HBD - BACSU - GREMLIN Contacts

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HBD - Probable 3-hydroxybutyryl-CoA dehydrogenase

UniProt:	P45856	Sequences: MEIKQIMVAGAGQMGSGIAQTAADAGFYVRMYDVNPEAAEAGLKRLKKQLARDAEKGKRTETEVKSVINRISISQTLEEAEHADIVIEAIAENMAAKTEMFKTLDRICPPHTILASNTSSLPITEIAAVTNRPQRVIGMHFMNPVPVMKLVEVIRGLATSEETALDVMALAEKMGKTAVEVNDFPGFVSNRVLLPMINEAIYCVYEGVAKPEAIDEVMKLGMNHPMGPLALADFIGLDTCLSIMEVLHSGLGDSKYRPCPLLRKYVKAGWLGKKSGRGFYDYEEKTS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	287 (279)
Sequences:	8916 (5399)
Seq/√Len:	323.2

ECOLI - PAAH FADB FADJ
BACSU - HBD FADN
HALSA - Q9HRI4 Q9HQ61
SULSO - Q97UK9 Q97UX0 Q7LXQ8 Q97VU5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
99_E	103_T	3.191	1.00
270_W	277_R	2.967	1.00
36_P	40_E	2.792	1.00
7_M	80_A	2.733	1.00
219_K	230_A	2.719	1.00
105_D	131_N	2.547	1.00
90_I	100_M	2.484	1.00
76_T	79_E	2.425	1.00
277_R	281_D	2.382	1.00
210_K	213_A	2.360	1.00
91_A	96_A	2.340	1.00
5_Q	28_Y	2.216	1.00
137_I	167_V	2.210	1.00
23_A	71_I	2.196	1.00
168_M	180_E	2.172	1.00
134_Q	160_S	2.172	1.00
161_E	165_L	2.142	1.00
61_E	65_K	2.123	1.00
245_E	263_R	2.106	1.00
6_I	22_A	2.086	1.00
105_D	130_T	2.064	1.00
151_V	171_A	2.061	1.00
84_D	109_P	2.009	1.00
43_L	73_I	1.948	1.00
7_M	83_A	1.939	1.00
132_R	135_R	1.929	1.00
204_V	214_I	1.922	1.00
94_M	125_E	1.904	1.00
265_Y	270_W	1.894	1.00
90_I	96_A	1.892	1.00
5_Q	82_H	1.862	1.00
22_A	170_L	1.854	1.00
271_L	275_S	1.833	1.00
160_S	163_T	1.828	1.00
153_V	168_M	1.820	1.00
86_V	108_C	1.805	1.00
54_A	64_V	1.803	1.00
98_T	129_V	1.803	1.00
155_R	161_E	1.785	1.00
168_M	172_E	1.724	1.00
111_H	135_R	1.723	1.00
103_T	106_R	1.720	1.00
39_A	73_I	1.667	1.00
5_Q	30_R	1.664	1.00
139_M	171_A	1.652	1.00
27_F	173_K	1.647	1.00
51_A	55_E	1.644	1.00
22_A	174_M	1.628	1.00
264_K	268_A	1.625	1.00
108_C	112_T	1.623	1.00
28_Y	70_R	1.621	1.00
116_S	123_I	1.610	1.00
13_Q	239_T	1.606	1.00
66_S	70_R	1.597	1.00
60_T	63_E	1.580	1.00
74_S	79_E	1.572	1.00
238_D	274_K	1.566	1.00
47_K	68_I	1.563	1.00
139_M	167_V	1.559	1.00
133_P	158_A	1.546	1.00
47_K	51_A	1.536	1.00
43_L	47_K	1.498	1.00
209_A	214_I	1.489	1.00
6_I	27_F	1.488	1.00
181_V	188_V	1.471	1.00
11_A	31_M	1.468	1.00
177_T	216_E	1.459	1.00
124_T	157_L	1.454	1.00
94_M	121_L	1.448	1.00
102_K	129_V	1.444	1.00
155_R	164_A	1.432	1.00
241_L	263_R	1.430	1.00
63_E	66_S	1.430	1.00
85_I	167_V	1.427	1.00
20_Q	49_Q	1.419	1.00
101_F	114_L	1.414	1.00
106_R	131_N	1.412	1.00
164_A	180_E	1.410	1.00
232_A	240_C	1.396	1.00
40_E	44_K	1.395	1.00
11_A	33_D	1.385	1.00
16_S	45_R	1.380	1.00
95_A	98_T	1.373	1.00
35_N	38_A	1.373	1.00
108_C	114_L	1.366	1.00
51_A	64_V	1.365	1.00
130_T	136_V	1.347	1.00
165_L	169_A	1.345	1.00
263_R	267_K	1.340	1.00
95_A	99_E	1.337	1.00
65_K	69_N	1.336	1.00
124_T	183_D	1.329	1.00
99_E	102_K	1.318	1.00
169_A	173_K	1.316	1.00
30_R	74_S	1.314	1.00
32_Y	77_L	1.310	1.00
169_A	172_E	1.308	1.00
20_Q	24_D	1.306	1.00
44_K	48_K	1.298	1.00
36_P	75_Q	1.289	1.00
78_E	103_T	1.276	1.00
109_P	112_T	1.275	1.00
241_L	266_V	1.262	1.00
171_A	178_A	1.259	1.00
85_I	170_L	1.255	1.00
125_E	128_A	1.254	1.00
204_V	211_P	1.247	1.00
19_A	31_M	1.246	1.00
50_L	67_V	1.245	1.00
245_E	249_S	1.239	1.00
102_K	106_R	1.234	1.00
94_M	98_T	1.228	1.00
64_V	68_I	1.224	1.00
260_P	264_K	1.222	1.00
28_Y	72_S	1.222	1.00
241_L	245_E	1.221	1.00
24_D	67_V	1.202	1.00
101_F	104_L	1.201	1.00
156_G	159_T	1.193	1.00
30_R	72_S	1.183	1.00
98_T	102_K	1.174	1.00
54_A	59_R	1.166	1.00
113_I	163_T	1.161	1.00
82_H	109_P	1.161	1.00
126_I	136_V	1.157	1.00
38_A	41_A	1.139	1.00
61_E	64_V	1.133	1.00
78_E	107_I	1.131	1.00
115_A	137_I	1.125	1.00
123_I	138_G	1.122	1.00
41_A	45_R	1.117	1.00
96_A	99_E	1.116	1.00
203_C	208_V	1.113	1.00
39_A	75_Q	1.113	1.00
137_I	163_T	1.104	1.00
138_G	154_I	1.103	1.00
37_E	40_E	1.094	1.00
47_K	64_V	1.092	1.00
179_V	217_V	1.090	1.00
11_A	42_G	1.086	1.00
62_T	66_S	1.082	1.00
101_F	126_I	1.074	1.00
32_Y	74_S	1.056	1.00
205_Y	259_C	1.042	1.00
40_E	43_L	1.040	1.00
84_D	111_H	1.039	1.00
218_M	222_M	1.039	1.00
202_Y	206_E	1.038	1.00
103_T	107_I	1.033	1.00
85_I	139_M	1.030	1.00
31_M	42_G	1.022	1.00
77_L	107_I	1.012	1.00
22_A	87_I	1.010	1.00
124_T	156_G	1.007	1.00
211_P	229_L	0.997	1.00
72_S	79_E	0.995	1.00
172_E	178_A	0.992	1.00
218_M	228_P	0.981	1.00
9_A	104_L	0.978	1.00
6_I	85_I	0.975	1.00
196_M	224_H	0.970	1.00
9_A	100_M	0.958	1.00
77_L	103_T	0.953	1.00
163_T	166_D	0.947	1.00
134_Q	158_A	0.939	1.00
120_S	243_I	0.938	1.00
32_Y	103_T	0.937	1.00
50_L	64_V	0.936	1.00
122_P	125_E	0.936	1.00
201_I	279_F	0.933	1.00
189_S	217_V	0.930	1.00
115_A	139_M	0.929	1.00
271_L	274_K	0.922	1.00
158_A	270_W	0.921	1.00
44_K	47_K	0.920	1.00
225_P	231_L	0.915	1.00
47_K	65_K	0.904	1.00
155_R	180_E	0.903	1.00
80_A	83_A	0.900	1.00
23_A	67_V	0.898	1.00
52_R	55_E	0.898	1.00
137_I	153_V	0.897	1.00
230_A	234_F	0.892	1.00
31_M	73_I	0.887	1.00
39_A	43_L	0.884	1.00
45_R	48_K	0.882	1.00
30_R	82_H	0.879	1.00
51_A	54_A	0.878	1.00
116_S	126_I	0.873	1.00
98_T	126_I	0.871	1.00
149_K	177_T	0.864	1.00
116_S	138_G	0.857	1.00
33_D	38_A	0.856	1.00
104_L	108_C	0.851	1.00
63_E	70_R	0.849	1.00
192_V	196_M	0.848	1.00
4_K	84_D	0.848	1.00
85_I	115_A	0.847	1.00
45_R	49_Q	0.847	1.00
198_N	259_C	0.843	1.00
49_Q	53_D	0.836	1.00
162_E	166_D	0.829	1.00
78_E	81_E	0.829	1.00
203_C	214_I	0.826	1.00
7_M	30_R	0.823	1.00
27_F	170_L	0.822	1.00
94_M	126_I	0.822	1.00
127_A	136_V	0.820	1.00
105_D	132_R	0.818	1.00
202_Y	259_C	0.815	1.00
93_N	242_S	0.811	1.00
113_I	137_I	0.801	1.00
165_L	168_M	0.799	1.00
9_A	32_Y	0.797	1.00
237_L	240_C	0.795	1.00
8_V	19_A	0.792	1.00
216_E	219_K	0.789	1.00
96_A	100_M	0.788	1.00
34_V	38_A	0.787	1.00
142_M	189_S	0.784	1.00
16_S	42_G	0.782	1.00
245_E	258_P	0.782	1.00
21_T	25_A	0.782	1.00
141_F	174_M	0.781	1.00
167_V	171_A	0.781	1.00
67_V	70_R	0.778	1.00
20_Q	146_P	0.773	1.00
197_I	232_A	0.767	1.00
189_S	222_M	0.767	1.00
121_L	125_E	0.767	1.00
118_T	138_G	0.766	1.00
232_A	237_L	0.766	1.00
199_E	206_E	0.763	0.99
54_A	61_E	0.762	0.99
139_M	153_V	0.760	0.99
202_Y	205_Y	0.758	0.99
269_G	275_S	0.757	0.99
5_Q	83_A	0.757	0.99
21_T	174_M	0.755	0.99
249_S	252_G	0.750	0.99
77_L	80_A	0.748	0.99
177_T	220_L	0.745	0.99
165_L	180_E	0.745	0.99
101_F	130_T	0.744	0.99
235_I	240_C	0.743	0.99
150_L	179_V	0.738	0.99
168_M	178_A	0.737	0.99
30_R	83_A	0.736	0.99
14_M	117_N	0.736	0.99
237_L	266_V	0.735	0.99
179_V	188_V	0.727	0.99
98_T	128_A	0.726	0.99
142_M	150_L	0.724	0.99
53_D	59_R	0.721	0.99
139_M	170_L	0.720	0.99
6_I	170_L	0.719	0.99
261_L	279_F	0.719	0.99
34_V	91_A	0.718	0.99
85_I	113_I	0.718	0.99
248_H	252_G	0.713	0.99
16_S	41_A	0.713	0.99
153_V	178_A	0.710	0.99
30_R	79_E	0.705	0.99
53_D	58_K	0.703	0.99
170_L	174_M	0.702	0.99
213_A	216_E	0.702	0.99
17_G	146_P	0.701	0.99
93_N	96_A	0.701	0.99
200_A	229_L	0.700	0.99
194_L	240_C	0.699	0.99
105_D	136_V	0.698	0.99
62_T	65_K	0.696	0.99
53_D	147_V	0.696	0.99
159_T	163_T	0.696	0.99
21_T	176_K	0.696	0.99
32_Y	80_A	0.695	0.99
77_L	100_M	0.695	0.99
25_A	175_G	0.694	0.99
98_T	125_E	0.693	0.99
14_M	18_I	0.691	0.99
135_R	160_S	0.691	0.99
64_V	67_V	0.690	0.99
226_M	234_F	0.683	0.99
46_L	71_I	0.683	0.99
110_P	131_N	0.679	0.99
212_E	216_E	0.675	0.99
75_Q	79_E	0.673	0.99
161_E	180_E	0.673	0.99
252_G	255_K	0.673	0.99
122_P	183_D	0.672	0.99
164_A	168_M	0.672	0.99
211_P	280_Y	0.671	0.99
93_N	99_E	0.670	0.99
193_L	197_I	0.670	0.99
63_E	67_V	0.668	0.99
266_V	271_L	0.667	0.99
48_K	51_A	0.665	0.99
241_L	267_K	0.664	0.99
76_T	103_T	0.660	0.99
198_N	202_Y	0.659	0.99
18_I	89_A	0.657	0.99
191_R	199_E	0.656	0.98
86_V	104_L	0.653	0.98
37_E	41_A	0.651	0.98
162_E	165_L	0.649	0.98
216_E	220_L	0.642	0.98
201_I	232_A	0.642	0.98
239_T	243_I	0.641	0.98
201_I	261_L	0.639	0.98
127_A	156_G	0.638	0.98
166_D	173_K	0.635	0.98
66_S	69_N	0.635	0.98
153_V	171_A	0.631	0.98
42_G	46_L	0.628	0.98
205_Y	260_P	0.628	0.98
150_L	217_V	0.626	0.98
234_F	273_K	0.626	0.98
264_K	267_K	0.626	0.98
21_T	145_V	0.623	0.98
217_V	222_M	0.622	0.98
204_V	229_L	0.621	0.98
270_W	275_S	0.620	0.98
273_K	282_Y	0.617	0.98
195_P	198_N	0.617	0.98
261_L	265_Y	0.616	0.98
106_R	109_P	0.615	0.98
194_L	197_I	0.613	0.98
48_K	52_R	0.611	0.98
123_I	183_D	0.610	0.98
229_L	279_F	0.609	0.98
209_A	213_A	0.603	0.97
46_L	49_Q	0.602	0.97
51_A	61_E	0.600	0.97
143_N	235_I	0.597	0.97
42_G	73_I	0.595	0.97
242_S	245_E	0.595	0.97
128_A	158_A	0.595	0.97
138_G	183_D	0.593	0.97
197_I	240_C	0.592	0.97
13_Q	143_N	0.591	0.97
143_N	231_L	0.591	0.97
30_R	80_A	0.590	0.97
115_A	167_V	0.589	0.97
242_S	246_V	0.588	0.97
7_M	32_Y	0.587	0.97
204_V	261_L	0.587	0.97
80_A	107_I	0.583	0.97
226_M	230_A	0.579	0.97
113_I	166_D	0.578	0.97
34_V	90_I	0.576	0.97
190_N	195_P	0.575	0.97
4_K	173_K	0.574	0.97
104_L	107_I	0.567	0.96
119_S	190_N	0.567	0.96
231_L	235_I	0.565	0.96
114_L	136_V	0.560	0.96
109_P	135_R	0.560	0.96
114_L	130_T	0.560	0.96
33_D	39_A	0.557	0.96
166_D	169_A	0.557	0.96
46_L	73_I	0.557	0.96
6_I	87_I	0.556	0.96
193_L	235_I	0.554	0.96
238_D	271_L	0.552	0.96
22_A	27_F	0.551	0.96
11_A	19_A	0.549	0.96
185_P	246_V	0.548	0.95
65_K	68_I	0.547	0.95
5_Q	84_D	0.546	0.95
172_E	177_T	0.546	0.95
20_Q	53_D	0.545	0.95
258_P	262_L	0.545	0.95
260_P	263_R	0.543	0.95
154_I	187_F	0.536	0.95
54_A	57_G	0.535	0.95
236_G	239_T	0.534	0.95
59_R	67_V	0.533	0.95
110_P	132_R	0.532	0.95
24_D	53_D	0.531	0.95
248_H	258_P	0.529	0.95
196_M	218_M	0.528	0.94
202_Y	257_R	0.526	0.94
83_A	86_V	0.525	0.94
111_H	166_D	0.524	0.94
121_L	246_V	0.524	0.94
170_L	173_K	0.522	0.94
193_L	232_A	0.522	0.94
21_T	146_P	0.521	0.94
178_A	181_V	0.520	0.94
205_Y	261_L	0.520	0.94
34_V	93_N	0.520	0.94
41_A	44_K	0.520	0.94
198_N	244_M	0.520	0.94
78_E	106_R	0.518	0.94
133_P	156_G	0.518	0.94
193_L	225_P	0.517	0.94
35_N	41_A	0.516	0.94
93_N	98_T	0.514	0.94
130_T	133_P	0.514	0.94
118_T	187_F	0.512	0.94
236_G	274_K	0.512	0.94
265_Y	277_R	0.512	0.94
237_L	241_L	0.510	0.93
197_I	201_I	0.510	0.93
123_I	156_G	0.508	0.93
4_K	27_F	0.508	0.93
51_A	68_I	0.507	0.93
102_K	131_N	0.507	0.93
198_N	256_Y	0.506	0.93
235_I	239_T	0.505	0.93
237_L	265_Y	0.504	0.93
189_S	195_P	0.504	0.93
193_L	231_L	0.503	0.93
101_F	108_C	0.503	0.93
104_L	114_L	0.503	0.93
213_A	221_G	0.503	0.93
188_V	209_A	0.502	0.93
137_I	164_A	0.500	0.93

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
1wdkA	2	0.9826	100	0.234	Contact Map
2wtbA	1	0.9129	100	0.242	Contact Map
4b3hA	1	0.9895	100	0.245	Contact Map
3zwcA	1	0.9861	100	0.261	Contact Map
3k6jA	1	0.9582	100	0.266	Contact Map
4j0eA	2	0.9826	100	0.272	Contact Map
1zcjA	1	0.9861	100	0.272	Contact Map
1f0yA	2	0.9861	100	0.296	Contact Map
4r1nA	2	0.9826	100	0.301	Contact Map
3mogA	3	1	100	0.318	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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