NRNA - BACSU - GREMLIN Contacts

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NRNA - Bifunctional oligoribonuclease and PAP phosphatase NrnA

UniProt:	O34600	Sequences: MKTELIRTISLYDTIILHRHVRPDPDAYGSQCGLTEILRETYPEKNIFAVGTPEPSLSFLYSLDEVDNETYEGALVIVCDTANQERIDDQRYPSGAKLMKIDHHPNEDPYGDLLWVDTSASSVSEMIYELYLEGKEHGWKLNTKAAELIYAGIVGDTGRFLFPNTTEKTLKYAGELIQYPFSSSELFNQLYETKLNVVKLNGFIFQNVSLSENGAASVFIKKDTLEKFGTTASEASQLVGTLGNISGIRAWVFFVEEDDQIRVRFRSKGPVINGLARKYNGGGHPLASGASIYSWDEADRILADLETLCKEHE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	313 (280)
Sequences:	5636 (4172)
Seq/√Len:	249.3

BACSU - NRNA YYBT PPAC
HALSA - Q9HHX6 Q9HSF1 Q9HRL0 Q9HQW0
SULSO - Q97VZ4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
129_E	168_K	4.259	1.00
124_S	152_G	3.559	1.00
135_K	175_E	3.187	1.00
40_E	142_N	3.182	1.00
171_K	178_Q	3.076	1.00
37_I	131_Y	3.053	1.00
19_R	27_A	2.840	1.00
182_S	185_E	2.778	1.00
128_Y	175_E	2.727	1.00
35_T	39_R	2.539	1.00
160_F	173_A	2.532	1.00
128_Y	172_Y	2.471	1.00
142_N	145_A	2.397	1.00
36_E	142_N	2.358	1.00
115_W	126_M	2.279	1.00
14_T	44_E	2.163	1.00
35_T	45_K	2.156	1.00
12_Y	15_I	2.152	1.00
221_K	224_T	2.094	1.00
16_I	74_A	2.091	1.00
150_Y	181_F	2.087	1.00
15_I	75_L	2.028	1.00
151_A	186_L	1.977	1.00
208_V	216_A	1.972	1.00
185_E	189_Q	1.952	1.00
36_E	145_A	1.949	1.00
30_S	124_S	1.926	1.00
167_E	178_Q	1.924	1.00
17_L	79_C	1.916	1.00
158_G	162_F	1.892	1.00
167_E	171_K	1.889	1.00
171_K	174_G	1.884	1.00
216_A	248_I	1.790	1.00
36_E	40_E	1.781	1.00
33_G	127_I	1.759	1.00
263_V	290_A	1.737	1.00
274_G	277_R	1.704	1.00
254_F	261_I	1.702	1.00
203_F	206_Q	1.695	1.00
121_S	125_E	1.679	1.00
21_V	89_D	1.666	1.00
214_G	249_R	1.662	1.00
30_S	123_V	1.661	1.00
153_I	173_A	1.649	1.00
17_L	35_T	1.638	1.00
78_V	87_I	1.633	1.00
260_Q	293_Y	1.626	1.00
207_N	218_V	1.594	1.00
38_L	47_I	1.591	1.00
79_C	123_V	1.573	1.00
34_L	77_I	1.571	1.00
14_T	46_N	1.568	1.00
33_G	149_I	1.558	1.00
36_E	39_R	1.553	1.00
78_V	81_T	1.543	1.00
121_S	157_T	1.536	1.00
17_L	34_L	1.535	1.00
195_L	199_K	1.527	1.00
211_S	217_S	1.522	1.00
171_K	175_E	1.521	1.00
18_H	76_V	1.501	1.00
17_L	31_Q	1.495	1.00
150_Y	173_A	1.474	1.00
170_L	174_G	1.470	1.00
75_L	96_A	1.470	1.00
267_S	272_I	1.457	1.00
77_I	99_M	1.456	1.00
147_E	181_F	1.453	1.00
120_A	126_M	1.451	1.00
265_F	276_A	1.436	1.00
175_E	178_Q	1.429	1.00
58_S	62_S	1.421	1.00
31_Q	47_I	1.418	1.00
201_N	241_T	1.406	1.00
101_I	130_L	1.403	1.00
128_Y	135_K	1.398	1.00
199_K	202_G	1.397	1.00
36_E	144_K	1.380	1.00
37_I	139_W	1.353	1.00
170_L	177_I	1.346	1.00
15_I	43_P	1.344	1.00
30_S	79_C	1.335	1.00
62_S	65_E	1.334	1.00
124_S	149_I	1.300	1.00
117_D	168_K	1.298	1.00
149_I	176_L	1.298	1.00
168_K	172_Y	1.295	1.00
25_P	151_A	1.293	1.00
249_R	270_P	1.292	1.00
125_E	169_T	1.292	1.00
231_T	234_E	1.283	1.00
198_V	245_I	1.270	1.00
265_F	272_I	1.268	1.00
56_S	61_Y	1.266	1.00
124_S	153_I	1.254	1.00
32_C	148_L	1.253	1.00
174_G	178_Q	1.252	1.00
209_S	217_S	1.248	1.00
208_V	242_L	1.244	1.00
41_T	139_W	1.244	1.00
35_T	47_I	1.242	1.00
143_T	180_P	1.242	1.00
207_N	224_T	1.234	1.00
76_V	95_G	1.233	1.00
81_T	87_I	1.231	1.00
14_T	74_A	1.220	1.00
167_E	170_L	1.219	1.00
55_P	58_S	1.217	1.00
57_L	61_Y	1.214	1.00
177_I	183_S	1.206	1.00
165_T	170_L	1.205	1.00
154_V	159_R	1.200	1.00
143_T	181_F	1.195	1.00
33_G	145_A	1.166	1.00
204_I	218_V	1.146	1.00
25_P	155_G	1.145	1.00
203_F	224_T	1.142	1.00
203_F	207_N	1.142	1.00
37_I	41_T	1.141	1.00
260_Q	291_S	1.133	1.00
46_N	73_G	1.128	1.00
109_P	112_D	1.116	1.00
97_K	112_D	1.115	1.00
128_Y	149_I	1.112	1.00
141_L	179_Y	1.108	1.00
37_I	137_H	1.105	1.00
15_I	77_I	1.102	1.00
34_L	127_I	1.096	1.00
256_E	259_D	1.094	1.00
33_G	124_S	1.091	1.00
250_A	271_V	1.090	1.00
99_M	113_L	1.081	1.00
36_E	131_Y	1.080	1.00
203_F	228_F	1.076	1.00
143_T	147_E	1.076	1.00
122_S	152_G	1.075	1.00
41_T	137_H	1.074	1.00
249_R	269_G	1.069	1.00
33_G	36_E	1.069	1.00
16_I	73_G	1.068	1.00
222_K	226_E	1.064	1.00
12_Y	75_L	1.061	1.00
19_R	31_Q	1.057	1.00
240_G	243_G	1.055	1.00
217_S	254_F	1.054	1.00
120_A	129_E	1.052	1.00
155_G	190_L	1.037	1.00
31_Q	79_C	1.028	1.00
240_G	244_N	1.027	1.00
146_A	176_L	1.011	1.00
84_Q	93_P	1.006	1.00
29_G	124_S	1.003	1.00
226_E	229_G	1.002	1.00
172_Y	175_E	1.001	1.00
204_I	238_L	0.999	1.00
18_H	48_F	0.994	1.00
239_V	251_W	0.988	1.00
167_E	174_G	0.978	1.00
210_L	248_I	0.973	1.00
13_D	71_Y	0.972	1.00
241_T	245_I	0.964	1.00
98_L	111_G	0.954	1.00
69_E	73_G	0.943	1.00
195_L	210_L	0.941	1.00
38_L	99_M	0.937	1.00
208_V	218_V	0.936	1.00
272_I	288_S	0.921	1.00
61_Y	147_E	0.920	1.00
121_S	169_T	0.919	1.00
18_H	87_I	0.916	1.00
34_L	38_L	0.916	1.00
73_G	96_A	0.914	1.00
56_S	59_F	0.914	1.00
42_Y	45_K	0.914	1.00
200_L	234_E	0.910	1.00
168_K	171_K	0.905	1.00
201_N	205_F	0.902	1.00
159_R	187_F	0.901	1.00
116_V	136_E	0.899	1.00
34_L	79_C	0.896	1.00
39_R	65_E	0.896	1.00
181_F	186_L	0.894	1.00
194_K	246_S	0.893	1.00
222_K	256_E	0.882	1.00
61_Y	64_D	0.881	1.00
196_N	230_T	0.881	1.00
105_P	285_P	0.876	1.00
218_V	242_L	0.875	1.00
25_P	60_L	0.867	0.99
60_L	151_A	0.867	0.99
75_L	97_K	0.865	0.99
243_G	251_W	0.864	0.99
145_A	149_I	0.861	0.99
207_N	219_F	0.857	0.99
13_D	44_E	0.852	0.99
200_L	238_L	0.845	0.99
201_N	204_I	0.844	0.99
280_N	293_Y	0.844	0.99
187_F	191_Y	0.842	0.99
117_D	126_M	0.841	0.99
222_K	225_L	0.840	0.99
56_S	60_L	0.839	0.99
129_E	172_Y	0.839	0.99
61_Y	148_L	0.838	0.99
54_E	57_L	0.834	0.99
38_L	77_I	0.829	0.99
117_D	129_E	0.825	0.99
64_D	147_E	0.824	0.99
194_K	197_V	0.824	0.99
69_E	72_E	0.822	0.99
143_T	182_S	0.820	0.99
107_E	114_L	0.818	0.99
37_I	145_A	0.816	0.99
199_K	203_F	0.809	0.99
53_P	58_S	0.801	0.99
123_V	127_I	0.798	0.99
170_L	173_A	0.797	0.99
13_D	74_A	0.797	0.99
257_E	260_Q	0.795	0.99
29_G	33_G	0.795	0.99
241_T	244_N	0.794	0.99
175_E	179_Y	0.792	0.99
127_I	131_Y	0.791	0.99
40_E	140_K	0.788	0.99
264_R	289_G	0.788	0.99
106_N	114_L	0.788	0.99
267_S	286_L	0.787	0.99
63_L	189_Q	0.784	0.99
29_G	148_L	0.778	0.99
59_F	63_L	0.776	0.99
32_C	61_Y	0.776	0.99
273_N	277_R	0.772	0.99
129_E	136_E	0.772	0.99
53_P	63_L	0.768	0.99
238_L	241_T	0.764	0.99
92_Y	95_G	0.763	0.99
196_N	229_G	0.761	0.99
11_L	97_K	0.761	0.99
76_V	92_Y	0.761	0.99
215_A	250_A	0.756	0.99
213_N	249_R	0.752	0.99
225_L	230_T	0.750	0.99
232_A	236_S	0.749	0.98
202_G	206_Q	0.747	0.98
223_D	256_E	0.745	0.98
143_T	179_Y	0.745	0.98
122_S	125_E	0.743	0.98
223_D	226_E	0.737	0.98
198_V	202_G	0.736	0.98
127_I	149_I	0.734	0.98
201_N	238_L	0.732	0.98
27_A	79_C	0.730	0.98
242_L	248_I	0.725	0.98
100_K	107_E	0.724	0.98
243_G	266_R	0.724	0.98
141_L	146_A	0.723	0.98
24_D	156_D	0.717	0.98
199_K	206_Q	0.716	0.98
269_G	286_L	0.715	0.98
200_L	220_I	0.711	0.98
34_L	99_M	0.705	0.98
256_E	261_I	0.705	0.98
82_A	111_G	0.704	0.98
83_N	107_E	0.702	0.98
259_D	293_Y	0.702	0.98
63_L	66_V	0.700	0.98
239_V	253_F	0.697	0.98
201_N	245_I	0.696	0.98
118_T	129_E	0.695	0.98
237_Q	241_T	0.694	0.98
265_F	275_L	0.693	0.97
78_V	111_G	0.692	0.97
141_L	149_I	0.692	0.97
109_P	114_L	0.691	0.97
147_E	185_E	0.689	0.97
207_N	211_S	0.689	0.97
219_F	261_I	0.686	0.97
20_H	24_D	0.684	0.97
242_L	251_W	0.682	0.97
25_P	57_L	0.680	0.97
279_Y	292_I	0.672	0.97
146_A	181_F	0.672	0.97
20_H	23_P	0.671	0.97
23_P	27_A	0.671	0.97
16_I	48_F	0.671	0.97
252_V	275_L	0.670	0.97
72_E	94_S	0.669	0.97
60_L	148_L	0.667	0.97
210_L	216_A	0.664	0.97
29_G	152_G	0.664	0.97
235_A	255_V	0.659	0.97
167_E	177_I	0.659	0.97
120_A	125_E	0.659	0.97
265_F	290_A	0.657	0.97
66_V	144_K	0.657	0.97
106_N	109_P	0.656	0.97
40_E	145_A	0.654	0.96
160_F	170_L	0.652	0.96
221_K	256_E	0.652	0.96
85_E	108_D	0.649	0.96
79_C	124_S	0.642	0.96
212_E	215_A	0.640	0.96
150_Y	154_V	0.637	0.96
57_L	60_L	0.637	0.96
200_L	204_I	0.637	0.96
120_A	168_K	0.634	0.96
135_K	138_G	0.633	0.96
218_V	253_F	0.628	0.96
71_Y	74_A	0.626	0.95
27_A	31_Q	0.625	0.95
35_T	49_A	0.624	0.95
195_L	208_V	0.623	0.95
125_E	168_K	0.623	0.95
162_F	287_A	0.622	0.95
111_G	114_L	0.619	0.95
193_T	246_S	0.619	0.95
252_V	265_F	0.619	0.95
104_H	156_D	0.617	0.95
240_G	266_R	0.616	0.95
52_T	56_S	0.614	0.95
18_H	50_V	0.613	0.95
14_T	72_E	0.612	0.95
68_N	71_Y	0.602	0.94
276_A	289_G	0.601	0.94
38_L	45_K	0.601	0.94
141_L	145_A	0.601	0.94
147_E	186_L	0.599	0.94
197_V	234_E	0.596	0.94
159_R	191_Y	0.595	0.94
28_Y	49_A	0.594	0.94
12_Y	74_A	0.593	0.94
192_E	246_S	0.592	0.94
41_T	45_K	0.591	0.94
131_Y	145_A	0.588	0.94
161_L	187_F	0.587	0.94
14_T	71_Y	0.586	0.94
24_D	80_D	0.583	0.93
13_D	43_P	0.582	0.93
78_V	100_K	0.581	0.93
39_R	44_E	0.580	0.93
232_A	257_E	0.579	0.93
106_N	273_N	0.578	0.93
250_A	267_S	0.578	0.93
220_I	224_T	0.576	0.93
215_A	275_L	0.576	0.93
202_G	205_F	0.575	0.93
141_L	176_L	0.574	0.93
280_N	290_A	0.573	0.93
107_E	277_R	0.573	0.93
80_D	156_D	0.572	0.93
281_G	287_A	0.569	0.93
144_K	147_E	0.567	0.92
131_Y	138_G	0.567	0.92
156_D	281_G	0.566	0.92
41_T	140_K	0.562	0.92
20_H	86_R	0.558	0.92
263_V	276_A	0.557	0.92
243_G	248_I	0.555	0.92
39_R	45_K	0.554	0.92
79_C	127_I	0.553	0.92
219_F	256_E	0.552	0.91
238_L	253_F	0.552	0.91
33_G	148_L	0.552	0.91
117_D	120_A	0.551	0.91
15_I	45_K	0.550	0.91
36_E	148_L	0.549	0.91
282_G	289_G	0.549	0.91
101_I	127_I	0.549	0.91
163_P	286_L	0.548	0.91
131_Y	139_W	0.547	0.91
16_I	76_V	0.545	0.91
52_T	55_P	0.545	0.91
29_G	145_A	0.543	0.91
276_A	279_Y	0.543	0.91
17_L	38_L	0.541	0.91
204_I	209_S	0.541	0.91
54_E	64_D	0.541	0.91
50_V	89_D	0.539	0.90
100_K	111_G	0.539	0.90
233_S	236_S	0.539	0.90
97_K	113_L	0.539	0.90
183_S	187_F	0.536	0.90
225_L	228_F	0.536	0.90
131_Y	137_H	0.536	0.90
13_D	73_G	0.535	0.90
272_I	275_L	0.534	0.90
28_Y	32_C	0.534	0.90
122_S	153_I	0.533	0.90
154_V	190_L	0.531	0.90
82_A	110_Y	0.531	0.90
15_I	38_L	0.531	0.90
225_L	229_G	0.530	0.90
16_I	95_G	0.525	0.89
17_L	45_K	0.525	0.89
21_V	86_R	0.524	0.89
153_I	172_Y	0.521	0.89
236_S	239_V	0.520	0.89
184_S	188_N	0.519	0.89
53_P	59_F	0.517	0.89
151_A	154_V	0.517	0.89
40_E	139_W	0.515	0.88
130_L	136_E	0.514	0.88
193_T	201_N	0.513	0.88
125_E	172_Y	0.512	0.88
73_G	95_G	0.512	0.88
62_S	66_V	0.511	0.88
113_L	117_D	0.510	0.88
75_L	99_M	0.509	0.88
106_N	115_W	0.508	0.88
74_A	95_G	0.508	0.88
265_F	270_P	0.507	0.88
239_V	266_R	0.503	0.87
160_F	165_T	0.503	0.87
38_L	41_T	0.503	0.87
113_L	130_L	0.502	0.87
150_Y	183_S	0.502	0.87
32_C	62_S	0.501	0.87
100_K	116_V	0.501	0.87
157_T	164_N	0.501	0.87
12_Y	97_K	0.500	0.87

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
3devA	2	0.9968	100	0.18	Contact Map
4py9A	2	0.9776	100	0.202	Contact Map
4ls9A	2	0.9617	100	0.23	Contact Map
4rpaA	3	0.9329	100	0.309	Contact Map
2hawA	2	0.9329	100	0.311	Contact Map
1k20A	2	0.9233	100	0.347	Contact Map
2eb0A	2	0.9042	100	0.353	Contact Map
2qb7A	1	0.9744	100	0.407	Contact Map
1wpnA	2	0.5687	100	0.476	Contact Map
2zxrA	1	0.8115	100	0.542	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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