YDEC - BACSU - GREMLIN Contacts

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YDEC - Uncharacterized HTH-type transcriptional regulator YdeC

UniProt:	P96660	Sequences: MKNFVIDQNLKELTEHRTVELPVACYKTTINQNINGYIPLHWHDEIQFVLILKGIALFQINEEKIEVHEGDGLFINSGYLHMAEEKEGSDCTYICLNVSPHFVLSQELYSSYVQPYMFSTNLPYLFLAGNQQWAKNILDAVKKINQLIQQKTSLYEIDITMQLTLMWKNLVVNGFQLEYDQSEMIKSHRMKQMLNWIHLHYVEKITLEDIAKAGQLSRSECCRYFKRMLNKTPLRYVMDYRIQKSLLLLQHPESNVTEVSYQVGFNSTSYFISKFQQAMNMTPLSYKKMNS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	291 (250)
Sequences:	30021 (25924)
Seq/√Len:	1639.6

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
246_L	279_M	3.319	1.00
231_K	239_D	3.202	1.00
242_I	279_M	3.137	1.00
198_H	240_Y	3.096	1.00
254_S	262_Q	3.087	1.00
208_E	218_R	2.965	1.00
244_K	247_L	2.861	1.00
196_W	200_H	2.824	1.00
200_H	203_E	2.782	1.00
239_D	278_A	2.625	1.00
193_M	221_C	2.404	1.00
248_L	262_Q	2.334	1.00
245_S	271_F	2.325	1.00
275_F	286_Y	2.320	1.00
225_F	236_Y	2.191	1.00
206_T	209_D	2.043	1.00
248_L	263_V	2.039	1.00
57_L	64_K	2.032	1.00
201_Y	240_Y	1.969	1.00
197_I	237_V	1.966	1.00
254_S	258_E	1.946	1.00
57_L	66_E	1.895	1.00
190_M	229_L	1.865	1.00
234_L	238_M	1.858	1.00
193_M	214_G	1.831	1.00
196_W	213_A	1.829	1.00
242_I	278_A	1.815	1.00
248_L	254_S	1.789	1.00
59_Q	64_K	1.784	1.00
194_L	229_L	1.782	1.00
207_L	222_C	1.767	1.00
255_N	258_E	1.736	1.00
249_L	256_V	1.711	1.00
268_T	272_I	1.703	1.00
220_E	224_Y	1.695	1.00
274_K	277_Q	1.695	1.00
162_Q	165_L	1.676	1.00
195_N	199_L	1.670	1.00
55_I	66_E	1.668	1.00
210_I	233_P	1.665	1.00
231_K	235_R	1.657	1.00
246_L	286_Y	1.650	1.00
196_W	205_I	1.636	1.00
68_H	71_D	1.626	1.00
138_L	142_K	1.622	1.00
165_L	169_N	1.588	1.00
221_C	233_P	1.587	1.00
257_T	268_T	1.586	1.00
240_Y	244_K	1.559	1.00
198_H	236_Y	1.544	1.00
233_P	237_V	1.540	1.00
53_K	92_T	1.536	1.00
55_I	68_H	1.536	1.00
270_Y	274_K	1.534	1.00
244_K	248_L	1.523	1.00
201_Y	244_K	1.514	1.00
220_E	223_R	1.510	1.00
218_R	222_C	1.510	1.00
247_L	251_H	1.505	1.00
59_Q	82_M	1.499	1.00
46_I	77_S	1.496	1.00
216_L	220_E	1.481	1.00
265_F	274_K	1.479	1.00
281_M	285_S	1.476	1.00
258_E	262_Q	1.464	1.00
57_L	84_E	1.441	1.00
202_V	262_Q	1.440	1.00
259_V	263_V	1.431	1.00
222_C	233_P	1.426	1.00
257_T	261_Y	1.422	1.00
197_I	240_Y	1.420	1.00
258_E	261_Y	1.418	1.00
61_N	79_Y	1.410	1.00
187_S	228_M	1.392	1.00
284_L	288_K	1.382	1.00
269_S	272_I	1.381	1.00
209_D	213_A	1.374	1.00
245_S	263_V	1.373	1.00
244_K	263_V	1.370	1.00
208_E	212_K	1.366	1.00
52_L	94_I	1.353	1.00
219_S	223_R	1.343	1.00
193_M	210_I	1.335	1.00
161_M	168_K	1.333	1.00
232_T	235_R	1.313	1.00
161_M	165_L	1.307	1.00
239_D	243_Q	1.307	1.00
161_M	164_T	1.279	1.00
194_L	198_H	1.278	1.00
272_I	282_T	1.277	1.00
252_P	287_K	1.272	1.00
216_L	221_C	1.266	1.00
203_E	209_D	1.265	1.00
238_M	274_K	1.264	1.00
41_H	81_H	1.238	1.00
217_S	220_E	1.231	1.00
240_Y	243_Q	1.228	1.00
272_I	284_L	1.217	1.00
254_S	259_V	1.195	1.00
189_R	216_L	1.190	1.00
53_K	69_E	1.189	1.00
76_N	79_Y	1.185	1.00
273_S	277_Q	1.174	1.00
139_D	143_K	1.167	1.00
43_H	81_H	1.155	1.00
52_L	92_T	1.149	1.00
139_D	142_K	1.126	1.00
246_L	250_Q	1.122	1.00
205_I	210_I	1.095	1.00
47_Q	81_H	1.093	1.00
158_D	162_Q	1.089	1.00
207_L	233_P	1.084	1.00
224_Y	227_R	1.071	1.00
202_V	244_K	1.067	1.00
210_I	213_A	1.060	1.00
243_Q	246_L	1.053	1.00
204_K	266_N	1.052	1.00
284_L	287_K	1.048	1.00
151_K	155_Y	1.043	1.00
188_H	192_Q	1.042	1.00
192_Q	213_A	1.042	1.00
267_S	273_S	1.041	1.00
285_S	288_K	1.036	1.00
40_L	80_L	1.035	1.00
211_A	218_R	1.033	1.00
158_D	165_L	1.029	1.00
224_Y	228_M	1.026	1.00
160_T	164_T	1.026	1.00
214_G	221_C	1.026	1.00
197_I	233_P	1.025	1.00
196_W	214_G	1.023	1.00
282_T	285_S	1.022	1.00
209_D	212_K	1.015	1.00
169_N	173_N	1.013	1.00
56_A	91_C	1.010	1.00
204_K	209_D	1.007	1.00
165_L	168_K	0.997	1.00
189_R	224_Y	0.996	1.00
164_T	168_K	0.994	1.00
191_K	195_N	0.992	1.00
248_L	259_V	0.992	1.00
252_P	259_V	0.987	1.00
189_R	214_G	0.985	1.00
272_I	276_Q	0.976	1.00
142_K	146_Q	0.969	1.00
168_K	172_V	0.960	1.00
43_H	47_Q	0.958	1.00
194_L	236_Y	0.957	1.00
241_R	263_V	0.956	1.00
196_W	210_I	0.954	1.00
71_D	126_F	0.947	1.00
274_K	278_A	0.936	1.00
238_M	277_Q	0.935	1.00
246_L	275_F	0.934	1.00
51_I	56_A	0.931	1.00
192_Q	195_N	0.930	1.00
235_R	238_M	0.928	1.00
60_I	63_E	0.926	1.00
279_M	286_Y	0.919	1.00
219_S	222_C	0.909	1.00
235_R	239_D	0.903	1.00
234_L	270_Y	0.892	1.00
256_V	259_V	0.891	1.00
46_I	74_F	0.889	1.00
238_M	278_A	0.887	1.00
56_A	67_V	0.885	1.00
59_Q	84_E	0.870	1.00
201_Y	237_V	0.869	1.00
207_L	218_R	0.867	1.00
225_F	229_L	0.865	1.00
270_Y	273_S	0.864	1.00
216_L	224_Y	0.861	1.00
242_I	274_K	0.856	1.00
234_L	237_V	0.853	1.00
190_M	224_Y	0.850	1.00
59_Q	62_E	0.847	1.00
143_K	147_L	0.846	1.00
191_K	194_L	0.842	1.00
57_L	86_K	0.838	1.00
50_L	72_G	0.835	1.00
225_F	233_P	0.833	1.00
53_K	90_D	0.832	1.00
91_C	95_C	0.831	1.00
40_L	82_M	0.829	1.00
190_M	193_M	0.829	1.00
192_Q	214_G	0.820	1.00
135_K	139_D	0.815	1.00
210_I	221_C	0.814	1.00
55_I	86_K	0.799	1.00
200_H	213_A	0.799	1.00
157_I	160_T	0.798	1.00
276_Q	282_T	0.798	1.00
249_L	259_V	0.798	1.00
58_F	73_L	0.792	1.00
201_Y	263_V	0.790	1.00
49_V	95_C	0.789	1.00
136_N	169_N	0.788	1.00
56_A	66_E	0.787	1.00
143_K	162_Q	0.785	1.00
47_Q	97_N	0.782	1.00
125_L	129_G	0.781	1.00
245_S	248_L	0.774	1.00
222_C	232_T	0.773	1.00
250_Q	286_Y	0.768	1.00
242_I	271_F	0.766	1.00
134_A	138_L	0.766	1.00
158_D	161_M	0.764	1.00
75_I	81_H	0.763	1.00
51_I	54_G	0.761	1.00
193_M	233_P	0.758	1.00
100_P	104_L	0.757	1.00
201_Y	205_I	0.757	1.00
186_K	227_R	0.754	1.00
201_Y	241_R	0.750	1.00
267_S	270_Y	0.749	1.00
67_V	73_L	0.748	1.00
260_S	268_T	0.747	1.00
261_Y	266_N	0.746	1.00
276_Q	285_S	0.746	1.00
200_H	209_D	0.744	1.00
235_R	278_A	0.738	1.00
136_N	139_D	0.738	1.00
114_Q	118_F	0.737	1.00
223_R	227_R	0.736	1.00
269_S	282_T	0.734	1.00
189_R	192_Q	0.733	1.00
236_Y	240_Y	0.732	1.00
156_E	160_T	0.730	1.00
281_M	286_Y	0.730	1.00
158_D	172_V	0.729	1.00
145_N	149_Q	0.729	1.00
222_C	234_L	0.726	1.00
193_M	225_F	0.724	1.00
190_M	228_M	0.719	1.00
135_K	138_L	0.712	1.00
197_I	236_Y	0.709	1.00
222_C	226_K	0.697	1.00
158_D	168_K	0.696	1.00
205_I	209_D	0.695	1.00
136_N	143_K	0.694	1.00
194_L	225_F	0.693	1.00
266_N	270_Y	0.686	1.00
249_L	287_K	0.684	1.00
190_M	194_L	0.683	1.00
187_S	224_Y	0.682	1.00
49_V	75_I	0.677	1.00
207_L	234_L	0.674	1.00
193_M	196_W	0.673	1.00
42_W	80_L	0.669	1.00
169_N	172_V	0.662	1.00
51_I	67_V	0.660	1.00
113_V	117_M	0.658	1.00
101_H	104_L	0.657	1.00
269_S	273_S	0.656	1.00
275_F	281_M	0.654	1.00
231_K	236_Y	0.647	1.00
162_Q	169_N	0.645	1.00
55_I	89_S	0.643	1.00
259_V	287_K	0.641	1.00
186_K	189_R	0.641	1.00
140_A	144_I	0.641	1.00
205_I	241_R	0.637	1.00
139_D	146_Q	0.637	1.00
226_K	232_T	0.636	1.00
190_M	221_C	0.634	1.00
193_M	197_I	0.626	1.00
267_S	277_Q	0.626	1.00
256_V	284_L	0.625	1.00
157_I	161_M	0.625	1.00
198_H	244_K	0.624	1.00
237_V	241_R	0.624	1.00
154_L	157_I	0.622	1.00
242_I	265_F	0.620	1.00
271_F	283_P	0.620	1.00
56_A	83_A	0.620	1.00
49_V	73_L	0.618	1.00
104_L	107_E	0.617	1.00
92_T	95_C	0.615	1.00
155_Y	158_D	0.615	1.00
210_I	214_G	0.615	1.00
121_N	124_Y	0.614	1.00
61_N	80_L	0.612	1.00
243_Q	278_A	0.604	1.00
193_M	213_A	0.603	1.00
255_N	259_V	0.602	1.00
221_C	229_L	0.601	1.00
268_T	271_F	0.598	1.00
71_D	128_A	0.597	1.00
155_Y	159_I	0.597	1.00
229_L	236_Y	0.595	1.00
247_L	250_Q	0.595	1.00
153_S	156_E	0.594	1.00
197_I	205_I	0.592	1.00
212_K	215_Q	0.589	1.00
237_V	240_Y	0.589	1.00
49_V	58_F	0.588	1.00
58_F	75_I	0.587	1.00
205_I	237_V	0.585	1.00
110_S	114_Q	0.585	1.00
100_P	103_V	0.584	1.00
184_M	187_S	0.584	1.00
207_L	219_S	0.583	1.00
147_L	172_V	0.581	1.00
190_M	214_G	0.581	1.00
146_Q	150_Q	0.580	1.00
238_M	242_I	0.579	1.00
211_A	214_G	0.578	1.00
111_S	115_P	0.577	1.00
51_I	93_Y	0.576	1.00
195_N	198_H	0.576	1.00
122_L	125_L	0.575	1.00
226_K	229_L	0.573	1.00
60_I	75_I	0.572	1.00
243_Q	279_M	0.571	1.00
186_K	228_M	0.571	1.00
159_I	162_Q	0.570	1.00
159_I	163_L	0.570	1.00
48_F	74_F	0.568	1.00
49_V	93_Y	0.567	1.00
51_I	91_C	0.565	1.00
238_M	265_F	0.565	1.00
136_N	140_A	0.565	1.00
143_K	165_L	0.564	1.00
238_M	270_Y	0.564	1.00
50_L	141_V	0.562	1.00
115_P	118_F	0.560	1.00
157_I	168_K	0.559	1.00
245_S	259_V	0.557	1.00
265_F	270_Y	0.557	1.00
152_T	155_Y	0.555	1.00
157_I	164_T	0.554	1.00
140_A	143_K	0.551	1.00
83_A	93_Y	0.550	1.00
271_F	275_F	0.548	1.00
249_L	286_Y	0.548	1.00
187_S	191_K	0.546	1.00
101_H	105_S	0.546	1.00
52_L	142_K	0.544	1.00
58_F	83_A	0.544	1.00
133_W	136_N	0.541	1.00
251_H	254_S	0.540	1.00
140_A	162_Q	0.539	1.00
124_Y	128_A	0.539	1.00
163_L	167_W	0.536	1.00
214_G	218_R	0.534	1.00
41_H	47_Q	0.534	1.00
274_K	279_M	0.533	1.00
46_I	49_V	0.533	1.00
188_H	228_M	0.532	1.00
122_L	127_L	0.532	1.00
196_W	209_D	0.531	1.00
158_D	169_N	0.530	1.00
52_L	138_L	0.529	1.00
244_K	262_Q	0.527	1.00
248_L	251_H	0.526	1.00
37_Y	84_E	0.523	1.00
58_F	67_V	0.522	1.00
83_A	95_C	0.516	1.00
210_I	241_R	0.515	1.00
44_D	78_G	0.514	1.00
162_Q	166_M	0.513	1.00
111_S	114_Q	0.511	1.00
260_S	263_V	0.508	1.00
260_S	265_F	0.507	1.00
196_W	201_Y	0.506	1.00
148_I	151_K	0.506	1.00
200_H	205_I	0.505	1.00
50_L	134_A	0.505	1.00
133_W	173_N	0.504	1.00
45_E	97_N	0.502	1.00
154_L	158_D	0.501	1.00
143_K	146_Q	0.501	1.00
124_Y	127_L	0.501	1.00
67_V	71_D	0.501	1.00
145_N	148_I	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	0.866	100	0.255	Contact Map
1bl0A	1	0.3643	100	0.477	Contact Map
3oioA	1	0.3746	100	0.478	Contact Map
3oouA	1	0.3608	100	0.483	Contact Map
3mn2A	1	0.3608	100	0.488	Contact Map
3mklA	1	0.3746	100	0.492	Contact Map
2k9sA	1	0.3643	100	0.496	Contact Map
3lsgA	2	0.3505	100	0.497	Contact Map
3w6vA	1	0.3608	100	0.497	Contact Map
1d5yA	1	0.3643	100	0.501	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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