NADD - BACSU - GREMLIN Contacts

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NADD - Nicotinate-nucleotide adenylyltransferase

UniProt:	P54455	Sequences: MKKIGIFGGTFDPPHNGHLLMANEVLYQAGLDEIWFMPNQIPPHKQNEDYTDSFHRVEMLKLAIQSNPSFKLELVEMEREGPSYTFDTVSLLKQRYPNDQLFFIIGADMIEYLPKWYKLDELLNLIQFIGVKRPGFHVETPYPLLFADVPEFEVSSTMIRERFKSKKPTDYLIPDKVKKYVEENGLYES	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	189 (184)
Sequences:	4110 (2989)
Seq/√Len:	220.3

ECOLI - NADD
BACSU - NADD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
74_L	78_E	3.968	1.00
33_E	71_K	3.377	1.00
26_L	69_S	2.957	1.00
118_K	121_E	2.939	1.00
12_D	51_T	2.659	1.00
36_F	70_F	2.542	1.00
5_G	31_L	2.518	1.00
29_A	129_I	2.439	1.00
90_S	121_E	2.362	1.00
14_P	60_L	2.360	1.00
58_E	61_K	2.314	1.00
55_H	184_N	2.302	1.00
55_H	180_Y	2.167	1.00
89_V	126_I	2.156	1.00
55_H	58_E	1.980	1.00
57_V	74_L	1.933	1.00
23_N	67_N	1.923	1.00
169_T	173_I	1.903	1.00
22_A	36_F	1.901	1.00
53_S	77_M	1.890	1.00
122_L	128_F	1.861	1.00
59_M	180_Y	1.850	1.00
35_W	73_E	1.847	1.00
90_S	118_K	1.844	1.00
52_D	55_H	1.832	1.00
3_K	100_Q	1.796	1.00
93_K	125_L	1.768	1.00
79_R	87_D	1.768	1.00
62_L	180_Y	1.764	1.00
158_M	162_R	1.752	1.00
14_P	63_A	1.750	1.00
89_V	122_L	1.735	1.00
4_I	99_D	1.735	1.00
75_V	91_L	1.728	1.00
161_E	165_S	1.728	1.00
57_V	72_L	1.712	1.00
103_F	128_F	1.700	1.00
64_I	72_L	1.668	1.00
175_D	178_K	1.593	1.00
163_F	169_T	1.584	1.00
86_F	118_K	1.570	1.00
60_L	72_L	1.551	1.00
86_F	90_S	1.542	1.00
178_K	182_E	1.504	1.00
25_V	104_I	1.485	1.00
36_F	64_I	1.463	1.00
113_L	122_L	1.455	1.00
67_N	171_Y	1.429	1.00
60_L	64_I	1.351	1.00
44_H	115_K	1.347	1.00
35_W	101_L	1.328	1.00
65_Q	176_K	1.324	1.00
100_Q	127_Q	1.304	1.00
169_T	178_K	1.301	1.00
5_G	104_I	1.294	1.00
102_F	129_I	1.289	1.00
10_T	42_P	1.284	1.00
127_Q	145_L	1.264	1.00
35_W	96_Y	1.263	1.00
75_V	95_R	1.262	1.00
58_E	62_L	1.248	1.00
12_D	49_D	1.234	1.00
158_M	161_E	1.231	1.00
57_V	61_K	1.219	1.00
79_R	91_L	1.217	1.00
12_D	50_Y	1.200	1.00
21_M	131_V	1.186	1.00
86_F	125_L	1.170	1.00
121_E	125_L	1.168	1.00
62_L	176_K	1.156	1.00
16_N	174_P	1.139	1.00
113_L	123_L	1.138	1.00
110_I	130_G	1.129	1.00
61_K	74_L	1.126	1.00
179_K	183_E	1.124	1.00
91_L	95_R	1.123	1.00
113_L	119_L	1.122	1.00
35_W	71_K	1.120	1.00
162_R	167_K	1.109	1.00
85_T	103_F	1.103	1.00
112_Y	115_K	1.097	1.00
37_M	75_V	1.092	1.00
7_F	21_M	1.077	1.00
40_Q	80_E	1.072	1.00
20_L	152_F	1.071	1.00
170_D	178_K	1.071	1.00
75_V	79_R	1.069	1.00
86_F	117_Y	1.062	1.00
43_P	83_S	1.049	1.00
134_P	151_E	1.048	1.00
170_D	175_D	1.043	1.00
91_L	94_Q	1.039	1.00
37_M	73_E	1.023	1.00
159_I	173_I	0.998	1.00
123_L	128_F	0.990	1.00
87_D	90_S	0.989	1.00
180_Y	184_N	0.988	1.00
19_L	174_P	0.987	1.00
132_K	148_D	0.981	1.00
45_K	156_S	0.978	1.00
23_N	26_L	0.974	1.00
14_P	59_M	0.973	1.00
25_V	131_V	0.963	1.00
26_L	34_I	0.956	1.00
154_V	172_L	0.953	1.00
40_Q	77_M	0.943	1.00
51_T	186_L	0.940	1.00
3_K	102_F	0.934	1.00
24_E	28_Q	0.929	1.00
86_F	121_E	0.921	0.99
51_T	55_H	0.918	0.99
6_I	37_M	0.912	0.99
96_Y	101_L	0.907	0.99
20_L	23_N	0.901	0.99
109_M	112_Y	0.898	0.99
29_A	145_L	0.896	0.99
25_V	147_A	0.896	0.99
180_Y	186_L	0.891	0.99
121_E	124_N	0.891	0.99
55_H	59_M	0.887	0.99
75_V	92_L	0.878	0.99
31_L	104_I	0.869	0.99
6_I	89_V	0.865	0.99
132_K	151_E	0.858	0.99
90_S	125_L	0.854	0.99
19_L	171_Y	0.853	0.99
173_I	178_K	0.848	0.99
93_K	101_L	0.846	0.99
4_I	101_L	0.843	0.99
14_P	36_F	0.836	0.99
28_Q	148_D	0.831	0.99
131_V	149_V	0.830	0.99
20_L	24_E	0.825	0.99
57_V	77_M	0.820	0.99
19_L	63_A	0.808	0.99
44_H	112_Y	0.802	0.99
40_Q	43_P	0.802	0.99
102_F	127_Q	0.792	0.98
87_D	117_Y	0.792	0.98
127_Q	143_P	0.783	0.98
67_N	70_F	0.782	0.98
81_G	87_D	0.778	0.98
85_T	89_V	0.774	0.98
40_Q	53_S	0.772	0.98
168_P	171_Y	0.769	0.98
38_P	60_L	0.769	0.98
12_D	47_N	0.762	0.98
123_L	144_L	0.761	0.98
129_I	145_L	0.757	0.98
22_A	70_F	0.757	0.98
62_L	177_V	0.753	0.98
162_R	168_P	0.746	0.98
3_K	32_D	0.745	0.98
107_A	136_F	0.743	0.98
162_R	172_L	0.742	0.98
74_L	77_M	0.738	0.97
21_M	149_V	0.736	0.97
19_L	64_I	0.736	0.97
92_L	96_Y	0.734	0.97
23_N	27_Y	0.734	0.97
27_Y	167_K	0.728	0.97
107_A	132_K	0.728	0.97
58_E	180_Y	0.725	0.97
64_I	70_F	0.723	0.97
21_M	25_V	0.721	0.97
42_P	45_K	0.721	0.97
79_R	83_S	0.720	0.97
24_E	150_P	0.716	0.97
134_P	153_E	0.708	0.97
89_V	125_L	0.706	0.97
37_M	92_L	0.702	0.97
10_T	50_Y	0.702	0.97
3_K	30_G	0.700	0.97
12_D	160_R	0.699	0.97
23_N	168_P	0.697	0.96
4_I	35_W	0.692	0.96
31_L	102_F	0.691	0.96
36_F	60_L	0.691	0.96
110_I	144_L	0.689	0.96
16_N	173_I	0.687	0.96
163_F	173_I	0.683	0.96
129_I	147_A	0.681	0.96
37_M	88_T	0.681	0.96
27_Y	168_P	0.678	0.96
63_A	177_V	0.678	0.96
66_S	176_K	0.677	0.96
59_M	177_V	0.675	0.96
76_E	83_S	0.675	0.96
16_N	171_Y	0.673	0.96
168_P	178_K	0.670	0.96
17_G	152_F	0.668	0.96
9_G	15_H	0.664	0.95
6_I	92_L	0.661	0.95
47_N	50_Y	0.661	0.95
54_F	58_E	0.659	0.95
51_T	59_M	0.656	0.95
44_H	109_M	0.656	0.95
113_L	128_F	0.652	0.95
163_F	178_K	0.648	0.95
16_N	20_L	0.648	0.95
76_E	88_T	0.642	0.94
20_L	172_L	0.638	0.94
85_T	122_L	0.636	0.94
54_F	74_L	0.631	0.94
7_F	103_F	0.630	0.94
171_Y	175_D	0.628	0.94
162_R	169_T	0.626	0.94
35_W	92_L	0.626	0.94
105_I	109_M	0.622	0.93
93_K	126_I	0.621	0.93
57_V	60_L	0.620	0.93
107_A	135_G	0.620	0.93
104_I	129_I	0.619	0.93
132_K	149_V	0.619	0.93
25_V	129_I	0.618	0.93
42_P	109_M	0.618	0.93
32_D	99_D	0.615	0.93
16_N	154_V	0.610	0.93
154_V	159_I	0.609	0.93
10_T	39_N	0.608	0.93
63_A	66_S	0.606	0.93
22_A	34_I	0.605	0.93
15_H	84_Y	0.601	0.92
34_I	104_I	0.600	0.92
43_P	82_P	0.598	0.92
41_I	82_P	0.598	0.92
176_K	179_K	0.594	0.92
105_I	110_I	0.594	0.92
158_M	172_L	0.589	0.92
90_S	94_Q	0.589	0.92
107_A	111_E	0.589	0.92
4_I	33_E	0.587	0.91
179_K	182_E	0.585	0.91
24_E	149_V	0.584	0.91
62_L	65_Q	0.583	0.91
78_E	95_R	0.581	0.91
7_F	22_A	0.573	0.90
17_G	154_V	0.572	0.90
152_F	158_M	0.566	0.90
77_M	80_E	0.565	0.90
53_S	57_V	0.557	0.89
20_L	150_P	0.555	0.89
20_L	171_Y	0.548	0.88
10_T	44_H	0.547	0.88
23_N	70_F	0.547	0.88
39_N	83_S	0.546	0.88
107_A	138_V	0.543	0.88
181_V	186_L	0.541	0.88
25_V	29_A	0.540	0.88
25_V	149_V	0.538	0.87
92_L	101_L	0.535	0.87
93_K	100_Q	0.534	0.87
86_F	119_L	0.531	0.87
100_Q	143_P	0.530	0.87
16_N	152_F	0.525	0.86
96_Y	99_D	0.524	0.86
93_K	98_N	0.524	0.86
89_V	93_K	0.524	0.86
119_L	128_F	0.523	0.86
132_K	146_F	0.522	0.86
39_N	43_P	0.521	0.86
159_I	172_L	0.518	0.85
7_F	36_F	0.517	0.85
44_H	119_L	0.516	0.85
29_A	147_A	0.515	0.85
86_F	89_V	0.513	0.85
22_A	60_L	0.508	0.84
6_I	101_L	0.508	0.84
34_I	70_F	0.507	0.84
119_L	123_L	0.506	0.84
16_N	159_I	0.506	0.84
161_E	164_K	0.503	0.84
111_E	114_P	0.503	0.84
7_F	20_L	0.503	0.84
24_E	131_V	0.500	0.83
63_A	174_P	0.500	0.83

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
1k4mA	3	0.9894	100	0.222	Contact Map
4x0eA	1	0.9735	100	0.236	Contact Map
1kqnA	3	0.9788	100	0.244	Contact Map
1yumA	4	0.9947	100	0.25	Contact Map
2qtrA	2	1	100	0.267	Contact Map
1kamA	3	0.9683	100	0.267	Contact Map
4wsoA	1	0.9841	100	0.273	Contact Map
1nupA	4	0.9894	100	0.277	Contact Map
2h29A	2	0.9947	100	0.277	Contact Map
3h05A	2	0.836	100	0.366	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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