GLTR - BACSU - GREMLIN Contacts

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GLTR - HTH-type transcriptional regulator GltR

UniProt:	P94501	Sequences: MNIQLLQVFLTTAREGSISKAALTLNYAQSNVTNKIQQLENDLQTKLFYRHSRGITLTPPGQILVSYSEKILHTIEEARAAMGESSAPSGPLRIGSMETTAAVWLPQLLAHYNNLYPNVDLNLVTGPTEQQIQAVLHYELNGAFISGPIEHPDLVQEKVLDEEMVLVTSASHPVISSIQDVQTQTMLVFRKGCSYRAKLNHILQEEGLLPIKLMEFGILEAIIGCVSAGLGISLLPRSIIASHEKEGRIRSHTISDKYSFVSTMFIRRKDTLITPALSAFLTHMRDHFQIKRPDQS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	296 (281)
Sequences:	79335 (57269)
Seq/√Len:	3416.4

ECOLI - OXYR NAC YNEJ CYNR NHAR CYSB AAER ABGR LYSR YBHD CBL TDCA YAFC DMLR LEUO YFIE YFER TTDR DSDC YCAN YEIE YBDO YDCI PGRR HCAR YDHB YGFI YHJC METR ALLS YEEY YAHB ILVY YBEF YIAU YNFL GCVA YIDZ ICIA XAPR YHAJ LRHA YJIE HDFR PERR
BACSU - GLTR YWBI YUST CYSL YCGK ALSR GLTC YOFA YTLI YYBE YWQM YVBU BSDA CITR CZCR YXJO 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
70_K	74_T	3.652	1.00
15_E	24_T	3.392	1.00
157_E	285_R	2.667	1.00
95_G	140_L	2.525	1.00
67_Y	81_A	2.487	1.00
11_T	24_T	2.419	1.00
161_D	262_S	2.239	1.00
158_K	262_S	2.238	1.00
91_P	122_N	2.235	1.00
226_V	233_S	2.227	1.00
158_K	161_D	2.221	1.00
172_H	184_Q	2.218	1.00
45_T	60_P	2.149	1.00
91_P	120_D	2.100	1.00
163_E	237_R	2.097	1.00
8_V	35_K	2.091	1.00
111_H	283_H	2.054	1.00
10_L	69_E	2.052	1.00
177_S	180_D	2.047	1.00
20_K	23_L	2.023	1.00
67_Y	74_T	2.020	1.00
161_D	260_F	2.019	1.00
10_L	14_R	2.003	1.00
227_S	248_R	1.990	1.00
165_V	237_R	1.985	1.00
93_R	122_N	1.963	1.00
11_T	15_E	1.954	1.00
10_L	65_V	1.921	1.00
11_T	14_R	1.921	1.00
14_R	69_E	1.915	1.00
223_I	243_H	1.904	1.00
168_T	252_H	1.868	1.00
13_A	57_L	1.865	1.00
227_S	243_H	1.864	1.00
8_V	32_V	1.857	1.00
71_I	75_I	1.853	1.00
187_L	231_G	1.851	1.00
65_V	69_E	1.829	1.00
165_V	251_S	1.779	1.00
185_T	213_L	1.753	1.00
49_Y	56_T	1.713	1.00
156_Q	264_M	1.700	1.00
63_I	81_A	1.700	1.00
13_A	65_V	1.668	1.00
134_A	139_E	1.666	1.00
64_L	78_A	1.660	1.00
18_I	36_I	1.639	1.00
15_E	20_K	1.625	1.00
155_V	269_K	1.589	1.00
10_L	68_S	1.564	1.00
14_R	24_T	1.534	1.00
67_Y	70_K	1.534	1.00
157_E	267_R	1.516	1.00
17_S	20_K	1.509	1.00
133_Q	137_H	1.508	1.00
5_L	35_K	1.498	1.00
112_Y	280_F	1.496	1.00
5_L	42_D	1.493	1.00
9_F	65_V	1.472	1.00
8_V	27_Y	1.470	1.00
5_L	38_Q	1.460	1.00
46_K	49_Y	1.442	1.00
87_A	118_N	1.439	1.00
11_T	25_L	1.439	1.00
28_A	31_N	1.436	1.00
281_L	285_R	1.434	1.00
155_V	267_R	1.424	1.00
67_Y	77_E	1.418	1.00
112_Y	119_V	1.417	1.00
102_A	220_E	1.417	1.00
145_I	266_I	1.415	1.00
19_S	29_Q	1.414	1.00
267_R	281_L	1.407	1.00
147_G	264_M	1.385	1.00
51_H	56_T	1.384	1.00
273_I	277_L	1.380	1.00
59_P	62_Q	1.379	1.00
196_R	200_N	1.372	1.00
93_R	124_V	1.363	1.00
71_I	78_A	1.357	1.00
115_L	283_H	1.357	1.00
134_A	140_L	1.353	1.00
279_A	282_T	1.353	1.00
74_T	77_E	1.350	1.00
10_L	72_L	1.348	1.00
135_V	143_A	1.346	1.00
89_S	118_N	1.337	1.00
170_A	248_R	1.330	1.00
136_L	153_D	1.316	1.00
64_L	79_R	1.316	1.00
162_E	238_S	1.308	1.00
265_F	281_L	1.302	1.00
111_H	115_L	1.289	1.00
66_S	70_K	1.284	1.00
222_I	233_S	1.279	1.00
170_A	250_R	1.263	1.00
142_G	265_F	1.262	1.00
224_G	227_S	1.257	1.00
113_N	213_L	1.254	1.00
3_I	75_I	1.252	1.00
67_Y	78_A	1.251	1.00
243_H	248_R	1.249	1.00
184_Q	232_I	1.246	1.00
42_D	79_R	1.240	1.00
168_T	232_I	1.239	1.00
142_G	277_L	1.235	1.00
158_K	264_M	1.227	1.00
63_I	66_S	1.220	1.00
237_R	251_S	1.220	1.00
27_Y	31_N	1.216	1.00
110_A	114_N	1.197	1.00
113_N	185_T	1.196	1.00
241_A	245_K	1.183	1.00
237_R	241_A	1.178	1.00
9_F	48_F	1.176	1.00
110_A	228_A	1.175	1.00
34_N	38_Q	1.172	1.00
156_Q	266_I	1.162	1.00
9_F	13_A	1.152	1.00
173_P	184_Q	1.142	1.00
126_G	134_A	1.139	1.00
62_Q	66_S	1.135	1.00
63_I	67_Y	1.132	1.00
122_N	215_E	1.121	1.00
172_H	175_I	1.119	1.00
37_Q	41_N	1.113	1.00
107_Q	228_A	1.110	1.00
116_Y	279_A	1.106	1.00
34_N	37_Q	1.104	1.00
6_L	68_S	1.097	1.00
70_K	77_E	1.093	1.00
185_T	211_I	1.089	1.00
251_S	254_I	1.088	1.00
157_E	281_L	1.080	1.00
282_T	285_R	1.079	1.00
223_I	227_S	1.071	1.00
11_T	21_A	1.070	1.00
167_V	251_S	1.067	1.00
101_A	125_T	1.065	1.00
18_I	55_I	1.065	1.00
111_H	114_N	1.060	1.00
224_G	228_A	1.054	1.00
9_F	47_L	1.054	1.00
71_I	74_T	1.046	1.00
33_T	37_Q	1.044	1.00
278_S	282_T	1.039	1.00
112_Y	283_H	1.035	1.00
203_L	208_L	1.031	1.00
136_L	151_H	1.031	1.00
108_L	284_M	1.030	1.00
216_F	222_I	1.029	1.00
242_S	246_E	1.025	1.00
12_T	21_A	1.019	1.00
79_R	83_G	1.019	1.00
187_L	222_I	1.016	1.00
35_K	38_Q	1.016	1.00
92_L	280_F	1.016	1.00
163_E	260_F	1.016	1.00
169_S	229_G	1.008	1.00
168_T	172_H	1.005	1.00
197_A	200_N	0.999	1.00
73_H	77_E	0.998	1.00
283_H	286_D	0.993	1.00
4_Q	7_Q	0.992	1.00
124_V	134_A	0.992	1.00
188_V	212_K	0.980	1.00
64_L	68_S	0.976	1.00
7_Q	76_E	0.971	1.00
12_T	18_I	0.966	1.00
57_L	61_G	0.963	1.00
178_I	256_D	0.963	1.00
38_Q	41_N	0.961	1.00
27_Y	32_V	0.960	1.00
112_Y	116_Y	0.959	1.00
167_V	240_I	0.957	1.00
76_E	79_R	0.952	1.00
8_V	25_L	0.947	1.00
76_E	80_A	0.944	1.00
13_A	48_F	0.943	1.00
166_L	232_I	0.943	1.00
172_H	176_S	0.942	1.00
21_A	32_V	0.935	1.00
216_F	225_C	0.923	1.00
134_A	137_H	0.921	1.00
9_F	57_L	0.918	1.00
20_K	24_T	0.917	1.00
9_F	39_L	0.914	1.00
70_K	73_H	0.907	1.00
274_T	277_L	0.906	1.00
108_L	283_H	0.903	1.00
115_L	286_D	0.897	1.00
45_T	82_M	0.890	1.00
147_G	262_S	0.882	1.00
16_G	56_T	0.880	1.00
98_E	218_I	0.880	1.00
95_G	143_A	0.880	1.00
95_G	145_I	0.873	1.00
48_F	55_I	0.866	1.00
66_S	69_E	0.861	1.00
75_I	79_R	0.858	1.00
199_L	203_L	0.857	1.00
202_I	206_E	0.856	1.00
174_V	184_Q	0.854	1.00
140_L	143_A	0.853	1.00
120_D	211_I	0.850	1.00
185_T	212_K	0.848	1.00
19_S	23_L	0.845	1.00
132_I	136_L	0.844	1.00
110_A	230_L	0.835	1.00
155_V	158_K	0.834	1.00
25_L	32_V	0.832	1.00
168_T	173_P	0.830	1.00
197_A	201_H	0.830	1.00
268_R	271_T	0.827	1.00
60_P	82_M	0.826	1.00
124_V	140_L	0.824	1.00
119_V	276_A	0.822	1.00
94_I	142_G	0.821	1.00
51_H	54_G	0.821	1.00
154_L	266_I	0.818	1.00
77_E	81_A	0.816	1.00
13_A	61_G	0.815	1.00
243_H	246_E	0.814	1.00
60_P	63_I	0.812	1.00
177_S	255_S	0.811	1.00
90_G	276_A	0.809	1.00
29_Q	33_T	0.809	1.00
273_I	278_S	0.809	1.00
13_A	16_G	0.807	1.00
167_V	233_S	0.804	1.00
75_I	78_A	0.801	1.00
113_N	230_L	0.800	1.00
16_G	62_Q	0.798	1.00
14_R	65_V	0.794	1.00
240_I	243_H	0.791	1.00
9_F	64_L	0.791	1.00
176_S	185_T	0.790	1.00
282_T	286_D	0.786	1.00
179_Q	182_Q	0.781	1.00
74_T	78_A	0.781	1.00
15_E	21_A	0.778	1.00
275_P	279_A	0.777	1.00
16_G	54_G	0.776	1.00
4_Q	35_K	0.776	1.00
3_I	72_L	0.774	1.00
37_Q	46_K	0.773	1.00
7_Q	11_T	0.772	1.00
168_T	174_V	0.770	1.00
186_M	210_P	0.768	1.00
169_S	230_L	0.766	1.00
163_E	253_T	0.761	1.00
153_D	269_K	0.757	1.00
172_H	185_T	0.757	1.00
90_G	119_V	0.756	1.00
12_T	48_F	0.756	1.00
69_E	73_H	0.756	1.00
78_A	82_M	0.754	1.00
5_L	8_V	0.752	1.00
198_K	202_I	0.752	1.00
175_I	250_R	0.748	1.00
202_I	205_E	0.739	1.00
240_I	244_E	0.739	1.00
96_S	101_A	0.739	1.00
199_L	202_I	0.738	1.00
225_C	230_L	0.737	1.00
49_Y	58_T	0.736	1.00
62_Q	65_V	0.736	1.00
68_S	71_I	0.733	1.00
180_D	183_T	0.732	1.00
142_G	280_F	0.730	1.00
167_V	235_L	0.729	1.00
115_L	279_A	0.729	1.00
218_I	221_A	0.728	1.00
171_S	175_I	0.727	1.00
112_Y	279_A	0.726	1.00
18_I	32_V	0.724	1.00
182_Q	208_L	0.723	1.00
167_V	244_E	0.723	1.00
12_T	36_I	0.717	1.00
138_Y	268_R	0.717	1.00
279_A	283_H	0.714	1.00
173_P	176_S	0.713	1.00
88_P	116_Y	0.713	1.00
12_T	32_V	0.711	1.00
236_P	239_I	0.707	1.00
169_S	172_H	0.707	1.00
244_E	247_G	0.706	1.00
168_T	250_R	0.705	1.00
136_L	154_L	0.704	1.00
200_N	204_Q	0.701	1.00
177_S	256_D	0.700	1.00
60_P	64_L	0.693	1.00
201_H	205_E	0.690	1.00
59_P	63_I	0.688	1.00
93_R	140_L	0.686	1.00
7_Q	10_L	0.686	1.00
190_R	215_E	0.685	1.00
31_N	35_K	0.685	1.00
171_S	229_G	0.684	1.00
141_N	277_L	0.683	1.00
244_E	251_S	0.680	1.00
57_L	62_Q	0.676	1.00
93_R	141_N	0.671	1.00
56_T	62_Q	0.670	1.00
102_A	224_G	0.661	1.00
64_L	82_M	0.661	1.00
198_K	201_H	0.652	1.00
171_S	174_V	0.651	1.00
197_A	202_I	0.649	1.00
67_Y	71_I	0.649	1.00
49_Y	54_G	0.649	1.00
242_S	245_K	0.645	1.00
73_H	76_E	0.644	1.00
23_L	26_N	0.643	1.00
189_F	222_I	0.642	1.00
111_H	286_D	0.641	1.00
77_E	80_A	0.640	1.00
40_E	45_T	0.639	1.00
163_E	257_K	0.639	1.00
183_T	211_I	0.637	1.00
214_M	225_C	0.632	1.00
271_T	274_T	0.631	1.00
186_M	232_I	0.631	1.00
40_E	50_R	0.630	1.00
125_T	217_G	0.630	1.00
201_H	204_Q	0.628	1.00
166_L	234_L	0.625	1.00
120_D	215_E	0.623	1.00
107_Q	110_A	0.621	1.00
36_I	40_E	0.618	1.00
105_L	108_L	0.618	1.00
196_R	215_E	0.617	1.00
171_S	250_R	0.617	1.00
7_Q	72_L	0.615	1.00
96_S	105_L	0.615	1.00
275_P	278_S	0.615	1.00
166_L	181_V	0.609	1.00
146_S	261_V	0.607	1.00
179_Q	206_E	0.606	1.00
80_A	84_E	0.605	1.00
98_E	127_P	0.605	1.00
68_S	72_L	0.602	1.00
190_R	217_G	0.597	1.00
4_Q	38_Q	0.597	1.00
92_L	276_A	0.596	1.00
142_G	281_L	0.596	1.00
9_F	61_G	0.594	1.00
170_A	247_G	0.589	1.00
12_T	17_S	0.587	1.00
43_L	64_L	0.587	1.00
200_N	203_L	0.586	1.00
92_L	142_G	0.585	1.00
21_A	25_L	0.584	1.00
72_L	76_E	0.582	1.00
45_T	49_Y	0.576	1.00
107_Q	111_H	0.576	1.00
89_S	120_D	0.571	1.00
4_Q	8_V	0.570	1.00
43_L	82_M	0.570	1.00
63_I	82_M	0.565	1.00
45_T	85_S	0.564	1.00
116_Y	119_V	0.564	1.00
31_N	34_N	0.564	1.00
227_S	246_E	0.564	1.00
48_F	57_L	0.562	1.00
267_R	278_S	0.562	1.00
216_F	221_A	0.561	1.00
162_E	261_V	0.560	1.00
125_T	218_I	0.559	1.00
135_V	266_I	0.558	1.00
195_Y	199_L	0.557	1.00
135_V	154_L	0.557	1.00
95_G	126_G	0.555	1.00
160_L	263_T	0.554	1.00
166_L	186_M	0.553	1.00
95_G	124_V	0.552	1.00
280_F	284_M	0.552	1.00
203_L	210_P	0.551	1.00
222_I	226_V	0.550	1.00
172_H	232_I	0.549	1.00
13_A	62_Q	0.548	1.00
235_L	240_I	0.548	1.00
159_V	265_F	0.547	1.00
144_F	284_M	0.545	1.00
57_L	65_V	0.543	1.00
182_Q	209_L	0.542	1.00
30_S	34_N	0.542	1.00
168_T	175_I	0.542	1.00
164_M	234_L	0.541	1.00
28_A	34_N	0.540	1.00
100_T	104_W	0.537	1.00
155_V	270_D	0.535	1.00
18_I	29_Q	0.533	1.00
107_Q	224_G	0.531	1.00
225_C	231_G	0.531	1.00
191_K	215_E	0.531	1.00
90_G	118_N	0.530	1.00
195_Y	198_K	0.530	1.00
80_A	83_G	0.530	1.00
254_I	257_K	0.529	1.00
18_I	54_G	0.526	1.00
147_G	156_Q	0.526	1.00
104_W	108_L	0.524	1.00
43_L	46_K	0.524	1.00
84_E	88_P	0.522	1.00
8_V	36_I	0.521	1.00
27_Y	35_K	0.521	1.00
46_K	60_P	0.520	1.00
106_P	110_A	0.517	1.00
102_A	218_I	0.517	1.00
66_S	81_A	0.517	1.00
16_G	55_I	0.512	1.00
81_A	84_E	0.512	1.00
67_Y	82_M	0.511	1.00
219_L	236_P	0.510	1.00
109_L	121_L	0.509	1.00
78_A	81_A	0.509	1.00
136_L	139_E	0.503	1.00
96_S	123_L	0.503	1.00
8_V	21_A	0.500	1.00
110_A	113_N	0.500	1.00
277_L	281_L	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
1uthA	2	0.7534	100	0.088	Contact Map
2esnA	3	0.9764	100	0.09	Contact Map
3fxqA	3	0.9764	100	0.091	Contact Map
1al3A	1	0.7095	100	0.103	Contact Map
1ixcA	4	0.9696	100	0.104	Contact Map
3fzvA	4	0.9527	100	0.105	Contact Map
2h9bA	2	0.6926	100	0.105	Contact Map
2h98A	2	0.6926	100	0.106	Contact Map
4x6gA	4	1	100	0.107	Contact Map
3szpA	3	0.9628	100	0.119	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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