RTCA - HALSA - GREMLIN Contacts

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RTCA - RNA 3'-terminal phosphate cyclase

UniProt:	Q9HRE8	Sequences: MHVLDGSSGGGQLVRTALTCAAVSGESFRMRYVRRARSNPGLQAQHCAAVNAVADICDAATDGVEVGSEAFSFEPEVAAEEADDDEEPTLGGTTSVEVGTAGSIPLVFDSLLPLAGALDEPITATLTGGTDAKWAPPMDYFQHVKLPLLREHGIDATVSVDRRGFYPRGGGEATLTVEPSTPTPITLTERGDREALTAYSVAESSLADDEVAEQQATAAAPDAAHEIAYTDADSAGSAVVLAAEYEHSRAGFAALGERGVSADAVGENAADALAAFESGPGAVDSHLADQLVPVVAVAGGEVRAPEVTTHIETCVDLLAEFDYDIDIEHTDDGAVVLSA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	339 (308)
Sequences:	975 (719)
Seq/√Len:	41.0

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
22_A	73_F	5.065	1.00
266_G	270_A	4.744	1.00
50_V	71_F	3.700	1.00
260_V	268_N	3.432	1.00
292_V	318_L	3.376	1.00
214_Q	263_D	3.276	1.00
146_L	156_A	3.204	1.00
283_V	291_L	3.162	1.00
139_D	163_R	3.039	1.00
29_R	70_A	2.987	1.00
108_F	175_L	2.924	1.00
18_L	53_V	2.837	1.00
193_R	245_Y	2.734	1.00
115_A	122_I	2.681	1.00
319_A	324_D	2.672	1.00
29_R	72_S	2.593	1.00
307_V	311_I	2.561	1.00
200_S	215_Q	2.530	1.00
195_A	244_E	2.515	1.00
218_A	266_G	2.439	1.00
93_T	123_T	2.433	1.00
215_Q	237_S	2.352	1.00
132_A	135_A	2.231	1.00
111_L	124_A	2.189	1.00
282_A	303_R	2.108	0.99
315_V	325_I	2.058	0.99
47_C	64_V	2.052	0.99
219_A	270_A	2.041	0.99
144_V	251_G	2.027	0.99
140_Y	251_G	2.025	0.99
22_A	57_C	2.014	0.99
98_V	107_V	2.002	0.99
123_T	174_T	1.966	0.99
207_A	211_V	1.943	0.99
157_T	176_T	1.939	0.99
21_A	27_S	1.930	0.99
198_A	241_L	1.893	0.99
152_H	185_I	1.879	0.98
137_P	240_V	1.865	0.98
316_D	319_A	1.864	0.98
127_T	172_E	1.842	0.98
197_T	244_E	1.829	0.98
97_E	127_T	1.815	0.98
22_A	53_V	1.781	0.98
254_A	269_A	1.764	0.98
285_S	308_T	1.759	0.98
314_C	318_L	1.723	0.97
216_A	227_I	1.679	0.97
18_L	50_V	1.664	0.97
159_S	174_T	1.646	0.96
164_G	167_P	1.638	0.96
150_R	155_D	1.631	0.96
218_A	267_E	1.618	0.96
186_T	301_E	1.616	0.96
201_V	238_A	1.611	0.96
116_G	154_I	1.607	0.96
288_A	311_I	1.597	0.96
200_S	212_A	1.566	0.95
51_N	64_V	1.548	0.95
148_L	287_L	1.542	0.95
318_L	321_F	1.539	0.95
104_I	138_M	1.538	0.95
11_G	45_Q	1.537	0.95
267_E	271_D	1.517	0.94
316_D	320_E	1.499	0.94
16_T	314_C	1.465	0.93
309_T	312_E	1.463	0.93
219_A	266_G	1.447	0.93
19_T	23_V	1.446	0.93
62_D	72_S	1.442	0.93
189_E	247_H	1.431	0.92
198_A	225_H	1.431	0.92
243_A	273_L	1.428	0.92
108_F	173_A	1.427	0.92
131_D	163_R	1.425	0.92
95_S	127_T	1.414	0.92
165_F	203_E	1.413	0.92
145_K	287_L	1.388	0.91
219_A	239_V	1.383	0.91
241_L	273_L	1.378	0.91
194_E	246_E	1.375	0.91
23_V	114_L	1.373	0.91
58_D	90_L	1.372	0.91
193_R	243_A	1.365	0.90
245_Y	277_E	1.363	0.90
112_L	308_T	1.354	0.90
63_G	68_S	1.347	0.90
305_P	308_T	1.344	0.90
98_V	126_L	1.328	0.89
123_T	176_T	1.325	0.89
18_L	47_C	1.314	0.89
289_D	310_H	1.305	0.88
219_A	269_A	1.305	0.88
138_M	158_V	1.299	0.88
116_G	156_A	1.299	0.88
56_I	115_A	1.298	0.88
198_A	238_A	1.296	0.88
89_T	92_G	1.262	0.86
48_A	51_N	1.261	0.86
167_P	170_G	1.250	0.86
54_A	61_T	1.250	0.86
143_H	242_A	1.232	0.85
161_D	172_E	1.216	0.84
52_A	96_V	1.214	0.84
31_R	70_A	1.209	0.84
209_D	213_E	1.192	0.83
202_A	212_A	1.182	0.83
165_F	201_V	1.182	0.83
125_T	172_E	1.179	0.82
152_H	295_V	1.172	0.82
275_A	285_S	1.165	0.82
292_V	304_A	1.154	0.81
53_V	59_A	1.152	0.81
291_L	302_V	1.142	0.80
105_P	141_F	1.140	0.80
204_S	235_A	1.129	0.80
215_Q	265_V	1.128	0.79
200_S	237_S	1.123	0.79
276_F	285_S	1.117	0.79
161_D	174_T	1.117	0.79
71_F	321_F	1.117	0.79
131_D	137_P	1.116	0.79
53_V	73_F	1.103	0.78
53_V	110_S	1.102	0.78
218_A	270_A	1.102	0.78
124_A	175_L	1.101	0.78
48_A	96_V	1.094	0.77
164_G	169_G	1.093	0.77
140_Y	287_L	1.083	0.77
269_A	273_L	1.081	0.76
148_L	187_L	1.080	0.76
140_Y	144_V	1.077	0.76
319_A	325_I	1.076	0.76
39_N	43_Q	1.069	0.76
106_L	109_D	1.056	0.75
38_S	43_Q	1.050	0.74
11_G	37_R	1.038	0.74
46_H	102_G	1.037	0.73
101_A	129_G	1.036	0.73
281_G	305_P	1.031	0.73
21_A	28_F	1.023	0.72
239_V	266_G	1.013	0.72
15_R	109_D	1.012	0.72
129_G	289_D	1.008	0.71
256_G	259_G	1.002	0.71
198_A	216_A	1.001	0.71
34_R	41_G	0.999	0.71
28_F	71_F	0.997	0.70
314_C	317_L	0.996	0.70
95_S	125_T	0.996	0.70
169_G	236_G	0.995	0.70
310_H	313_T	0.989	0.70
117_A	180_S	0.989	0.70
104_I	173_A	0.984	0.69
56_I	111_L	0.982	0.69
40_P	170_G	0.977	0.69
160_V	199_Y	0.977	0.69
129_G	136_P	0.976	0.69
224_A	227_I	0.973	0.69
310_H	317_L	0.971	0.68
12_Q	310_H	0.970	0.68
24_S	321_F	0.968	0.68
311_I	315_V	0.959	0.67
40_P	169_G	0.955	0.67
101_A	136_P	0.952	0.67
307_V	315_V	0.950	0.67
12_Q	101_A	0.947	0.66
136_P	289_D	0.946	0.66
101_A	106_L	0.942	0.66
145_K	149_L	0.939	0.66
141_F	158_V	0.936	0.66
125_T	161_D	0.935	0.65
18_L	28_F	0.933	0.65
37_R	46_H	0.931	0.65
130_T	171_G	0.929	0.65
112_L	154_I	0.928	0.65
195_A	222_D	0.927	0.65
162_R	190_R	0.924	0.65
121_P	178_E	0.922	0.64
288_A	308_T	0.919	0.64
52_A	107_V	0.917	0.64
270_A	274_A	0.908	0.63
56_I	122_I	0.904	0.63
60_A	76_E	0.899	0.62
94_T	124_A	0.896	0.62
118_L	122_I	0.895	0.62
184_P	298_A	0.893	0.62
295_V	302_V	0.890	0.62
37_R	63_G	0.889	0.61
37_R	101_A	0.888	0.61
52_A	126_L	0.888	0.61
129_G	310_H	0.887	0.61
137_P	165_F	0.886	0.61
45_Q	101_A	0.884	0.61
117_A	152_H	0.882	0.61
245_Y	282_A	0.877	0.60
138_M	160_V	0.874	0.60
61_T	64_V	0.869	0.60
239_V	270_A	0.868	0.60
204_S	232_A	0.866	0.59
215_Q	239_V	0.860	0.59
283_V	287_L	0.858	0.59
28_F	321_F	0.857	0.59
315_V	327_I	0.852	0.58
11_G	129_G	0.850	0.58
53_V	96_V	0.833	0.56
262_A	265_V	0.830	0.56
152_H	184_P	0.829	0.56
140_Y	284_D	0.829	0.56
292_V	315_V	0.828	0.56
37_R	43_Q	0.825	0.56
12_Q	106_L	0.824	0.56
101_A	167_P	0.821	0.55
312_E	316_D	0.819	0.55
101_A	169_G	0.813	0.55
167_P	234_S	0.813	0.55
34_R	42_L	0.813	0.55
200_S	219_A	0.809	0.54
100_T	310_H	0.808	0.54
146_L	158_V	0.806	0.54
98_V	104_I	0.806	0.54
37_R	103_S	0.806	0.54
30_M	173_A	0.806	0.54
57_C	76_E	0.801	0.54
170_G	236_G	0.795	0.53
196_L	243_A	0.794	0.53
37_R	45_Q	0.794	0.53
57_C	74_E	0.793	0.53
57_C	60_A	0.791	0.53
99_G	107_V	0.791	0.53
49_A	110_S	0.790	0.52
138_M	238_A	0.790	0.52
136_P	310_H	0.788	0.52
288_A	305_P	0.787	0.52
60_A	74_E	0.786	0.52
109_D	290_Q	0.785	0.52
252_F	276_F	0.783	0.52
282_A	295_V	0.782	0.52
46_H	106_L	0.782	0.52
45_Q	106_L	0.781	0.52
199_Y	228_A	0.779	0.51
249_R	253_A	0.777	0.51
295_V	315_V	0.777	0.51
262_A	266_G	0.777	0.51
69_E	295_V	0.777	0.51
257_E	260_V	0.776	0.51
286_H	290_Q	0.768	0.50
17_A	142_Q	0.767	0.50
11_G	289_D	0.766	0.50
113_P	300_G	0.763	0.50
131_D	201_V	0.763	0.50
172_E	318_L	0.762	0.50
196_L	225_H	0.760	0.50
45_Q	310_H	0.757	0.49
196_L	273_L	0.756	0.49
56_I	94_T	0.753	0.49
139_D	199_Y	0.749	0.49
12_Q	45_Q	0.745	0.48
131_D	238_A	0.744	0.48
51_N	178_E	0.742	0.48
17_A	21_A	0.742	0.48
91_G	120_E	0.739	0.48
55_D	217_T	0.736	0.47
198_A	243_A	0.736	0.47
18_L	73_F	0.735	0.47
275_A	278_S	0.735	0.47
202_A	211_V	0.735	0.47
250_A	284_D	0.729	0.47
289_D	313_T	0.726	0.47
252_F	273_L	0.721	0.46
100_T	136_P	0.721	0.46
102_G	106_L	0.717	0.46
215_Q	266_G	0.716	0.46
107_V	124_A	0.709	0.45
37_R	290_Q	0.708	0.45
12_Q	289_D	0.706	0.45
125_T	174_T	0.706	0.45
148_L	291_L	0.705	0.45
312_E	317_L	0.700	0.44
160_V	173_A	0.700	0.44
119_D	217_T	0.698	0.44
10_G	130_T	0.691	0.43
297_V	310_H	0.685	0.43
167_P	236_G	0.683	0.43
309_T	313_T	0.681	0.42
89_T	118_L	0.676	0.42
108_F	112_L	0.676	0.42
32_Y	36_A	0.673	0.42
110_S	113_P	0.673	0.42
12_Q	37_R	0.671	0.42
37_R	310_H	0.671	0.42
37_R	289_D	0.670	0.41
241_L	323_Y	0.669	0.41
17_A	328_E	0.669	0.41
238_A	266_G	0.669	0.41
17_A	68_S	0.665	0.41
140_Y	289_D	0.664	0.41
106_L	129_G	0.664	0.41
48_A	107_V	0.664	0.41
139_D	142_Q	0.662	0.41
103_S	132_A	0.662	0.41
281_G	303_R	0.660	0.41
141_F	323_Y	0.659	0.40
71_F	270_A	0.657	0.40
23_V	197_T	0.657	0.40
117_A	138_M	0.657	0.40
195_A	224_A	0.656	0.40
64_V	68_S	0.655	0.40
259_G	265_V	0.655	0.40
295_V	325_I	0.654	0.40
115_A	147_P	0.654	0.40
91_G	119_D	0.651	0.40
23_V	123_T	0.651	0.40
181_T	278_S	0.651	0.40
10_G	34_R	0.648	0.39
158_V	172_E	0.645	0.39
10_G	15_R	0.642	0.39
43_Q	66_V	0.642	0.39
52_A	111_L	0.639	0.39
219_A	238_A	0.638	0.39
304_A	307_V	0.636	0.38
166_Y	259_G	0.633	0.38
69_E	104_I	0.632	0.38
101_A	289_D	0.632	0.38
168_R	294_V	0.632	0.38
104_I	124_A	0.632	0.38
18_L	61_T	0.629	0.38
96_V	111_L	0.628	0.38
113_P	289_D	0.628	0.38
145_K	311_I	0.626	0.38
143_H	240_V	0.625	0.37
219_A	241_L	0.624	0.37
35_R	47_C	0.624	0.37
45_Q	109_D	0.624	0.37
284_D	308_T	0.624	0.37
103_S	113_P	0.621	0.37
14_V	28_F	0.617	0.37
315_V	318_L	0.616	0.37
254_A	265_V	0.616	0.37
95_S	172_E	0.614	0.37
146_L	157_T	0.613	0.36
163_R	171_G	0.613	0.36
70_A	175_L	0.610	0.36
290_Q	310_H	0.609	0.36
137_P	253_A	0.607	0.36
132_A	140_Y	0.607	0.36
45_Q	289_D	0.606	0.36
37_R	313_T	0.605	0.36
131_D	139_D	0.603	0.36
165_F	252_F	0.602	0.35
76_E	173_A	0.602	0.35
14_V	33_V	0.601	0.35
142_Q	202_A	0.598	0.35
102_G	135_A	0.597	0.35
11_G	15_R	0.595	0.35
236_G	266_G	0.594	0.35
45_Q	287_L	0.594	0.35
202_A	210_E	0.592	0.35
285_S	306_E	0.591	0.35
89_T	117_A	0.591	0.35
37_R	136_P	0.590	0.34
16_T	293_P	0.589	0.34
304_A	311_I	0.589	0.34
169_G	234_S	0.588	0.34
103_S	203_E	0.588	0.34
37_R	106_L	0.587	0.34
145_K	308_T	0.587	0.34
106_L	310_H	0.586	0.34
170_G	234_S	0.584	0.34
129_G	313_T	0.584	0.34
250_A	255_L	0.583	0.34
96_V	276_F	0.583	0.34
37_R	129_G	0.581	0.34
45_Q	129_G	0.580	0.34
46_H	49_A	0.580	0.34
126_L	175_L	0.573	0.33
158_V	175_L	0.573	0.33
104_I	198_A	0.571	0.33
18_L	64_V	0.571	0.33
94_T	122_I	0.570	0.33
112_L	149_L	0.570	0.33
77_V	217_T	0.568	0.33
107_V	110_S	0.567	0.33
191_G	245_Y	0.566	0.32
108_F	138_M	0.563	0.32
211_V	237_S	0.562	0.32
141_F	175_L	0.561	0.32
293_P	314_C	0.560	0.32
162_R	172_E	0.559	0.32
29_R	177_V	0.559	0.32
305_P	311_I	0.558	0.32
101_A	310_H	0.558	0.32
248_S	276_F	0.558	0.32
200_S	239_V	0.557	0.32
117_A	244_E	0.557	0.32
272_A	290_Q	0.556	0.32
133_K	257_E	0.556	0.32
99_G	265_V	0.556	0.32
77_V	89_T	0.555	0.32
141_F	190_R	0.554	0.32
201_V	242_A	0.553	0.31
129_G	132_A	0.553	0.31
28_F	53_V	0.552	0.31
164_G	171_G	0.551	0.31
275_A	306_E	0.550	0.31
140_Y	240_V	0.548	0.31
41_G	171_G	0.547	0.31
106_L	289_D	0.546	0.31
11_G	101_A	0.546	0.31
193_R	196_L	0.543	0.31
324_D	327_I	0.543	0.31
21_A	309_T	0.543	0.31
218_A	221_P	0.542	0.31
236_G	269_A	0.542	0.31
103_S	121_P	0.538	0.30
145_K	294_V	0.537	0.30
136_P	169_G	0.537	0.30
13_L	109_D	0.536	0.30
162_R	229_Y	0.535	0.30
116_G	294_V	0.535	0.30
149_L	154_I	0.534	0.30
29_R	325_I	0.534	0.30
253_A	304_A	0.532	0.30
139_D	281_G	0.528	0.29
245_Y	276_F	0.527	0.29
245_Y	248_S	0.526	0.29
257_E	265_V	0.526	0.29
49_A	177_V	0.525	0.29
252_F	269_A	0.523	0.29
131_D	240_V	0.522	0.29
168_R	252_F	0.522	0.29
177_V	261_S	0.521	0.29
203_E	232_A	0.519	0.29
11_G	106_L	0.519	0.29
96_V	126_L	0.517	0.29
276_F	305_P	0.517	0.29
40_P	167_P	0.516	0.29
242_A	249_R	0.514	0.28
147_P	253_A	0.514	0.28
23_V	178_E	0.513	0.28
261_S	264_A	0.512	0.28
14_V	40_P	0.511	0.28
267_E	270_A	0.511	0.28
33_V	40_P	0.510	0.28
25_G	42_L	0.510	0.28
46_H	129_G	0.510	0.28
263_D	266_G	0.509	0.28
159_S	184_P	0.508	0.28
162_R	217_T	0.506	0.28
92_G	122_I	0.506	0.28
19_T	22_A	0.505	0.28
61_T	177_V	0.504	0.28
17_A	317_L	0.504	0.28
16_T	318_L	0.504	0.28
23_V	172_E	0.503	0.28
59_A	74_E	0.503	0.28
105_P	239_V	0.503	0.28
222_D	227_I	0.502	0.28
241_L	244_E	0.502	0.28
53_V	114_L	0.501	0.27
151_E	308_T	0.501	0.27
231_D	234_S	0.500	0.27

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	0.9617	100	0.071	Contact Map
3tutA	1	0.9587	100	0.113	Contact Map
4clqA	1	0.9499	100	0.145	Contact Map
2o0bA	1	0.8083	97	0.932	Contact Map
3r38A	2	0.5752	91.8	0.95	Contact Map
3rmtA	4	0.8024	91	0.951	Contact Map
3nvsA	1	0.8289	90.8	0.951	Contact Map
2yvwA	1	0.7699	86.4	0.955	Contact Map
1ejdA	4	0.2094	39.9	0.968	Contact Map
2pqcA	1	0.2183	32.2	0.969	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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