K	0.502	1.00
119_I	305_I	0.500	1.00
307_H	310_I	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
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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
1uthA	2	0.6845	100	0.165	Contact Map
2esnA	3	0.9243	100	0.165	Contact Map
3fxqA	3	0.9085	100	0.183	Contact Map
3fzvA	4	0.8896	100	0.19	Contact Map
4x6gA	4	0.9211	100	0.194	Contact Map
1al3A	1	0.6372	100	0.194	Contact Map
1ixcA	4	0.8991	100	0.194	Contact Map
2h98A	2	0.6246	100	0.195	Contact Map
3szpA	3	0.9022	100	0.197	Contact Map
2h9bA	2	0.6246	100	0.198	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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