RIR2 - ECOLI - GREMLIN Contacts

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RIR2 - Ribonucleoside-diphosphate reductase 1 subunit beta

UniProt:	P69924	Sequences: MAYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLVSDNVQVAPQEVEVSSYLVGQIDSEVDTDDLSNFQL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10661
Length:	376 (311)
Sequences:	2134 (711)
Seq/√Len:	40.3

ECOLI - RIR2 RIR4
BACSU - YOSP RIR2
HALSA - Q9HMU4
SULSO - Q97VV7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
149_K	286_D	6.328	1.00
289_D	306_C	4.951	1.00
54_V	122_S	4.608	1.00
314_N	327_Q	4.353	1.00
285_K	310_E	4.186	1.00
68_E	71_K	4.097	1.00
148_Q	152_E	3.423	1.00
72_H	76_S	3.397	1.00
270_K	323_D	3.283	1.00
278_V	325_P	3.257	1.00
203_A	277_F	3.183	1.00
196_L	272_E	3.112	1.00
281_A	326_F	3.099	1.00
274_Y	325_P	3.017	1.00
198_L	249_M	2.764	1.00
274_Y	317_M	2.753	1.00
199_M	273_C	2.619	1.00
285_K	306_C	2.540	1.00
67_P	70_E	2.472	1.00
250_L	268_E	2.464	1.00
281_A	313_T	2.461	1.00
274_Y	323_D	2.422	1.00
274_Y	322_L	2.399	1.00
271_Q	275_D	2.319	1.00
88_Q	158_Y	2.132	0.99
56_V	125_H	2.115	0.99
205_E	239_E	2.059	0.99
310_E	328_T	2.050	0.99
278_V	326_F	2.046	0.99
274_Y	278_V	2.040	0.99
275_D	279_Q	1.976	0.99
199_M	320_V	1.975	0.99
116_E	205_E	1.961	0.99
62_D	65_A	1.936	0.99
116_E	239_E	1.860	0.98
29_Y	107_T	1.858	0.98
44_Q	115_S	1.848	0.98
70_E	224_L	1.844	0.98
85_D	123_Y	1.843	0.98
51_P	122_S	1.829	0.98
145_E	149_K	1.827	0.98
45_L	50_R	1.820	0.98
75_I	131_V	1.815	0.98
156_S	279_Q	1.795	0.98
60_R	64_Q	1.759	0.97
160_E	196_L	1.751	0.97
110_E	113_A	1.738	0.97
282_Q	286_D	1.731	0.97
36_I	252_L	1.714	0.97
192_K	272_E	1.681	0.97
44_Q	112_W	1.654	0.96
34_Y	102_I	1.647	0.96
273_C	322_L	1.643	0.96
209_F	239_E	1.640	0.96
250_L	322_L	1.615	0.96
149_K	279_Q	1.614	0.96
66_L	225_M	1.608	0.96
63_Y	75_I	1.607	0.96
303_D	307_Q	1.580	0.95
213_F	239_E	1.565	0.95
108_W	245_G	1.551	0.95
318_Q	324_L	1.548	0.95
111_T	115_S	1.544	0.95
234_L	237_R	1.542	0.95
306_C	310_E	1.540	0.94
110_E	117_T	1.536	0.94
267_E	271_Q	1.531	0.94
239_E	242_H	1.527	0.94
260_P	263_A	1.516	0.94
209_F	235_I	1.476	0.93
119_H	242_H	1.471	0.93
193_K	196_L	1.467	0.93
111_T	114_F	1.456	0.93
73_I	291_L	1.449	0.92
254_R	263_A	1.441	0.92
230_K	355_S	1.435	0.92
289_D	302_K	1.431	0.92
259_D	263_A	1.424	0.92
42_E	52_E	1.416	0.92
270_K	274_Y	1.400	0.91
296_S	303_D	1.376	0.90
214_A	335_W	1.344	0.89
254_R	270_K	1.330	0.89
278_V	282_Q	1.320	0.88
207_I	277_F	1.319	0.88
214_A	288_A	1.316	0.88
219_F	225_M	1.302	0.88
213_F	357_Y	1.299	0.88
213_F	242_H	1.284	0.87
152_E	156_S	1.264	0.86
63_Y	71_K	1.261	0.86
34_Y	252_L	1.259	0.86
205_E	213_F	1.228	0.84
45_L	51_P	1.217	0.84
69_H	296_S	1.214	0.84
71_K	75_I	1.212	0.84
60_R	129_N	1.208	0.83
220_A	229_A	1.205	0.83
281_A	310_E	1.197	0.83
272_E	275_D	1.195	0.83
195_Y	250_L	1.194	0.83
51_P	54_V	1.181	0.82
51_P	125_H	1.174	0.82
93_N	97_L	1.171	0.81
251_N	254_R	1.170	0.81
152_E	323_D	1.165	0.81
74_F	228_N	1.164	0.81
119_H	357_Y	1.163	0.81
89_G	117_T	1.159	0.81
293_R	301_N	1.149	0.80
116_E	209_F	1.132	0.79
243_L	315_I	1.128	0.79
308_Y	336_I	1.126	0.79
42_E	121_R	1.124	0.79
259_D	262_M	1.122	0.79
347_V	352_V	1.111	0.78
42_E	50_R	1.107	0.78
126_I	228_N	1.103	0.77
36_I	39_K	1.100	0.77
270_K	322_L	1.095	0.77
85_D	228_N	1.095	0.77
307_Q	328_T	1.089	0.76
267_E	270_K	1.082	0.76
35_D	39_K	1.082	0.76
275_D	282_Q	1.078	0.76
288_A	309_V	1.078	0.76
54_V	237_R	1.067	0.75
36_I	248_H	1.058	0.74
230_K	234_L	1.055	0.74
217_F	236_A	1.047	0.74
353_E	359_V	1.044	0.73
348_A	351_E	1.039	0.73
312_I	316_R	1.033	0.73
270_K	275_D	1.031	0.72
358_L	363_D	1.023	0.72
139_D	143_T	1.014	0.71
65_A	224_L	1.000	0.70
69_H	294_D	0.999	0.70
205_E	209_F	0.997	0.70
99_L	197_C	0.995	0.70
294_D	298_I	0.995	0.70
106_E	110_E	0.983	0.69
285_K	289_D	0.982	0.69
149_K	153_G	0.981	0.69
64_Q	69_H	0.976	0.68
150_R	287_W	0.974	0.68
119_H	213_F	0.973	0.68
100_I	194_L	0.971	0.68
54_V	234_L	0.959	0.67
314_N	328_T	0.958	0.67
81_Q	212_S	0.955	0.66
221_E	335_W	0.949	0.66
38_E	121_R	0.948	0.66
233_R	345_V	0.948	0.66
92_P	112_W	0.946	0.66
314_N	324_L	0.944	0.66
152_E	325_P	0.942	0.65
282_Q	285_K	0.938	0.65
107_T	117_T	0.937	0.65
53_E	353_E	0.937	0.65
192_K	268_E	0.935	0.65
209_F	213_F	0.933	0.65
48_F	111_T	0.932	0.65
122_S	231_I	0.914	0.63
344_N	356_S	0.914	0.63
223_E	355_S	0.913	0.63
282_Q	289_D	0.908	0.62
61_I	64_Q	0.905	0.62
317_M	325_P	0.904	0.62
351_E	354_V	0.903	0.62
252_L	255_S	0.903	0.62
261_E	266_A	0.900	0.62
247_Q	319_A	0.900	0.62
333_I	336_I	0.898	0.62
80_Y	287_W	0.896	0.61
365_E	368_T	0.891	0.61
45_L	118_I	0.890	0.61
196_L	268_E	0.885	0.60
64_Q	132_N	0.881	0.60
51_P	118_I	0.879	0.60
74_F	225_M	0.879	0.60
85_D	357_Y	0.878	0.60
286_D	289_D	0.876	0.60
85_D	238_D	0.876	0.60
95_A	98_P	0.876	0.60
194_L	198_L	0.869	0.59
269_C	272_E	0.867	0.59
201_V	246_T	0.866	0.59
53_E	359_V	0.862	0.58
110_E	272_E	0.861	0.58
220_A	233_R	0.859	0.58
272_E	276_L	0.850	0.57
26_V	31_Q	0.848	0.57
100_I	198_L	0.840	0.56
243_L	316_R	0.835	0.56
203_A	273_C	0.834	0.56
38_E	42_E	0.833	0.56
211_V	309_V	0.832	0.56
302_K	306_C	0.831	0.56
156_S	270_K	0.830	0.56
53_E	336_I	0.824	0.55
68_E	278_V	0.824	0.55
92_P	120_S	0.822	0.55
245_G	249_M	0.820	0.55
40_L	106_E	0.817	0.54
304_I	307_Q	0.814	0.54
364_S	368_T	0.813	0.54
64_Q	275_D	0.812	0.54
56_V	231_I	0.804	0.53
192_K	269_C	0.798	0.53
119_H	239_E	0.794	0.52
296_S	302_K	0.791	0.52
243_L	311_Y	0.791	0.52
281_A	285_K	0.791	0.52
119_H	238_D	0.788	0.52
306_C	309_V	0.787	0.52
301_N	304_I	0.785	0.51
242_H	357_Y	0.784	0.51
288_A	306_C	0.782	0.51
292_F	305_L	0.780	0.51
107_T	110_E	0.779	0.51
207_I	211_V	0.779	0.51
42_E	46_S	0.775	0.51
68_E	271_Q	0.771	0.50
81_Q	88_Q	0.764	0.50
41_I	121_R	0.764	0.50
62_D	219_F	0.763	0.49
68_E	273_C	0.759	0.49
196_L	269_C	0.758	0.49
271_Q	274_Y	0.756	0.49
94_V	97_L	0.751	0.48
198_L	254_R	0.750	0.48
124_T	128_R	0.749	0.48
310_E	326_F	0.746	0.48
79_K	137_V	0.745	0.48
150_R	283_Q	0.744	0.48
40_L	244_T	0.743	0.48
245_G	248_H	0.741	0.47
72_H	77_N	0.739	0.47
144_N	290_Y	0.739	0.47
239_E	357_Y	0.738	0.47
258_D	262_M	0.735	0.47
99_L	161_L	0.733	0.47
154_I	204_L	0.733	0.47
323_D	327_Q	0.732	0.47
214_A	303_D	0.732	0.47
40_L	245_G	0.732	0.47
311_Y	315_I	0.728	0.46
150_R	348_A	0.728	0.46
199_M	269_C	0.724	0.46
105_L	249_M	0.724	0.46
37_F	248_H	0.723	0.46
89_G	113_A	0.723	0.46
112_W	209_F	0.722	0.46
114_F	118_I	0.721	0.46
158_Y	210_Y	0.719	0.45
116_E	123_Y	0.718	0.45
274_Y	324_L	0.714	0.45
314_N	317_M	0.711	0.45
127_I	298_I	0.711	0.45
57_S	60_R	0.710	0.45
145_E	323_D	0.709	0.44
50_R	118_I	0.707	0.44
37_F	252_L	0.707	0.44
139_D	271_Q	0.707	0.44
66_L	297_M	0.704	0.44
216_S	232_I	0.700	0.44
119_H	209_F	0.699	0.44
254_R	322_L	0.699	0.44
125_H	128_R	0.696	0.43
61_I	286_D	0.694	0.43
195_Y	268_E	0.693	0.43
26_V	30_D	0.693	0.43
246_T	309_V	0.691	0.43
74_F	81_Q	0.690	0.43
212_S	235_I	0.690	0.43
235_I	238_D	0.689	0.43
214_A	305_L	0.686	0.42
81_Q	348_A	0.683	0.42
73_I	215_C	0.682	0.42
76_S	309_V	0.679	0.42
135_S	159_D	0.678	0.42
58_R	62_D	0.676	0.41
102_I	253_L	0.676	0.41
124_T	359_V	0.676	0.41
269_C	322_L	0.674	0.41
150_R	284_E	0.673	0.41
138_F	209_F	0.673	0.41
93_N	214_A	0.672	0.41
224_L	319_A	0.670	0.41
160_E	367_D	0.670	0.41
193_K	279_Q	0.667	0.41
93_N	98_P	0.666	0.41
151_A	308_Y	0.664	0.40
345_V	356_S	0.663	0.40
206_A	316_R	0.663	0.40
327_Q	330_S	0.662	0.40
44_Q	245_G	0.661	0.40
37_F	105_L	0.659	0.40
146_Q	290_Y	0.658	0.40
161_L	193_K	0.657	0.40
65_A	261_E	0.656	0.40
160_E	214_A	0.656	0.40
255_S	267_E	0.655	0.40
91_S	112_W	0.653	0.39
48_F	84_L	0.653	0.39
203_A	276_L	0.652	0.39
347_V	354_V	0.652	0.39
213_F	238_D	0.651	0.39
349_P	354_V	0.651	0.39
85_D	235_I	0.649	0.39
68_E	261_E	0.646	0.39
116_E	213_F	0.645	0.39
56_V	129_N	0.645	0.39
68_E	303_D	0.643	0.39
109_V	246_T	0.642	0.38
130_I	344_N	0.641	0.38
35_D	136_V	0.640	0.38
123_Y	242_H	0.640	0.38
161_L	196_L	0.640	0.38
251_N	320_V	0.640	0.38
250_L	269_C	0.638	0.38
220_A	225_M	0.636	0.38
289_D	293_R	0.634	0.38
143_T	323_D	0.634	0.38
255_S	275_D	0.630	0.37
97_L	113_A	0.629	0.37
44_Q	47_F	0.628	0.37
238_D	242_H	0.628	0.37
194_L	197_C	0.626	0.37
224_L	278_V	0.624	0.37
255_S	322_L	0.622	0.37
85_D	242_H	0.621	0.37
345_V	352_V	0.621	0.37
191_K	261_E	0.621	0.37
308_Y	349_P	0.620	0.37
213_F	349_P	0.619	0.36
318_Q	327_Q	0.618	0.36
223_E	341_V	0.618	0.36
44_Q	241_L	0.617	0.36
145_E	274_Y	0.616	0.36
111_T	117_T	0.616	0.36
56_V	227_G	0.615	0.36
231_I	283_Q	0.614	0.36
203_A	280_A	0.613	0.36
191_K	262_M	0.610	0.36
324_L	327_Q	0.610	0.36
214_A	309_V	0.609	0.36
293_R	298_I	0.609	0.36
67_P	303_D	0.608	0.36
68_E	160_E	0.608	0.36
36_I	253_L	0.607	0.35
201_V	243_L	0.607	0.35
35_D	64_Q	0.606	0.35
33_K	103_P	0.605	0.35
322_L	325_P	0.603	0.35
206_A	281_A	0.602	0.35
134_P	143_T	0.602	0.35
68_E	334_P	0.600	0.35
39_K	279_Q	0.597	0.35
237_R	313_T	0.597	0.35
48_F	118_I	0.596	0.35
255_S	303_D	0.594	0.34
214_A	219_F	0.594	0.34
122_S	204_L	0.593	0.34
149_K	155_S	0.590	0.34
85_D	119_H	0.589	0.34
61_I	303_D	0.587	0.34
29_Y	280_A	0.586	0.34
55_D	58_R	0.585	0.34
307_Q	330_S	0.584	0.34
201_V	211_V	0.584	0.34
279_Q	283_Q	0.579	0.33
317_M	324_L	0.579	0.33
236_A	246_T	0.578	0.33
206_A	243_L	0.578	0.33
145_E	282_Q	0.577	0.33
87_I	150_R	0.576	0.33
152_E	326_F	0.575	0.33
160_E	192_K	0.572	0.33
220_A	235_I	0.571	0.33
82_T	292_F	0.571	0.33
236_A	340_L	0.570	0.32
67_P	306_C	0.570	0.32
289_D	303_D	0.568	0.32
85_D	124_T	0.567	0.32
223_E	354_V	0.567	0.32
267_E	368_T	0.567	0.32
297_M	353_E	0.565	0.32
279_Q	282_Q	0.564	0.32
72_H	267_E	0.563	0.32
96_L	197_C	0.562	0.32
270_K	273_C	0.562	0.32
26_V	202_N	0.561	0.32
150_R	209_F	0.559	0.32
267_E	322_L	0.558	0.31
260_P	266_A	0.557	0.31
260_P	268_E	0.557	0.31
161_L	197_C	0.556	0.31
310_E	314_N	0.556	0.31
114_F	117_T	0.555	0.31
250_L	320_V	0.552	0.31
288_A	335_W	0.552	0.31
204_L	216_S	0.551	0.31
82_T	127_I	0.546	0.31
247_Q	251_N	0.546	0.31
112_W	348_A	0.545	0.30
247_Q	311_Y	0.545	0.30
209_F	357_Y	0.544	0.30
247_Q	320_V	0.542	0.30
78_L	228_N	0.542	0.30
160_E	191_K	0.541	0.30
71_K	307_Q	0.541	0.30
33_K	118_I	0.540	0.30
159_D	291_L	0.540	0.30
150_R	205_E	0.538	0.30
84_L	88_Q	0.538	0.30
65_A	136_V	0.537	0.30
153_G	279_Q	0.536	0.30
84_L	122_S	0.536	0.30
118_I	291_L	0.536	0.30
49_W	119_H	0.533	0.30
88_Q	210_Y	0.533	0.30
152_E	275_D	0.533	0.30
139_D	253_L	0.533	0.30
78_L	137_V	0.532	0.29
31_Q	104_E	0.532	0.29
76_S	291_L	0.528	0.29
58_R	61_I	0.526	0.29
271_Q	278_V	0.526	0.29
238_D	357_Y	0.526	0.29
273_C	355_S	0.525	0.29
332_P	351_E	0.525	0.29
65_A	323_D	0.523	0.29
281_A	309_V	0.523	0.29
29_Y	245_G	0.522	0.29
281_A	327_Q	0.522	0.29
81_Q	235_I	0.520	0.29
58_R	352_V	0.518	0.28
45_L	241_L	0.517	0.28
270_K	325_P	0.516	0.28
335_W	338_T	0.515	0.28
135_S	326_F	0.515	0.28
136_V	143_T	0.514	0.28
77_N	349_P	0.513	0.28
73_I	294_D	0.512	0.28
337_N	341_V	0.511	0.28
277_F	313_T	0.510	0.28
30_D	88_Q	0.509	0.28
200_S	276_L	0.508	0.28
263_A	266_A	0.508	0.28
134_P	271_Q	0.507	0.28
229_A	233_R	0.506	0.27
81_Q	216_S	0.506	0.27
150_R	202_N	0.505	0.27
217_F	340_L	0.505	0.27
53_E	214_A	0.505	0.27
261_E	267_E	0.503	0.27
44_Q	111_T	0.502	0.27
157_Y	272_E	0.502	0.27
35_D	97_L	0.502	0.27
38_E	41_I	0.502	0.27
195_Y	269_C	0.501	0.27
66_L	71_K	0.501	0.27
146_Q	291_L	0.500	0.27
123_Y	213_F	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
1mxrA	2	0.9016	100	0.116	Contact Map
2rccA	4	0.8218	100	0.173	Contact Map
1syyA	2	0.8298	100	0.216	Contact Map
1h0oA	2	0.758	100	0.227	Contact Map
1jk0A	1	0.7846	100	0.234	Contact Map
1jk0B	1	0.6968	100	0.236	Contact Map
2p1iA	2	0.6782	100	0.247	Contact Map
3n37A	2	0.742	100	0.253	Contact Map
4bmoA	2	0.766	100	0.259	Contact Map
3dhzA	2	0.7739	100	0.26	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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