YISR - BACSU - GREMLIN Contacts

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YISR - Uncharacterized HTH-type transcriptional regulator YisR

UniProt:	P40331	Sequences: MPRILFTVPPFPVFIAAGEGVFKKGETHVKRVFSVFDLIYVKQGTLYITENETSFSVEGGEYILLSPGLEHYGTKGSDEATSYYWLHFDEHRYEFTAKGGSNWSELQQEKGSFEELARYGLALPRKGKVQRPQFMAQQFEKLIDYSAENSDLPLRKQILFEELMLHLQKEAFQIPSAKERVAWEAARYLQEHYKEKTTIKDLSLALHYHQDYVSRCMQQVLGVTPAQYTNRVRMTEAKRLLSSTNDKMGVIAETVGMEDPTYFSKLFKQIEGISPIEYRKIVSRKVQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	287 (236)
Sequences:	32506 (27587)
Seq/√Len:	1795.8

ECOLI - RHAS RHAR YQHC YPDC ARAC YDIP MELR YIJO YBCM YIDL CHBR RCLR YEAM FEAR GADW ENVY ADIY GADX APPY EUTR YDEO MARA YKGA SOXS ROB XYLR
BACSU - YISR BTR YDEC YFIF YBFI YOBQ YTDP ADAA 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
223_V	231_R	3.314	1.00
238_K	271_E	3.298	1.00
190_Q	232_V	3.050	1.00
246_D	254_T	3.025	1.00
234_M	271_E	3.015	1.00
200_K	210_Q	2.840	1.00
236_E	239_R	2.837	1.00
188_Y	192_H	2.698	1.00
192_H	195_E	2.673	1.00
231_R	270_I	2.607	1.00
267_F	278_Y	2.444	1.00
240_L	254_T	2.315	1.00
237_A	263_F	2.313	1.00
185_A	213_V	2.281	1.00
217_M	228_Y	2.076	1.00
198_T	201_D	2.068	1.00
240_L	255_V	2.018	1.00
47_Y	54_S	1.964	1.00
246_D	250_V	1.957	1.00
193_Y	232_V	1.925	1.00
273_I	281_I	1.922	1.00
226_A	230_N	1.836	1.00
47_Y	56_S	1.827	1.00
189_L	229_T	1.808	1.00
185_A	206_L	1.800	1.00
186_A	221_L	1.795	1.00
240_L	246_D	1.783	1.00
188_Y	205_A	1.773	1.00
247_K	250_V	1.726	1.00
182_A	221_L	1.710	1.00
260_P	264_S	1.703	1.00
234_M	270_I	1.702	1.00
49_T	54_S	1.701	1.00
266_L	269_Q	1.692	1.00
202_L	225_P	1.657	1.00
199_I	214_S	1.638	1.00
159_L	162_E	1.634	1.00
238_K	278_Y	1.630	1.00
239_R	243_S	1.627	1.00
232_V	236_E	1.623	1.00
223_V	227_Q	1.618	1.00
187_R	191_E	1.617	1.00
212_Y	216_C	1.616	1.00
241_L	248_M	1.605	1.00
45_T	56_S	1.603	1.00
43_Q	82_S	1.598	1.00
236_E	240_L	1.590	1.00
58_E	61_E	1.576	1.00
188_Y	197_T	1.565	1.00
42_K	84_Y	1.523	1.00
213_V	225_P	1.508	1.00
249_G	260_P	1.498	1.00
190_Q	228_Y	1.477	1.00
210_Q	214_S	1.471	1.00
273_I	277_E	1.464	1.00
49_T	72_Y	1.464	1.00
179_E	220_V	1.456	1.00
225_P	229_T	1.454	1.00
212_Y	215_R	1.449	1.00
262_Y	266_L	1.440	1.00
250_V	253_E	1.422	1.00
193_Y	236_E	1.418	1.00
249_G	253_E	1.406	1.00
208_Y	212_Y	1.403	1.00
237_A	255_V	1.397	1.00
47_Y	74_T	1.394	1.00
276_I	280_K	1.392	1.00
186_A	190_Q	1.390	1.00
36_F	67_P	1.386	1.00
257_M	266_L	1.378	1.00
250_V	254_T	1.378	1.00
201_D	205_A	1.373	1.00
45_T	58_E	1.372	1.00
136_A	140_E	1.360	1.00
194_K	254_T	1.359	1.00
211_D	215_R	1.342	1.00
214_S	225_P	1.335	1.00
251_I	255_V	1.318	1.00
236_E	255_V	1.313	1.00
231_R	235_T	1.313	1.00
158_I	165_L	1.309	1.00
158_I	162_E	1.302	1.00
162_E	166_H	1.299	1.00
230_N	266_L	1.293	1.00
200_K	204_L	1.292	1.00
261_T	264_S	1.292	1.00
51_N	69_L	1.272	1.00
224_T	227_Q	1.258	1.00
189_L	232_V	1.237	1.00
195_E	201_D	1.234	1.00
244_T	279_R	1.226	1.00
232_V	235_T	1.215	1.00
208_Y	213_V	1.212	1.00
238_K	242_S	1.191	1.00
155_R	159_L	1.191	1.00
264_S	274_S	1.189	1.00
158_I	161_E	1.188	1.00
185_A	202_L	1.186	1.00
209_H	212_Y	1.175	1.00
181_V	208_Y	1.172	1.00
125_R	128_K	1.170	1.00
196_K	258_E	1.155	1.00
264_S	276_I	1.149	1.00
137_Q	141_K	1.145	1.00
66_S	69_L	1.131	1.00
42_K	82_S	1.119	1.00
235_T	238_K	1.107	1.00
180_R	184_E	1.097	1.00
125_R	129_V	1.093	1.00
246_D	251_I	1.091	1.00
43_Q	59_G	1.091	1.00
265_K	269_Q	1.078	1.00
197_T	202_L	1.074	1.00
216_C	219_Q	1.072	1.00
199_I	225_P	1.069	1.00
277_E	280_K	1.057	1.00
181_V	216_C	1.051	1.00
216_C	220_V	1.044	1.00
274_S	277_E	1.039	1.00
137_Q	140_E	1.035	1.00
157_Q	161_E	1.035	1.00
31_R	71_H	1.029	1.00
230_N	269_Q	1.028	1.00
37_D	71_H	1.017	1.00
203_S	210_Q	1.016	1.00
155_R	162_E	1.010	1.00
194_K	236_E	1.010	1.00
33_F	71_H	0.992	1.00
161_E	165_L	0.990	1.00
188_Y	206_L	0.989	1.00
276_I	279_R	0.983	1.00
259_D	265_K	0.978	1.00
201_D	204_L	0.975	1.00
186_A	228_Y	0.973	1.00
240_L	251_I	0.971	1.00
206_L	213_V	0.956	1.00
189_L	225_P	0.948	1.00
30_K	70_E	0.944	1.00
181_V	206_L	0.942	1.00
183_W	187_R	0.939	1.00
199_I	210_Q	0.938	1.00
248_M	251_I	0.935	1.00
266_L	270_I	0.930	1.00
264_S	268_K	0.930	1.00
140_E	144_D	0.926	1.00
120_G	124_P	0.919	1.00
129_V	132_P	0.918	1.00
184_E	205_A	0.915	1.00
165_L	169_K	0.911	1.00
202_L	205_A	0.904	1.00
227_Q	230_N	0.899	1.00
227_Q	231_R	0.897	1.00
143_I	147_A	0.897	1.00
233_R	255_V	0.892	1.00
46_L	81_T	0.885	1.00
241_L	251_I	0.884	1.00
211_D	214_S	0.883	1.00
230_N	270_I	0.883	1.00
238_K	267_F	0.879	1.00
226_A	262_Y	0.878	1.00
184_E	187_R	0.876	1.00
188_Y	202_L	0.876	1.00
162_E	165_L	0.873	1.00
217_M	225_P	0.872	1.00
49_T	52_E	0.870	1.00
271_E	278_Y	0.868	1.00
234_M	266_L	0.865	1.00
262_Y	265_K	0.861	1.00
50_E	53_T	0.851	1.00
268_K	274_S	0.846	1.00
41_V	46_L	0.845	1.00
277_E	281_I	0.842	1.00
196_K	201_D	0.841	1.00
244_T	251_I	0.832	1.00
241_L	279_R	0.830	1.00
193_Y	229_T	0.825	1.00
46_L	57_V	0.820	1.00
184_E	206_L	0.818	1.00
208_Y	216_C	0.818	1.00
49_T	74_T	0.807	1.00
217_M	221_L	0.806	1.00
183_W	186_A	0.806	1.00
193_Y	197_T	0.804	1.00
33_F	37_D	0.803	1.00
182_A	216_C	0.802	1.00
141_K	145_Y	0.802	1.00
90_E	94_E	0.792	1.00
252_A	260_P	0.790	1.00
192_H	205_A	0.781	1.00
45_T	76_G	0.781	1.00
123_L	126_K	0.776	1.00
193_Y	255_V	0.770	1.00
47_Y	76_G	0.767	1.00
36_F	64_L	0.765	1.00
39_I	85_W	0.765	1.00
30_K	72_Y	0.761	1.00
268_K	277_E	0.759	1.00
134_F	166_H	0.756	1.00
237_A	240_L	0.756	1.00
242_S	278_Y	0.755	1.00
40_Y	62_Y	0.755	1.00
253_E	258_E	0.753	1.00
214_S	218_Q	0.751	1.00
186_A	217_M	0.749	1.00
226_A	229_T	0.749	1.00
227_Q	270_I	0.745	1.00
154_L	157_Q	0.745	1.00
182_A	185_A	0.743	1.00
48_I	63_I	0.735	1.00
185_A	188_Y	0.734	1.00
182_A	220_V	0.730	1.00
192_H	201_D	0.729	1.00
81_T	85_W	0.729	1.00
215_R	219_Q	0.725	1.00
134_F	137_Q	0.722	1.00
259_D	262_Y	0.719	1.00
273_I	278_Y	0.719	1.00
46_L	56_S	0.718	1.00
128_K	132_P	0.717	1.00
228_Y	232_V	0.716	1.00
178_K	219_Q	0.711	1.00
185_A	217_M	0.710	1.00
214_S	224_T	0.707	1.00
185_A	189_L	0.704	1.00
234_M	263_F	0.704	1.00
37_D	87_H	0.702	1.00
251_I	279_R	0.698	1.00
214_S	226_A	0.696	1.00
155_R	165_L	0.690	1.00
182_A	186_A	0.681	1.00
153_P	157_Q	0.680	1.00
141_K	159_L	0.680	1.00
189_L	228_Y	0.678	1.00
185_A	225_P	0.678	1.00
179_E	216_C	0.676	1.00
155_R	158_I	0.674	1.00
121_L	125_R	0.673	1.00
122_A	125_R	0.673	1.00
121_L	124_P	0.672	1.00
261_T	274_S	0.669	1.00
235_T	270_I	0.668	1.00
181_V	184_E	0.667	1.00
197_T	201_D	0.667	1.00
134_F	138_Q	0.666	1.00
138_Q	141_K	0.664	1.00
258_E	262_Y	0.664	1.00
141_K	162_E	0.663	1.00
133_Q	136_A	0.663	1.00
166_H	170_E	0.662	1.00
202_L	213_V	0.657	1.00
245_N	251_I	0.655	1.00
124_P	128_K	0.643	1.00
193_Y	233_R	0.639	1.00
223_V	228_Y	0.637	1.00
234_M	257_M	0.635	1.00
155_R	169_K	0.633	1.00
261_T	265_K	0.630	1.00
190_Q	236_E	0.629	1.00
43_Q	80_A	0.627	1.00
188_Y	201_D	0.627	1.00
57_V	63_I	0.624	1.00
39_I	65_L	0.623	1.00
35_V	87_H	0.623	1.00
134_F	141_K	0.622	1.00
260_P	263_F	0.619	1.00
152_L	155_R	0.618	1.00
218_Q	224_T	0.616	1.00
65_L	71_H	0.615	1.00
178_K	181_V	0.615	1.00
133_Q	137_Q	0.613	1.00
39_I	83_Y	0.611	1.00
141_K	144_D	0.610	1.00
199_I	226_A	0.608	1.00
156_K	167_L	0.600	1.00
180_R	220_V	0.599	1.00
179_E	183_W	0.598	1.00
197_T	233_R	0.598	1.00
128_K	131_R	0.594	1.00
61_E	128_K	0.592	1.00
202_L	206_L	0.590	1.00
41_V	81_T	0.588	1.00
259_D	269_Q	0.586	1.00
92_R	95_F	0.586	1.00
154_L	158_I	0.586	1.00
138_Q	159_L	0.584	1.00
247_K	251_I	0.581	1.00
267_F	273_I	0.581	1.00
235_T	271_E	0.577	1.00
221_L	228_Y	0.575	1.00
36_F	39_I	0.572	1.00
41_V	57_V	0.568	1.00
168_Q	172_F	0.568	1.00
32_V	70_E	0.567	1.00
27_T	74_T	0.567	1.00
237_A	251_I	0.567	1.00
94_E	98_K	0.566	1.00
40_Y	139_F	0.564	1.00
229_T	233_R	0.563	1.00
199_I	211_D	0.563	1.00
230_N	262_Y	0.561	1.00
185_A	205_A	0.561	1.00
124_P	129_V	0.561	1.00
150_S	153_P	0.559	1.00
123_L	127_G	0.559	1.00
178_K	220_V	0.557	1.00
46_L	73_G	0.557	1.00
263_F	275_P	0.550	1.00
119_Y	123_L	0.549	1.00
143_I	146_S	0.548	1.00
230_N	234_M	0.545	1.00
204_L	207_H	0.545	1.00
155_R	166_H	0.544	1.00
50_E	65_L	0.540	1.00
176_S	179_E	0.540	1.00
51_N	70_E	0.538	1.00
42_K	140_E	0.538	1.00
203_S	206_L	0.537	1.00
137_Q	144_D	0.537	1.00
182_A	213_V	0.537	1.00
90_E	93_Y	0.537	1.00
41_V	83_Y	0.537	1.00
131_R	134_F	0.535	1.00
39_I	48_I	0.534	1.00
241_L	278_Y	0.533	1.00
138_Q	142_L	0.531	1.00
192_H	197_T	0.528	1.00
248_M	276_I	0.528	1.00
154_L	165_L	0.528	1.00
120_G	123_L	0.527	1.00
144_D	148_E	0.526	1.00
239_R	242_S	0.525	1.00
41_V	44_G	0.524	1.00
154_L	161_E	0.524	1.00
142_L	145_Y	0.522	1.00
149_N	152_L	0.522	1.00
240_L	243_S	0.522	1.00
152_L	156_K	0.521	1.00
197_T	229_T	0.520	1.00
132_P	136_A	0.520	1.00
230_N	257_M	0.520	1.00
182_A	206_L	0.519	1.00
145_Y	169_K	0.518	1.00
187_R	190_Q	0.517	1.00
266_L	271_E	0.516	1.00
189_L	197_T	0.515	1.00
227_Q	269_Q	0.512	1.00
119_Y	122_A	0.510	1.00
263_F	267_F	0.508	1.00
83_Y	87_H	0.505	1.00
48_I	57_V	0.505	1.00
235_T	239_R	0.504	1.00
252_A	257_M	0.503	1.00
166_H	169_K	0.500	1.00
127_G	131_R	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	0.8815	100	0.231	Contact Map
3oouA	1	0.3659	100	0.469	Contact Map
1bl0A	1	0.3833	100	0.47	Contact Map
3mn2A	1	0.3693	100	0.475	Contact Map
3oioA	1	0.3902	100	0.475	Contact Map
3w6vA	1	0.3798	100	0.478	Contact Map
3mklA	1	0.3868	100	0.478	Contact Map
2k9sA	1	0.3693	100	0.482	Contact Map
3lsgA	2	0.3554	100	0.491	Contact Map
1d5yA	1	0.3833	99.9	0.497	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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