RECF - BACSU - GREMLIN Contacts

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RECF - DNA replication and repair protein RecF

UniProt:	P05651	Sequences: MYIQNLELTSYRNYDHAELQFENKVNVIIGENAQGKTNLMEAIYVLSMAKSHRTSNDKELIRWDKDYAKIEGRVMKQNGAIPMQLVISKKGKKGKVNHIEQQKLSQYVGALNTIMFAPEDLNLVKGSPQVRRRFLDMEIGQVSPVYLHDLSLYQKILSQRNHFLKQLQTRKQTDRTMLDVLTDQLVEVAAKVVVKRLQFTAQLEKWAQPIHAGISRGLEELTLKYHTALDVSDPLDLSKIGDSYQEAFSKLREKEIERGVTLSGPHRDDVLFYVNGRDVQTYGSQGQQRTTALSLKLAEIDLIHEEIGEYPILLLDDVLSELDDYRQSHLLHTIQGRVQTFVTTTSVDGIDHETLRQAGMFRVQNGALVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	370 (340)
Sequences:	8040 (6814)
Seq/√Len:	369.5

ECOLI - RECF RECN
BACSU - RECF RECN YHAN YYDD SMC
HALSA - SPH2 SPH1 RAD50 Q9HS95
SULSO - Q97WH8 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	4.556	1.00
5_N	18_E	3.955	1.00
4_Q	75_M	3.818	1.00
7_E	18_E	3.047	1.00
5_N	73_R	2.811	1.00
4_Q	80_A	2.705	1.00
5_N	20_Q	2.568	1.00
255_E	262_L	2.509	1.00
241_G	245_Q	2.412	1.00
7_E	71_E	2.408	1.00
10_S	62_R	2.349	1.00
246_E	250_K	2.340	1.00
339_Q	342_V	2.306	1.00
195_K	198_Q	2.288	1.00
9_T	16_H	2.241	1.00
7_E	16_H	2.222	1.00
322_L	330_L	2.174	1.00
73_R	80_A	2.138	1.00
62_R	65_K	2.116	1.00
3_I	72_G	2.115	1.00
183_D	187_E	2.069	1.00
8_L	14_Y	2.062	1.00
258_R	262_L	1.978	1.00
161_N	165_K	1.967	1.00
146_Y	153_Y	1.946	1.00
237_L	241_G	1.936	1.00
245_Q	249_S	1.927	1.00
67_Y	86_V	1.925	1.00
262_L	266_H	1.917	1.00
350_I	354_T	1.903	1.00
163_F	167_L	1.891	1.00
159_Q	163_F	1.873	1.00
327_Q	346_S	1.854	1.00
158_S	162_H	1.854	1.00
328_S	332_H	1.828	1.00
184_Q	187_E	1.823	1.00
71_E	84_Q	1.822	1.00
177_M	181_L	1.806	1.00
180_V	184_Q	1.799	1.00
162_H	166_Q	1.789	1.00
238_S	242_D	1.776	1.00
10_S	65_K	1.757	1.00
252_R	256_I	1.739	1.00
111_L	115_M	1.739	1.00
111_L	114_I	1.708	1.00
15_D	62_R	1.698	1.00
148_H	152_L	1.688	1.00
350_I	355_L	1.663	1.00
9_T	69_K	1.652	1.00
266_H	269_D	1.640	1.00
81_I	97_N	1.629	1.00
247_A	250_K	1.590	1.00
191_K	195_K	1.571	1.00
263_S	267_R	1.567	1.00
143_S	147_L	1.563	1.00
255_E	259_G	1.560	1.00
69_K	84_Q	1.554	1.00
103_K	106_Q	1.532	1.00
290_T	326_R	1.530	1.00
202_Q	206_W	1.529	1.00
176_T	179_D	1.524	1.00
355_L	358_A	1.521	1.00
14_Y	17_A	1.511	1.00
236_D	239_K	1.508	1.00
254_K	258_R	1.508	1.00
21_F	341_F	1.506	1.00
157_L	161_N	1.495	1.00
256_I	259_G	1.494	1.00
166_Q	170_R	1.494	1.00
15_D	65_K	1.493	1.00
185_L	189_A	1.480	1.00
84_Q	95_K	1.479	1.00
140_G	143_S	1.449	1.00
239_K	243_S	1.433	1.00
193_V	197_L	1.433	1.00
26_N	361_F	1.429	1.00
238_S	241_G	1.423	1.00
40_M	314_L	1.416	1.00
130_V	133_R	1.404	1.00
355_L	360_M	1.401	1.00
259_G	263_S	1.390	1.00
4_Q	73_R	1.386	1.00
165_K	169_T	1.380	1.00
143_S	195_K	1.370	1.00
192_V	196_R	1.365	1.00
190_A	194_V	1.359	1.00
154_Q	158_S	1.359	1.00
146_Y	150_L	1.356	1.00
329_H	332_H	1.351	1.00
259_G	274_V	1.346	1.00
165_K	168_Q	1.344	1.00
244_Y	248_F	1.344	1.00
194_V	198_Q	1.340	1.00
285_Q	321_E	1.327	1.00
112_N	115_M	1.324	1.00
179_D	182_T	1.324	1.00
204_E	208_Q	1.306	1.00
183_D	186_V	1.301	1.00
240_I	243_S	1.300	1.00
96_V	101_Q	1.296	1.00
253_E	257_E	1.294	1.00
347_V	351_D	1.291	1.00
147_L	151_S	1.291	1.00
252_R	259_G	1.289	1.00
243_S	246_E	1.277	1.00
160_R	164_L	1.276	1.00
44_Y	49_A	1.271	1.00
17_A	21_F	1.270	1.00
259_G	262_L	1.268	1.00
150_L	154_Q	1.264	1.00
179_D	183_D	1.258	1.00
192_V	195_K	1.255	1.00
206_W	210_I	1.252	1.00
242_D	246_E	1.251	1.00
252_R	255_E	1.250	1.00
264_G	268_D	1.249	1.00
203_L	207_A	1.245	1.00
279_V	291_T	1.243	1.00
181_L	184_Q	1.242	1.00
274_V	278_D	1.241	1.00
267_R	278_D	1.233	1.00
254_K	257_E	1.230	1.00
66_D	89_K	1.229	1.00
191_K	194_V	1.229	1.00
142_V	146_Y	1.203	1.00
119_E	125_K	1.200	1.00
209_P	213_G	1.199	1.00
174_D	177_M	1.199	1.00
269_D	273_Y	1.199	1.00
285_Q	317_D	1.193	1.00
25_V	342_V	1.191	1.00
145_V	149_D	1.187	1.00
242_D	245_Q	1.183	1.00
69_K	86_V	1.177	1.00
149_D	191_K	1.171	1.00
3_I	43_I	1.165	1.00
210_I	213_G	1.158	1.00
180_V	183_D	1.155	1.00
61_I	68_A	1.151	1.00
95_K	100_E	1.150	1.00
33_A	287_Q	1.149	1.00
271_L	274_V	1.141	1.00
147_L	150_L	1.136	1.00
45_V	70_I	1.133	1.00
111_L	312_I	1.129	1.00
182_T	252_R	1.129	1.00
71_E	82_P	1.128	1.00
147_L	157_L	1.115	1.00
182_T	186_V	1.112	1.00
211_H	215_S	1.111	1.00
157_L	160_R	1.108	1.00
235_L	238_S	1.107	1.00
11_Y	42_A	1.106	1.00
201_A	204_E	1.104	1.00
267_R	270_V	1.103	1.00
156_I	159_Q	1.103	1.00
153_Y	156_I	1.093	1.00
243_S	247_A	1.092	1.00
8_L	39_L	1.090	1.00
259_G	266_H	1.089	1.00
260_V	264_G	1.087	1.00
338_V	342_V	1.083	1.00
271_L	278_D	1.081	1.00
206_W	209_P	1.081	1.00
96_V	110_A	1.079	1.00
164_L	168_Q	1.079	1.00
251_L	254_K	1.074	1.00
339_Q	345_T	1.071	1.00
31_E	325_Y	1.069	1.00
201_A	205_K	1.069	1.00
68_A	87_I	1.067	1.00
147_L	153_Y	1.061	1.00
279_V	283_G	1.060	1.00
267_R	275_N	1.059	1.00
275_N	278_D	1.058	1.00
159_Q	162_H	1.053	1.00
237_L	240_I	1.053	1.00
11_Y	68_A	1.053	1.00
252_R	260_V	1.052	1.00
177_M	180_V	1.048	1.00
175_R	184_Q	1.047	1.00
265_P	268_D	1.045	1.00
186_V	189_A	1.043	1.00
175_R	182_T	1.034	1.00
236_D	240_I	1.033	1.00
180_V	187_E	1.026	1.00
194_V	197_L	1.026	1.00
140_G	144_P	1.025	1.00
156_I	160_R	1.020	1.00
228_A	231_V	1.014	1.00
267_R	271_L	1.012	1.00
198_Q	202_Q	1.009	1.00
186_V	245_Q	1.009	1.00
256_I	267_R	1.008	1.00
179_D	252_R	1.003	1.00
227_T	231_V	0.999	1.00
224_K	227_T	0.998	1.00
354_T	358_A	0.985	1.00
253_E	256_I	0.985	1.00
272_F	275_N	0.980	1.00
226_H	230_D	0.977	1.00
106_Q	109_G	0.976	1.00
155_K	159_Q	0.976	1.00
122_N	126_G	0.975	1.00
13_N	38_N	0.973	1.00
43_I	314_L	0.970	1.00
264_G	267_R	0.966	1.00
270_V	274_V	0.963	1.00
191_K	196_R	0.952	1.00
153_Y	157_L	0.952	1.00
94_G	107_Y	0.949	1.00
32_N	326_R	0.947	1.00
94_G	101_Q	0.947	1.00
256_I	260_V	0.945	1.00
143_S	146_Y	0.944	1.00
175_R	194_V	0.942	1.00
185_L	188_V	0.937	1.00
149_D	152_L	0.937	1.00
200_T	203_L	0.933	1.00
217_G	220_E	0.933	1.00
75_M	80_A	0.926	1.00
245_Q	252_R	0.925	1.00
46_L	70_I	0.915	1.00
319_L	327_Q	0.915	1.00
274_V	277_R	0.913	1.00
184_Q	188_V	0.909	1.00
263_S	266_H	0.909	1.00
228_A	232_S	0.907	1.00
317_D	343_T	0.906	1.00
8_L	42_A	0.906	1.00
187_E	241_G	0.906	1.00
187_E	191_K	0.906	1.00
339_Q	346_S	0.905	1.00
182_T	189_A	0.903	1.00
314_L	341_F	0.901	1.00
273_Y	276_G	0.899	1.00
255_E	258_R	0.899	1.00
210_I	217_G	0.894	1.00
160_R	261_T	0.894	1.00
193_V	196_R	0.893	1.00
73_R	82_P	0.893	1.00
215_S	218_L	0.893	1.00
249_S	252_R	0.887	1.00
12_R	41_E	0.887	1.00
11_Y	60_L	0.881	1.00
255_E	266_H	0.873	1.00
6_L	72_G	0.871	1.00
174_D	181_L	0.869	1.00
287_Q	290_T	0.869	1.00
292_A	296_K	0.868	1.00
132_R	136_D	0.868	1.00
166_Q	169_T	0.864	1.00
261_T	264_G	0.861	1.00
176_T	180_V	0.861	1.00
241_G	248_F	0.859	1.00
208_Q	212_A	0.859	1.00
42_A	70_I	0.857	1.00
225_Y	228_A	0.855	1.00
267_R	274_V	0.854	1.00
127_S	130_V	0.851	1.00
271_L	277_R	0.849	1.00
170_R	173_T	0.843	1.00
181_L	185_L	0.842	1.00
358_A	361_F	0.840	1.00
57_D	60_L	0.835	1.00
205_K	209_P	0.835	1.00
252_R	272_F	0.834	1.00
152_L	156_I	0.834	1.00
151_S	154_Q	0.828	1.00
265_P	269_D	0.828	1.00
146_Y	149_D	0.826	1.00
186_V	190_A	0.823	1.00
289_R	321_E	0.820	1.00
156_I	188_V	0.820	1.00
203_L	206_W	0.817	1.00
188_V	191_K	0.815	1.00
259_G	267_R	0.815	1.00
224_K	228_A	0.812	1.00
283_G	291_T	0.809	1.00
239_K	242_D	0.808	1.00
28_I	361_F	0.807	1.00
149_D	153_Y	0.803	1.00
157_L	164_L	0.803	1.00
271_L	275_N	0.801	1.00
175_R	183_D	0.801	1.00
340_T	345_T	0.799	1.00
214_I	217_G	0.793	1.00
266_H	270_V	0.792	1.00
162_H	165_K	0.791	1.00
207_A	210_I	0.791	1.00
161_N	261_T	0.790	1.00
141_Q	144_P	0.788	1.00
83_M	107_Y	0.784	1.00
19_L	361_F	0.783	1.00
342_V	346_S	0.783	1.00
31_E	34_Q	0.782	1.00
270_V	277_R	0.779	1.00
154_Q	157_L	0.776	1.00
81_I	85_L	0.775	1.00
160_R	163_F	0.774	1.00
12_R	38_N	0.773	1.00
267_R	272_F	0.770	1.00
323_D	326_R	0.770	1.00
203_L	210_I	0.769	1.00
223_L	228_A	0.765	1.00
61_I	89_K	0.759	1.00
32_N	317_D	0.759	1.00
272_F	277_R	0.757	1.00
259_G	272_F	0.757	1.00
247_A	251_L	0.757	1.00
210_I	220_E	0.752	1.00
255_E	260_V	0.751	1.00
303_I	310_Y	0.744	1.00
150_L	153_Y	0.743	1.00
238_S	249_S	0.742	1.00
240_I	244_Y	0.742	1.00
264_G	272_F	0.741	1.00
267_R	277_R	0.739	1.00
229_L	232_S	0.736	1.00
203_L	217_G	0.735	1.00
262_L	265_P	0.735	1.00
93_K	100_E	0.735	1.00
252_R	266_H	0.732	1.00
105_S	108_V	0.730	1.00
175_R	179_D	0.729	1.00
118_P	121_L	0.726	1.00
148_H	151_S	0.726	1.00
252_R	267_R	0.725	1.00
300_I	313_L	0.724	1.00
331_L	354_T	0.724	1.00
40_M	343_T	0.722	1.00
323_D	327_Q	0.721	1.00
6_L	21_F	0.721	1.00
339_Q	343_T	0.719	1.00
257_E	260_V	0.713	1.00
26_N	359_G	0.713	1.00
76_K	79_G	0.708	0.99
290_T	322_L	0.706	0.99
260_V	266_H	0.706	0.99
248_F	263_S	0.705	0.99
178_L	186_V	0.704	0.99
28_I	39_L	0.703	0.99
47_S	113_T	0.702	0.99
265_P	272_F	0.702	0.99
256_I	270_V	0.700	0.99
152_L	155_K	0.698	0.99
245_Q	248_F	0.698	0.99
61_I	64_D	0.698	0.99
203_L	211_H	0.698	0.99
261_T	265_P	0.695	0.99
256_I	263_S	0.692	0.99
58_K	61_I	0.691	0.99
174_D	184_Q	0.691	0.99
145_V	148_H	0.689	0.99
188_V	192_V	0.685	0.99
225_Y	232_S	0.685	0.99
317_D	320_S	0.683	0.99
158_S	161_N	0.682	0.99
192_V	198_Q	0.680	0.99
86_V	93_K	0.680	0.99
157_L	162_H	0.679	0.99
151_S	155_K	0.676	0.99
202_Q	205_K	0.673	0.99
325_Y	328_S	0.670	0.99
265_P	270_V	0.669	0.99
263_S	274_V	0.667	0.99
101_Q	106_Q	0.666	0.99
211_H	217_G	0.663	0.99
101_Q	107_Y	0.663	0.99
342_V	345_T	0.663	0.99
171_K	174_D	0.662	0.99
179_D	186_V	0.662	0.99
140_G	147_L	0.662	0.99
29_I	360_M	0.660	0.99
117_A	120_D	0.659	0.99
245_Q	259_G	0.659	0.99
11_Y	45_V	0.658	0.99
351_D	355_L	0.658	0.99
273_Y	277_R	0.655	0.99
133_R	137_M	0.653	0.99
251_L	262_L	0.646	0.99
157_L	170_R	0.645	0.99
191_K	197_L	0.643	0.99
317_D	321_E	0.642	0.99
104_L	108_V	0.641	0.99
12_R	37_T	0.639	0.99
217_G	221_L	0.639	0.99
290_T	317_D	0.636	0.99
251_L	255_E	0.635	0.99
204_E	210_I	0.635	0.99
240_I	247_A	0.635	0.99
123_L	131_R	0.634	0.99
272_F	276_G	0.632	0.99
252_R	265_P	0.631	0.99
86_V	95_K	0.628	0.99
235_L	241_G	0.628	0.99
211_H	216_R	0.627	0.99
266_H	277_R	0.627	0.99
327_Q	348_D	0.624	0.99
191_K	198_Q	0.623	0.99
245_Q	256_I	0.623	0.99
252_R	270_V	0.621	0.99
248_F	252_R	0.620	0.99
146_Y	157_L	0.618	0.99
178_L	181_L	0.618	0.99
83_M	94_G	0.615	0.99
10_S	15_D	0.614	0.99
212_A	216_R	0.612	0.98
190_A	195_K	0.611	0.98
4_Q	20_Q	0.609	0.98
210_I	218_L	0.609	0.98
289_R	319_L	0.608	0.98
296_K	320_S	0.605	0.98
213_G	217_G	0.603	0.98
140_G	146_Y	0.600	0.98
315_L	320_S	0.599	0.98
289_R	320_S	0.598	0.98
176_T	184_Q	0.598	0.98
285_Q	289_R	0.597	0.98
320_S	323_D	0.596	0.98
113_T	117_A	0.596	0.98
23_N	26_N	0.592	0.98
178_L	182_T	0.591	0.98
163_F	170_R	0.591	0.98
176_T	181_L	0.590	0.98
146_Y	154_Q	0.590	0.98
120_D	123_L	0.584	0.98
212_A	220_E	0.582	0.98
202_Q	217_G	0.581	0.98
318_V	346_S	0.581	0.98
115_M	123_L	0.580	0.98
167_L	170_R	0.578	0.98
121_L	131_R	0.577	0.98
256_I	265_P	0.575	0.98
264_G	270_V	0.574	0.98
313_L	340_T	0.573	0.98
216_R	219_E	0.573	0.98
256_I	274_V	0.572	0.98
332_H	336_G	0.568	0.98
61_I	65_K	0.566	0.97
238_S	245_Q	0.564	0.97
339_Q	347_V	0.563	0.97
289_R	317_D	0.563	0.97
195_K	199_F	0.562	0.97
27_V	354_T	0.561	0.97
142_V	147_L	0.561	0.97
150_L	164_L	0.560	0.97
236_D	241_G	0.560	0.97
26_N	339_Q	0.558	0.97
223_L	226_H	0.557	0.97
266_H	273_Y	0.557	0.97
147_L	170_R	0.556	0.97
154_Q	164_L	0.554	0.97
252_R	274_V	0.553	0.97
161_N	164_L	0.553	0.97
85_L	94_G	0.551	0.97
177_M	182_T	0.545	0.97
184_Q	192_V	0.544	0.97
350_I	358_A	0.544	0.97
175_R	178_L	0.543	0.97
104_L	107_Y	0.542	0.97
121_L	124_V	0.542	0.97
38_N	41_E	0.540	0.97
159_Q	166_Q	0.539	0.97
178_L	185_L	0.533	0.96
57_D	61_I	0.531	0.96
174_D	189_A	0.531	0.96
211_H	214_I	0.529	0.96
173_T	176_T	0.529	0.96
256_I	278_D	0.528	0.96
324_D	348_D	0.527	0.96
203_L	213_G	0.527	0.96
131_R	139_I	0.526	0.96
202_Q	218_L	0.525	0.96
3_I	312_I	0.522	0.96
318_V	322_L	0.521	0.96
215_S	219_E	0.520	0.96
116_F	119_E	0.519	0.96
264_G	269_D	0.519	0.96
150_L	157_L	0.519	0.96
27_V	344_T	0.518	0.96
14_Y	39_L	0.518	0.96
319_L	346_S	0.518	0.96
163_F	166_Q	0.517	0.96
200_T	204_E	0.517	0.96
153_Y	185_L	0.516	0.96
174_D	178_L	0.516	0.96
179_D	185_L	0.516	0.96
268_D	271_L	0.514	0.96
242_D	248_F	0.513	0.96
296_K	299_E	0.513	0.96
10_S	16_H	0.512	0.96
180_V	185_L	0.511	0.95
160_R	167_L	0.511	0.95
260_V	267_R	0.511	0.95
42_A	46_L	0.511	0.95
44_Y	48_M	0.510	0.95
112_N	117_A	0.510	0.95
315_L	318_V	0.509	0.95
155_K	158_S	0.509	0.95
213_G	220_E	0.506	0.95
59_E	63_W	0.505	0.95
22_E	359_G	0.505	0.95
289_R	318_V	0.505	0.95
257_E	261_T	0.504	0.95
302_L	309_E	0.504	0.95
181_L	188_V	0.503	0.95
75_M	78_N	0.502	0.95
292_A	320_S	0.501	0.95
189_A	265_P	0.500	0.95

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
4ad8A	1	0.9189	100	0.37	Contact Map
3auyA	2	0.9135	100	0.373	Contact Map
4ux3A	1	0.9081	100	0.386	Contact Map
3zgxA	2	0.8378	100	0.388	Contact Map
1w1wA	2	0.7703	100	0.394	Contact Map
4abyA	1	0.8432	100	0.406	Contact Map
3qf7A	2	0.8811	100	0.438	Contact Map
2o5vA	1	0.9351	100	0.439	Contact Map
3qktA	2	0.827	100	0.456	Contact Map
4i99A	2	0.7622	100	0.482	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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