YVBU - BACSU - GREMLIN Contacts

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YVBU - Uncharacterized HTH-type transcriptional regulator YvbU

UniProt:	O32255	Sequences: MTITQLKVFVKIAETGSFTKAGQALNMTQPAVSHAISAIEAELDVKLIIRDRRNGLMLTDTGKQILVHIREVLKGIEKVEQVAAAEKGLELGTIHIGTFSTASAYFMPKLISEFKQKYPKLELVLHEGTVNEVKEWLHTRMIDVGILLYPTEEMEYIHLKKDKMAVVLRDDHPLASHSAITLKDLDHEPMIVCDGGYESPFIDMFRQAGATLHPAFTVYNINTSISMIREGLGLAILSEMSMSGMPLPEHVVTRELDPQVYRDVQLAVPSLKEASLAAKLFIEMAKELFGAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	292 (279)
Sequences:	79596 (58165)
Seq/√Len:	3482.2

ECOLI - OXYR LEUO LYSR CYSB CYNR AAER YFER YDHB TTDR YBHD DMLR NAC YAFC YAHB ALLS CBL YEEY YCAN PGRR ABGR ILVY METR NHAR DSDC YDCI YHJC YHAJ TDCA YEIE XAPR YFIE YBDO YNFL YBEF YNEJ HCAR GCVA ICIA YIDZ YIAU LRHA YGFI PERR YJIE HDFR
BACSU - YVBU CYSL YWBI YCGK GLTC YWQM YYBE ALSR GLTR CITR YOAU BSDA YTLI YUST YKUM YOFA YXJO CZCR YRAN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
71_E	75_G	3.573	1.00
15_T	24_A	3.396	1.00
157_I	286_K	2.673	1.00
97_G	142_I	2.569	1.00
68_H	82_V	2.414	1.00
228_I	235_A	2.287	1.00
11_K	24_A	2.229	1.00
161_K	263_D	2.205	1.00
163_K	239_E	2.194	1.00
172_H	188_E	2.192	1.00
93_T	124_V	2.173	1.00
158_H	161_K	2.166	1.00
93_T	122_E	2.096	1.00
20_K	23_Q	2.094	1.00
14_E	70_R	2.086	1.00
158_H	263_D	2.076	1.00
181_T	184_D	2.040	1.00
45_V	61_T	2.034	1.00
8_V	35_A	2.030	1.00
161_K	261_Y	2.015	1.00
225_I	245_M	1.979	1.00
113_E	284_M	1.979	1.00
10_V	66_L	1.972	1.00
95_H	124_V	1.970	1.00
68_H	75_G	1.962	1.00
229_R	250_H	1.958	1.00
10_V	70_R	1.935	1.00
11_K	14_E	1.894	1.00
10_V	14_E	1.887	1.00
191_I	233_G	1.885	1.00
72_V	76_I	1.878	1.00
8_V	32_V	1.877	1.00
11_K	15_T	1.864	1.00
13_A	58_L	1.857	1.00
165_A	239_E	1.839	1.00
168_L	254_R	1.833	1.00
229_R	245_M	1.833	1.00
66_L	70_R	1.808	1.00
18_F	36_I	1.795	1.00
49_I	57_M	1.725	1.00
65_I	79_V	1.704	1.00
165_A	253_T	1.680	1.00
189_P	215_A	1.676	1.00
64_Q	82_V	1.665	1.00
156_Y	265_Q	1.660	1.00
136_W	141_M	1.621	1.00
114_F	281_F	1.617	1.00
14_E	24_A	1.594	1.00
13_A	66_L	1.586	1.00
9_F	66_L	1.578	1.00
177_H	184_D	1.559	1.00
10_V	69_I	1.557	1.00
15_T	20_K	1.556	1.00
8_V	27_M	1.539	1.00
155_E	270_S	1.517	1.00
114_F	121_L	1.505	1.00
5_Q	35_A	1.500	1.00
19_T	29_Q	1.499	1.00
135_E	139_T	1.481	1.00
60_D	63_K	1.478	1.00
198_E	202_I	1.473	1.00
28_T	31_A	1.467	1.00
5_Q	42_E	1.464	1.00
89_L	120_K	1.464	1.00
157_I	268_V	1.453	1.00
17_S	20_K	1.449	1.00
5_Q	38_A	1.439	1.00
46_K	49_I	1.420	1.00
68_H	71_E	1.418	1.00
11_K	25_L	1.409	1.00
274_A	278_A	1.407	1.00
10_V	73_L	1.402	1.00
282_I	286_K	1.388	1.00
72_V	79_V	1.376	1.00
155_E	268_V	1.375	1.00
147_L	267_A	1.374	1.00
149_Y	265_Q	1.369	1.00
68_H	78_K	1.366	1.00
91_L	120_K	1.337	1.00
170_D	250_H	1.337	1.00
268_V	282_I	1.331	1.00
104_A	222_N	1.330	1.00
266_L	282_I	1.315	1.00
95_H	126_H	1.313	1.00
137_L	145_G	1.310	1.00
113_E	117_K	1.308	1.00
280_L	283_E	1.306	1.00
144_V	278_A	1.302	1.00
3_I	76_I	1.293	1.00
162_D	240_M	1.293	1.00
136_W	142_I	1.279	1.00
65_I	80_E	1.279	1.00
42_E	80_E	1.277	1.00
144_V	266_L	1.267	1.00
168_L	234_L	1.267	1.00
51_D	57_M	1.265	1.00
115_K	215_A	1.256	1.00
224_S	235_A	1.253	1.00
75_G	78_K	1.246	1.00
245_M	250_H	1.245	1.00
205_F	210_A	1.237	1.00
138_H	153_E	1.236	1.00
188_E	234_L	1.221	1.00
117_K	284_M	1.221	1.00
243_S	247_L	1.218	1.00
67_V	71_E	1.211	1.00
239_E	243_S	1.211	1.00
226_S	229_R	1.208	1.00
68_H	79_V	1.194	1.00
170_D	252_V	1.192	1.00
37_S	41_A	1.190	1.00
63_K	67_V	1.186	1.00
64_Q	67_V	1.186	1.00
9_F	48_I	1.182	1.00
112_S	116_Q	1.174	1.00
115_K	189_P	1.173	1.00
239_E	253_T	1.160	1.00
173_P	188_E	1.151	1.00
158_H	265_Q	1.145	1.00
156_Y	267_A	1.145	1.00
27_M	31_A	1.143	1.00
178_S	252_V	1.130	1.00
113_E	116_Q	1.128	1.00
199_S	203_D	1.128	1.00
9_F	13_A	1.125	1.00
9_F	47_L	1.117	1.00
128_G	136_W	1.111	1.00
34_H	38_A	1.111	1.00
34_H	37_S	1.110	1.00
191_I	224_S	1.109	1.00
94_I	281_F	1.106	1.00
124_V	217_T	1.104	1.00
112_S	230_E	1.101	1.00
33_S	37_S	1.096	1.00
167_V	253_T	1.089	1.00
114_F	284_M	1.083	1.00
283_E	286_K	1.083	1.00
179_A	257_D	1.082	1.00
118_Y	280_L	1.081	1.00
189_P	213_H	1.076	1.00
71_E	78_K	1.070	1.00
7_K	77_E	1.070	1.00
12_I	21_A	1.069	1.00
218_V	224_S	1.068	1.00
6_L	69_I	1.067	1.00
103_S	127_E	1.061	1.00
11_K	21_A	1.054	1.00
279_K	283_E	1.052	1.00
72_V	75_G	1.044	1.00
225_I	229_R	1.040	1.00
110_L	285_A	1.040	1.00
58_L	62_G	1.036	1.00
64_Q	68_H	1.035	1.00
18_F	56_L	1.026	1.00
169_R	231_G	1.019	1.00
109_K	230_E	1.019	1.00
226_S	230_E	1.018	1.00
253_T	256_L	1.015	1.00
4_T	7_K	1.014	1.00
167_V	242_M	1.013	1.00
35_A	38_A	1.011	1.00
180_I	184_D	1.009	1.00
157_I	282_I	1.005	1.00
80_E	84_A	0.997	1.00
163_K	261_Y	0.989	1.00
166_V	234_L	0.981	1.00
8_V	25_L	0.969	1.00
27_M	32_V	0.965	1.00
77_E	81_Q	0.962	1.00
13_A	48_I	0.954	1.00
65_I	69_I	0.954	1.00
77_E	80_E	0.954	1.00
12_I	18_F	0.953	1.00
114_F	118_Y	0.953	1.00
244_G	248_P	0.952	1.00
9_F	58_L	0.950	1.00
153_E	270_S	0.946	1.00
74_K	78_K	0.939	1.00
136_W	139_T	0.936	1.00
218_V	227_M	0.935	1.00
192_V	214_P	0.931	1.00
117_K	287_E	0.930	1.00
21_A	32_V	0.925	1.00
110_L	284_M	0.923	1.00
168_L	172_H	0.915	1.00
275_S	278_A	0.915	1.00
199_S	202_I	0.914	1.00
48_I	56_L	0.905	1.00
172_H	175_A	0.905	1.00
284_M	287_E	0.903	1.00
38_A	41_A	0.902	1.00
9_F	39_I	0.900	1.00
45_V	83_A	0.897	1.00
126_H	136_W	0.896	1.00
172_H	189_P	0.893	1.00
97_G	145_G	0.892	1.00
13_A	62_G	0.883	1.00
64_Q	86_E	0.879	1.00
20_K	24_A	0.875	1.00
142_I	145_G	0.871	1.00
67_V	70_R	0.870	1.00
122_E	213_H	0.869	1.00
176_S	189_P	0.860	1.00
97_G	147_L	0.857	1.00
154_M	267_A	0.855	1.00
19_T	23_Q	0.854	1.00
100_S	220_N	0.852	1.00
149_Y	263_D	0.851	1.00
155_E	158_H	0.843	1.00
242_M	245_M	0.842	1.00
269_P	272_K	0.842	1.00
173_P	178_S	0.840	1.00
190_M	212_L	0.839	1.00
121_L	277_A	0.839	1.00
168_L	173_P	0.838	1.00
204_M	208_A	0.836	1.00
96_I	144_V	0.835	1.00
184_D	187_H	0.834	1.00
167_V	235_A	0.831	1.00
71_E	74_K	0.827	1.00
25_L	32_V	0.827	1.00
134_K	138_H	0.827	1.00
283_E	287_E	0.826	1.00
245_M	248_P	0.818	1.00
61_T	86_E	0.814	1.00
198_E	204_M	0.813	1.00
126_H	142_I	0.812	1.00
92_G	277_A	0.808	1.00
189_P	214_P	0.805	1.00
172_H	176_S	0.805	1.00
9_F	65_I	0.800	1.00
274_A	279_K	0.796	1.00
61_T	83_A	0.794	1.00
163_K	255_E	0.793	1.00
16_G	57_M	0.790	1.00
12_I	36_I	0.787	1.00
37_S	46_K	0.786	1.00
29_Q	33_S	0.785	1.00
16_G	63_K	0.785	1.00
183_K	186_D	0.781	1.00
112_S	232_L	0.778	1.00
169_R	232_L	0.778	1.00
13_A	16_G	0.777	1.00
92_G	121_L	0.775	1.00
12_I	48_I	0.771	1.00
3_I	73_L	0.768	1.00
75_G	79_V	0.765	1.00
4_T	35_A	0.763	1.00
174_L	188_E	0.762	1.00
76_I	79_V	0.762	1.00
171_D	175_A	0.760	1.00
14_E	66_L	0.758	1.00
78_K	82_V	0.753	1.00
138_H	154_M	0.749	1.00
15_T	21_A	0.749	1.00
61_T	64_Q	0.746	1.00
181_T	257_D	0.744	1.00
144_V	281_F	0.742	1.00
115_K	232_L	0.741	1.00
163_K	259_Q	0.741	1.00
76_I	80_E	0.741	1.00
276_L	280_L	0.741	1.00
5_Q	8_V	0.732	1.00
227_M	232_L	0.730	1.00
167_V	237_L	0.727	1.00
204_M	207_Q	0.727	1.00
203_D	207_Q	0.724	1.00
90_E	118_Y	0.720	1.00
117_K	280_L	0.719	1.00
79_V	83_A	0.715	1.00
69_I	72_V	0.714	1.00
7_K	11_K	0.713	1.00
49_I	59_T	0.712	1.00
95_H	142_I	0.709	1.00
57_M	63_K	0.705	1.00
238_S	241_S	0.704	1.00
18_F	32_V	0.703	1.00
201_F	205_F	0.703	1.00
31_A	35_A	0.702	1.00
169_R	172_H	0.701	1.00
114_F	280_L	0.700	1.00
58_L	63_K	0.699	1.00
12_I	32_V	0.699	1.00
168_L	252_V	0.697	1.00
84_A	87_K	0.696	1.00
203_D	206_R	0.696	1.00
98_T	103_S	0.688	1.00
220_N	223_T	0.684	1.00
201_F	204_M	0.681	1.00
40_E	45_V	0.681	1.00
198_E	217_T	0.681	1.00
146_I	285_A	0.680	1.00
175_A	252_V	0.679	1.00
61_T	65_I	0.678	1.00
143_D	278_A	0.676	1.00
113_E	287_E	0.675	1.00
70_R	74_K	0.669	1.00
95_H	143_D	0.665	1.00
193_C	224_S	0.661	1.00
194_D	217_T	0.660	1.00
199_S	204_M	0.659	1.00
202_I	206_R	0.658	1.00
187_H	213_H	0.657	1.00
200_P	203_D	0.656	1.00
171_D	174_L	0.654	1.00
63_K	66_L	0.653	1.00
98_T	107_M	0.651	1.00
280_L	284_M	0.651	1.00
168_L	174_L	0.650	1.00
74_K	77_E	0.649	1.00
60_D	64_Q	0.648	1.00
170_D	249_E	0.645	1.00
216_F	227_M	0.643	1.00
140_R	269_P	0.643	1.00
40_E	50_R	0.639	1.00
94_I	277_A	0.638	1.00
78_K	81_Q	0.637	1.00
200_P	204_M	0.636	1.00
244_G	247_L	0.634	1.00
65_I	83_A	0.634	1.00
69_I	73_L	0.634	1.00
186_D	210_A	0.632	1.00
179_A	255_E	0.631	1.00
36_I	40_E	0.630	1.00
23_Q	26_N	0.630	1.00
122_E	217_T	0.629	1.00
171_D	252_V	0.622	1.00
7_K	10_V	0.622	1.00
171_D	231_G	0.621	1.00
12_I	17_S	0.621	1.00
104_A	226_S	0.617	1.00
127_E	219_Y	0.616	1.00
100_S	129_T	0.615	1.00
137_L	267_A	0.614	1.00
21_A	25_L	0.614	1.00
174_L	177_H	0.609	1.00
4_T	38_A	0.609	1.00
190_M	234_L	0.608	1.00
183_K	208_A	0.608	1.00
199_S	205_F	0.607	1.00
68_H	72_V	0.606	1.00
276_L	279_K	0.597	1.00
64_Q	83_A	0.597	1.00
166_V	185_L	0.597	1.00
194_D	219_Y	0.593	1.00
272_K	275_S	0.592	1.00
166_V	236_I	0.591	1.00
107_M	110_L	0.590	1.00
30_P	34_H	0.585	1.00
144_V	282_I	0.585	1.00
127_E	220_N	0.585	1.00
160_K	264_V	0.584	1.00
81_Q	85_A	0.582	1.00
227_M	233_G	0.580	1.00
137_L	154_M	0.578	1.00
281_F	285_A	0.577	1.00
94_I	144_V	0.574	1.00
224_S	228_I	0.571	1.00
174_L	180_I	0.571	1.00
148_L	262_R	0.570	1.00
91_L	122_E	0.570	1.00
166_V	190_M	0.570	1.00
4_T	8_V	0.569	1.00
28_T	34_H	0.568	1.00
58_L	66_L	0.568	1.00
202_I	205_F	0.567	1.00
31_A	34_H	0.567	1.00
155_E	271_L	0.567	1.00
97_G	128_G	0.563	1.00
111_I	123_L	0.562	1.00
177_H	180_I	0.561	1.00
48_I	58_L	0.561	1.00
109_K	112_S	0.556	1.00
43_L	65_I	0.555	1.00
7_K	73_L	0.553	1.00
164_M	236_I	0.551	1.00
162_D	262_R	0.551	1.00
43_L	83_A	0.548	1.00
268_V	279_K	0.547	1.00
205_F	212_L	0.543	1.00
218_V	223_T	0.539	1.00
97_G	126_H	0.539	1.00
173_P	177_H	0.538	1.00
109_K	113_E	0.538	1.00
45_V	49_I	0.538	1.00
92_G	120_K	0.535	1.00
43_L	46_K	0.530	1.00
73_L	77_E	0.529	1.00
102_A	106_F	0.529	1.00
237_L	242_M	0.529	1.00
85_A	90_E	0.526	1.00
195_G	217_T	0.524	1.00
8_V	36_I	0.523	1.00
179_A	184_D	0.522	1.00
73_L	76_I	0.521	1.00
186_D	211_T	0.520	1.00
221_I	238_S	0.520	1.00
36_I	48_I	0.520	1.00
9_F	62_G	0.519	1.00
118_Y	121_L	0.518	1.00
67_V	82_V	0.518	1.00
198_E	203_D	0.517	1.00
104_A	220_N	0.516	1.00
68_H	83_A	0.514	1.00
172_H	234_L	0.514	1.00
149_Y	156_Y	0.513	1.00
173_P	176_S	0.512	1.00
146_I	266_L	0.511	1.00
116_Q	175_A	0.510	1.00
198_E	205_F	0.508	1.00
46_K	61_T	0.507	1.00
18_F	29_Q	0.507	1.00
168_L	175_A	0.506	1.00
18_F	50_R	0.503	1.00
92_G	118_Y	0.502	1.00
16_G	56_L	0.501	1.00
135_E	141_M	0.500	1.00
159_L	266_L	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
2esnA	3	0.9863	100	0.087	Contact Map
1uthA	2	0.75	100	0.091	Contact Map
1al3A	1	0.7021	100	0.092	Contact Map
3fxqA	3	0.9829	100	0.092	Contact Map
1ixcA	4	0.9829	100	0.094	Contact Map
3fzvA	4	0.9692	100	0.096	Contact Map
2h98A	2	0.6815	100	0.1	Contact Map
2h9bA	2	0.6815	100	0.103	Contact Map
4x6gA	4	0.9966	100	0.106	Contact Map
3szpA	3	0.9795	100	0.107	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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