LRHA - ECOLI - GREMLIN Contacts

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LRHA - Probable HTH-type transcriptional regulator LrhA

UniProt:	P36771	Sequences: MISANRPIINLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILRFNDEACSSLMFSNLQGVLTIGASDESADTILPFLLNRVSSVYPKLALDVRVKRNAYMAEMLESQEVDLMVTTHRPSAFKALNLRTSPTHWYCAAEYILQKGEPIPLVLLDDPSPFRDMVLATLNKADIPWRLAYVASTLPAVRAAVKAGLGVTARPVEMMSPDLRVLSGVDGLPPLPDTEYLLCYDPSSNNELAQVIYQAMESYHNPWQYSPMSAPEGDDSLLIERDIE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12123
Length:	312 (275)
Sequences:	79601 (58363)
Seq/√Len:	3519.4

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
80_K	84_F	3.654	1.00
25_L	34_A	3.433	1.00
164_L	285_E	2.718	1.00
77_Y	91_S	2.463	1.00
104_G	149_V	2.416	1.00
21_A	34_A	2.305	1.00
229_V	236_T	2.299	1.00
120_R	287_Y	2.280	1.00
170_P	240_V	2.259	1.00
168_T	263_E	2.221	1.00
100_V	131_D	2.216	1.00
165_N	168_T	2.208	1.00
100_V	129_A	2.144	1.00
165_N	263_E	2.112	1.00
30_A	33_A	2.095	1.00
55_K	70_H	2.094	1.00
168_T	261_D	2.074	1.00
24_D	79_R	2.066	1.00
18_T	45_Q	2.041	1.00
120_R	283_A	2.003	1.00
77_Y	84_F	1.987	1.00
102_T	131_D	1.986	1.00
20_V	75_L	1.980	1.00
20_V	79_R	1.979	1.00
226_R	246_D	1.960	1.00
20_V	24_D	1.916	1.00
21_A	25_L	1.905	1.00
21_A	24_D	1.902	1.00
140_M	152_M	1.900	1.00
172_H	240_V	1.887	1.00
81_I	85_N	1.877	1.00
23_A	67_L	1.875	1.00
188_P	191_L	1.864	1.00
18_T	42_V	1.861	1.00
179_Y	195_P	1.847	1.00
75_L	79_R	1.812	1.00
28_F	46_M	1.773	1.00
230_K	246_D	1.772	1.00
59_A	66_L	1.748	1.00
73_Q	91_S	1.681	1.00
163_A	265_L	1.676	1.00
74_L	88_A	1.675	1.00
143_M	148_E	1.627	1.00
23_A	75_L	1.610	1.00
121_V	280_I	1.575	1.00
25_L	30_A	1.573	1.00
20_V	78_A	1.566	1.00
162_K	270_P	1.556	1.00
19_F	75_L	1.541	1.00
184_G	191_L	1.539	1.00
18_T	37_R	1.538	1.00
24_D	34_A	1.537	1.00
15_L	52_L	1.509	1.00
196_S	216_A	1.503	1.00
29_A	39_Q	1.501	1.00
15_L	45_Q	1.494	1.00
96_N	127_K	1.487	1.00
121_V	128_L	1.479	1.00
77_Y	80_K	1.469	1.00
156_H	265_L	1.456	1.00
164_L	268_Y	1.452	1.00
15_L	48_R	1.452	1.00
142_E	146_S	1.450	1.00
27_T	30_A	1.447	1.00
38_T	41_A	1.444	1.00
69_E	72_I	1.438	1.00
12_D	15_L	1.426	1.00
56_E	59_A	1.419	1.00
281_Y	285_E	1.415	1.00
21_A	35_V	1.408	1.00
162_K	268_Y	1.399	1.00
154_T	267_C	1.396	1.00
20_V	82_L	1.387	1.00
273_N	277_A	1.387	1.00
77_Y	87_E	1.376	1.00
268_Y	281_Y	1.356	1.00
81_I	88_A	1.346	1.00
102_T	133_R	1.341	1.00
111_D	223_P	1.335	1.00
120_R	124_V	1.335	1.00
98_Q	127_K	1.333	1.00
169_S	241_E	1.320	1.00
279_V	282_Q	1.315	1.00
266_L	281_Y	1.298	1.00
143_M	149_V	1.297	1.00
144_L	152_M	1.294	1.00
13_L	85_N	1.291	1.00
250_L	254_D	1.291	1.00
74_L	89_C	1.283	1.00
199_R	203_L	1.282	1.00
175_C	235_V	1.280	1.00
61_H	66_L	1.276	1.00
124_V	283_A	1.272	1.00
225_V	236_T	1.264	1.00
151_L	277_A	1.262	1.00
84_F	87_E	1.260	1.00
230_K	251_S	1.254	1.00
151_L	266_L	1.252	1.00
76_G	80_K	1.238	1.00
145_E	160_A	1.225	1.00
77_Y	88_A	1.223	1.00
227_A	230_K	1.213	1.00
122_S	216_A	1.212	1.00
172_H	254_D	1.208	1.00
73_Q	76_G	1.196	1.00
47_Q	51_Q	1.190	1.00
165_N	265_L	1.176	1.00
72_I	76_G	1.175	1.00
119_N	123_S	1.175	1.00
240_V	244_S	1.159	1.00
19_F	58_F	1.154	1.00
37_R	41_A	1.145	1.00
163_A	267_C	1.144	1.00
120_R	123_S	1.138	1.00
192_L	197_P	1.136	1.00
190_V	193_D	1.134	1.00
52_L	89_C	1.121	1.00
44_Q	47_Q	1.120	1.00
119_N	231_A	1.118	1.00
19_F	23_A	1.111	1.00
44_Q	48_R	1.110	1.00
125_Y	279_V	1.100	1.00
187_I	191_L	1.094	1.00
269_D	272_S	1.090	1.00
206_L	211_I	1.089	1.00
282_Q	285_E	1.079	1.00
219_A	225_V	1.078	1.00
19_F	57_L	1.076	1.00
135_K	143_M	1.075	1.00
190_V	197_P	1.069	1.00
28_F	65_K	1.068	1.00
283_A	287_Y	1.068	1.00
80_K	87_E	1.068	1.00
43_S	47_Q	1.067	1.00
101_L	280_I	1.059	1.00
110_A	134_V	1.057	1.00
73_Q	77_Y	1.051	1.00
131_D	218_V	1.051	1.00
14_D	17_R	1.049	1.00
81_I	84_F	1.049	1.00
278_Q	282_Q	1.042	1.00
226_R	230_K	1.041	1.00
185_E	253_V	1.036	1.00
16_L	78_A	1.035	1.00
116_F	231_A	1.031	1.00
22_V	31_A	1.030	1.00
240_V	254_D	1.030	1.00
21_A	31_A	1.028	1.00
17_R	86_D	1.028	1.00
164_L	281_Y	1.025	1.00
176_A	232_G	1.023	1.00
121_V	283_A	1.022	1.00
117_L	284_M	1.022	1.00
198_F	234_G	1.019	1.00
45_Q	48_R	1.018	1.00
244_S	248_R	1.017	1.00
227_A	231_A	1.006	1.00
175_C	179_Y	1.001	1.00
245_P	249_V	0.996	1.00
177_A	251_S	0.993	1.00
247_L	250_L	0.980	1.00
200_D	205_T	0.976	1.00
89_C	93_M	0.975	1.00
190_V	198_F	0.971	1.00
170_P	261_D	0.968	1.00
173_W	235_V	0.968	1.00
86_D	90_S	0.968	1.00
246_D	251_S	0.967	1.00
190_V	195_P	0.961	1.00
86_D	89_C	0.961	1.00
200_D	203_L	0.956	1.00
67_L	71_G	0.952	1.00
83_R	87_E	0.946	1.00
23_A	58_F	0.943	1.00
283_A	286_S	0.942	1.00
37_R	42_V	0.940	1.00
219_A	228_A	0.940	1.00
18_T	35_V	0.939	1.00
11_L	52_L	0.938	1.00
121_V	125_Y	0.935	1.00
174_Y	243_M	0.935	1.00
143_M	146_S	0.934	1.00
180_I	195_P	0.933	1.00
74_L	78_A	0.928	1.00
124_V	286_S	0.920	1.00
133_R	143_M	0.910	1.00
19_F	67_L	0.909	1.00
31_A	42_V	0.908	1.00
160_A	270_P	0.906	1.00
175_C	253_V	0.905	1.00
55_K	92_L	0.905	1.00
22_V	28_F	0.904	1.00
48_R	51_Q	0.903	1.00
117_L	283_A	0.897	1.00
274_N	277_A	0.894	1.00
19_F	49_L	0.890	1.00
104_G	140_M	0.889	1.00
58_F	65_K	0.884	1.00
30_A	34_A	0.883	1.00
246_D	249_V	0.880	1.00
76_G	79_R	0.872	1.00
149_V	152_M	0.869	1.00
195_P	235_V	0.865	1.00
191_L	195_P	0.864	1.00
26_N	66_L	0.858	1.00
61_H	64_N	0.857	1.00
175_C	180_I	0.856	1.00
122_S	196_S	0.851	1.00
129_A	214_R	0.844	1.00
80_K	83_R	0.843	1.00
156_H	263_E	0.842	1.00
254_D	257_P	0.841	1.00
162_K	165_N	0.838	1.00
23_A	71_G	0.837	1.00
174_Y	236_T	0.835	1.00
99_G	276_L	0.830	1.00
107_D	221_T	0.829	1.00
192_L	196_S	0.827	1.00
191_L	197_P	0.825	1.00
104_G	154_T	0.825	1.00
128_L	276_L	0.824	1.00
179_Y	196_S	0.824	1.00
282_Q	286_S	0.819	1.00
200_D	204_A	0.818	1.00
29_A	33_A	0.818	1.00
161_F	267_C	0.816	1.00
141_A	145_E	0.816	1.00
133_R	149_V	0.811	1.00
103_I	151_L	0.809	1.00
14_D	45_Q	0.806	1.00
70_H	92_L	0.805	1.00
35_V	42_V	0.805	1.00
205_T	209_A	0.804	1.00
135_K	140_M	0.796	1.00
170_P	254_D	0.793	1.00
177_A	249_V	0.793	1.00
104_G	152_M	0.790	1.00
13_L	82_L	0.790	1.00
187_I	190_V	0.786	1.00
196_S	214_R	0.782	1.00
180_I	185_E	0.781	1.00
119_N	233_L	0.778	1.00
199_R	205_T	0.775	1.00
273_N	278_Q	0.775	1.00
47_Q	56_E	0.774	1.00
19_F	74_L	0.769	1.00
26_N	72_I	0.767	1.00
176_A	233_L	0.766	1.00
23_A	26_N	0.765	1.00
99_G	128_L	0.753	1.00
85_N	88_A	0.748	1.00
117_L	287_Y	0.743	1.00
84_F	88_A	0.743	1.00
275_E	279_V	0.742	1.00
189_L	192_L	0.741	1.00
25_L	31_A	0.740	1.00
228_A	233_L	0.739	1.00
24_D	75_L	0.738	1.00
39_Q	43_S	0.737	1.00
87_E	91_S	0.737	1.00
183_K	196_S	0.737	1.00
26_N	64_N	0.736	1.00
85_N	89_C	0.736	1.00
151_L	280_I	0.736	1.00
122_S	233_L	0.735	1.00
97_L	125_Y	0.734	1.00
22_V	46_M	0.734	1.00
70_H	73_Q	0.733	1.00
145_E	161_F	0.729	1.00
191_L	194_D	0.728	1.00
22_V	58_F	0.720	1.00
120_R	286_S	0.714	1.00
243_M	246_D	0.714	1.00
15_L	18_T	0.713	1.00
121_V	279_V	0.710	1.00
17_R	21_A	0.710	1.00
124_V	279_V	0.710	1.00
88_A	92_L	0.709	1.00
251_S	255_G	0.704	1.00
59_A	68_T	0.702	1.00
199_R	218_V	0.697	1.00
28_F	42_V	0.692	1.00
105_A	110_A	0.692	1.00
67_L	72_I	0.691	1.00
174_Y	238_R	0.690	1.00
179_Y	183_K	0.689	1.00
176_A	179_Y	0.688	1.00
78_A	81_I	0.682	1.00
204_A	207_N	0.681	1.00
204_A	208_K	0.679	1.00
203_L	207_N	0.678	1.00
79_R	83_R	0.678	1.00
41_A	45_Q	0.675	1.00
202_V	206_L	0.674	1.00
22_V	42_V	0.673	1.00
201_M	205_T	0.673	1.00
179_Y	182_Q	0.671	1.00
66_L	72_I	0.670	1.00
239_P	242_M	0.665	1.00
221_T	224_A	0.662	1.00
72_I	75_L	0.660	1.00
70_H	74_L	0.659	1.00
189_L	259_L	0.650	1.00
50_E	55_K	0.649	1.00
87_E	90_S	0.649	1.00
150_D	277_A	0.649	1.00
11_L	89_C	0.648	1.00
147_Q	269_D	0.648	1.00
230_K	249_V	0.644	1.00
102_T	149_V	0.643	1.00
279_V	283_A	0.643	1.00
59_A	64_N	0.641	1.00
174_Y	247_L	0.637	1.00
250_L	256_L	0.637	1.00
69_E	73_Q	0.635	1.00
83_R	86_D	0.634	1.00
186_P	256_L	0.632	1.00
178_E	232_G	0.629	1.00
74_L	92_L	0.629	1.00
102_T	150_D	0.627	1.00
111_D	227_A	0.622	1.00
202_V	205_T	0.621	1.00
129_A	218_V	0.621	1.00
198_F	225_V	0.615	1.00
251_S	254_D	0.615	1.00
107_D	136_R	0.614	1.00
201_M	204_A	0.614	1.00
77_Y	81_I	0.613	1.00
14_D	48_R	0.608	1.00
33_A	36_C	0.607	1.00
105_A	114_L	0.607	1.00
196_S	215_L	0.604	1.00
245_P	248_R	0.603	1.00
17_R	20_V	0.602	1.00
50_E	60_R	0.600	1.00
217_Y	228_A	0.598	1.00
155_T	262_T	0.596	1.00
46_M	50_E	0.596	1.00
101_L	276_L	0.595	1.00
206_L	213_W	0.595	1.00
22_V	27_T	0.594	1.00
78_A	82_L	0.594	1.00
192_L	195_P	0.594	1.00
153_V	284_M	0.592	1.00
173_W	237_A	0.587	1.00
31_A	35_V	0.585	1.00
181_L	184_G	0.585	1.00
114_L	117_L	0.584	1.00
189_L	197_P	0.582	1.00
247_L	254_D	0.581	1.00
197_P	213_W	0.577	1.00
268_Y	278_Q	0.576	1.00
116_F	120_R	0.575	1.00
243_M	247_L	0.573	1.00
190_V	196_S	0.571	1.00
169_S	262_T	0.571	1.00
151_L	281_Y	0.569	1.00
90_S	94_F	0.568	1.00
73_Q	92_L	0.566	1.00
280_I	284_M	0.563	1.00
205_T	208_K	0.563	1.00
134_V	220_S	0.562	1.00
228_A	234_G	0.562	1.00
275_E	278_Q	0.559	1.00
193_D	196_S	0.558	1.00
98_Q	129_A	0.557	1.00
55_K	59_A	0.556	1.00
28_F	64_N	0.556	1.00
67_L	75_L	0.554	1.00
167_R	264_Y	0.551	1.00
253_V	257_P	0.551	1.00
41_A	44_Q	0.550	1.00
116_F	119_N	0.550	1.00
14_D	18_T	0.550	1.00
134_V	221_T	0.550	1.00
144_L	267_C	0.549	1.00
101_L	151_L	0.546	1.00
203_L	206_L	0.546	1.00
179_Y	235_V	0.546	1.00
40_S	44_Q	0.545	1.00
195_P	198_F	0.543	1.00
144_L	161_F	0.543	1.00
109_S	113_I	0.540	1.00
178_E	182_Q	0.539	1.00
17_R	82_L	0.535	1.00
219_A	224_A	0.535	1.00
53_V	92_L	0.534	1.00
162_K	271_S	0.534	1.00
171_T	237_A	0.534	1.00
175_C	255_G	0.532	1.00
178_E	181_L	0.531	1.00
192_L	198_F	0.530	1.00
38_T	44_Q	0.528	1.00
58_F	67_L	0.527	1.00
225_V	229_V	0.527	1.00
76_G	91_S	0.522	1.00
118_L	130_L	0.522	1.00
238_R	243_M	0.521	1.00
53_V	74_L	0.521	1.00
125_Y	128_L	0.514	1.00
53_V	56_E	0.513	1.00
99_G	127_K	0.513	1.00
181_L	187_I	0.510	1.00
82_L	86_D	0.510	1.00
175_C	181_L	0.510	1.00
257_P	260_P	0.507	1.00
174_Y	252_G	0.505	1.00
194_D	197_P	0.504	1.00
222_L	239_P	0.503	1.00
111_D	221_T	0.502	1.00
180_I	184_G	0.502	1.00
183_K	186_P	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
1ixcA	4	0.8974	100	0.209	Contact Map
2esnA	3	0.9135	100	0.215	Contact Map
2h98A	2	0.6474	100	0.219	Contact Map
2h9bA	2	0.6474	100	0.222	Contact Map
1uthA	2	0.6795	100	0.222	Contact Map
3fzvA	4	0.8814	100	0.226	Contact Map
1al3A	1	0.6923	100	0.234	Contact Map
4x6gA	4	0.9359	100	0.235	Contact Map
3fxqA	3	0.891	100	0.239	Contact Map
3szpA	3	0.8846	100	0.244	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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