METR - ECOLI - GREMLIN Contacts

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METR - HTH-type transcriptional regulator MetR

UniProt:	P0A9F9	Sequences: MIEVKHLKTLQALRNCGSLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRKSQPLRFTPQGEILLQLANQVLPQISQALQACNEPQQTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHYSPMFDYEVRLVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQMVAARMGIAALPHWVVESFERQGLVVTKTLGEGLWSRLYAAVRDGEQRQPVTEAFIRSARNHACDHLPFVKSAERPTYDAPTVRPGSPARL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10591
Length:	317 (284)
Sequences:	79387 (57596)
Seq/√Len:	3417.7

ECOLI - METR OXYR AAER LYSR CYSB DMLR YHJC ALLS CYNR TTDR YDHB YBHD TDCA CBL NAC YAFC PGRR HCAR LEUO YBDO GCVA YFIE YFER DSDC ILVY YDCI ABGR XAPR YNEJ YEIE YBEF YCAN YAHB YIDZ YIAU YNFL YEEY NHAR ICIA YHAJ YGFI YJIE HDFR PERR LRHA
BACSU - YWQM YCGK YWBI CYSL GLTC CITR GLTR ALSR YYBE YVBU YTLI BSDA YUST YOFA YKUM YXJO CZCR 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
71_Q	75_Q	3.578	1.00
16_C	25_T	3.355	1.00
156_S	286_R	2.646	1.00
68_L	82_A	2.452	1.00
94_A	139_L	2.446	1.00
12_A	25_T	2.383	1.00
228_V	235_A	2.193	1.00
160_D	263_R	2.192	1.00
90_R	121_D	2.189	1.00
157_P	263_R	2.181	1.00
157_P	160_D	2.177	1.00
171_H	187_E	2.170	1.00
110_N	288_H	2.158	1.00
46_F	61_Q	2.130	1.00
162_E	239_H	2.089	1.00
9_T	36_Q	2.059	1.00
90_R	119_E	2.051	1.00
11_Q	70_N	2.030	1.00
68_L	75_Q	1.996	1.00
11_Q	15_N	1.994	1.00
21_A	24_A	1.993	1.00
160_D	261_W	1.987	1.00
229_A	250_L	1.967	1.00
164_R	239_H	1.959	1.00
180_T	183_D	1.950	1.00
110_N	284_S	1.940	1.00
12_A	16_C	1.938	1.00
92_R	121_D	1.936	1.00
225_I	245_F	1.935	1.00
15_N	70_N	1.934	1.00
14_R	58_F	1.899	1.00
11_Q	66_L	1.894	1.00
12_A	15_N	1.893	1.00
190_L	233_G	1.892	1.00
9_T	33_L	1.858	1.00
72_V	76_I	1.849	1.00
167_L	254_K	1.811	1.00
66_L	70_N	1.805	1.00
164_R	253_T	1.766	1.00
229_A	245_F	1.763	1.00
188_T	215_L	1.753	1.00
155_Y	265_Y	1.703	1.00
50_V	57_R	1.681	1.00
176_K	183_D	1.676	1.00
19_L	37_F	1.675	1.00
14_R	66_L	1.664	1.00
65_L	79_A	1.663	1.00
64_I	82_A	1.652	1.00
130_P	142_V	1.646	1.00
133_A	138_E	1.630	1.00
16_C	21_A	1.596	1.00
11_Q	69_A	1.562	1.00
154_H	270_D	1.552	1.00
15_N	25_T	1.545	1.00
68_L	71_Q	1.519	1.00
111_F	281_F	1.519	1.00
6_H	36_Q	1.508	1.00
156_S	268_V	1.498	1.00
6_H	43_R	1.491	1.00
18_S	21_A	1.488	1.00
132_P	136_Q	1.481	1.00
10_L	66_L	1.463	1.00
9_T	28_Q	1.457	1.00
29_T	32_A	1.443	1.00
6_H	39_D	1.437	1.00
111_F	118_V	1.435	1.00
20_A	30_Q	1.427	1.00
282_I	286_R	1.410	1.00
47_R	50_V	1.408	1.00
144_T	267_A	1.408	1.00
268_V	282_I	1.402	1.00
12_A	26_L	1.397	1.00
154_H	268_V	1.396	1.00
101_I	222_L	1.395	1.00
68_L	78_Q	1.379	1.00
146_D	265_Y	1.375	1.00
86_P	117_Q	1.371	1.00
60_P	63_E	1.362	1.00
52_K	57_R	1.358	1.00
11_Q	73_L	1.356	1.00
72_V	79_A	1.354	1.00
199_L	203_R	1.345	1.00
133_A	139_L	1.336	1.00
92_R	123_K	1.330	1.00
75_Q	78_Q	1.328	1.00
114_N	284_S	1.320	1.00
280_A	283_R	1.318	1.00
266_A	282_I	1.314	1.00
4_V	76_I	1.310	1.00
65_L	80_L	1.310	1.00
134_L	142_V	1.304	1.00
88_Q	117_Q	1.296	1.00
135_Q	152_G	1.295	1.00
110_N	114_N	1.295	1.00
3_E	6_H	1.293	1.00
141_L	266_A	1.280	1.00
161_Y	240_W	1.275	1.00
67_Q	71_Q	1.270	1.00
224_L	235_A	1.266	1.00
169_P	250_L	1.266	1.00
274_R	278_T	1.257	1.00
68_L	79_A	1.251	1.00
141_L	278_T	1.250	1.00
167_L	234_I	1.249	1.00
187_E	234_I	1.246	1.00
245_F	250_L	1.232	1.00
226_Q	229_A	1.225	1.00
157_P	265_Y	1.221	1.00
43_R	80_L	1.221	1.00
112_H	215_L	1.219	1.00
239_H	253_T	1.214	1.00
28_Q	32_A	1.209	1.00
169_P	252_V	1.207	1.00
64_I	67_Q	1.193	1.00
10_L	49_F	1.189	1.00
35_H	39_D	1.184	1.00
112_H	188_T	1.181	1.00
109_E	113_K	1.179	1.00
239_H	243_E	1.177	1.00
10_L	14_R	1.152	1.00
109_E	230_A	1.151	1.00
155_Y	267_A	1.145	1.00
63_E	67_Q	1.128	1.00
38_S	42_Q	1.125	1.00
178_R	257_G	1.122	1.00
172_P	187_E	1.121	1.00
35_H	38_S	1.120	1.00
64_I	68_L	1.116	1.00
121_D	217_S	1.106	1.00
177_T	252_V	1.104	1.00
284_S	288_H	1.087	1.00
71_Q	78_Q	1.087	1.00
188_T	214_S	1.085	1.00
115_W	280_A	1.083	1.00
106_P	230_A	1.080	1.00
7_L	69_A	1.075	1.00
100_C	124_S	1.072	1.00
206_L	211_V	1.072	1.00
110_N	113_K	1.072	1.00
243_E	247_R	1.071	1.00
166_V	253_T	1.068	1.00
156_S	282_I	1.067	1.00
19_L	56_L	1.067	1.00
10_L	48_L	1.066	1.00
12_A	22_A	1.064	1.00
5_K	8_K	1.059	1.00
72_V	75_Q	1.053	1.00
190_L	224_L	1.053	1.00
36_Q	39_D	1.053	1.00
253_T	256_L	1.045	1.00
179_I	183_D	1.044	1.00
283_R	286_R	1.041	1.00
135_Q	150_R	1.041	1.00
226_Q	230_A	1.041	1.00
34_S	38_S	1.041	1.00
13_L	22_A	1.037	1.00
225_I	229_A	1.033	1.00
279_E	283_R	1.024	1.00
111_F	284_S	1.023	1.00
107_A	285_A	1.019	1.00
80_L	84_N	1.016	1.00
269_R	272_E	1.015	1.00
91_L	281_F	1.014	1.00
162_E	261_W	1.009	1.00
218_V	224_L	1.006	1.00
168_A	231_R	0.998	1.00
123_K	133_A	0.991	1.00
244_S	248_Q	0.990	1.00
8_K	77_S	0.990	1.00
74_P	78_Q	0.981	1.00
13_L	19_L	0.973	1.00
284_S	287_N	0.973	1.00
58_F	62_G	0.971	1.00
165_L	234_I	0.952	1.00
111_F	115_W	0.952	1.00
28_Q	33_L	0.951	1.00
65_L	69_A	0.951	1.00
166_V	242_V	0.949	1.00
14_R	49_F	0.946	1.00
9_T	26_L	0.943	1.00
77_S	80_L	0.936	1.00
39_D	42_Q	0.934	1.00
114_N	287_N	0.933	1.00
22_A	33_L	0.932	1.00
10_L	40_L	0.927	1.00
218_V	227_M	0.924	1.00
10_L	58_F	0.924	1.00
167_L	171_H	0.912	1.00
133_A	136_Q	0.907	1.00
200_D	203_R	0.905	1.00
77_S	81_Q	0.900	1.00
21_A	25_T	0.893	1.00
71_Q	74_P	0.892	1.00
97_C	220_N	0.891	1.00
107_A	284_S	0.889	1.00
46_F	83_C	0.887	1.00
5_K	36_Q	0.886	1.00
171_H	174_A	0.884	1.00
49_F	56_L	0.881	1.00
275_Q	278_T	0.879	1.00
17_G	57_R	0.865	1.00
200_D	204_H	0.861	1.00
94_A	130_P	0.858	1.00
139_L	142_V	0.856	1.00
67_Q	70_N	0.855	1.00
89_T	277_V	0.847	1.00
61_Q	83_C	0.844	1.00
20_A	24_A	0.842	1.00
14_R	62_G	0.841	1.00
146_D	263_R	0.838	1.00
94_A	144_T	0.835	1.00
76_I	80_L	0.832	1.00
131_Q	135_Q	0.830	1.00
154_H	157_P	0.829	1.00
109_E	232_M	0.828	1.00
118_V	277_V	0.819	1.00
171_H	175_A	0.817	1.00
242_V	245_F	0.817	1.00
26_L	33_L	0.817	1.00
93_I	141_L	0.814	1.00
94_A	142_V	0.811	1.00
205_F	209_A	0.810	1.00
52_K	55_P	0.810	1.00
153_L	267_A	0.807	1.00
107_A	288_H	0.807	1.00
183_D	186_S	0.805	1.00
75_Q	79_A	0.803	1.00
76_I	79_A	0.802	1.00
172_P	177_T	0.802	1.00
78_Q	82_A	0.800	1.00
245_F	248_Q	0.800	1.00
123_K	139_L	0.799	1.00
171_H	188_T	0.796	1.00
167_L	172_P	0.794	1.00
30_Q	34_S	0.791	1.00
166_V	235_A	0.791	1.00
61_Q	64_I	0.790	1.00
14_R	17_G	0.790	1.00
173_L	187_E	0.789	1.00
17_G	55_P	0.788	1.00
89_T	118_V	0.787	1.00
15_N	66_L	0.787	1.00
10_L	65_L	0.786	1.00
112_H	232_M	0.785	1.00
229_A	248_Q	0.784	1.00
119_E	214_S	0.784	1.00
276_P	280_A	0.783	1.00
13_L	49_F	0.780	1.00
4_V	73_L	0.778	1.00
38_S	47_R	0.776	1.00
17_G	63_E	0.776	1.00
16_C	22_A	0.775	1.00
162_E	259_G	0.774	1.00
168_A	232_M	0.774	1.00
180_T	257_G	0.770	1.00
175_A	188_T	0.770	1.00
13_L	37_F	0.770	1.00
8_K	12_A	0.769	1.00
283_R	287_N	0.766	1.00
189_L	213_P	0.758	1.00
182_E	185_A	0.757	1.00
202_W	206_L	0.756	1.00
6_H	9_T	0.754	1.00
79_A	83_C	0.751	1.00
162_E	255_T	0.747	1.00
227_M	232_M	0.744	1.00
69_A	72_V	0.737	1.00
19_L	33_L	0.737	1.00
246_E	249_G	0.736	1.00
152_G	270_D	0.731	1.00
95_I	100_C	0.731	1.00
13_L	33_L	0.730	1.00
87_Q	115_W	0.730	1.00
70_N	74_P	0.730	1.00
129_D	132_P	0.729	1.00
166_V	237_L	0.728	1.00
141_L	281_F	0.726	1.00
50_V	59_T	0.722	1.00
63_E	66_L	0.722	1.00
114_N	280_A	0.720	1.00
135_Q	153_L	0.720	1.00
220_N	223_L	0.719	1.00
272_E	275_Q	0.716	1.00
168_A	171_H	0.710	1.00
167_L	252_V	0.710	1.00
185_A	211_V	0.702	1.00
111_F	280_A	0.702	1.00
140_D	278_T	0.700	1.00
174_A	252_V	0.700	1.00
280_A	284_S	0.698	1.00
110_N	287_N	0.697	1.00
8_K	11_Q	0.696	1.00
193_P	217_S	0.694	1.00
137_G	269_R	0.692	1.00
61_Q	65_L	0.690	1.00
170_D	231_R	0.685	1.00
238_P	241_V	0.685	1.00
166_V	246_E	0.682	1.00
170_D	174_A	0.682	1.00
204_H	208_P	0.680	1.00
32_A	36_Q	0.680	1.00
205_F	208_P	0.679	1.00
58_F	63_E	0.676	1.00
101_I	226_Q	0.676	1.00
60_P	64_I	0.674	1.00
57_R	63_E	0.672	1.00
50_V	55_P	0.669	1.00
274_R	279_E	0.668	1.00
167_L	173_L	0.662	1.00
92_R	139_L	0.662	1.00
199_L	217_S	0.658	1.00
178_R	255_T	0.657	1.00
65_L	83_C	0.656	1.00
92_R	140_D	0.656	1.00
78_Q	81_Q	0.655	1.00
189_L	234_I	0.654	1.00
246_E	253_T	0.654	1.00
216_K	227_M	0.648	1.00
68_L	72_V	0.646	1.00
41_E	51_R	0.646	1.00
119_E	217_S	0.644	1.00
5_K	39_D	0.643	1.00
204_H	207_Q	0.642	1.00
192_Y	224_L	0.640	1.00
124_S	219_D	0.638	1.00
165_L	236_A	0.636	1.00
41_E	46_F	0.636	1.00
24_A	27_H	0.632	1.00
201_V	205_F	0.627	1.00
145_S	262_S	0.625	1.00
74_P	77_S	0.624	1.00
182_E	209_A	0.623	1.00
242_V	246_E	0.623	1.00
129_D	133_A	0.614	1.00
203_R	207_Q	0.614	1.00
37_F	41_E	0.613	1.00
244_S	247_R	0.612	1.00
104_L	107_A	0.612	1.00
13_L	18_S	0.611	1.00
165_L	184_L	0.610	1.00
276_P	279_E	0.610	1.00
95_I	104_L	0.607	1.00
106_P	109_E	0.605	1.00
202_W	205_F	0.604	1.00
172_P	175_A	0.603	1.00
206_L	213_P	0.603	1.00
173_L	176_K	0.601	1.00
170_D	173_L	0.601	1.00
8_K	73_L	0.599	1.00
91_L	277_V	0.597	1.00
64_I	83_C	0.596	1.00
170_D	252_V	0.593	1.00
10_L	62_G	0.593	1.00
106_P	110_N	0.592	1.00
69_A	73_L	0.590	1.00
172_P	176_K	0.589	1.00
22_A	26_L	0.588	1.00
200_D	205_F	0.586	1.00
81_Q	85_E	0.586	1.00
201_V	204_H	0.585	1.00
141_L	282_I	0.585	1.00
193_P	219_D	0.584	1.00
88_Q	119_E	0.582	1.00
46_F	50_V	0.581	1.00
281_F	285_A	0.581	1.00
224_L	228_V	0.580	1.00
44_L	65_L	0.578	1.00
73_L	77_S	0.575	1.00
134_L	153_L	0.574	1.00
32_A	35_H	0.570	1.00
169_P	249_G	0.569	1.00
44_L	83_C	0.568	1.00
5_K	9_T	0.567	1.00
3_E	39_D	0.567	1.00
91_L	141_L	0.567	1.00
199_L	205_F	0.565	1.00
218_V	223_L	0.565	1.00
19_L	55_P	0.564	1.00
143_M	285_A	0.561	1.00
163_V	236_A	0.560	1.00
134_L	267_A	0.559	1.00
49_F	58_F	0.555	1.00
31_S	35_H	0.554	1.00
124_S	220_N	0.553	1.00
268_V	279_E	0.553	1.00
161_Y	262_S	0.552	1.00
14_R	63_E	0.551	1.00
165_L	189_L	0.550	1.00
158_M	266_A	0.548	1.00
173_L	179_I	0.545	1.00
227_M	233_G	0.545	1.00
29_T	35_H	0.544	1.00
115_W	118_V	0.543	1.00
89_T	117_Q	0.536	1.00
44_L	47_R	0.536	1.00
58_F	66_L	0.536	1.00
203_R	206_L	0.534	1.00
159_F	264_L	0.534	1.00
237_L	242_V	0.533	1.00
94_A	123_K	0.532	1.00
186_S	214_S	0.529	1.00
221_T	238_P	0.529	1.00
101_I	220_N	0.528	1.00
67_Q	82_A	0.524	1.00
19_L	30_Q	0.523	1.00
99_S	103_W	0.523	1.00
9_T	37_F	0.523	1.00
28_Q	36_Q	0.522	1.00
171_H	234_I	0.520	1.00
47_R	61_Q	0.520	1.00
82_A	85_E	0.519	1.00
108_L	120_M	0.518	1.00
146_D	155_Y	0.517	1.00
130_P	137_G	0.517	1.00
194_V	217_S	0.515	1.00
278_T	282_I	0.513	1.00
182_E	211_V	0.512	1.00
154_H	271_G	0.511	1.00
17_G	56_L	0.508	1.00
96_E	99_S	0.508	1.00
103_W	107_A	0.507	1.00
106_P	226_Q	0.505	1.00
68_L	83_C	0.503	1.00
166_V	251_V	0.503	1.00
135_Q	138_E	0.500	1.00
19_L	51_R	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
3fxqA	3	0.9085	100	0.157	Contact Map
2esnA	3	0.9117	100	0.157	Contact Map
1uthA	2	0.7003	100	0.164	Contact Map
3fzvA	4	0.8927	100	0.167	Contact Map
1ixcA	4	0.9054	100	0.169	Contact Map
1al3A	1	0.7035	100	0.176	Contact Map
2h98A	2	0.6625	100	0.179	Contact Map
2h9bA	2	0.6656	100	0.181	Contact Map
4x6gA	4	0.9401	100	0.181	Contact Map
3hhgA	3	0.9085	100	0.185	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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