NAMA - BACSU - GREMLIN Contacts

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NAMA - NADPH dehydrogenase

UniProt:	P54550	Sequences: MARKLFTPITIKDMTLKNRIVMSPMCMYSSHEKDGKLTPFHMAHYISRAIGQVGLIIVEASAVNPQGRITDQDLGIWSDEHIEGFAKLTEQVKEQGSKIGIQLAHAGRKAELEGDIFAPSAIAFDEQSATPVEMSAEKVKETVQEFKQAAARAKEAGFDVIEIHAAHGYLIHEFLSPLSNHRTDEYGGSPENRYRFLREIIDEVKQVWDGPLFVRVSASDYTDKGLDIADHIGFAKWMKEQGVDLIDCSSGALVHADINVFPGYQVSFAEKIREQADMATGAVGMITDGSMAEEILQNGRADLIFIGRELLRDPFFARTAAKQLNTEIPAPVQYERGW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	338 (324)
Sequences:	11182 (7419)
Seq/√Len:	412.2

ECOLI - FADH NEMA
BACSU - NAMA YQIG
HALSA - Q9HQZ6
SULSO - Q97WT9 Q97X55

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
136_A	185_E	3.594	1.00
202_D	241_Q	3.525	1.00
100_G	160_V	3.123	1.00
64_N	145_E	2.948	1.00
189_S	192_N	2.547	1.00
151_A	207_V	2.520	1.00
147_K	203_E	2.499	1.00
21_V	303_L	2.476	1.00
132_V	138_K	2.455	1.00
10_T	15_T	2.435	1.00
92_V	99_I	2.397	1.00
237_W	240_E	2.393	1.00
9_I	303_L	2.308	1.00
39_P	87_K	2.305	1.00
270_E	300_R	2.296	1.00
134_M	142_T	2.281	1.00
294_E	298_N	2.221	1.00
53_V	310_L	2.160	1.00
93_K	159_D	2.135	1.00
79_D	152_R	2.115	1.00
239_K	277_D	2.100	1.00
213_F	245_L	2.096	1.00
117_F	134_M	2.086	1.00
46_I	95_Q	2.073	1.00
313_D	319_T	2.041	1.00
134_M	138_K	2.017	1.00
154_K	208_W	2.007	1.00
281_G	305_F	1.969	1.00
6_F	321_A	1.951	1.00
46_I	91_Q	1.937	1.00
144_Q	148_Q	1.928	1.00
318_R	322_K	1.903	1.00
151_A	155_E	1.898	1.00
236_K	275_Q	1.893	1.00
121_A	133_E	1.882	1.00
171_I	197_L	1.871	1.00
293_E	297_Q	1.868	1.00
61_S	101_I	1.852	1.00
86_A	90_E	1.844	1.00
148_Q	152_R	1.823	1.00
171_I	196_F	1.821	1.00
4_K	7_T	1.811	1.00
136_A	140_K	1.788	1.00
141_E	145_E	1.786	1.00
13_D	210_G	1.773	1.00
147_K	207_V	1.766	1.00
140_K	199_E	1.727	1.00
82_I	155_E	1.727	1.00
233_G	237_W	1.701	1.00
90_E	94_E	1.686	1.00
186_Y	199_E	1.671	1.00
4_K	293_E	1.659	1.00
192_N	195_R	1.657	1.00
165_A	214_V	1.650	1.00
197_L	214_V	1.648	1.00
115_D	132_V	1.619	1.00
136_A	186_Y	1.612	1.00
89_T	158_F	1.598	1.00
171_I	200_I	1.596	1.00
135_S	138_K	1.591	1.00
136_A	139_V	1.584	1.00
42_M	87_K	1.575	1.00
270_E	274_E	1.574	1.00
79_D	155_E	1.568	1.00
150_A	204_V	1.562	1.00
144_Q	203_E	1.547	1.00
194_Y	237_W	1.540	1.00
66_Q	141_E	1.536	1.00
85_F	158_F	1.535	1.00
324_L	327_E	1.518	1.00
140_K	185_E	1.514	1.00
177_P	225_G	1.513	1.00
39_P	43_A	1.480	1.00
21_V	281_G	1.468	1.00
197_L	234_F	1.466	1.00
122_I	181_H	1.463	1.00
43_A	46_I	1.461	1.00
273_R	302_D	1.456	1.00
316_F	320_A	1.440	1.00
47_S	315_F	1.424	1.00
76_I	101_I	1.412	1.00
198_R	237_W	1.408	1.00
58_V	99_I	1.408	1.00
194_Y	233_G	1.406	1.00
82_I	152_R	1.402	1.00
154_K	210_G	1.396	1.00
148_Q	151_A	1.396	1.00
25_M	307_G	1.374	1.00
17_K	98_K	1.369	1.00
20_I	317_A	1.364	1.00
198_R	241_Q	1.360	1.00
318_R	321_A	1.348	1.00
37_L	85_F	1.347	1.00
22_M	48_R	1.346	1.00
103_L	149_A	1.331	1.00
147_K	151_A	1.330	1.00
190_P	194_Y	1.329	1.00
227_D	230_D	1.325	1.00
165_A	171_I	1.316	1.00
201_I	238_M	1.305	1.00
16_L	55_L	1.305	1.00
271_K	275_Q	1.304	1.00
42_M	91_Q	1.298	1.00
4_K	297_Q	1.293	1.00
286_I	295_I	1.292	1.00
122_I	131_P	1.288	1.00
143_V	203_E	1.287	1.00
76_I	149_A	1.283	1.00
203_E	206_Q	1.270	1.00
289_G	320_A	1.254	1.00
117_F	132_V	1.246	1.00
194_Y	198_R	1.245	1.00
292_A	306_I	1.245	1.00
283_V	305_F	1.241	1.00
147_K	206_Q	1.229	1.00
203_E	207_V	1.228	1.00
271_K	274_E	1.227	1.00
140_K	186_Y	1.221	1.00
46_I	94_E	1.198	1.00
84_G	87_K	1.197	1.00
198_R	202_D	1.196	1.00
36_K	80_E	1.189	1.00
239_K	278_M	1.184	1.00
237_W	241_Q	1.184	1.00
167_H	249_S	1.180	1.00
22_M	56_I	1.179	1.00
118_A	121_A	1.177	1.00
14_M	98_K	1.176	1.00
101_I	153_A	1.175	1.00
42_M	46_I	1.174	1.00
195_R	199_E	1.165	1.00
133_E	183_T	1.164	1.00
144_Q	147_K	1.149	1.00
98_K	159_D	1.145	1.00
282_A	301_A	1.144	1.00
310_L	317_A	1.140	1.00
9_I	279_A	1.131	1.00
123_A	130_T	1.130	1.00
58_V	158_F	1.129	1.00
90_E	93_K	1.129	1.00
138_K	141_E	1.129	1.00
172_H	176_S	1.126	1.00
289_G	323_Q	1.125	1.00
143_V	199_E	1.117	1.00
228_I	271_K	1.116	1.00
190_P	233_G	1.113	1.00
295_I	301_A	1.113	1.00
281_G	303_L	1.107	1.00
93_K	99_I	1.105	1.00
120_S	181_H	1.097	1.00
89_T	99_I	1.096	1.00
165_A	197_L	1.080	1.00
266_V	295_I	1.075	1.00
143_V	147_K	1.070	1.00
82_I	156_A	1.066	1.00
69_I	106_A	1.065	1.00
79_D	83_E	1.064	1.00
37_L	84_G	1.062	1.00
13_D	211_P	1.062	1.00
289_G	293_E	1.057	1.00
208_W	212_L	1.056	1.00
119_P	179_S	1.055	1.00
27_M	40_F	1.054	1.00
38_T	41_H	1.046	1.00
233_G	236_K	1.046	1.00
214_V	243_V	1.045	1.00
87_K	90_E	1.044	1.00
10_T	13_D	1.042	1.00
185_E	195_R	1.037	1.00
35_G	68_R	1.030	1.00
62_A	73_D	1.027	1.00
202_D	206_Q	1.024	1.00
145_E	148_Q	1.023	1.00
74_L	85_F	1.020	1.00
148_Q	207_V	1.015	1.00
22_M	310_L	1.002	1.00
89_T	156_A	0.999	1.00
4_K	296_L	0.997	1.00
232_I	275_Q	0.990	1.00
16_L	54_G	0.990	1.00
214_V	238_M	0.986	1.00
12_K	244_D	0.976	1.00
140_K	143_V	0.973	1.00
143_V	200_I	0.972	1.00
228_I	232_I	0.968	1.00
194_Y	234_F	0.965	1.00
201_I	243_V	0.964	1.00
16_L	21_V	0.962	1.00
108_R	179_S	0.960	1.00
139_V	143_V	0.958	1.00
42_M	88_L	0.957	1.00
16_L	303_L	0.950	1.00
121_A	130_T	0.947	1.00
175_L	197_L	0.942	1.00
232_I	236_K	0.939	1.00
178_L	224_K	0.938	1.00
18_N	54_G	0.938	1.00
75_G	81_H	0.937	1.00
301_A	304_I	0.933	1.00
232_I	271_K	0.932	1.00
53_V	317_A	0.931	1.00
20_I	316_F	0.928	1.00
216_V	231_H	0.926	1.00
76_I	153_A	0.921	1.00
163_I	204_V	0.920	1.00
52_Q	318_R	0.917	1.00
162_E	247_D	0.916	1.00
154_K	209_D	0.915	1.00
100_G	211_P	0.913	1.00
137_E	140_K	0.911	1.00
286_I	304_I	0.911	1.00
78_S	81_H	0.904	1.00
99_I	158_F	0.899	1.00
36_K	81_H	0.898	1.00
160_V	213_F	0.898	1.00
186_Y	202_D	0.897	1.00
205_K	244_D	0.894	1.00
86_A	155_E	0.894	1.00
17_K	97_S	0.891	1.00
37_L	74_L	0.886	1.00
190_P	237_W	0.884	1.00
204_V	212_L	0.884	1.00
23_S	247_D	0.884	1.00
117_F	138_K	0.881	1.00
99_I	159_D	0.881	1.00
190_P	230_D	0.881	1.00
143_V	196_F	0.878	1.00
170_L	196_F	0.877	1.00
293_E	296_L	0.877	1.00
150_A	208_W	0.876	1.00
290_S	323_Q	0.874	1.00
267_S	270_E	0.873	1.00
60_A	104_A	0.869	1.00
246_I	278_M	0.867	1.00
201_I	241_Q	0.866	1.00
55_L	100_G	0.866	1.00
263_G	291_M	0.861	1.00
199_E	202_D	0.860	1.00
83_E	86_A	0.859	1.00
13_D	209_D	0.858	1.00
140_K	203_E	0.857	1.00
5_L	292_A	0.856	1.00
163_I	200_I	0.849	1.00
9_I	12_K	0.846	1.00
194_Y	197_L	0.844	1.00
55_L	160_V	0.836	1.00
235_A	246_I	0.835	1.00
23_S	307_G	0.834	1.00
143_V	186_Y	0.830	1.00
14_M	100_G	0.828	1.00
23_S	305_F	0.826	1.00
226_L	234_F	0.818	1.00
135_S	140_K	0.817	1.00
306_I	309_E	0.816	1.00
286_I	292_A	0.816	1.00
22_M	25_M	0.813	1.00
39_P	42_M	0.813	1.00
57_I	100_G	0.810	1.00
62_A	68_R	0.808	1.00
245_L	281_G	0.808	1.00
215_R	247_D	0.803	1.00
191_E	233_G	0.803	1.00
100_G	213_F	0.800	1.00
62_A	77_W	0.800	1.00
37_L	88_L	0.797	1.00
315_F	319_T	0.796	1.00
51_G	318_R	0.795	1.00
91_Q	95_Q	0.792	1.00
236_K	240_E	0.792	1.00
133_E	181_H	0.792	1.00
121_A	181_H	0.791	1.00
17_K	52_Q	0.790	1.00
185_E	192_N	0.789	1.00
250_S	265_Q	0.786	1.00
136_A	143_V	0.783	1.00
109_K	124_F	0.783	1.00
205_K	212_L	0.782	1.00
14_M	211_P	0.782	1.00
218_A	248_C	0.776	1.00
22_M	53_V	0.773	1.00
142_T	145_E	0.772	1.00
106_A	110_A	0.772	1.00
58_V	101_I	0.771	1.00
132_V	135_S	0.768	1.00
147_K	200_I	0.767	1.00
43_A	47_S	0.764	1.00
163_I	201_I	0.761	1.00
248_C	280_T	0.761	1.00
196_F	200_I	0.761	1.00
290_S	294_E	0.756	1.00
77_W	81_H	0.752	1.00
115_D	129_A	0.752	1.00
57_I	160_V	0.752	1.00
30_S	41_H	0.747	1.00
188_G	193_R	0.746	1.00
306_I	310_L	0.746	1.00
152_R	155_E	0.745	1.00
63_V	146_F	0.744	1.00
154_K	207_V	0.742	1.00
58_V	85_F	0.740	1.00
108_R	131_P	0.736	1.00
272_I	276_A	0.727	1.00
78_S	82_I	0.727	1.00
91_Q	94_E	0.724	1.00
172_H	231_H	0.723	1.00
125_D	224_K	0.721	1.00
134_M	139_V	0.718	1.00
164_H	169_Y	0.718	1.00
306_I	316_F	0.716	1.00
266_V	282_A	0.715	1.00
230_D	233_G	0.713	1.00
226_L	231_H	0.712	1.00
248_C	272_I	0.712	1.00
64_N	142_T	0.710	1.00
120_S	133_E	0.706	1.00
292_A	320_A	0.704	1.00
14_M	160_V	0.704	1.00
21_V	57_I	0.702	1.00
139_V	197_L	0.697	1.00
226_L	229_A	0.697	1.00
45_Y	56_I	0.696	1.00
51_G	317_A	0.696	1.00
247_D	305_F	0.695	1.00
86_A	89_T	0.695	1.00
178_L	222_T	0.694	1.00
191_E	237_W	0.693	1.00
109_K	223_D	0.690	1.00
235_A	276_A	0.688	1.00
44_H	48_R	0.685	1.00
63_V	200_I	0.684	1.00
49_A	95_Q	0.681	1.00
229_A	232_I	0.680	1.00
151_A	154_K	0.680	1.00
16_L	98_K	0.680	1.00
49_A	92_V	0.678	1.00
15_T	98_K	0.678	1.00
93_K	98_K	0.676	1.00
83_E	87_K	0.676	1.00
21_V	55_L	0.673	0.99
36_K	78_S	0.670	0.99
235_A	272_I	0.669	0.99
118_A	179_S	0.669	0.99
226_L	230_D	0.669	0.99
20_I	53_V	0.667	0.99
63_V	145_E	0.666	0.99
11_I	279_A	0.666	0.99
92_V	97_S	0.665	0.99
188_G	192_N	0.663	0.99
276_A	279_A	0.661	0.99
64_N	141_E	0.660	0.99
213_F	281_G	0.659	0.99
36_K	84_G	0.653	0.99
147_K	204_V	0.650	0.99
291_M	294_E	0.650	0.99
291_M	295_I	0.648	0.99
63_V	104_A	0.648	0.99
273_R	276_A	0.648	0.99
24_P	215_R	0.648	0.99
101_I	158_F	0.646	0.99
287_T	291_M	0.644	0.99
67_G	105_H	0.643	0.99
214_V	246_I	0.642	0.99
201_I	214_V	0.639	0.99
61_S	76_I	0.639	0.99
65_P	77_W	0.637	0.99
288_D	291_M	0.636	0.99
33_K	72_Q	0.636	0.99
294_E	297_Q	0.635	0.99
53_V	56_I	0.634	0.99
175_L	194_Y	0.633	0.99
309_E	316_F	0.633	0.99
164_H	167_H	0.633	0.99
17_K	321_A	0.626	0.99
6_F	317_A	0.626	0.99
8_P	15_T	0.625	0.99
30_S	74_L	0.624	0.99
247_D	283_V	0.623	0.99
21_V	305_F	0.622	0.99
239_K	276_A	0.622	0.99
295_I	300_R	0.619	0.99
201_I	212_L	0.618	0.99
245_L	303_L	0.616	0.99
185_E	199_E	0.614	0.99
48_R	315_F	0.612	0.99
172_H	220_D	0.612	0.99
108_R	173_E	0.610	0.99
119_P	122_I	0.607	0.99
190_P	226_L	0.606	0.99
175_L	234_F	0.604	0.99
117_F	142_T	0.604	0.99
211_P	244_D	0.598	0.99
87_K	91_Q	0.595	0.99
118_A	131_P	0.594	0.99
122_I	179_S	0.593	0.99
76_I	81_H	0.588	0.99
55_L	98_K	0.587	0.99
140_K	144_Q	0.586	0.99
296_L	304_I	0.586	0.99
205_K	208_W	0.586	0.99
234_F	237_W	0.585	0.99
318_R	324_L	0.585	0.99
312_R	327_E	0.584	0.99
82_I	89_T	0.583	0.99
200_I	203_E	0.582	0.99
23_S	57_I	0.581	0.99
76_I	152_R	0.581	0.99
220_D	253_L	0.581	0.99
146_F	171_I	0.580	0.99
238_M	243_V	0.580	0.99
66_Q	142_T	0.579	0.98
306_I	320_A	0.578	0.98
136_A	199_E	0.577	0.98
171_I	204_V	0.576	0.98
134_M	170_L	0.573	0.98
309_E	312_R	0.572	0.98
121_A	131_P	0.571	0.98
315_F	318_R	0.569	0.98
105_H	142_T	0.569	0.98
211_P	245_L	0.567	0.98
142_T	170_L	0.565	0.98
149_A	152_R	0.564	0.98
266_V	269_A	0.557	0.98
198_R	233_G	0.555	0.98
82_I	86_A	0.553	0.98
162_E	213_F	0.549	0.98
147_K	208_W	0.548	0.98
17_K	96_G	0.548	0.98
294_E	300_R	0.548	0.98
110_A	116_I	0.547	0.98
74_L	88_L	0.544	0.98
66_Q	145_E	0.543	0.98
296_L	301_A	0.542	0.98
163_I	212_L	0.542	0.98
268_F	271_K	0.541	0.98
26_C	69_I	0.539	0.98
139_V	171_I	0.539	0.98
73_D	106_A	0.538	0.98
218_A	268_F	0.538	0.98
187_G	193_R	0.537	0.98
62_A	106_A	0.535	0.97
41_H	59_E	0.535	0.97
213_F	247_D	0.535	0.97
11_I	16_L	0.534	0.97
205_K	209_D	0.533	0.97
219_S	268_F	0.533	0.97
319_T	324_L	0.532	0.97
248_C	282_A	0.531	0.97
37_L	41_H	0.531	0.97
123_A	128_S	0.531	0.97
83_E	90_E	0.528	0.97
204_V	208_W	0.527	0.97
190_P	234_F	0.526	0.97
119_P	173_E	0.525	0.97
142_T	146_F	0.523	0.97
25_M	311_L	0.521	0.97
124_F	129_A	0.521	0.97
161_I	208_W	0.518	0.97
139_V	186_Y	0.517	0.97
52_Q	321_A	0.516	0.97
289_G	316_F	0.515	0.97
231_H	235_A	0.514	0.97
270_E	273_R	0.514	0.97
216_V	248_C	0.514	0.97
58_V	61_S	0.510	0.97
69_I	73_D	0.510	0.97
51_G	315_F	0.509	0.97
136_A	184_D	0.509	0.97
125_D	128_S	0.509	0.97
269_A	280_T	0.507	0.97
176_S	220_D	0.507	0.97
231_H	272_I	0.506	0.96
292_A	304_I	0.506	0.96
204_V	207_V	0.506	0.96
267_S	271_K	0.506	0.96
201_I	205_K	0.505	0.96
124_F	128_S	0.505	0.96
250_S	268_F	0.504	0.96
220_D	251_G	0.504	0.96
89_T	101_I	0.502	0.96
235_A	275_Q	0.502	0.96
209_D	242_G	0.502	0.96
100_G	244_D	0.502	0.96
217_S	220_D	0.500	0.96
44_H	59_E	0.500	0.96
69_I	104_A	0.500	0.96
24_P	247_D	0.500	0.96

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
3k30A	2	0.9822	100	0.218	Contact Map
2hsaB	2	0.9822	100	0.221	Contact Map
1o94A	2	0.9822	100	0.223	Contact Map
4qnwA	1	0.9793	100	0.23	Contact Map
3tjlA	2	0.9941	100	0.231	Contact Map
4tmbA	2	0.9941	100	0.232	Contact Map
4e2bA	1	0.9675	100	0.233	Contact Map
3l5aA	1	0.9882	100	0.235	Contact Map
4gbuA	2	0.9882	100	0.238	Contact Map
1ps9A	1	0.9911	100	0.24	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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