YVDE - BACSU - GREMLIN Contacts

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YVDE - Uncharacterized HTH-type transcriptional regulator YvdE

UniProt:	O06987	Sequences: MATLSDVAKKANVSKMTVSRVINHPETVTDELKKLVHSAMKELNYIPNYAARALVQNRTQVVKLLILEEMDTTEPYYMNLLTGISRELDRNHYALQLVTRNSLNIGQCDGIIATGLRKNDFEGVIKAFEKPLVVFGQNEMGYDFIDVNNEKGTFMATRHVMGLGEREVVFFGIDLDEPFERAREQGYIRAMNKSFKKSNMFRIDNSSKKSECLARELLKSMDNQAAFVCASDRIALGVIRAAQSLGKRIPEDVAVTGNDGVFLDRISSPRLTTVRQPVVEMGEACAKMLLKKMNEDGAAQGSLFFEPELIVRESTL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	316 (308)
Sequences:	33556 (24478)
Seq/√Len:	1394.8

ECOLI - RBSR GALS GALR EBGR PURR IDNR ASCG CYTR GNTR LACI MALI CRA YCJW TRER TORT ALSB RBSB YTFQ XYLF ARAF YPHF XYLR LSRB DGAL
BACSU - YVDE GANR NTDR MSMR RBSR EXUR CCPA KDGR YKVZ DEGA ARAR CCPB RBSB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
150_E	189_R	3.268	1.00
165_E	225_A	3.121	1.00
10_K	42_E	3.080	1.00
248_R	251_E	3.024	1.00
156_A	256_T	2.678	1.00
165_E	254_A	2.582	1.00
184_E	188_I	2.513	1.00
110_G	289_L	2.498	1.00
260_G	275_R	2.434	1.00
154_F	193_K	2.280	1.00
143_D	292_K	2.248	1.00
30_D	34_K	2.233	1.00
38_S	42_E	2.211	1.00
211_E	244_S	2.144	1.00
34_K	38_S	2.120	1.00
215_R	245_L	2.096	1.00
87_E	90_R	2.069	1.00
161_M	194_S	2.066	1.00
87_E	287_K	2.064	1.00
158_R	190_A	2.046	1.00
151_K	155_M	2.023	1.00
21_V	36_V	2.021	1.00
284_A	287_K	1.991	1.00
154_F	189_R	1.971	1.00
215_R	241_A	1.969	1.00
154_F	190_A	1.950	1.00
88_L	286_A	1.930	1.00
22_I	40_M	1.909	1.00
33_K	37_H	1.907	1.00
153_T	157_T	1.900	1.00
5_S	15_K	1.892	1.00
83_G	282_G	1.868	1.00
210_S	237_G	1.857	1.00
152_G	258_N	1.856	1.00
157_T	187_Y	1.852	1.00
150_E	185_Q	1.835	1.00
158_R	162_G	1.806	1.00
87_E	283_E	1.798	1.00
160_V	226_A	1.790	1.00
153_T	228_V	1.779	1.00
242_A	253_V	1.768	1.00
275_R	308_E	1.762	1.00
10_K	39_A	1.762	1.00
11_A	39_A	1.756	1.00
219_K	245_L	1.742	1.00
158_R	194_S	1.734	1.00
270_R	313_E	1.720	1.00
284_A	303_L	1.712	1.00
86_R	279_V	1.684	1.00
211_E	241_A	1.671	1.00
291_K	296_D	1.664	1.00
170_F	230_A	1.659	1.00
229_C	238_V	1.653	1.00
214_A	238_V	1.645	1.00
154_F	158_R	1.629	1.00
243_Q	268_S	1.625	1.00
83_G	279_V	1.622	1.00
155_M	307_P	1.603	1.00
169_V	224_Q	1.600	1.00
248_R	252_D	1.597	1.00
241_A	245_L	1.595	1.00
63_K	108_C	1.592	1.00
277_P	280_E	1.590	1.00
247_K	252_D	1.571	1.00
135_F	285_C	1.562	1.00
159_H	163_L	1.552	1.00
87_E	91_N	1.538	1.00
37_H	41_K	1.513	1.00
91_N	290_L	1.485	1.00
241_A	244_S	1.483	1.00
167_E	223_N	1.467	1.00
280_E	284_A	1.463	1.00
161_M	190_A	1.454	1.00
21_V	40_M	1.445	1.00
148_N	151_K	1.444	1.00
260_G	312_R	1.441	1.00
151_K	154_F	1.440	1.00
37_H	40_M	1.430	1.00
7_V	39_A	1.427	1.00
185_Q	189_R	1.426	1.00
159_H	311_V	1.407	1.00
159_H	162_G	1.383	1.00
182_A	185_Q	1.382	1.00
60_Q	109_D	1.378	1.00
201_F	216_E	1.376	1.00
280_E	283_E	1.370	1.00
188_I	192_N	1.361	1.00
152_G	307_P	1.353	1.00
10_K	43_L	1.335	1.00
190_A	193_K	1.332	1.00
87_E	286_A	1.328	1.00
242_A	247_K	1.310	1.00
5_S	9_K	1.299	1.00
157_T	190_A	1.295	1.00
169_V	217_L	1.288	1.00
30_D	33_K	1.282	1.00
35_L	39_A	1.274	1.00
153_T	186_G	1.270	1.00
214_A	242_A	1.268	1.00
215_R	219_K	1.266	1.00
20_R	25_P	1.264	1.00
221_M	224_Q	1.261	1.00
167_E	225_A	1.254	1.00
6_D	9_K	1.252	1.00
157_T	186_G	1.248	1.00
204_D	209_K	1.248	1.00
211_E	215_R	1.248	1.00
39_A	42_E	1.248	1.00
60_Q	93_Y	1.243	1.00
165_E	226_A	1.242	1.00
214_A	227_F	1.239	1.00
211_E	240_R	1.236	1.00
157_T	161_M	1.236	1.00
215_R	244_S	1.234	1.00
29_T	32_L	1.231	1.00
62_V	88_L	1.228	1.00
186_G	190_A	1.217	1.00
167_E	199_N	1.215	1.00
7_V	11_A	1.213	1.00
239_I	255_V	1.205	1.00
39_A	43_L	1.205	1.00
287_K	291_K	1.204	1.00
290_L	294_N	1.204	1.00
84_I	286_A	1.197	1.00
158_R	193_K	1.192	1.00
155_M	158_R	1.182	1.00
7_V	43_L	1.181	1.00
4_L	15_K	1.179	1.00
32_L	35_L	1.178	1.00
256_T	272_T	1.176	1.00
150_E	154_F	1.169	1.00
112_I	285_C	1.165	1.00
21_V	28_V	1.163	1.00
84_I	112_I	1.156	1.00
150_E	182_A	1.130	1.00
123_G	127_A	1.128	1.00
64_L	84_I	1.128	1.00
190_A	194_S	1.124	1.00
187_Y	191_M	1.123	1.00
216_E	220_S	1.119	1.00
88_L	95_L	1.115	1.00
34_K	37_H	1.114	1.00
168_V	191_M	1.113	1.00
98_V	103_L	1.109	1.00
279_V	283_E	1.106	1.00
232_D	273_T	1.088	1.00
161_M	196_K	1.083	1.00
38_S	41_K	1.080	1.00
284_A	288_M	1.079	1.00
171_F	238_V	1.079	1.00
282_G	286_A	1.078	1.00
91_N	287_K	1.074	1.00
227_F	238_V	1.071	1.00
150_E	186_G	1.070	1.00
232_D	257_G	1.058	1.00
170_F	184_E	1.058	1.00
24_H	33_K	1.057	1.00
163_L	311_V	1.056	1.00
208_K	212_C	1.056	1.00
237_G	241_A	1.048	1.00
189_R	193_K	1.048	1.00
156_A	228_V	1.047	1.00
213_L	216_E	1.047	1.00
4_L	18_V	1.047	1.00
167_E	222_D	1.046	1.00
166_R	225_A	1.042	1.00
64_L	95_L	1.035	1.00
288_M	303_L	1.034	1.00
61_V	96_Q	1.032	1.00
185_Q	188_I	1.025	1.00
229_C	235_A	1.020	1.00
91_N	294_N	1.010	1.00
40_M	43_L	1.006	1.00
50_A	53_A	1.004	1.00
63_K	103_L	1.002	1.00
284_A	305_F	1.002	1.00
151_K	306_E	1.001	1.00
162_G	194_S	0.999	1.00
48_N	54_L	0.994	1.00
93_Y	290_L	0.989	1.00
191_M	196_K	0.968	1.00
11_A	18_V	0.968	1.00
283_E	287_K	0.963	1.00
161_M	166_R	0.961	1.00
210_S	214_A	0.961	1.00
206_S	209_K	0.955	1.00
168_V	226_A	0.949	1.00
289_L	293_M	0.948	1.00
85_S	89_D	0.947	1.00
163_L	254_A	0.945	1.00
48_N	51_A	0.940	1.00
156_A	274_V	0.933	1.00
229_C	234_I	0.932	1.00
209_K	212_C	0.929	1.00
239_I	249_I	0.928	1.00
181_R	185_Q	0.927	1.00
144_F	302_S	0.926	1.00
51_A	54_L	0.922	1.00
239_I	267_S	0.922	1.00
212_C	216_E	0.920	1.00
214_A	218_L	0.917	1.00
308_E	311_V	0.916	1.00
61_V	94_A	0.915	1.00
24_H	37_H	0.913	1.00
178_P	182_A	0.907	1.00
47_P	52_R	0.900	1.00
188_I	198_S	0.896	1.00
275_R	310_I	0.896	1.00
227_F	253_V	0.894	1.00
143_D	288_M	0.892	1.00
187_Y	228_V	0.890	1.00
166_R	196_K	0.888	1.00
147_V	277_P	0.882	1.00
207_S	240_R	0.880	1.00
288_M	291_K	0.879	1.00
151_K	307_P	0.877	1.00
112_I	289_L	0.876	1.00
157_T	191_M	0.876	1.00
90_R	283_E	0.872	1.00
86_R	283_E	0.869	1.00
62_V	112_I	0.869	1.00
21_V	37_H	0.868	1.00
175_L	202_R	0.864	1.00
201_F	213_L	0.863	1.00
277_P	308_E	0.860	1.00
277_P	305_F	0.854	1.00
147_V	307_P	0.850	1.00
146_D	304_F	0.841	1.00
148_N	306_E	0.837	1.00
172_G	184_E	0.836	1.00
148_N	304_F	0.835	1.00
260_G	310_I	0.833	1.00
145_I	288_M	0.833	1.00
84_I	282_G	0.832	1.00
212_C	215_R	0.831	1.00
146_D	302_S	0.829	1.00
82_T	86_R	0.829	1.00
191_M	198_S	0.824	1.00
232_D	260_G	0.824	1.00
160_V	256_T	0.824	1.00
13_V	36_V	0.822	1.00
176_D	181_R	0.821	1.00
169_V	227_F	0.818	1.00
247_K	253_V	0.818	1.00
76_Y	278_V	0.814	1.00
286_A	290_L	0.814	1.00
243_Q	270_R	0.811	1.00
173_I	205_N	0.810	1.00
64_L	81_L	0.807	1.00
218_L	241_A	0.804	1.00
80_L	135_F	0.803	1.00
17_T	20_R	0.800	1.00
171_F	229_C	0.800	1.00
49_Y	52_R	0.796	1.00
3_T	6_D	0.793	1.00
59_T	109_D	0.792	1.00
16_M	20_R	0.790	1.00
167_E	197_K	0.785	1.00
104_N	128_F	0.783	1.00
214_A	241_A	0.783	1.00
147_V	276_Q	0.783	1.00
31_E	34_K	0.778	1.00
149_N	183_R	0.778	1.00
83_G	87_E	0.775	1.00
189_R	192_N	0.774	1.00
223_N	247_K	0.774	1.00
143_D	301_G	0.772	1.00
209_K	213_L	0.767	1.00
228_V	256_T	0.765	1.00
79_N	279_V	0.758	1.00
184_E	200_M	0.750	1.00
31_E	35_L	0.749	1.00
218_L	245_L	0.747	1.00
242_A	255_V	0.747	1.00
155_M	274_V	0.746	1.00
20_R	27_T	0.745	1.00
263_L	267_S	0.745	1.00
110_G	293_M	0.743	1.00
260_G	264_D	0.743	1.00
182_A	186_G	0.742	1.00
85_S	99_T	0.741	1.00
20_R	26_E	0.739	1.00
83_G	283_E	0.738	1.00
81_L	85_S	0.735	1.00
257_G	273_T	0.735	1.00
58_R	109_D	0.734	1.00
242_A	249_I	0.734	1.00
225_A	254_A	0.729	1.00
84_I	95_L	0.728	1.00
61_V	106_G	0.726	1.00
62_V	286_A	0.720	1.00
67_L	77_Y	0.719	1.00
236_L	267_S	0.718	1.00
214_A	217_L	0.718	1.00
138_N	302_S	0.715	1.00
132_L	142_Y	0.713	1.00
170_F	228_V	0.712	1.00
201_F	220_S	0.710	1.00
240_R	243_Q	0.709	1.00
161_M	191_M	0.706	1.00
124_V	127_A	0.704	1.00
21_V	33_K	0.702	1.00
240_R	270_R	0.701	1.00
168_V	225_A	0.701	1.00
85_S	95_L	0.701	1.00
126_K	141_G	0.699	1.00
63_K	111_I	0.695	1.00
126_K	132_L	0.693	1.00
232_D	235_A	0.692	1.00
81_L	97_L	0.692	1.00
86_R	90_R	0.686	1.00
264_D	267_S	0.685	1.00
125_I	132_L	0.685	1.00
159_H	272_T	0.684	1.00
263_L	266_I	0.683	1.00
240_R	244_S	0.681	1.00
159_H	309_L	0.681	1.00
291_K	295_E	0.680	1.00
184_E	202_R	0.679	1.00
34_K	41_K	0.678	1.00
58_R	294_N	0.676	1.00
216_E	219_K	0.675	1.00
259_D	276_Q	0.675	1.00
203_I	234_I	0.673	1.00
270_R	312_R	0.673	1.00
210_S	213_L	0.668	1.00
13_V	32_L	0.667	1.00
112_I	135_F	0.666	1.00
155_M	159_H	0.661	1.00
295_E	298_A	0.660	1.00
240_R	268_S	0.652	1.00
82_T	85_S	0.651	1.00
220_S	224_Q	0.651	1.00
235_A	257_G	0.648	1.00
154_F	186_G	0.644	1.00
110_G	133_V	0.643	1.00
220_S	223_N	0.640	1.00
134_V	142_Y	0.639	1.00
170_F	187_Y	0.639	1.00
35_L	38_S	0.637	1.00
5_S	55_V	0.636	1.00
214_A	237_G	0.636	1.00
27_T	32_L	0.635	1.00
180_E	205_N	0.635	1.00
96_Q	108_C	0.634	1.00
133_V	289_L	0.632	1.00
269_P	272_T	0.629	1.00
18_V	40_M	0.625	1.00
82_T	279_V	0.624	1.00
79_N	278_V	0.624	1.00
187_Y	198_S	0.624	1.00
272_T	309_L	0.623	1.00
168_V	187_Y	0.623	1.00
201_F	217_L	0.622	1.00
7_V	18_V	0.619	1.00
267_S	270_R	0.618	1.00
123_G	126_K	0.616	1.00
291_K	301_G	0.615	1.00
46_I	105_I	0.614	1.00
172_G	202_R	0.613	1.00
93_Y	293_M	0.612	1.00
41_K	44_N	0.611	1.00
239_I	243_Q	0.610	1.00
93_Y	109_D	0.609	1.00
160_V	228_V	0.606	1.00
74_E	233_R	0.605	1.00
18_V	21_V	0.605	1.00
149_N	182_A	0.604	1.00
231_S	259_D	0.602	1.00
154_F	157_T	0.600	1.00
110_G	285_C	0.600	1.00
205_N	230_A	0.600	1.00
20_R	28_V	0.598	1.00
207_S	237_G	0.596	1.00
274_V	307_P	0.595	1.00
258_N	276_Q	0.594	1.00
242_A	245_L	0.594	1.00
173_I	180_E	0.593	1.00
76_Y	80_L	0.589	1.00
268_S	313_E	0.588	1.00
136_G	179_F	0.587	1.00
288_M	292_K	0.585	1.00
111_I	130_K	0.585	1.00
80_L	278_V	0.583	1.00
46_I	50_A	0.582	1.00
279_V	282_G	0.582	1.00
83_G	278_V	0.581	1.00
104_N	130_K	0.581	1.00
203_I	209_K	0.581	1.00
236_L	261_V	0.578	1.00
133_V	292_K	0.578	1.00
62_V	110_G	0.577	1.00
156_A	226_A	0.575	1.00
133_V	145_I	0.574	1.00
62_V	293_M	0.573	1.00
82_T	101_N	0.571	1.00
143_D	300_Q	0.570	1.00
284_A	291_K	0.566	1.00
240_R	265_R	0.565	1.00
136_G	149_N	0.565	1.00
265_R	270_R	0.565	1.00
159_H	256_T	0.565	1.00
88_L	290_L	0.565	1.00
243_Q	248_R	0.562	1.00
104_N	107_Q	0.560	1.00
180_E	230_A	0.560	1.00
228_V	258_N	0.558	1.00
247_K	250_P	0.556	1.00
25_P	28_V	0.556	1.00
238_V	242_A	0.555	1.00
103_L	108_C	0.555	1.00
211_E	237_G	0.553	1.00
133_V	288_M	0.553	1.00
292_K	295_E	0.552	1.00
281_M	305_F	0.551	1.00
13_V	18_V	0.550	1.00
126_K	142_Y	0.550	1.00
18_V	36_V	0.549	1.00
231_S	234_I	0.548	1.00
121_F	124_V	0.547	1.00
62_V	93_Y	0.547	1.00
218_L	242_A	0.546	1.00
229_C	257_G	0.542	1.00
96_Q	106_G	0.541	1.00
145_I	284_A	0.541	1.00
208_K	211_E	0.541	1.00
79_N	262_F	0.536	1.00
146_D	149_N	0.533	1.00
11_A	21_V	0.531	1.00
264_D	271_L	0.531	1.00
217_L	221_M	0.530	1.00
133_V	285_C	0.529	1.00
167_E	224_Q	0.528	1.00
304_F	307_P	0.528	1.00
77_Y	114_T	0.524	1.00
53_A	56_Q	0.523	1.00
75_P	233_R	0.522	1.00
163_L	225_A	0.521	1.00
167_E	221_M	0.520	1.00
244_S	268_S	0.519	1.00
16_M	25_P	0.518	1.00
157_T	228_V	0.517	1.00
224_Q	227_F	0.516	1.00
232_D	261_V	0.516	1.00
84_I	88_L	0.515	1.00
172_G	200_M	0.513	1.00
213_L	217_L	0.511	1.00
6_D	10_K	0.509	1.00
147_V	258_N	0.509	1.00
24_H	27_T	0.508	1.00
211_E	214_A	0.507	1.00
61_V	109_D	0.507	1.00
188_I	200_M	0.506	1.00
28_V	33_K	0.506	1.00
149_N	179_F	0.506	1.00
73_T	79_N	0.505	1.00
52_R	56_Q	0.504	1.00
209_K	234_I	0.503	1.00
230_A	234_I	0.502	1.00
71_D	82_T	0.501	1.00
87_E	290_L	0.501	1.00
196_K	199_N	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
3dbiA	2	0.8101	100	0.102	Contact Map
2hsgA	1	0.981	100	0.104	Contact Map
4o5aA	2	0.7975	100	0.106	Contact Map
1qpzA	2	0.9873	100	0.109	Contact Map
3jvdA	2	0.7848	100	0.111	Contact Map
2o20A	2	0.8165	100	0.111	Contact Map
3ctpA	2	0.7911	100	0.112	Contact Map
3bilA	2	0.7563	100	0.113	Contact Map
1jyeA	2	0.8006	100	0.119	Contact Map
3e3mA	2	0.788	100	0.121	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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