NAGD - ECOLI - GREMLIN Contacts

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NAGD - Ribonucleotide monophosphatase NagD

UniProt:	P0AF24	Sequences: MTIKNVICDIDGVLMHDNVAVPGAAEFLHGIMDKGLPLVLLTNYPSQTGQDLANRFATAGVDVPDSVFYTSAMATADFLRRQEGKKAYVVGEGALIHELYKAGFTITDVNPDFVIVGETRSYNWDMMHKAAYFVANGARFIATNPDTHGRGFYPACGALCAGIEKISGRKPFYVGKPSPWIIRAALNKMQAHSEETVIVGDNLRTDILAGFQAGLETILVLSGVSSLDDIDSMPFRPSWIYPSVAEIDVI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10634
Length:	250 (243)
Sequences:	4232 (2890)
Seq/√Len:	185.4

ECOLI - NAGD
BACSU - YUTF ARAL
HALSA - Q9HRF8 Q9HR34
SULSO - Q97W80

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_K	195_E	5.206	1.00
210_G	217_T	5.122	1.00
32_M	67_V	3.325	1.00
197_V	218_I	3.307	1.00
208_L	212_Q	2.985	1.00
179_P	183_R	2.892	1.00
142_A	160_C	2.831	1.00
216_E	238_S	2.817	1.00
50_Q	65_D	2.396	1.00
164_E	170_K	2.340	1.00
86_K	105_T	2.320	1.00
30_G	34_K	2.246	1.00
5_N	189_M	2.239	1.00
164_E	171_P	2.233	1.00
243_S	246_E	2.006	1.00
207_I	217_T	1.991	1.00
30_G	33_D	1.975	1.00
54_N	58_T	1.837	1.00
242_P	246_E	1.833	1.00
29_H	33_D	1.829	1.00
191_A	196_T	1.814	1.00
140_F	171_P	1.811	1.00
147_T	165_K	1.761	1.00
221_L	242_P	1.749	1.00
20_A	25_A	1.700	1.00
186_L	196_T	1.699	1.00
198_I	215_L	1.694	1.00
50_Q	54_N	1.634	1.00
8_C	199_V	1.627	1.00
75_T	115_I	1.613	1.00
39_V	188_K	1.605	1.00
89_V	99_L	1.601	1.00
226_S	229_D	1.596	1.00
16_H	19_V	1.563	1.00
161_A	164_E	1.547	1.00
182_I	209_A	1.546	1.00
211_F	238_S	1.530	1.00
221_L	240_I	1.517	1.00
46_S	118_E	1.514	1.00
7_I	41_L	1.511	1.00
53_A	65_D	1.501	1.00
225_S	229_D	1.498	1.00
10_I	40_L	1.488	1.00
75_T	141_I	1.473	1.00
225_S	230_I	1.465	1.00
14_L	40_L	1.458	1.00
123_N	126_M	1.450	1.00
10_I	15_M	1.446	1.00
182_I	198_I	1.442	1.00
5_N	191_A	1.440	1.00
49_G	73_M	1.437	1.00
119_T	126_M	1.429	1.00
139_R	172_F	1.424	1.00
25_A	29_H	1.418	1.00
161_A	165_K	1.416	1.00
21_V	243_S	1.386	1.00
4_K	36_L	1.380	1.00
76_A	102_A	1.373	1.00
92_E	120_R	1.368	1.00
26_E	245_A	1.357	1.00
85_K	112_D	1.353	1.00
93_G	97_H	1.341	1.00
6_V	197_V	1.339	1.00
141_I	174_V	1.336	1.00
132_Y	135_A	1.317	1.00
31_I	36_L	1.315	1.00
29_H	62_D	1.309	1.00
178_S	212_Q	1.309	1.00
86_K	112_D	1.297	1.00
82_Q	139_R	1.294	1.00
218_I	241_Y	1.293	1.00
183_R	193_S	1.287	1.00
134_V	163_I	1.277	1.00
51_D	54_N	1.259	1.00
184_A	187_N	1.254	1.00
6_V	36_L	1.252	1.00
53_A	57_A	1.252	1.00
48_T	51_D	1.237	1.00
47_Q	55_R	1.232	1.00
221_L	225_S	1.228	1.00
192_H	195_E	1.212	1.00
208_L	235_F	1.209	1.00
14_L	61_V	1.207	1.00
227_L	231_D	1.206	1.00
57_A	65_D	1.192	1.00
87_A	104_F	1.189	1.00
26_E	29_H	1.182	1.00
77_D	81_R	1.178	1.00
37_P	67_V	1.174	1.00
32_M	38_L	1.174	1.00
74_A	181_I	1.172	1.00
14_L	28_L	1.169	1.00
8_C	27_F	1.168	1.00
54_N	57_A	1.163	1.00
53_A	68_F	1.155	1.00
221_L	227_L	1.145	1.00
64_P	67_V	1.141	1.00
97_H	100_Y	1.135	1.00
134_V	167_S	1.129	1.00
49_G	98_E	1.122	1.00
24_A	61_V	1.121	1.00
7_I	185_A	1.113	1.00
72_A	76_A	1.112	1.00
6_V	31_I	1.111	1.00
10_I	13_V	1.106	1.00
132_Y	153_Y	1.102	1.00
182_I	215_L	1.089	1.00
169_R	172_F	1.088	1.00
227_L	242_P	1.086	1.00
25_A	61_V	1.081	1.00
127_M	162_G	1.072	1.00
80_R	104_F	1.059	1.00
116_V	160_C	1.057	1.00
128_H	153_Y	1.053	1.00
128_H	154_P	1.052	1.00
23_G	26_E	1.048	1.00
216_E	239_W	1.035	1.00
185_A	189_M	1.034	1.00
39_V	189_M	1.032	1.00
111_P	133_F	1.031	1.00
202_N	205_T	1.029	1.00
40_L	63_V	1.029	1.00
219_L	225_S	1.029	1.00
5_N	37_P	1.019	1.00
183_R	187_N	1.015	1.00
147_T	161_A	1.013	0.99
45_P	71_S	1.003	0.99
129_K	133_F	1.002	0.99
20_A	59_A	1.001	0.99
230_I	237_P	0.999	0.99
197_V	216_E	0.997	0.99
8_C	38_L	0.992	0.99
42_T	70_T	0.990	0.99
69_Y	184_A	0.985	0.99
202_N	224_V	0.979	0.99
90_V	130_A	0.979	0.99
75_T	143_T	0.976	0.99
132_Y	150_R	0.970	0.99
69_Y	185_A	0.969	0.99
145_P	173_Y	0.966	0.99
113_F	139_R	0.965	0.99
8_C	244_V	0.964	0.99
38_L	67_V	0.964	0.99
88_Y	133_F	0.961	0.99
118_E	122_Y	0.960	0.99
99_L	115_I	0.954	0.99
77_D	184_A	0.953	0.99
78_F	174_V	0.951	0.99
41_L	198_I	0.951	0.99
130_A	163_I	0.949	0.99
160_C	173_Y	0.940	0.99
78_F	141_I	0.938	0.99
18_N	58_T	0.937	0.99
21_V	24_A	0.930	0.99
75_T	174_V	0.926	0.99
32_M	62_D	0.920	0.99
211_F	217_T	0.919	0.99
17_D	149_G	0.918	0.99
147_T	204_R	0.917	0.99
142_A	156_C	0.916	0.99
134_V	137_G	0.913	0.99
230_I	240_I	0.908	0.99
57_A	62_D	0.902	0.99
50_Q	97_H	0.899	0.99
52_L	68_F	0.896	0.99
13_V	118_E	0.892	0.99
55_R	59_A	0.891	0.99
5_N	196_T	0.890	0.99
81_R	187_N	0.889	0.99
18_N	55_R	0.888	0.99
128_H	132_Y	0.885	0.99
131_A	166_I	0.885	0.99
23_G	245_A	0.882	0.99
204_R	224_V	0.880	0.99
15_M	59_A	0.880	0.99
146_D	205_T	0.876	0.99
100_Y	106_I	0.874	0.99
86_K	110_N	0.869	0.98
69_Y	188_K	0.866	0.98
142_A	173_Y	0.864	0.98
96_I	106_I	0.861	0.98
207_I	211_F	0.861	0.98
156_C	160_C	0.858	0.98
96_I	100_Y	0.857	0.98
41_L	181_I	0.853	0.98
13_V	182_I	0.852	0.98
228_D	231_D	0.843	0.98
39_V	67_V	0.843	0.98
93_G	96_I	0.842	0.98
84_G	105_T	0.838	0.98
37_P	189_M	0.837	0.98
52_L	70_T	0.836	0.98
203_L	233_M	0.836	0.98
97_H	101_K	0.832	0.98
114_V	130_A	0.827	0.98
94_A	98_E	0.824	0.98
86_K	107_T	0.822	0.98
15_M	40_L	0.822	0.98
76_A	80_R	0.819	0.98
158_A	162_G	0.804	0.97
87_A	115_I	0.803	0.97
125_D	129_K	0.802	0.97
28_L	40_L	0.799	0.97
14_L	244_V	0.795	0.97
158_A	165_K	0.793	0.97
23_G	243_S	0.793	0.97
186_L	215_L	0.791	0.97
24_A	244_V	0.791	0.97
219_L	240_I	0.785	0.97
73_M	98_E	0.785	0.97
191_A	195_E	0.784	0.97
63_V	67_V	0.774	0.97
13_V	209_A	0.772	0.97
72_A	75_T	0.770	0.97
184_A	188_K	0.768	0.97
76_A	98_E	0.765	0.97
211_F	235_F	0.764	0.97
172_F	180_W	0.764	0.97
39_V	69_Y	0.761	0.96
186_L	193_S	0.760	0.96
40_L	61_V	0.759	0.96
227_L	230_I	0.758	0.96
89_V	96_I	0.758	0.96
148_H	152_F	0.754	0.96
116_V	140_F	0.753	0.96
217_T	238_S	0.750	0.96
82_Q	172_F	0.740	0.96
122_Y	159_L	0.738	0.96
22_P	245_A	0.737	0.96
79_L	104_F	0.736	0.96
32_M	64_P	0.735	0.96
47_Q	52_L	0.735	0.96
98_E	101_K	0.733	0.96
185_A	209_A	0.733	0.96
198_I	209_A	0.722	0.95
158_A	166_I	0.720	0.95
134_V	169_R	0.718	0.95
197_V	239_W	0.718	0.95
122_Y	127_M	0.717	0.95
7_I	196_T	0.716	0.95
88_Y	114_V	0.712	0.95
10_I	14_L	0.712	0.95
138_A	169_R	0.710	0.95
74_A	184_A	0.708	0.95
27_F	38_L	0.707	0.95
55_R	58_T	0.707	0.95
24_A	243_S	0.707	0.95
45_P	117_G	0.705	0.95
134_V	140_F	0.703	0.95
20_A	61_V	0.701	0.94
122_Y	126_M	0.699	0.94
88_Y	130_A	0.698	0.94
71_S	144_N	0.694	0.94
51_D	97_H	0.692	0.94
25_A	60_G	0.688	0.94
79_L	115_I	0.687	0.94
116_V	142_A	0.682	0.94
85_K	104_F	0.680	0.93
10_I	56_F	0.679	0.93
16_H	21_V	0.679	0.93
71_S	143_T	0.675	0.93
57_A	63_V	0.671	0.93
8_C	14_L	0.667	0.93
20_A	60_G	0.667	0.93
91_G	95_L	0.665	0.93
15_M	56_F	0.663	0.93
116_V	159_L	0.661	0.93
131_A	135_A	0.660	0.92
136_N	194_E	0.655	0.92
51_D	94_A	0.655	0.92
127_M	131_A	0.652	0.92
162_G	165_K	0.651	0.92
237_P	240_I	0.651	0.92
42_T	52_L	0.650	0.92
220_V	223_G	0.647	0.92
78_F	113_F	0.646	0.92
133_F	136_N	0.644	0.92
198_I	210_G	0.643	0.91
118_E	159_L	0.642	0.91
148_H	202_N	0.638	0.91
77_D	80_R	0.634	0.91
76_A	104_F	0.633	0.91
182_I	185_A	0.631	0.91
192_H	196_T	0.627	0.90
77_D	188_K	0.626	0.90
10_I	52_L	0.626	0.90
182_I	210_G	0.624	0.90
115_I	141_I	0.622	0.90
44_Y	52_L	0.620	0.90
78_F	82_Q	0.620	0.90
145_P	160_C	0.617	0.90
53_A	64_P	0.613	0.89
80_R	102_A	0.612	0.89
219_L	222_S	0.612	0.89
50_Q	101_K	0.611	0.89
140_F	169_R	0.611	0.89
78_F	172_F	0.608	0.89
7_I	181_I	0.608	0.89
16_H	155_A	0.607	0.89
95_L	143_T	0.606	0.89
32_M	40_L	0.604	0.89
148_H	224_V	0.601	0.88
108_D	129_K	0.600	0.88
88_Y	126_M	0.598	0.88
203_L	207_I	0.598	0.88
122_Y	162_G	0.597	0.88
203_L	211_F	0.596	0.88
87_A	91_G	0.595	0.88
144_N	156_C	0.592	0.88
145_P	164_E	0.590	0.88
9_D	12_G	0.586	0.87
145_P	178_S	0.585	0.87
186_L	213_A	0.583	0.87
5_N	39_V	0.578	0.86
28_L	32_M	0.576	0.86
193_S	215_L	0.576	0.86
131_A	163_I	0.574	0.86
107_T	111_P	0.570	0.86
139_R	169_R	0.569	0.86
24_A	28_L	0.569	0.86
8_C	28_L	0.569	0.86
127_M	163_I	0.565	0.85
132_Y	152_F	0.564	0.85
108_D	111_P	0.564	0.85
74_A	174_V	0.563	0.85
15_M	55_R	0.563	0.85
137_G	169_R	0.563	0.85
7_I	215_L	0.562	0.85
182_I	213_A	0.561	0.85
26_E	30_G	0.560	0.85
66_S	188_K	0.556	0.84
27_F	245_A	0.555	0.84
229_D	232_S	0.552	0.84
48_T	94_A	0.550	0.84
27_F	31_I	0.548	0.83
31_I	35_G	0.543	0.83
220_V	241_Y	0.542	0.83
134_V	138_A	0.541	0.83
18_N	59_A	0.541	0.83
10_I	205_T	0.541	0.83
183_R	186_L	0.536	0.82
128_H	131_A	0.535	0.82
77_D	187_N	0.534	0.82
47_Q	51_D	0.533	0.82
187_N	190_Q	0.533	0.82
114_V	117_G	0.532	0.82
179_P	213_A	0.530	0.81
69_Y	74_A	0.526	0.81
180_W	183_R	0.523	0.81
119_T	124_W	0.523	0.81
4_K	196_T	0.521	0.80
92_E	95_L	0.518	0.80
218_I	239_W	0.516	0.80
14_L	20_A	0.515	0.80
39_V	185_A	0.514	0.79
228_D	232_S	0.514	0.79
160_C	164_E	0.513	0.79
77_D	102_A	0.506	0.78
7_I	198_I	0.505	0.78
154_P	158_A	0.503	0.78
13_V	152_F	0.502	0.78
204_R	208_L	0.501	0.78
89_V	92_E	0.500	0.78
130_A	134_V	0.500	0.78

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
3kc2A	2	0.972	100	0.37	Contact Map
2ho4A	1	0.976	100	0.405	Contact Map
1zjjA	2	0.984	100	0.446	Contact Map
4i9fA	2	0.98	100	0.469	Contact Map
2oycA	2	1	100	0.478	Contact Map
2c4nA	3	1	100	0.487	Contact Map
3pdwA	1	0.976	100	0.499	Contact Map
3eprA	3	1	100	0.5	Contact Map
1vjrA	1	1	100	0.502	Contact Map
1yv9A	2	1	100	0.518	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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