YVOA - BACSU - GREMLIN Contacts

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YVOA - HTH-type transcriptional repressor YvoA

UniProt:	O34817	Sequences: MNINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRGTFVSKPKMEQALQGLTSFTEDMKSRGMTPGSRLIDYQLIDSTEELAAILGCGHPSSIHKITRVRLANDIPMAIESSHIPFELAGELNESHFQSSIYDHIERYNSIPISRAKQELEPSAATTEEANILGIQKGAPVLLIKRTTYLQNGTAFEHAKSVYRGDRYTFVHYMDRLS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	243 (196)
Sequences:	25518 (19306)
Seq/√Len:	1379.0

ECOLI - YIDP PHNF YIHL MNGR FRLR YEGW NANR PDHR YIEP FADR EXUR GLCC LLDR DGOR YJJM UXUR YDFH MCBR CSIR
BACSU - YVOA YURK YYDK TRER YMFC YBGA GMUR YCBG YDHC LUTR YHCF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_Q	27_E	3.810	1.00
29_Q	32_M	3.654	1.00
16_M	57_N	3.154	1.00
22_Q	43_Q	3.020	1.00
20_K	61_E	3.012	1.00
65_Y	75_S	2.823	1.00
106_D	191_T	2.589	1.00
37_E	48_R	2.557	1.00
18_Q	22_Q	2.531	1.00
15_I	46_I	2.525	1.00
186_E	189_A	2.476	1.00
66_R	72_T	2.347	1.00
67_L	70_R	2.230	1.00
16_M	61_E	2.192	1.00
99_T	103_R	2.146	1.00
33_P	73_F	2.117	1.00
113_T	116_L	2.105	1.00
15_I	44_F	2.103	1.00
21_T	25_N	2.099	1.00
9_I	17_E	1.896	1.00
110_I	187_P	1.890	1.00
18_Q	44_F	1.837	1.00
16_M	20_K	1.831	1.00
59_V	66_R	1.790	1.00
53_Q	56_S	1.753	1.00
116_L	138_N	1.734	1.00
70_R	73_F	1.703	1.00
20_K	24_K	1.689	1.00
135_R	143_A	1.687	1.00
11_I	14_Q	1.656	1.00
38_R	42_E	1.649	1.00
117_A	183_Q	1.619	1.00
14_Q	18_Q	1.618	1.00
191_T	195_A	1.604	1.00
36_S	39_E	1.587	1.00
22_Q	28_L	1.571	1.00
39_E	43_Q	1.562	1.00
191_T	194_E	1.552	1.00
59_V	64_L	1.519	1.00
20_K	63_L	1.507	1.00
92_D	140_I	1.503	1.00
18_Q	21_T	1.492	1.00
112_S	117_A	1.430	1.00
98_M	199_G	1.420	1.00
12_Y	57_N	1.418	1.00
23_I	74_V	1.408	1.00
101_G	136_L	1.399	1.00
37_E	52_R	1.390	1.00
40_Y	51_V	1.390	1.00
67_L	73_F	1.386	1.00
112_S	116_L	1.385	1.00
28_L	74_V	1.378	1.00
57_N	60_N	1.367	1.00
30_P	76_K	1.357	1.00
56_S	66_R	1.347	1.00
55_L	64_L	1.342	1.00
65_Y	73_F	1.333	1.00
131_I	147_S	1.314	1.00
181_A	189_A	1.313	1.00
95_S	107_Y	1.297	1.00
106_D	187_P	1.294	1.00
10_P	13_Y	1.293	1.00
64_L	72_T	1.271	1.00
46_I	51_V	1.256	1.00
39_E	42_E	1.245	1.00
9_I	14_Q	1.238	1.00
102_S	195_A	1.238	1.00
189_A	193_E	1.237	1.00
67_L	71_G	1.235	1.00
56_S	60_N	1.228	1.00
187_P	191_T	1.226	1.00
144_I	148_H	1.222	1.00
132_T	135_R	1.221	1.00
125_P	128_I	1.215	1.00
24_K	63_L	1.206	1.00
103_R	136_L	1.197	1.00
189_A	205_P	1.194	1.00
119_I	132_T	1.188	1.00
123_G	126_S	1.179	1.00
33_P	71_G	1.178	1.00
179_S	183_Q	1.164	1.00
57_N	61_E	1.156	1.00
102_S	191_T	1.150	1.00
130_K	146_S	1.150	1.00
22_Q	26_G	1.150	1.00
116_L	148_H	1.149	1.00
56_S	59_V	1.143	1.00
131_I	135_R	1.141	1.00
98_M	195_A	1.133	1.00
192_T	196_N	1.128	1.00
55_L	72_T	1.127	1.00
96_R	145_E	1.120	1.00
98_M	102_S	1.111	1.00
112_S	185_L	1.099	1.00
122_C	126_S	1.084	1.00
168_D	172_R	1.064	1.00
13_Y	17_E	1.048	1.00
13_Y	57_N	1.032	1.00
167_Y	171_E	1.025	1.00
176_I	180_R	1.015	1.00
143_A	147_S	1.013	1.00
195_A	199_G	1.006	1.00
144_I	194_E	0.997	1.00
132_T	136_L	0.995	1.00
22_Q	44_F	0.993	1.00
28_L	32_M	0.987	1.00
166_I	170_I	0.982	1.00
132_T	146_S	0.979	1.00
109_L	127_S	0.974	1.00
110_I	130_K	0.971	1.00
47_S	50_T	0.964	1.00
174_N	200_I	0.961	1.00
12_Y	16_M	0.956	1.00
134_V	146_S	0.942	1.00
53_Q	57_N	0.936	1.00
109_L	151_F	0.931	1.00
180_R	184_E	0.923	1.00
11_I	50_T	0.919	1.00
9_I	13_Y	0.908	1.00
117_A	185_L	0.899	1.00
103_R	106_D	0.898	1.00
108_Q	130_K	0.895	1.00
114_E	118_A	0.893	1.00
69_G	72_T	0.891	1.00
169_H	174_N	0.891	1.00
117_A	179_S	0.889	1.00
31_D	65_Y	0.887	1.00
201_Q	204_A	0.887	1.00
141_P	152_E	0.885	1.00
31_D	76_K	0.884	1.00
165_S	168_D	0.876	1.00
19_L	40_Y	0.871	1.00
12_Y	53_Q	0.869	1.00
106_D	188_S	0.868	1.00
177_P	193_E	0.865	1.00
86_L	89_F	0.864	1.00
17_E	20_K	0.845	1.00
105_I	109_L	0.841	1.00
112_S	136_L	0.839	1.00
116_L	119_I	0.824	1.00
115_E	119_I	0.821	1.00
37_E	66_R	0.813	1.00
106_D	130_K	0.813	1.00
124_H	128_I	0.809	1.00
189_A	192_T	0.808	1.00
103_R	107_Y	0.802	1.00
105_I	194_E	0.801	1.00
150_P	153_L	0.798	1.00
188_S	191_T	0.797	1.00
120_L	132_T	0.791	1.00
133_R	182_K	0.791	1.00
40_Y	55_L	0.791	1.00
166_I	169_H	0.786	1.00
41_A	51_V	0.783	1.00
152_E	155_G	0.783	1.00
104_L	134_V	0.779	1.00
190_A	200_I	0.774	1.00
33_P	36_S	0.773	1.00
121_G	124_H	0.761	1.00
30_P	75_S	0.760	1.00
17_E	21_T	0.754	1.00
188_S	194_E	0.748	1.00
102_S	106_D	0.747	1.00
116_L	136_L	0.744	1.00
18_Q	43_Q	0.744	1.00
34_L	64_L	0.741	1.00
35_P	43_Q	0.740	1.00
121_G	125_P	0.740	1.00
22_Q	25_N	0.737	1.00
145_E	148_H	0.735	1.00
180_R	183_Q	0.733	1.00
130_K	175_S	0.731	1.00
101_G	139_D	0.730	1.00
119_I	135_R	0.726	1.00
177_P	180_R	0.724	1.00
114_E	117_A	0.720	1.00
111_D	127_S	0.719	1.00
171_E	177_P	0.709	1.00
146_S	150_P	0.708	1.00
137_A	143_A	0.704	1.00
154_A	158_N	0.698	1.00
158_N	161_H	0.698	1.00
129_H	133_R	0.695	1.00
132_T	193_E	0.694	1.00
44_F	51_V	0.693	1.00
141_P	144_I	0.692	1.00
55_L	59_V	0.692	1.00
97_G	101_G	0.691	1.00
200_I	204_A	0.691	1.00
188_S	192_T	0.689	1.00
126_S	152_E	0.681	1.00
127_S	151_F	0.681	1.00
109_L	182_K	0.680	1.00
106_D	110_I	0.679	1.00
38_R	41_A	0.676	1.00
154_A	157_L	0.676	1.00
105_I	190_A	0.675	1.00
41_A	44_F	0.673	1.00
190_A	195_A	0.670	1.00
193_E	196_N	0.666	1.00
192_T	195_A	0.666	1.00
184_E	189_A	0.665	1.00
28_L	34_L	0.663	1.00
124_H	127_S	0.663	1.00
176_I	179_S	0.661	1.00
91_E	94_K	0.660	1.00
16_M	54_A	0.655	1.00
105_I	134_V	0.652	1.00
103_R	191_T	0.651	1.00
102_S	105_I	0.651	1.00
114_E	185_L	0.649	1.00
98_M	202_K	0.648	1.00
59_V	72_T	0.646	1.00
27_E	43_Q	0.643	1.00
19_L	28_L	0.641	1.00
50_T	54_A	0.639	1.00
181_A	186_E	0.634	1.00
151_F	155_G	0.632	1.00
15_I	51_V	0.630	1.00
194_E	197_I	0.628	1.00
128_I	132_T	0.628	1.00
91_E	95_S	0.624	1.00
136_L	139_D	0.624	1.00
131_I	150_P	0.618	1.00
51_V	64_L	0.618	1.00
55_L	66_R	0.613	1.00
129_H	179_S	0.612	1.00
196_N	200_I	0.612	1.00
178_I	194_E	0.604	1.00
8_P	14_Q	0.604	1.00
112_S	182_K	0.601	1.00
37_E	72_T	0.600	1.00
15_I	18_Q	0.598	1.00
21_T	24_K	0.597	1.00
94_K	201_Q	0.594	1.00
165_S	170_I	0.593	1.00
93_M	137_A	0.591	1.00
169_H	172_R	0.591	1.00
137_A	142_M	0.586	1.00
165_S	169_H	0.585	1.00
115_E	118_A	0.584	1.00
42_E	45_G	0.574	1.00
78_K	81_Q	0.573	1.00
41_A	48_R	0.572	1.00
88_S	92_D	0.571	1.00
15_I	19_L	0.569	1.00
109_L	187_P	0.566	1.00
50_T	53_Q	0.563	1.00
36_S	69_G	0.562	1.00
178_I	193_E	0.562	1.00
150_P	154_A	0.561	1.00
116_L	135_R	0.561	1.00
38_R	48_R	0.560	1.00
95_S	111_D	0.559	1.00
109_L	185_L	0.558	1.00
193_E	197_I	0.558	1.00
92_D	96_R	0.548	1.00
131_I	143_A	0.547	1.00
84_Q	92_D	0.542	1.00
94_K	100_P	0.542	1.00
40_Y	44_F	0.540	1.00
109_L	129_H	0.539	1.00
15_I	54_A	0.537	1.00
155_G	158_N	0.536	1.00
14_Q	17_E	0.535	1.00
134_V	150_P	0.533	1.00
28_L	35_P	0.532	1.00
190_A	204_A	0.531	1.00
107_Y	110_I	0.531	1.00
130_K	148_H	0.531	1.00
107_Y	111_D	0.529	1.00
83_L	202_K	0.529	1.00
94_K	97_G	0.525	1.00
13_Y	16_M	0.524	1.00
157_L	161_H	0.523	1.00
147_S	150_P	0.523	1.00
21_T	27_E	0.521	1.00
157_L	160_S	0.520	1.00
117_A	182_K	0.519	1.00
141_P	145_E	0.518	1.00
123_G	127_S	0.517	1.00
127_S	154_A	0.516	1.00
58_L	64_L	0.515	1.00
68_K	71_G	0.513	1.00
177_P	189_A	0.512	1.00
80_E	83_L	0.509	1.00
174_N	197_I	0.505	1.00
78_K	82_A	0.505	1.00
153_L	156_E	0.504	1.00
190_A	198_L	0.503	1.00
96_R	100_P	0.503	1.00
129_H	151_F	0.501	1.00
73_F	76_K	0.501	1.00
8_P	13_Y	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
4u0wA	2	0.9959	100	0.127	Contact Map
2ra5A	2	0.6091	100	0.175	Contact Map
3f8mA	2	0.9424	100	0.186	Contact Map
3edpA	2	0.9053	100	0.206	Contact Map
3eetA	2	0.9465	100	0.213	Contact Map
3bwgA	2	0.9383	100	0.222	Contact Map
3sxyA	2	0.7654	100	0.417	Contact Map
1hw1A	2	0.8354	100	0.428	Contact Map
3c7jA	4	0.8477	100	0.431	Contact Map
4p96A	2	0.8848	100	0.432	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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