YBCM - ECOLI - GREMLIN Contacts

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YBCM - Uncharacterized HTH-type transcriptional regulator YbcM

UniProt:	P77634	Sequences: MLARGKTNLKIEEIRMHKHHEIHRVKPLMPALCRIRQGKKVINWETHTLTVDNNQIILFPCGYEFYIENYPEAGLYLAEMLYLPIDLIESFQKLYTVTDQIRNKTSFFLPQNPELIYCWEQLKTSVSRGFSTKIQEHLAMGVLLSLGVNHVNHLLLSYSKQSLISRCYNLLLSEPGTKWTANKVARYLYISVSTLHRRLASEGVSFQSILDDVRLNNALSAIQTTVKPISEIARENGYKCPSRFTERFHNRFNITPREIRKASRE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13629
Length:	265 (231)
Sequences:	36183 (30097)
Seq/√Len:	1980.2

ECOLI - YBCM YPDC YDIP YQHC RHAR RHAS MELR ARAC GADW YIJO APPY RCLR FEAR CHBR YIDL ENVY GADX YDEO YEAM ADIY EUTR YKGA MARA ROB SOXS XYLR
BACSU - YISR YBFI YDEC YFIF BTR YOBQ YTDP YESS ADAA YDEE YESN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
204_V	212_D	3.255	1.00
219_L	252_F	3.222	1.00
172_L	213_V	3.041	1.00
215_L	252_F	2.984	1.00
227_K	235_E	2.924	1.00
170_L	174_E	2.809	1.00
217_N	220_S	2.777	1.00
182_N	192_V	2.735	1.00
212_D	251_R	2.599	1.00
248_F	259_I	2.550	1.00
174_E	177_T	2.544	1.00
167_C	195_L	2.252	1.00
218_A	244_F	2.228	1.00
221_A	235_E	2.216	1.00
199_L	209_I	2.191	1.00
221_A	236_N	2.021	1.00
175_P	213_V	1.984	1.00
180_T	183_K	1.969	1.00
227_K	231_E	1.944	1.00
168_Y	202_E	1.926	1.00
170_L	187_Y	1.892	1.00
167_C	188_L	1.827	1.00
215_L	251_R	1.825	1.00
41_V	48_T	1.816	1.00
171_L	210_L	1.813	1.00
164_I	202_E	1.788	1.00
207_Q	211_D	1.783	1.00
228_P	231_E	1.767	1.00
221_A	227_K	1.747	1.00
241_P	245_T	1.720	1.00
184_V	206_F	1.672	1.00
194_T	198_R	1.654	1.00
41_V	50_T	1.650	1.00
169_N	173_S	1.645	1.00
219_L	259_I	1.621	1.00
43_N	48_T	1.613	1.00
181_A	196_H	1.595	1.00
247_R	250_N	1.581	1.00
138_L	141_G	1.578	1.00
204_V	208_S	1.563	1.00
217_N	221_A	1.558	1.00
220_S	224_T	1.558	1.00
213_V	217_N	1.545	1.00
52_D	55_Q	1.545	1.00
37_Q	77_L	1.537	1.00
230_S	241_P	1.527	1.00
170_L	179_W	1.513	1.00
195_L	206_F	1.512	1.00
243_R	247_R	1.509	1.00
39_K	50_T	1.499	1.00
172_L	209_I	1.498	1.00
36_R	79_E	1.496	1.00
192_V	196_H	1.479	1.00
175_P	217_N	1.479	1.00
222_I	229_I	1.477	1.00
168_Y	172_L	1.451	1.00
231_E	235_E	1.451	1.00
206_F	210_L	1.446	1.00
171_L	213_V	1.441	1.00
194_T	197_R	1.437	1.00
254_I	258_E	1.436	1.00
230_S	234_R	1.423	1.00
231_E	234_R	1.410	1.00
176_G	235_E	1.405	1.00
43_N	66_Y	1.404	1.00
167_C	184_V	1.400	1.00
218_A	236_N	1.398	1.00
190_I	194_T	1.392	1.00
141_G	145_S	1.385	1.00
238_Y	247_R	1.381	1.00
257_R	261_K	1.379	1.00
232_I	236_N	1.370	1.00
30_P	61_C	1.369	1.00
217_N	236_N	1.367	1.00
39_K	52_D	1.342	1.00
212_D	216_N	1.332	1.00
116_I	120_E	1.309	1.00
196_H	206_F	1.301	1.00
182_N	186_R	1.293	1.00
193_S	197_R	1.288	1.00
242_S	245_T	1.285	1.00
205_S	208_S	1.283	1.00
213_V	216_N	1.268	1.00
41_V	68_E	1.268	1.00
45_E	63_Y	1.265	1.00
211_D	247_R	1.249	1.00
183_K	187_Y	1.247	1.00
225_T	260_R	1.238	1.00
177_T	183_K	1.234	1.00
60_P	63_Y	1.228	1.00
137_H	144_L	1.224	1.00
190_I	195_L	1.218	1.00
245_T	255_T	1.197	1.00
137_H	140_M	1.189	1.00
191_S	194_T	1.179	1.00
137_H	141_G	1.168	1.00
245_T	257_R	1.163	1.00
163_L	190_I	1.158	1.00
246_E	250_N	1.147	1.00
105_T	108_F	1.132	1.00
216_N	219_L	1.124	1.00
37_Q	53_N	1.118	1.00
219_L	223_Q	1.110	1.00
227_K	232_I	1.104	1.00
36_R	77_L	1.091	1.00
185_A	192_V	1.082	1.00
176_G	217_N	1.077	1.00
170_L	188_L	1.075	1.00
31_A	65_F	1.074	1.00
181_A	206_F	1.071	1.00
27_P	65_F	1.067	1.00
117_Y	121_Q	1.063	1.00
184_V	187_Y	1.036	1.00
120_E	124_T	1.034	1.00
255_T	258_E	1.033	1.00
162_S	166_R	1.025	1.00
240_C	246_E	1.024	1.00
178_K	183_K	1.023	1.00
211_D	250_N	1.020	1.00
25_V	65_F	1.019	1.00
198_R	201_S	1.011	1.00
229_I	232_I	1.009	1.00
258_E	261_K	1.008	1.00
165_S	169_N	1.005	1.00
208_S	211_D	1.001	1.00
179_W	184_V	0.994	1.00
117_Y	120_E	0.991	1.00
178_K	239_K	0.988	1.00
168_Y	209_I	0.979	1.00
163_L	188_L	0.977	1.00
105_T	109_L	0.973	1.00
257_R	260_R	0.960	1.00
166_R	187_Y	0.955	1.00
252_F	259_I	0.955	1.00
134_I	138_L	0.952	1.00
183_K	186_R	0.951	1.00
221_A	232_I	0.950	1.00
132_T	136_E	0.948	1.00
163_L	198_R	0.944	1.00
40_K	76_Y	0.941	1.00
171_L	206_F	0.940	1.00
247_R	251_R	0.939	1.00
208_S	212_D	0.933	1.00
245_T	249_H	0.932	1.00
170_L	184_V	0.931	1.00
181_A	192_V	0.930	1.00
136_E	140_M	0.923	1.00
27_P	31_A	0.911	1.00
166_R	169_N	0.909	1.00
193_S	196_H	0.908	1.00
44_W	47_H	0.901	1.00
134_I	141_G	0.882	1.00
243_R	246_E	0.880	1.00
114_E	117_Y	0.877	1.00
188_L	195_L	0.877	1.00
43_N	46_T	0.873	1.00
215_L	247_R	0.871	1.00
219_L	248_F	0.867	1.00
190_I	198_R	0.864	1.00
249_H	255_T	0.858	1.00
164_I	198_R	0.851	1.00
199_L	206_F	0.849	1.00
222_I	232_I	0.840	1.00
35_I	40_K	0.835	1.00
174_E	187_Y	0.833	1.00
140_M	144_L	0.832	1.00
211_D	251_R	0.831	1.00
166_R	188_L	0.830	1.00
209_I	213_V	0.828	1.00
207_Q	210_L	0.827	1.00
175_P	210_L	0.826	1.00
43_N	68_E	0.823	1.00
40_K	51_V	0.820	1.00
175_P	179_W	0.820	1.00
225_T	232_I	0.820	1.00
214_R	236_N	0.819	1.00
165_S	168_Y	0.819	1.00
254_I	259_I	0.811	1.00
168_Y	199_L	0.808	1.00
164_I	167_C	0.807	1.00
215_L	244_F	0.802	1.00
37_Q	75_L	0.801	1.00
40_K	50_T	0.801	1.00
41_V	70_Y	0.801	1.00
133_K	136_E	0.798	1.00
207_Q	243_R	0.797	1.00
218_A	221_A	0.793	1.00
141_G	144_L	0.792	1.00
199_L	202_E	0.788	1.00
30_P	58_L	0.785	1.00
234_R	239_K	0.780	1.00
175_P	236_N	0.778	1.00
160_K	201_S	0.778	1.00
39_K	70_Y	0.773	1.00
208_S	251_R	0.769	1.00
171_L	209_I	0.768	1.00
179_W	183_K	0.762	1.00
164_I	168_Y	0.760	1.00
114_E	145_S	0.756	1.00
167_C	170_L	0.752	1.00
31_A	82_Y	0.748	1.00
196_H	200_A	0.747	1.00
197_R	201_S	0.744	1.00
161_Q	198_R	0.744	1.00
42_I	57_I	0.741	1.00
174_E	183_K	0.740	1.00
144_L	148_V	0.739	1.00
196_H	205_S	0.738	1.00
223_Q	259_I	0.737	1.00
55_Q	108_F	0.732	1.00
244_F	248_F	0.730	1.00
175_P	214_R	0.730	1.00
121_Q	125_S	0.730	1.00
33_C	78_A	0.729	1.00
163_L	166_R	0.723	1.00
167_C	199_L	0.723	1.00
85_I	89_E	0.720	1.00
222_I	260_R	0.717	1.00
196_H	207_Q	0.705	1.00
33_C	80_M	0.705	1.00
167_C	206_F	0.703	1.00
233_A	241_P	0.703	1.00
249_H	258_E	0.699	1.00
35_I	38_G	0.698	1.00
104_K	107_F	0.697	1.00
200_A	205_S	0.697	1.00
111_Q	114_E	0.695	1.00
113_P	117_Y	0.693	1.00
184_V	195_L	0.691	1.00
118_C	121_Q	0.688	1.00
211_D	243_R	0.687	1.00
114_E	118_C	0.685	1.00
239_K	243_R	0.678	1.00
228_P	232_I	0.671	1.00
241_P	244_F	0.670	1.00
34_R	56_I	0.669	1.00
117_Y	124_T	0.669	1.00
59_F	65_F	0.659	1.00
242_S	255_T	0.654	1.00
89_E	93_K	0.653	1.00
248_F	254_I	0.653	1.00
216_N	252_F	0.653	1.00
204_V	209_I	0.650	1.00
167_C	187_Y	0.649	1.00
170_L	183_K	0.647	1.00
35_I	78_A	0.645	1.00
240_C	243_R	0.644	1.00
104_K	108_F	0.643	1.00
121_Q	141_G	0.642	1.00
172_L	217_N	0.642	1.00
114_E	121_Q	0.641	1.00
113_P	116_I	0.640	1.00
221_A	224_T	0.638	1.00
104_K	109_L	0.636	1.00
121_Q	138_L	0.633	1.00
211_D	215_L	0.632	1.00
29_M	82_Y	0.631	1.00
121_Q	124_T	0.631	1.00
51_V	57_I	0.626	1.00
160_K	163_L	0.624	1.00
131_S	135_Q	0.618	1.00
86_D	89_E	0.618	1.00
181_A	207_Q	0.617	1.00
127_S	131_S	0.616	1.00
138_L	145_S	0.615	1.00
76_Y	80_M	0.614	1.00
145_S	148_V	0.610	1.00
118_C	122_L	0.605	1.00
26_K	64_E	0.604	1.00
186_R	189_Y	0.604	1.00
218_A	232_I	0.601	1.00
185_A	188_L	0.597	1.00
219_L	254_I	0.597	1.00
161_Q	165_S	0.596	1.00
164_I	195_L	0.594	1.00
167_C	171_L	0.594	1.00
134_I	137_H	0.593	1.00
215_L	238_Y	0.592	1.00
179_W	214_R	0.590	1.00
35_I	51_V	0.586	1.00
242_S	246_E	0.584	1.00
244_F	256_P	0.584	1.00
90_S	94_L	0.581	1.00
133_K	137_H	0.580	1.00
35_I	76_Y	0.579	1.00
210_L	213_V	0.579	1.00
216_N	251_R	0.577	1.00
222_I	259_I	0.577	1.00
184_V	188_L	0.573	1.00
220_S	223_Q	0.571	1.00
107_F	110_P	0.571	1.00
33_C	42_I	0.570	1.00
202_E	209_I	0.569	1.00
112_N	116_I	0.569	1.00
158_Y	161_Q	0.567	1.00
45_E	64_E	0.567	1.00
109_L	112_N	0.567	1.00
33_C	57_I	0.566	1.00
169_N	172_L	0.564	1.00
210_L	214_R	0.563	1.00
36_R	120_E	0.560	1.00
248_F	252_F	0.560	1.00
232_I	260_R	0.557	1.00
44_W	59_F	0.557	1.00
181_A	193_S	0.555	1.00
208_S	250_N	0.554	1.00
240_C	250_N	0.552	1.00
171_L	179_W	0.551	1.00
90_S	93_K	0.550	1.00
72_E	75_L	0.548	1.00
167_C	198_R	0.545	1.00
184_V	214_R	0.545	1.00
106_S	109_L	0.544	1.00
33_C	59_F	0.542	1.00
195_L	202_E	0.542	1.00
79_E	82_Y	0.538	1.00
28_L	84_P	0.538	1.00
179_W	210_L	0.537	1.00
40_K	67_I	0.536	1.00
229_I	257_R	0.536	1.00
30_P	60_P	0.535	1.00
134_I	148_V	0.532	1.00
87_L	90_S	0.532	1.00
134_I	144_L	0.532	1.00
217_N	235_E	0.531	1.00
69_N	76_Y	0.529	1.00
238_Y	243_R	0.528	1.00
160_K	194_T	0.526	1.00
105_T	110_P	0.526	1.00
35_I	53_N	0.523	1.00
131_S	134_I	0.522	1.00
238_Y	244_F	0.521	1.00
34_R	119_W	0.520	1.00
107_F	111_Q	0.520	1.00
39_K	71_P	0.519	1.00
111_Q	116_I	0.518	1.00
133_K	140_M	0.517	1.00
174_E	179_W	0.517	1.00
30_P	33_C	0.515	1.00
138_L	142_V	0.513	1.00
216_N	220_S	0.512	1.00
164_I	188_L	0.512	1.00
224_T	227_K	0.512	1.00
32_L	56_I	0.508	1.00
247_R	252_F	0.504	1.00
188_L	192_V	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
3gbgA	1	0.9547	100	0.208	Contact Map
3mklA	1	0.4151	100	0.455	Contact Map
1bl0A	1	0.4	100	0.46	Contact Map
3oouA	1	0.3925	100	0.463	Contact Map
3oioA	1	0.4113	100	0.464	Contact Map
3w6vA	1	0.3962	100	0.469	Contact Map
3mn2A	1	0.3962	100	0.469	Contact Map
2k9sA	1	0.3962	99.9	0.476	Contact Map
3lsgA	2	0.3811	99.9	0.49	Contact Map
1d5yA	1	0.4	99.9	0.49	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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