DMLR - ECOLI - GREMLIN Contacts

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DMLR - HTH-type transcriptional regulator DmlR

UniProt:	P76250	Sequences: MNNLPLLNDLRVFMLVARRAGFAAVAEELGVSPAFVSKRIALLEQTLNVVLLHRTTRRVTITEEGERIYEWAQRILQDVGQMMDELSDVRQVPQGMLRIISSFGFGRQVVAPALLALAKAYPQLELRFDVEDRLVDLVNEGVDLDIRIGDDIAPNLIARKLATNYRILCASPEFIAQHGAPKHLTDLSALPCLVIKERDHPFGVWQLRNKEGPHAIKVTGPLSSNHGEIVHQWCLDGQGIALRSWWDVSENIASGHLVQVLPEYYQPANVWAVYVSRLATSAKVRITVEFLRQYFAEHYPNFSLEHA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13506
Length:	307 (288)
Sequences:	79839 (58162)
Seq/√Len:	3427.2

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
74_R	78_D	3.628	1.00
19_R	28_E	3.422	1.00
159_R	292_R	2.739	1.00
100_I	142_V	2.555	1.00
71_W	85_E	2.440	1.00
234_C	241_A	2.306	1.00
15_L	28_E	2.264	1.00
116_A	294_Y	2.251	1.00
174_F	190_L	2.236	1.00
163_T	269_N	2.223	1.00
165_Y	245_W	2.221	1.00
160_K	163_T	2.211	1.00
96_M	127_R	2.155	1.00
160_K	269_N	2.119	1.00
24_A	27_E	2.112	1.00
96_M	125_E	2.106	1.00
18_R	73_Q	2.078	1.00
49_V	64_E	2.055	1.00
183_H	186_D	2.044	1.00
12_V	39_R	2.039	1.00
163_T	267_P	2.021	1.00
14_M	69_Y	1.991	1.00
116_A	290_F	1.983	1.00
231_H	251_N	1.980	1.00
71_W	78_D	1.976	1.00
98_R	127_R	1.964	1.00
14_M	73_Q	1.952	1.00
15_L	18_R	1.916	1.00
14_M	18_R	1.910	1.00
235_L	256_H	1.908	1.00
15_L	19_R	1.893	1.00
193_L	239_G	1.886	1.00
12_V	36_V	1.876	1.00
75_I	79_V	1.874	1.00
17_A	61_I	1.870	1.00
167_I	245_W	1.869	1.00
235_L	251_N	1.836	1.00
69_Y	73_Q	1.821	1.00
22_F	40_I	1.801	1.00
170_A	260_V	1.760	1.00
53_H	60_T	1.749	1.00
68_I	82_M	1.716	1.00
191_P	221_P	1.712	1.00
67_R	85_E	1.691	1.00
158_A	271_W	1.674	1.00
179_G	186_D	1.641	1.00
17_A	69_Y	1.610	1.00
136_D	141_G	1.608	1.00
117_L	287_T	1.604	1.00
167_I	259_Q	1.580	1.00
157_I	276_S	1.573	1.00
18_R	28_E	1.571	1.00
14_M	72_A	1.571	1.00
19_R	24_A	1.567	1.00
13_F	69_Y	1.543	1.00
12_V	31_V	1.534	1.00
92_V	123_Q	1.515	1.00
9_D	39_R	1.495	1.00
23_A	33_P	1.494	1.00
9_D	46_T	1.487	1.00
63_E	66_E	1.485	1.00
159_R	274_Y	1.477	1.00
204_V	208_R	1.465	1.00
117_L	124_L	1.452	1.00
50_V	53_H	1.446	1.00
71_W	74_R	1.442	1.00
32_S	35_F	1.440	1.00
21_G	24_A	1.439	1.00
9_D	42_L	1.437	1.00
15_L	29_L	1.425	1.00
288_V	292_R	1.416	1.00
14_M	76_L	1.409	1.00
147_R	273_V	1.405	1.00
6_L	9_D	1.404	1.00
157_I	274_Y	1.398	1.00
149_G	271_W	1.391	1.00
71_W	81_Q	1.380	1.00
280_T	284_V	1.377	1.00
94_Q	123_Q	1.364	1.00
274_Y	288_V	1.358	1.00
75_I	82_M	1.357	1.00
7_L	79_V	1.348	1.00
138_V	155_N	1.345	1.00
107_R	228_E	1.345	1.00
116_A	120_A	1.336	1.00
136_D	142_V	1.332	1.00
272_A	288_V	1.326	1.00
286_I	289_E	1.323	1.00
98_R	129_D	1.312	1.00
55_T	60_T	1.303	1.00
137_L	145_D	1.301	1.00
172_P	256_H	1.300	1.00
164_N	246_W	1.296	1.00
144_L	284_V	1.293	1.00
170_A	240_I	1.284	1.00
144_L	272_A	1.280	1.00
230_V	241_A	1.273	1.00
120_A	290_F	1.272	1.00
190_L	240_I	1.264	1.00
78_D	81_Q	1.263	1.00
118_A	221_P	1.257	1.00
68_I	83_M	1.256	1.00
245_W	249_S	1.235	1.00
70_E	74_R	1.225	1.00
232_Q	235_L	1.219	1.00
71_W	82_M	1.210	1.00
66_E	70_E	1.203	1.00
41_A	45_Q	1.203	1.00
118_A	191_P	1.200	1.00
249_S	253_A	1.198	1.00
115_L	119_K	1.195	1.00
251_N	256_H	1.190	1.00
160_K	271_W	1.187	1.00
67_R	70_E	1.180	1.00
211_E	216_I	1.178	1.00
180_A	258_V	1.175	1.00
13_F	52_L	1.170	1.00
46_T	83_M	1.161	1.00
175_I	190_L	1.159	1.00
116_A	119_K	1.156	1.00
158_A	273_V	1.151	1.00
31_V	35_F	1.151	1.00
245_W	259_Q	1.150	1.00
13_F	17_A	1.126	1.00
38_K	41_A	1.125	1.00
115_L	236_D	1.120	1.00
38_K	42_L	1.118	1.00
259_Q	262_P	1.114	1.00
13_F	51_L	1.111	1.00
131_E	135_V	1.110	1.00
193_L	230_V	1.107	1.00
97_L	287_T	1.098	1.00
289_E	292_R	1.097	1.00
191_P	219_T	1.094	1.00
275_V	278_L	1.092	1.00
121_Y	286_I	1.089	1.00
74_R	81_Q	1.089	1.00
127_R	223_S	1.086	1.00
37_S	41_A	1.084	1.00
290_F	294_Y	1.083	1.00
172_P	258_V	1.079	1.00
10_L	72_A	1.078	1.00
133_R	145_D	1.076	1.00
22_F	59_V	1.067	1.00
75_I	78_D	1.067	1.00
11_R	80_G	1.066	1.00
8_N	11_R	1.063	1.00
117_L	290_F	1.061	1.00
16_V	25_V	1.060	1.00
224_S	230_V	1.058	1.00
15_L	25_V	1.053	1.00
285_R	289_E	1.053	1.00
67_R	71_W	1.050	1.00
106_G	130_V	1.044	1.00
113_A	291_L	1.038	1.00
231_H	235_L	1.036	1.00
39_R	42_L	1.034	1.00
112_P	236_D	1.031	1.00
171_S	237_G	1.029	1.00
159_R	288_V	1.026	1.00
138_V	153_A	1.021	1.00
182_K	186_D	1.014	1.00
61_I	65_G	1.013	1.00
232_Q	236_D	1.012	1.00
165_Y	267_P	1.006	1.00
83_M	87_S	1.004	1.00
80_G	83_M	0.985	1.00
168_L	240_I	0.983	1.00
80_G	84_D	0.971	1.00
31_V	36_V	0.969	1.00
250_E	254_S	0.968	1.00
17_A	52_L	0.964	1.00
169_C	248_V	0.962	1.00
77_Q	81_Q	0.962	1.00
12_V	29_L	0.960	1.00
117_L	121_Y	0.957	1.00
16_V	22_F	0.952	1.00
290_F	293_Q	0.950	1.00
181_P	263_E	0.946	1.00
120_A	293_Q	0.939	1.00
5_P	46_T	0.934	1.00
170_A	174_F	0.934	1.00
194_V	220_G	0.933	1.00
68_I	72_A	0.931	1.00
13_F	61_I	0.928	1.00
136_D	139_N	0.927	1.00
224_S	233_W	0.921	1.00
184_L	264_Y	0.917	1.00
42_L	45_Q	0.915	1.00
169_C	259_Q	0.915	1.00
281_S	284_V	0.914	1.00
129_D	136_D	0.910	1.00
125_E	219_T	0.906	1.00
113_A	290_F	0.905	1.00
25_V	36_V	0.900	1.00
52_L	59_V	0.898	1.00
13_F	43_L	0.898	1.00
49_V	86_L	0.897	1.00
132_D	135_V	0.895	1.00
205_W	208_R	0.894	1.00
24_A	28_E	0.888	1.00
174_F	191_P	0.887	1.00
103_F	226_H	0.885	1.00
17_A	65_G	0.884	1.00
67_R	89_V	0.884	1.00
142_V	145_D	0.876	1.00
174_F	177_Q	0.875	1.00
149_G	269_N	0.874	1.00
70_E	73_Q	0.870	1.00
100_I	147_R	0.867	1.00
155_N	276_S	0.864	1.00
8_N	39_R	0.858	1.00
20_A	60_T	0.857	1.00
289_E	293_Q	0.849	1.00
186_D	189_A	0.848	1.00
170_A	175_I	0.847	1.00
23_A	27_E	0.846	1.00
124_L	283_K	0.843	1.00
74_R	77_Q	0.842	1.00
99_I	144_L	0.840	1.00
135_V	139_N	0.839	1.00
175_I	180_A	0.834	1.00
156_L	273_V	0.834	1.00
169_C	241_A	0.828	1.00
178_H	191_P	0.827	1.00
100_I	145_D	0.825	1.00
191_P	220_G	0.824	1.00
29_L	36_V	0.822	1.00
174_F	178_H	0.820	1.00
55_T	58_R	0.818	1.00
176_A	190_L	0.818	1.00
64_E	89_V	0.817	1.00
205_W	209_N	0.815	1.00
248_V	251_N	0.809	1.00
192_C	218_V	0.808	1.00
157_I	160_K	0.804	1.00
207_L	211_E	0.800	1.00
64_E	86_L	0.797	1.00
7_L	76_L	0.795	1.00
17_A	20_A	0.794	1.00
20_A	66_E	0.790	1.00
115_L	238_Q	0.790	1.00
13_F	68_I	0.790	1.00
95_G	283_K	0.788	1.00
33_P	37_S	0.786	1.00
41_A	50_V	0.779	1.00
280_T	285_R	0.777	1.00
129_D	142_V	0.776	1.00
185_T	188_S	0.775	1.00
210_K	214_H	0.775	1.00
251_N	254_S	0.774	1.00
18_R	69_Y	0.767	1.00
171_S	238_Q	0.767	1.00
19_R	25_V	0.765	1.00
79_V	82_M	0.764	1.00
16_V	40_I	0.763	1.00
16_V	52_L	0.763	1.00
79_V	83_M	0.762	1.00
93_P	121_Y	0.761	1.00
78_D	82_M	0.757	1.00
173_E	177_Q	0.753	1.00
81_Q	85_E	0.750	1.00
64_E	67_R	0.749	1.00
256_H	259_Q	0.747	1.00
120_A	286_I	0.747	1.00
282_A	286_I	0.746	1.00
118_A	238_Q	0.746	1.00
20_A	58_R	0.746	1.00
233_W	238_Q	0.739	1.00
144_L	287_T	0.736	1.00
9_D	12_V	0.735	1.00
116_A	293_Q	0.735	1.00
113_A	294_Y	0.733	1.00
138_V	156_L	0.726	1.00
169_C	243_R	0.725	1.00
11_R	15_L	0.722	1.00
5_P	83_M	0.721	1.00
204_V	223_S	0.721	1.00
188_S	216_I	0.718	1.00
87_S	90_R	0.715	1.00
183_H	263_E	0.714	1.00
185_T	214_H	0.714	1.00
248_V	252_I	0.713	1.00
61_I	66_E	0.710	1.00
72_A	75_I	0.710	1.00
60_T	66_E	0.708	1.00
101_S	106_G	0.707	1.00
209_N	212_G	0.706	1.00
82_M	86_L	0.706	1.00
22_F	36_V	0.705	1.00
117_L	286_I	0.703	1.00
244_S	247_D	0.701	1.00
98_R	142_V	0.698	1.00
53_H	62_T	0.697	1.00
252_I	259_Q	0.697	1.00
53_H	58_R	0.693	1.00
16_V	36_V	0.691	1.00
226_H	229_I	0.691	1.00
171_S	174_F	0.690	1.00
169_C	252_I	0.689	1.00
73_Q	77_Q	0.684	1.00
210_K	213_P	0.683	1.00
170_A	176_A	0.681	1.00
35_F	39_R	0.681	1.00
95_G	124_L	0.676	1.00
64_E	68_I	0.674	1.00
209_N	213_P	0.672	1.00
278_L	281_S	0.672	1.00
189_A	219_T	0.671	1.00
252_I	255_G	0.671	1.00
146_I	291_L	0.668	1.00
66_E	69_Y	0.668	1.00
98_R	143_D	0.667	1.00
63_E	67_R	0.666	1.00
222_L	233_W	0.661	1.00
77_Q	80_G	0.660	1.00
143_D	284_V	0.656	1.00
256_H	260_V	0.653	1.00
196_K	223_S	0.652	1.00
44_E	49_V	0.651	1.00
195_I	230_V	0.650	1.00
140_E	275_V	0.649	1.00
125_E	223_S	0.648	1.00
81_Q	84_D	0.645	1.00
173_E	176_A	0.641	1.00
22_F	58_R	0.639	1.00
286_I	290_F	0.639	1.00
72_A	76_L	0.638	1.00
68_I	86_L	0.637	1.00
8_N	42_L	0.636	1.00
250_E	253_A	0.636	1.00
208_R	212_G	0.635	1.00
44_E	54_R	0.631	1.00
165_Y	265_Y	0.630	1.00
101_S	110_V	0.630	1.00
11_R	14_M	0.629	1.00
170_A	258_V	0.626	1.00
192_C	240_I	0.625	1.00
27_E	30_G	0.625	1.00
97_L	283_K	0.622	1.00
173_E	237_G	0.621	1.00
165_Y	261_L	0.620	1.00
40_I	44_E	0.619	1.00
71_W	75_I	0.617	1.00
107_R	232_Q	0.616	1.00
262_P	265_Y	0.615	1.00
25_V	29_L	0.615	1.00
168_L	187_L	0.615	1.00
211_E	218_V	0.603	1.00
144_L	288_V	0.599	1.00
177_Q	258_V	0.599	1.00
16_V	21_G	0.598	1.00
287_T	291_L	0.598	1.00
282_A	285_R	0.597	1.00
67_R	86_L	0.596	1.00
196_K	225_N	0.594	1.00
162_A	270_V	0.592	1.00
183_H	264_Y	0.591	1.00
206_Q	210_K	0.591	1.00
110_V	113_A	0.590	1.00
134_L	145_D	0.590	1.00
84_D	88_D	0.588	1.00
179_G	182_K	0.586	1.00
137_L	273_V	0.582	1.00
172_P	255_G	0.578	1.00
100_I	133_R	0.575	1.00
148_I	268_A	0.573	1.00
173_E	258_V	0.573	1.00
168_L	242_L	0.573	1.00
233_W	239_G	0.571	1.00
230_V	234_C	0.571	1.00
130_V	226_H	0.571	1.00
61_I	69_Y	0.571	1.00
207_L	210_K	0.570	1.00
97_L	144_L	0.569	1.00
166_R	242_L	0.568	1.00
168_L	192_C	0.568	1.00
35_F	38_K	0.566	1.00
8_N	12_V	0.565	1.00
274_Y	285_R	0.565	1.00
112_P	116_A	0.563	1.00
157_I	277_R	0.563	1.00
175_I	178_H	0.560	1.00
47_L	68_I	0.558	1.00
47_L	86_L	0.556	1.00
34_A	38_K	0.556	1.00
176_A	182_K	0.556	1.00
176_A	179_G	0.555	1.00
112_P	115_L	0.555	1.00
11_R	76_L	0.554	1.00
205_W	210_K	0.553	1.00
164_N	268_A	0.553	1.00
224_S	229_I	0.553	1.00
137_L	156_L	0.550	1.00
47_L	50_V	0.549	1.00
255_G	259_Q	0.549	1.00
130_V	225_N	0.549	1.00
204_V	207_L	0.548	1.00
32_S	38_K	0.547	1.00
175_I	179_G	0.547	1.00
94_Q	125_E	0.547	1.00
161_L	272_A	0.546	1.00
181_P	261_L	0.544	1.00
49_V	53_H	0.543	1.00
174_F	240_I	0.541	1.00
52_L	61_I	0.540	1.00
206_Q	209_N	0.536	1.00
70_E	85_E	0.535	1.00
243_R	248_V	0.530	1.00
76_L	80_G	0.527	1.00
13_F	65_G	0.527	1.00
197_E	223_S	0.527	1.00
76_L	79_V	0.518	1.00
22_F	33_P	0.517	1.00
227_G	244_S	0.517	1.00
12_V	40_I	0.517	1.00
181_P	186_D	0.516	1.00
105_F	109_V	0.516	1.00
185_T	216_I	0.510	1.00
31_V	39_R	0.509	1.00
95_G	121_Y	0.509	1.00
100_I	129_D	0.509	1.00
146_I	272_A	0.509	1.00
208_R	211_E	0.507	1.00
170_A	177_Q	0.507	1.00
50_V	64_E	0.506	1.00
284_V	288_V	0.505	1.00
12_V	25_V	0.504	1.00
6_L	42_L	0.504	1.00
95_G	123_Q	0.503	1.00
40_I	52_L	0.501	1.00
149_G	158_A	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
2esnA	3	0.9511	100	0.113	Contact Map
1uthA	2	0.7264	100	0.117	Contact Map
3hhgA	3	0.9577	100	0.123	Contact Map
3fzvA	4	0.9283	100	0.124	Contact Map
1ixcA	4	0.9446	100	0.126	Contact Map
3szpA	3	0.9414	100	0.127	Contact Map
3fxqA	3	0.9414	100	0.128	Contact Map
1al3A	1	0.7003	100	0.133	Contact Map
4x6gA	4	0.9805	100	0.133	Contact Map
2h98A	2	0.684	100	0.138	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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