MTA - BACSU - GREMLIN Contacts

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MTA - HTH-type transcriptional activator mta

UniProt:	P71039	Sequences: MKYQVKQVAEISGVSIRTLHHYDNIELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRLDEIKEMLDHPNFDRKAALQSQKEILMKKKQRMDEMIQTIDRTLLSVDGGETMNKRDLFAGLSMKDIEEHQQTYADEVRKLYGKEIAEETEKRTSAYSADDWRTIMAEFDSIYRRIAARMKHGPDDAEIQAAVGAFRDHICQYHYDCTLDIFRGLGEVYITDERFTDSINQYGEGLAAFLREAIIIYCDHQENPRP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	257 (227)
Sequences:	4559 (3662)
Seq/√Len:	243.0

ECOLI - SOXR ZNTR CUER
BACSU - MTA BMRR YDFL BLTR YYAN ADHR YFMP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
91_K	95_D	5.862	1.00
84_K	102_D	5.256	1.00
42_S	45_D	4.210	1.00
176_R	196_A	3.808	1.00
28_L	52_I	3.469	1.00
16_I	20_H	3.138	1.00
48_R	70_D	3.074	1.00
5_V	20_H	2.929	1.00
88_M	98_I	2.863	1.00
23_D	29_N	2.833	1.00
91_K	94_M	2.807	1.00
61_R	64_E	2.743	1.00
31_S	45_D	2.589	1.00
90_K	93_R	2.552	1.00
34_T	40_L	2.437	1.00
77_K	105_L	2.384	1.00
64_E	67_E	2.361	1.00
83_Q	86_I	2.307	1.00
218_E	222_T	2.304	1.00
81_Q	105_L	2.272	1.00
88_M	102_D	2.266	1.00
84_K	98_I	2.234	1.00
21_H	25_I	2.208	1.00
81_Q	109_D	2.129	1.00
195_G	199_D	2.086	1.00
56_K	62_L	2.004	1.00
87_L	94_M	1.943	1.00
59_G	90_K	1.912	1.00
6_K	10_E	1.898	1.00
77_K	109_D	1.882	1.00
90_K	94_M	1.759	1.00
84_K	88_M	1.732	1.00
8_V	49_L	1.693	1.00
187_D	190_I	1.660	1.00
4_Q	40_L	1.642	1.00
183_H	189_E	1.596	1.00
87_L	98_I	1.595	1.00
91_K	98_I	1.567	1.00
85_E	89_K	1.546	1.00
18_T	21_H	1.530	1.00
200_H	204_Y	1.526	1.00
84_K	105_L	1.524	1.00
25_I	62_L	1.514	1.00
75_D	78_A	1.504	1.00
32_A	40_L	1.495	1.00
167_M	171_D	1.492	1.00
87_L	101_I	1.478	1.00
21_H	62_L	1.460	1.00
4_Q	7_Q	1.452	1.00
7_Q	10_E	1.440	1.00
80_L	101_I	1.436	1.00
80_L	105_L	1.436	1.00
176_R	179_A	1.423	1.00
137_D	141_K	1.419	1.00
146_E	150_E	1.406	1.00
21_H	24_N	1.356	1.00
88_M	91_K	1.353	1.00
132_Q	135_Y	1.327	1.00
212_I	215_G	1.321	1.00
171_D	175_R	1.309	1.00
53_L	56_K	1.302	1.00
94_M	98_I	1.296	1.00
159_S	162_D	1.270	1.00
93_R	97_M	1.266	1.00
132_Q	136_A	1.251	1.00
31_S	42_S	1.243	1.00
86_I	90_K	1.241	1.00
9_A	15_S	1.235	1.00
190_I	194_V	1.234	1.00
136_A	140_R	1.234	1.00
226_F	230_I	1.201	1.00
9_A	12_S	1.195	1.00
172_S	176_R	1.190	1.00
5_V	16_I	1.190	1.00
8_V	46_L	1.188	1.00
3_Y	43_D	1.184	1.00
178_A	182_K	1.164	1.00
86_I	89_K	1.154	1.00
173_I	177_I	1.154	1.00
154_R	159_S	1.151	1.00
36_A	40_L	1.145	1.00
145_K	149_E	1.141	1.00
33_L	45_D	1.133	1.00
153_K	157_A	1.133	1.00
137_D	140_R	1.122	1.00
48_R	69_L	1.114	1.00
87_L	97_M	1.113	1.00
135_Y	139_V	1.110	1.00
64_E	82_S	1.099	1.00
33_L	40_L	1.085	1.00
216_L	219_V	1.082	1.00
50_Q	54_F	1.078	1.00
84_K	101_I	1.074	1.00
66_K	70_D	1.072	1.00
15_S	18_T	1.050	1.00
77_K	81_Q	1.032	1.00
164_R	168_A	1.031	1.00
102_D	106_L	1.026	1.00
133_Q	138_E	1.016	1.00
193_A	196_A	1.011	1.00
60_F	68_M	1.009	1.00
26_E	29_N	1.009	1.00
199_D	203_Q	1.004	1.00
118_D	121_A	1.003	1.00
19_L	23_D	1.001	1.00
135_Y	138_E	0.992	1.00
56_K	59_G	0.988	1.00
121_A	124_S	0.984	1.00
14_V	49_L	0.984	1.00
138_E	142_L	0.975	1.00
180_R	193_A	0.975	1.00
92_Q	95_D	0.966	1.00
173_I	176_R	0.963	1.00
8_V	12_S	0.963	1.00
144_G	147_I	0.960	1.00
179_A	183_H	0.959	1.00
136_A	139_V	0.949	1.00
60_F	79_A	0.945	1.00
170_F	174_Y	0.939	1.00
169_E	203_Q	0.916	1.00
216_L	220_Y	0.913	1.00
138_E	225_R	0.908	1.00
117_R	120_F	0.892	1.00
174_Y	178_A	0.886	1.00
14_V	18_T	0.886	1.00
172_S	175_R	0.886	1.00
60_F	83_Q	0.884	1.00
138_E	141_K	0.883	1.00
92_Q	96_E	0.879	0.99
115_N	119_L	0.879	0.99
85_E	88_M	0.878	0.99
76_R	108_V	0.874	0.99
82_S	85_E	0.866	0.99
107_S	112_E	0.865	0.99
17_R	21_H	0.864	0.99
192_A	195_G	0.863	0.99
201_I	206_Y	0.859	0.99
198_R	208_C	0.845	0.99
27_L	52_I	0.838	0.99
134_T	138_E	0.838	0.99
169_E	196_A	0.836	0.99
177_I	181_M	0.832	0.99
179_A	182_K	0.828	0.99
8_V	45_D	0.826	0.99
169_E	173_I	0.826	0.99
181_M	184_G	0.822	0.99
189_E	192_A	0.822	0.99
215_G	219_V	0.820	0.99
133_Q	136_A	0.817	0.99
50_Q	104_T	0.816	0.99
134_T	137_D	0.816	0.99
136_A	141_K	0.804	0.99
152_E	156_S	0.800	0.99
94_M	97_M	0.797	0.99
209_T	212_I	0.790	0.99
22_Y	49_L	0.789	0.99
19_L	30_P	0.788	0.99
201_I	208_C	0.788	0.99
148_A	151_T	0.786	0.99
180_R	183_H	0.781	0.99
152_E	158_Y	0.781	0.99
193_A	197_F	0.781	0.99
130_E	134_T	0.780	0.99
178_A	184_G	0.779	0.99
12_S	46_L	0.778	0.99
175_R	179_A	0.778	0.99
205_H	212_I	0.776	0.99
125_M	128_I	0.776	0.99
105_L	109_D	0.772	0.99
225_R	228_D	0.771	0.99
191_Q	195_G	0.768	0.99
3_Y	46_L	0.767	0.99
115_N	118_D	0.766	0.99
89_K	92_Q	0.764	0.99
171_D	174_Y	0.763	0.99
56_K	65_I	0.756	0.98
57_E	97_M	0.754	0.98
154_R	158_Y	0.753	0.98
164_R	167_M	0.752	0.98
226_F	229_S	0.749	0.98
165_T	168_A	0.748	0.98
106_L	111_G	0.748	0.98
14_V	94_M	0.743	0.98
168_A	171_D	0.743	0.98
56_K	61_R	0.743	0.98
12_S	28_L	0.741	0.98
3_Y	40_L	0.740	0.98
108_V	111_G	0.737	0.98
153_K	158_Y	0.736	0.98
142_L	145_K	0.735	0.98
186_D	191_Q	0.734	0.98
62_L	65_I	0.733	0.98
182_K	193_A	0.730	0.98
139_V	143_Y	0.727	0.98
206_Y	212_I	0.726	0.98
124_S	129_E	0.725	0.98
227_T	230_I	0.725	0.98
151_T	158_Y	0.724	0.98
29_N	33_L	0.724	0.98
132_Q	140_R	0.719	0.98
78_A	82_S	0.717	0.98
155_T	158_Y	0.715	0.98
149_E	153_K	0.714	0.98
190_I	193_A	0.714	0.98
219_V	226_F	0.711	0.98
211_D	214_R	0.703	0.98
12_S	49_L	0.696	0.97
169_E	172_S	0.691	0.97
23_D	28_L	0.691	0.97
223_D	226_F	0.690	0.97
89_K	93_R	0.689	0.97
148_A	154_R	0.686	0.97
83_Q	97_M	0.680	0.97
132_Q	138_E	0.680	0.97
210_L	213_F	0.677	0.97
88_M	92_Q	0.675	0.97
162_D	165_T	0.675	0.97
225_R	229_S	0.675	0.97
185_P	190_I	0.673	0.97
133_Q	137_D	0.673	0.97
149_E	152_E	0.666	0.97
119_L	122_G	0.665	0.97
44_A	47_E	0.664	0.97
154_R	157_A	0.662	0.96
15_S	21_H	0.661	0.96
135_Y	140_R	0.660	0.96
54_F	104_T	0.656	0.96
9_A	16_I	0.654	0.96
168_A	175_R	0.652	0.96
40_L	45_D	0.652	0.96
120_F	124_S	0.647	0.96
83_Q	101_I	0.644	0.96
108_V	112_E	0.643	0.96
23_D	41_Y	0.638	0.96
51_Q	74_F	0.637	0.96
197_F	213_F	0.637	0.96
141_K	145_K	0.634	0.95
19_L	49_L	0.632	0.95
210_L	214_R	0.630	0.95
206_Y	210_L	0.629	0.95
130_E	133_Q	0.628	0.95
153_K	159_S	0.627	0.95
6_K	16_I	0.625	0.95
126_K	129_E	0.625	0.95
163_W	166_I	0.624	0.95
180_R	190_I	0.623	0.95
157_A	161_D	0.621	0.95
124_S	127_D	0.621	0.95
90_K	97_M	0.619	0.95
198_R	202_C	0.618	0.95
148_A	152_E	0.618	0.95
177_I	182_K	0.617	0.95
217_G	220_Y	0.617	0.95
15_S	38_Y	0.613	0.95
151_T	157_A	0.612	0.95
176_R	180_R	0.611	0.94
17_R	51_Q	0.607	0.94
18_T	49_L	0.607	0.94
33_L	38_Y	0.605	0.94
213_F	216_L	0.604	0.94
139_V	142_L	0.601	0.94
4_Q	20_H	0.601	0.94
151_T	156_S	0.600	0.94
170_F	173_I	0.599	0.94
201_I	204_Y	0.598	0.94
156_S	159_S	0.597	0.94
98_I	102_D	0.595	0.94
194_V	214_R	0.594	0.94
223_D	229_S	0.593	0.94
51_Q	76_R	0.592	0.94
219_V	222_T	0.589	0.93
31_S	44_A	0.586	0.93
115_N	120_F	0.586	0.93
53_L	57_E	0.582	0.93
123_L	128_I	0.582	0.93
84_K	87_L	0.581	0.93
5_V	39_R	0.581	0.93
12_S	56_K	0.580	0.93
124_S	128_I	0.579	0.93
146_E	149_E	0.578	0.93
196_A	199_D	0.574	0.92
96_E	99_Q	0.574	0.92
116_K	121_A	0.574	0.92
121_A	125_M	0.570	0.92
49_L	53_L	0.568	0.92
200_H	203_Q	0.567	0.92
8_V	28_L	0.567	0.92
185_P	194_V	0.567	0.92
22_Y	37_G	0.566	0.92
143_Y	147_I	0.563	0.92
142_L	154_R	0.560	0.92
195_G	198_R	0.559	0.91
106_L	110_G	0.558	0.91
136_A	144_G	0.558	0.91
15_S	230_I	0.558	0.91
217_G	221_I	0.557	0.91
169_E	174_Y	0.556	0.91
17_R	23_D	0.554	0.91
119_L	124_S	0.554	0.91
166_I	170_F	0.554	0.91
23_D	56_K	0.548	0.91
123_L	126_K	0.547	0.91
221_I	224_E	0.546	0.90
132_Q	139_V	0.545	0.90
220_Y	226_F	0.543	0.90
81_Q	85_E	0.540	0.90
92_Q	160_A	0.539	0.90
210_L	217_G	0.538	0.90
88_M	95_D	0.535	0.90
25_I	63_D	0.532	0.89
162_D	203_Q	0.532	0.89
103_R	118_D	0.531	0.89
160_A	163_W	0.531	0.89
153_K	156_S	0.530	0.89
166_I	204_Y	0.530	0.89
212_I	216_L	0.529	0.89
45_D	48_R	0.528	0.89
168_A	172_S	0.524	0.89
177_I	213_F	0.520	0.88
174_Y	179_A	0.519	0.88
218_E	223_D	0.518	0.88
30_P	33_L	0.518	0.88
219_V	223_D	0.517	0.88
121_A	129_E	0.516	0.88
167_M	172_S	0.513	0.88
140_R	145_K	0.512	0.87
50_Q	83_Q	0.511	0.87
95_D	99_Q	0.510	0.87
135_Y	143_Y	0.509	0.87
23_D	52_I	0.508	0.87
212_I	220_Y	0.508	0.87
176_R	193_A	0.507	0.87
122_G	125_M	0.507	0.87
156_S	160_A	0.505	0.87
23_D	32_A	0.503	0.87
175_R	178_A	0.502	0.86
23_D	30_P	0.502	0.86
150_E	153_K	0.501	0.86
83_Q	90_K	0.501	0.86
202_C	206_Y	0.500	0.86

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
3qaoA	2	0.5409	100	0.286	Contact Map
1r8eA	2	0.9222	100	0.434	Contact Map
3gp4A	4	0.4903	99.9	0.511	Contact Map
1r8dA	2	0.4241	99.9	0.512	Contact Map
3hh0A	4	0.5097	99.9	0.515	Contact Map
3gpvA	2	0.428	99.9	0.523	Contact Map
2vz4A	2	0.3891	99.9	0.528	Contact Map
4ua1A	2	0.463	99.9	0.528	Contact Map
1q06A	2	0.4708	99.9	0.531	Contact Map
2zhgA	2	0.463	99.9	0.536	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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