YJJM - ECOLI - GREMLIN Contacts

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YJJM - Probable HTH-type transcriptional regulator YjjM

UniProt:	P39399	Sequences: MSRSQNLRHNVINQVIDDMARGHIPSPLPSQSALAEMYNISRTTVRHILSHLRECGVLTQVGNDYVIARKPDHDDGFACTTASMSEQNKVFEQAFFTMINQRQLRPGETFSELQLARAAGVSPVVVREYLLKFGRYNLIHSEKRGQWSMKQFDQSYAEQLFELREMLETHSLQHFLNLPDHDPRWLQAKTMLERHRLLRDNIGNSFRMFSQLDRDFHSLLLSAADNIFFDQSLEIISVIFHFHYQWDESDLKQRNIIAVDEHMTILSALICRSDLDATLALRNHLNSAKQSMIRSINENTRYAH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12589
Length:	304 (233)
Sequences:	342 (278)
Seq/√Len:	18.2

ECOLI - YJJM NANR YDFH MCBR CSIR PDHR GLCC YIEP EXUR UXUR DGOR
BACSU - GNTR YDHC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
217_H	262_H	4.871	1.00
173_Q	278_T	4.485	1.00
217_H	284_H	4.332	1.00
168_E	217_H	3.616	1.00
162_E	226_N	3.595	1.00
261_E	284_H	3.532	1.00
189_K	270_I	3.357	1.00
112_E	123_P	3.342	1.00
276_D	280_A	3.238	0.99
262_H	284_H	3.089	0.99
92_E	132_K	3.024	0.99
168_E	262_H	2.928	0.99
172_L	281_L	2.654	0.97
273_S	276_D	2.478	0.96
119_A	157_A	2.379	0.95
91_F	119_A	2.364	0.95
105_R	108_E	2.321	0.94
164_R	213_D	2.280	0.94
159_Q	227_I	2.256	0.94
181_H	184_R	2.238	0.93
176_L	269_L	2.187	0.92
172_L	176_L	2.145	0.92
164_R	168_E	2.137	0.92
96_F	136_Y	2.072	0.90
177_N	272_R	1.949	0.87
95_F	147_W	1.942	0.87
191_M	212_L	1.933	0.87
168_E	213_D	1.919	0.86
141_S	147_W	1.868	0.85
131_L	134_G	1.831	0.84
165_E	289_K	1.808	0.83
216_F	220_L	1.756	0.81
122_S	127_R	1.741	0.80
114_Q	265_I	1.729	0.80
205_S	208_M	1.708	0.79
168_E	281_L	1.698	0.79
99_I	138_L	1.695	0.78
265_I	277_A	1.683	0.78
161_F	288_A	1.640	0.76
92_E	136_Y	1.640	0.76
105_R	110_F	1.557	0.72
194_R	215_D	1.553	0.72
214_R	240_F	1.532	0.71
209_F	213_D	1.532	0.71
90_V	94_A	1.531	0.71
125_V	162_E	1.513	0.70
196_R	263_M	1.503	0.69
168_E	284_H	1.489	0.69
244_Y	284_H	1.482	0.68
112_E	284_H	1.470	0.68
105_R	186_L	1.462	0.67
121_V	191_M	1.461	0.67
192_L	266_L	1.455	0.67
125_V	129_Y	1.450	0.66
112_E	138_L	1.446	0.66
91_F	159_Q	1.429	0.65
277_A	281_L	1.427	0.65
217_H	261_E	1.400	0.64
124_V	172_L	1.394	0.63
213_D	262_H	1.376	0.62
134_G	139_I	1.354	0.61
254_R	261_E	1.346	0.60
272_R	294_R	1.344	0.60
213_D	241_H	1.340	0.60
91_F	127_R	1.324	0.59
226_N	284_H	1.314	0.59
111_S	160_L	1.307	0.58
133_F	139_I	1.307	0.58
192_L	213_D	1.301	0.58
119_A	139_I	1.300	0.58
70_K	183_P	1.268	0.56
159_Q	226_N	1.265	0.56
260_D	264_T	1.261	0.55
213_D	236_I	1.259	0.55
187_Q	197_L	1.257	0.55
130_L	147_W	1.249	0.55
244_Y	254_R	1.249	0.55
276_D	279_L	1.228	0.53
130_L	212_L	1.211	0.52
93_Q	265_I	1.196	0.51
119_A	267_S	1.187	0.51
138_L	284_H	1.180	0.50
98_M	118_A	1.170	0.50
78_A	273_S	1.170	0.50
268_A	280_A	1.158	0.49
91_F	116_A	1.146	0.48
136_Y	224_A	1.140	0.48
154_Q	269_L	1.137	0.48
112_E	226_N	1.130	0.47
110_F	139_I	1.129	0.47
110_F	119_A	1.126	0.47
112_E	127_R	1.124	0.47
163_L	167_L	1.121	0.47
265_I	281_L	1.116	0.46
68_A	182_D	1.114	0.46
265_I	280_A	1.105	0.46
216_F	262_H	1.095	0.45
165_E	282_R	1.080	0.44
213_D	221_L	1.068	0.43
125_V	145_G	1.040	0.42
171_S	277_A	1.037	0.42
139_I	150_K	1.027	0.41
102_R	145_G	1.003	0.40
125_V	213_D	0.997	0.39
168_E	212_L	0.990	0.39
130_L	139_I	0.984	0.38
189_K	211_Q	0.974	0.38
264_T	283_N	0.974	0.38
105_R	268_A	0.972	0.38
86_E	105_R	0.970	0.38
266_L	282_R	0.969	0.38
107_G	128_E	0.968	0.38
193_E	197_L	0.963	0.37
152_F	171_S	0.961	0.37
179_P	184_R	0.956	0.37
110_F	149_M	0.954	0.37
175_F	178_L	0.952	0.37
164_R	221_L	0.944	0.36
74_D	118_A	0.943	0.36
269_L	277_A	0.938	0.36
89_K	193_E	0.935	0.36
226_N	241_H	0.928	0.35
91_F	122_S	0.924	0.35
91_F	102_R	0.920	0.35
62_G	66_V	0.918	0.35
267_S	273_S	0.914	0.34
133_F	216_F	0.911	0.34
115_L	126_V	0.910	0.34
193_E	271_C	0.907	0.34
164_R	285_L	0.906	0.34
119_A	133_F	0.905	0.34
164_R	281_L	0.902	0.34
195_H	258_A	0.900	0.34
130_L	258_A	0.900	0.34
176_L	281_L	0.896	0.33
159_Q	265_I	0.892	0.33
74_D	283_N	0.886	0.33
74_D	267_S	0.885	0.33
163_L	171_S	0.883	0.33
125_V	136_Y	0.883	0.33
144_R	152_F	0.879	0.33
122_S	125_V	0.877	0.32
265_I	268_A	0.877	0.32
120_G	172_L	0.877	0.32
177_N	208_M	0.875	0.32
257_I	267_S	0.875	0.32
139_I	234_E	0.872	0.32
244_Y	261_E	0.871	0.32
89_K	94_A	0.859	0.31
168_E	285_L	0.858	0.31
85_S	105_R	0.857	0.31
171_S	221_L	0.855	0.31
197_L	275_L	0.850	0.31
72_D	181_H	0.848	0.31
115_L	236_I	0.844	0.31
117_R	227_I	0.838	0.30
177_N	274_D	0.834	0.30
131_L	139_I	0.834	0.30
102_R	127_R	0.827	0.30
133_F	165_E	0.822	0.30
89_K	149_M	0.813	0.29
186_L	190_T	0.810	0.29
275_L	279_L	0.807	0.29
133_F	149_M	0.804	0.29
126_V	129_Y	0.800	0.28
124_V	131_L	0.799	0.28
125_V	142_E	0.798	0.28
193_E	222_S	0.797	0.28
264_T	268_A	0.793	0.28
64_D	272_R	0.792	0.28
96_F	122_S	0.783	0.28
220_L	278_T	0.783	0.28
168_E	251_L	0.778	0.27
167_L	233_L	0.773	0.27
272_R	282_R	0.770	0.27
135_R	153_D	0.768	0.27
80_T	132_K	0.763	0.27
80_T	172_L	0.762	0.27
128_E	160_L	0.761	0.26
91_F	106_P	0.756	0.26
217_H	281_L	0.745	0.26
176_L	274_D	0.737	0.25
209_F	258_A	0.737	0.25
88_N	213_D	0.732	0.25
205_S	290_Q	0.730	0.25
281_L	285_L	0.727	0.25
198_L	254_R	0.726	0.25
160_L	258_A	0.726	0.25
186_L	274_D	0.724	0.25
125_V	144_R	0.724	0.25
91_F	147_W	0.718	0.24
244_Y	258_A	0.713	0.24
83_S	293_I	0.713	0.24
77_F	270_I	0.713	0.24
96_F	188_A	0.712	0.24
159_Q	269_L	0.712	0.24
120_G	267_S	0.710	0.24
117_R	272_R	0.710	0.24
99_I	264_T	0.706	0.24
109_T	112_E	0.704	0.24
91_F	121_V	0.703	0.24
98_M	104_L	0.702	0.24
151_Q	178_L	0.701	0.24
124_V	147_W	0.697	0.24
165_E	285_L	0.696	0.23
198_L	272_R	0.693	0.23
125_V	163_L	0.692	0.23
103_Q	227_I	0.689	0.23
118_A	173_Q	0.686	0.23
261_E	287_S	0.683	0.23
63_N	66_V	0.679	0.23
112_E	148_S	0.671	0.22
164_R	216_F	0.670	0.22
177_N	264_T	0.669	0.22
99_I	163_L	0.668	0.22
155_S	167_L	0.668	0.22
209_F	228_F	0.663	0.22
129_Y	163_L	0.663	0.22
95_F	148_S	0.661	0.22
153_D	183_P	0.659	0.22
67_I	83_S	0.655	0.22
142_E	145_G	0.655	0.22
170_H	278_T	0.654	0.22
125_V	242_F	0.653	0.22
196_R	200_D	0.651	0.22
68_A	81_T	0.648	0.21
114_Q	276_D	0.647	0.21
162_E	289_K	0.646	0.21
162_E	284_H	0.645	0.21
122_S	225_D	0.644	0.21
187_Q	275_L	0.643	0.21
213_D	228_F	0.643	0.21
99_I	150_K	0.642	0.21
102_R	124_V	0.641	0.21
272_R	296_I	0.638	0.21
71_P	126_V	0.637	0.21
101_Q	223_A	0.633	0.21
140_H	159_Q	0.633	0.21
244_Y	292_M	0.633	0.21
112_E	221_L	0.633	0.21
166_M	272_R	0.628	0.21
82_A	197_L	0.628	0.21
166_M	170_H	0.625	0.20
125_V	152_F	0.624	0.20
122_S	146_Q	0.623	0.20
261_E	273_S	0.622	0.20
125_V	143_K	0.621	0.20
162_E	174_H	0.619	0.20
270_I	286_N	0.615	0.20
193_E	220_L	0.612	0.20
128_E	153_D	0.610	0.20
248_E	292_M	0.609	0.20
164_R	192_L	0.609	0.20
240_F	254_R	0.608	0.20
91_F	132_K	0.603	0.20
82_A	128_E	0.602	0.20
96_F	228_F	0.600	0.19
117_R	257_I	0.594	0.19
268_A	282_R	0.593	0.19
69_R	174_H	0.593	0.19
123_P	269_L	0.592	0.19
139_I	290_Q	0.589	0.19
106_P	155_S	0.589	0.19
77_F	219_L	0.585	0.19
64_D	67_I	0.583	0.19
255_N	285_L	0.582	0.19
80_T	133_F	0.581	0.19
122_S	129_Y	0.580	0.19
115_L	150_K	0.580	0.19
125_V	132_K	0.580	0.19
157_A	185_W	0.578	0.19
95_F	240_F	0.578	0.19
163_L	170_H	0.578	0.19
186_L	279_L	0.576	0.19
253_Q	272_R	0.576	0.19
172_L	274_D	0.576	0.19
100_N	155_S	0.575	0.19
175_F	184_R	0.575	0.19
79_C	100_N	0.573	0.18
129_Y	149_M	0.571	0.18
137_N	161_F	0.571	0.18
267_S	283_N	0.570	0.18
156_Y	239_I	0.570	0.18
91_F	172_L	0.568	0.18
138_L	226_N	0.568	0.18
139_I	284_H	0.567	0.18
174_H	181_H	0.565	0.18
131_L	141_S	0.565	0.18
94_A	114_Q	0.564	0.18
230_D	270_I	0.564	0.18
200_D	278_T	0.562	0.18
195_H	237_S	0.561	0.18
123_P	133_F	0.559	0.18
87_Q	121_V	0.558	0.18
197_L	272_R	0.557	0.18
129_Y	250_D	0.557	0.18
124_V	181_H	0.556	0.18
126_V	141_S	0.555	0.18
160_L	167_L	0.555	0.18
89_K	207_R	0.555	0.18
142_E	172_L	0.555	0.18
79_C	224_A	0.554	0.18
122_S	149_M	0.553	0.18
102_R	171_S	0.552	0.18
162_E	178_L	0.551	0.18
276_D	294_R	0.550	0.18
105_R	274_D	0.549	0.18
217_H	226_N	0.548	0.18
237_S	241_H	0.548	0.18
116_A	288_A	0.546	0.17
169_T	213_D	0.546	0.17
174_H	207_R	0.545	0.17
71_P	197_L	0.544	0.17
182_D	264_T	0.541	0.17
223_A	253_Q	0.541	0.17
173_Q	277_A	0.540	0.17
111_S	265_I	0.540	0.17
122_S	174_H	0.537	0.17
81_T	181_H	0.536	0.17
93_Q	220_L	0.536	0.17
92_E	152_F	0.534	0.17
80_T	249_S	0.532	0.17
128_E	255_N	0.532	0.17
147_W	280_A	0.529	0.17
245_Q	254_R	0.528	0.17
160_L	228_F	0.527	0.17
69_R	267_S	0.526	0.17
172_L	188_A	0.525	0.17
85_S	283_N	0.525	0.17
210_S	243_H	0.524	0.17
102_R	116_A	0.523	0.17
163_L	281_L	0.521	0.17
177_N	182_D	0.521	0.17
64_D	215_D	0.521	0.17
191_M	258_A	0.519	0.17
88_N	143_K	0.517	0.16
174_H	220_L	0.515	0.16
236_I	239_I	0.515	0.16
158_E	293_I	0.515	0.16
220_L	225_D	0.515	0.16
82_A	97_T	0.514	0.16
78_A	117_R	0.514	0.16
120_G	201_N	0.513	0.16
76_G	93_Q	0.512	0.16
172_L	278_T	0.512	0.16
97_T	257_I	0.508	0.16
195_H	213_D	0.506	0.16
114_Q	229_F	0.502	0.16
174_H	226_N	0.502	0.16
171_S	244_Y	0.500	0.16

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
3sxyA	2	0.6579	100	0.45	Contact Map
3ihuA	1	0.6711	100	0.452	Contact Map
2hs5A	1	0.6809	100	0.455	Contact Map
3c7jA	4	0.7763	100	0.457	Contact Map
4p9fA	1	0.6908	100	0.459	Contact Map
4p96A	2	0.7303	100	0.475	Contact Map
2di3A	2	0.6842	100	0.48	Contact Map
1hw1A	2	0.6776	100	0.498	Contact Map
3sxmA	2	0.4441	99.8	0.722	Contact Map
3by6A	2	0.4046	99.8	0.728	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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