MCBR - ECOLI - GREMLIN Contacts

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MCBR - HTH-type transcriptional regulator McbR

UniProt:	P76114	Sequences: MPGTGKMKHVSLTLQVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQAFTVPEVGKRQLDEINRIRYELELMAVALAVENLTPQDLAELQELLEKLQQAQEKGDMEQIINVNRLFRLAIYHRSNMPILCEMIEQLWVRMGPGLHYLYEAINPAELREHIENYHLLLAALKAKDKEGCRHCLAEIMQQNIAILYQQYNR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13773
Length:	221 (203)
Sequences:	23628 (17405)
Seq/√Len:	1221.6

ECOLI - MCBR YDFH YJJM CSIR PDHR NANR YIEP GLCC UXUR EXUR DGOR LLDR FADR FRLR YEGW YIDP
BACSU - YDHC GNTR YCBG LUTR YVOA YMFC YURK TRER YYDK
SULSO - Q97YR4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
113_Q	193_K	3.648	1.00
98_A	201_R	3.279	1.00
196_D	199_G	2.921	1.00
120_Q	186_H	2.705	1.00
23_Q	28_A	2.701	1.00
30_K	33_A	2.606	1.00
23_Q	43_Q	2.403	1.00
91_E	95_M	2.318	1.00
111_E	141_A	2.242	1.00
37_T	48_I	2.207	1.00
84_E	149_P	2.098	1.00
90_Y	209_Q	2.082	1.00
17_E	57_R	2.036	1.00
65_S	75_P	2.034	1.00
87_R	99_L	1.963	1.00
102_E	197_K	1.962	1.00
21_K	61_V	1.953	1.00
16_V	46_M	1.934	1.00
144_H	152_C	1.842	1.00
66_V	72_F	1.822	1.00
109_L	193_K	1.791	1.00
16_V	44_L	1.760	1.00
191_A	199_G	1.748	1.00
94_L	205_A	1.744	1.00
19_D	23_Q	1.742	1.00
108_D	147_N	1.741	1.00
141_A	144_H	1.735	1.00
105_T	108_D	1.681	1.00
98_A	197_K	1.634	1.00
116_L	189_L	1.631	1.00
184_N	210_Q	1.627	1.00
88_I	154_M	1.605	1.00
127_D	130_Q	1.603	1.00
201_R	205_A	1.595	1.00
94_L	201_R	1.589	1.00
199_G	203_C	1.585	1.00
95_M	98_A	1.568	1.00
22_H	26_I	1.538	1.00
187_L	203_C	1.527	1.00
10_V	18_N	1.493	1.00
118_K	134_V	1.490	1.00
143_Y	155_I	1.429	1.00
120_Q	182_I	1.427	1.00
108_D	145_R	1.426	1.00
139_R	185_Y	1.426	1.00
153_E	157_Q	1.423	1.00
97_V	200_C	1.416	1.00
150_I	161_R	1.415	1.00
90_Y	205_A	1.413	1.00
67_A	70_Q	1.390	1.00
113_Q	189_L	1.388	1.00
140_L	156_E	1.386	1.00
17_E	61_V	1.382	1.00
38_K	42_E	1.367	1.00
115_L	134_V	1.365	1.00
190_A	194_A	1.351	1.00
104_L	109_L	1.344	1.00
90_Y	212_I	1.333	1.00
194_A	199_G	1.331	1.00
197_K	201_R	1.301	1.00
84_E	150_I	1.301	1.00
36_I	39_N	1.279	1.00
186_H	190_A	1.263	1.00
113_Q	117_E	1.232	1.00
39_N	43_Q	1.225	1.00
115_L	141_A	1.216	1.00
114_E	118_K	1.209	1.00
90_Y	94_L	1.207	1.00
118_K	137_L	1.205	1.00
34_R	73_T	1.198	1.00
40_L	51_V	1.195	1.00
116_L	186_H	1.189	1.00
15_Q	19_D	1.187	1.00
67_A	73_T	1.169	1.00
137_L	141_A	1.165	1.00
205_A	209_Q	1.164	1.00
184_N	207_I	1.155	1.00
59_V	66_V	1.155	1.00
202_H	206_E	1.149	1.00
94_L	98_A	1.146	1.00
140_L	144_H	1.145	1.00
19_D	22_H	1.141	1.00
19_D	44_L	1.138	1.00
89_R	93_E	1.127	1.00
115_L	137_L	1.115	1.00
97_V	204_L	1.110	1.00
142_I	192_L	1.107	1.00
23_Q	44_L	1.107	1.00
104_L	108_D	1.104	1.00
104_L	195_K	1.095	1.00
141_A	145_R	1.092	1.00
98_A	198_E	1.089	1.00
199_G	202_H	1.087	1.00
109_L	189_L	1.083	1.00
135_N	139_R	1.072	1.00
96_A	143_Y	1.069	1.00
116_L	120_Q	1.069	1.00
189_L	193_K	1.061	1.00
83_D	212_I	1.060	1.00
97_V	101_V	1.059	1.00
104_L	145_R	1.055	1.00
116_L	119_L	1.054	1.00
84_E	148_M	1.054	1.00
130_Q	133_N	1.054	1.00
113_Q	186_H	1.046	1.00
29_L	74_V	1.041	1.00
134_V	137_L	1.037	1.00
87_R	148_M	1.025	1.00
111_E	144_H	1.025	1.00
65_S	73_T	1.024	1.00
190_A	193_K	1.023	1.00
109_L	195_K	1.012	1.00
10_V	15_Q	1.010	1.00
111_E	114_E	1.009	1.00
78_G	81_Q	1.008	1.00
53_E	56_L	1.004	1.00
154_M	157_Q	1.003	1.00
59_V	64_L	0.996	1.00
99_L	103_N	0.979	1.00
55_L	72_F	0.968	1.00
67_A	71_A	0.967	1.00
23_Q	29_L	0.965	1.00
95_M	201_R	0.957	1.00
191_A	196_D	0.955	1.00
101_V	197_K	0.953	1.00
24_L	74_V	0.950	1.00
138_F	189_L	0.949	1.00
139_R	207_I	0.939	1.00
13_T	57_R	0.938	1.00
117_E	120_Q	0.936	1.00
152_C	156_E	0.931	1.00
93_E	139_R	0.926	1.00
133_N	137_L	0.924	1.00
187_L	206_E	0.923	1.00
185_Y	207_I	0.921	1.00
183_E	187_L	0.920	1.00
111_E	115_L	0.916	1.00
110_A	114_E	0.911	1.00
101_V	192_L	0.908	1.00
57_R	60_S	0.907	1.00
187_L	199_G	0.906	1.00
187_L	190_A	0.906	1.00
37_T	52_R	0.906	1.00
103_N	147_N	0.897	1.00
17_E	21_K	0.892	1.00
64_L	72_F	0.888	1.00
146_S	152_C	0.887	1.00
109_L	113_Q	0.887	1.00
34_R	71_A	0.885	1.00
115_L	118_K	0.883	1.00
198_E	202_H	0.869	1.00
95_M	99_L	0.868	1.00
41_A	51_V	0.861	1.00
70_Q	73_T	0.860	1.00
182_I	186_H	0.856	1.00
21_K	63_A	0.855	1.00
88_I	150_I	0.847	1.00
188_L	204_L	0.841	1.00
47_S	50_P	0.837	1.00
21_K	25_S	0.829	1.00
113_Q	190_A	0.824	1.00
56_L	59_V	0.823	1.00
12_L	15_Q	0.823	1.00
187_L	191_A	0.822	1.00
81_Q	150_I	0.817	1.00
101_V	195_K	0.816	1.00
198_E	201_R	0.812	1.00
100_A	145_R	0.809	1.00
118_K	121_Q	0.809	1.00
150_I	154_M	0.804	1.00
122_A	130_Q	0.804	1.00
108_D	111_E	0.803	1.00
39_N	42_E	0.799	1.00
135_N	185_Y	0.798	1.00
191_A	203_C	0.795	1.00
89_R	208_M	0.794	1.00
150_I	153_E	0.794	1.00
55_L	64_L	0.793	1.00
106_P	110_A	0.793	1.00
56_L	66_V	0.789	1.00
12_L	50_P	0.785	1.00
104_L	192_L	0.784	1.00
101_V	200_C	0.782	1.00
188_L	203_C	0.775	1.00
112_L	141_A	0.772	1.00
106_P	195_K	0.769	1.00
14_L	57_R	0.769	1.00
11_S	14_L	0.768	1.00
99_L	102_E	0.765	1.00
117_E	121_Q	0.759	1.00
87_R	212_I	0.758	1.00
98_A	102_E	0.755	1.00
80_R	147_N	0.750	1.00
99_L	148_M	0.750	1.00
203_C	206_E	0.745	1.00
140_L	159_W	0.745	1.00
40_L	55_L	0.740	1.00
46_M	51_V	0.734	1.00
117_E	186_H	0.733	1.00
179_R	183_E	0.733	1.00
87_R	103_N	0.732	1.00
88_I	151_L	0.729	1.00
136_R	159_W	0.721	1.00
86_N	211_N	0.720	1.00
80_R	84_E	0.720	1.00
13_T	17_E	0.719	1.00
119_L	131_I	0.718	1.00
209_Q	213_A	0.717	1.00
110_A	193_K	0.712	1.00
136_R	163_G	0.707	1.00
112_L	189_L	0.704	1.00
130_Q	134_V	0.699	1.00
110_A	113_Q	0.699	1.00
202_H	205_A	0.698	1.00
206_E	210_Q	0.696	1.00
188_L	200_C	0.693	1.00
140_L	152_C	0.692	1.00
122_A	134_V	0.691	1.00
111_E	137_L	0.690	1.00
108_D	141_A	0.687	1.00
209_Q	212_I	0.682	1.00
88_I	96_A	0.682	1.00
10_V	14_L	0.680	1.00
118_K	122_A	0.680	1.00
114_E	117_E	0.673	1.00
118_K	130_Q	0.673	1.00
29_L	33_A	0.670	1.00
120_Q	124_E	0.667	1.00
184_N	187_L	0.667	1.00
87_R	95_M	0.666	1.00
28_A	43_Q	0.665	1.00
91_E	151_L	0.664	1.00
109_L	192_L	0.664	1.00
57_R	61_V	0.663	1.00
116_L	182_I	0.660	1.00
137_L	140_L	0.658	1.00
188_L	207_I	0.650	1.00
50_P	54_A	0.647	1.00
108_D	144_H	0.643	1.00
13_T	53_E	0.639	1.00
122_A	127_D	0.637	1.00
69_A	72_F	0.628	1.00
100_A	104_L	0.626	1.00
100_A	146_S	0.626	1.00
97_V	197_K	0.625	1.00
32_G	76_E	0.619	1.00
210_Q	214_I	0.616	1.00
96_A	151_L	0.615	1.00
23_Q	27_G	0.604	1.00
88_I	92_L	0.601	1.00
94_L	204_L	0.591	1.00
90_Y	208_M	0.588	1.00
119_L	182_I	0.585	1.00
96_A	146_S	0.585	1.00
91_E	94_L	0.578	1.00
44_L	51_V	0.574	1.00
31_P	76_E	0.572	1.00
98_A	205_A	0.570	1.00
153_E	161_R	0.568	1.00
35_L	64_L	0.563	1.00
93_E	185_Y	0.560	1.00
107_Q	111_E	0.559	1.00
131_I	181_H	0.556	1.00
94_L	197_K	0.556	1.00
149_P	152_C	0.555	1.00
88_I	91_E	0.555	1.00
38_K	41_A	0.554	1.00
23_Q	26_I	0.553	1.00
112_L	145_R	0.552	1.00
136_R	140_L	0.550	1.00
56_L	60_S	0.547	1.00
20_L	40_L	0.547	1.00
80_R	149_P	0.543	1.00
14_L	18_N	0.543	1.00
106_P	193_K	0.542	1.00
210_Q	213_A	0.537	1.00
92_L	155_I	0.536	1.00
100_A	142_I	0.536	1.00
164_P	168_Y	0.536	1.00
97_V	142_I	0.533	1.00
112_L	116_L	0.530	1.00
81_Q	149_P	0.529	1.00
25_S	63_A	0.528	1.00
73_T	76_E	0.527	1.00
42_E	45_G	0.526	1.00
112_L	115_L	0.524	1.00
29_L	35_L	0.522	1.00
188_L	191_A	0.521	1.00
153_E	156_E	0.516	1.00
184_N	206_E	0.516	1.00
87_R	91_E	0.513	1.00
192_L	200_C	0.513	1.00
183_E	186_H	0.511	1.00
99_L	146_S	0.510	1.00
81_Q	161_R	0.508	1.00
75_P	164_P	0.508	1.00
87_R	90_Y	0.507	1.00
177_E	180_E	0.506	1.00
204_L	208_M	0.506	1.00
123_Q	126_G	0.505	1.00
206_E	209_Q	0.505	1.00
177_E	214_I	0.504	1.00
36_I	69_A	0.503	1.00
38_K	48_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
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
2hs5A	1	0.9367	100	0.114	Contact Map
3sxyA	2	0.905	100	0.118	Contact Map
3c7jA	4	0.9774	100	0.118	Contact Map
3ihuA	1	0.9231	100	0.124	Contact Map
4p9fA	1	0.9548	100	0.125	Contact Map
4p96A	2	0.9683	100	0.153	Contact Map
2di3A	2	0.9457	100	0.173	Contact Map
1hw1A	2	0.9276	100	0.195	Contact Map
3ic7A	2	0.4977	99.8	0.522	Contact Map
3by6A	2	0.5566	99.8	0.529	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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