YMFC - BACSU - GREMLIN Contacts

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YMFC - Uncharacterized HTH-type transcriptional regulator YmfC

UniProt:	O31761	Sequences: MSTKADNRHLYLKVIERIKEDIKNGIYTEKEKLPSEFELSKKLGVSRATLREALRILEEEHVIIRRHGVGTFVHSKPLFLSGIEQLNSVTKMIEQANMTPGTIFLSSQVLMPSEDDTKRFHLAEGQELFYLERVRTADGQPIVYCIDKIPMNILPNSFSHQQESMFDLLEKNSGSVISYAVTDIEPIGYHDTISPVLECDPETALLLLKQTHYDQHDKPVLYSLNYFRADKFRFHVLRKRF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	241 (194)
Sequences:	27694 (21434)
Seq/√Len:	1538.8

ECOLI - YEGW YIDP FRLR PHNF YIHL MNGR NANR PDHR UXUR FADR YIEP EXUR LLDR DGOR YJJM GLCC MCBR YDFH CSIR
BACSU - YMFC YURK YVOA YYDK TRER YBGA GMUR YCBG LUTR YDHC GNTR
SULSO - Q97YR4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_D	26_I	3.743	1.00
28_T	31_E	3.603	1.00
15_I	56_I	3.289	1.00
19_K	60_E	3.049	1.00
21_D	42_K	2.984	1.00
64_I	74_H	2.895	1.00
36_E	47_R	2.626	1.00
17_R	21_D	2.620	1.00
14_V	45_V	2.593	1.00
185_E	188_G	2.473	1.00
121_H	182_T	2.458	1.00
65_R	71_T	2.361	1.00
66_R	69_V	2.322	1.00
15_I	60_E	2.270	1.00
106_S	190_H	2.253	1.00
32_K	72_F	2.176	1.00
14_V	43_L	2.153	1.00
20_E	24_N	2.081	1.00
113_S	116_D	1.991	1.00
17_R	43_L	1.916	1.00
58_E	65_R	1.900	1.00
15_I	19_K	1.867	1.00
8_R	16_E	1.866	1.00
52_E	55_R	1.862	1.00
99_T	103_I	1.824	1.00
135_R	143_V	1.814	1.00
37_F	41_K	1.737	1.00
69_V	72_F	1.703	1.00
21_D	27_Y	1.702	1.00
110_L	186_P	1.691	1.00
13_K	17_R	1.668	1.00
19_K	23_K	1.662	1.00
10_L	13_K	1.661	1.00
35_S	38_E	1.654	1.00
116_D	138_D	1.647	1.00
38_E	42_K	1.596	1.00
58_E	63_I	1.585	1.00
190_H	194_S	1.575	1.00
66_R	72_F	1.506	1.00
190_H	193_I	1.504	1.00
19_K	62_V	1.502	1.00
17_R	20_E	1.497	1.00
132_E	135_R	1.495	1.00
92_M	140_Q	1.492	1.00
64_I	72_F	1.456	1.00
56_I	59_E	1.433	1.00
39_L	50_L	1.402	1.00
27_Y	73_V	1.399	1.00
180_A	188_G	1.396	1.00
11_Y	56_I	1.390	1.00
130_Y	146_I	1.364	1.00
112_P	116_D	1.359	1.00
131_L	147_D	1.349	1.00
22_I	73_V	1.346	1.00
36_E	51_R	1.345	1.00
117_T	182_T	1.339	1.00
144_Y	148_K	1.334	1.00
55_R	65_R	1.330	1.00
29_E	75_S	1.317	1.00
188_G	192_T	1.312	1.00
54_L	63_I	1.291	1.00
55_R	59_E	1.289	1.00
38_E	41_K	1.289	1.00
63_I	71_T	1.276	1.00
101_G	136_T	1.255	1.00
186_P	190_H	1.234	1.00
56_I	60_E	1.228	1.00
166_F	170_E	1.223	1.00
8_R	13_K	1.217	1.00
131_L	135_R	1.211	1.00
12_L	16_E	1.207	1.00
141_P	152_N	1.193	1.00
119_R	132_E	1.193	1.00
112_P	117_T	1.193	1.00
103_I	136_T	1.184	1.00
55_R	58_E	1.174	1.00
23_K	62_V	1.162	1.00
125_G	128_L	1.159	1.00
188_G	204_A	1.159	1.00
66_R	70_G	1.153	1.00
12_L	56_I	1.153	1.00
45_V	50_L	1.148	1.00
175_S	179_Y	1.147	1.00
9_H	12_L	1.144	1.00
32_K	70_G	1.139	1.00
54_L	71_T	1.130	1.00
97_N	101_G	1.118	1.00
191_D	195_P	1.109	1.00
98_M	198_E	1.081	1.00
21_D	25_G	1.078	1.00
178_S	182_T	1.076	1.00
21_D	43_L	1.059	1.00
116_D	148_K	1.058	1.00
143_V	147_D	1.040	1.00
106_S	186_P	1.029	1.00
8_R	12_L	1.028	1.00
179_Y	183_D	1.025	1.00
110_L	130_Y	1.022	1.00
46_S	49_T	1.016	1.00
132_E	136_T	1.010	1.00
96_A	145_C	1.004	1.00
132_E	146_I	0.999	1.00
194_S	198_E	0.989	1.00
133_R	181_V	0.982	1.00
117_T	121_H	0.982	1.00
112_P	184_I	0.977	1.00
27_Y	31_E	0.973	1.00
167_D	171_K	0.967	1.00
95_Q	107_S	0.961	1.00
134_V	146_I	0.954	1.00
164_S	167_D	0.949	1.00
30_K	75_S	0.946	1.00
11_Y	52_E	0.937	1.00
102_T	194_S	0.932	1.00
144_Y	193_I	0.931	1.00
98_M	102_T	0.930	1.00
121_H	178_S	0.925	1.00
102_T	190_H	0.913	1.00
103_I	106_S	0.908	1.00
123_A	126_Q	0.903	1.00
165_M	169_L	0.900	1.00
128_L	132_E	0.896	1.00
188_G	191_D	0.888	1.00
98_M	194_S	0.881	1.00
108_Q	130_Y	0.875	1.00
10_L	49_T	0.868	1.00
176_V	192_T	0.867	1.00
68_G	71_T	0.866	1.00
114_E	118_K	0.866	1.00
105_L	109_V	0.861	1.00
52_E	56_I	0.859	1.00
179_Y	182_T	0.850	1.00
92_M	96_A	0.849	1.00
130_Y	174_G	0.843	1.00
16_E	19_K	0.843	1.00
11_Y	15_I	0.842	1.00
18_I	39_L	0.835	1.00
30_K	64_I	0.834	1.00
33_L	63_I	0.821	1.00
124_E	128_L	0.820	1.00
141_P	144_Y	0.820	1.00
109_V	151_M	0.816	1.00
200_D	203_T	0.815	1.00
122_L	126_Q	0.809	1.00
117_T	184_I	0.796	1.00
32_K	35_S	0.790	1.00
40_S	50_L	0.787	1.00
187_I	190_H	0.786	1.00
16_E	20_E	0.784	1.00
21_D	24_N	0.783	1.00
109_V	127_E	0.779	1.00
195_P	199_C	0.779	1.00
127_E	151_M	0.777	1.00
116_D	136_T	0.769	1.00
145_C	148_K	0.763	1.00
117_T	178_S	0.763	1.00
91_K	94_E	0.762	1.00
157_S	160_H	0.759	1.00
106_S	130_Y	0.759	1.00
112_P	136_T	0.757	1.00
165_M	168_L	0.752	1.00
37_F	40_S	0.752	1.00
29_E	74_H	0.740	1.00
36_E	65_R	0.736	1.00
137_A	143_V	0.736	1.00
58_E	71_T	0.733	1.00
170_E	176_V	0.728	1.00
102_T	106_S	0.723	1.00
97_N	100_P	0.722	1.00
39_L	54_L	0.721	1.00
106_S	187_I	0.718	1.00
114_E	117_T	0.717	1.00
17_R	42_K	0.716	1.00
115_D	119_R	0.715	1.00
180_A	185_E	0.712	1.00
168_L	171_K	0.711	1.00
183_D	188_G	0.708	1.00
14_V	50_L	0.705	1.00
175_S	178_S	0.701	1.00
187_I	193_I	0.697	1.00
90_T	94_E	0.697	1.00
49_T	53_A	0.693	1.00
116_D	119_R	0.692	1.00
105_L	193_I	0.691	1.00
164_S	168_L	0.689	1.00
189_Y	199_C	0.676	1.00
14_V	53_A	0.674	1.00
106_S	110_L	0.673	1.00
107_S	110_L	0.672	1.00
199_C	203_T	0.671	1.00
34_P	42_K	0.664	1.00
40_S	43_L	0.663	1.00
43_L	50_L	0.662	1.00
132_E	192_T	0.662	1.00
129_F	178_S	0.661	1.00
54_L	58_E	0.654	1.00
101_G	139_G	0.653	1.00
189_Y	194_S	0.652	1.00
41_K	44_G	0.649	1.00
107_S	111_M	0.646	1.00
94_E	97_N	0.639	1.00
152_N	155_P	0.638	1.00
104_F	134_V	0.638	1.00
15_I	53_A	0.636	1.00
131_L	150_P	0.636	1.00
150_P	153_I	0.635	1.00
117_T	120_F	0.631	1.00
91_K	95_Q	0.630	1.00
176_V	179_Y	0.630	1.00
12_L	15_I	0.628	1.00
120_F	132_E	0.625	1.00
50_L	63_I	0.624	1.00
191_D	194_S	0.623	1.00
119_R	135_R	0.617	1.00
37_F	47_R	0.616	1.00
147_D	150_P	0.616	1.00
122_L	125_G	0.616	1.00
87_N	90_T	0.606	1.00
26_I	42_K	0.605	1.00
49_T	52_E	0.600	1.00
86_L	90_T	0.595	1.00
192_T	196_V	0.595	1.00
164_S	169_L	0.594	1.00
14_V	17_R	0.593	1.00
177_I	192_T	0.592	1.00
18_I	27_Y	0.591	1.00
115_D	118_K	0.590	1.00
154_L	158_F	0.590	1.00
32_K	69_V	0.589	1.00
127_E	154_L	0.587	1.00
67_H	70_G	0.585	1.00
141_P	145_C	0.584	1.00
127_E	150_P	0.583	1.00
98_M	201_P	0.582	1.00
157_S	161_Q	0.580	1.00
20_E	23_K	0.579	1.00
27_Y	33_L	0.579	1.00
187_I	191_D	0.577	1.00
124_E	127_E	0.577	1.00
192_T	195_P	0.577	1.00
35_S	68_G	0.575	1.00
109_V	112_P	0.575	1.00
103_I	107_S	0.574	1.00
131_L	143_V	0.572	1.00
102_T	105_L	0.565	1.00
118_K	121_H	0.565	1.00
54_L	65_R	0.563	1.00
40_S	47_R	0.563	1.00
177_I	193_I	0.561	1.00
105_L	134_V	0.556	1.00
193_I	196_V	0.554	1.00
72_F	75_S	0.554	1.00
158_F	161_Q	0.553	1.00
137_A	142_I	0.553	1.00
116_D	135_R	0.552	1.00
154_L	157_S	0.551	1.00
96_A	101_G	0.551	1.00
189_Y	193_I	0.549	1.00
171_K	199_C	0.548	1.00
106_S	132_E	0.547	1.00
39_L	43_L	0.546	1.00
48_A	52_E	0.545	1.00
164_S	171_K	0.544	1.00
169_L	175_S	0.542	1.00
113_S	117_T	0.542	1.00
127_E	131_L	0.541	1.00
126_Q	152_N	0.540	1.00
114_E	184_I	0.540	1.00
155_P	158_F	0.539	1.00
163_E	167_D	0.536	1.00
9_H	13_K	0.534	1.00
13_K	16_E	0.531	1.00
111_M	127_E	0.529	1.00
171_K	174_G	0.528	1.00
121_H	175_S	0.527	1.00
126_Q	130_Y	0.526	1.00
145_C	149_I	0.526	1.00
55_R	71_T	0.524	1.00
92_M	95_Q	0.520	1.00
99_T	142_I	0.520	1.00
167_D	170_E	0.519	1.00
105_L	189_Y	0.516	1.00
176_V	195_P	0.514	1.00
96_A	100_P	0.510	1.00
20_E	26_I	0.505	1.00
109_V	129_F	0.505	1.00
98_M	138_D	0.504	1.00
128_L	131_L	0.504	1.00
174_G	196_V	0.501	1.00
146_I	193_I	0.500	1.00
189_Y	203_T	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	0.157	Contact Map
2ra5A	2	0.61	100	0.193	Contact Map
3f8mA	2	0.9419	100	0.199	Contact Map
3edpA	2	0.9087	100	0.222	Contact Map
3bwgA	2	0.9461	100	0.228	Contact Map
3eetA	2	0.9502	100	0.233	Contact Map
1hw1A	2	0.834	100	0.426	Contact Map
3sxyA	2	0.7718	100	0.427	Contact Map
4p96A	2	0.888	100	0.432	Contact Map
3c7jA	4	0.8465	100	0.433	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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