RCLR - ECOLI - GREMLIN Contacts

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RCLR - RCS-specific HTH-type transcriptional activator RclR

UniProt:	P77379	Sequences: MDALSRLLMLNAPQGTIDKNCVLGSDWQLPHGAGELSVIRWHALTQGAAKLEMPTGEIFTLRPGNVVLLPQNSAHRLSHVDNESTCIVCGTLRLQHSARYFLTSLPETLFLAPVNHSVEYNWLREAIPFLQQESRSAMPGVDALCSQICATFFTLAVREWIAQVNTEKNILSLLLHPRLGAVIQQMLEMPGHAWTVESLASIAHMSRASFAQLFRDVSGTTPLAVLTKLRLQIAAQMFSRETLPVVVIAESVGYASESSFHKAFVREFGCTPGEYRERVRQLAP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13581
Length:	284 (242)
Sequences:	35601 (29993)
Seq/√Len:	1928.0

ECOLI - RCLR YQHC YDIP RHAR MELR CHBR YPDC RHAS YIDL ARAC YBCM FEAR YIJO YEAM EUTR GADW APPY GADX ENVY ADIY YDEO ROB MARA SOXS YKGA XYLR
BACSU - YDEC YBFI YISR YFIF BTR YOBQ YTDP ADAA YESS YDEE YESN YBFP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
235_A	268_F	3.311	1.00
220_T	228_K	3.302	1.00
187_L	229_L	3.082	1.00
243_L	251_S	3.075	1.00
231_L	268_F	2.955	1.00
197_E	207_R	2.865	1.00
185_Q	189_M	2.801	1.00
233_I	236_Q	2.781	1.00
228_K	267_E	2.677	1.00
189_M	192_H	2.614	1.00
264_F	275_Y	2.610	1.00
237_M	251_S	2.406	1.00
234_A	260_F	2.359	1.00
182_V	210_F	2.320	1.00
237_M	252_V	2.147	1.00
214_F	225_V	2.141	1.00
195_T	198_S	2.067	1.00
243_L	247_V	2.039	1.00
190_P	229_L	2.031	1.00
185_Q	202_I	1.953	1.00
50_K	58_I	1.952	1.00
270_C	278_R	1.920	1.00
237_M	243_L	1.873	1.00
183_I	218_S	1.853	1.00
223_L	227_T	1.840	1.00
182_V	203_A	1.811	1.00
231_L	267_E	1.802	1.00
186_M	226_L	1.797	1.00
179_L	218_S	1.795	1.00
244_P	247_V	1.790	1.00
50_K	60_T	1.760	1.00
257_E	261_H	1.749	1.00
263_A	266_R	1.726	1.00
235_A	275_Y	1.710	1.00
52_E	58_I	1.710	1.00
199_L	222_P	1.685	1.00
209_S	213_L	1.674	1.00
196_V	211_A	1.634	1.00
233_I	237_M	1.611	1.00
207_R	211_A	1.606	1.00
48_A	60_T	1.598	1.00
229_L	233_I	1.591	1.00
184_Q	188_E	1.590	1.00
62_R	65_N	1.581	1.00
220_T	224_A	1.580	1.00
246_V	257_E	1.575	1.00
92_L	95_Q	1.555	1.00
270_C	274_E	1.553	1.00
148_I	151_T	1.547	1.00
187_L	225_V	1.546	1.00
210_F	222_P	1.501	1.00
247_V	251_S	1.500	1.00
185_Q	194_W	1.496	1.00
183_I	187_L	1.484	1.00
236_Q	240_R	1.472	1.00
222_P	226_L	1.460	1.00
50_K	78_S	1.457	1.00
190_P	233_I	1.452	1.00
209_S	212_Q	1.445	1.00
247_V	250_E	1.443	1.00
176_H	217_V	1.443	1.00
94_L	97_S	1.441	1.00
259_S	263_A	1.439	1.00
246_V	250_E	1.439	1.00
238_F	245_V	1.435	1.00
52_E	76_R	1.434	1.00
254_Y	263_A	1.432	1.00
233_I	252_V	1.429	1.00
234_A	252_V	1.428	1.00
186_M	229_L	1.408	1.00
48_A	62_R	1.400	1.00
273_G	277_E	1.393	1.00
248_I	252_V	1.390	1.00
205_M	209_S	1.385	1.00
191_G	251_S	1.383	1.00
151_T	155_L	1.377	1.00
124_R	128_P	1.372	1.00
258_S	261_H	1.368	1.00
182_V	199_L	1.357	1.00
39_I	71_Q	1.343	1.00
208_A	212_Q	1.318	1.00
211_A	222_P	1.315	1.00
227_T	263_A	1.311	1.00
46_Q	86_C	1.305	1.00
229_L	232_Q	1.292	1.00
228_K	232_Q	1.291	1.00
198_S	202_I	1.290	1.00
221_T	224_A	1.272	1.00
197_E	201_S	1.236	1.00
205_M	210_F	1.229	1.00
55_T	73_S	1.215	1.00
241_E	276_R	1.213	1.00
261_H	271_T	1.212	1.00
178_R	205_M	1.208	1.00
206_S	209_S	1.198	1.00
147_Q	154_T	1.177	1.00
192_H	198_S	1.164	1.00
70_P	73_S	1.161	1.00
147_Q	151_T	1.161	1.00
147_Q	150_A	1.148	1.00
235_A	239_S	1.134	1.00
262_K	266_R	1.127	1.00
46_Q	63_P	1.127	1.00
261_H	273_G	1.117	1.00
232_Q	235_A	1.102	1.00
200_A	207_R	1.096	1.00
196_V	222_P	1.089	1.00
243_L	248_I	1.087	1.00
213_L	216_D	1.072	1.00
177_P	181_A	1.067	1.00
271_T	274_E	1.062	1.00
125_E	128_P	1.053	1.00
191_G	233_I	1.052	1.00
185_Q	203_A	1.050	1.00
274_E	277_E	1.044	1.00
91_T	95_Q	1.036	1.00
125_E	129_F	1.033	1.00
45_T	88_V	1.028	1.00
213_L	217_V	1.026	1.00
180_G	184_Q	1.020	1.00
227_T	266_R	1.018	1.00
45_T	86_C	1.018	1.00
199_L	202_I	1.003	1.00
224_A	227_T	1.001	1.00
46_Q	84_S	0.997	1.00
186_M	222_P	0.996	1.00
273_G	276_R	0.994	1.00
146_S	150_A	0.994	1.00
245_V	248_I	0.988	1.00
33_A	74_A	0.983	1.00
194_W	199_L	0.981	1.00
128_P	132_Q	0.981	1.00
137_A	141_V	0.978	1.00
193_A	255_A	0.976	1.00
178_R	213_L	0.972	1.00
36_L	75_H	0.971	1.00
208_A	211_A	0.970	1.00
268_F	275_Y	0.968	1.00
183_I	225_V	0.962	1.00
40_R	75_H	0.957	1.00
237_M	248_I	0.953	1.00
256_S	262_K	0.950	1.00
198_S	201_S	0.947	1.00
144_L	148_I	0.945	1.00
178_R	203_A	0.943	1.00
261_H	265_V	0.939	1.00
263_A	267_E	0.934	1.00
196_V	207_R	0.928	1.00
44_L	49_A	0.918	1.00
235_A	264_F	0.911	1.00
224_A	228_K	0.910	1.00
185_Q	199_L	0.906	1.00
181_A	202_I	0.899	1.00
155_L	159_E	0.898	1.00
52_E	78_S	0.895	1.00
203_A	210_F	0.891	1.00
88_V	92_L	0.889	1.00
181_A	184_Q	0.884	1.00
189_M	202_I	0.879	1.00
259_S	262_K	0.876	1.00
34_G	75_H	0.871	1.00
154_T	158_R	0.868	1.00
190_P	194_W	0.865	1.00
122_W	125_E	0.863	1.00
241_E	248_I	0.861	1.00
214_F	218_S	0.859	1.00
190_P	226_L	0.855	1.00
50_K	80_V	0.854	1.00
144_L	151_T	0.854	1.00
225_V	229_L	0.853	1.00
265_V	271_T	0.853	1.00
48_A	80_V	0.852	1.00
205_M	213_L	0.849	1.00
230_R	252_V	0.844	1.00
151_T	154_T	0.843	1.00
39_I	68_L	0.842	1.00
181_A	203_A	0.841	1.00
231_L	263_A	0.831	1.00
238_F	248_I	0.829	1.00
224_A	267_E	0.827	1.00
179_L	213_L	0.827	1.00
122_W	155_L	0.827	1.00
49_A	61_L	0.826	1.00
52_E	56_G	0.825	1.00
223_L	226_L	0.822	1.00
86_C	89_C	0.814	1.00
250_E	255_A	0.813	1.00
227_T	267_E	0.809	1.00
49_A	85_T	0.808	1.00
223_L	259_S	0.806	1.00
194_W	198_S	0.804	1.00
214_F	222_P	0.803	1.00
193_A	198_S	0.803	1.00
274_E	278_R	0.801	1.00
238_F	276_R	0.795	1.00
234_A	237_M	0.794	1.00
179_L	182_V	0.793	1.00
189_M	198_S	0.792	1.00
183_I	214_F	0.786	1.00
231_L	260_F	0.783	1.00
180_G	183_I	0.780	1.00
117_S	120_Y	0.780	1.00
121_N	125_E	0.779	1.00
91_T	94_L	0.777	1.00
190_P	252_V	0.777	1.00
179_L	217_V	0.776	1.00
42_H	89_C	0.775	1.00
53_M	57_E	0.766	1.00
239_S	275_Y	0.762	1.00
212_Q	216_D	0.760	1.00
270_C	275_Y	0.760	1.00
129_F	133_E	0.754	1.00
179_L	183_I	0.753	1.00
49_A	60_T	0.747	1.00
182_V	185_Q	0.745	1.00
33_A	76_R	0.739	1.00
249_A	257_E	0.737	1.00
129_F	148_I	0.734	1.00
85_T	89_C	0.731	1.00
211_A	215_R	0.730	1.00
265_V	274_E	0.729	1.00
150_A	154_T	0.725	1.00
176_H	213_L	0.718	1.00
244_P	248_I	0.714	1.00
36_L	40_R	0.712	1.00
186_M	225_V	0.712	1.00
105_L	108_T	0.711	1.00
131_Q	135_R	0.708	1.00
211_A	223_L	0.707	1.00
178_R	181_A	0.704	1.00
260_F	264_F	0.704	1.00
86_C	92_L	0.703	1.00
69_L	75_H	0.697	1.00
88_V	91_T	0.695	1.00
43_A	66_V	0.694	1.00
182_V	222_P	0.691	1.00
211_A	221_T	0.688	1.00
142_D	146_S	0.688	1.00
190_P	230_R	0.686	1.00
255_A	259_S	0.685	1.00
182_V	214_F	0.681	1.00
227_T	259_S	0.680	1.00
215_R	221_T	0.680	1.00
51_L	67_V	0.679	1.00
122_W	129_F	0.674	1.00
61_L	67_V	0.673	1.00
175_L	216_D	0.671	1.00
155_L	158_R	0.666	1.00
44_L	47_G	0.664	1.00
199_L	210_F	0.663	1.00
129_F	132_Q	0.663	1.00
100_Y	103_T	0.662	1.00
182_V	186_M	0.661	1.00
175_L	178_R	0.656	1.00
144_L	154_T	0.655	1.00
109_L	112_A	0.651	1.00
258_S	271_T	0.650	1.00
234_A	248_I	0.650	1.00
256_S	259_S	0.648	1.00
132_Q	136_S	0.648	1.00
257_E	260_F	0.642	1.00
120_Y	124_R	0.641	1.00
220_T	225_V	0.638	1.00
200_A	203_A	0.627	1.00
231_L	254_Y	0.623	1.00
129_F	151_T	0.623	1.00
199_L	203_A	0.622	1.00
89_C	92_L	0.620	1.00
232_Q	268_F	0.620	1.00
122_W	126_A	0.618	1.00
42_H	69_L	0.618	1.00
106_P	109_L	0.614	1.00
196_V	223_L	0.612	1.00
264_F	270_C	0.609	1.00
35_E	74_A	0.608	1.00
121_N	124_R	0.606	1.00
144_L	147_Q	0.606	1.00
45_T	128_P	0.605	1.00
44_L	61_L	0.605	1.00
235_A	270_C	0.603	1.00
53_M	56_G	0.601	1.00
175_L	217_V	0.600	1.00
176_H	180_G	0.597	1.00
108_T	112_A	0.597	1.00
93_R	96_H	0.594	1.00
232_Q	267_E	0.594	1.00
218_S	225_V	0.593	1.00
126_A	148_I	0.593	1.00
185_Q	198_S	0.593	1.00
187_L	233_I	0.591	1.00
108_T	111_L	0.587	1.00
237_M	240_R	0.586	1.00
126_A	129_F	0.586	1.00
240_R	243_L	0.585	1.00
248_I	276_R	0.579	1.00
196_V	208_A	0.579	1.00
148_I	155_L	0.572	1.00
258_S	262_K	0.571	1.00
138_M	141_V	0.570	1.00
179_L	210_F	0.569	1.00
134_S	137_A	0.569	1.00
107_E	110_F	0.567	1.00
242_T	248_I	0.567	1.00
194_W	230_R	0.567	1.00
130_L	133_E	0.560	1.00
113_P	116_H	0.560	1.00
52_E	55_T	0.559	1.00
143_A	147_Q	0.558	1.00
260_F	272_P	0.556	1.00
210_F	218_S	0.555	1.00
42_H	87_I	0.555	1.00
105_L	109_L	0.554	1.00
43_A	127_I	0.553	1.00
49_A	77_L	0.553	1.00
92_L	96_H	0.552	1.00
143_A	146_S	0.549	1.00
193_A	230_R	0.547	1.00
254_Y	260_F	0.546	1.00
53_M	69_L	0.545	1.00
149_C	156_A	0.545	1.00
125_E	132_Q	0.544	1.00
87_I	91_T	0.543	1.00
238_F	275_Y	0.542	1.00
245_V	273_G	0.542	1.00
194_W	226_L	0.541	1.00
182_V	202_I	0.541	1.00
254_Y	259_S	0.541	1.00
226_L	230_R	0.541	1.00
224_A	266_R	0.541	1.00
92_L	97_S	0.539	1.00
41_W	68_L	0.538	1.00
232_Q	236_Q	0.538	1.00
119_E	122_W	0.538	1.00
84_S	92_L	0.538	1.00
184_Q	187_L	0.537	1.00
141_V	145_C	0.534	1.00
39_I	42_H	0.531	1.00
203_A	207_R	0.531	1.00
236_Q	239_S	0.530	1.00
256_S	266_R	0.528	1.00
42_H	67_V	0.528	1.00
185_Q	190_P	0.527	1.00
177_P	217_V	0.526	1.00
186_M	194_W	0.526	1.00
173_L	176_H	0.526	1.00
93_R	97_S	0.526	1.00
41_W	66_V	0.525	1.00
182_V	213_L	0.525	1.00
189_M	194_W	0.521	1.00
43_A	120_Y	0.520	1.00
144_L	155_L	0.519	1.00
227_T	231_L	0.518	1.00
42_H	51_L	0.515	1.00
201_S	204_H	0.513	1.00
103_T	106_P	0.512	1.00
263_A	268_F	0.511	1.00
226_L	229_L	0.511	1.00
210_F	213_L	0.510	1.00
55_T	74_A	0.508	1.00
158_R	162_A	0.506	1.00
144_L	158_R	0.502	1.00
51_L	77_L	0.502	1.00
145_C	149_C	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
3gbgA	1	0.8873	100	0.223	Contact Map
1bl0A	1	0.3873	100	0.446	Contact Map
3oioA	1	0.3944	100	0.449	Contact Map
3oouA	1	0.3697	100	0.45	Contact Map
3w6vA	1	0.3838	100	0.454	Contact Map
3mn2A	1	0.3732	100	0.457	Contact Map
3mklA	1	0.3908	100	0.46	Contact Map
2k9sA	1	0.3732	100	0.462	Contact Map
3lsgA	2	0.3592	100	0.472	Contact Map
1d5yA	1	0.3873	99.9	0.477	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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