RECF - ECOLI - GREMLIN Contacts

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RECF - DNA replication and repair protein RecF

UniProt:	P0A7H0	Sequences: MSLTRLLIRDFRNIETADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQEAFVLHGRLQGEERETAIGLTKDKQGDSKVRIDGTDGHKVAELAHLMPMQLITPEGFTLLNGGPKYRRAFLDWGCFHNEPGFFTAWSNLKRLLKQRNAALRQVTRYEQLRPWDKELIPLAEQISTWRAEYSAGIAADMADTCKQFLPEFSLTFSFQRGWEKETEYAEVLERNFERDRQLTYTAHGPHKADLRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRESGRRCLYLIDDFASELDDERRGLLASRLKATQSQVFVSAISAEHVIDMSDENSKMFTVEKGKITD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10828
Length:	357 (328)
Sequences:	5707 (4567)
Seq/√Len:	252.2

ECOLI - RECF RECN
BACSU - RECF RECN
HALSA - SPH2 RAD50 SPH1
SULSO - RAD50

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
46_L	72_G	5.077	1.00
259_R	262_G	3.891	1.00
4_T	75_Q	3.753	1.00
241_D	248_A	3.409	1.00
10_D	62_R	3.236	1.00
5_R	18_D	2.923	1.00
260_A	263_A	2.734	1.00
308_L	316_L	2.655	1.00
5_R	20_A	2.463	1.00
7_L	18_D	2.283	1.00
119_P	122_F	2.202	1.00
21_L	328_F	2.197	1.00
232_E	236_R	2.172	1.00
104_K	107_E	2.159	1.00
5_R	73_R	2.153	1.00
231_A	235_E	2.133	1.00
3_L	72_G	2.128	1.00
179_K	183_P	2.127	1.00
8_I	14_I	2.122	1.00
84_G	96_R	2.118	1.00
62_R	65_Q	2.100	1.00
10_D	65_Q	2.088	1.00
3_L	43_I	2.086	1.00
7_L	16_T	2.076	1.00
120_E	126_N	2.058	1.00
15_E	62_R	2.044	1.00
162_N	247_T	2.012	1.00
73_R	80_E	2.011	1.00
67_A	86_T	1.982	1.00
9_R	16_T	1.956	1.00
112_M	115_Q	1.954	1.00
7_L	71_H	1.934	1.00
227_E	231_A	1.927	1.00
66_E	89_K	1.909	1.00
81_T	98_D	1.908	1.00
259_R	263_A	1.896	1.00
238_F	242_R	1.832	1.00
178_D	238_F	1.827	1.00
228_T	232_E	1.800	1.00
199_I	203_M	1.797	1.00
112_M	116_L	1.789	1.00
14_I	17_A	1.781	1.00
290_T	296_R	1.751	1.00
147_F	154_L	1.750	1.00
252_H	256_L	1.717	1.00
148_F	151_W	1.708	1.00
40_L	300_L	1.680	1.00
144_E	191_W	1.675	1.00
173_Q	177_W	1.670	1.00
119_P	124_L	1.669	1.00
314_G	318_S	1.663	1.00
69_V	84_G	1.658	1.00
241_D	249_H	1.653	1.00
154_L	158_L	1.647	1.00
118_T	126_N	1.637	1.00
113_P	116_L	1.632	1.00
175_R	238_F	1.585	1.00
163_A	167_Q	1.572	1.00
113_P	117_I	1.555	1.00
240_R	244_L	1.536	1.00
15_E	65_Q	1.534	1.00
189_S	193_A	1.529	1.00
118_T	124_L	1.516	1.00
327_V	332_I	1.516	1.00
4_T	80_E	1.496	1.00
240_R	243_Q	1.496	1.00
251_P	256_L	1.495	1.00
68_F	87_K	1.492	1.00
229_E	232_E	1.479	1.00
182_I	231_A	1.476	1.00
149_T	153_N	1.475	1.00
112_M	298_L	1.475	1.00
235_E	238_F	1.474	1.00
162_N	166_R	1.465	1.00
69_V	86_T	1.465	1.00
252_H	255_D	1.464	1.00
154_L	157_L	1.456	1.00
161_R	165_L	1.454	1.00
313_R	333_S	1.448	1.00
196_S	200_A	1.438	1.00
241_D	252_H	1.437	1.00
245_T	252_H	1.433	1.00
150_A	187_Q	1.428	1.00
183_P	227_E	1.425	1.00
114_M	117_I	1.424	1.00
109_A	116_L	1.422	1.00
245_T	256_L	1.377	1.00
233_V	236_R	1.375	1.00
231_A	238_F	1.353	1.00
63_H	261_D	1.343	1.00
179_K	182_I	1.323	1.00
207_C	211_L	1.308	1.00
180_E	184_L	1.299	1.00
239_E	243_Q	1.299	1.00
265_V	269_L	1.284	1.00
157_L	184_L	1.277	1.00
241_D	245_T	1.276	1.00
336_H	339_D	1.267	1.00
71_H	84_G	1.258	1.00
245_T	249_H	1.244	1.00
61_I	89_K	1.243	1.00
147_F	151_W	1.241	1.00
118_T	122_F	1.235	1.00
148_F	152_S	1.234	1.00
131_Y	134_A	1.232	1.00
315_L	318_S	1.227	1.00
248_A	252_H	1.214	1.00
148_F	154_L	1.205	1.00
132_R	139_G	1.205	1.00
25_F	329_V	1.201	1.00
73_R	82_A	1.200	1.00
112_M	117_I	1.191	1.00
202_D	205_D	1.185	1.00
109_A	113_P	1.183	1.00
181_L	185_A	1.177	1.00
151_W	154_L	1.176	1.00
237_N	241_D	1.175	1.00
109_A	117_I	1.172	1.00
276_L	312_R	1.165	1.00
156_R	160_Q	1.163	1.00
259_R	265_V	1.162	1.00
31_A	311_E	1.158	1.00
123_T	127_G	1.156	1.00
96_R	101_D	1.148	1.00
238_F	245_T	1.148	1.00
122_F	125_L	1.148	1.00
86_T	94_K	1.147	1.00
47_G	114_M	1.147	1.00
161_R	247_T	1.146	1.00
109_A	112_M	1.143	1.00
178_D	182_I	1.137	1.00
244_L	248_A	1.135	1.00
28_L	328_F	1.133	1.00
143_N	147_F	1.131	1.00
206_T	209_Q	1.129	1.00
249_H	252_H	1.123	1.00
44_Y	49_G	1.123	1.00
147_F	158_L	1.122	1.00
157_L	164_A	1.118	1.00
9_R	69_V	1.117	1.00
180_E	183_P	1.117	1.00
245_T	248_A	1.114	1.00
43_I	328_F	1.102	1.00
227_E	235_E	1.097	1.00
122_F	126_N	1.094	1.00
150_A	184_L	1.091	1.00
228_T	231_A	1.088	1.00
229_E	233_V	1.082	1.00
119_P	126_N	1.081	1.00
182_I	186_E	1.081	1.00
180_E	185_A	1.079	1.00
238_F	241_D	1.074	1.00
154_L	161_R	1.071	1.00
238_F	253_K	1.070	1.00
189_S	195_Y	1.064	1.00
97_I	102_G	1.058	1.00
177_W	181_L	1.056	1.00
249_H	256_L	1.056	1.00
187_Q	191_W	1.053	1.00
160_Q	164_A	1.051	1.00
164_A	168_V	1.049	1.00
190_T	193_A	1.046	1.00
159_K	163_A	1.040	1.00
190_T	194_E	1.037	1.00
269_L	277_L	1.034	1.00
202_D	206_T	1.033	1.00
158_L	162_N	1.028	1.00
119_P	125_L	1.027	1.00
95_V	108_L	1.020	1.00
118_T	125_L	1.013	1.00
83_I	95_V	1.010	1.00
120_E	123_T	1.010	1.00
265_V	277_L	1.001	1.00
191_W	194_E	0.999	1.00
50_R	53_R	0.991	1.00
146_G	150_A	0.990	1.00
327_V	333_S	0.989	1.00
146_G	149_T	0.987	1.00
13_N	38_S	0.987	1.00
260_A	265_V	0.986	1.00
155_K	165_L	0.985	1.00
151_W	155_K	0.984	1.00
154_L	164_A	0.983	1.00
194_E	198_G	0.983	1.00
141_F	145_P	0.983	1.00
253_K	258_I	0.982	1.00
124_L	127_G	0.981	1.00
234_L	241_D	0.978	1.00
106_A	109_A	0.975	1.00
183_P	187_Q	0.973	1.00
200_A	204_A	0.970	1.00
27_F	331_A	0.970	1.00
141_F	144_E	0.967	1.00
201_A	205_D	0.962	1.00
245_T	251_P	0.962	1.00
8_I	39_V	0.958	1.00
119_P	127_G	0.955	1.00
192_R	199_I	0.955	1.00
234_L	238_F	0.952	1.00
11_F	68_F	0.950	1.00
11_F	60_V	0.946	1.00
237_N	249_H	0.945	1.00
12_R	38_S	0.941	1.00
234_L	249_H	0.940	1.00
237_N	240_R	0.936	1.00
95_V	102_G	0.933	1.00
299_Y	325_S	0.932	1.00
4_T	73_R	0.927	1.00
249_H	253_K	0.925	1.00
181_L	184_L	0.925	1.00
94_K	101_D	0.923	1.00
192_R	195_Y	0.922	1.00
177_W	185_A	0.919	1.00
203_M	207_C	0.913	1.00
176_P	179_K	0.909	1.00
200_A	203_M	0.906	1.00
43_I	300_L	0.902	1.00
11_F	42_A	0.902	1.00
200_A	217_T	0.902	1.00
230_Y	234_L	0.899	1.00
196_S	199_I	0.898	1.00
242_R	249_H	0.898	1.00
233_V	249_H	0.895	1.00
231_A	242_R	0.895	1.00
154_L	252_H	0.893	1.00
242_R	246_Y	0.892	1.00
245_T	253_K	0.889	1.00
178_D	235_E	0.889	1.00
167_Q	170_R	0.885	1.00
178_D	181_L	0.884	1.00
205_D	209_Q	0.883	1.00
176_P	180_E	0.880	1.00
199_I	207_C	0.879	1.00
83_I	108_L	0.876	1.00
241_D	255_D	0.876	1.00
278_M	282_R	0.875	1.00
61_I	68_F	0.875	1.00
231_A	246_Y	0.871	1.00
191_W	196_S	0.869	1.00
157_L	161_R	0.868	1.00
235_E	245_T	0.868	1.00
4_T	20_A	0.864	0.99
289_L	296_R	0.863	0.99
167_Q	171_Y	0.862	0.99
6_L	72_G	0.855	0.99
233_V	237_N	0.852	0.99
246_Y	250_G	0.851	0.99
241_D	253_K	0.847	0.99
46_L	70_L	0.844	0.99
311_E	314_G	0.843	0.99
216_L	220_F	0.843	0.99
219_S	223_G	0.842	0.99
235_E	241_D	0.842	0.99
58_G	61_I	0.841	0.99
61_I	87_K	0.837	0.99
144_E	148_F	0.832	0.99
156_R	159_K	0.831	0.99
204_A	208_K	0.831	0.99
262_G	265_V	0.828	0.99
235_E	253_K	0.823	0.99
132_R	136_L	0.820	0.99
194_E	197_A	0.819	0.99
188_I	195_Y	0.816	0.99
253_K	257_R	0.813	0.99
45_T	60_V	0.811	0.99
252_H	258_I	0.811	0.99
218_F	223_G	0.804	0.99
141_F	148_F	0.801	0.99
250_G	254_A	0.795	0.99
109_A	115_Q	0.794	0.99
241_D	258_I	0.790	0.99
106_A	114_M	0.790	0.99
227_E	241_D	0.788	0.99
105_V	117_I	0.787	0.99
217_T	221_Q	0.784	0.99
148_F	158_L	0.780	0.99
253_K	256_L	0.779	0.99
119_P	123_T	0.779	0.99
173_Q	176_P	0.778	0.99
286_G	299_Y	0.777	0.99
242_R	253_K	0.777	0.99
107_E	110_H	0.777	0.99
182_I	185_A	0.774	0.99
21_L	28_L	0.773	0.99
136_L	139_G	0.771	0.99
235_E	239_E	0.769	0.99
86_T	96_R	0.768	0.99
204_A	207_C	0.767	0.99
177_W	184_L	0.767	0.99
42_A	70_L	0.766	0.99
305_A	313_R	0.762	0.99
85_L	95_V	0.756	0.99
179_K	184_L	0.756	0.99
28_L	39_V	0.756	0.99
178_D	234_L	0.754	0.99
109_A	114_M	0.751	0.99
154_L	181_L	0.750	0.99
206_T	210_F	0.750	0.99
186_E	190_T	0.749	0.99
160_Q	177_W	0.746	0.99
172_E	175_R	0.743	0.98
175_R	179_K	0.738	0.98
144_E	147_F	0.738	0.98
326_Q	331_A	0.736	0.98
192_R	196_S	0.734	0.98
271_R	307_E	0.732	0.98
327_V	331_A	0.729	0.98
31_A	34_S	0.725	0.98
13_N	40_L	0.719	0.98
105_V	109_A	0.719	0.98
155_K	159_K	0.719	0.98
179_K	231_A	0.717	0.98
12_R	37_T	0.717	0.98
227_E	238_F	0.716	0.98
166_R	169_T	0.715	0.98
219_S	257_R	0.713	0.98
333_S	336_H	0.711	0.98
6_L	21_L	0.711	0.98
162_N	165_L	0.709	0.98
199_I	202_D	0.707	0.98
41_E	328_F	0.706	0.98
235_E	242_R	0.706	0.98
197_A	200_A	0.703	0.98
251_P	258_I	0.703	0.98
231_A	237_N	0.700	0.98
147_F	157_L	0.700	0.98
242_R	258_I	0.700	0.98
242_R	245_T	0.698	0.98
132_R	137_D	0.697	0.98
303_D	330_S	0.694	0.98
158_L	161_R	0.693	0.98
235_E	249_H	0.692	0.98
187_Q	190_T	0.691	0.98
199_I	209_Q	0.689	0.97
151_W	161_R	0.688	0.97
151_W	158_L	0.688	0.97
231_A	253_K	0.687	0.97
251_P	255_D	0.687	0.97
241_D	244_L	0.686	0.97
187_Q	194_E	0.685	0.97
196_S	256_L	0.685	0.97
204_A	215_S	0.682	0.97
121_G	124_L	0.682	0.97
177_W	180_E	0.670	0.97
147_F	150_A	0.667	0.97
238_F	258_I	0.666	0.97
165_L	169_T	0.666	0.97
111_L	115_Q	0.665	0.97
132_R	135_F	0.665	0.97
275_K	307_E	0.662	0.97
158_L	164_A	0.661	0.97
275_K	304_F	0.659	0.97
185_A	192_R	0.659	0.97
43_I	72_G	0.657	0.97
150_A	154_L	0.653	0.97
174_L	179_K	0.652	0.97
195_Y	199_I	0.651	0.96
327_V	330_S	0.650	0.96
133_R	137_D	0.648	0.96
205_D	208_K	0.647	0.96
250_G	253_K	0.645	0.96
239_E	242_R	0.643	0.96
334_A	338_I	0.643	0.96
185_A	251_P	0.640	0.96
247_T	255_D	0.640	0.96
12_R	41_E	0.640	0.96
158_L	165_L	0.639	0.96
12_R	309_D	0.639	0.96
241_D	256_L	0.639	0.96
71_H	82_A	0.638	0.96
238_F	256_L	0.636	0.96
231_A	245_T	0.634	0.96
12_R	32_N	0.633	0.96
155_K	158_L	0.630	0.96
231_A	258_I	0.628	0.96
251_P	254_A	0.628	0.96
148_F	165_L	0.627	0.96
154_L	165_L	0.626	0.96
178_D	185_A	0.626	0.96
271_R	303_D	0.625	0.96
299_Y	327_V	0.624	0.96
148_F	164_A	0.621	0.95
119_P	132_R	0.619	0.95
182_I	230_Y	0.618	0.95
132_R	140_C	0.617	0.95
136_L	256_L	0.615	0.95
173_Q	184_L	0.614	0.95
23_P	26_N	0.614	0.95
187_Q	193_A	0.613	0.95
118_T	123_T	0.611	0.95
208_K	215_S	0.611	0.95
269_L	276_L	0.609	0.95
168_V	171_Y	0.609	0.95
211_L	214_F	0.607	0.95
310_D	335_E	0.607	0.95
151_W	165_L	0.606	0.95
166_R	170_R	0.605	0.95
220_F	223_G	0.604	0.95
231_A	234_L	0.603	0.95
153_N	156_R	0.603	0.95
250_G	258_I	0.602	0.95
221_Q	257_R	0.602	0.95
250_G	257_R	0.602	0.95
8_I	42_A	0.602	0.95
157_L	160_Q	0.601	0.95
161_R	167_Q	0.600	0.94
134_A	138_W	0.600	0.94
275_K	305_A	0.598	0.94
133_R	140_C	0.598	0.94
200_A	206_T	0.590	0.94
261_D	265_V	0.589	0.94
108_L	117_I	0.587	0.94
10_D	15_E	0.587	0.94
203_M	211_L	0.586	0.94
219_S	222_R	0.583	0.94
232_E	235_E	0.579	0.93
259_R	264_P	0.576	0.93
278_M	306_S	0.575	0.93
175_R	235_E	0.575	0.93
237_N	248_A	0.574	0.93
228_T	234_L	0.572	0.93
147_F	162_N	0.572	0.93
143_N	148_F	0.570	0.93
122_F	127_G	0.570	0.93
283_L	316_L	0.568	0.93
17_A	39_V	0.566	0.93
105_V	108_L	0.566	0.93
202_D	209_Q	0.565	0.93
13_N	312_R	0.564	0.92
197_A	206_T	0.562	0.92
117_I	122_F	0.560	0.92
176_P	185_A	0.560	0.92
63_H	263_A	0.556	0.92
121_G	125_L	0.556	0.92
193_A	197_A	0.555	0.92
173_Q	180_E	0.555	0.92
227_E	233_V	0.555	0.92
141_F	158_L	0.555	0.92
11_F	45_T	0.554	0.92
264_P	267_D	0.553	0.92
335_E	338_I	0.553	0.92
217_T	259_R	0.552	0.92
219_S	259_R	0.551	0.92
179_K	185_A	0.550	0.92
282_R	285_Q	0.550	0.92
161_R	164_A	0.544	0.91
38_S	41_E	0.544	0.91
158_L	181_L	0.543	0.91
32_N	38_S	0.543	0.91
107_E	115_Q	0.542	0.91
117_I	275_K	0.542	0.91
105_V	116_L	0.541	0.91
184_L	187_Q	0.540	0.91
228_T	238_F	0.539	0.91
13_N	17_A	0.538	0.91
327_V	334_A	0.537	0.91
120_E	124_L	0.537	0.91
192_R	207_C	0.533	0.90
150_A	153_N	0.532	0.90
184_L	189_S	0.532	0.90
223_G	226_K	0.529	0.90
54_S	57_I	0.528	0.90
198_G	201_A	0.528	0.90
154_L	185_A	0.526	0.90
244_L	249_H	0.523	0.89
180_E	193_A	0.522	0.89
190_T	200_A	0.521	0.89
216_L	221_Q	0.520	0.89
14_I	39_V	0.520	0.89
254_A	258_I	0.519	0.89
139_G	285_Q	0.517	0.89
157_L	165_L	0.516	0.89
149_T	152_S	0.515	0.89
303_D	307_E	0.515	0.89
250_G	255_D	0.513	0.89
51_A	60_V	0.511	0.88
191_W	195_Y	0.510	0.88
104_K	117_I	0.509	0.88
32_N	312_R	0.509	0.88
133_R	136_L	0.509	0.88
104_K	112_M	0.507	0.88
197_A	201_A	0.507	0.88
317_A	329_V	0.506	0.88
287_E	290_T	0.505	0.88
12_R	312_R	0.504	0.88
25_F	327_V	0.504	0.88
203_M	206_T	0.504	0.88
268_T	274_L	0.504	0.88
97_I	111_L	0.503	0.88
282_R	312_R	0.502	0.87
3_L	298_L	0.501	0.87
118_T	127_G	0.500	0.87

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
3auyA	2	0.9356	100	0.384	Contact Map
4abyA	1	0.8683	100	0.384	Contact Map
4ad8A	1	0.9272	100	0.389	Contact Map
2o5vA	1	0.972	100	0.404	Contact Map
3zgxA	2	0.8543	100	0.408	Contact Map
1w1wA	2	0.7843	100	0.424	Contact Map
3qf7A	2	0.902	100	0.44	Contact Map
4ux3A	1	0.8964	100	0.452	Contact Map
3qktA	2	0.8683	100	0.46	Contact Map
4i99A	2	0.7899	100	0.476	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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