YDIP - ECOLI - GREMLIN Contacts

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YDIP - Uncharacterized HTH-type transcriptional regulator YdiP

UniProt:	P77402	Sequences: MYQRCFDNASETLFVAGKTPRLSRFAFSDDPKWESGHHVHDNETELIYVKKGVARFTIDSSLYVAHADDIVVIERGRLHAVASDVNDPATTCTCALYGFQFQGAEENQLLQPHSCPVIAAGQGKEVIKTLFNELSVILPQSKNSQTSSLWDAFAYTLAILYYENFKNAYRSEQGYIKKDVLIKDILFYLNNNYREKITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWSLTNTELSQAEISWRVGYENVDHFAKLFLRHVGCSPSDYRRQFKNCFAEQEILSEFPQPVSLVG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13975
Length:	303 (248)
Sequences:	28668 (24577)
Seq/√Len:	1560.6

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
238_K	271_V	3.206	1.00
223_I	231_Q	3.151	1.00
234_M	271_V	3.104	1.00
246_L	254_R	2.926	1.00
190_N	232_R	2.915	1.00
236_E	239_W	2.832	1.00
200_E	210_V	2.831	1.00
188_Y	192_N	2.822	1.00
192_N	195_E	2.725	1.00
231_Q	270_H	2.482	1.00
237_A	263_F	2.371	1.00
267_F	278_Y	2.361	1.00
185_I	213_I	2.292	1.00
240_S	254_R	2.260	1.00
217_F	228_Y	2.100	1.00
55_R	62_L	2.053	1.00
193_Y	232_R	2.002	1.00
240_S	255_V	1.996	1.00
273_C	281_Q	1.968	1.00
246_L	250_E	1.949	1.00
198_T	201_Q	1.919	1.00
189_L	229_V	1.917	1.00
234_M	270_H	1.879	1.00
55_R	64_V	1.875	1.00
240_S	246_L	1.853	1.00
182_I	221_Y	1.805	1.00
185_I	206_F	1.804	1.00
226_I	230_I	1.790	1.00
188_Y	205_K	1.775	1.00
186_L	221_Y	1.759	1.00
57_T	62_L	1.757	1.00
53_V	64_V	1.729	1.00
51_K	90_T	1.717	1.00
212_Y	216_E	1.690	1.00
199_L	214_C	1.687	1.00
247_S	250_E	1.680	1.00
187_F	191_N	1.679	1.00
202_L	225_P	1.669	1.00
190_N	228_Y	1.637	1.00
241_L	248_Q	1.635	1.00
50_K	92_C	1.613	1.00
152_A	156_T	1.576	1.00
238_K	278_Y	1.572	1.00
153_F	156_T	1.570	1.00
266_L	269_R	1.567	1.00
225_P	229_V	1.562	1.00
260_V	264_A	1.561	1.00
66_H	69_D	1.560	1.00
189_L	232_R	1.558	1.00
53_V	66_H	1.554	1.00
236_E	240_S	1.547	1.00
232_R	236_E	1.540	1.00
213_I	225_P	1.536	1.00
223_I	227_N	1.533	1.00
239_W	243_N	1.531	1.00
152_A	155_Y	1.525	1.00
188_Y	197_I	1.524	1.00
249_A	260_V	1.512	1.00
249_A	253_W	1.494	1.00
273_C	277_D	1.481	1.00
59_D	77_R	1.480	1.00
262_H	266_L	1.471	1.00
179_D	220_E	1.469	1.00
44_T	75_R	1.469	1.00
152_A	159_I	1.467	1.00
128_K	132_N	1.459	1.00
57_T	80_A	1.458	1.00
193_Y	236_E	1.450	1.00
250_E	253_W	1.437	1.00
250_E	254_R	1.436	1.00
212_Y	215_H	1.433	1.00
276_S	280_R	1.424	1.00
210_V	214_C	1.413	1.00
208_A	212_Y	1.402	1.00
185_I	202_L	1.400	1.00
194_R	254_R	1.394	1.00
200_E	204_K	1.391	1.00
214_C	225_P	1.390	1.00
251_I	255_V	1.388	1.00
237_A	255_V	1.381	1.00
211_S	215_H	1.352	1.00
151_D	155_Y	1.349	1.00
201_Q	205_K	1.345	1.00
257_Y	266_L	1.331	1.00
244_T	279_R	1.331	1.00
55_R	82_A	1.296	1.00
186_L	190_N	1.295	1.00
208_A	213_I	1.291	1.00
261_D	264_A	1.280	1.00
181_L	208_A	1.267	1.00
224_S	227_N	1.254	1.00
264_A	274_S	1.233	1.00
209_S	212_Y	1.229	1.00
236_E	255_V	1.225	1.00
51_K	67_A	1.207	1.00
231_Q	235_T	1.197	1.00
195_E	201_Q	1.190	1.00
264_A	276_S	1.181	1.00
74_E	77_R	1.157	1.00
230_I	266_L	1.153	1.00
50_K	90_T	1.152	1.00
232_R	235_T	1.131	1.00
129_T	132_N	1.118	1.00
246_L	251_I	1.105	1.00
238_K	242_T	1.100	1.00
40_H	79_H	1.098	1.00
129_T	133_E	1.095	1.00
265_K	269_R	1.088	1.00
38_H	79_H	1.077	1.00
155_Y	159_I	1.077	1.00
235_T	238_K	1.074	1.00
277_D	280_R	1.067	1.00
45_E	79_H	1.057	1.00
199_L	225_P	1.057	1.00
216_E	219_K	1.053	1.00
194_R	236_E	1.052	1.00
40_H	45_E	1.047	1.00
37_H	78_L	1.042	1.00
276_S	279_R	1.042	1.00
196_K	201_Q	1.037	1.00
117_V	120_A	1.037	1.00
132_N	136_V	1.034	1.00
188_Y	206_F	1.029	1.00
183_K	187_F	1.027	1.00
197_I	202_L	1.025	1.00
116_P	119_A	1.023	1.00
189_L	225_P	1.015	1.00
259_N	265_K	1.013	1.00
159_I	163_E	1.010	1.00
203_S	210_V	1.006	1.00
196_K	258_E	1.004	1.00
181_L	216_E	0.998	1.00
180_V	184_D	0.996	1.00
181_L	206_F	0.991	1.00
184_D	205_K	0.984	1.00
201_Q	204_K	0.979	1.00
230_I	269_R	0.971	1.00
240_S	251_I	0.966	1.00
202_L	205_K	0.966	1.00
248_Q	251_I	0.964	1.00
156_T	160_L	0.963	1.00
244_T	251_I	0.961	1.00
216_E	220_E	0.959	1.00
188_Y	202_L	0.956	1.00
274_S	277_D	0.952	1.00
206_F	213_I	0.951	1.00
54_A	65_A	0.949	1.00
156_T	159_I	0.946	1.00
264_A	268_L	0.932	1.00
234_M	266_L	0.929	1.00
57_T	82_A	0.925	1.00
149_L	156_T	0.917	1.00
69_D	119_A	0.915	1.00
54_A	89_A	0.913	1.00
126_V	129_T	0.911	1.00
226_I	262_H	0.911	1.00
53_V	84_D	0.906	1.00
211_S	214_C	0.906	1.00
186_L	228_Y	0.904	1.00
233_R	255_V	0.903	1.00
208_A	216_E	0.902	1.00
277_D	281_Q	0.895	1.00
266_L	270_H	0.893	1.00
44_T	72_V	0.892	1.00
49_V	54_A	0.889	1.00
227_N	231_Q	0.888	1.00
238_K	267_F	0.888	1.00
45_E	95_A	0.888	1.00
199_L	210_V	0.884	1.00
58_I	61_S	0.882	1.00
148_S	152_A	0.878	1.00
271_V	278_Y	0.870	1.00
56_F	71_V	0.867	1.00
227_N	230_I	0.866	1.00
133_E	156_T	0.864	1.00
148_S	155_Y	0.862	1.00
193_Y	229_V	0.858	1.00
184_D	187_F	0.857	1.00
37_H	80_A	0.853	1.00
241_L	251_I	0.847	1.00
182_I	216_E	0.846	1.00
55_R	84_D	0.836	1.00
148_S	151_D	0.829	1.00
121_G	124_K	0.826	1.00
226_I	229_V	0.824	1.00
184_D	206_F	0.819	1.00
48_Y	70_I	0.811	1.00
230_I	270_H	0.810	1.00
234_M	263_F	0.808	1.00
193_Y	197_I	0.808	1.00
262_H	265_K	0.804	1.00
193_Y	255_V	0.802	1.00
160_L	164_N	0.801	1.00
98_G	102_Q	0.799	1.00
51_K	88_P	0.797	1.00
237_A	240_S	0.794	1.00
178_K	219_K	0.791	1.00
47_I	93_T	0.791	1.00
183_K	186_L	0.790	1.00
268_L	277_D	0.789	1.00
54_A	64_V	0.786	1.00
217_F	221_Y	0.786	1.00
57_T	60_S	0.782	1.00
182_I	220_E	0.778	1.00
189_L	228_Y	0.775	1.00
182_I	185_I	0.774	1.00
214_C	224_S	0.768	1.00
253_W	258_E	0.766	1.00
268_L	274_S	0.765	1.00
217_F	225_P	0.764	1.00
192_N	205_K	0.764	1.00
125_E	128_K	0.763	1.00
202_L	213_I	0.763	1.00
215_H	219_K	0.761	1.00
141_S	146_T	0.761	1.00
149_L	153_F	0.760	1.00
192_N	201_Q	0.758	1.00
241_L	279_R	0.757	1.00
193_Y	233_R	0.751	1.00
146_T	150_W	0.745	1.00
185_I	225_P	0.742	1.00
214_C	218_T	0.740	1.00
227_N	270_H	0.736	1.00
259_N	262_H	0.733	1.00
147_S	151_D	0.732	1.00
150_W	154_A	0.732	1.00
133_E	137_I	0.729	1.00
43_E	95_A	0.729	1.00
65_A	71_V	0.729	1.00
113_H	116_P	0.727	1.00
34_E	82_A	0.720	1.00
261_D	274_S	0.718	1.00
73_I	79_H	0.712	1.00
185_I	217_F	0.712	1.00
185_I	188_Y	0.709	1.00
102_Q	106_E	0.709	1.00
124_K	128_K	0.708	1.00
179_D	216_E	0.706	1.00
242_T	278_Y	0.704	1.00
197_I	201_Q	0.698	1.00
186_L	217_F	0.697	1.00
273_C	278_Y	0.694	1.00
252_S	260_V	0.694	1.00
99_F	102_Q	0.692	1.00
136_V	140_Q	0.691	1.00
49_V	52_G	0.691	1.00
228_Y	232_R	0.689	1.00
126_V	133_E	0.688	1.00
185_I	189_L	0.688	1.00
133_E	136_V	0.687	1.00
181_L	184_D	0.683	1.00
165_F	169_Y	0.682	1.00
267_F	273_C	0.681	1.00
197_I	233_R	0.678	1.00
126_V	130_L	0.674	1.00
133_E	153_F	0.673	1.00
150_W	153_F	0.673	1.00
258_E	262_H	0.671	1.00
182_I	213_I	0.670	1.00
47_I	91_T	0.669	1.00
199_L	226_I	0.665	1.00
47_I	73_I	0.664	1.00
135_S	139_P	0.661	1.00
137_I	163_E	0.660	1.00
261_D	265_K	0.659	1.00
125_E	129_T	0.655	1.00
214_C	226_I	0.654	1.00
247_S	251_I	0.647	1.00
251_I	279_R	0.647	1.00
54_A	81_V	0.646	1.00
166_K	170_R	0.645	1.00
126_V	160_L	0.644	1.00
182_I	186_L	0.642	1.00
223_I	228_Y	0.636	1.00
45_E	73_I	0.631	1.00
185_I	205_K	0.630	1.00
53_V	87_D	0.629	1.00
49_V	89_A	0.627	1.00
49_V	65_A	0.626	1.00
245_E	251_I	0.625	1.00
147_S	150_W	0.623	1.00
129_T	136_V	0.620	1.00
56_F	73_I	0.619	1.00
263_F	275_P	0.619	1.00
248_Q	276_S	0.619	1.00
178_K	181_L	0.619	1.00
150_W	156_T	0.618	1.00
190_N	236_E	0.618	1.00
123_G	126_V	0.617	1.00
130_L	134_L	0.616	1.00
49_V	91_T	0.615	1.00
138_L	141_S	0.613	1.00
218_T	224_S	0.612	1.00
229_V	233_R	0.611	1.00
46_L	70_I	0.610	1.00
58_I	73_I	0.609	1.00
48_Y	131_F	0.609	1.00
149_L	152_A	0.598	1.00
178_K	220_E	0.597	1.00
47_I	71_V	0.597	1.00
149_L	159_I	0.596	1.00
48_Y	124_K	0.595	1.00
140_Q	143_N	0.592	1.00
59_D	78_L	0.592	1.00
189_L	197_I	0.591	1.00
203_S	206_F	0.590	1.00
230_I	234_M	0.589	1.00
116_P	120_A	0.589	1.00
127_I	130_L	0.587	1.00
234_M	257_Y	0.583	1.00
229_V	232_R	0.580	1.00
204_K	207_R	0.579	1.00
164_N	168_A	0.579	1.00
160_L	163_E	0.579	1.00
81_V	93_T	0.577	1.00
39_V	78_L	0.575	1.00
260_V	263_F	0.571	1.00
202_L	206_F	0.568	1.00
230_I	262_H	0.567	1.00
230_I	257_Y	0.566	1.00
130_L	133_E	0.566	1.00
176_I	179_D	0.564	1.00
100_Q	103_G	0.562	1.00
89_A	93_T	0.562	1.00
188_Y	193_Y	0.561	1.00
47_I	56_F	0.561	1.00
46_L	72_V	0.556	1.00
162_Y	166_K	0.555	1.00
187_F	190_N	0.554	1.00
259_N	269_R	0.550	1.00
163_E	167_N	0.549	1.00
132_N	135_S	0.546	1.00
103_G	106_E	0.545	1.00
143_N	146_T	0.545	1.00
98_G	101_F	0.544	1.00
148_S	156_T	0.544	1.00
34_E	80_A	0.543	1.00
126_V	136_V	0.541	1.00
161_Y	165_F	0.539	1.00
243_N	246_L	0.538	1.00
237_A	251_I	0.537	1.00
114_S	117_V	0.537	1.00
182_I	206_F	0.535	1.00
213_I	221_Y	0.534	1.00
235_T	271_V	0.532	1.00
145_Q	149_L	0.532	1.00
206_F	210_V	0.529	1.00
110_L	114_S	0.529	1.00
197_I	229_V	0.527	1.00
235_T	270_H	0.525	1.00
145_Q	148_S	0.520	1.00
263_F	267_F	0.520	1.00
92_C	95_A	0.517	1.00
221_Y	228_Y	0.515	1.00
218_T	221_Y	0.514	1.00
185_I	216_E	0.514	1.00
62_L	82_A	0.514	1.00
39_V	76_G	0.513	1.00
99_F	103_G	0.513	1.00
239_W	242_T	0.512	1.00
56_F	81_V	0.512	1.00
179_D	183_K	0.511	1.00
196_K	233_R	0.509	1.00
227_N	269_R	0.509	1.00
202_L	233_R	0.508	1.00
180_V	220_E	0.507	1.00
44_T	47_I	0.507	1.00
45_E	93_T	0.506	1.00
252_S	257_Y	0.505	1.00
188_Y	201_Q	0.505	1.00
213_I	216_E	0.505	1.00
134_L	137_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	0.8449	100	0.305	Contact Map
3oioA	1	0.3696	100	0.525	Contact Map
3oouA	1	0.3465	100	0.525	Contact Map
3mn2A	1	0.3498	100	0.531	Contact Map
1bl0A	1	0.3828	100	0.531	Contact Map
3mklA	1	0.3663	100	0.533	Contact Map
3w6vA	1	0.3663	100	0.536	Contact Map
2k9sA	1	0.3498	100	0.537	Contact Map
3lsgA	2	0.3366	100	0.544	Contact Map
1d5yA	1	0.4158	99.9	0.554	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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