NPD - ECOLI - GREMLIN Contacts

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NPD - NAD-dependent protein deacylase

UniProt:	P75960	Sequences: MEKPRVLVLTGAGISAESGIRTFRAADGLWEEHRVEDVATPEGFDRDPELVQAFYNARRRQLQQPEIQPNAAHLALAKLQDALGDRFLLVTQNIDNLHERAGNTNVIHMHGELLKVRCSQSGQVLDWTGDVTPEDKCHCCQFPAPLRPHVVWFGEMPLGMDEIYMALSMADIFIAIGTSGHVYPAAGFVHEAKLHGAHTVELNLEPSQVGNEFAEKYYGPASQVVPEFVEKLLKGLKAGSIA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13443
Length:	242 (223)
Sequences:	5764 (4016)
Seq/√Len:	268.9

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
17_E	222_S	3.734	1.00
18_S	70_N	2.959	1.00
88_L	166_A	2.821	1.00
71_A	226_P	2.650	1.00
99_E	108_H	2.494	1.00
176_I	221_A	2.449	1.00
80_Q	104_T	2.447	1.00
14_I	72_A	2.426	1.00
78_K	81_D	2.362	1.00
219_G	224_V	2.353	1.00
42_E	154_G	2.272	1.00
115_K	149_H	2.246	1.00
192_A	197_A	2.180	1.00
183_Y	187_G	2.085	1.00
16_A	22_T	2.056	1.00
77_A	81_D	2.053	1.00
219_G	223_Q	2.040	1.00
8_V	76_L	2.021	1.00
183_Y	186_A	2.007	1.00
34_R	37_D	1.982	1.00
80_Q	105_N	1.975	1.00
72_A	225_V	1.972	1.00
118_C	121_S	1.965	1.00
80_Q	103_N	1.935	1.00
123_Q	141_Q	1.923	1.00
220_P	223_Q	1.917	1.00
125_L	146_L	1.883	1.00
204_L	220_P	1.864	1.00
5_R	169_M	1.825	1.00
76_L	89_L	1.804	1.00
78_K	82_A	1.804	1.00
5_R	87_F	1.802	1.00
5_R	86_R	1.788	1.00
72_A	221_A	1.768	1.00
121_S	142_F	1.725	1.00
17_E	220_P	1.695	1.00
227_E	230_E	1.691	1.00
68_Q	100_R	1.672	1.00
123_Q	140_C	1.663	1.00
139_C	142_F	1.659	1.00
8_V	174_I	1.652	1.00
124_V	149_H	1.621	1.00
71_A	74_L	1.621	1.00
88_L	107_I	1.616	1.00
75_A	225_V	1.603	1.00
41_P	45_D	1.602	1.00
159_G	162_E	1.557	1.00
107_I	162_E	1.551	1.00
44_F	119_S	1.517	1.00
75_A	229_V	1.506	1.00
7_L	170_A	1.471	1.00
202_L	224_V	1.470	1.00
193_K	214_A	1.449	1.00
198_H	214_A	1.444	1.00
172_I	200_V	1.433	1.00
167_L	188_F	1.397	1.00
89_L	103_N	1.357	1.00
49_E	53_A	1.354	1.00
22_T	25_A	1.351	1.00
10_T	98_H	1.350	1.00
112_E	115_K	1.340	1.00
117_R	149_H	1.335	1.00
103_N	106_V	1.313	1.00
207_S	210_G	1.311	1.00
109_M	185_A	1.310	1.00
10_T	14_I	1.305	1.00
53_A	57_A	1.302	1.00
40_T	43_G	1.300	1.00
82_A	85_D	1.284	1.00
75_A	226_P	1.281	1.00
68_Q	74_L	1.272	1.00
117_R	124_V	1.271	1.00
167_L	173_F	1.267	1.00
165_M	169_M	1.267	1.00
164_Y	191_E	1.255	1.00
75_A	79_L	1.244	1.00
108_H	112_E	1.243	1.00
107_I	166_A	1.228	1.00
176_I	225_V	1.224	1.00
168_S	191_E	1.224	1.00
217_Y	224_V	1.218	1.00
172_I	198_H	1.218	1.00
201_E	207_S	1.217	1.00
79_L	229_V	1.205	1.00
125_L	140_C	1.200	1.00
74_L	78_K	1.200	1.00
77_A	101_A	1.199	1.00
201_E	213_F	1.184	1.00
118_C	142_F	1.180	1.00
5_R	166_A	1.178	1.00
198_H	215_E	1.172	1.00
47_D	50_L	1.171	1.00
78_K	229_V	1.160	1.00
99_E	106_V	1.151	1.00
10_T	76_L	1.150	1.00
96_N	100_R	1.145	1.00
20_I	67_I	1.142	1.00
176_I	202_L	1.139	1.00
45_D	119_S	1.132	1.00
70_N	222_S	1.119	1.00
10_T	89_L	1.118	1.00
201_E	210_G	1.115	1.00
5_R	171_D	1.109	1.00
25_A	31_E	1.093	1.00
21_R	32_E	1.079	1.00
6_V	85_D	1.071	1.00
75_A	78_K	1.068	1.00
96_N	114_L	1.064	1.00
7_L	90_V	1.064	1.00
44_F	48_P	1.061	1.00
118_C	139_C	1.060	1.00
147_R	155_E	1.060	1.00
160_M	188_F	1.055	1.00
162_E	165_M	1.041	1.00
96_N	108_H	1.041	1.00
115_K	124_V	1.037	1.00
199_T	213_F	1.030	1.00
109_M	156_M	1.024	1.00
98_H	103_N	1.017	1.00
210_G	216_K	1.013	1.00
8_V	86_R	1.010	1.00
40_T	155_E	1.009	1.00
116_V	146_L	1.004	1.00
55_Y	58_R	1.001	1.00
162_E	166_A	0.994	1.00
21_R	61_Q	0.989	1.00
62_L	67_I	0.984	1.00
109_M	163_I	0.984	1.00
44_F	147_R	0.983	1.00
206_P	218_Y	0.980	1.00
219_G	227_E	0.973	1.00
77_A	103_N	0.967	1.00
57_A	61_Q	0.966	1.00
33_H	37_D	0.965	1.00
223_Q	227_E	0.965	1.00
27_D	31_E	0.962	1.00
226_P	229_V	0.961	1.00
119_S	144_A	0.961	1.00
51_V	152_W	0.960	1.00
38_V	43_G	0.955	1.00
24_R	28_G	0.931	1.00
9_L	185_A	0.930	1.00
174_I	200_V	0.925	1.00
81_D	104_T	0.924	1.00
39_A	43_G	0.923	1.00
52_Q	137_C	0.920	1.00
39_A	152_W	0.918	1.00
50_L	53_A	0.918	1.00
30_W	39_A	0.916	1.00
120_Q	144_A	0.914	1.00
96_N	99_E	0.914	1.00
40_T	44_F	0.913	1.00
37_D	50_L	0.902	1.00
41_P	154_G	0.902	1.00
210_G	213_F	0.886	1.00
119_S	145_P	0.885	1.00
164_Y	168_S	0.877	1.00
7_L	173_F	0.873	1.00
193_K	196_G	0.868	1.00
96_N	112_E	0.865	1.00
4_P	171_D	0.863	1.00
127_W	130_D	0.863	1.00
136_K	139_C	0.848	1.00
117_R	147_R	0.847	1.00
44_F	152_W	0.842	1.00
56_N	59_R	0.838	0.99
72_A	220_P	0.838	0.99
192_A	198_H	0.837	0.99
121_S	139_C	0.832	0.99
71_A	75_A	0.830	0.99
39_A	58_R	0.821	0.99
57_A	60_R	0.812	0.99
223_Q	226_P	0.812	0.99
6_V	172_I	0.811	0.99
10_T	176_I	0.805	0.99
180_G	201_E	0.800	0.99
105_N	162_E	0.798	0.99
175_A	178_T	0.786	0.99
21_R	27_D	0.782	0.99
202_L	217_Y	0.780	0.99
90_V	185_A	0.779	0.99
137_C	142_F	0.775	0.99
138_H	145_P	0.775	0.99
151_V	155_E	0.771	0.99
72_A	176_I	0.771	0.99
7_L	167_L	0.771	0.99
202_L	228_F	0.770	0.99
166_A	169_M	0.765	0.99
33_H	50_L	0.762	0.99
5_R	88_L	0.762	0.99
9_L	173_F	0.761	0.99
12_A	15_S	0.756	0.99
37_D	43_G	0.753	0.99
158_L	161_D	0.747	0.99
54_F	58_R	0.744	0.99
9_L	188_F	0.741	0.99
71_A	222_S	0.741	0.99
205_E	216_K	0.739	0.99
207_S	213_F	0.737	0.99
179_S	182_V	0.737	0.99
78_K	230_E	0.737	0.99
50_L	54_F	0.726	0.99
153_F	182_V	0.724	0.99
100_R	114_L	0.723	0.99
37_D	46_R	0.722	0.99
82_A	229_V	0.722	0.99
127_W	131_V	0.717	0.98
76_L	176_I	0.716	0.98
163_I	188_F	0.714	0.98
205_E	218_Y	0.714	0.98
225_V	229_V	0.708	0.98
14_I	98_H	0.705	0.98
200_V	215_E	0.704	0.98
138_H	143_P	0.702	0.98
42_E	46_R	0.700	0.98
224_V	228_F	0.700	0.98
7_L	166_A	0.699	0.98
35_V	38_V	0.697	0.98
89_L	98_H	0.696	0.98
17_E	70_N	0.696	0.98
121_S	144_A	0.694	0.98
170_A	197_A	0.688	0.98
128_T	131_V	0.688	0.98
147_R	152_W	0.686	0.98
190_H	212_E	0.684	0.98
137_C	140_C	0.683	0.98
170_A	173_F	0.683	0.98
72_A	222_S	0.682	0.98
6_V	171_D	0.676	0.98
94_I	150_V	0.674	0.98
175_A	209_V	0.671	0.98
15_S	95_D	0.666	0.97
8_V	87_F	0.662	0.97
14_I	176_I	0.660	0.97
161_D	164_Y	0.658	0.97
184_P	189_V	0.654	0.97
94_I	113_L	0.653	0.97
174_I	228_F	0.648	0.97
30_W	153_F	0.647	0.97
160_M	164_Y	0.644	0.97
222_S	226_P	0.642	0.97
121_S	126_D	0.642	0.97
47_D	51_V	0.640	0.97
175_A	199_T	0.640	0.97
201_E	216_K	0.636	0.97
34_R	43_G	0.635	0.97
175_A	180_G	0.635	0.97
118_C	144_A	0.632	0.97
156_M	184_P	0.630	0.96
116_V	127_W	0.629	0.96
6_V	87_F	0.628	0.96
44_F	52_Q	0.626	0.96
90_V	163_I	0.625	0.96
86_R	105_N	0.622	0.96
63_Q	66_E	0.612	0.96
96_N	113_L	0.608	0.96
16_A	25_A	0.607	0.96
204_L	218_Y	0.604	0.96
62_L	114_L	0.603	0.96
149_H	158_L	0.602	0.95
183_Y	190_H	0.599	0.95
88_L	105_N	0.595	0.95
43_G	47_D	0.595	0.95
21_R	25_A	0.593	0.95
121_S	125_L	0.591	0.95
91_T	108_H	0.591	0.95
62_L	113_L	0.590	0.95
41_P	44_F	0.587	0.95
152_W	155_E	0.585	0.95
161_D	165_M	0.583	0.95
148_P	155_E	0.582	0.95
7_L	188_F	0.580	0.94
21_R	31_E	0.578	0.94
60_R	66_E	0.575	0.94
121_S	124_V	0.573	0.94
217_Y	228_F	0.573	0.94
87_F	166_A	0.572	0.94
25_A	205_E	0.571	0.94
135_D	138_H	0.569	0.94
38_V	54_F	0.567	0.94
220_P	224_V	0.566	0.94
90_V	166_A	0.565	0.94
9_L	89_L	0.563	0.94
55_Y	150_V	0.562	0.94
40_T	47_D	0.561	0.93
39_A	44_F	0.561	0.93
63_Q	128_T	0.559	0.93
132_T	135_D	0.559	0.93
108_H	114_L	0.558	0.93
48_P	52_Q	0.555	0.93
76_L	87_F	0.555	0.93
6_V	79_L	0.552	0.93
126_D	129_G	0.552	0.93
148_P	152_W	0.548	0.93
8_V	176_I	0.548	0.93
51_V	55_Y	0.547	0.93
44_F	145_P	0.547	0.93
164_Y	188_F	0.544	0.92
163_I	167_L	0.543	0.92
200_V	228_F	0.542	0.92
167_L	189_V	0.541	0.92
173_F	189_V	0.540	0.92
76_L	103_N	0.540	0.92
226_P	230_E	0.539	0.92
193_K	197_A	0.538	0.92
8_V	79_L	0.533	0.92
190_H	209_V	0.533	0.92
43_G	50_L	0.532	0.92
123_Q	126_D	0.529	0.91
173_F	197_A	0.527	0.91
39_A	153_F	0.526	0.91
60_R	63_Q	0.526	0.91
75_A	176_I	0.524	0.91
73_H	92_Q	0.524	0.91
61_Q	66_E	0.523	0.91
204_L	219_G	0.522	0.91
55_Y	152_W	0.521	0.91
168_S	195_H	0.519	0.91
16_A	221_A	0.517	0.90
80_Q	98_H	0.516	0.90
210_G	218_Y	0.516	0.90
12_A	22_T	0.516	0.90
193_K	199_T	0.514	0.90
151_V	182_V	0.514	0.90
26_A	31_E	0.512	0.90
77_A	80_Q	0.511	0.90
44_F	47_D	0.510	0.90
4_P	85_D	0.510	0.90
51_V	150_V	0.507	0.90
130_D	133_P	0.505	0.89
63_Q	114_L	0.505	0.89
200_V	203_N	0.504	0.89
87_F	169_M	0.503	0.89
14_I	70_N	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
1s5pA	1	0.9298	100	0.132	Contact Map
1m2kA	1	0.9752	100	0.137	Contact Map
1yc5A	1	0.905	100	0.14	Contact Map
3riyA	1	0.938	100	0.146	Contact Map
3u31A	1	0.9752	100	0.147	Contact Map
1q14A	3	0.9215	100	0.152	Contact Map
5btrA	1	0.9628	100	0.152	Contact Map
4twjA	1	0.9008	100	0.153	Contact Map
4iaoA	1	0.9711	100	0.156	Contact Map
1q1aA	1	0.9752	100	0.16	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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