RF2 - BACSU - GREMLIN Contacts

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RF2 - Peptide chain release factor 2

UniProt:	P28367	Sequences: MELSEIRAELENMASRLADFRGSLDLESKEARIAELDEQMADPEFWNDQQKAQTVINEANGLKDYVNSYKKLNESHEELQMTHDLLKEEPDTDLQLELEKELKSLTKEFNEFELQLLLSEPYDKNNAILELHPGAGGTESQDWGSMLLRMYTRWGERRGFKVETLDYLPGDEAGIKSVTLLIKGHNAYGYLKAEKGVHRLVRISPFDSSGRRHTSFVSCEVMPEFNDEIDIDIRTEDIKVDTYRASGAGGQHVNTTDSAVRITHLPTNVVVTCQTERSQIKNRERAMKMLKAKLYQRRIEEQQAELDEIRGEQKEIGWGSQIRSYVFHPYSMVKDHRTNTEMGNVQAVMDGDIDTFIDAYLRSKLS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	366 (336)
Sequences:	5925 (3041)
Seq/√Len:	165.9

ECOLI - RF2 RF1
BACSU - RF2 RF1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
298_R	301_E	4.493	1.00
296_Q	300_E	3.257	1.00
300_E	304_A	3.094	1.00
129_L	180_L	3.060	1.00
32_R	58_E	3.029	1.00
158_R	354_D	3.027	1.00
297_R	301_E	2.805	1.00
327_F	349_M	2.781	1.00
30_E	70_K	2.770	1.00
243_Y	272_T	2.751	1.00
77_E	81_M	2.639	1.00
155_G	182_I	2.625	1.00
240_V	262_I	2.568	1.00
126_N	224_E	2.551	1.00
152_T	162_V	2.533	1.00
244_R	257_D	2.510	1.00
48_D	51_K	2.497	1.00
238_I	262_I	2.487	1.00
344_N	347_A	2.458	1.00
238_I	287_M	2.388	1.00
148_L	180_L	2.369	1.00
71_K	108_E	2.349	1.00
36_L	55_V	2.300	1.00
262_I	287_M	2.216	1.00
301_E	305_E	2.193	1.00
239_K	265_L	2.191	1.00
148_L	178_V	2.153	1.00
44_E	47_N	2.130	1.00
280_I	284_E	2.127	1.00
158_R	190_Y	2.105	1.00
348_V	356_F	2.092	1.00
51_K	54_T	2.033	1.00
35_E	39_Q	2.031	1.00
248_A	252_H	2.024	1.00
245_A	252_H	2.010	1.00
135_A	216_F	2.004	1.00
78_E	81_M	1.977	1.00
63_K	67_N	1.951	1.00
163_E	183_K	1.938	1.00
347_A	352_D	1.919	1.00
299_I	303_Q	1.887	1.00
39_Q	51_K	1.874	1.00
131_L	144_G	1.832	1.00
248_A	277_R	1.829	1.00
148_L	152_T	1.805	1.00
79_L	102_L	1.793	1.00
207_D	211_R	1.788	1.00
74_E	78_E	1.776	1.00
147_L	217_V	1.773	1.00
252_H	256_T	1.769	1.00
108_E	111_E	1.741	1.00
252_H	277_R	1.732	1.00
154_W	354_D	1.705	1.00
241_D	263_T	1.697	1.00
295_Y	299_I	1.690	1.00
340_T	355_T	1.665	1.00
83_H	106_T	1.656	1.00
37_D	63_K	1.650	1.00
252_H	258_S	1.646	1.00
104_S	108_E	1.644	1.00
303_Q	307_D	1.642	1.00
163_E	181_L	1.625	1.00
299_I	302_Q	1.619	1.00
276_E	281_K	1.615	1.00
126_N	183_K	1.613	1.00
207_D	213_H	1.605	1.00
162_V	180_L	1.601	1.00
40_M	56_I	1.600	1.00
59_A	63_K	1.599	1.00
39_Q	42_D	1.588	1.00
167_Y	175_I	1.552	1.00
252_H	255_T	1.542	1.00
34_A	37_D	1.541	1.00
37_D	59_A	1.524	1.00
276_E	285_R	1.507	1.00
148_L	164_T	1.503	1.00
263_T	270_V	1.499	1.00
333_V	356_F	1.483	1.00
240_V	283_R	1.483	1.00
327_F	345_V	1.460	1.00
298_R	302_Q	1.449	1.00
242_T	260_V	1.413	1.00
228_E	291_K	1.413	1.00
245_A	255_T	1.412	1.00
69_Y	73_N	1.405	1.00
149_R	350_D	1.402	1.00
275_T	285_R	1.400	1.00
75_S	108_E	1.389	1.00
242_T	257_D	1.386	1.00
284_E	288_K	1.385	1.00
161_K	183_K	1.385	1.00
302_Q	306_L	1.366	1.00
50_Q	54_T	1.355	1.00
289_M	293_K	1.355	1.00
164_T	178_V	1.340	1.00
50_Q	53_Q	1.334	1.00
305_E	308_E	1.333	1.00
239_K	263_T	1.332	1.00
107_K	111_E	1.327	1.00
285_R	288_K	1.318	1.00
100_K	104_S	1.309	1.00
157_R	352_D	1.305	1.00
68_S	115_Q	1.302	1.00
131_L	178_V	1.278	1.00
238_I	265_L	1.276	1.00
155_G	162_V	1.273	1.00
96_L	100_K	1.256	1.00
345_V	349_M	1.253	1.00
280_I	283_R	1.253	1.00
160_F	191_L	1.246	1.00
229_I	295_Y	1.245	1.00
342_M	348_V	1.243	1.00
52_A	56_I	1.236	1.00
331_S	346_Q	1.234	1.00
97_E	101_E	1.232	1.00
216_F	316_I	1.218	1.00
203_I	210_G	1.213	1.00
40_M	45_F	1.207	1.00
300_E	303_Q	1.202	1.00
67_N	71_K	1.200	1.00
27_E	31_A	1.194	1.00
269_V	297_R	1.189	1.00
264_H	268_N	1.186	1.00
138_T	170_G	1.184	1.00
32_R	35_E	1.179	1.00
33_I	59_A	1.178	1.00
324_S	336_H	1.175	1.00
75_S	101_E	1.170	1.00
124_K	186_N	1.166	1.00
348_V	353_I	1.163	1.00
131_L	219_C	1.152	1.00
314_K	320_S	1.148	1.00
181_L	224_E	1.144	1.00
259_A	274_Q	1.139	1.00
264_H	267_T	1.137	1.00
106_T	110_N	1.110	1.00
153_R	350_D	1.108	1.00
333_V	348_V	1.098	1.00
281_K	288_K	1.092	1.00
152_T	180_L	1.092	1.00
68_S	71_K	1.092	1.00
342_M	355_T	1.091	1.00
207_D	210_G	1.088	1.00
128_I	181_L	1.085	1.00
303_Q	306_L	1.085	1.00
95_Q	99_E	1.082	1.00
128_I	165_L	1.068	0.99
99_E	103_K	1.067	0.99
42_D	45_F	1.065	0.99
190_Y	358_D	1.064	0.99
182_I	191_L	1.059	0.99
304_A	308_E	1.057	0.99
235_T	238_I	1.055	0.99
252_H	257_D	1.050	0.99
243_Y	261_R	1.049	0.99
127_A	189_G	1.048	0.99
157_R	350_D	1.048	0.99
49_Q	52_A	1.048	0.99
71_K	75_S	1.047	0.99
75_S	109_F	1.042	0.99
122_Y	125_N	1.037	0.99
81_M	84_D	1.033	0.99
307_D	311_G	1.032	0.99
96_L	99_E	1.031	0.99
73_N	77_E	1.031	0.99
242_T	252_H	1.027	0.99
342_M	345_V	1.025	0.99
175_I	178_V	1.022	0.99
34_A	38_E	1.022	0.99
70_K	73_N	1.018	0.99
142_D	172_E	1.014	0.99
129_L	182_I	1.011	0.99
190_Y	354_D	1.009	0.99
272_T	275_T	1.002	0.99
344_N	355_T	1.002	0.99
340_T	359_A	1.000	0.99
233_I	287_M	0.997	0.99
72_L	76_H	0.995	0.99
49_Q	53_Q	0.993	0.99
32_R	39_Q	0.991	0.99
146_M	327_F	0.982	0.99
355_T	359_A	0.979	0.99
94_L	98_L	0.978	0.99
100_K	103_K	0.976	0.99
220_E	310_R	0.972	0.99
302_Q	305_E	0.967	0.99
154_W	190_Y	0.957	0.99
195_K	220_E	0.956	0.99
301_E	304_A	0.952	0.99
124_K	185_H	0.944	0.99
144_G	217_V	0.941	0.99
241_D	261_R	0.938	0.99
80_Q	84_D	0.935	0.99
46_W	52_A	0.928	0.99
61_G	185_H	0.927	0.99
78_E	105_L	0.926	0.99
148_L	175_I	0.925	0.99
160_F	187_A	0.921	0.98
122_Y	299_I	0.920	0.98
30_E	73_N	0.919	0.98
193_A	360_Y	0.918	0.98
66_V	70_K	0.918	0.98
164_T	167_Y	0.916	0.98
114_L	117_L	0.915	0.98
46_W	49_Q	0.908	0.98
296_Q	299_I	0.907	0.98
67_N	70_K	0.907	0.98
33_I	66_V	0.906	0.98
275_T	289_M	0.906	0.98
28_S	31_A	0.906	0.98
30_E	34_A	0.899	0.98
269_V	294_L	0.898	0.98
252_H	280_I	0.897	0.98
31_A	35_E	0.897	0.98
238_I	266_P	0.889	0.98
353_I	357_I	0.888	0.98
126_N	181_L	0.888	0.98
331_S	345_V	0.886	0.98
275_T	281_K	0.884	0.98
354_D	358_D	0.880	0.98
64_D	67_N	0.876	0.98
141_Q	172_E	0.875	0.98
352_D	355_T	0.874	0.98
190_Y	361_L	0.871	0.98
271_V	294_L	0.865	0.98
265_L	268_N	0.859	0.98
153_R	156_E	0.859	0.98
33_I	63_K	0.858	0.98
272_T	289_M	0.853	0.97
353_I	356_F	0.851	0.97
235_T	287_M	0.850	0.97
93_D	97_E	0.849	0.97
310_R	313_Q	0.840	0.97
154_W	160_F	0.838	0.97
27_E	73_N	0.838	0.97
255_T	260_V	0.834	0.97
283_R	287_M	0.832	0.97
81_M	85_L	0.831	0.97
242_T	248_A	0.830	0.97
262_I	283_R	0.830	0.97
201_V	324_S	0.830	0.97
129_L	191_L	0.827	0.97
133_P	140_S	0.820	0.97
165_L	181_L	0.817	0.97
291_K	295_Y	0.816	0.97
38_E	41_A	0.813	0.97
277_R	288_K	0.808	0.97
145_S	170_G	0.807	0.96
324_S	332_M	0.806	0.96
33_I	62_L	0.804	0.96
79_L	105_L	0.803	0.96
340_T	348_V	0.803	0.96
133_P	168_L	0.801	0.96
326_V	332_M	0.801	0.96
103_K	106_T	0.793	0.96
40_M	59_A	0.789	0.96
181_L	288_K	0.789	0.96
39_Q	55_V	0.789	0.96
167_Y	178_V	0.787	0.96
230_D	291_K	0.787	0.96
281_K	284_E	0.784	0.96
201_V	326_V	0.783	0.96
297_R	300_E	0.779	0.96
76_H	80_Q	0.778	0.96
123_D	192_K	0.777	0.96
33_I	37_D	0.776	0.96
357_I	361_L	0.776	0.96
88_E	91_D	0.771	0.95
203_I	209_S	0.771	0.95
225_F	230_D	0.771	0.95
334_K	341_E	0.770	0.95
122_Y	295_Y	0.769	0.95
145_S	175_I	0.761	0.95
229_I	291_K	0.761	0.95
110_N	113_E	0.760	0.95
97_E	100_K	0.758	0.95
72_L	75_S	0.756	0.95
102_L	106_T	0.756	0.95
103_K	107_K	0.747	0.95
105_L	109_F	0.745	0.95
248_A	255_T	0.745	0.95
241_D	265_L	0.742	0.94
141_Q	145_S	0.741	0.94
294_L	297_R	0.740	0.94
256_T	278_S	0.738	0.94
75_S	105_L	0.737	0.94
243_Y	274_Q	0.733	0.94
54_T	58_E	0.731	0.94
240_V	260_V	0.731	0.94
338_T	359_A	0.729	0.94
104_S	107_K	0.728	0.94
81_M	88_E	0.727	0.94
338_T	360_Y	0.725	0.94
85_L	88_E	0.723	0.94
240_V	287_M	0.723	0.94
79_L	109_F	0.722	0.94
346_Q	350_D	0.721	0.94
70_K	74_E	0.719	0.93
336_H	339_N	0.718	0.93
92_T	96_L	0.716	0.93
165_L	289_M	0.714	0.93
231_I	291_K	0.712	0.93
93_D	96_L	0.710	0.93
75_S	79_L	0.709	0.93
27_E	30_E	0.708	0.93
148_L	162_V	0.708	0.93
152_T	156_E	0.708	0.93
42_D	47_N	0.704	0.93
25_D	28_S	0.703	0.93
157_R	354_D	0.701	0.93
253_V	257_D	0.701	0.93
246_S	256_T	0.698	0.92
329_P	332_M	0.697	0.92
133_P	141_Q	0.696	0.92
45_F	55_V	0.696	0.92
255_T	280_I	0.696	0.92
146_M	349_M	0.695	0.92
330_Y	334_K	0.695	0.92
90_P	98_L	0.694	0.92
37_D	41_A	0.692	0.92
239_K	272_T	0.692	0.92
58_E	61_G	0.692	0.92
31_A	34_A	0.690	0.92
79_L	83_H	0.690	0.92
64_D	68_S	0.689	0.92
154_W	158_R	0.688	0.92
244_R	252_H	0.688	0.92
315_E	320_S	0.686	0.92
263_T	272_T	0.682	0.92
82_T	86_L	0.682	0.92
358_D	362_R	0.676	0.91
115_Q	186_N	0.676	0.91
152_T	178_V	0.675	0.91
83_H	87_K	0.674	0.91
65_Y	115_Q	0.674	0.91
333_V	345_V	0.672	0.91
86_L	98_L	0.672	0.91
86_L	94_L	0.672	0.91
125_N	225_F	0.671	0.91
71_K	74_E	0.670	0.91
233_I	262_I	0.667	0.91
197_V	313_Q	0.667	0.91
45_F	52_A	0.666	0.91
171_D	321_Q	0.665	0.90
148_L	167_Y	0.664	0.90
273_C	285_R	0.663	0.90
338_T	356_F	0.662	0.90
305_E	309_I	0.662	0.90
330_Y	341_E	0.661	0.90
56_I	59_A	0.661	0.90
267_T	294_L	0.660	0.90
255_T	272_T	0.657	0.90
287_M	291_K	0.655	0.90
25_D	29_K	0.653	0.90
94_L	97_E	0.652	0.90
82_T	98_L	0.652	0.90
30_E	66_V	0.651	0.90
45_F	51_K	0.649	0.89
86_L	102_L	0.646	0.89
79_L	101_E	0.641	0.89
273_C	289_M	0.638	0.89
231_I	294_L	0.637	0.89
237_D	266_P	0.637	0.89
75_S	112_F	0.637	0.89
107_K	110_N	0.636	0.88
135_A	316_I	0.635	0.88
131_L	148_L	0.633	0.88
154_W	357_I	0.632	0.88
239_K	287_M	0.632	0.88
77_E	80_Q	0.631	0.88
31_A	42_D	0.631	0.88
227_D	302_Q	0.630	0.88
262_I	271_V	0.629	0.88
166_D	179_T	0.629	0.88
189_G	361_L	0.627	0.88
225_F	292_A	0.625	0.88
141_Q	176_K	0.624	0.87
243_Y	263_T	0.624	0.87
265_L	269_V	0.622	0.87
138_T	172_E	0.622	0.87
79_L	106_T	0.621	0.87
35_E	38_E	0.621	0.87
139_E	213_H	0.621	0.87
150_M	353_I	0.621	0.87
142_D	145_S	0.619	0.87
245_A	259_A	0.614	0.87
338_T	341_E	0.612	0.86
248_A	257_D	0.612	0.86
271_V	289_M	0.611	0.86
145_S	167_Y	0.610	0.86
343_G	347_A	0.610	0.86
331_S	341_E	0.609	0.86
342_M	356_F	0.608	0.86
127_A	188_Y	0.608	0.86
308_E	311_G	0.608	0.86
271_V	293_K	0.606	0.86
55_V	59_A	0.604	0.86
84_D	88_E	0.603	0.86
197_V	314_K	0.603	0.86
61_G	119_S	0.603	0.86
218_S	316_I	0.602	0.86
29_K	65_Y	0.601	0.85
356_F	359_A	0.601	0.85
332_M	336_H	0.600	0.85
82_T	94_L	0.597	0.85
132_H	218_S	0.596	0.85
40_M	52_A	0.596	0.85
243_Y	259_A	0.596	0.85
138_T	171_D	0.596	0.85
153_R	157_R	0.595	0.85
225_F	295_Y	0.594	0.85
234_R	237_D	0.593	0.85
228_E	231_I	0.591	0.85
149_R	153_R	0.590	0.84
183_K	187_A	0.588	0.84
60_N	63_K	0.587	0.84
83_H	102_L	0.587	0.84
62_L	66_V	0.586	0.84
76_H	109_F	0.585	0.84
197_V	216_F	0.583	0.84
38_E	42_D	0.583	0.84
281_K	285_R	0.583	0.84
306_L	310_R	0.581	0.84
142_D	327_F	0.581	0.84
285_R	289_M	0.580	0.83
133_P	167_Y	0.577	0.83
86_L	95_Q	0.576	0.83
347_A	350_D	0.567	0.82
209_S	213_H	0.567	0.82
78_E	82_T	0.565	0.82
255_T	281_K	0.564	0.82
245_A	272_T	0.563	0.82
187_A	191_L	0.563	0.82
131_L	217_V	0.562	0.81
51_K	55_V	0.561	0.81
145_S	172_E	0.561	0.81
118_L	192_K	0.561	0.81
197_V	320_S	0.560	0.81
134_G	216_F	0.559	0.81
91_D	94_L	0.557	0.81
252_H	278_S	0.556	0.81
81_M	97_E	0.555	0.81
166_D	177_S	0.554	0.81
146_M	205_P	0.554	0.81
54_T	57_N	0.553	0.80
243_Y	270_V	0.553	0.80
135_A	317_G	0.552	0.80
168_L	177_S	0.549	0.80
68_S	112_F	0.548	0.80
82_T	85_L	0.546	0.80
208_S	213_H	0.542	0.79
225_F	299_I	0.541	0.79
197_V	218_S	0.540	0.79
140_S	213_H	0.537	0.79
229_I	299_I	0.537	0.79
294_L	298_R	0.535	0.78
195_K	313_Q	0.533	0.78
160_F	190_Y	0.531	0.78
29_K	62_L	0.530	0.78
218_S	315_E	0.530	0.78
52_A	59_A	0.529	0.77
146_M	200_L	0.529	0.77
85_L	98_L	0.529	0.77
237_D	265_L	0.528	0.77
61_G	124_K	0.524	0.77
109_F	113_E	0.524	0.77
149_R	152_T	0.523	0.77
326_V	330_Y	0.523	0.77
271_V	276_E	0.522	0.77
242_T	255_T	0.522	0.77
309_I	313_Q	0.521	0.76
144_G	175_I	0.520	0.76
233_I	291_K	0.519	0.76
228_E	288_K	0.518	0.76
130_E	211_R	0.518	0.76
220_E	293_K	0.517	0.76
248_A	283_R	0.517	0.76
133_P	176_K	0.515	0.76
53_Q	56_I	0.515	0.76
222_M	292_A	0.514	0.75
316_I	320_S	0.514	0.75
140_S	197_V	0.513	0.75
240_V	263_T	0.512	0.75
331_S	336_H	0.512	0.75
260_V	271_V	0.512	0.75
134_G	197_V	0.512	0.75
242_T	280_I	0.512	0.75
132_H	220_E	0.511	0.75
84_D	87_K	0.511	0.75
246_S	272_T	0.511	0.75
30_E	33_I	0.510	0.75
333_V	342_M	0.510	0.75
216_F	320_S	0.508	0.75
163_E	281_K	0.507	0.74
140_S	217_V	0.507	0.74
257_D	280_I	0.506	0.74
135_A	140_S	0.504	0.74
57_N	124_K	0.504	0.74
307_D	310_R	0.502	0.74
318_W	324_S	0.501	0.74
140_S	168_L	0.501	0.74
239_K	256_T	0.501	0.74
82_T	101_E	0.500	0.73
252_H	275_T	0.500	0.73

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	0.8415	100	0.127	Contact Map
2ihr1	1	0.9536	100	0.135	Contact Map
1gqeA	1	0.9891	100	0.136	Contact Map
3d5aX	1	0.929	100	0.138	Contact Map
2b3tB	1	0.8005	100	0.141	Contact Map
1rq0A	3	0.8415	100	0.192	Contact Map
2rsmA	1	0.3142	100	0.706	Contact Map
3j7yp	1	0.1585	100	0.745	Contact Map
1j26A	1	0.2377	100	0.795	Contact Map
4dh9Y	1	0.2596	99.9	0.807	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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