HDFR - ECOLI - GREMLIN Contacts

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HDFR - HTH-type transcriptional regulator HdfR

UniProt:	P0A8R9	Sequences: MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGEKLLPYAETLMSTWQAARKEVAHTSRHNEFSIGASASLWECMLNQWLGRLYQNQDAHTGLQFEARIAQRQSLVKQLHERQLDLLITTEAPKMDEFSSQLLGYFTLALYTSAPSKLKGDLNYLRLEWGPDFQQHEAGLIGADEVPILTTSSAELAQQQIAMLNGCTWLPVSWARKKGGLHTVVDSTTLSRPLYAIWLQNSDKNALIRDLLKINVLDEVY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11449
Length:	279 (266)
Sequences:	78513 (57029)
Seq/√Len:	3496.7

ECOLI - HDFR OXYR LYSR CYNR YNEJ CYSB YFER TDCA NAC YBHD YDCI NHAR METR CBL YEIE ABGR YBDO HCAR DMLR YEEY AAER YNFL LEUO XAPR TTDR YAFC YFIE ILVY ICIA YGFI DSDC YDHB YAHB ALLS PGRR YHJC YBEF GCVA YIDZ LRHA YHAJ YJIE YCAN YIAU PERR
BACSU - YCGK YYBE CYSL GLTR YWBI YKUM CITR BSDA YOFA YWQM GLTC YUST ALSR YTLI YVBU YXJO YOAU CZCR 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
70_T	74_T	3.643	1.00
15_T	24_S	3.434	1.00
159_Q	274_V	2.631	1.00
94_G	142_L	2.578	1.00
67_Y	81_E	2.505	1.00
11_E	24_S	2.392	1.00
219_I	226_T	2.314	1.00
90_E	124_E	2.251	1.00
163_Y	251_P	2.227	1.00
160_L	163_Y	2.218	1.00
160_L	251_P	2.184	1.00
165_T	230_V	2.148	1.00
45_V	60_A	2.129	1.00
90_E	122_Q	2.125	1.00
8_T	35_R	2.110	1.00
20_R	23_E	2.083	1.00
67_Y	74_T	2.039	1.00
10_L	69_E	2.035	1.00
14_R	69_E	2.015	1.00
163_Y	249_S	2.007	1.00
10_L	14_R	1.993	1.00
92_S	124_E	1.992	1.00
110_R	272_I	1.985	1.00
10_L	65_L	1.963	1.00
11_E	14_R	1.947	1.00
11_E	15_T	1.944	1.00
167_A	230_V	1.943	1.00
13_S	57_L	1.897	1.00
8_T	32_V	1.894	1.00
71_L	75_W	1.873	1.00
65_L	69_E	1.845	1.00
220_A	238_G	1.844	1.00
170_T	242_V	1.828	1.00
18_F	36_I	1.777	1.00
49_T	56_R	1.739	1.00
64_L	78_A	1.720	1.00
63_K	81_E	1.715	1.00
158_S	253_Y	1.714	1.00
167_A	241_T	1.714	1.00
13_S	65_L	1.670	1.00
136_Q	141_Q	1.655	1.00
15_T	20_R	1.625	1.00
10_L	68_A	1.591	1.00
14_R	24_S	1.587	1.00
157_S	258_Q	1.583	1.00
5_L	35_R	1.560	1.00
111_L	269_L	1.548	1.00
182_Y	185_L	1.547	1.00
9_F	65_L	1.540	1.00
67_Y	70_T	1.525	1.00
135_K	139_E	1.516	1.00
5_L	42_Q	1.514	1.00
17_H	20_R	1.512	1.00
8_T	27_L	1.500	1.00
111_L	121_L	1.492	1.00
19_G	29_Q	1.492	1.00
159_Q	256_W	1.490	1.00
5_L	38_Q	1.488	1.00
28_T	31_A	1.488	1.00
59_A	62_E	1.464	1.00
11_E	25_L	1.455	1.00
147_T	255_I	1.448	1.00
46_N	49_T	1.445	1.00
157_S	256_W	1.426	1.00
67_Y	77_A	1.426	1.00
101_E	213_E	1.411	1.00
149_E	253_Y	1.402	1.00
71_L	78_A	1.389	1.00
10_L	72_M	1.384	1.00
256_W	270_L	1.374	1.00
51_H	56_R	1.368	1.00
92_S	126_R	1.358	1.00
136_Q	142_L	1.347	1.00
137_L	145_L	1.345	1.00
64_L	79_R	1.340	1.00
172_A	238_G	1.330	1.00
88_H	120_G	1.322	1.00
74_T	77_A	1.320	1.00
270_L	274_V	1.320	1.00
164_F	231_S	1.319	1.00
144_L	266_I	1.318	1.00
138_H	155_E	1.315	1.00
268_D	271_K	1.310	1.00
254_A	270_L	1.302	1.00
3_T	75_W	1.300	1.00
215_A	226_T	1.287	1.00
42_Q	79_R	1.285	1.00
144_L	254_A	1.284	1.00
114_N	118_H	1.280	1.00
262_K	266_I	1.276	1.00
66_P	70_T	1.269	1.00
217_Q	220_A	1.258	1.00
170_T	225_C	1.255	1.00
67_Y	78_A	1.248	1.00
63_K	66_P	1.244	1.00
110_R	114_N	1.242	1.00
160_L	253_Y	1.229	1.00
114_N	272_I	1.221	1.00
27_L	31_A	1.220	1.00
109_G	113_Q	1.208	1.00
9_F	48_F	1.206	1.00
172_A	240_H	1.190	1.00
230_V	241_T	1.188	1.00
158_S	255_I	1.187	1.00
62_E	66_P	1.181	1.00
37_R	41_N	1.179	1.00
230_V	234_R	1.175	1.00
9_F	13_S	1.173	1.00
112_Y	206_I	1.170	1.00
34_F	38_Q	1.163	1.00
109_G	221_M	1.161	1.00
128_A	136_Q	1.135	1.00
34_F	37_R	1.126	1.00
193_Q	196_A	1.125	1.00
9_F	47_L	1.121	1.00
33_S	37_R	1.116	1.00
110_R	113_Q	1.111	1.00
174_S	177_K	1.109	1.00
91_F	269_L	1.104	1.00
70_T	77_A	1.100	1.00
170_T	174_S	1.098	1.00
209_T	215_A	1.096	1.00
118_H	268_D	1.096	1.00
63_K	67_Y	1.094	1.00
100_W	127_I	1.093	1.00
18_F	55_I	1.089	1.00
12_V	21_A	1.085	1.00
124_E	208_T	1.085	1.00
106_Q	221_M	1.083	1.00
6_L	68_A	1.078	1.00
11_E	21_A	1.073	1.00
111_L	272_I	1.072	1.00
169_Y	241_T	1.064	1.00
257_L	260_S	1.064	1.00
183_L	224_G	1.063	1.00
71_L	74_T	1.062	1.00
217_Q	221_M	1.057	1.00
267_R	271_K	1.051	1.00
174_S	178_G	1.050	1.00
138_H	153_M	1.049	1.00
171_S	222_L	1.041	1.00
35_R	38_Q	1.036	1.00
4_E	7_K	1.034	1.00
192_Q	196_A	1.034	1.00
79_R	83_A	1.032	1.00
7_K	76_Q	1.028	1.00
169_Y	233_A	1.027	1.00
194_H	198_L	1.027	1.00
165_T	249_S	1.021	1.00
180_L	240_H	1.020	1.00
159_Q	270_L	1.015	1.00
271_K	274_V	1.014	1.00
107_W	273_N	1.006	1.00
57_L	61_G	1.000	1.00
196_A	200_G	0.996	1.00
8_T	25_L	0.995	1.00
216_Q	220_A	0.992	1.00
73_S	77_A	0.988	1.00
27_L	32_V	0.987	1.00
13_S	48_F	0.987	1.00
64_L	68_A	0.977	1.00
126_R	136_Q	0.972	1.00
111_L	118_H	0.968	1.00
76_Q	79_R	0.965	1.00
193_Q	197_G	0.962	1.00
136_Q	139_E	0.956	1.00
9_F	57_L	0.956	1.00
12_V	18_F	0.954	1.00
76_Q	80_K	0.952	1.00
63_K	85_T	0.951	1.00
38_Q	41_N	0.949	1.00
21_A	32_V	0.946	1.00
168_L	225_C	0.945	1.00
209_T	218_Q	0.943	1.00
107_W	272_I	0.940	1.00
9_F	39_L	0.932	1.00
20_R	24_S	0.921	1.00
263_N	266_I	0.917	1.00
45_V	82_V	0.915	1.00
94_G	145_L	0.912	1.00
48_F	55_I	0.910	1.00
94_G	147_T	0.905	1.00
142_L	145_L	0.901	1.00
70_T	73_S	0.901	1.00
194_H	197_G	0.899	1.00
89_N	265_L	0.892	1.00
198_L	202_D	0.892	1.00
16_R	56_R	0.891	1.00
66_P	69_E	0.887	1.00
13_S	61_G	0.872	1.00
97_A	211_S	0.867	1.00
157_S	160_L	0.865	1.00
156_F	255_I	0.863	1.00
19_G	23_E	0.862	1.00
197_G	201_A	0.860	1.00
134_V	138_H	0.859	1.00
170_T	175_K	0.857	1.00
93_I	144_L	0.853	1.00
121_L	265_L	0.852	1.00
60_A	85_T	0.849	1.00
89_N	121_L	0.842	1.00
51_H	54_N	0.842	1.00
25_L	32_V	0.841	1.00
149_E	251_P	0.839	1.00
175_K	180_L	0.837	1.00
109_G	223_N	0.835	1.00
60_A	82_V	0.834	1.00
75_W	78_A	0.831	1.00
169_Y	226_T	0.831	1.00
75_W	79_R	0.826	1.00
126_R	142_L	0.826	1.00
77_A	81_E	0.822	1.00
9_F	64_L	0.820	1.00
155_E	258_Q	0.819	1.00
13_S	16_R	0.816	1.00
29_Q	33_S	0.809	1.00
122_Q	204_V	0.807	1.00
3_T	72_M	0.806	1.00
16_R	62_E	0.804	1.00
60_A	63_K	0.802	1.00
37_R	46_N	0.801	1.00
14_R	65_L	0.801	1.00
74_T	78_A	0.795	1.00
12_V	36_I	0.791	1.00
195_E	199_I	0.788	1.00
171_S	223_N	0.786	1.00
16_R	54_N	0.781	1.00
112_Y	223_N	0.778	1.00
15_T	21_A	0.777	1.00
218_Q	223_N	0.776	1.00
12_V	48_F	0.775	1.00
264_A	268_D	0.775	1.00
4_E	35_R	0.771	1.00
83_A	86_S	0.770	1.00
5_L	8_T	0.764	1.00
165_T	247_T	0.761	1.00
68_A	71_L	0.760	1.00
7_K	11_E	0.757	1.00
12_V	32_V	0.755	1.00
171_S	174_S	0.754	1.00
260_S	263_N	0.748	1.00
95_A	100_W	0.747	1.00
78_A	82_V	0.744	1.00
170_T	176_L	0.744	1.00
169_Y	228_L	0.743	1.00
144_L	269_L	0.741	1.00
138_H	156_F	0.740	1.00
174_S	225_C	0.740	1.00
196_A	199_I	0.737	1.00
49_T	58_T	0.737	1.00
18_F	32_V	0.733	1.00
211_S	214_L	0.732	1.00
173_P	177_K	0.731	1.00
31_A	35_R	0.730	1.00
220_A	236_K	0.730	1.00
111_L	268_D	0.728	1.00
165_T	243_V	0.728	1.00
69_E	73_S	0.727	1.00
62_E	65_L	0.722	1.00
175_K	178_G	0.721	1.00
198_L	201_A	0.717	1.00
114_N	268_D	0.717	1.00
143_D	266_I	0.716	1.00
57_L	62_E	0.714	1.00
229_P	232_W	0.713	1.00
60_A	64_L	0.705	1.00
170_T	240_H	0.705	1.00
40_E	45_V	0.700	1.00
92_S	142_L	0.700	1.00
56_R	62_E	0.699	1.00
92_S	143_D	0.695	1.00
140_R	257_L	0.693	1.00
173_P	222_L	0.692	1.00
268_D	272_I	0.690	1.00
262_K	267_R	0.688	1.00
183_L	186_E	0.686	1.00
59_A	63_K	0.685	1.00
177_K	240_H	0.679	1.00
7_K	10_L	0.677	1.00
40_E	50_R	0.671	1.00
91_F	265_L	0.671	1.00
23_E	26_Y	0.668	1.00
64_L	82_V	0.667	1.00
49_T	54_N	0.665	1.00
168_L	227_W	0.663	1.00
194_H	199_I	0.658	1.00
175_K	179_D	0.656	1.00
67_Y	71_L	0.656	1.00
73_S	76_Q	0.655	1.00
172_A	237_G	0.653	1.00
176_L	179_D	0.652	1.00
182_Y	187_W	0.651	1.00
68_A	72_M	0.651	1.00
183_L	187_W	0.650	1.00
12_V	17_H	0.650	1.00
101_E	217_Q	0.649	1.00
173_P	176_L	0.647	1.00
122_Q	208_T	0.645	1.00
77_A	80_K	0.644	1.00
127_I	210_S	0.639	1.00
191_F	195_E	0.639	1.00
104_L	107_W	0.639	1.00
36_I	40_E	0.637	1.00
197_G	202_D	0.635	1.00
192_Q	208_T	0.634	1.00
95_A	104_L	0.627	1.00
97_A	129_Q	0.625	1.00
21_A	25_L	0.625	1.00
264_A	267_R	0.620	1.00
137_L	255_I	0.620	1.00
218_Q	224_G	0.616	1.00
4_E	38_Q	0.615	1.00
146_I	273_N	0.615	1.00
89_N	120_G	0.614	1.00
18_F	54_N	0.611	1.00
106_Q	109_G	0.609	1.00
207_L	218_Q	0.609	1.00
148_T	250_R	0.606	1.00
144_L	270_L	0.604	1.00
89_N	118_H	0.604	1.00
4_E	8_T	0.603	1.00
7_K	72_M	0.602	1.00
88_H	122_Q	0.602	1.00
91_F	144_L	0.602	1.00
192_Q	198_L	0.602	1.00
197_G	200_G	0.600	1.00
195_E	198_L	0.600	1.00
269_L	273_N	0.598	1.00
118_H	121_L	0.598	1.00
80_K	84_H	0.597	1.00
174_S	179_D	0.595	1.00
137_L	156_F	0.593	1.00
127_I	211_S	0.593	1.00
106_Q	110_R	0.592	1.00
45_V	49_T	0.592	1.00
173_P	240_H	0.590	1.00
30_S	34_F	0.587	1.00
94_G	128_A	0.584	1.00
184_R	205_P	0.584	1.00
209_T	214_L	0.583	1.00
43_L	64_L	0.583	1.00
63_K	82_V	0.582	1.00
72_M	76_Q	0.582	1.00
199_I	203_E	0.582	1.00
9_F	61_G	0.581	1.00
238_G	241_T	0.581	1.00
162_G	252_L	0.578	1.00
31_A	34_F	0.578	1.00
256_W	267_R	0.577	1.00
99_L	103_M	0.576	1.00
178_G	181_N	0.572	1.00
48_F	57_L	0.571	1.00
94_G	126_R	0.571	1.00
28_T	34_F	0.571	1.00
164_F	250_R	0.569	1.00
166_L	227_W	0.568	1.00
215_A	219_I	0.566	1.00
183_L	215_A	0.565	1.00
43_L	82_V	0.564	1.00
199_I	202_D	0.564	1.00
57_L	65_L	0.562	1.00
157_S	259_N	0.559	1.00
170_T	177_K	0.553	1.00
43_L	46_N	0.547	1.00
189_P	192_Q	0.545	1.00
108_L	123_F	0.543	1.00
8_T	36_I	0.542	1.00
101_E	211_S	0.541	1.00
46_N	60_A	0.540	1.00
161_L	254_A	0.538	1.00
18_F	29_Q	0.538	1.00
18_F	50_R	0.538	1.00
228_L	233_A	0.538	1.00
16_R	55_I	0.536	1.00
27_L	35_R	0.536	1.00
66_P	81_E	0.530	1.00
13_S	62_E	0.529	1.00
80_K	83_A	0.528	1.00
8_T	21_A	0.528	1.00
103_M	107_W	0.526	1.00
106_Q	217_Q	0.524	1.00
105_N	109_G	0.523	1.00
72_M	75_W	0.521	1.00
216_Q	233_A	0.521	1.00
266_I	270_L	0.520	1.00
95_A	125_A	0.519	1.00
71_L	79_R	0.519	1.00
81_E	84_H	0.519	1.00
149_E	158_S	0.516	1.00
6_L	64_L	0.515	1.00
265_L	268_D	0.513	1.00
212_A	229_P	0.513	1.00
138_H	141_Q	0.512	1.00
67_Y	82_V	0.505	1.00
181_N	244_D	0.503	1.00
96_S	99_L	0.502	1.00
176_L	180_L	0.502	1.00
185_L	189_P	0.502	1.00
109_G	112_Y	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
2esnA	3	0.9857	100	0.128	Contact Map
4x6gA	4	0.9892	100	0.131	Contact Map
3fxqA	3	0.9857	100	0.132	Contact Map
1uthA	2	0.7348	100	0.136	Contact Map
2h98A	2	0.6738	100	0.142	Contact Map
1ixcA	4	0.9857	100	0.142	Contact Map
1al3A	1	0.6846	100	0.143	Contact Map
2h9bA	2	0.6738	100	0.144	Contact Map
3fzvA	4	0.9606	100	0.151	Contact Map
3hhgA	3	0.9785	100	0.164	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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