RIBD - BACSU - GREMLIN Contacts

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RIBD - Riboflavin biosynthesis protein RibD

UniProt:	P17618	Sequences: MEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHAEVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMRDPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTLKAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADNPSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEEKKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFVKEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGRDIKLTAKPTKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	361 (350)
Sequences:	3021 (2300)
Seq/√Len:	122.9

ECOLI - RIBD
BACSU - RIBD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_L	39_M	4.217	1.00
98_A	130_A	3.883	1.00
85_E	113_M	3.733	1.00
67_I	87_I	3.449	1.00
112_S	116_E	3.396	1.00
97_V	111_I	3.163	1.00
242_F	275_V	3.035	1.00
66_D	96_F	2.950	1.00
99_M	138_L	2.874	1.00
261_N	282_E	2.849	1.00
127_A	131_E	2.824	1.00
149_T	186_H	2.758	1.00
131_E	142_R	2.669	1.00
85_E	89_N	2.594	1.00
178_D	311_Y	2.530	1.00
63_E	91_G	2.520	1.00
139_H	306_Q	2.411	1.00
289_V	299_F	2.385	1.00
44_K	47_E	2.312	1.00
75_S	84_A	2.308	1.00
88_I	113_M	2.253	1.00
28_A	67_I	2.242	1.00
94_R	120_E	2.232	1.00
200_N	230_K	2.208	1.00
21_E	187_Q	2.204	1.00
215_V	240_W	2.168	1.00
278_I	282_E	2.152	1.00
67_I	92_I	2.149	1.00
139_H	143_T	2.145	1.00
5_Y	36_I	2.072	1.00
135_E	307_E	2.071	1.00
122_R	125_I	2.041	1.00
172_S	350_R	1.999	1.00
139_H	145_L	1.946	1.00
272_I	304_C	1.930	1.00
315_K	339_L	1.925	1.00
193_V	197_K	1.919	1.00
75_S	109_R	1.918	1.00
278_I	281_E	1.915	1.00
148_V	276_L	1.899	1.00
182_Y	288_Y	1.885	1.00
100_R	111_I	1.823	1.00
30_V	67_I	1.789	1.00
190_L	295_V	1.775	1.00
154_A	312_F	1.763	1.00
9_A	70_T	1.758	1.00
188_S	217_V	1.749	1.00
88_I	119_I	1.748	1.00
299_F	304_C	1.741	1.00
191_V	291_G	1.738	1.00
202_S	230_K	1.728	1.00
43_L	53_H	1.727	1.00
242_F	278_I	1.714	1.00
45_Y	79_K	1.701	1.00
86_L	90_S	1.699	1.00
55_I	62_A	1.692	1.00
197_K	224_S	1.692	1.00
342_F	356_A	1.681	1.00
77_Y	85_E	1.672	1.00
35_Q	61_H	1.653	1.00
193_V	225_I	1.645	1.00
112_S	115_K	1.639	1.00
309_I	353_K	1.621	1.00
315_K	337_V	1.615	1.00
145_L	277_K	1.611	1.00
17_E	185_T	1.607	1.00
172_S	175_A	1.604	1.00
94_R	122_R	1.596	1.00
87_I	92_I	1.567	1.00
344_D	355_T	1.527	1.00
15_Q	41_A	1.523	1.00
150_L	296_H	1.520	1.00
155_S	317_I	1.517	1.00
135_E	147_Y	1.517	1.00
7_K	126_L	1.513	1.00
204_T	237_A	1.506	1.00
219_L	295_V	1.495	1.00
194_G	198_A	1.491	1.00
155_S	315_K	1.490	1.00
276_L	299_F	1.488	1.00
103_N	141_M	1.486	1.00
169_W	176_R	1.477	1.00
196_V	231_V	1.474	1.00
172_S	351_D	1.457	1.00
84_A	113_M	1.446	1.00
215_V	284_I	1.444	1.00
311_Y	353_K	1.438	1.00
182_Y	309_I	1.437	1.00
75_S	113_M	1.430	1.00
166_D	334_M	1.429	1.00
160_I	293_S	1.411	1.00
307_E	355_T	1.395	1.00
252_K	256_S	1.394	1.00
174_A	349_G	1.370	1.00
84_A	88_I	1.358	1.00
48_A	56_H	1.354	1.00
100_R	123_E	1.334	1.00
191_V	196_V	1.333	1.00
243_T	262_I	1.332	1.00
178_D	353_K	1.332	1.00
126_L	129_Q	1.325	1.00
218_I	231_V	1.318	1.00
223_L	243_T	1.317	1.00
132_R	135_E	1.311	1.00
171_T	175_A	1.306	1.00
55_I	86_L	1.296	1.00
166_D	333_S	1.292	1.00
20_T	45_Y	1.292	1.00
7_K	129_Q	1.286	1.00
147_Y	307_E	1.281	1.00
221_T	244_T	1.280	1.00
38_G	57_M	1.278	1.00
154_A	325_L	1.276	1.00
193_V	224_S	1.271	1.00
219_L	275_V	1.264	1.00
77_Y	81_P	1.258	1.00
266_E	274_D	1.258	1.00
238_P	261_N	1.255	1.00
58_A	62_A	1.250	1.00
5_Y	31_V	1.232	0.99
225_I	241_I	1.226	0.99
138_L	142_R	1.225	0.99
218_I	225_I	1.224	0.99
140_F	280_A	1.219	0.99
317_I	334_M	1.216	0.99
190_L	299_F	1.214	0.99
197_K	226_P	1.207	0.99
244_T	270_I	1.203	0.99
184_K	205_C	1.193	0.99
340_L	356_A	1.192	0.99
152_A	310_F	1.186	0.99
99_M	131_E	1.182	0.99
190_L	219_L	1.180	0.99
220_D	224_S	1.175	0.99
140_F	285_M	1.174	0.99
124_G	127_A	1.169	0.99
111_I	123_E	1.164	0.99
252_K	264_T	1.160	0.99
17_E	25_L	1.158	0.99
178_D	346_T	1.151	0.99
16_G	19_Q	1.151	0.99
8_L	36_I	1.140	0.99
37_V	61_H	1.139	0.99
28_A	87_I	1.134	0.99
37_V	62_A	1.133	0.99
19_Q	184_K	1.133	0.99
32_K	61_H	1.128	0.99
150_L	300_V	1.128	0.99
227_E	254_R	1.110	0.99
149_T	309_I	1.110	0.99
152_A	296_H	1.110	0.99
242_F	263_F	1.105	0.99
31_V	68_Y	1.101	0.99
52_V	56_H	1.100	0.99
166_D	335_K	1.095	0.99
109_R	113_M	1.093	0.99
48_A	53_H	1.089	0.99
48_A	52_V	1.088	0.99
197_K	220_D	1.079	0.99
150_L	305_F	1.078	0.99
157_D	318_G	1.076	0.98
345_I	352_I	1.053	0.98
16_G	41_A	1.049	0.98
8_L	11_D	1.049	0.98
342_F	354_L	1.045	0.98
53_H	56_H	1.045	0.98
57_M	62_A	1.041	0.98
47_E	53_H	1.035	0.98
14_K	17_E	1.033	0.98
229_A	232_I	1.033	0.98
32_K	37_V	1.031	0.98
219_L	270_I	1.030	0.98
76_H	106_V	1.012	0.98
289_V	295_V	1.009	0.98
196_V	225_I	1.002	0.98
8_L	12_L	0.998	0.98
42_H	47_E	0.995	0.97
134_N	138_L	0.994	0.97
97_V	123_E	0.992	0.97
312_F	354_L	0.989	0.97
39_M	57_M	0.988	0.97
263_F	278_I	0.988	0.97
66_D	94_R	0.988	0.97
43_L	47_E	0.987	0.97
52_V	86_L	0.978	0.97
217_V	279_L	0.966	0.97
59_G	62_A	0.966	0.97
16_G	20_T	0.964	0.97
25_L	134_N	0.963	0.97
193_V	232_I	0.963	0.97
113_M	117_A	0.963	0.97
109_R	112_S	0.960	0.97
186_H	286_S	0.960	0.97
277_K	281_E	0.957	0.97
284_I	287_V	0.954	0.97
240_W	282_E	0.953	0.97
154_A	310_F	0.948	0.97
191_V	218_I	0.947	0.97
55_I	90_S	0.946	0.97
152_A	325_L	0.943	0.97
136_K	140_F	0.942	0.96
225_I	232_I	0.941	0.96
216_R	239_T	0.940	0.96
144_G	280_A	0.936	0.96
12_L	39_M	0.934	0.96
167_S	176_R	0.932	0.96
150_L	289_V	0.930	0.96
193_V	220_D	0.926	0.96
10_L	130_A	0.922	0.96
96_F	125_I	0.922	0.96
96_F	122_R	0.917	0.96
300_V	326_I	0.916	0.96
25_L	42_H	0.915	0.96
230_K	233_C	0.915	0.96
231_V	239_T	0.912	0.96
270_I	275_V	0.910	0.96
30_V	54_A	0.907	0.96
178_D	182_Y	0.906	0.96
170_I	334_M	0.905	0.96
143_T	280_A	0.903	0.96
187_Q	285_M	0.903	0.96
226_P	229_A	0.898	0.95
3_E	126_L	0.897	0.95
190_L	287_V	0.896	0.95
14_K	133_L	0.895	0.95
53_H	57_M	0.889	0.95
99_M	133_L	0.888	0.95
75_S	88_I	0.883	0.95
232_I	260_V	0.876	0.95
145_L	273_P	0.873	0.95
190_L	289_V	0.871	0.95
92_I	95_V	0.861	0.94
161_A	169_W	0.858	0.94
200_N	228_D	0.857	0.94
196_V	229_A	0.856	0.94
7_K	11_D	0.856	0.94
156_L	356_A	0.853	0.94
148_V	289_V	0.852	0.94
30_V	86_L	0.850	0.94
16_G	42_H	0.849	0.94
347_Q	352_I	0.849	0.94
38_G	58_A	0.844	0.94
274_D	278_I	0.843	0.94
178_D	181_Q	0.840	0.93
38_G	52_V	0.836	0.93
253_K	257_A	0.835	0.93
244_T	247_A	0.834	0.93
37_V	57_M	0.834	0.93
193_V	221_T	0.830	0.93
221_T	270_I	0.829	0.93
321_H	324_S	0.824	0.93
271_Q	274_D	0.823	0.93
13_A	133_L	0.821	0.93
84_A	87_I	0.820	0.93
149_T	286_S	0.818	0.93
13_A	134_N	0.816	0.92
340_L	354_L	0.815	0.92
246_R	264_T	0.812	0.92
193_V	226_P	0.812	0.92
297_G	301_K	0.809	0.92
131_E	138_L	0.806	0.92
12_L	38_G	0.806	0.92
240_W	263_F	0.802	0.92
178_D	309_I	0.796	0.92
225_I	255_L	0.796	0.92
225_I	229_A	0.795	0.91
88_I	117_A	0.794	0.91
115_K	121_V	0.793	0.91
30_V	92_I	0.790	0.91
310_F	325_L	0.789	0.91
253_K	256_S	0.788	0.91
194_G	224_S	0.788	0.91
343_T	355_T	0.784	0.91
32_K	64_G	0.782	0.91
291_G	296_H	0.781	0.91
76_H	82_P	0.779	0.91
179_A	334_M	0.778	0.91
42_H	133_L	0.775	0.90
243_T	247_A	0.775	0.90
159_K	324_S	0.774	0.90
148_V	287_V	0.772	0.90
106_V	110_G	0.771	0.90
178_D	348_I	0.769	0.90
52_V	89_N	0.769	0.90
193_V	255_L	0.768	0.90
233_C	236_I	0.767	0.90
100_R	127_A	0.764	0.90
346_T	355_T	0.761	0.90
238_P	282_E	0.761	0.90
295_V	299_F	0.761	0.90
155_S	162_T	0.757	0.89
145_L	306_Q	0.756	0.89
102_P	138_L	0.756	0.89
32_K	65_A	0.754	0.89
161_A	167_S	0.754	0.89
219_L	242_F	0.753	0.89
162_T	166_D	0.751	0.89
174_A	350_R	0.750	0.89
136_K	286_S	0.750	0.89
31_V	65_A	0.748	0.89
37_V	59_G	0.747	0.89
6_M	124_G	0.747	0.89
255_L	259_G	0.739	0.88
189_I	213_Q	0.738	0.88
93_K	120_E	0.738	0.88
12_L	41_A	0.738	0.88
84_A	109_R	0.738	0.88
99_M	127_A	0.736	0.88
174_A	177_Q	0.732	0.88
3_E	7_K	0.730	0.88
333_S	336_D	0.729	0.88
234_D	237_A	0.729	0.88
324_S	328_G	0.729	0.88
105_L	141_M	0.728	0.87
225_I	231_V	0.726	0.87
347_Q	350_R	0.726	0.87
265_L	274_D	0.725	0.87
348_I	353_K	0.724	0.87
115_K	123_E	0.723	0.87
319_G	328_G	0.723	0.87
75_S	85_E	0.720	0.87
188_S	287_V	0.720	0.87
52_V	81_P	0.719	0.87
123_E	126_L	0.717	0.87
168_K	334_M	0.717	0.87
11_D	14_K	0.716	0.87
232_I	239_T	0.714	0.86
30_V	38_G	0.710	0.86
10_L	98_A	0.709	0.86
176_R	311_Y	0.701	0.85
97_V	121_V	0.693	0.85
251_K	255_L	0.692	0.85
105_L	109_R	0.688	0.84
319_G	330_G	0.685	0.84
149_T	182_Y	0.682	0.84
225_I	251_K	0.681	0.84
14_K	129_Q	0.680	0.84
188_S	284_I	0.680	0.84
345_I	354_L	0.679	0.84
64_G	93_K	0.679	0.84
316_L	340_L	0.677	0.83
324_S	327_S	0.676	0.83
240_W	261_N	0.675	0.83
111_I	115_K	0.674	0.83
172_S	349_G	0.671	0.83
309_I	355_T	0.670	0.83
195_T	201_P	0.670	0.83
294_A	298_S	0.668	0.83
60_A	63_E	0.668	0.83
233_C	237_A	0.667	0.82
173_E	177_Q	0.664	0.82
10_L	14_K	0.664	0.82
55_I	87_I	0.662	0.82
233_C	258_F	0.660	0.82
241_I	255_L	0.660	0.82
42_H	45_Y	0.659	0.82
296_H	305_F	0.659	0.82
30_V	62_A	0.658	0.82
104_P	141_M	0.655	0.81
221_T	269_R	0.654	0.81
272_I	302_E	0.651	0.81
97_V	115_K	0.650	0.81
67_I	91_G	0.649	0.81
219_L	299_F	0.649	0.81
162_T	317_I	0.648	0.81
102_P	142_R	0.647	0.81
175_A	351_D	0.647	0.81
22_S	45_Y	0.644	0.80
149_T	307_E	0.644	0.80
12_L	15_Q	0.643	0.80
75_S	106_V	0.642	0.80
191_V	203_L	0.641	0.80
59_G	90_S	0.641	0.80
172_S	348_I	0.641	0.80
136_K	186_H	0.640	0.80
232_I	255_L	0.640	0.80
25_L	286_S	0.639	0.80
99_M	123_E	0.639	0.80
66_D	93_K	0.637	0.79
42_H	53_H	0.636	0.79
339_L	350_R	0.636	0.79
136_K	285_M	0.635	0.79
21_E	285_M	0.635	0.79
25_L	133_L	0.634	0.79
159_K	320_T	0.634	0.79
205_C	213_Q	0.633	0.79
343_T	356_A	0.633	0.79
67_I	70_T	0.632	0.79
100_R	115_K	0.631	0.79
186_H	288_Y	0.629	0.79
200_N	229_A	0.629	0.79
216_R	237_A	0.627	0.78
182_Y	186_H	0.623	0.78
272_I	276_L	0.618	0.77
274_D	277_K	0.618	0.77
289_V	305_F	0.617	0.77
223_L	247_A	0.616	0.77
97_V	124_G	0.616	0.77
232_I	258_F	0.614	0.77
99_M	130_A	0.611	0.77
99_M	134_N	0.611	0.77
269_R	294_A	0.609	0.76
42_H	134_N	0.608	0.76
180_Q	205_C	0.606	0.76
111_I	121_V	0.606	0.76
273_P	302_E	0.606	0.76
234_D	239_T	0.605	0.76
342_F	352_I	0.603	0.76
6_M	9_A	0.603	0.76
215_V	238_P	0.603	0.76
175_A	311_Y	0.602	0.76
346_T	353_K	0.598	0.75
175_A	178_D	0.596	0.75
16_G	45_Y	0.595	0.75
272_I	299_F	0.595	0.75
325_L	328_G	0.594	0.75
182_Y	311_Y	0.593	0.75
317_I	331_F	0.592	0.74
193_V	229_A	0.592	0.74
152_A	308_I	0.590	0.74
175_A	349_G	0.590	0.74
334_M	337_V	0.589	0.74
216_R	238_P	0.589	0.74
332_Q	336_D	0.588	0.74
261_N	264_T	0.586	0.74
202_S	233_C	0.583	0.73
25_L	136_K	0.580	0.73
293_S	327_S	0.579	0.73
233_C	239_T	0.578	0.73
21_E	212_K	0.578	0.73
162_T	331_F	0.578	0.73
23_N	26_V	0.576	0.72
301_K	329_E	0.572	0.72
243_T	264_T	0.571	0.72
6_M	125_I	0.570	0.72
266_E	271_Q	0.569	0.71
244_T	267_T	0.567	0.71
159_K	319_G	0.566	0.71
205_C	208_P	0.566	0.71
40_G	53_H	0.565	0.71
256_S	262_I	0.565	0.71
37_V	58_A	0.564	0.71
98_A	124_G	0.564	0.71
144_G	277_K	0.564	0.71
137_F	141_M	0.563	0.71
327_S	330_G	0.561	0.70
95_V	119_I	0.559	0.70
187_Q	212_K	0.556	0.70
191_V	201_P	0.555	0.70
245_A	264_T	0.554	0.69
156_L	312_F	0.553	0.69
317_I	337_V	0.553	0.69
65_A	92_I	0.552	0.69
166_D	317_I	0.552	0.69
184_K	213_Q	0.552	0.69
19_Q	41_A	0.551	0.69
204_T	216_R	0.550	0.69
244_T	264_T	0.547	0.68
189_I	208_P	0.547	0.68
175_A	348_I	0.545	0.68
181_Q	185_T	0.545	0.68
103_N	107_A	0.544	0.68
77_Y	82_P	0.543	0.68
171_T	313_A	0.543	0.68
217_V	275_V	0.543	0.68
162_T	169_W	0.542	0.68
30_V	52_V	0.541	0.68
344_D	353_K	0.540	0.68
155_S	170_I	0.539	0.67
162_T	167_S	0.537	0.67
313_A	351_D	0.537	0.67
220_D	223_L	0.537	0.67
103_N	106_V	0.535	0.67
196_V	220_D	0.534	0.67
305_F	308_I	0.532	0.66
128_D	132_R	0.532	0.66
223_L	251_K	0.531	0.66
187_Q	286_S	0.530	0.66
190_L	284_I	0.530	0.66
289_V	296_H	0.529	0.66
195_T	203_L	0.529	0.66
6_M	70_T	0.529	0.66
9_A	28_A	0.529	0.66
288_Y	299_F	0.527	0.66
251_K	254_R	0.527	0.66
190_L	217_V	0.527	0.66
74_C	83_C	0.525	0.65
170_I	313_A	0.524	0.65
247_A	255_L	0.524	0.65
86_L	89_N	0.523	0.65
3_E	125_I	0.523	0.65
272_I	289_V	0.521	0.65
11_D	36_I	0.520	0.65
272_I	298_S	0.519	0.64
308_I	356_A	0.519	0.64
310_F	356_A	0.518	0.64
221_T	267_T	0.517	0.64
16_G	25_L	0.517	0.64
149_T	288_Y	0.516	0.64
197_K	225_I	0.516	0.64
342_F	345_I	0.515	0.64
161_A	168_K	0.515	0.64
217_V	240_W	0.514	0.64
171_T	179_A	0.514	0.64
204_T	234_D	0.514	0.64
55_I	92_I	0.513	0.64
156_L	165_G	0.513	0.64
166_D	170_I	0.512	0.63
92_I	119_I	0.512	0.63
192_G	299_F	0.511	0.63
192_G	291_G	0.511	0.63
159_K	317_I	0.511	0.63
242_F	270_I	0.510	0.63
30_V	55_I	0.510	0.63
84_A	117_A	0.510	0.63
187_Q	284_I	0.509	0.63
45_Y	48_A	0.509	0.63
311_Y	348_I	0.508	0.63
115_K	122_R	0.507	0.63
188_S	215_V	0.505	0.62
10_L	70_T	0.503	0.62
317_I	321_H	0.503	0.62
45_Y	283_G	0.501	0.62
140_F	283_G	0.501	0.62
252_K	262_I	0.500	0.62

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
2b3zA	3	0.9917	100	0.227	Contact Map
2g6vA	2	0.9584	100	0.24	Contact Map
3zpgA	2	0.9529	100	0.274	Contact Map
2hxvA	2	0.9446	100	0.279	Contact Map
2p4gA	2	0.6399	100	0.632	Contact Map
2aznA	2	0.5983	100	0.639	Contact Map
3g8qA	2	0.7673	100	0.643	Contact Map
4ha7A	2	0.5706	100	0.651	Contact Map
1z3aA	2	0.3823	100	0.717	Contact Map
2nx8A	2	0.4044	100	0.718	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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