YEAM - ECOLI - GREMLIN Contacts

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YEAM - Uncharacterized HTH-type transcriptional regulator YeaM

UniProt:	P76241	Sequences: MMHRLNLNGYEPDRHHEAAVAFCIHAGTDELTSPVHQHRKGQLILALHGAITCTVENALWMVPPQYAVWIPGGVEHSNQVTANAELCFLFIEPSAVTMPTTCCTLKISPLCRELILTLANRTTTQRAEPMTRRLIQVLFDELPQQPQQQLHLPVSSHPKIRTMVEMMAKGPVEWGALGQWAGFFAMSERNLARLIVKETGLSFRQWRQQLQLIMALQGLVKGDTVQKVAHTLGYDSTTAFITMFKKGLGQTPGRYIARLTTVSPQSAKPDPRQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13499
Length:	273 (226)
Sequences:	34425 (28557)
Seq/√Len:	1899.6

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
216_L	248_L	3.206	1.00
201_L	209_Q	3.116	1.00
212_L	248_L	3.004	1.00
178_G	188_E	2.976	1.00
168_A	210_L	2.942	1.00
223_D	231_T	2.898	1.00
214_M	217_Q	2.773	1.00
166_M	170_G	2.759	1.00
170_G	173_E	2.570	1.00
209_Q	247_G	2.518	1.00
244_F	255_Y	2.423	1.00
215_A	240_F	2.329	1.00
163_M	191_L	2.211	1.00
218_G	231_T	2.200	1.00
195_I	206_W	2.118	1.00
176_A	179_Q	2.021	1.00
250_Q	258_R	1.975	1.00
218_G	232_L	1.949	1.00
171_P	210_L	1.929	1.00
52_T	59_L	1.870	1.00
166_M	183_F	1.865	1.00
223_D	227_K	1.830	1.00
167_M	207_R	1.808	1.00
218_G	223_D	1.798	1.00
133_R	136_Q	1.792	1.00
212_L	247_G	1.782	1.00
52_T	61_M	1.728	1.00
136_Q	140_D	1.716	1.00
204_R	208_Q	1.716	1.00
190_N	194_L	1.711	1.00
163_M	184_F	1.697	1.00
160_I	199_T	1.696	1.00
164_V	199_T	1.689	1.00
180_W	203_F	1.668	1.00
237_T	241_I	1.667	1.00
54_T	59_L	1.663	1.00
216_L	255_Y	1.660	1.00
177_L	192_A	1.655	1.00
224_T	227_K	1.642	1.00
217_Q	221_K	1.620	1.00
226_Q	237_T	1.612	1.00
243_M	246_K	1.600	1.00
50_A	61_M	1.589	1.00
48_H	85_E	1.579	1.00
165_E	169_K	1.577	1.00
168_A	206_W	1.572	1.00
166_M	175_G	1.551	1.00
214_M	218_G	1.535	1.00
188_E	192_A	1.508	1.00
63_P	66_Y	1.508	1.00
210_L	214_M	1.502	1.00
203_F	207_R	1.498	1.00
186_M	190_N	1.497	1.00
219_L	225_V	1.493	1.00
41_G	72_G	1.469	1.00
227_K	231_T	1.455	1.00
201_L	205_Q	1.444	1.00
239_A	243_M	1.444	1.00
190_N	193_R	1.430	1.00
47_L	87_C	1.428	1.00
171_P	214_M	1.422	1.00
191_L	203_F	1.416	1.00
227_K	230_H	1.394	1.00
234_Y	243_M	1.393	1.00
226_Q	230_H	1.382	1.00
250_Q	254_R	1.374	1.00
172_V	231_T	1.365	1.00
253_G	257_A	1.364	1.00
215_A	232_L	1.362	1.00
157_H	198_E	1.361	1.00
228_V	232_L	1.357	1.00
50_A	63_P	1.348	1.00
52_T	79_Q	1.346	1.00
56_E	74_V	1.336	1.00
164_V	168_A	1.331	1.00
238_T	241_I	1.315	1.00
178_G	182_G	1.302	1.00
214_M	232_L	1.287	1.00
163_M	180_W	1.277	1.00
167_M	210_L	1.268	1.00
192_A	203_F	1.268	1.00
179_Q	183_F	1.258	1.00
173_E	179_Q	1.255	1.00
133_R	140_D	1.254	1.00
208_Q	243_M	1.240	1.00
189_R	193_R	1.240	1.00
241_I	251_T	1.230	1.00
209_Q	213_I	1.218	1.00
54_T	77_S	1.211	1.00
210_L	213_I	1.199	1.00
202_S	205_Q	1.194	1.00
186_M	191_L	1.174	1.00
159_K	186_M	1.172	1.00
71_P	74_V	1.169	1.00
241_I	253_G	1.166	1.00
112_R	116_L	1.159	1.00
42_Q	76_H	1.156	1.00
36_H	76_H	1.156	1.00
187_S	190_N	1.156	1.00
216_L	220_V	1.131	1.00
101_T	104_T	1.125	1.00
117_T	121_R	1.090	1.00
48_H	64_P	1.088	1.00
213_I	216_L	1.084	1.00
251_T	254_R	1.072	1.00
129_P	133_R	1.064	1.00
223_D	228_V	1.063	1.00
194_L	197_K	1.056	1.00
175_G	180_W	1.050	1.00
113_E	117_T	1.043	1.00
38_H	76_H	1.031	1.00
254_R	257_A	1.026	1.00
177_L	203_F	1.023	1.00
132_R	139_F	1.020	1.00
166_M	184_F	1.012	1.00
116_L	120_N	1.012	1.00
159_K	194_L	1.010	1.00
35_V	75_E	1.007	1.00
132_R	136_Q	1.003	1.00
181_A	188_E	0.996	1.00
208_Q	246_K	0.991	1.00
158_P	162_T	0.990	1.00
179_Q	182_G	0.985	1.00
194_L	198_E	0.982	1.00
174_W	235_D	0.979	1.00
242_T	246_K	0.974	1.00
131_T	141_E	0.973	1.00
128_E	131_T	0.971	1.00
171_P	175_G	0.968	1.00
159_K	184_F	0.966	1.00
172_V	214_M	0.962	1.00
161_R	165_E	0.952	1.00
225_V	228_V	0.950	1.00
222_G	228_V	0.938	1.00
105_L	108_S	0.937	1.00
205_Q	208_Q	0.935	1.00
253_G	256_I	0.933	1.00
236_S	242_T	0.932	1.00
104_T	108_S	0.929	1.00
164_V	206_W	0.927	1.00
162_T	183_F	0.926	1.00
180_W	183_F	0.926	1.00
47_L	85_E	0.925	1.00
218_G	228_V	0.918	1.00
129_P	132_R	0.909	1.00
113_E	116_L	0.903	1.00
177_L	188_E	0.903	1.00
100_T	104_T	0.898	1.00
241_I	245_K	0.898	1.00
108_S	112_R	0.891	1.00
243_M	247_G	0.881	1.00
129_P	136_Q	0.872	1.00
248_L	255_Y	0.871	1.00
103_C	107_I	0.866	1.00
254_R	258_R	0.864	1.00
166_M	180_W	0.864	1.00
189_R	192_A	0.858	1.00
51_I	84_A	0.854	1.00
211_Q	232_L	0.850	1.00
140_D	144_Q	0.850	1.00
228_V	256_I	0.849	1.00
46_A	51_I	0.846	1.00
186_M	194_L	0.846	1.00
184_F	191_L	0.837	1.00
206_W	210_L	0.833	1.00
167_M	203_F	0.819	1.00
160_I	163_M	0.818	1.00
135_I	141_E	0.815	1.00
127_A	131_T	0.809	1.00
117_T	120_N	0.809	1.00
162_T	165_E	0.807	1.00
41_G	69_W	0.807	1.00
101_T	105_L	0.807	1.00
174_W	179_Q	0.804	1.00
133_R	137_V	0.803	1.00
195_I	199_T	0.800	1.00
205_Q	209_Q	0.800	1.00
205_Q	247_G	0.795	1.00
239_A	242_T	0.795	1.00
216_L	244_F	0.792	1.00
171_P	207_R	0.792	1.00
38_H	42_Q	0.791	1.00
160_I	194_L	0.791	1.00
52_T	81_T	0.789	1.00
54_T	57_N	0.778	1.00
70_I	76_H	0.778	1.00
219_L	228_V	0.775	1.00
128_E	132_R	0.773	1.00
51_I	62_V	0.771	1.00
53_C	68_V	0.771	1.00
204_R	207_R	0.765	1.00
164_V	195_I	0.764	1.00
212_L	240_F	0.763	1.00
175_G	179_Q	0.761	1.00
195_I	203_F	0.760	1.00
114_L	117_T	0.759	1.00
44_I	88_F	0.759	1.00
208_Q	247_G	0.750	1.00
160_I	164_V	0.749	1.00
55_V	58_A	0.749	1.00
162_T	184_F	0.748	1.00
161_R	164_V	0.747	1.00
54_T	79_Q	0.746	1.00
212_L	243_M	0.744	1.00
122_T	125_Q	0.740	1.00
245_K	254_R	0.740	1.00
204_R	239_A	0.737	1.00
170_G	183_F	0.735	1.00
45_L	67_A	0.734	1.00
135_I	139_F	0.733	1.00
230_H	235_D	0.731	1.00
130_M	133_R	0.731	1.00
35_V	77_S	0.730	1.00
215_A	218_G	0.727	1.00
171_P	232_L	0.726	1.00
160_I	198_E	0.725	1.00
110_L	117_T	0.725	1.00
245_K	251_T	0.724	1.00
219_L	256_I	0.720	1.00
167_M	206_W	0.719	1.00
50_A	81_T	0.714	1.00
192_A	196_V	0.712	1.00
156_S	197_K	0.708	1.00
163_M	166_M	0.708	1.00
250_Q	255_Y	0.705	1.00
192_A	202_S	0.694	1.00
180_W	191_L	0.693	1.00
128_E	139_F	0.690	1.00
42_Q	90_F	0.689	1.00
51_I	61_M	0.685	1.00
220_V	255_Y	0.681	1.00
157_H	194_L	0.675	1.00
46_A	49_G	0.674	1.00
121_R	125_Q	0.672	1.00
128_E	137_V	0.667	1.00
110_L	114_L	0.662	1.00
237_T	240_F	0.661	1.00
229_A	237_T	0.658	1.00
170_G	179_Q	0.655	1.00
163_M	167_M	0.651	1.00
105_L	109_P	0.648	1.00
114_L	118_L	0.643	1.00
235_D	239_A	0.641	1.00
163_M	195_I	0.641	1.00
62_V	68_V	0.633	1.00
37_Q	75_E	0.631	1.00
236_S	239_A	0.630	1.00
84_A	88_F	0.630	1.00
193_R	197_K	0.629	1.00
171_P	211_Q	0.627	1.00
163_M	203_F	0.624	1.00
201_L	206_W	0.624	1.00
159_K	162_T	0.622	1.00
46_A	86_L	0.621	1.00
163_M	183_F	0.618	1.00
224_T	228_V	0.618	1.00
238_T	251_T	0.617	1.00
100_T	103_C	0.616	1.00
196_V	202_S	0.616	1.00
212_L	234_Y	0.615	1.00
167_M	175_G	0.610	1.00
51_I	78_N	0.607	1.00
44_I	70_I	0.604	1.00
137_V	142_L	0.604	1.00
109_P	113_E	0.604	1.00
109_P	112_R	0.601	1.00
238_T	242_T	0.599	1.00
213_I	247_G	0.598	1.00
175_G	211_Q	0.597	1.00
132_R	135_I	0.594	1.00
222_G	256_I	0.594	1.00
119_A	123_T	0.591	1.00
168_A	214_M	0.590	1.00
137_V	141_E	0.586	1.00
130_M	134_L	0.581	1.00
225_V	253_G	0.577	1.00
192_A	204_R	0.577	1.00
170_G	175_G	0.576	1.00
111_C	115_I	0.574	1.00
215_A	228_V	0.574	1.00
134_L	139_F	0.574	1.00
208_Q	239_A	0.571	1.00
207_R	211_Q	0.570	1.00
177_L	204_R	0.569	1.00
156_S	198_E	0.565	1.00
53_C	78_N	0.562	1.00
131_T	137_V	0.562	1.00
41_G	44_I	0.560	1.00
191_L	199_T	0.551	1.00
160_I	191_L	0.551	1.00
44_I	86_L	0.551	1.00
111_C	114_L	0.551	1.00
129_P	143_P	0.547	1.00
104_T	107_I	0.547	1.00
219_L	255_Y	0.545	1.00
130_M	140_D	0.545	1.00
103_C	106_K	0.545	1.00
44_I	53_C	0.544	1.00
207_R	210_L	0.544	1.00
134_L	137_V	0.541	1.00
131_T	135_I	0.538	1.00
234_Y	240_F	0.537	1.00
182_G	185_A	0.536	1.00
110_L	113_E	0.535	1.00
107_I	121_R	0.535	1.00
43_L	67_A	0.535	1.00
174_W	211_Q	0.535	1.00
240_F	252_P	0.534	1.00
43_L	69_W	0.532	1.00
133_R	139_F	0.532	1.00
156_S	159_K	0.529	1.00
229_A	234_Y	0.528	1.00
56_E	75_E	0.527	1.00
244_F	250_Q	0.526	1.00
158_P	198_E	0.526	1.00
181_A	184_F	0.526	1.00
48_H	83_N	0.525	1.00
121_R	124_T	0.525	1.00
218_G	221_K	0.524	1.00
180_W	184_F	0.521	1.00
157_H	161_R	0.521	1.00
236_S	246_K	0.517	1.00
40_K	90_F	0.516	1.00
139_F	143_P	0.516	1.00
46_A	84_A	0.514	1.00
137_V	140_D	0.513	1.00
199_T	206_W	0.513	1.00
240_F	244_F	0.512	1.00
166_M	179_Q	0.509	1.00
80_V	84_A	0.508	1.00
180_W	211_Q	0.508	1.00
102_C	106_K	0.506	1.00
119_A	122_T	0.504	1.00
132_R	140_D	0.504	1.00
165_E	168_A	0.503	1.00
46_A	62_V	0.501	1.00
132_R	141_E	0.500	1.00
213_I	248_L	0.500	1.00
68_V	78_N	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	0.8681	100	0.29	Contact Map
3oioA	1	0.4066	100	0.492	Contact Map
3oouA	1	0.381	100	0.493	Contact Map
3mn2A	1	0.3846	100	0.497	Contact Map
1bl0A	1	0.4212	100	0.498	Contact Map
3w6vA	1	0.4029	100	0.5	Contact Map
3mklA	1	0.4029	99.9	0.505	Contact Map
2k9sA	1	0.3846	99.9	0.509	Contact Map
3lsgA	2	0.37	99.9	0.513	Contact Map
1d5yA	1	0.4322	99.9	0.522	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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