NPD - BACSU - GREMLIN Contacts

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NPD - NAD-dependent protein deacetylase

UniProt:	O07595	Sequences: METFKSILHEAQRIVVLTGAGMSTESGIPDFRSAGGIWTEDASRMEAMSLDYFLSYPRLFWPKFKELFQMKMSGSFEPNEGHLLLAELEKQGKQVDIFTQNIDGLHKKAGSRHVYELHGSIQTAACPACGARYDLPHLLEREVPECTAAGNNGDICGTVLKTDVVLFGDAVMHFDTLYEKLDQADLLLVIGTSLEVAPARFVPEDASLIPGMKKVIINLEPTYCDSLFDMVIHQKIGEFARSLGMKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	247 (224)
Sequences:	5813 (4067)
Seq/√Len:	271.7

ECOLI - NPD
BACSU - NPD
SULSO - NPD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_E	237_G	3.802	1.00
26_S	79_N	3.246	1.00
42_A	45_M	2.745	1.00
107_K	116_E	2.639	1.00
96_D	180_K	2.635	1.00
80_E	241_R	2.538	1.00
87_E	90_K	2.535	1.00
22_M	81_G	2.518	1.00
190_I	236_I	2.465	1.00
123_T	163_D	2.432	1.00
42_A	46_E	2.431	1.00
234_Q	239_F	2.396	1.00
51_D	168_G	2.387	1.00
197_A	201_F	2.161	1.00
206_A	212_M	2.129	1.00
197_A	200_R	2.114	1.00
16_V	85_L	2.114	1.00
86_A	90_K	2.111	1.00
24_T	30_D	2.096	1.00
235_K	238_E	2.076	1.00
126_C	129_C	2.069	1.00
89_E	113_H	2.054	1.00
81_G	240_A	1.948	1.00
13_R	183_Q	1.896	1.00
219_L	235_K	1.861	1.00
133_Y	160_L	1.852	1.00
13_R	95_V	1.850	1.00
87_E	91_Q	1.845	1.00
234_Q	238_E	1.838	1.00
16_V	188_L	1.804	1.00
77_E	108_K	1.786	1.00
153_G	156_C	1.764	1.00
81_G	236_I	1.754	1.00
13_R	94_Q	1.753	1.00
85_L	97_I	1.736	1.00
80_E	83_L	1.704	1.00
96_D	115_Y	1.695	1.00
115_Y	176_T	1.621	1.00
25_E	235_K	1.592	1.00
131_A	155_I	1.592	1.00
207_S	229_D	1.570	1.00
132_R	163_D	1.541	1.00
84_L	240_A	1.537	1.00
217_I	239_F	1.524	1.00
89_E	111_S	1.510	1.00
213_K	229_D	1.505	1.00
15_V	184_A	1.503	1.00
50_L	54_L	1.502	1.00
53_F	127_P	1.501	1.00
179_E	183_Q	1.496	1.00
111_S	114_V	1.491	1.00
49_S	52_Y	1.484	1.00
84_L	88_L	1.454	1.00
129_C	156_C	1.438	1.00
18_T	106_H	1.431	1.00
125_A	163_D	1.425	1.00
131_A	154_D	1.414	1.00
186_L	215_V	1.403	1.00
120_S	123_T	1.394	1.00
13_R	185_D	1.385	1.00
77_E	83_L	1.376	1.00
222_T	225_D	1.367	1.00
30_D	33_S	1.365	1.00
62_P	66_E	1.364	1.00
116_E	120_S	1.359	1.00
35_G	39_T	1.359	1.00
117_L	199_A	1.356	1.00
178_Y	205_D	1.355	1.00
84_L	241_R	1.352	1.00
89_E	112_R	1.339	1.00
181_L	202_V	1.339	1.00
58_R	62_P	1.335	1.00
73_S	76_F	1.327	1.00
190_I	240_A	1.326	1.00
150_G	153_G	1.309	1.00
181_L	187_L	1.293	1.00
216_I	222_T	1.270	1.00
125_A	132_R	1.266	1.00
56_Y	59_L	1.265	1.00
18_T	22_M	1.263	1.00
186_L	213_K	1.258	1.00
182_D	205_D	1.256	1.00
13_R	180_K	1.251	1.00
232_I	239_F	1.248	1.00
133_Y	154_D	1.239	1.00
216_I	225_D	1.234	1.00
28_I	76_F	1.221	1.00
190_I	217_I	1.219	1.00
216_I	228_F	1.218	1.00
18_T	97_I	1.216	1.00
115_Y	180_K	1.199	1.00
16_V	94_Q	1.197	1.00
83_L	87_E	1.194	1.00
86_A	109_A	1.190	1.00
104_G	108_K	1.188	1.00
15_V	98_F	1.173	1.00
123_T	132_R	1.157	1.00
33_S	39_T	1.150	1.00
84_L	87_E	1.148	1.00
18_T	85_L	1.127	1.00
53_F	57_P	1.124	1.00
161_K	169_D	1.121	1.00
107_K	114_V	1.114	1.00
47_A	52_Y	1.113	1.00
11_A	186_L	1.113	1.00
32_R	36_G	1.111	1.00
14_I	93_K	1.105	1.00
104_G	116_E	1.097	1.00
126_C	156_C	1.093	1.00
12_Q	185_D	1.089	1.00
213_K	230_M	1.085	1.00
29_P	40_E	1.072	1.00
117_L	171_V	1.072	1.00
54_L	127_P	1.071	1.00
79_N	237_G	1.070	1.00
46_E	59_L	1.065	1.00
188_L	215_V	1.054	1.00
104_G	122_Q	1.051	1.00
49_S	169_D	1.050	1.00
127_P	158_T	1.050	1.00
178_Y	182_D	1.045	1.00
128_A	158_T	1.042	1.00
174_F	202_V	1.029	1.00
176_T	179_E	1.028	1.00
151_N	154_D	1.025	1.00
124_A	160_L	1.003	1.00
50_L	168_G	0.999	1.00
225_D	231_V	0.980	1.00
17_L	199_A	0.979	1.00
221_P	233_H	0.978	1.00
48_M	52_Y	0.972	1.00
60_F	166_L	0.972	1.00
214_K	228_F	0.971	1.00
71_K	75_S	0.964	1.00
38_W	48_M	0.961	1.00
53_F	161_K	0.958	1.00
46_E	55_S	0.955	1.00
86_A	111_S	0.946	1.00
127_P	159_V	0.942	1.00
97_I	111_S	0.938	1.00
238_E	242_S	0.938	1.00
104_G	107_K	0.932	1.00
176_T	180_K	0.926	1.00
117_L	177_L	0.921	1.00
48_M	166_L	0.905	1.00
125_A	161_K	0.901	1.00
129_C	158_T	0.900	1.00
29_P	72_M	0.892	1.00
53_F	166_L	0.892	1.00
80_E	84_L	0.886	1.00
90_K	112_R	0.886	1.00
104_G	120_S	0.883	1.00
225_D	228_F	0.878	1.00
81_G	190_I	0.874	1.00
41_D	44_R	0.865	1.00
217_I	232_I	0.863	1.00
18_T	190_I	0.858	1.00
238_E	241_R	0.854	1.00
14_I	186_L	0.850	1.00
15_V	187_L	0.847	1.00
59_L	62_P	0.840	1.00
137_H	140_E	0.831	0.99
106_H	111_S	0.828	0.99
124_A	135_L	0.828	0.99
194_L	216_I	0.819	0.99
13_R	96_D	0.813	0.99
63_K	67_L	0.806	0.99
165_V	169_D	0.801	0.99
29_P	35_G	0.799	0.99
49_S	53_F	0.797	0.99
98_F	199_A	0.791	0.99
163_D	172_M	0.791	0.99
15_V	181_L	0.786	0.99
11_A	14_I	0.785	0.99
215_V	230_M	0.784	0.99
20_A	23_S	0.782	0.99
17_L	202_V	0.778	0.99
108_K	122_Q	0.775	0.99
17_L	187_L	0.774	0.99
80_E	237_G	0.771	0.99
134_D	137_H	0.764	0.99
171_V	198_P	0.763	0.99
48_M	67_L	0.761	0.99
206_A	213_K	0.760	0.99
174_F	178_Y	0.759	0.99
14_I	185_D	0.758	0.99
64_F	67_L	0.756	0.99
234_Q	242_S	0.749	0.99
237_G	241_R	0.749	0.99
97_I	106_H	0.743	0.99
33_S	220_E	0.742	0.99
207_S	227_L	0.740	0.99
136_P	140_E	0.739	0.99
189_V	192_T	0.738	0.99
173_H	176_T	0.737	0.99
113_H	176_T	0.737	0.99
81_G	235_K	0.735	0.99
25_E	79_N	0.729	0.99
85_L	190_I	0.729	0.99
222_T	228_F	0.728	0.99
180_K	183_Q	0.727	0.99
137_H	141_R	0.727	0.99
167_F	196_V	0.719	0.99
136_P	139_L	0.715	0.98
71_K	74_G	0.707	0.98
220_E	231_V	0.705	0.98
141_R	154_D	0.704	0.98
48_M	53_F	0.699	0.98
189_V	194_L	0.698	0.98
125_A	172_M	0.690	0.98
177_L	202_V	0.689	0.98
31_F	36_G	0.688	0.98
204_E	227_L	0.682	0.98
198_P	203_P	0.682	0.98
22_M	106_H	0.681	0.98
23_S	103_D	0.672	0.98
184_A	212_M	0.672	0.98
137_H	154_D	0.668	0.98
22_M	190_I	0.667	0.98
151_N	155_I	0.666	0.98
175_D	178_Y	0.663	0.97
15_V	202_V	0.659	0.97
189_V	214_K	0.658	0.97
133_Y	141_R	0.656	0.97
46_E	52_Y	0.655	0.97
102_I	121_I	0.653	0.97
188_L	243_L	0.652	0.97
94_Q	113_H	0.651	0.97
162_T	169_D	0.648	0.97
16_V	95_V	0.647	0.97
193_S	196_V	0.643	0.97
15_V	180_K	0.641	0.97
126_C	153_G	0.641	0.97
56_Y	60_F	0.638	0.97
84_L	190_I	0.637	0.97
126_C	158_T	0.637	0.97
66_E	72_M	0.636	0.97
220_E	233_H	0.636	0.97
59_L	63_K	0.633	0.97
184_A	187_L	0.633	0.97
239_F	243_L	0.632	0.97
86_A	89_E	0.625	0.96
89_E	106_H	0.624	0.96
116_E	122_Q	0.623	0.96
161_K	166_L	0.620	0.96
60_F	64_F	0.619	0.96
42_A	52_Y	0.617	0.96
104_G	121_I	0.614	0.96
39_T	44_R	0.613	0.96
61_W	151_N	0.613	0.96
215_V	243_L	0.613	0.96
52_Y	59_L	0.613	0.96
74_G	122_Q	0.611	0.96
24_T	33_S	0.606	0.96
96_D	113_H	0.605	0.96
204_E	224_C	0.600	0.96
73_S	122_Q	0.599	0.95
216_I	231_V	0.599	0.95
125_A	130_G	0.591	0.95
73_S	121_I	0.589	0.95
102_I	164_V	0.586	0.95
29_P	33_S	0.585	0.95
201_F	204_E	0.584	0.95
231_V	234_Q	0.584	0.95
82_H	100_Q	0.583	0.95
53_F	159_V	0.582	0.95
162_T	166_L	0.582	0.95
38_W	167_F	0.579	0.95
10_E	213_K	0.579	0.95
72_M	75_S	0.578	0.95
52_Y	63_K	0.578	0.95
29_P	39_T	0.576	0.94
178_Y	202_V	0.576	0.94
52_Y	56_Y	0.576	0.94
14_I	95_V	0.576	0.94
152_N	159_V	0.575	0.94
12_Q	93_K	0.574	0.94
47_A	63_K	0.574	0.94
51_D	55_S	0.571	0.94
14_I	188_L	0.567	0.94
28_I	73_S	0.567	0.94
57_P	61_W	0.567	0.94
16_V	88_L	0.566	0.94
174_F	177_L	0.561	0.94
64_F	166_L	0.561	0.94
215_V	232_I	0.561	0.94
166_L	169_D	0.561	0.94
16_V	190_I	0.558	0.93
177_L	184_A	0.555	0.93
187_L	212_M	0.554	0.93
53_F	61_W	0.548	0.93
135_L	139_L	0.548	0.93
81_G	84_L	0.548	0.93
11_A	185_D	0.547	0.93
127_P	161_K	0.546	0.93
219_L	234_Q	0.546	0.93
189_V	228_F	0.539	0.92
235_K	239_F	0.539	0.92
98_F	177_L	0.537	0.92
149_A	153_G	0.535	0.92
189_V	224_C	0.535	0.92
205_D	209_I	0.532	0.92
98_F	180_K	0.531	0.92
131_A	134_D	0.531	0.92
24_T	219_L	0.530	0.92
173_H	178_Y	0.528	0.91
165_V	171_V	0.527	0.91
149_A	156_C	0.526	0.91
175_D	179_E	0.524	0.91
99_T	116_E	0.523	0.91
228_F	231_V	0.523	0.91
23_S	82_H	0.522	0.91
151_N	156_C	0.522	0.91
48_M	63_K	0.521	0.91
41_D	59_L	0.521	0.91
81_G	237_G	0.521	0.91
96_D	114_V	0.519	0.91
95_V	180_K	0.518	0.91
181_L	214_K	0.514	0.90
204_E	209_I	0.511	0.90
120_S	163_D	0.511	0.90
215_V	218_N	0.509	0.90
51_D	54_L	0.509	0.90
72_M	76_F	0.508	0.90
17_L	97_I	0.508	0.90
221_P	231_V	0.508	0.90
138_L	142_E	0.508	0.90
148_A	151_N	0.507	0.90
64_F	121_I	0.505	0.90
44_R	47_A	0.505	0.90
90_K	93_K	0.505	0.90
232_I	243_L	0.505	0.90
107_K	111_S	0.503	0.89
24_T	194_L	0.503	0.89
150_G	159_V	0.502	0.89
217_I	243_L	0.500	0.89

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
1m2kA	1	0.9514	100	0.117	Contact Map
1yc5A	1	0.9231	100	0.124	Contact Map
4iaoA	1	0.9717	100	0.127	Contact Map
3riyA	1	0.9757	100	0.13	Contact Map
4twjA	1	0.8988	100	0.133	Contact Map
3u31A	1	0.9757	100	0.135	Contact Map
2hjhA	2	0.9717	100	0.135	Contact Map
5btrA	1	0.9595	100	0.142	Contact Map
1q14A	3	0.9231	100	0.15	Contact Map
4kxqA	1	0.9595	100	0.156	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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