RTCA - SULSO - GREMLIN Contacts

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RTCA - RNA 3'-terminal phosphate cyclase

UniProt:	Q97W04	Sequences: MIEIDGSFGEGGGQILRTSLTLSVITGKPFRIFNIRANRPNPGLQRQHLWAVRAMKMISNAETKGDEVGSKELTFIPHEIKGNSIIDIDIGTAGSVTLIMQTMIPAIINKNMRIKIKGGTDVPKSPTIDYIRLVYLEILRKIGIESKVNLIKRGHYPEGGGEVIIENVNGNPSDFSLLELGKLIMIKGISHVSSLPSHIAERQKDSAKAILSKLGVQIEIETDVRQGEVSKGSGIALAAIGEKSIIGADSLGERGKRAEIVGEEAARKLIDNLNTKAAVDVHMSDMLMIFTSLFGGEYIGAELTSHAYTNMEIIRKFLDVKIEISGKRPFRFKAKIF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	337 (315)
Sequences:	981 (733)
Seq/√Len:	41.3

ECOLI - RTCA
HALSA - RTCA
SULSO - RTCA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_V	75_F	5.046	1.00
262_G	266_A	4.986	1.00
52_V	73_L	3.704	1.00
256_K	264_E	3.695	1.00
202_R	259_E	3.605	1.00
288_M	314_I	3.604	1.00
136_L	146_S	3.480	1.00
279_V	287_L	3.234	1.00
129_D	153_R	3.061	1.00
31_R	72_E	2.948	1.00
183_L	241_G	2.884	1.00
100_M	165_I	2.853	1.00
20_L	55_M	2.853	1.00
188_G	237_L	2.720	1.00
315_R	321_K	2.675	1.00
31_R	74_T	2.653	1.00
303_L	307_A	2.575	1.00
190_S	203_Q	2.509	1.00
185_M	240_I	2.402	1.00
203_Q	233_S	2.389	1.00
122_V	125_S	2.381	1.00
130_Y	247_G	2.281	1.00
84_S	113_R	2.234	1.00
23_S	29_P	2.228	1.00
134_V	247_G	2.227	1.00
278_A	299_I	2.222	1.00
206_S	262_G	2.190	1.00
49_L	66_D	2.180	1.00
103_M	114_I	2.153	0.99
311_M	322_I	2.126	0.99
312_E	315_R	2.076	0.99
208_K	212_S	2.059	0.99
207_A	266_A	2.045	0.99
281_V	304_T	2.043	0.99
113_R	164_I	2.035	0.99
24_V	59_S	1.969	0.99
89_D	117_K	1.964	0.99
147_K	166_E	1.961	0.99
24_V	55_M	1.948	0.99
250_S	265_A	1.910	0.99
26_T	318_L	1.908	0.99
157_P	160_G	1.845	0.98
142_I	175_F	1.841	0.98
284_S	307_A	1.834	0.98
90_I	99_I	1.772	0.98
107_I	112_M	1.755	0.98
117_K	162_E	1.745	0.98
195_L	199_I	1.719	0.97
20_L	52_V	1.692	0.97
191_H	234_G	1.683	0.97
149_N	164_I	1.681	0.97
154_G	157_P	1.671	0.97
21_T	25_I	1.633	0.96
127_T	236_A	1.590	0.96
187_K	240_I	1.589	0.96
53_R	66_D	1.579	0.95
310_N	314_I	1.571	0.95
94_G	98_L	1.565	0.95
13_G	47_Q	1.558	0.95
121_D	153_R	1.545	0.95
210_I	263_E	1.545	0.95
206_S	263_E	1.537	0.95
96_V	128_I	1.536	0.95
18_T	310_N	1.506	0.94
138_I	283_M	1.505	0.94
140_R	145_E	1.503	0.94
192_V	200_A	1.500	0.94
190_S	200_A	1.493	0.94
155_H	193_S	1.492	0.94
113_R	166_E	1.479	0.94
287_L	298_Y	1.458	0.93
239_A	269_L	1.447	0.93
207_A	265_A	1.438	0.93
263_E	267_R	1.429	0.92
65_G	70_S	1.427	0.92
312_E	316_K	1.424	0.92
305_S	308_Y	1.420	0.92
292_S	318_L	1.403	0.92
108_I	144_I	1.387	0.91
104_I	304_T	1.381	0.91
64_K	74_T	1.381	0.91
155_H	191_H	1.376	0.91
285_D	306_H	1.359	0.90
20_L	49_L	1.353	0.90
90_I	116_I	1.318	0.89
87_D	117_K	1.292	0.88
55_M	61_A	1.283	0.88
207_A	235_I	1.277	0.87
135_Y	283_M	1.277	0.87
207_A	262_G	1.276	0.87
197_S	201_E	1.276	0.87
100_M	163_V	1.271	0.87
210_I	267_R	1.269	0.87
288_M	300_G	1.266	0.87
56_K	63_T	1.260	0.87
33_F	72_E	1.259	0.87
95_S	98_L	1.246	0.86
128_I	148_V	1.237	0.86
188_G	234_G	1.229	0.85
142_I	291_T	1.225	0.85
183_L	239_A	1.225	0.85
121_D	127_T	1.222	0.85
159_G	232_G	1.206	0.84
272_N	281_V	1.201	0.84
41_N	45_Q	1.195	0.84
97_T	131_I	1.186	0.83
252_G	255_G	1.182	0.83
60_N	81_K	1.178	0.83
151_I	162_E	1.175	0.82
151_I	164_I	1.171	0.82
83_N	86_I	1.165	0.82
54_A	88_I	1.161	0.82
241_G	273_L	1.154	0.81
99_I	102_T	1.152	0.81
119_G	285_D	1.148	0.81
204_K	222_T	1.147	0.81
176_S	297_E	1.143	0.81
133_L	238_A	1.142	0.81
50_W	53_R	1.137	0.80
114_I	165_I	1.137	0.80
271_D	281_V	1.132	0.80
130_Y	283_M	1.127	0.80
145_E	168_V	1.122	0.79
265_A	269_L	1.117	0.79
138_I	177_L	1.114	0.79
186_I	220_I	1.108	0.79
314_I	317_F	1.106	0.78
98_L	101_Q	1.102	0.78
130_Y	134_V	1.101	0.78
184_I	242_E	1.092	0.78
150_L	189_I	1.088	0.77
315_R	322_I	1.085	0.77
58_I	86_I	1.081	0.77
188_G	220_I	1.081	0.77
237_L	269_L	1.076	0.76
192_V	199_I	1.074	0.76
13_G	39_R	1.071	0.76
179_E	243_K	1.069	0.76
93_A	98_L	1.069	0.76
97_T	100_M	1.068	0.76
58_I	112_M	1.055	0.75
30_F	73_L	1.041	0.74
23_S	30_F	1.027	0.73
42_P	159_G	1.025	0.73
20_L	30_F	1.020	0.73
174_D	294_F	1.013	0.72
55_M	75_F	1.012	0.72
128_I	150_L	1.005	0.71
127_T	249_D	1.002	0.71
93_A	119_G	0.992	0.70
115_K	162_E	0.991	0.70
250_S	261_V	0.991	0.70
235_I	266_A	0.989	0.70
39_R	48_H	0.981	0.70
48_H	94_G	0.981	0.70
284_S	304_T	0.975	0.69
54_A	116_I	0.974	0.69
126_P	285_D	0.971	0.69
120_T	161_G	0.969	0.69
111_N	168_V	0.969	0.69
306_H	309_T	0.969	0.69
96_V	163_V	0.967	0.68
102_T	105_P	0.964	0.68
36_R	43_G	0.963	0.68
277_A	301_A	0.950	0.67
42_P	160_G	0.937	0.66
291_T	311_M	0.937	0.66
301_A	304_T	0.936	0.66
13_G	119_G	0.933	0.66
190_S	233_S	0.931	0.65
14_Q	93_A	0.928	0.65
82_G	110_K	0.927	0.65
307_A	311_M	0.923	0.65
87_D	115_K	0.920	0.65
145_E	175_F	0.919	0.64
152_K	180_L	0.917	0.64
39_R	65_G	0.913	0.64
310_N	313_I	0.912	0.64
206_S	266_A	0.912	0.64
30_F	317_F	0.908	0.63
306_H	313_I	0.907	0.63
63_T	66_D	0.905	0.63
19_S	132_R	0.903	0.63
105_P	296_G	0.902	0.63
115_K	151_I	0.901	0.63
311_M	324_I	0.899	0.63
17_R	101_Q	0.892	0.62
16_L	200_A	0.892	0.62
119_G	126_P	0.888	0.62
39_R	47_Q	0.887	0.62
131_I	148_V	0.887	0.62
55_M	102_T	0.885	0.61
40_P	45_Q	0.885	0.61
235_I	262_G	0.883	0.61
154_G	159_G	0.876	0.61
50_W	88_I	0.876	0.61
91_G	99_I	0.876	0.61
303_L	311_M	0.874	0.60
14_Q	306_H	0.872	0.60
127_T	155_H	0.871	0.60
92_T	172_P	0.862	0.59
73_L	317_F	0.861	0.59
93_A	126_P	0.860	0.59
95_S	105_P	0.860	0.59
47_Q	93_A	0.858	0.59
258_A	262_G	0.856	0.59
90_I	96_V	0.852	0.59
93_A	159_G	0.848	0.58
282_H	286_M	0.848	0.58
104_I	144_I	0.848	0.58
138_I	287_L	0.846	0.58
26_T	317_F	0.844	0.58
234_G	262_G	0.844	0.58
185_M	217_Q	0.841	0.58
39_R	93_A	0.840	0.57
190_S	207_A	0.836	0.57
203_Q	261_V	0.836	0.57
98_L	102_T	0.831	0.57
288_M	311_M	0.830	0.57
186_I	269_L	0.830	0.57
258_A	261_V	0.829	0.56
279_V	283_M	0.826	0.56
255_G	261_V	0.824	0.56
186_I	270_I	0.818	0.55
71_K	291_T	0.809	0.55
162_E	314_I	0.808	0.54
234_G	239_A	0.808	0.54
232_G	262_G	0.807	0.54
119_G	306_H	0.807	0.54
86_I	112_M	0.807	0.54
36_R	44_L	0.804	0.54
101_Q	286_M	0.804	0.54
39_R	95_S	0.802	0.54
128_I	234_G	0.801	0.54
59_S	76_I	0.797	0.53
253_E	256_K	0.793	0.53
218_I	222_T	0.793	0.53
32_I	163_V	0.792	0.53
314_I	318_L	0.788	0.53
278_A	291_T	0.786	0.52
20_L	75_F	0.781	0.52
54_A	99_I	0.779	0.52
108_I	146_S	0.772	0.51
135_Y	139_L	0.771	0.51
203_Q	262_G	0.770	0.51
39_R	45_Q	0.765	0.50
232_G	259_E	0.765	0.50
160_G	195_L	0.761	0.50
123_P	253_E	0.759	0.50
62_E	76_I	0.759	0.50
12_G	17_R	0.757	0.50
122_V	251_L	0.756	0.50
47_Q	98_L	0.750	0.49
92_T	98_L	0.749	0.49
47_Q	306_H	0.746	0.49
13_G	285_D	0.739	0.48
121_D	191_H	0.738	0.48
238_A	245_I	0.736	0.48
53_R	168_V	0.732	0.47
285_D	309_T	0.732	0.47
266_A	270_I	0.731	0.47
130_Y	280_D	0.730	0.47
157_P	232_G	0.728	0.47
203_Q	235_I	0.728	0.47
115_K	164_I	0.728	0.47
194_S	231_K	0.721	0.46
62_E	78_H	0.718	0.46
163_V	197_S	0.717	0.46
51_A	102_T	0.715	0.46
126_P	306_H	0.713	0.46
142_I	174_D	0.711	0.45
170_G	173_S	0.710	0.45
66_D	70_S	0.708	0.45
14_Q	39_R	0.705	0.45
59_S	78_H	0.705	0.45
150_L	163_V	0.704	0.45
92_T	306_H	0.702	0.45
136_L	148_V	0.700	0.44
47_Q	101_Q	0.700	0.44
39_R	285_D	0.700	0.44
88_I	272_N	0.699	0.44
210_I	266_A	0.697	0.44
19_S	325_S	0.695	0.44
20_L	63_T	0.695	0.44
14_Q	98_L	0.692	0.44
185_M	219_E	0.692	0.44
71_K	96_V	0.691	0.44
19_S	70_S	0.691	0.44
246_I	280_D	0.689	0.43
58_I	103_M	0.688	0.43
249_D	265_A	0.688	0.43
39_R	286_M	0.687	0.43
100_M	104_I	0.682	0.43
179_E	299_I	0.682	0.43
233_S	252_G	0.681	0.43
305_S	309_T	0.680	0.43
95_S	122_V	0.678	0.42
59_S	62_E	0.676	0.42
206_S	209_A	0.676	0.42
148_V	165_I	0.676	0.42
99_I	114_I	0.675	0.42
201_E	205_D	0.674	0.42
45_Q	68_V	0.672	0.42
296_G	306_H	0.671	0.42
188_G	204_K	0.666	0.41
92_T	126_P	0.663	0.41
286_M	306_H	0.661	0.41
271_D	274_N	0.658	0.41
281_V	302_E	0.657	0.41
13_G	17_R	0.657	0.41
246_I	272_N	0.656	0.40
58_I	107_I	0.655	0.40
211_L	266_A	0.651	0.40
34_N	38_N	0.649	0.40
86_I	114_I	0.649	0.40
210_I	270_I	0.649	0.40
39_R	119_G	0.647	0.40
241_G	278_A	0.647	0.40
16_L	35_I	0.646	0.40
98_L	306_H	0.644	0.39
130_Y	285_D	0.643	0.39
31_R	194_S	0.642	0.39
14_Q	47_Q	0.640	0.39
244_S	272_N	0.640	0.39
121_D	129_D	0.640	0.39
207_A	211_L	0.638	0.39
59_S	219_E	0.638	0.39
93_A	306_H	0.638	0.39
39_R	309_T	0.637	0.39
80_I	223_D	0.636	0.39
121_D	234_G	0.635	0.39
186_I	239_A	0.633	0.38
261_V	265_A	0.633	0.38
289_I	310_N	0.632	0.38
241_G	244_S	0.630	0.38
292_S	322_I	0.627	0.38
321_K	324_I	0.625	0.38
32_I	146_S	0.624	0.38
291_T	298_Y	0.624	0.38
37_A	49_L	0.623	0.38
82_G	109_N	0.622	0.37
105_P	285_D	0.620	0.37
93_A	285_D	0.619	0.37
170_G	274_N	0.619	0.37
135_Y	304_T	0.618	0.37
72_E	165_I	0.618	0.37
248_A	272_N	0.616	0.37
39_R	126_P	0.613	0.37
131_I	165_I	0.612	0.37
93_A	157_P	0.608	0.36
308_Y	312_E	0.608	0.36
148_V	162_E	0.607	0.36
47_Q	285_D	0.606	0.36
55_M	88_I	0.606	0.36
54_A	103_M	0.606	0.36
129_D	132_R	0.603	0.36
98_L	105_P	0.602	0.36
64_K	182_K	0.600	0.36
14_Q	285_D	0.600	0.36
88_I	103_M	0.597	0.35
248_A	269_L	0.595	0.35
116_I	165_I	0.595	0.35
12_G	36_R	0.592	0.35
119_G	143_G	0.591	0.35
16_L	73_L	0.590	0.35
293_L	306_H	0.590	0.35
220_I	243_K	0.590	0.35
277_A	284_S	0.589	0.35
152_K	162_E	0.588	0.35
291_T	322_I	0.588	0.35
96_V	114_I	0.586	0.34
177_L	299_I	0.584	0.34
259_E	262_G	0.583	0.34
39_R	306_H	0.583	0.34
100_M	116_I	0.582	0.34
199_I	233_S	0.581	0.34
29_P	173_S	0.581	0.34
18_T	289_I	0.579	0.34
132_R	192_V	0.578	0.34
188_G	239_A	0.578	0.34
48_H	51_A	0.577	0.34
51_A	167_N	0.576	0.34
88_I	116_I	0.574	0.33
143_G	255_G	0.573	0.33
39_R	98_L	0.572	0.33
130_Y	236_A	0.572	0.33
54_A	90_I	0.571	0.33
181_G	242_E	0.570	0.33
133_L	236_A	0.569	0.33
123_P	141_K	0.569	0.33
268_K	286_M	0.567	0.33
14_Q	17_R	0.567	0.33
73_L	266_A	0.564	0.33
73_L	108_I	0.563	0.32
202_R	232_G	0.563	0.32
288_M	322_I	0.563	0.32
92_T	119_G	0.562	0.32
20_L	272_N	0.562	0.32
19_S	313_I	0.561	0.32
48_H	98_L	0.560	0.32
308_Y	313_I	0.558	0.32
59_S	201_E	0.556	0.32
25_I	106_A	0.556	0.32
12_G	120_T	0.556	0.32
48_H	119_G	0.555	0.32
98_L	285_D	0.555	0.32
311_M	314_I	0.554	0.32
25_I	113_R	0.554	0.32
206_S	210_I	0.551	0.31
95_S	306_H	0.551	0.31
253_E	261_V	0.550	0.31
68_V	114_I	0.549	0.31
233_S	247_G	0.549	0.31
131_I	174_D	0.549	0.31
299_I	327_K	0.548	0.31
232_G	239_A	0.546	0.31
219_E	222_T	0.544	0.31
172_P	294_F	0.544	0.31
16_L	42_P	0.541	0.31
190_S	265_A	0.539	0.31
237_L	240_I	0.539	0.31
148_V	201_E	0.539	0.31
264_E	288_M	0.539	0.31
21_T	24_V	0.537	0.30
31_R	167_N	0.535	0.30
119_G	125_S	0.535	0.30
197_S	202_R	0.534	0.30
284_S	303_L	0.533	0.30
28_K	60_N	0.533	0.30
155_H	248_A	0.531	0.30
28_K	131_I	0.531	0.30
30_F	55_M	0.530	0.30
137_E	249_D	0.529	0.30
206_S	211_L	0.529	0.30
172_P	293_L	0.529	0.30
237_L	320_V	0.528	0.30
305_S	312_E	0.527	0.30
128_I	153_R	0.527	0.30
181_G	239_A	0.527	0.30
95_S	296_G	0.526	0.29
177_L	279_V	0.526	0.29
95_S	104_I	0.525	0.29
16_L	30_F	0.524	0.29
106_A	230_S	0.523	0.29
83_N	231_K	0.523	0.29
195_L	259_E	0.523	0.29
19_S	23_S	0.522	0.29
198_H	204_K	0.521	0.29
158_E	248_A	0.521	0.29
269_L	276_K	0.520	0.29
291_T	312_E	0.520	0.29
97_T	235_I	0.519	0.29
232_G	252_G	0.516	0.29
42_P	157_P	0.516	0.29
280_D	304_T	0.515	0.29
158_E	290_F	0.514	0.29
204_K	282_H	0.514	0.29
108_I	135_Y	0.513	0.29
247_G	280_D	0.512	0.28
173_S	176_S	0.512	0.28
75_F	248_A	0.512	0.28
43_G	161_G	0.509	0.28
279_V	307_A	0.509	0.28
20_L	66_D	0.507	0.28
153_R	161_G	0.507	0.28
47_Q	92_T	0.506	0.28
111_N	169_N	0.505	0.28
154_G	161_G	0.505	0.28
128_I	163_V	0.505	0.28
230_S	311_M	0.505	0.28
113_R	146_S	0.501	0.28
94_G	99_I	0.500	0.28

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
4o89A	1	0.9941	100	0.048	Contact Map
3tutA	1	0.9822	100	0.093	Contact Map
4clqA	1	0.9792	100	0.134	Contact Map
2o0bA	1	0.7834	95.2	0.943	Contact Map
3nvsA	1	0.8042	94.1	0.946	Contact Map
1rf6A	1	0.822	93.4	0.948	Contact Map
2yvwA	1	0.7389	92.8	0.949	Contact Map
3rmtA	4	0.822	90.4	0.952	Contact Map
3zh4A	1	0.7537	87.5	0.954	Contact Map
2pqcA	1	0.8902	86.9	0.955	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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