TDCA - ECOLI - GREMLIN Contacts

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TDCA - HTH-type transcriptional regulator TdcA

UniProt:	P0ACQ7	Sequences: MSTILLPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELVVRKNTGVTLTPAGQLLLSRSESITREMKNMVNEISGMSSEAVVEVSFGFPSLIGFTFMSGMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSAEMKLQDLHVEPLFESEFVLVASKSRTCTGTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADFLTVIPCDMTSPFGSNQFITIPVEETLPVAQYAAVWSKNYRIKKAASVLVELAKEYSSYNGCRRRQLIEVG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10989
Length:	312 (286)
Sequences:	79376 (57344)
Seq/√Len:	3390.8

ECOLI - TDCA OXYR LYSR NAC CYNR CYSB AAER YBHD ABGR CBL YFER LEUO XAPR DMLR TTDR YBDO YDCI PGRR YFIE YHJC METR YDHB DSDC YAFC YAHB HCAR NHAR ALLS YEEY YNFL ILVY YEIE YCAN YBEF YIAU YHAJ YGFI YNEJ YIDZ GCVA ICIA PERR YJIE LRHA HDFR
BACSU - YWBI YCGK CYSL GLTC YTLI YYBE ALSR GLTR BSDA YUST YOFA YVBU YWQM CITR YXJO CZCR YKUM YRAN YOAU

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
76_S	80_E	3.583	1.00
21_S	30_E	3.382	1.00
166_E	295_K	2.714	1.00
102_G	147_L	2.507	1.00
73_R	87_E	2.414	1.00
237_V	244_T	2.298	1.00
17_E	30_E	2.235	1.00
118_K	297_Y	2.234	1.00
181_R	195_E	2.221	1.00
167_P	170_E	2.204	1.00
170_E	272_Q	2.202	1.00
172_E	248_C	2.202	1.00
98_E	129_S	2.162	1.00
26_S	29_K	2.107	1.00
98_E	127_Q	2.104	1.00
167_P	272_Q	2.100	1.00
20_R	75_E	2.076	1.00
188_T	191_S	2.030	1.00
51_V	66_A	2.026	1.00
14_V	41_I	2.017	1.00
16_Q	71_L	1.994	1.00
170_E	270_V	1.991	1.00
238_L	258_Q	1.982	1.00
100_S	129_S	1.974	1.00
234_Y	253_P	1.967	1.00
118_K	293_L	1.965	1.00
73_R	80_E	1.958	1.00
16_Q	75_E	1.930	1.00
198_V	242_F	1.908	1.00
17_E	20_R	1.908	1.00
177_A	262_I	1.890	1.00
77_I	81_M	1.878	1.00
16_Q	20_R	1.877	1.00
14_V	38_V	1.874	1.00
17_E	21_S	1.869	1.00
19_I	63_L	1.862	1.00
174_V	248_C	1.836	1.00
71_L	75_E	1.811	1.00
24_I	42_I	1.802	1.00
138_F	150_A	1.753	1.00
55_V	62_T	1.737	1.00
238_L	253_P	1.724	1.00
70_L	84_M	1.707	1.00
196_Q	224_I	1.707	1.00
69_L	87_E	1.663	1.00
174_V	261_T	1.661	1.00
165_V	274_A	1.652	1.00
141_A	146_R	1.638	1.00
119_F	290_L	1.614	1.00
19_I	71_L	1.595	1.00
20_R	30_E	1.588	1.00
15_F	71_L	1.570	1.00
16_Q	74_S	1.568	1.00
21_S	26_S	1.558	1.00
164_H	279_K	1.552	1.00
14_V	33_L	1.531	1.00
94_E	125_K	1.512	1.00
140_P	144_D	1.511	1.00
25_G	35_Q	1.497	1.00
119_F	126_A	1.497	1.00
11_H	41_I	1.485	1.00
65_P	68_Q	1.477	1.00
11_H	48_Y	1.474	1.00
166_E	277_W	1.457	1.00
52_E	55_V	1.439	1.00
34_T	37_A	1.438	1.00
8_K	11_H	1.430	1.00
23_S	26_S	1.426	1.00
73_R	76_S	1.424	1.00
11_H	44_D	1.422	1.00
207_Y	211_L	1.416	1.00
16_Q	78_T	1.412	1.00
17_E	31_L	1.410	1.00
291_V	295_K	1.410	1.00
283_I	287_A	1.384	1.00
164_H	277_W	1.379	1.00
152_G	276_V	1.377	1.00
73_R	83_N	1.376	1.00
179_K	258_Q	1.369	1.00
154_L	274_A	1.369	1.00
186_T	191_S	1.367	1.00
77_I	84_M	1.356	1.00
277_W	291_V	1.354	1.00
109_F	231_V	1.352	1.00
96_V	125_K	1.349	1.00
9_T	81_M	1.336	1.00
118_K	122_V	1.335	1.00
275_A	291_V	1.325	1.00
100_S	131_Y	1.317	1.00
289_V	292_E	1.311	1.00
171_S	249_D	1.295	1.00
149_F	287_A	1.292	1.00
143_R	162_D	1.289	1.00
142_I	150_A	1.288	1.00
141_A	147_L	1.287	1.00
57_K	62_T	1.283	1.00
195_E	243_L	1.271	1.00
177_A	243_L	1.267	1.00
70_L	85_V	1.264	1.00
149_F	275_A	1.256	1.00
120_K	224_I	1.256	1.00
233_I	244_T	1.254	1.00
80_E	83_N	1.250	1.00
122_V	293_L	1.235	1.00
72_S	76_S	1.219	1.00
235_N	238_L	1.209	1.00
179_K	260_I	1.206	1.00
248_C	261_T	1.206	1.00
68_Q	72_S	1.201	1.00
248_C	252_S	1.196	1.00
73_R	84_M	1.192	1.00
43_N	47_D	1.184	1.00
69_L	72_S	1.183	1.00
120_K	196_Q	1.173	1.00
182_T	195_E	1.171	1.00
167_P	274_A	1.169	1.00
117_N	121_E	1.163	1.00
15_F	54_V	1.163	1.00
214_L	219_I	1.157	1.00
165_V	276_V	1.149	1.00
118_K	121_E	1.148	1.00
252_S	255_G	1.146	1.00
253_P	258_Q	1.144	1.00
33_L	37_A	1.139	1.00
48_Y	85_V	1.134	1.00
15_F	19_I	1.127	1.00
40_K	43_N	1.121	1.00
15_F	53_L	1.117	1.00
198_V	233_I	1.116	1.00
117_N	239_N	1.111	1.00
40_K	44_D	1.110	1.00
99_V	290_L	1.107	1.00
129_S	226_K	1.101	1.00
292_E	295_K	1.084	1.00
39_S	43_N	1.083	1.00
123_F	289_V	1.080	1.00
24_I	61_V	1.078	1.00
76_S	83_N	1.077	1.00
119_F	293_L	1.076	1.00
293_L	297_Y	1.072	1.00
196_Q	222_E	1.068	1.00
227_T	233_I	1.068	1.00
278_S	281_Y	1.065	1.00
13_V	82_K	1.063	1.00
18_V	27_A	1.062	1.00
12_L	74_S	1.060	1.00
10_Q	13_V	1.058	1.00
17_E	27_A	1.058	1.00
261_T	264_V	1.053	1.00
176_V	261_T	1.051	1.00
288_S	292_E	1.049	1.00
77_I	80_E	1.045	1.00
187_T	191_S	1.039	1.00
69_L	73_R	1.038	1.00
178_S	240_A	1.034	1.00
41_I	44_D	1.033	1.00
115_M	294_A	1.027	1.00
114_G	239_N	1.023	1.00
143_R	160_L	1.023	1.00
166_E	291_V	1.020	1.00
234_Y	238_L	1.018	1.00
63_L	67_G	1.013	1.00
235_N	239_N	1.006	1.00
85_V	89_S	0.999	1.00
176_V	251_T	0.990	1.00
175_L	243_L	0.987	1.00
177_A	181_R	0.987	1.00
19_I	54_V	0.975	1.00
172_E	270_V	0.974	1.00
33_L	38_V	0.973	1.00
208_S	211_L	0.972	1.00
102_G	138_F	0.972	1.00
82_K	86_N	0.969	1.00
82_K	85_V	0.967	1.00
199_L	223_N	0.967	1.00
7_P	48_Y	0.960	1.00
14_V	31_L	0.959	1.00
122_V	296_E	0.955	1.00
79_R	83_N	0.955	1.00
119_F	123_F	0.951	1.00
189_L	266_E	0.949	1.00
18_V	24_I	0.945	1.00
15_F	63_L	0.941	1.00
181_R	184_T	0.938	1.00
70_L	74_S	0.936	1.00
293_L	296_E	0.935	1.00
131_Y	141_A	0.926	1.00
227_T	236_L	0.918	1.00
141_A	144_D	0.918	1.00
115_M	293_L	0.914	1.00
54_V	61_V	0.912	1.00
284_K	287_A	0.908	1.00
15_F	45_I	0.907	1.00
156_A	160_L	0.903	1.00
44_D	47_D	0.902	1.00
27_A	38_V	0.897	1.00
127_Q	222_E	0.895	1.00
51_V	88_I	0.893	1.00
19_I	67_G	0.885	1.00
147_L	150_A	0.883	1.00
162_D	279_K	0.879	1.00
26_S	30_E	0.877	1.00
181_R	196_Q	0.871	1.00
72_S	75_E	0.870	1.00
191_S	194_N	0.863	1.00
126_A	286_A	0.851	1.00
102_G	152_G	0.851	1.00
177_A	182_T	0.851	1.00
154_L	272_Q	0.851	1.00
22_G	62_T	0.846	1.00
176_V	244_T	0.845	1.00
105_S	229_S	0.844	1.00
163_L	276_V	0.844	1.00
196_Q	223_N	0.843	1.00
183_C	195_E	0.842	1.00
76_S	79_R	0.841	1.00
101_F	149_F	0.841	1.00
181_R	185_G	0.839	1.00
25_G	29_K	0.837	1.00
57_K	60_G	0.834	1.00
210_L	214_L	0.832	1.00
139_L	143_R	0.832	1.00
292_E	296_E	0.831	1.00
254_F	257_N	0.828	1.00
131_Y	147_L	0.823	1.00
164_H	167_P	0.817	1.00
10_Q	41_I	0.816	1.00
185_G	196_Q	0.812	1.00
102_G	150_A	0.809	1.00
31_L	38_V	0.809	1.00
208_S	212_T	0.801	1.00
22_G	68_Q	0.800	1.00
9_T	78_T	0.799	1.00
283_I	288_S	0.793	1.00
19_I	22_G	0.789	1.00
15_F	70_L	0.788	1.00
213_T	217_N	0.787	1.00
66_A	88_I	0.787	1.00
190_E	193_K	0.786	1.00
43_N	52_E	0.784	1.00
97_V	286_A	0.783	1.00
117_N	241_D	0.781	1.00
178_S	241_D	0.778	1.00
20_R	71_L	0.777	1.00
18_V	54_V	0.776	1.00
80_E	84_M	0.772	1.00
149_F	290_L	0.766	1.00
35_Q	39_S	0.765	1.00
18_V	42_I	0.765	1.00
188_T	265_E	0.763	1.00
172_E	263_P	0.760	1.00
285_K	289_V	0.756	1.00
21_S	27_A	0.755	1.00
81_M	84_M	0.753	1.00
81_M	85_V	0.752	1.00
137_S	140_P	0.752	1.00
95_A	123_F	0.751	1.00
69_L	91_M	0.750	1.00
115_M	297_Y	0.746	1.00
172_E	268_L	0.743	1.00
180_S	184_T	0.742	1.00
83_N	87_E	0.742	1.00
120_K	241_D	0.741	1.00
97_V	126_A	0.740	1.00
236_L	241_D	0.738	1.00
122_V	289_V	0.736	1.00
118_K	296_E	0.736	1.00
22_G	60_G	0.735	1.00
66_A	69_L	0.733	1.00
184_T	260_I	0.732	1.00
11_H	14_V	0.729	1.00
253_P	256_S	0.727	1.00
66_A	91_M	0.725	1.00
89_S	92_S	0.725	1.00
176_V	246_I	0.724	1.00
7_P	85_V	0.724	1.00
177_A	183_C	0.723	1.00
63_L	68_Q	0.722	1.00
143_R	163_L	0.721	1.00
62_T	68_Q	0.717	1.00
84_M	88_I	0.717	1.00
24_I	38_V	0.714	1.00
177_A	260_I	0.714	1.00
207_Y	226_K	0.714	1.00
103_F	108_G	0.712	1.00
213_T	216_R	0.712	1.00
100_S	147_L	0.710	1.00
247_P	250_M	0.708	1.00
13_V	17_E	0.705	1.00
74_S	77_I	0.704	1.00
119_F	289_V	0.703	1.00
55_V	64_T	0.703	1.00
193_K	219_I	0.702	1.00
55_V	60_G	0.698	1.00
37_A	41_I	0.690	1.00
238_L	256_S	0.689	1.00
190_E	217_N	0.689	1.00
75_E	79_R	0.688	1.00
210_L	213_T	0.688	1.00
18_V	38_V	0.688	1.00
188_T	266_E	0.682	1.00
209_E	213_T	0.679	1.00
178_S	181_R	0.678	1.00
151_I	294_A	0.677	1.00
66_A	70_L	0.677	1.00
212_T	216_R	0.676	1.00
281_Y	284_K	0.675	1.00
148_D	287_A	0.669	1.00
46_E	51_V	0.666	1.00
194_N	222_E	0.663	1.00
100_S	148_D	0.663	1.00
145_G	278_S	0.661	1.00
200_P	233_I	0.661	1.00
229_S	232_T	0.661	1.00
212_T	215_Q	0.659	1.00
65_P	69_L	0.658	1.00
79_R	82_K	0.657	1.00
254_F	261_T	0.657	1.00
211_L	215_Q	0.656	1.00
68_Q	71_L	0.655	1.00
225_V	236_L	0.653	1.00
83_N	86_N	0.652	1.00
289_V	293_L	0.651	1.00
103_F	112_M	0.651	1.00
74_S	78_T	0.641	1.00
201_Q	226_K	0.641	1.00
197_W	221_I	0.640	1.00
46_E	56_R	0.639	1.00
24_I	60_G	0.637	1.00
180_S	260_I	0.637	1.00
127_Q	226_K	0.637	1.00
99_V	286_A	0.635	1.00
70_L	88_I	0.630	1.00
29_K	32_G	0.629	1.00
180_S	240_A	0.629	1.00
179_K	257_N	0.625	1.00
176_V	254_F	0.625	1.00
175_L	192_L	0.625	1.00
73_R	77_I	0.623	1.00
10_Q	44_D	0.620	1.00
42_I	46_E	0.620	1.00
180_S	183_C	0.619	1.00
251_T	254_F	0.618	1.00
13_V	16_Q	0.615	1.00
108_G	135_L	0.614	1.00
197_W	243_L	0.613	1.00
27_A	31_L	0.613	1.00
96_V	127_Q	0.612	1.00
18_V	23_S	0.609	1.00
109_F	235_N	0.605	1.00
285_K	288_S	0.600	1.00
169_F	273_Y	0.598	1.00
142_I	276_V	0.598	1.00
175_L	245_V	0.597	1.00
208_S	213_T	0.595	1.00
112_M	115_M	0.593	1.00
211_L	214_L	0.591	1.00
69_L	88_I	0.589	1.00
290_L	294_A	0.588	1.00
137_S	141_A	0.587	1.00
206_Y	210_L	0.587	1.00
86_N	90_G	0.586	1.00
149_F	291_V	0.586	1.00
99_V	149_F	0.584	1.00
201_Q	228_D	0.583	1.00
236_L	242_F	0.578	1.00
175_L	197_W	0.578	1.00
233_I	237_V	0.577	1.00
214_L	221_I	0.575	1.00
63_L	71_L	0.574	1.00
114_G	118_K	0.573	1.00
164_H	280_N	0.573	1.00
36_P	40_K	0.571	1.00
142_I	163_L	0.570	1.00
49_F	70_L	0.568	1.00
277_W	288_S	0.566	1.00
13_V	78_T	0.566	1.00
171_S	271_A	0.565	1.00
227_T	232_T	0.564	1.00
49_F	88_I	0.563	1.00
183_C	186_T	0.563	1.00
182_T	185_G	0.562	1.00
54_V	63_L	0.562	1.00
206_Y	209_E	0.560	1.00
153_T	271_A	0.559	1.00
183_C	187_T	0.558	1.00
114_G	117_N	0.558	1.00
177_A	184_T	0.558	1.00
116_I	128_V	0.558	1.00
182_T	186_T	0.554	1.00
173_F	245_V	0.554	1.00
34_T	40_K	0.554	1.00
51_V	55_V	0.550	1.00
37_A	40_K	0.550	1.00
10_Q	14_V	0.548	1.00
138_F	145_G	0.543	1.00
181_R	243_L	0.540	1.00
72_S	87_E	0.537	1.00
123_F	126_A	0.532	1.00
207_Y	210_L	0.531	1.00
209_E	212_T	0.531	1.00
102_G	131_Y	0.529	1.00
107_I	111_F	0.526	1.00
78_T	82_K	0.526	1.00
230_V	247_P	0.526	1.00
246_I	251_T	0.525	1.00
202_T	226_K	0.523	1.00
15_F	67_G	0.521	1.00
14_V	42_I	0.521	1.00
42_I	54_V	0.520	1.00
49_F	52_E	0.520	1.00
78_T	81_M	0.519	1.00
73_R	88_I	0.518	1.00
74_S	81_M	0.516	1.00
97_V	125_K	0.516	1.00
168_L	275_A	0.516	1.00
52_E	66_A	0.512	1.00
140_P	146_R	0.512	1.00
33_L	41_I	0.509	1.00
151_I	275_A	0.507	1.00
14_V	27_A	0.506	1.00
109_F	229_S	0.504	1.00
287_A	291_V	0.503	1.00
24_I	56_R	0.503	1.00
176_V	259_F	0.502	1.00
24_I	35_Q	0.501	1.00
154_L	165_V	0.501	1.00
86_N	89_S	0.501	1.00
19_I	68_Q	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
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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
3fxqA	3	0.9423	100	0.113	Contact Map
2esnA	3	0.9487	100	0.117	Contact Map
1uthA	2	0.7212	100	0.119	Contact Map
1al3A	1	0.7051	100	0.133	Contact Map
1ixcA	4	0.9295	100	0.134	Contact Map
3fzvA	4	0.9167	100	0.138	Contact Map
2h98A	2	0.6731	100	0.14	Contact Map
4x6gA	4	0.9744	100	0.143	Contact Map
2h9bA	2	0.6763	100	0.148	Contact Map
3szpA	3	0.9199	100	0.162	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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