RF1 - ECOLI - GREMLIN Contacts

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RF1 - Peptide chain release factor 1

UniProt:	P0A7I0	Sequences: MKPSIVAKLEALHERHEEVQALLGDAQTIADQERFRALSREYAQLSDVSRCFTDWQQVQEDIETAQMMLDDPEMREMAQDELREAKEKSEQLEQQLQVLLLPKDPDDERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMSASEGEHGGYKEIIAKISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSACTVAVMPELPDAELPDINPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLLGSGDRSDRNRTYNFPQGRVTDHRINLTLYRLDEVMEGKLDMLIEPIIQEHQADQLAALSEQE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10761
Length:	360 (338)
Sequences:	5951 (3119)
Seq/√Len:	169.6

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
282_E	285_K	4.374	1.00
280_A	284_A	3.172	1.00
284_A	288_Q	3.068	1.00
15_R	41_E	2.960	1.00
142_R	338_D	2.945	1.00
113_L	164_A	2.942	1.00
281_A	285_K	2.726	1.00
312_F	333_M	2.701	1.00
227_F	256_E	2.692	1.00
13_H	53_T	2.656	1.00
139_A	166_I	2.636	1.00
60_E	64_T	2.561	1.00
224_I	246_I	2.505	1.00
31_D	34_R	2.466	1.00
110_N	208_E	2.466	1.00
136_S	146_V	2.460	1.00
222_L	246_I	2.430	1.00
228_R	241_D	2.401	1.00
328_R	331_E	2.366	1.00
222_L	271_L	2.363	1.00
19_V	38_L	2.337	1.00
132_F	164_A	2.314	1.00
246_I	271_L	2.194	1.00
285_K	289_A	2.168	1.00
223_R	249_L	2.147	1.00
264_H	268_A	2.114	1.00
27_Q	30_A	2.105	1.00
132_F	162_I	2.094	1.00
142_R	174_R	2.062	1.00
34_R	37_A	2.050	1.00
332_V	340_L	2.048	1.00
232_A	236_H	1.989	1.00
229_S	236_H	1.981	1.00
119_T	200_A	1.970	1.00
18_E	22_L	1.954	1.00
91_Q	95_Q	1.952	1.00
61_D	64_T	1.948	1.00
66_Q	86_K	1.909	1.00
331_E	336_K	1.908	1.00
46_S	50_R	1.878	1.00
283_M	287_Q	1.874	1.00
147_E	167_S	1.853	1.00
54_D	88_K	1.852	1.00
115_V	128_A	1.833	1.00
232_A	261_R	1.825	1.00
22_L	34_R	1.820	1.00
131_L	201_C	1.812	1.00
57_Q	61_D	1.775	1.00
132_F	136_S	1.757	1.00
191_E	195_R	1.752	1.00
138_Y	338_D	1.711	1.00
236_H	240_T	1.706	1.00
279_H	283_M	1.693	1.00
236_H	261_R	1.689	1.00
62_I	82_L	1.676	1.00
324_L	339_M	1.665	1.00
225_D	247_T	1.663	1.00
287_Q	291_A	1.650	1.00
260_E	265_K	1.626	1.00
22_L	25_D	1.625	1.00
146_V	164_A	1.618	1.00
236_H	242_S	1.613	1.00
20_Q	46_S	1.612	1.00
51_C	95_Q	1.596	1.00
147_E	165_K	1.590	1.00
283_M	286_R	1.587	1.00
110_N	167_S	1.583	1.00
88_K	91_Q	1.581	1.00
42_Y	46_S	1.558	1.00
191_E	197_H	1.548	1.00
236_H	239_T	1.526	1.00
23_L	39_S	1.524	1.00
58_V	89_S	1.522	1.00
260_E	269_K	1.518	1.00
80_D	84_E	1.508	1.00
151_A	159_Y	1.508	1.00
224_I	267_K	1.490	1.00
17_E	20_Q	1.483	1.00
20_Q	42_Y	1.478	1.00
247_T	254_V	1.472	1.00
132_F	148_I	1.468	1.00
317_V	340_L	1.460	1.00
282_E	286_R	1.439	1.00
229_S	239_T	1.437	1.00
80_D	83_R	1.425	1.00
312_F	329_L	1.424	1.00
226_T	244_I	1.401	1.00
145_R	167_S	1.392	1.00
33_E	37_A	1.382	1.00
259_D	269_K	1.381	1.00
133_R	334_E	1.370	1.00
273_V	277_R	1.364	1.00
58_V	85_A	1.364	1.00
58_V	92_L	1.361	1.00
268_A	272_S	1.347	1.00
148_I	162_I	1.343	1.00
286_R	290_E	1.343	1.00
226_T	241_D	1.330	1.00
52_F	56_Q	1.323	1.00
33_E	36_R	1.320	1.00
51_C	99_L	1.311	1.00
289_A	292_S	1.301	1.00
139_A	146_V	1.290	1.00
223_R	247_T	1.288	1.00
141_A	336_K	1.270	1.00
269_K	272_S	1.250	1.00
329_L	333_M	1.241	1.00
115_V	162_I	1.241	1.00
264_H	267_K	1.231	1.00
222_L	249_L	1.228	1.00
210_P	213_E	1.227	1.00
15_R	18_E	1.221	1.00
144_W	175_L	1.218	1.00
90_E	94_Q	1.213	1.00
284_A	287_Q	1.210	1.00
326_L	332_V	1.204	1.00
10_E	14_E	1.203	1.00
35_F	39_S	1.197	1.00
87_E	91_Q	1.189	1.00
315_G	330_D	1.182	1.00
253_I	281_A	1.173	1.00
23_L	28_T	1.166	1.00
122_D	154_G	1.162	1.00
165_K	208_E	1.161	1.00
187_V	194_G	1.161	1.00
84_E	88_K	1.160	1.00
200_A	300_S	1.158	1.00
16_H	42_Y	1.157	1.00
50_R	54_D	1.147	1.00
76_E	80_D	1.146	1.00
309_T	320_H	1.145	1.00
88_K	92_L	1.138	1.00
137_R	334_E	1.136	1.00
317_V	332_V	1.132	1.00
108_E	170_G	1.117	1.00
287_Q	290_E	1.117	1.00
115_V	203_V	1.104	1.00
243_A	258_Q	1.102	1.00
326_L	339_M	1.101	1.00
32_Q	35_F	1.094	1.00
112_F	149_M	1.087	1.00
51_C	54_D	1.086	1.00
332_V	337_L	1.085	1.00
112_F	165_K	1.081	1.00
136_S	164_A	1.081	1.00
61_D	85_A	1.080	1.00
265_K	272_S	1.078	1.00
166_I	175_L	1.068	1.00
25_D	28_T	1.067	1.00
64_T	67_M	1.065	1.00
219_P	222_L	1.061	1.00
288_Q	292_S	1.056	0.99
227_F	245_R	1.052	0.99
191_E	194_G	1.051	0.99
69_L	82_L	1.049	0.99
74_M	78_A	1.049	0.99
81_E	85_A	1.048	0.99
62_I	89_S	1.047	0.99
236_H	241_D	1.046	0.99
174_R	342_E	1.040	0.99
298_L	305_D	1.040	0.99
17_E	21_A	1.039	0.99
248_H	252_G	1.027	0.99
214_L	275_G	1.027	0.99
128_A	201_C	1.026	0.99
53_T	56_Q	1.026	0.99
141_A	334_E	1.024	0.99
111_A	173_G	1.022	0.99
106_D	109_R	1.017	0.99
291_A	295_R	1.017	0.99
75_R	79_Q	1.016	0.99
15_R	22_L	1.011	0.99
324_L	343_P	1.010	0.99
328_R	339_M	1.009	0.99
113_L	166_I	1.009	0.99
54_D	58_V	1.006	0.99
226_T	236_H	1.005	0.99
59_Q	89_S	1.004	0.99
159_Y	162_I	0.998	0.99
286_R	289_A	0.998	0.99
62_I	85_A	0.996	0.99
58_V	88_K	0.994	0.99
217_I	271_L	0.992	0.99
56_Q	60_E	0.986	0.99
256_E	259_D	0.983	0.99
63_E	67_M	0.977	0.99
130_D	312_F	0.977	0.99
32_Q	36_R	0.975	0.99
126_L	156_H	0.973	0.99
55_W	59_Q	0.969	0.99
326_L	329_L	0.965	0.99
179_S	204_A	0.964	0.99
10_E	56_Q	0.957	0.99
174_R	338_D	0.954	0.99
177_F	344_I	0.952	0.99
138_Y	174_R	0.949	0.99
14_E	18_E	0.948	0.99
339_M	343_P	0.947	0.99
49_S	53_T	0.946	0.99
108_E	169_D	0.943	0.99
204_A	294_R	0.940	0.99
222_L	250_P	0.939	0.99
50_R	53_T	0.938	0.99
13_H	17_E	0.937	0.99
225_D	245_R	0.936	0.99
71_D	74_M	0.935	0.99
280_A	283_M	0.934	0.99
285_K	288_Q	0.929	0.99
294_R	297_L	0.929	0.99
29_I	35_F	0.927	0.99
253_I	278_I	0.926	0.99
83_R	87_E	0.924	0.99
29_I	32_Q	0.916	0.99
315_G	329_L	0.916	0.99
98_V	101_L	0.915	0.99
125_A	156_H	0.908	0.98
16_H	49_S	0.903	0.98
64_T	68_M	0.900	0.98
144_W	171_V	0.897	0.98
54_D	92_L	0.893	0.98
106_D	283_M	0.890	0.98
148_I	151_A	0.888	0.98
47_D	50_R	0.888	0.98
132_F	159_Y	0.887	0.98
44_Q	169_D	0.887	0.98
90_E	93_E	0.886	0.98
259_D	265_K	0.883	0.98
259_D	273_V	0.883	0.98
337_L	341_I	0.882	0.98
211_D	275_G	0.881	0.98
248_H	251_T	0.878	0.98
275_G	279_H	0.875	0.98
338_D	342_E	0.873	0.98
267_K	271_L	0.873	0.98
110_N	165_K	0.871	0.98
236_H	264_H	0.868	0.98
13_H	56_Q	0.867	0.98
213_E	216_D	0.861	0.98
11_A	14_E	0.861	0.98
256_E	273_V	0.861	0.98
94_Q	97_Q	0.859	0.98
174_R	345_I	0.857	0.98
16_H	20_Q	0.856	0.98
16_H	46_S	0.854	0.98
92_L	95_Q	0.852	0.98
138_Y	144_W	0.851	0.98
239_T	244_I	0.847	0.98
70_D	78_A	0.846	0.98
62_I	86_K	0.845	0.98
137_R	140_E	0.844	0.97
23_L	42_Y	0.842	0.97
117_A	124_A	0.840	0.97
249_L	252_G	0.839	0.97
149_M	165_K	0.838	0.97
281_A	284_A	0.833	0.97
336_K	339_M	0.825	0.97
309_T	316_R	0.825	0.97
219_P	271_L	0.823	0.97
21_A	24_G	0.820	0.97
113_L	175_L	0.819	0.97
151_A	162_I	0.816	0.97
226_T	232_A	0.816	0.97
246_I	267_K	0.809	0.97
311_N	316_R	0.807	0.97
22_L	38_L	0.806	0.97
16_H	45_L	0.802	0.97
129_G	154_G	0.798	0.96
342_E	346_Q	0.798	0.96
318_T	325_T	0.797	0.96
109_R	210_P	0.796	0.96
185_Q	309_T	0.795	0.96
255_V	278_I	0.795	0.96
129_G	159_Y	0.793	0.96
337_L	340_L	0.785	0.96
261_R	272_S	0.779	0.96
265_K	268_A	0.777	0.96
185_Q	311_N	0.775	0.96
224_I	244_I	0.772	0.96
136_S	140_E	0.767	0.96
55_W	89_S	0.767	0.96
322_I	343_P	0.765	0.96
227_F	258_Q	0.764	0.96
25_D	30_A	0.762	0.95
278_I	281_A	0.759	0.95
165_K	272_S	0.754	0.95
187_V	193_Q	0.751	0.95
324_L	332_V	0.749	0.95
69_L	78_A	0.747	0.95
232_A	239_T	0.746	0.95
117_A	125_A	0.746	0.95
55_W	58_V	0.746	0.95
224_I	271_L	0.744	0.95
202_T	301_G	0.742	0.95
54_D	57_Q	0.740	0.95
117_A	152_S	0.738	0.95
141_A	338_D	0.737	0.95
107_D	176_K	0.736	0.95
59_Q	63_E	0.735	0.94
98_V	349_Q	0.728	0.94
240_T	262_S	0.727	0.94
125_A	129_G	0.723	0.94
341_I	345_I	0.722	0.94
85_A	89_S	0.721	0.94
28_T	38_L	0.720	0.94
213_E	279_H	0.718	0.94
106_D	279_H	0.715	0.94
136_S	162_I	0.714	0.94
149_M	273_V	0.713	0.94
314_Q	325_T	0.709	0.93
313_P	316_R	0.708	0.93
209_L	213_E	0.708	0.93
87_E	90_E	0.706	0.93
322_I	344_I	0.706	0.93
65_A	85_A	0.705	0.93
58_V	62_I	0.704	0.93
239_T	264_H	0.703	0.93
14_E	17_E	0.703	0.93
28_T	34_R	0.702	0.93
41_E	44_Q	0.702	0.93
320_H	323_N	0.701	0.93
257_C	269_K	0.700	0.93
225_D	249_L	0.699	0.93
211_D	272_S	0.699	0.93
130_D	333_M	0.698	0.93
228_R	236_H	0.697	0.93
271_L	275_G	0.697	0.93
37_A	41_E	0.697	0.93
314_Q	318_T	0.696	0.93
239_T	256_E	0.695	0.93
119_T	302_D	0.695	0.93
74_M	77_M	0.692	0.93
330_D	334_E	0.692	0.93
155_E	306_R	0.692	0.93
223_R	256_E	0.690	0.92
53_T	57_Q	0.690	0.92
289_A	293_T	0.689	0.92
317_V	329_L	0.688	0.92
83_R	86_K	0.684	0.92
251_T	278_I	0.683	0.92
200_A	302_D	0.682	0.92
62_I	66_Q	0.681	0.92
247_T	256_E	0.678	0.92
28_T	35_F	0.677	0.92
132_F	151_A	0.677	0.92
230_S	240_T	0.677	0.92
20_Q	24_G	0.676	0.92
39_S	42_Y	0.675	0.92
79_Q	83_R	0.673	0.91
221_D	250_P	0.666	0.91
95_Q	99_L	0.664	0.91
65_A	82_L	0.662	0.91
61_D	65_A	0.658	0.91
132_F	146_V	0.657	0.90
134_M	337_L	0.654	0.90
43_A	46_S	0.653	0.90
48_V	99_L	0.653	0.90
211_D	214_L	0.652	0.90
257_C	273_V	0.650	0.90
60_E	63_E	0.649	0.90
237_V	241_D	0.649	0.90
217_I	246_I	0.647	0.90
109_R	209_L	0.647	0.90
99_L	170_G	0.647	0.90
44_Q	103_K	0.646	0.90
21_A	25_D	0.646	0.90
138_Y	142_R	0.643	0.89
255_V	273_V	0.640	0.89
152_S	161_E	0.639	0.89
322_I	340_L	0.639	0.89
18_E	21_A	0.638	0.89
123_E	197_H	0.638	0.89
45_L	49_S	0.634	0.89
327_Y	331_E	0.634	0.89
125_A	160_K	0.631	0.89
111_A	172_Y	0.629	0.88
150_S	163_I	0.628	0.88
181_G	297_L	0.627	0.88
138_Y	341_I	0.626	0.88
340_L	343_P	0.625	0.88
81_E	84_E	0.623	0.88
173_G	345_I	0.623	0.88
229_S	243_A	0.622	0.88
193_Q	197_H	0.622	0.88
179_S	297_L	0.622	0.88
212_A	286_R	0.621	0.88
227_F	243_A	0.621	0.88
68_M	78_A	0.620	0.88
209_L	276_A	0.619	0.88
316_R	320_H	0.618	0.88
249_L	253_I	0.618	0.88
232_A	241_D	0.615	0.87
115_V	132_F	0.615	0.87
126_L	312_F	0.614	0.87
117_A	151_A	0.614	0.87
133_R	137_R	0.613	0.87
85_A	88_K	0.613	0.87
292_S	295_R	0.611	0.87
65_A	69_L	0.611	0.87
227_F	247_T	0.611	0.87
13_H	49_S	0.608	0.87
218_N	221_D	0.606	0.87
122_D	156_H	0.606	0.87
315_G	325_T	0.605	0.86
214_L	217_I	0.605	0.86
12_L	48_V	0.605	0.86
47_D	51_C	0.601	0.86
84_E	87_E	0.600	0.86
35_F	42_Y	0.600	0.86
223_R	271_L	0.599	0.86
37_A	40_R	0.598	0.86
118_G	200_A	0.597	0.86
255_V	277_R	0.597	0.86
66_Q	82_L	0.596	0.86
239_T	265_K	0.595	0.86
171_V	175_L	0.593	0.85
126_L	129_G	0.593	0.85
115_V	201_C	0.592	0.85
192_S	197_H	0.592	0.85
167_S	171_V	0.590	0.85
137_R	141_A	0.590	0.85
38_L	42_Y	0.588	0.85
48_V	96_L	0.587	0.85
92_L	96_L	0.586	0.85
265_K	269_K	0.586	0.85
322_I	325_T	0.585	0.85
129_G	151_A	0.585	0.85
269_K	273_V	0.584	0.85
23_L	35_F	0.581	0.84
246_I	255_V	0.580	0.84
14_E	25_D	0.580	0.84
181_G	200_A	0.578	0.84
51_C	92_L	0.577	0.84
200_A	305_D	0.576	0.84
229_S	256_E	0.575	0.84
116_R	202_T	0.573	0.83
326_L	340_L	0.569	0.83
209_L	279_H	0.567	0.83
124_A	181_G	0.566	0.83
65_A	68_M	0.565	0.83
236_H	262_S	0.563	0.82
86_K	90_E	0.563	0.82
118_G	181_G	0.562	0.82
82_L	89_S	0.561	0.82
10_E	13_H	0.560	0.82
181_G	202_T	0.558	0.82
94_Q	98_V	0.558	0.82
63_E	66_Q	0.558	0.82
150_S	161_E	0.558	0.82
278_I	282_E	0.557	0.82
133_R	136_S	0.556	0.82
255_V	260_E	0.556	0.82
239_T	260_E	0.555	0.81
290_E	294_R	0.553	0.81
326_L	331_E	0.552	0.81
331_E	334_E	0.550	0.81
64_T	71_D	0.550	0.81
30_A	35_F	0.548	0.81
117_A	160_K	0.548	0.81
227_F	254_V	0.547	0.80
130_D	189_A	0.545	0.80
181_G	305_D	0.544	0.80
116_R	204_A	0.543	0.80
224_I	247_T	0.541	0.80
82_L	86_K	0.540	0.80
36_R	39_S	0.540	0.80
315_G	320_H	0.540	0.80
129_G	156_H	0.540	0.80
232_A	267_K	0.537	0.79
68_M	74_M	0.537	0.79
176_K	348_H	0.537	0.79
34_R	38_L	0.535	0.79
209_L	283_M	0.534	0.79
130_D	184_V	0.532	0.79
144_W	174_R	0.530	0.78
118_G	160_K	0.529	0.78
221_D	249_L	0.529	0.78
122_D	155_E	0.527	0.78
311_N	314_Q	0.527	0.78
102_P	176_K	0.526	0.78
128_A	159_Y	0.525	0.78
44_Q	108_E	0.524	0.78
10_E	52_F	0.524	0.78
212_A	275_G	0.523	0.77
226_T	239_T	0.522	0.77
19_V	42_Y	0.521	0.77
230_S	256_E	0.521	0.77
206_M	276_A	0.520	0.77
241_D	264_H	0.519	0.77
73_E	77_M	0.517	0.77
242_S	264_H	0.515	0.76
177_F	348_H	0.514	0.76
225_D	256_E	0.514	0.76
47_D	95_Q	0.513	0.76
217_I	275_G	0.510	0.76
116_R	161_E	0.510	0.76
12_L	45_L	0.510	0.76
65_A	78_A	0.509	0.76
226_T	264_H	0.507	0.75
58_V	61_D	0.506	0.75
298_L	301_G	0.505	0.75
204_A	277_R	0.505	0.75
181_G	298_L	0.505	0.75
69_L	77_M	0.504	0.75
223_R	240_T	0.502	0.75
89_S	93_E	0.502	0.75
77_M	80_D	0.501	0.74
317_V	326_L	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
2b3tB	1	0.8333	100	0.088	Contact Map
3d5aX	1	0.9833	100	0.098	Contact Map
1zbtA	1	0.8833	100	0.102	Contact Map
2ihr1	1	0.9528	100	0.157	Contact Map
1rq0A	3	0.8861	100	0.158	Contact Map
1gqeA	1	0.95	100	0.173	Contact Map
2rsmA	1	0.3194	100	0.702	Contact Map
3j7yp	1	0.1611	100	0.746	Contact Map
1j26A	1	0.2417	100	0.794	Contact Map
4dh9Y	1	0.2639	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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