HCAR - ECOLI - GREMLIN Contacts

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HCAR - Hca operon transcriptional activator HcaR

UniProt:	Q47141	Sequences: MELRHLRYFVAVAQALNFTRAAEKLHTSQPSLSSQIRDLENCVGVPLLVRDKRKVALTAAGECFLQDALAILEQAENAKLRARKIVQEDRQLTIGFVPSAEVNLLPKVLPMFRLRQPDTLIELVSLITTQQEEKIRRGELDVGLMRHPVYSPEIDYLELFDEPLVVVLPVDHPLAHEKEITAAQLDGVNFVSTDPVYSGSLAPIVKAWFAQENSQPNIVQVATNILVTMNLVGMGLGVTLIPGYMNNFNTGQVVFRPIAGNVPSIALLMAWKKGEMKPALRDFIAIVQERLASVTA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13455
Length:	296 (282)
Sequences:	79738 (58144)
Seq/√Len:	3462.4

ECOLI - HCAR OXYR CYSB CYNR LYSR YBHD YNFL YFER CBL XAPR TDCA ABGR NAC TTDR PGRR YNEJ YEEY ALLS LEUO AAER METR ILVY YFIE DMLR YDHB YAFC NHAR YEIE YDCI YAHB YBDO DSDC YCAN YIDZ YHJC YBEF ICIA YGFI YHAJ GCVA YIAU YJIE LRHA PERR HDFR
BACSU - YWBI ALSR YCGK GLTC CYSL YYBE YWQM YTLI BSDA GLTR CITR YUST YOFA YVBU YXJO YKUM 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
70_A	74_Q	3.623	1.00
15_A	24_K	3.388	1.00
157_L	288_Q	2.703	1.00
67_D	81_R	2.449	1.00
95_G	140_L	2.448	1.00
11_A	24_K	2.321	1.00
232_V	239_T	2.266	1.00
161_D	266_A	2.238	1.00
158_E	161_D	2.225	1.00
91_Q	122_E	2.217	1.00
172_H	188_V	2.213	1.00
163_P	243_G	2.175	1.00
158_E	266_A	2.162	1.00
91_Q	120_L	2.125	1.00
45_V	60_A	2.092	1.00
20_R	23_E	2.089	1.00
8_Y	35_Q	2.054	1.00
111_M	286_I	2.042	1.00
181_T	184_Q	2.040	1.00
161_D	264_S	2.016	1.00
233_G	252_Q	1.997	1.00
10_V	69_L	1.988	1.00
14_Q	69_L	1.986	1.00
67_D	74_Q	1.980	1.00
93_T	122_E	1.964	1.00
10_V	65_L	1.964	1.00
10_V	14_Q	1.929	1.00
165_V	243_G	1.915	1.00
11_A	15_A	1.907	1.00
11_A	14_Q	1.901	1.00
191_V	237_G	1.857	1.00
71_I	75_A	1.857	1.00
8_Y	32_L	1.850	1.00
13_A	57_L	1.831	1.00
65_L	69_L	1.822	1.00
168_L	256_R	1.817	1.00
49_V	56_A	1.739	1.00
189_N	219_V	1.731	1.00
165_V	255_F	1.716	1.00
63_C	81_R	1.686	1.00
18_F	36_I	1.683	1.00
64_F	78_A	1.682	1.00
156_Y	268_L	1.679	1.00
131_Q	143_G	1.661	1.00
134_K	139_E	1.657	1.00
13_A	65_L	1.623	1.00
15_A	20_R	1.592	1.00
155_D	273_K	1.584	1.00
10_V	68_A	1.569	1.00
112_F	283_F	1.556	1.00
177_E	184_Q	1.553	1.00
14_Q	24_K	1.553	1.00
133_E	137_R	1.543	1.00
229_M	247_N	1.537	1.00
9_F	65_L	1.527	1.00
8_Y	27_T	1.502	1.00
157_L	271_W	1.491	1.00
5_H	35_Q	1.479	1.00
5_H	42_C	1.477	1.00
202_A	206_K	1.475	1.00
67_D	70_A	1.475	1.00
19_T	29_Q	1.474	1.00
46_P	49_V	1.463	1.00
112_F	119_T	1.460	1.00
17_N	20_R	1.452	1.00
5_H	38_D	1.451	1.00
59_A	62_E	1.447	1.00
233_G	247_N	1.445	1.00
11_A	25_L	1.441	1.00
28_S	31_S	1.435	1.00
284_I	288_Q	1.425	1.00
155_D	271_W	1.424	1.00
67_D	77_N	1.405	1.00
271_W	284_I	1.405	1.00
145_M	270_A	1.401	1.00
276_M	280_L	1.400	1.00
102_V	226_L	1.378	1.00
170_V	252_Q	1.373	1.00
147_H	268_L	1.373	1.00
10_V	72_L	1.373	1.00
93_T	124_V	1.361	1.00
89_D	118_D	1.349	1.00
282_D	285_A	1.347	1.00
71_I	78_A	1.346	1.00
51_D	56_A	1.344	1.00
134_K	140_L	1.338	1.00
111_M	115_R	1.331	1.00
269_M	284_I	1.322	1.00
74_Q	77_N	1.313	1.00
162_E	244_Y	1.313	1.00
136_R	153_E	1.310	1.00
64_F	79_K	1.299	1.00
135_I	143_G	1.299	1.00
115_R	286_I	1.287	1.00
168_L	238_V	1.278	1.00
42_C	79_K	1.278	1.00
3_L	75_A	1.272	1.00
113_R	219_V	1.267	1.00
142_V	269_M	1.267	1.00
188_V	238_V	1.266	1.00
142_V	280_L	1.263	1.00
230_N	233_G	1.262	1.00
228_T	239_T	1.252	1.00
66_Q	70_A	1.248	1.00
113_R	189_N	1.226	1.00
67_D	78_A	1.219	1.00
158_E	268_L	1.215	1.00
63_C	66_Q	1.205	1.00
110_P	114_L	1.203	1.00
170_V	254_V	1.203	1.00
178_K	254_V	1.185	1.00
37_R	41_N	1.182	1.00
243_G	255_F	1.182	1.00
27_T	31_S	1.172	1.00
62_E	66_Q	1.171	1.00
156_Y	270_A	1.165	1.00
9_F	48_L	1.164	1.00
110_P	234_M	1.162	1.00
173_P	188_V	1.149	1.00
9_F	13_A	1.145	1.00
111_M	114_L	1.142	1.00
34_S	38_D	1.131	1.00
34_S	37_R	1.108	1.00
122_E	221_V	1.107	1.00
116_Q	282_D	1.106	1.00
179_E	259_A	1.104	1.00
189_N	217_N	1.095	1.00
285_A	288_Q	1.091	1.00
272_K	275_E	1.088	1.00
167_V	255_F	1.087	1.00
70_A	77_N	1.087	1.00
209_F	214_S	1.083	1.00
63_C	67_D	1.083	1.00
6_L	68_A	1.081	1.00
18_F	55_V	1.076	1.00
107_K	234_M	1.074	1.00
33_S	37_R	1.071	1.00
112_F	286_I	1.066	1.00
11_A	21_A	1.065	1.00
180_I	184_Q	1.064	1.00
255_F	258_I	1.064	1.00
222_A	228_T	1.062	1.00
9_F	47_L	1.060	1.00
71_I	74_Q	1.058	1.00
191_V	228_T	1.054	1.00
92_L	283_F	1.052	1.00
281_R	285_A	1.050	1.00
157_L	284_I	1.049	1.00
230_N	234_M	1.043	1.00
229_M	233_G	1.042	1.00
203_P	207_A	1.030	1.00
79_K	83_R	1.029	1.00
108_V	287_V	1.027	1.00
136_R	151_S	1.026	1.00
7_R	76_E	1.025	1.00
12_V	21_A	1.022	1.00
4_R	7_R	1.020	1.00
35_Q	38_D	1.019	1.00
169_P	235_G	1.007	1.00
163_P	264_S	1.002	1.00
76_E	80_L	0.999	1.00
166_V	238_V	0.987	1.00
203_P	206_K	0.986	1.00
73_E	77_N	0.984	1.00
192_S	218_I	0.980	1.00
76_E	79_K	0.979	1.00
27_T	32_L	0.978	1.00
57_L	61_G	0.967	1.00
124_V	134_K	0.966	1.00
64_F	68_A	0.963	1.00
8_Y	25_L	0.960	1.00
112_F	116_Q	0.960	1.00
13_A	48_L	0.957	1.00
182_A	260_G	0.957	1.00
12_V	18_F	0.950	1.00
286_I	289_E	0.949	1.00
134_K	137_R	0.941	1.00
38_D	41_N	0.933	1.00
63_C	85_I	0.930	1.00
9_F	57_L	0.929	1.00
108_V	286_I	0.929	1.00
21_A	32_L	0.924	1.00
277_K	280_L	0.923	1.00
222_A	231_L	0.921	1.00
9_F	39_L	0.919	1.00
115_R	289_E	0.918	1.00
168_L	172_H	0.918	1.00
20_R	24_K	0.911	1.00
95_G	131_Q	0.907	1.00
45_V	82_A	0.904	1.00
120_L	217_N	0.898	1.00
70_A	73_E	0.889	1.00
48_L	55_V	0.888	1.00
140_L	143_G	0.886	1.00
246_N	250_T	0.885	1.00
172_H	175_A	0.880	1.00
66_Q	69_L	0.876	1.00
119_T	279_A	0.869	1.00
176_H	189_N	0.867	1.00
16_L	56_A	0.866	1.00
153_E	273_K	0.859	1.00
184_Q	187_G	0.859	1.00
147_H	266_A	0.855	1.00
172_H	189_N	0.855	1.00
51_D	54_K	0.855	1.00
19_T	23_E	0.854	1.00
189_N	218_I	0.853	1.00
285_A	289_E	0.846	1.00
95_G	145_M	0.846	1.00
98_P	224_N	0.845	1.00
60_A	85_I	0.844	1.00
155_D	158_E	0.840	1.00
168_L	173_P	0.838	1.00
13_A	61_G	0.838	1.00
154_I	270_A	0.838	1.00
132_E	136_R	0.837	1.00
90_R	279_A	0.832	1.00
173_P	178_K	0.827	1.00
124_V	140_L	0.825	1.00
25_L	32_L	0.824	1.00
167_V	239_T	0.824	1.00
94_I	142_V	0.822	1.00
183_A	186_D	0.820	1.00
110_P	236_L	0.816	1.00
276_M	281_R	0.815	1.00
246_N	249_N	0.809	1.00
13_A	16_L	0.809	1.00
29_Q	33_S	0.808	1.00
60_A	82_A	0.807	1.00
37_R	46_P	0.805	1.00
95_G	143_G	0.804	1.00
75_A	79_K	0.802	1.00
16_L	62_E	0.802	1.00
174_L	188_V	0.800	1.00
208_W	212_E	0.799	1.00
172_H	176_H	0.794	1.00
163_P	257_P	0.793	1.00
171_D	175_A	0.792	1.00
14_Q	65_L	0.789	1.00
181_T	259_A	0.786	1.00
247_N	252_Q	0.785	1.00
130_Q	133_E	0.784	1.00
75_A	78_A	0.784	1.00
60_A	63_C	0.783	1.00
113_R	236_L	0.782	1.00
163_P	262_V	0.779	1.00
77_N	81_R	0.778	1.00
9_F	64_F	0.778	1.00
278_P	282_D	0.776	1.00
205_V	209_F	0.775	1.00
90_R	119_T	0.773	1.00
15_A	21_A	0.771	1.00
16_L	54_K	0.770	1.00
3_L	72_L	0.770	1.00
74_Q	78_A	0.769	1.00
4_R	35_Q	0.763	1.00
5_H	8_Y	0.762	1.00
169_P	236_L	0.759	1.00
231_L	236_L	0.758	1.00
7_R	11_A	0.754	1.00
190_F	216_P	0.748	1.00
115_R	282_D	0.748	1.00
12_V	48_L	0.747	1.00
207_A	211_Q	0.746	1.00
142_V	283_F	0.745	1.00
88_E	116_Q	0.739	1.00
112_F	282_D	0.737	1.00
83_R	86_V	0.733	1.00
68_A	71_I	0.729	1.00
96_F	101_E	0.728	1.00
12_V	36_I	0.725	1.00
78_A	82_A	0.724	1.00
18_F	32_L	0.724	1.00
136_R	154_I	0.722	1.00
167_V	241_I	0.722	1.00
233_G	250_T	0.720	1.00
69_L	73_E	0.719	1.00
242_P	245_M	0.717	1.00
208_W	211_Q	0.717	1.00
62_E	65_L	0.712	1.00
169_P	172_H	0.711	1.00
49_V	58_T	0.709	1.00
93_T	140_L	0.706	1.00
57_L	62_E	0.705	1.00
56_A	62_E	0.703	1.00
183_A	212_E	0.701	1.00
31_S	35_Q	0.697	1.00
12_V	32_L	0.696	1.00
282_D	286_I	0.692	1.00
204_I	208_W	0.692	1.00
138_G	272_K	0.690	1.00
186_D	214_S	0.690	1.00
194_D	221_V	0.690	1.00
60_A	64_F	0.689	1.00
59_A	63_C	0.686	1.00
207_A	210_A	0.686	1.00
224_N	227_V	0.683	1.00
175_A	254_V	0.683	1.00
181_T	260_G	0.682	1.00
179_E	257_P	0.679	1.00
171_D	235_G	0.671	1.00
111_M	289_E	0.670	1.00
141_D	280_L	0.669	1.00
49_V	54_K	0.666	1.00
168_L	254_V	0.666	1.00
77_N	80_L	0.666	1.00
7_R	10_V	0.664	1.00
187_G	217_N	0.663	1.00
93_T	141_D	0.663	1.00
73_E	76_E	0.662	1.00
64_F	82_A	0.660	1.00
171_D	174_L	0.657	1.00
168_L	174_L	0.656	1.00
202_A	221_V	0.656	1.00
201_L	205_V	0.655	1.00
220_Q	231_L	0.654	1.00
193_T	228_T	0.653	1.00
120_L	221_V	0.651	1.00
40_E	45_V	0.650	1.00
206_K	210_A	0.647	1.00
102_V	230_N	0.646	1.00
204_I	207_A	0.643	1.00
96_F	105_L	0.641	1.00
23_E	26_H	0.639	1.00
174_L	177_E	0.635	1.00
92_L	279_A	0.634	1.00
170_V	251_G	0.634	1.00
190_F	238_V	0.634	1.00
67_D	71_I	0.632	1.00
278_P	281_R	0.631	1.00
68_A	72_L	0.630	1.00
36_I	40_E	0.627	1.00
40_E	50_R	0.625	1.00
144_L	287_V	0.625	1.00
171_D	254_V	0.624	1.00
130_Q	134_K	0.621	1.00
205_V	208_W	0.617	1.00
166_V	185_L	0.615	1.00
80_L	84_K	0.610	1.00
160_F	267_L	0.607	1.00
101_E	128_T	0.607	1.00
21_A	25_L	0.606	1.00
142_V	284_I	0.605	1.00
107_K	110_P	0.604	1.00
271_W	281_R	0.601	1.00
89_D	120_L	0.601	1.00
201_L	204_I	0.599	1.00
209_F	216_P	0.597	1.00
4_R	38_D	0.593	1.00
166_V	240_L	0.590	1.00
7_R	72_L	0.590	1.00
194_D	223_T	0.589	1.00
92_L	142_V	0.589	1.00
202_A	205_V	0.585	1.00
135_I	270_A	0.585	1.00
146_R	265_I	0.584	1.00
155_D	274_G	0.582	1.00
12_V	17_N	0.581	1.00
63_C	82_A	0.580	1.00
222_A	227_V	0.580	1.00
228_T	232_V	0.578	1.00
105_L	108_V	0.578	1.00
43_V	82_A	0.577	1.00
107_K	111_M	0.576	1.00
90_R	118_D	0.575	1.00
164_L	240_L	0.574	1.00
57_L	65_L	0.570	1.00
173_P	177_E	0.570	1.00
174_L	180_I	0.570	1.00
4_R	8_Y	0.568	1.00
283_F	287_V	0.567	1.00
45_V	49_V	0.566	1.00
135_I	154_I	0.566	1.00
162_E	265_I	0.565	1.00
48_L	57_L	0.564	1.00
43_V	64_F	0.564	1.00
30_P	34_S	0.561	1.00
116_Q	119_T	0.559	1.00
172_H	238_V	0.557	1.00
9_F	61_G	0.557	1.00
231_L	237_G	0.557	1.00
202_A	208_W	0.556	1.00
114_L	175_A	0.555	1.00
84_K	88_E	0.554	1.00
31_S	34_S	0.554	1.00
109_L	121_I	0.554	1.00
166_V	190_F	0.553	1.00
72_L	76_E	0.553	1.00
18_F	54_K	0.551	1.00
195_P	221_V	0.548	1.00
28_S	34_S	0.547	1.00
248_F	251_G	0.547	1.00
203_P	208_W	0.546	1.00
179_E	184_Q	0.545	1.00
159_L	269_M	0.543	1.00
95_G	124_V	0.543	1.00
131_Q	138_G	0.543	1.00
247_N	250_T	0.541	1.00
100_A	104_L	0.540	1.00
66_Q	81_R	0.539	1.00
72_L	75_A	0.537	1.00
199_G	202_A	0.537	1.00
18_F	29_Q	0.536	1.00
43_V	46_P	0.534	1.00
133_E	139_E	0.534	1.00
8_Y	36_I	0.532	1.00
206_K	209_F	0.531	1.00
13_A	62_E	0.528	1.00
177_E	180_I	0.527	1.00
80_L	83_R	0.527	1.00
193_T	225_I	0.522	1.00
147_H	156_Y	0.521	1.00
67_D	82_A	0.517	1.00
173_P	176_H	0.516	1.00
225_I	242_P	0.516	1.00
27_T	35_Q	0.514	1.00
104_L	108_V	0.512	1.00
107_K	230_N	0.508	1.00
280_L	284_I	0.506	1.00
46_P	60_A	0.505	1.00
16_L	55_V	0.504	1.00
78_A	81_R	0.503	1.00
84_K	87_Q	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
2h98A	2	0.7027	100	0.065	Contact Map
2h9bA	2	0.7027	100	0.067	Contact Map
1ixcA	4	0.9899	100	0.071	Contact Map
2esnA	3	0.9797	100	0.09	Contact Map
1al3A	1	0.7061	100	0.094	Contact Map
1uthA	2	0.75	100	0.097	Contact Map
4x6gA	4	0.9932	100	0.097	Contact Map
3fxqA	3	0.973	100	0.099	Contact Map
3fzvA	4	0.9561	100	0.1	Contact Map
3szpA	3	0.9662	100	0.117	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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