TTDR - ECOLI - GREMLIN Contacts

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TTDR - HTH-type transcriptional activator TtdR

UniProt:	P45463	Sequences: MLNSWPLAKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDVTQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEIPDYYIAHLLTKNKRILCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTHGIWELGNGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLRSEWDVLPFLESGKLVQVLPEYAQSANIWAVYREPLYRSMKLRVCVEFLAAWCQQRLGKPDEGYQVM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12694
Length:	310 (288)
Sequences:	79782 (58104)
Seq/√Len:	3423.8

ECOLI - TTDR DMLR GCVA OXYR AAER YHJC LYSR YAFC PGRR YFER DSDC YCAN CYSB CYNR NAC YAHB ALLS LEUO TDCA YDHB YBHD CBL METR YIAU NHAR YBDO YEEY ABGR YDCI HCAR ILVY YBEF XAPR YNFL YHAJ ICIA YNEJ YEIE YIDZ YFIE PERR YGFI LRHA YJIE HDFR
BACSU - YWBI CYSL YCGK YTLI GLTC ALSR GLTR YYBE YWQM YVBU CITR BSDA YUST YOFA YKUM CZCR YXJO 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
75_E	79_Q	3.524	1.00
20_S	29_T	3.362	1.00
160_H	293_A	2.691	1.00
101_G	143_I	2.548	1.00
72_H	86_D	2.403	1.00
235_A	242_M	2.306	1.00
166_K	246_E	2.227	1.00
175_Y	191_H	2.206	1.00
117_E	295_W	2.195	1.00
164_K	270_N	2.176	1.00
16_E	29_T	2.150	1.00
161_L	164_K	2.135	1.00
19_H	74_L	2.133	1.00
25_A	28_A	2.129	1.00
97_M	128_H	2.106	1.00
97_M	126_Q	2.053	1.00
161_L	270_N	2.034	1.00
184_S	187_E	2.033	1.00
15_V	70_Y	1.993	1.00
232_L	252_F	1.993	1.00
50_T	65_S	1.979	1.00
13_V	40_R	1.977	1.00
164_K	268_S	1.961	1.00
99_R	128_H	1.956	1.00
72_H	79_Q	1.930	1.00
117_E	291_F	1.909	1.00
194_L	240_G	1.900	1.00
76_I	80_Y	1.892	1.00
23_F	41_I	1.890	1.00
15_V	74_L	1.886	1.00
16_E	19_H	1.886	1.00
13_V	37_V	1.884	1.00
18_V	62_L	1.870	1.00
15_V	19_H	1.841	1.00
16_E	20_S	1.839	1.00
236_L	257_K	1.811	1.00
236_L	252_F	1.807	1.00
70_Y	74_L	1.798	1.00
168_I	246_E	1.785	1.00
134_R	146_D	1.768	1.00
54_N	61_A	1.728	1.00
69_C	83_L	1.721	1.00
192_D	222_H	1.673	1.00
118_L	288_C	1.660	1.00
68_R	86_D	1.653	1.00
180_P	187_E	1.643	1.00
159_A	272_W	1.635	1.00
171_A	261_V	1.622	1.00
19_H	29_T	1.608	1.00
14_L	70_Y	1.581	1.00
137_D	142_N	1.571	1.00
18_V	70_Y	1.570	1.00
15_V	73_A	1.564	1.00
13_V	32_Q	1.550	1.00
20_S	25_A	1.542	1.00
158_I	277_E	1.537	1.00
24_S	34_P	1.523	1.00
118_L	125_L	1.513	1.00
93_R	124_E	1.511	1.00
64_E	67_Q	1.504	1.00
10_D	40_R	1.483	1.00
168_I	260_Q	1.480	1.00
10_D	47_T	1.466	1.00
33_T	36_F	1.457	1.00
205_I	209_G	1.457	1.00
7_L	10_D	1.451	1.00
15_V	77_L	1.443	1.00
160_H	275_Y	1.430	1.00
51_T	54_N	1.430	1.00
281_R	285_L	1.425	1.00
136_I	140_Q	1.422	1.00
22_S	25_A	1.412	1.00
10_D	43_I	1.410	1.00
16_E	30_L	1.395	1.00
72_H	75_E	1.393	1.00
289_V	293_A	1.389	1.00
148_R	274_V	1.375	1.00
158_I	275_Y	1.372	1.00
150_N	272_W	1.371	1.00
76_I	83_L	1.367	1.00
72_H	82_R	1.356	1.00
139_V	156_Y	1.335	1.00
108_R	229_E	1.332	1.00
95_E	124_E	1.332	1.00
8_A	80_Y	1.330	1.00
117_E	121_N	1.329	1.00
273_A	289_V	1.326	1.00
145_L	285_L	1.320	1.00
275_Y	289_V	1.301	1.00
287_V	290_E	1.301	1.00
99_R	130_E	1.283	1.00
138_L	146_D	1.276	1.00
137_D	143_I	1.271	1.00
191_H	241_I	1.271	1.00
165_N	247_W	1.265	1.00
145_L	273_A	1.264	1.00
171_A	241_I	1.264	1.00
212_Q	217_V	1.260	1.00
119_M	222_H	1.253	1.00
231_V	242_M	1.251	1.00
69_C	84_V	1.245	1.00
56_S	61_A	1.242	1.00
67_Q	71_E	1.237	1.00
173_P	257_K	1.231	1.00
246_E	250_L	1.230	1.00
42_Q	46_N	1.227	1.00
79_Q	82_R	1.213	1.00
121_N	291_F	1.205	1.00
194_L	231_V	1.195	1.00
71_E	75_E	1.192	1.00
233_Q	236_L	1.191	1.00
176_L	191_H	1.184	1.00
72_H	83_L	1.183	1.00
252_F	257_K	1.176	1.00
117_E	120_R	1.169	1.00
116_T	120_R	1.168	1.00
181_Q	259_V	1.168	1.00
68_R	71_E	1.167	1.00
119_M	192_D	1.164	1.00
250_L	254_E	1.163	1.00
47_T	84_V	1.163	1.00
14_L	53_L	1.159	1.00
161_L	272_W	1.151	1.00
98_I	288_C	1.145	1.00
246_E	260_Q	1.132	1.00
32_Q	36_F	1.130	1.00
14_L	52_L	1.129	1.00
159_A	274_V	1.127	1.00
12_Q	81_Q	1.120	1.00
39_K	42_Q	1.118	1.00
14_L	18_V	1.118	1.00
17_I	26_A	1.104	1.00
257_K	261_V	1.101	1.00
38_T	42_Q	1.099	1.00
118_L	291_F	1.091	1.00
23_F	60_V	1.090	1.00
39_K	43_I	1.087	1.00
290_E	293_A	1.080	1.00
192_D	220_S	1.080	1.00
128_H	224_S	1.079	1.00
75_E	82_R	1.077	1.00
291_F	295_W	1.073	1.00
116_T	237_E	1.072	1.00
225_S	231_V	1.071	1.00
122_Y	287_V	1.066	1.00
11_L	73_A	1.063	1.00
286_R	290_E	1.061	1.00
9_K	12_Q	1.061	1.00
6_P	47_T	1.056	1.00
76_I	79_Q	1.052	1.00
62_L	66_G	1.052	1.00
16_E	26_A	1.050	1.00
172_A	238_G	1.050	1.00
114_A	292_L	1.044	1.00
40_R	43_I	1.034	1.00
232_L	236_L	1.018	1.00
68_R	72_H	1.017	1.00
139_V	154_P	1.003	1.00
160_H	289_V	0.999	1.00
169_L	241_I	0.998	1.00
233_Q	237_E	0.997	1.00
183_Q	187_E	0.995	1.00
113_P	237_E	0.994	1.00
81_Q	85_D	0.992	1.00
166_K	268_S	0.991	1.00
84_V	88_T	0.989	1.00
13_V	30_L	0.984	1.00
101_G	134_R	0.983	1.00
18_V	53_L	0.982	1.00
81_Q	84_V	0.980	1.00
173_P	259_V	0.980	1.00
32_Q	37_V	0.978	1.00
121_N	294_A	0.974	1.00
175_Y	178_K	0.973	1.00
170_C	249_V	0.969	1.00
14_L	62_L	0.959	1.00
118_L	122_Y	0.959	1.00
251_P	255_S	0.955	1.00
171_A	175_Y	0.952	1.00
17_I	23_F	0.948	1.00
262_L	265_Y	0.938	1.00
175_Y	192_D	0.936	1.00
137_D	140_Q	0.935	1.00
291_F	294_A	0.935	1.00
69_C	73_A	0.934	1.00
78_T	82_R	0.930	1.00
195_V	221_G	0.926	1.00
53_L	60_V	0.925	1.00
156_Y	277_E	0.924	1.00
225_S	234_W	0.921	1.00
257_K	260_Q	0.920	1.00
50_T	87_V	0.918	1.00
282_S	285_L	0.917	1.00
18_V	66_G	0.917	1.00
114_A	291_F	0.913	1.00
126_Q	220_S	0.908	1.00
260_Q	263_P	0.899	1.00
26_A	37_V	0.895	1.00
14_L	44_L	0.894	1.00
143_I	146_D	0.893	1.00
175_Y	179_Y	0.883	1.00
43_I	46_N	0.881	1.00
101_G	148_R	0.880	1.00
206_W	209_G	0.877	1.00
171_A	176_L	0.875	1.00
71_E	74_L	0.875	1.00
276_R	279_L	0.874	1.00
25_A	29_T	0.867	1.00
150_N	270_N	0.859	1.00
100_I	145_L	0.858	1.00
130_E	137_D	0.856	1.00
157_Y	274_V	0.854	1.00
290_E	294_A	0.850	1.00
24_S	28_A	0.848	1.00
170_C	242_M	0.848	1.00
125_L	284_K	0.847	1.00
104_F	227_S	0.847	1.00
170_C	260_Q	0.842	1.00
17_I	41_I	0.841	1.00
21_G	61_A	0.840	1.00
187_E	190_R	0.840	1.00
179_Y	192_D	0.835	1.00
192_D	221_G	0.835	1.00
176_L	181_Q	0.831	1.00
56_S	59_G	0.827	1.00
30_L	37_V	0.826	1.00
208_L	212_Q	0.821	1.00
185_L	265_Y	0.820	1.00
177_Q	191_H	0.818	1.00
9_K	40_R	0.818	1.00
75_E	78_T	0.817	1.00
166_K	266_A	0.816	1.00
249_V	252_F	0.805	1.00
101_G	146_D	0.804	1.00
8_A	77_L	0.801	1.00
65_S	87_V	0.799	1.00
14_L	69_C	0.798	1.00
42_Q	51_T	0.798	1.00
18_V	21_G	0.797	1.00
158_I	161_L	0.796	1.00
281_R	286_R	0.796	1.00
17_I	53_L	0.794	1.00
135_Q	139_V	0.787	1.00
21_G	67_Q	0.785	1.00
94_P	122_Y	0.785	1.00
172_A	239_K	0.784	1.00
96_G	284_K	0.778	1.00
174_E	178_K	0.778	1.00
130_E	143_I	0.775	1.00
205_I	224_S	0.774	1.00
252_F	255_S	0.773	1.00
19_H	70_Y	0.771	1.00
186_Q	189_S	0.769	1.00
80_Y	83_L	0.767	1.00
116_T	239_K	0.765	1.00
34_P	38_T	0.764	1.00
79_Q	83_L	0.762	1.00
145_L	288_C	0.758	1.00
6_P	84_V	0.754	1.00
20_S	26_A	0.754	1.00
234_W	239_K	0.753	1.00
21_G	59_G	0.749	1.00
121_N	287_V	0.749	1.00
62_L	67_Q	0.747	1.00
68_R	90_I	0.747	1.00
65_S	90_I	0.747	1.00
88_T	91_K	0.746	1.00
170_C	244_R	0.745	1.00
82_R	86_D	0.742	1.00
117_E	294_A	0.739	1.00
283_M	287_V	0.738	1.00
61_A	67_Q	0.737	1.00
253_L	260_Q	0.735	1.00
170_C	253_L	0.734	1.00
147_I	292_L	0.734	1.00
256_G	260_Q	0.733	1.00
211_G	215_K	0.732	1.00
99_R	143_I	0.730	1.00
186_Q	215_K	0.728	1.00
189_S	217_V	0.728	1.00
10_D	13_V	0.726	1.00
193_C	219_V	0.726	1.00
119_M	239_K	0.724	1.00
139_V	157_Y	0.721	1.00
80_Y	84_V	0.721	1.00
114_A	295_W	0.719	1.00
23_F	37_V	0.716	1.00
65_S	68_R	0.715	1.00
249_V	253_L	0.712	1.00
83_L	87_V	0.712	1.00
73_A	76_I	0.711	1.00
253_L	256_G	0.710	1.00
245_S	248_D	0.710	1.00
17_I	37_V	0.709	1.00
118_L	287_V	0.708	1.00
171_A	177_Q	0.707	1.00
210_N	213_E	0.705	1.00
12_Q	16_E	0.705	1.00
54_N	63_T	0.702	1.00
102_C	107_G	0.701	1.00
36_F	40_R	0.699	1.00
190_R	220_S	0.697	1.00
172_A	175_Y	0.696	1.00
23_F	59_G	0.695	1.00
96_G	125_L	0.691	1.00
223_L	234_W	0.687	1.00
99_R	144_D	0.685	1.00
144_D	285_L	0.676	1.00
205_I	208_L	0.675	1.00
54_N	59_G	0.675	1.00
65_S	69_C	0.675	1.00
45_E	50_T	0.674	1.00
206_W	210_N	0.674	1.00
98_I	284_K	0.671	1.00
227_S	230_I	0.670	1.00
74_L	78_T	0.670	1.00
73_A	77_L	0.668	1.00
196_T	231_V	0.667	1.00
82_R	85_D	0.664	1.00
102_C	111_I	0.664	1.00
78_T	81_Q	0.663	1.00
126_Q	224_S	0.658	1.00
138_L	274_V	0.658	1.00
64_E	68_R	0.652	1.00
26_A	30_L	0.651	1.00
197_K	224_S	0.645	1.00
45_E	55_R	0.643	1.00
193_C	241_I	0.642	1.00
210_N	214_K	0.641	1.00
174_E	177_Q	0.641	1.00
209_G	213_E	0.639	1.00
17_I	22_S	0.638	1.00
67_Q	70_Y	0.637	1.00
69_C	87_V	0.635	1.00
176_L	179_Y	0.633	1.00
211_G	214_K	0.632	1.00
287_V	291_F	0.630	1.00
174_E	238_G	0.628	1.00
41_I	45_E	0.625	1.00
28_A	31_G	0.624	1.00
208_L	211_G	0.623	1.00
141_D	276_R	0.623	1.00
251_P	254_E	0.621	1.00
68_R	87_V	0.620	1.00
171_A	259_V	0.620	1.00
262_L	266_A	0.619	1.00
72_H	76_I	0.617	1.00
288_C	292_L	0.616	1.00
163_T	271_I	0.614	1.00
169_L	193_C	0.613	1.00
9_K	43_I	0.613	1.00
180_P	183_Q	0.612	1.00
212_Q	219_V	0.611	1.00
169_L	188_L	0.610	1.00
207_E	211_G	0.607	1.00
231_V	235_A	0.606	1.00
12_Q	15_V	0.603	1.00
111_I	114_A	0.603	1.00
234_W	240_G	0.599	1.00
62_L	70_Y	0.599	1.00
206_W	211_G	0.597	1.00
204_G	207_E	0.595	1.00
98_I	145_L	0.595	1.00
108_R	233_Q	0.595	1.00
177_Q	180_P	0.593	1.00
197_K	226_N	0.593	1.00
177_Q	183_Q	0.592	1.00
184_S	264_E	0.591	1.00
279_L	282_S	0.590	1.00
283_M	286_R	0.589	1.00
145_L	289_V	0.589	1.00
165_N	269_A	0.588	1.00
158_I	278_P	0.588	1.00
107_G	131_L	0.588	1.00
169_L	243_L	0.588	1.00
85_D	89_Q	0.586	1.00
167_R	243_L	0.585	1.00
95_E	126_Q	0.585	1.00
173_P	256_G	0.581	1.00
138_L	157_Y	0.581	1.00
48_L	87_V	0.581	1.00
134_R	141_D	0.580	1.00
33_T	39_K	0.578	1.00
275_Y	286_R	0.575	1.00
35_A	39_K	0.574	1.00
149_I	269_A	0.572	1.00
48_L	69_C	0.572	1.00
9_K	13_V	0.568	1.00
209_G	212_Q	0.563	1.00
256_G	261_V	0.563	1.00
53_L	62_L	0.560	1.00
36_F	39_K	0.560	1.00
176_L	180_P	0.560	1.00
178_K	259_V	0.559	1.00
113_P	117_E	0.559	1.00
41_I	53_L	0.558	1.00
50_T	54_N	0.557	1.00
198_E	224_S	0.554	1.00
71_E	86_D	0.551	1.00
113_P	116_T	0.549	1.00
48_L	51_T	0.549	1.00
106_F	110_H	0.548	1.00
228_G	245_S	0.548	1.00
77_L	80_Y	0.548	1.00
225_S	230_I	0.547	1.00
171_A	178_K	0.546	1.00
12_Q	77_L	0.545	1.00
96_G	122_Y	0.544	1.00
244_R	249_V	0.543	1.00
115_I	127_V	0.543	1.00
175_Y	241_I	0.541	1.00
73_A	80_Y	0.540	1.00
13_V	41_I	0.539	1.00
147_I	273_A	0.539	1.00
263_P	266_A	0.534	1.00
77_L	81_Q	0.526	1.00
152_E	155_D	0.526	1.00
51_T	65_S	0.525	1.00
23_F	55_R	0.525	1.00
182_P	187_E	0.524	1.00
162_L	273_A	0.524	1.00
204_G	208_L	0.523	1.00
96_G	124_E	0.521	1.00
72_H	87_V	0.520	1.00
258_L	261_V	0.518	1.00
150_N	159_A	0.516	1.00
13_V	26_A	0.515	1.00
174_E	259_V	0.511	1.00
285_L	289_V	0.510	1.00
23_F	34_P	0.508	1.00
85_D	88_T	0.502	1.00
103_S	106_F	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
1uthA	2	0.7194	100	0.128	Contact Map
2esnA	3	0.9452	100	0.133	Contact Map
3szpA	3	0.9323	100	0.136	Contact Map
1ixcA	4	0.9387	100	0.137	Contact Map
3hhgA	3	0.9484	100	0.144	Contact Map
3fxqA	3	0.9323	100	0.145	Contact Map
3fzvA	4	0.9194	100	0.147	Contact Map
1al3A	1	0.7	100	0.152	Contact Map
2h98A	2	0.6806	100	0.153	Contact Map
4x6gA	4	0.9742	100	0.154	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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