RF1 - BACSU - GREMLIN Contacts

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RF1 - Peptide chain release factor 1

UniProt:	P45872	Sequences: MLDRLKSIEERYEKLNELLSDPEVVNDPKKLREYSKEQSDIQETVDVYRQYRDASEQLADAKAMLEEKLDAEMRDMVKEEISELQKETETLSERLKVLLIPKDPNDDKNVIMEIRGAAGGEEAALFAGNLYRMYSRYAELQGWKTEVMEANVTGTGGYKEIIFMITGSGAYSKLKYENGAHRVQRVPETESGGRIHTSTATVACLPEAEEVEVDIHEKDIRVDTFASSGPGGQSVNTTMSAVRLTHLPTGVVVSCQDEKSQIKNKEKAMKVLRARIYDKFQQEAQAEYDQTRKSAVGSGDRSERIRTYNFPQNRVTDHRIGLTIQKLDQILEGKLDEVVEALIVEDQASKLQQSEG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	356 (334)
Sequences:	5967 (3109)
Seq/√Len:	170.1

ECOLI - RF1 RF2
BACSU - RF1 RF2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
280_F	283_E	4.417	1.00
278_D	282_Q	3.219	1.00
282_Q	286_A	3.083	1.00
141_Q	336_D	2.989	1.00
11_R	37_E	2.985	1.00
112_M	163_F	2.958	1.00
279_K	283_E	2.768	1.00
310_F	331_L	2.746	1.00
9_E	49_R	2.717	1.00
225_F	254_S	2.652	1.00
138_A	165_I	2.636	1.00
56_E	60_D	2.578	1.00
109_N	207_E	2.499	1.00
222_V	244_L	2.498	1.00
135_S	145_T	2.493	1.00
27_D	30_K	2.475	1.00
326_K	329_Q	2.440	1.00
226_A	239_M	2.436	1.00
220_I	244_L	2.422	1.00
220_I	269_M	2.370	1.00
50_Q	87_E	2.365	1.00
131_Y	163_F	2.351	1.00
15_L	34_Y	2.320	1.00
221_R	247_L	2.216	1.00
283_E	287_E	2.193	1.00
244_L	269_M	2.187	1.00
262_I	266_E	2.136	1.00
23_E	26_N	2.120	1.00
141_Q	173_K	2.084	1.00
131_Y	161_I	2.083	1.00
330_I	338_V	2.049	1.00
30_K	33_E	2.040	1.00
230_P	234_S	2.025	1.00
14_K	18_L	2.003	1.00
227_S	234_S	1.993	1.00
118_A	199_T	1.958	1.00
57_Q	60_D	1.947	1.00
62_K	85_Q	1.903	1.00
146_E	166_T	1.895	1.00
42_Q	46_D	1.880	1.00
329_Q	334_K	1.870	1.00
281_Q	285_Q	1.852	1.00
114_I	127_A	1.845	1.00
18_L	30_K	1.828	1.00
130_L	200_A	1.813	1.00
230_P	259_K	1.812	1.00
87_E	90_T	1.796	1.00
137_Y	336_D	1.783	1.00
131_Y	135_S	1.779	1.00
58_L	81_I	1.750	1.00
53_D	57_Q	1.737	1.00
234_S	238_T	1.734	1.00
277_Y	281_Q	1.732	1.00
190_E	194_R	1.731	1.00
322_L	337_E	1.720	1.00
285_Q	289_D	1.700	1.00
234_S	259_K	1.672	1.00
223_D	245_T	1.667	1.00
18_L	21_D	1.645	1.00
281_Q	284_A	1.644	1.00
258_E	263_K	1.638	1.00
83_E	87_E	1.637	1.00
109_N	166_T	1.633	1.00
16_N	42_Q	1.629	1.00
145_T	163_F	1.621	1.00
234_S	240_S	1.609	1.00
146_E	164_M	1.598	1.00
190_E	196_H	1.588	1.00
19_L	35_S	1.578	1.00
38_Q	42_Q	1.564	1.00
16_N	38_Q	1.547	1.00
13_E	16_N	1.547	1.00
86_K	90_T	1.534	1.00
258_E	267_K	1.522	1.00
150_A	158_Y	1.514	1.00
131_Y	147_V	1.498	1.00
234_S	237_T	1.484	1.00
245_T	252_V	1.482	1.00
310_F	327_L	1.481	1.00
222_V	265_K	1.471	1.00
315_V	338_V	1.445	1.00
144_K	166_T	1.436	1.00
280_F	284_A	1.432	1.00
257_D	267_K	1.410	1.00
132_R	332_E	1.405	1.00
54_A	87_E	1.402	1.00
227_S	237_T	1.401	1.00
266_E	270_K	1.381	1.00
224_T	242_V	1.381	1.00
29_K	33_E	1.374	1.00
48_Y	52_R	1.369	1.00
284_A	288_Y	1.369	1.00
271_V	275_R	1.355	1.00
147_V	161_I	1.342	1.00
287_E	290_Q	1.341	1.00
224_T	239_M	1.336	1.00
138_A	145_T	1.333	1.00
47_V	98_L	1.318	1.00
221_R	245_T	1.311	1.00
267_K	270_K	1.295	1.00
220_I	247_L	1.292	1.00
79_E	83_E	1.290	1.00
114_I	161_I	1.285	1.00
324_I	330_I	1.283	1.00
29_K	32_R	1.283	1.00
140_L	334_K	1.270	1.00
211_V	277_Y	1.258	1.00
54_A	88_T	1.254	1.00
251_V	279_K	1.238	1.00
262_I	265_K	1.237	1.00
143_W	174_L	1.236	1.00
282_Q	285_Q	1.231	1.00
327_L	331_L	1.230	1.00
313_N	328_D	1.221	1.00
186_V	193_G	1.197	1.00
19_L	24_V	1.194	1.00
12_Y	38_Q	1.190	1.00
31_L	35_S	1.186	1.00
75_D	79_E	1.173	1.00
330_I	335_L	1.168	1.00
307_T	318_H	1.167	1.00
315_V	330_I	1.165	1.00
121_E	153_T	1.165	1.00
164_M	207_E	1.162	1.00
136_R	332_E	1.156	1.00
11_R	14_K	1.154	1.00
107_D	169_G	1.137	1.00
46_D	50_Q	1.135	1.00
285_Q	288_Y	1.131	1.00
199_T	298_S	1.131	1.00
76_M	80_E	1.130	1.00
74_R	78_K	1.120	1.00
263_K	270_K	1.118	1.00
28_P	31_L	1.110	1.00
111_I	164_M	1.107	1.00
241_A	256_Q	1.099	1.00
114_I	202_V	1.095	1.00
111_I	148_M	1.090	1.00
21_D	24_V	1.088	1.00
85_Q	89_E	1.081	1.00
173_K	340_E	1.081	1.00
286_A	290_Q	1.078	1.00
47_V	50_Q	1.078	1.00
324_I	337_E	1.073	1.00
110_V	172_S	1.070	1.00
135_S	163_F	1.062	1.00
234_S	239_M	1.062	1.00
322_L	341_A	1.059	1.00
217_E	220_I	1.057	0.99
190_E	193_G	1.050	0.99
296_V	303_E	1.049	0.99
140_L	332_E	1.043	0.99
225_F	243_R	1.042	0.99
324_I	327_L	1.041	0.99
49_R	52_R	1.039	0.99
326_K	337_E	1.039	0.99
50_Q	54_A	1.035	0.99
112_M	165_I	1.033	0.99
127_A	200_A	1.026	0.99
224_T	234_S	1.024	0.99
246_H	250_G	1.024	0.99
165_I	174_L	1.020	0.99
46_D	49_R	1.018	0.99
60_D	63_A	1.016	0.99
284_A	287_E	1.015	0.99
73_M	77_V	1.014	0.99
51_Y	55_S	1.007	0.99
158_Y	161_I	1.007	0.99
13_E	17_E	1.005	0.99
129_N	310_F	1.002	0.99
105_N	108_K	1.001	0.99
289_D	293_K	1.000	0.99
215_I	269_M	0.993	0.99
52_R	56_E	0.993	0.99
28_P	32_R	0.991	0.99
337_E	341_A	0.990	0.99
137_Y	173_K	0.988	0.99
125_L	155_T	0.985	0.99
54_A	91_L	0.977	0.99
11_R	18_L	0.974	0.99
176_Y	342_L	0.971	0.99
283_E	286_A	0.969	0.99
254_S	257_D	0.966	0.99
75_D	78_K	0.965	0.99
178_N	203_A	0.956	0.99
54_A	80_E	0.948	0.99
173_K	336_D	0.947	0.99
45_V	49_R	0.946	0.99
203_A	292_R	0.944	0.99
76_M	79_E	0.943	0.99
82_S	85_Q	0.938	0.99
251_V	276_I	0.934	0.99
223_D	243_R	0.933	0.99
10_E	14_K	0.933	0.99
9_E	13_E	0.932	0.99
40_D	168_S	0.929	0.99
147_V	150_A	0.927	0.99
107_D	168_S	0.927	0.99
278_D	281_Q	0.924	0.99
313_N	327_L	0.922	0.99
79_E	82_S	0.916	0.99
59_A	63_A	0.915	0.99
12_Y	45_V	0.914	0.99
143_W	170_A	0.913	0.99
97_V	100_I	0.908	0.98
25_V	31_L	0.905	0.98
105_N	281_Q	0.905	0.98
220_I	248_P	0.902	0.98
43_E	46_D	0.899	0.98
292_R	295_A	0.898	0.98
173_K	343_I	0.895	0.98
234_S	262_I	0.894	0.98
246_H	249_T	0.893	0.98
78_K	82_S	0.893	0.98
257_D	271_V	0.890	0.98
336_D	340_E	0.889	0.98
335_L	339_V	0.887	0.98
81_I	85_Q	0.886	0.98
137_Y	143_W	0.884	0.98
25_V	28_P	0.877	0.98
12_Y	42_Q	0.876	0.98
257_D	263_K	0.876	0.98
72_E	76_M	0.873	0.98
131_Y	158_Y	0.872	0.98
210_E	273_R	0.871	0.98
124_A	155_T	0.871	0.98
70_D	74_R	0.869	0.98
60_D	64_M	0.869	0.98
9_E	52_R	0.867	0.98
254_S	271_V	0.867	0.98
109_N	164_M	0.865	0.98
112_M	174_L	0.858	0.98
148_M	164_M	0.855	0.98
334_K	337_E	0.854	0.98
244_L	265_K	0.852	0.98
265_K	269_M	0.844	0.98
247_L	250_G	0.842	0.97
58_L	88_T	0.840	0.97
12_Y	41_I	0.840	0.97
57_Q	84_L	0.835	0.97
150_A	161_I	0.834	0.97
273_R	277_Y	0.832	0.97
307_T	314_R	0.829	0.97
335_L	338_V	0.827	0.97
237_T	242_V	0.824	0.97
217_E	269_M	0.824	0.97
17_E	20_S	0.824	0.97
184_Q	307_T	0.822	0.97
309_N	314_R	0.820	0.97
224_T	230_P	0.820	0.97
84_L	88_T	0.815	0.97
19_L	38_Q	0.812	0.97
211_V	273_R	0.810	0.97
108_K	209_E	0.805	0.97
55_S	59_A	0.802	0.97
136_R	139_E	0.800	0.97
128_G	153_T	0.800	0.97
116_G	123_A	0.798	0.97
316_T	323_T	0.798	0.97
12_Y	16_N	0.798	0.97
279_K	282_Q	0.797	0.96
54_A	84_L	0.796	0.96
340_E	344_V	0.795	0.96
255_C	267_K	0.794	0.96
164_M	270_K	0.791	0.96
263_K	266_E	0.790	0.96
259_K	270_K	0.789	0.96
128_G	158_Y	0.784	0.96
18_L	34_Y	0.781	0.96
253_V	276_I	0.780	0.96
184_Q	309_N	0.775	0.96
58_L	84_L	0.769	0.96
69_L	77_V	0.768	0.96
225_F	256_Q	0.765	0.96
21_D	26_N	0.764	0.96
50_Q	53_D	0.760	0.95
82_S	86_K	0.759	0.95
33_E	37_E	0.755	0.95
213_V	273_R	0.755	0.95
339_V	343_I	0.754	0.95
201_T	299_G	0.754	0.95
322_L	330_I	0.753	0.95
276_I	279_K	0.752	0.95
73_M	76_M	0.751	0.95
222_V	269_M	0.749	0.95
86_K	89_E	0.747	0.95
320_I	341_A	0.746	0.95
222_V	242_V	0.745	0.95
64_M	67_E	0.739	0.95
71_A	75_D	0.737	0.95
116_G	124_A	0.736	0.95
238_T	260_S	0.733	0.94
51_Y	54_A	0.732	0.94
245_T	254_S	0.730	0.94
148_M	271_V	0.729	0.94
16_N	20_S	0.728	0.94
186_V	192_G	0.728	0.94
135_S	139_E	0.726	0.94
212_E	273_R	0.725	0.94
230_P	237_T	0.725	0.94
106_D	175_K	0.724	0.94
118_A	300_D	0.724	0.94
320_I	342_L	0.723	0.94
315_V	327_L	0.722	0.94
140_L	336_D	0.722	0.94
10_E	13_E	0.721	0.94
60_D	67_E	0.715	0.94
58_L	85_Q	0.715	0.94
318_H	321_G	0.713	0.94
24_V	30_K	0.710	0.93
208_A	212_E	0.710	0.93
65_L	81_I	0.709	0.93
24_V	34_Y	0.708	0.93
124_A	128_G	0.707	0.93
116_G	151_N	0.707	0.93
328_D	332_E	0.707	0.93
62_K	66_E	0.706	0.93
129_N	331_L	0.705	0.93
312_Q	323_T	0.703	0.93
105_N	277_Y	0.700	0.93
135_S	161_I	0.699	0.93
97_V	347_Q	0.699	0.93
49_R	53_D	0.698	0.93
54_A	58_L	0.697	0.93
226_A	234_S	0.697	0.93
269_M	273_R	0.693	0.93
37_E	40_D	0.692	0.93
131_Y	150_A	0.689	0.92
61_A	65_L	0.689	0.92
24_V	31_L	0.688	0.92
237_T	254_S	0.687	0.92
131_Y	145_T	0.687	0.92
312_Q	316_T	0.687	0.92
223_D	247_L	0.682	0.92
43_E	47_V	0.682	0.92
67_E	70_D	0.682	0.92
221_R	254_S	0.680	0.92
199_T	300_D	0.679	0.92
219_D	248_P	0.678	0.92
228_S	238_T	0.675	0.92
133_M	335_L	0.674	0.92
70_D	73_M	0.674	0.92
137_Y	141_Q	0.673	0.92
320_I	338_V	0.673	0.92
44_T	98_L	0.672	0.91
98_L	169_G	0.670	0.91
311_P	314_R	0.670	0.91
235_V	239_M	0.669	0.91
237_T	262_I	0.669	0.91
41_I	45_V	0.666	0.91
55_S	88_T	0.662	0.91
213_V	276_I	0.660	0.91
17_E	21_D	0.659	0.91
35_S	38_Q	0.657	0.91
149_E	162_I	0.654	0.90
108_K	208_A	0.651	0.90
154_G	304_R	0.648	0.90
180_A	295_A	0.648	0.90
325_Q	329_Q	0.644	0.90
215_I	244_L	0.643	0.90
9_E	45_V	0.642	0.89
210_E	270_K	0.642	0.89
39_S	42_Q	0.642	0.89
56_E	59_A	0.642	0.89
40_D	102_K	0.638	0.89
14_K	17_E	0.638	0.89
255_C	271_V	0.637	0.89
314_R	318_H	0.637	0.89
192_G	196_H	0.635	0.89
249_T	276_I	0.635	0.89
253_V	271_V	0.633	0.89
244_L	253_V	0.632	0.89
57_Q	61_A	0.631	0.89
58_L	62_K	0.631	0.89
72_E	75_D	0.628	0.88
221_R	269_M	0.627	0.88
172_S	343_I	0.627	0.88
124_A	159_K	0.625	0.88
263_K	267_K	0.623	0.88
122_E	196_H	0.622	0.88
290_Q	293_K	0.622	0.88
115_R	201_T	0.619	0.88
78_K	85_Q	0.617	0.88
287_E	291_T	0.616	0.87
10_E	21_D	0.615	0.87
225_F	241_A	0.615	0.87
19_L	31_L	0.615	0.87
137_Y	339_V	0.612	0.87
65_L	73_M	0.611	0.87
230_P	239_M	0.611	0.87
227_S	241_A	0.610	0.87
63_A	67_E	0.610	0.87
132_R	136_R	0.610	0.87
288_Y	292_R	0.609	0.87
338_V	341_A	0.608	0.87
170_A	174_L	0.608	0.87
121_E	155_T	0.608	0.87
225_F	245_T	0.607	0.87
324_I	338_V	0.605	0.87
267_K	271_V	0.605	0.87
110_V	171_Y	0.604	0.86
208_A	274_A	0.604	0.86
61_A	77_V	0.603	0.86
34_Y	38_Q	0.602	0.86
125_L	310_F	0.601	0.86
114_I	131_Y	0.598	0.86
247_L	251_V	0.596	0.86
237_T	263_K	0.595	0.86
180_A	199_T	0.594	0.86
87_E	91_L	0.593	0.85
151_N	160_E	0.592	0.85
8_I	44_T	0.590	0.85
253_V	275_R	0.588	0.85
125_L	128_G	0.586	0.85
166_T	170_A	0.581	0.84
253_V	258_E	0.581	0.84
132_R	135_S	0.580	0.84
26_N	31_L	0.580	0.84
136_R	140_L	0.579	0.84
65_L	74_R	0.579	0.84
128_G	150_A	0.578	0.84
216_H	219_D	0.577	0.84
178_N	295_A	0.577	0.84
208_A	281_Q	0.576	0.84
227_S	254_S	0.575	0.84
208_A	277_Y	0.574	0.84
128_G	155_T	0.572	0.83
31_L	38_Q	0.571	0.83
11_R	15_L	0.571	0.83
30_K	34_Y	0.570	0.83
191_S	196_H	0.570	0.83
143_W	173_K	0.568	0.83
313_N	323_T	0.568	0.83
114_I	200_A	0.568	0.83
33_E	36_K	0.567	0.83
320_I	323_T	0.566	0.83
180_A	201_T	0.565	0.83
117_A	199_T	0.563	0.82
58_L	80_E	0.561	0.82
234_S	260_S	0.561	0.82
225_F	252_V	0.560	0.82
276_I	280_F	0.560	0.82
116_G	150_A	0.558	0.82
180_A	303_E	0.557	0.82
175_K	346_D	0.553	0.81
115_R	203_A	0.549	0.81
224_T	237_T	0.547	0.81
123_A	180_A	0.545	0.80
222_V	245_T	0.544	0.80
149_E	160_E	0.542	0.80
230_P	265_K	0.541	0.80
129_N	183_V	0.540	0.80
237_T	258_E	0.538	0.79
199_T	303_E	0.535	0.79
118_A	123_A	0.535	0.79
129_N	188_E	0.532	0.79
205_L	274_A	0.531	0.79
329_Q	332_E	0.530	0.78
228_S	254_S	0.528	0.78
203_A	275_R	0.528	0.78
61_A	64_M	0.528	0.78
83_E	86_K	0.527	0.78
64_M	77_V	0.526	0.78
54_A	57_Q	0.526	0.78
59_A	62_K	0.526	0.78
223_D	254_S	0.525	0.78
309_N	312_Q	0.525	0.78
38_Q	41_I	0.522	0.77
32_R	35_S	0.521	0.77
117_A	180_A	0.521	0.77
313_N	318_H	0.521	0.77
211_V	281_Q	0.520	0.77
289_D	292_R	0.517	0.77
33_E	40_D	0.517	0.77
219_D	247_L	0.517	0.77
239_M	262_I	0.515	0.77
242_V	253_V	0.514	0.76
228_S	239_M	0.513	0.76
101_P	175_K	0.512	0.76
47_V	91_L	0.512	0.76
210_E	266_E	0.511	0.76
84_L	87_E	0.511	0.76
176_Y	345_E	0.511	0.76
71_A	74_R	0.510	0.76
252_V	256_Q	0.509	0.76
221_R	238_T	0.508	0.76
116_G	159_K	0.508	0.76
36_K	107_D	0.507	0.75
176_Y	339_V	0.505	0.75
121_E	125_L	0.505	0.75
296_V	299_G	0.505	0.75
180_A	296_V	0.504	0.75
40_D	107_D	0.504	0.75
96_K	344_V	0.504	0.75
234_S	254_S	0.504	0.75
113_E	194_R	0.503	0.75
70_D	75_D	0.502	0.75
240_S	262_I	0.502	0.75
81_I	88_T	0.501	0.75
234_S	257_D	0.501	0.75
226_A	238_T	0.500	0.74

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
1zbtA	1	0.8876	100	0.088	Contact Map
3d5aX	1	0.9916	100	0.092	Contact Map
2b3tB	1	0.8399	100	0.098	Contact Map
1rq0A	3	0.8933	100	0.153	Contact Map
2ihr1	1	0.9551	100	0.153	Contact Map
1gqeA	1	0.9607	100	0.161	Contact Map
2rsmA	1	0.3202	100	0.706	Contact Map
3j7yp	1	0.1629	100	0.742	Contact Map
1j26A	1	0.2444	100	0.79	Contact Map
4dh9Y	1	0.2669	99.9	0.805	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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