RF2 - ECOLI - GREMLIN Contacts

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RF2 - Peptide chain release factor 2

UniProt:	P07012	Sequences: MFEINPVNNRIQDLTERSDVLRGYLDYDAKKERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEADDEETFNEAVAELDALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRTSGAGGQHVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYELEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSRIKDLRTGVETRNTQAVLDGSLDQFIEASLKAGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10762
Length:	365 (335)
Sequences:	5943 (3102)
Seq/√Len:	169.5

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
299_E	302_K	4.414	1.00
297_E	301_Q	3.191	1.00
301_Q	305_A	3.060	1.00
130_L	181_I	3.021	1.00
33_R	59_E	2.996	1.00
159_R	354_D	2.980	1.00
328_L	349_L	2.736	1.00
31_K	71_D	2.729	1.00
298_L	302_K	2.724	1.00
244_Y	273_Q	2.723	1.00
78_E	82_G	2.577	1.00
156_A	183_I	2.572	1.00
241_I	263_I	2.527	1.00
49_E	52_R	2.489	1.00
127_D	225_E	2.488	1.00
245_R	258_E	2.480	1.00
153_L	163_T	2.480	1.00
239_L	263_I	2.457	1.00
344_N	347_A	2.405	1.00
239_L	288_M	2.362	1.00
149_E	181_I	2.348	1.00
72_Q	109_K	2.309	1.00
37_V	56_L	2.260	1.00
263_I	288_M	2.180	1.00
240_R	266_I	2.162	1.00
302_K	306_E	2.159	1.00
281_H	285_D	2.124	1.00
149_E	179_V	2.097	1.00
159_R	191_W	2.088	1.00
45_D	48_N	2.081	1.00
348_V	356_F	2.062	1.00
36_E	40_E	2.031	1.00
246_T	253_H	1.999	1.00
249_A	253_H	1.996	1.00
136_S	217_F	1.993	1.00
52_R	55_A	1.988	1.00
79_D	82_G	1.954	1.00
69_T	116_R	1.943	1.00
64_E	68_D	1.910	1.00
347_A	352_S	1.905	1.00
112_Q	116_R	1.896	1.00
164_E	184_S	1.892	1.00
300_M	304_N	1.864	1.00
40_E	52_R	1.850	1.00
80_V	103_L	1.815	1.00
132_I	145_A	1.811	1.00
249_A	278_R	1.811	1.00
208_D	212_R	1.776	1.00
148_L	218_S	1.753	1.00
253_H	257_T	1.751	1.00
149_E	153_L	1.747	1.00
75_Q	79_D	1.732	1.00
109_K	112_Q	1.715	1.00
253_H	278_R	1.706	1.00
155_W	354_D	1.687	1.00
296_Y	300_M	1.679	1.00
105_A	109_K	1.658	1.00
242_D	264_T	1.641	1.00
253_H	259_S	1.635	1.00
304_N	308_Q	1.635	1.00
84_L	107_E	1.627	1.00
340_V	355_Q	1.626	1.00
38_N	64_E	1.618	1.00
164_E	182_K	1.611	1.00
300_M	303_K	1.606	1.00
40_E	43_Q	1.589	1.00
277_D	282_K	1.581	1.00
127_D	184_S	1.578	1.00
208_D	214_H	1.569	1.00
41_L	57_G	1.568	1.00
163_T	181_I	1.567	1.00
60_R	64_E	1.566	1.00
35_E	38_N	1.538	1.00
253_H	256_R	1.537	1.00
149_E	165_I	1.518	1.00
38_N	60_R	1.487	1.00
168_E	176_I	1.487	1.00
241_I	284_K	1.484	1.00
277_D	286_Q	1.482	1.00
264_T	271_V	1.468	1.00
333_I	356_F	1.460	1.00
328_L	345_T	1.446	1.00
229_D	292_K	1.443	1.00
299_E	303_K	1.423	1.00
246_T	256_R	1.419	1.00
150_R	350_D	1.394	1.00
276_N	286_Q	1.391	1.00
70_L	74_K	1.387	1.00
76_G	109_K	1.377	1.00
243_V	258_E	1.367	1.00
285_D	289_K	1.366	1.00
162_K	184_S	1.362	1.00
243_V	261_V	1.358	1.00
303_K	307_K	1.345	1.00
290_Q	294_K	1.336	1.00
101_A	105_A	1.331	1.00
51_E	54_Q	1.330	1.00
51_E	55_A	1.320	1.00
240_R	264_T	1.319	1.00
306_E	309_A	1.316	1.00
286_Q	289_K	1.300	1.00
158_S	352_S	1.294	1.00
108_E	112_Q	1.291	1.00
132_I	179_V	1.279	1.00
165_I	179_V	1.276	1.00
156_A	163_T	1.257	1.00
345_T	349_L	1.247	1.00
97_N	101_A	1.245	1.00
161_F	192_L	1.244	1.00
281_H	284_K	1.240	1.00
331_S	346_Q	1.231	1.00
239_L	266_I	1.228	1.00
342_T	348_V	1.224	1.00
68_D	72_Q	1.219	1.00
53_A	57_G	1.217	1.00
28_D	32_E	1.216	1.00
230_I	296_Y	1.216	1.00
315_S	321_S	1.214	1.00
301_Q	304_N	1.201	1.00
33_R	36_E	1.192	1.00
270_I	298_L	1.191	1.00
41_L	46_V	1.191	1.00
34_L	60_R	1.179	1.00
139_T	171_G	1.168	1.00
204_K	211_G	1.157	1.00
325_S	336_L	1.154	1.00
348_V	353_L	1.151	1.00
76_G	102_E	1.148	1.00
125_S	187_Y	1.146	1.00
132_I	220_A	1.143	1.00
182_K	225_E	1.137	1.00
69_T	72_Q	1.136	1.00
217_F	316_D	1.128	1.00
260_A	275_Q	1.126	1.00
98_E	102_E	1.117	1.00
154_R	350_D	1.110	1.00
153_L	181_I	1.100	1.00
43_Q	46_V	1.097	1.00
282_K	289_K	1.097	1.00
333_I	348_V	1.095	1.00
76_G	110_L	1.091	1.00
304_N	307_K	1.090	1.00
129_Y	182_K	1.086	1.00
265_H	269_G	1.075	1.00
191_W	358_E	1.067	1.00
342_T	355_Q	1.067	1.00
208_D	211_G	1.067	1.00
129_Y	166_I	1.065	1.00
183_I	192_L	1.058	0.99
100_V	104_D	1.054	0.99
305_A	309_A	1.052	0.99
107_E	111_A	1.048	0.99
253_H	258_E	1.046	0.99
236_P	239_L	1.043	0.99
72_Q	76_G	1.038	0.99
50_P	53_A	1.035	0.99
244_Y	262_R	1.031	0.99
344_N	355_Q	1.029	0.99
123_Y	126_A	1.026	0.99
191_W	354_D	1.023	0.99
128_C	190_G	1.020	0.99
96_F	100_V	1.019	0.99
243_V	253_H	1.017	0.99
82_G	85_E	1.017	0.99
158_S	350_D	1.016	0.99
176_I	179_V	1.015	0.99
308_Q	312_D	1.010	0.99
97_N	100_V	1.007	0.99
143_D	173_V	1.007	0.99
73_M	77_L	1.006	0.99
35_E	39_A	1.005	0.99
340_V	359_A	1.003	0.99
71_D	74_K	1.000	0.99
130_L	183_I	0.995	0.99
273_Q	276_N	0.989	0.99
342_T	345_T	0.986	0.99
95_T	99_A	0.985	0.99
355_Q	359_A	0.984	0.99
302_K	305_A	0.981	0.99
303_K	306_E	0.981	0.99
74_K	78_E	0.976	0.99
147_M	328_L	0.974	0.99
265_H	268_T	0.970	0.99
50_P	54_Q	0.964	0.99
234_I	288_M	0.963	0.99
155_W	191_W	0.958	0.99
101_A	104_D	0.955	0.99
196_T	221_F	0.949	0.99
33_R	40_E	0.949	0.99
145_A	218_S	0.949	0.99
68_D	71_D	0.942	0.99
221_F	311_E	0.942	0.99
125_S	186_D	0.939	0.99
194_T	360_S	0.936	0.99
67_V	71_D	0.927	0.99
242_D	262_R	0.926	0.99
47_W	53_A	0.924	0.99
142_Q	173_V	0.923	0.99
123_Y	300_M	0.920	0.99
329_D	332_R	0.919	0.99
297_E	300_M	0.918	0.99
311_E	314_K	0.918	0.99
270_I	295_L	0.912	0.98
79_D	106_L	0.912	0.98
31_K	74_K	0.912	0.98
31_K	35_E	0.911	0.98
149_E	176_I	0.907	0.98
161_F	188_A	0.907	0.98
81_S	85_E	0.907	0.98
253_H	281_H	0.899	0.98
276_N	290_Q	0.895	0.98
353_L	357_I	0.894	0.98
62_S	186_D	0.894	0.98
276_N	282_K	0.894	0.98
165_I	168_E	0.893	0.98
32_E	36_E	0.888	0.98
65_A	68_D	0.885	0.98
47_W	50_P	0.884	0.98
29_A	32_E	0.879	0.98
127_D	182_K	0.877	0.98
34_L	67_V	0.875	0.98
239_L	267_P	0.874	0.98
191_W	361_L	0.873	0.98
34_L	64_E	0.867	0.98
266_I	269_G	0.866	0.98
331_S	345_T	0.861	0.98
354_D	358_E	0.856	0.98
82_G	86_L	0.848	0.98
154_R	157_E	0.847	0.98
236_P	288_M	0.844	0.97
130_L	192_L	0.844	0.97
273_Q	290_Q	0.842	0.97
352_S	355_Q	0.833	0.97
202_V	325_S	0.832	0.97
256_R	261_V	0.832	0.97
104_D	107_E	0.830	0.97
284_K	288_M	0.828	0.97
272_T	295_L	0.825	0.97
39_A	42_E	0.824	0.97
166_I	182_K	0.823	0.97
146_S	171_G	0.823	0.97
325_S	332_R	0.819	0.97
94_E	98_E	0.817	0.97
353_L	356_F	0.817	0.97
155_W	161_F	0.815	0.97
263_I	284_K	0.813	0.97
28_D	74_K	0.811	0.97
134_A	141_A	0.810	0.97
292_K	296_Y	0.804	0.97
40_E	56_L	0.802	0.97
243_V	249_A	0.802	0.97
202_V	327_V	0.801	0.97
327_V	332_R	0.800	0.97
126_A	227_D	0.797	0.96
34_L	63_L	0.797	0.96
226_V	231_D	0.796	0.96
104_D	108_E	0.796	0.96
282_K	285_D	0.793	0.96
146_S	176_I	0.789	0.96
278_R	289_K	0.789	0.96
298_L	301_Q	0.788	0.96
80_V	106_L	0.787	0.96
103_L	107_E	0.787	0.96
41_L	60_R	0.786	0.96
26_D	29_A	0.783	0.96
34_L	38_N	0.780	0.96
182_K	289_K	0.779	0.96
168_E	179_V	0.777	0.96
340_V	348_V	0.776	0.96
28_D	31_K	0.774	0.96
204_K	329_D	0.774	0.96
134_A	169_S	0.772	0.96
230_I	292_K	0.771	0.96
123_Y	296_Y	0.771	0.96
231_D	292_K	0.770	0.96
334_K	341_E	0.764	0.95
204_K	210_G	0.763	0.95
111_A	114_E	0.762	0.95
357_I	361_L	0.757	0.95
77_L	81_S	0.756	0.95
295_L	298_L	0.755	0.95
124_D	193_R	0.754	0.95
94_E	97_N	0.744	0.95
73_M	76_G	0.741	0.95
244_Y	275_Q	0.740	0.95
76_G	106_L	0.739	0.95
142_Q	146_S	0.738	0.95
249_A	256_R	0.737	0.95
338_T	359_A	0.736	0.94
242_D	266_I	0.736	0.94
198_V	313_N	0.730	0.94
26_D	30_K	0.730	0.94
43_Q	48_N	0.729	0.94
257_T	279_S	0.726	0.94
241_I	261_V	0.726	0.94
87_A	99_A	0.725	0.94
106_L	110_L	0.722	0.94
338_T	360_S	0.722	0.94
254_V	258_E	0.721	0.94
241_I	288_M	0.721	0.94
80_V	110_L	0.718	0.94
155_W	159_R	0.716	0.94
82_G	89_E	0.716	0.94
346_Q	350_D	0.716	0.94
86_L	89_E	0.715	0.94
219_S	317_I	0.715	0.94
232_I	292_K	0.715	0.94
32_E	35_E	0.715	0.94
72_Q	75_Q	0.712	0.93
166_I	290_Q	0.711	0.93
247_S	257_T	0.711	0.93
158_S	354_D	0.711	0.93
55_A	59_E	0.710	0.93
136_S	318_G	0.709	0.93
38_N	42_E	0.705	0.93
330_D	334_K	0.704	0.93
105_A	108_E	0.704	0.93
71_D	75_Q	0.702	0.93
76_G	113_L	0.702	0.93
76_G	80_V	0.701	0.93
256_R	281_H	0.698	0.93
264_T	273_Q	0.698	0.93
134_A	142_Q	0.697	0.93
336_L	339_G	0.697	0.93
91_D	99_A	0.697	0.93
240_R	273_Q	0.695	0.93
46_V	56_L	0.695	0.93
153_L	157_E	0.693	0.93
358_E	362_K	0.693	0.93
93_E	97_N	0.693	0.93
83_L	87_A	0.690	0.92
274_C	286_Q	0.690	0.92
149_E	163_T	0.690	0.92
80_V	84_L	0.688	0.92
238_D	267_P	0.688	0.92
89_E	92_D	0.688	0.92
147_M	349_L	0.684	0.92
245_R	253_H	0.682	0.92
153_L	179_V	0.681	0.92
126_A	226_V	0.680	0.92
59_E	62_S	0.679	0.92
84_L	88_V	0.679	0.92
306_E	310_M	0.678	0.92
227_D	230_I	0.678	0.92
83_L	99_A	0.678	0.92
98_E	101_A	0.677	0.92
234_I	263_I	0.676	0.92
65_A	116_R	0.675	0.92
95_T	98_E	0.675	0.92
57_G	60_R	0.675	0.92
333_I	345_T	0.674	0.91
338_T	356_F	0.669	0.91
288_M	292_K	0.668	0.91
172_E	322_Q	0.666	0.91
256_R	273_Q	0.660	0.91
78_E	81_S	0.660	0.91
46_V	52_R	0.659	0.91
151_M	353_L	0.659	0.91
217_F	318_G	0.650	0.90
263_I	272_T	0.649	0.90
244_Y	264_T	0.648	0.90
46_V	53_A	0.645	0.90
149_E	168_E	0.645	0.90
226_V	293_A	0.643	0.89
232_I	295_L	0.643	0.89
268_T	295_L	0.640	0.89
167_E	180_T	0.638	0.89
116_R	187_Y	0.638	0.89
310_M	313_N	0.635	0.89
108_E	111_A	0.634	0.89
111_A	115_F	0.633	0.89
274_C	290_Q	0.633	0.89
65_A	69_T	0.631	0.89
338_T	341_E	0.629	0.88
87_A	95_T	0.628	0.88
132_I	149_E	0.627	0.88
142_Q	177_K	0.627	0.88
356_F	359_A	0.626	0.88
63_L	67_V	0.625	0.88
36_E	39_A	0.622	0.88
190_G	361_L	0.622	0.88
31_K	67_V	0.622	0.88
332_R	336_L	0.622	0.88
56_L	60_R	0.621	0.88
85_E	89_E	0.619	0.88
266_I	270_I	0.617	0.87
128_C	189_Y	0.615	0.87
87_A	103_L	0.613	0.87
272_T	294_K	0.613	0.87
244_Y	260_A	0.613	0.87
240_R	288_M	0.611	0.87
272_T	290_Q	0.611	0.87
155_W	357_I	0.611	0.87
80_V	102_E	0.610	0.87
331_S	341_E	0.610	0.87
246_T	260_A	0.609	0.87
77_L	110_L	0.607	0.87
229_D	232_I	0.606	0.87
342_T	356_F	0.606	0.87
343_R	347_A	0.603	0.86
235_N	238_D	0.603	0.86
143_D	146_S	0.602	0.86
92_D	95_T	0.600	0.86
184_S	188_A	0.597	0.86
62_S	120_S	0.597	0.86
140_E	214_H	0.597	0.86
61_S	64_E	0.596	0.86
330_D	341_E	0.592	0.85
307_K	311_E	0.592	0.85
198_V	217_F	0.592	0.85
146_S	168_E	0.591	0.85
249_A	258_E	0.591	0.85
286_Q	290_Q	0.589	0.85
150_R	154_R	0.588	0.85
80_V	107_E	0.587	0.85
119_F	193_R	0.587	0.85
41_L	53_A	0.586	0.85
30_K	66_V	0.585	0.85
309_A	312_D	0.585	0.85
143_D	328_L	0.585	0.85
169_S	178_S	0.584	0.84
133_Q	219_S	0.584	0.84
83_L	95_T	0.583	0.84
84_L	103_L	0.583	0.84
256_R	282_K	0.582	0.84
139_T	173_V	0.581	0.84
210_G	214_H	0.581	0.84
282_K	286_Q	0.580	0.84
226_V	296_Y	0.580	0.84
188_A	192_L	0.578	0.84
32_E	43_Q	0.577	0.84
154_R	158_S	0.576	0.84
132_I	218_S	0.576	0.84
209_S	214_H	0.575	0.84
246_T	273_Q	0.572	0.83
39_A	43_Q	0.571	0.83
347_A	350_D	0.570	0.83
55_A	58_K	0.569	0.83
141_A	198_V	0.567	0.83
79_D	83_L	0.565	0.83
244_Y	271_V	0.564	0.82
146_S	173_V	0.560	0.82
141_A	214_H	0.557	0.82
147_M	206_P	0.556	0.82
52_R	56_L	0.555	0.81
167_E	178_S	0.555	0.81
253_H	279_S	0.554	0.81
134_A	168_E	0.553	0.81
83_L	102_E	0.550	0.81
83_L	86_L	0.550	0.81
66_V	116_R	0.548	0.81
150_R	153_L	0.548	0.81
87_A	96_F	0.545	0.80
82_G	98_E	0.544	0.80
161_F	191_W	0.543	0.80
230_I	300_M	0.542	0.80
141_A	218_S	0.541	0.80
272_T	277_D	0.541	0.80
198_V	219_S	0.540	0.80
135_G	217_F	0.539	0.79
234_I	292_K	0.539	0.79
81_S	84_L	0.539	0.79
226_V	300_M	0.537	0.79
243_V	281_H	0.536	0.79
62_S	125_S	0.535	0.79
53_A	60_R	0.532	0.79
223_Y	293_A	0.532	0.79
131_D	212_R	0.532	0.79
31_K	34_L	0.531	0.78
295_L	299_E	0.530	0.78
30_K	63_L	0.529	0.78
217_F	321_S	0.529	0.78
333_I	342_T	0.529	0.78
147_M	201_L	0.528	0.78
69_T	113_L	0.526	0.78
135_G	198_V	0.525	0.78
134_A	177_K	0.523	0.77
331_S	336_L	0.522	0.77
243_V	256_R	0.521	0.77
241_I	264_T	0.521	0.77
258_E	281_H	0.521	0.77
247_S	273_Q	0.521	0.77
107_E	110_L	0.521	0.77
48_N	53_A	0.519	0.77
249_A	284_K	0.518	0.77
261_V	272_T	0.517	0.77
238_D	266_I	0.516	0.77
221_F	294_K	0.516	0.77
240_R	257_T	0.513	0.76
139_T	172_E	0.512	0.76
54_Q	57_G	0.510	0.76
124_D	190_G	0.510	0.76
198_V	321_S	0.508	0.75
253_H	276_N	0.507	0.75
194_T	357_I	0.507	0.75
85_E	88_V	0.505	0.75
133_Q	221_F	0.504	0.75
136_S	141_A	0.503	0.75
147_M	217_F	0.503	0.75
76_G	79_D	0.502	0.75
247_S	258_E	0.501	0.74
198_V	218_S	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	0.8438	100	0.127	Contact Map
1gqeA	1	0.9918	100	0.128	Contact Map
2ihr1	1	0.9534	100	0.132	Contact Map
3d5aX	1	0.9288	100	0.139	Contact Map
2b3tB	1	0.7973	100	0.142	Contact Map
1rq0A	3	0.8411	100	0.191	Contact Map
2rsmA	1	0.3151	100	0.705	Contact Map
3j7yp	1	0.1589	100	0.744	Contact Map
1j26A	1	0.2384	100	0.793	Contact Map
4dh9Y	1	0.2904	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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