RFCL - SULSO - GREMLIN Contacts

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RFCL - Replication factor C large subunit

UniProt:	Q9UXF6	Sequences: MIQWFLKYRPRSLKDVENQDDAKKQLQEWIESWLNGNSNVKAVLLHGPPGVGKTVLAEALAHDYNFELLEMNASDSRKLQDIKSIAEKAAVYGSIFGTKGKLILLDEVDGINVREDTGAIQGILELIEKTKYPIIMTANDPWNPGLRELRNKAKMIELSKLGKYPLRRILKKICQAEKIICDDEALNYIIDSSEGDARYAINILQGIGEGYGKVTLNLVESLAKRKERELDPFETLRDIFWARYAWQAKNAATSAQIDYDMLIRWISENIPIQYDNIEDIWRAFDALSRASIFLKRAKSGDWDLLSYAYDMMSSGVAFAEPEKKKPNWKPKWKKYQFPSYIQLLSKSKDIRDTRDEIIKKLAIHSSFNKALNDTYPFFLLFYKKYDKHLNLNTKEKEYLSSISKS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	405 (318)
Sequences:	10649 (6771)
Seq/√Len:	379.7

ECOLI - RARA DPO3X
BACSU - YRVN DPO3X RUVB
HALSA - RFCL RFCS Q9HN59
SULSO - RFCL RFCS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_D	165_P	3.979	1.00
6_L	10_P	3.224	1.00
162_G	165_P	3.166	1.00
167_R	187_N	2.776	1.00
205_Q	210_G	2.643	1.00
171_K	183_D	2.550	1.00
27_Q	31_E	2.521	1.00
171_K	186_L	2.520	1.00
277_I	281_W	2.513	1.00
240_F	272_I	2.502	1.00
326_P	330_P	2.341	1.00
167_R	171_K	2.329	1.00
205_Q	209_E	2.317	1.00
180_I	213_K	2.257	1.00
267_S	271_P	2.219	1.00
282_R	286_A	2.172	1.00
16_V	59_A	2.158	1.00
206_G	210_G	2.156	1.00
277_I	280_I	2.137	1.00
259_Y	262_L	2.109	1.00
80_Q	84_S	2.088	1.00
215_T	218_L	2.061	1.00
219_V	223_A	2.024	1.00
294_L	297_A	2.008	1.00
16_V	56_L	2.002	1.00
261_M	265_W	1.972	1.00
259_Y	263_I	1.938	1.00
166_L	190_I	1.923	1.00
301_D	305_L	1.906	1.00
291_S	295_K	1.897	1.00
84_S	88_K	1.880	1.00
269_N	272_I	1.861	1.00
167_R	186_L	1.848	1.00
285_D	289_R	1.832	1.00
84_S	87_E	1.822	1.00
248_A	251_A	1.813	1.00
12_S	15_D	1.811	1.00
172_K	176_A	1.799	1.00
306_S	310_D	1.794	1.00
78_K	81_D	1.772	1.00
67_E	92_Y	1.768	1.00
216_L	220_E	1.761	1.00
228_R	231_D	1.739	1.00
250_N	254_S	1.725	1.00
284_F	288_S	1.720	1.00
287_L	291_S	1.713	1.00
243_R	246_W	1.707	1.00
20_D	168_R	1.686	1.00
136_M	139_N	1.684	1.00
67_E	99_K	1.681	1.00
289_R	293_F	1.680	1.00
259_Y	265_W	1.676	1.00
308_A	312_M	1.669	1.00
266_I	270_I	1.667	1.00
182_D	213_K	1.647	1.00
300_G	303_D	1.646	1.00
327_N	331_K	1.619	1.00
264_R	268_E	1.596	1.00
235_T	242_A	1.564	1.00
262_L	266_I	1.549	1.00
169_I	197_A	1.546	1.00
163_K	191_D	1.540	1.00
288_S	291_S	1.518	1.00
262_L	270_I	1.515	1.00
286_A	290_A	1.491	1.00
206_G	209_E	1.489	1.00
233_F	239_I	1.486	1.00
284_F	287_L	1.483	1.00
286_A	297_A	1.483	1.00
87_E	90_A	1.470	1.00
231_D	234_E	1.467	1.00
79_L	83_K	1.466	1.00
163_K	190_I	1.464	1.00
170_L	186_L	1.463	1.00
248_A	255_A	1.450	1.00
262_L	265_W	1.438	1.00
267_S	270_I	1.435	1.00
166_L	200_A	1.433	1.00
290_A	294_L	1.425	1.00
287_L	290_A	1.422	1.00
291_S	294_L	1.418	1.00
283_A	286_A	1.416	1.00
58_E	70_E	1.406	1.00
312_M	316_V	1.388	1.00
273_Q	277_I	1.371	1.00
268_E	272_I	1.366	1.00
265_W	269_N	1.352	1.00
282_R	285_D	1.349	1.00
260_D	264_R	1.348	1.00
216_L	219_V	1.336	1.00
44_L	108_V	1.332	1.00
289_R	292_I	1.332	1.00
220_E	223_A	1.330	1.00
74_S	122_G	1.316	1.00
309_Y	312_M	1.312	1.00
299_S	302_W	1.306	1.00
325_K	328_W	1.302	1.00
80_Q	83_K	1.297	1.00
22_A	156_I	1.293	1.00
292_I	296_R	1.278	1.00
248_A	252_A	1.276	1.00
22_A	25_Q	1.274	1.00
186_L	190_I	1.261	1.00
290_A	295_K	1.255	1.00
171_K	175_Q	1.250	1.00
283_A	290_A	1.249	1.00
233_F	237_R	1.229	1.00
259_Y	272_I	1.225	1.00
293_F	297_A	1.223	1.00
181_C	186_L	1.218	1.00
329_K	333_K	1.216	1.00
273_Q	276_N	1.213	1.00
319_A	323_K	1.208	1.00
45_L	158_L	1.202	1.00
229_E	242_A	1.200	1.00
46_H	157_E	1.193	1.00
190_I	200_A	1.192	1.00
316_V	319_A	1.191	1.00
237_R	241_W	1.189	1.00
163_K	187_N	1.186	1.00
278_E	281_W	1.186	1.00
276_N	279_D	1.185	1.00
11_R	15_D	1.184	1.00
211_Y	215_T	1.181	1.00
325_K	329_K	1.181	1.00
187_N	191_D	1.181	1.00
182_D	185_A	1.178	1.00
161_L	197_A	1.172	1.00
239_I	242_A	1.170	1.00
148_E	152_K	1.156	1.00
298_K	302_W	1.154	1.00
217_N	221_S	1.150	1.00
218_L	222_L	1.148	1.00
61_A	102_L	1.148	1.00
318_F	322_E	1.147	1.00
25_Q	30_I	1.146	1.00
328_W	332_W	1.138	1.00
137_T	140_D	1.137	1.00
283_A	287_L	1.136	1.00
299_S	305_L	1.135	1.00
16_V	23_K	1.134	1.00
234_E	237_R	1.132	1.00
249_K	253_T	1.130	1.00
220_E	224_K	1.128	1.00
68_L	104_L	1.128	1.00
251_A	255_A	1.113	1.00
265_W	268_E	1.109	1.00
112_N	118_G	1.105	1.00
281_W	285_D	1.104	1.00
217_N	220_E	1.099	1.00
14_K	27_Q	1.097	1.00
188_Y	191_D	1.092	1.00
91_V	96_F	1.091	1.00
87_E	91_V	1.084	1.00
315_G	318_F	1.080	1.00
169_I	172_K	1.071	1.00
238_D	241_W	1.063	1.00
306_S	309_Y	1.062	1.00
288_S	292_I	1.054	1.00
287_L	297_A	1.054	1.00
77_R	118_G	1.053	1.00
233_F	236_L	1.051	1.00
21_D	159_S	1.051	1.00
293_F	296_R	1.049	1.00
88_K	92_Y	1.049	1.00
302_W	306_S	1.048	1.00
248_A	256_Q	1.041	1.00
77_R	112_N	1.037	1.00
173_I	176_A	1.036	1.00
193_S	200_A	1.031	1.00
292_I	297_A	1.020	1.00
264_R	271_P	1.012	1.00
316_V	320_E	1.011	1.00
265_W	271_P	1.006	1.00
69_L	88_K	0.995	1.00
263_I	267_S	0.992	1.00
305_L	308_A	0.982	1.00
287_L	292_I	0.979	1.00
302_W	305_L	0.974	1.00
73_A	76_S	0.971	1.00
79_L	118_G	0.969	1.00
279_D	283_A	0.968	1.00
219_V	222_L	0.965	1.00
134_I	139_N	0.965	1.00
274_Y	277_I	0.964	1.00
284_F	291_S	0.960	1.00
318_F	324_K	0.959	1.00
227_E	238_D	0.959	1.00
25_Q	28_E	0.953	1.00
327_N	330_P	0.952	1.00
227_E	231_D	0.950	1.00
328_W	331_K	0.946	1.00
299_S	303_D	0.945	1.00
56_L	158_L	0.943	1.00
188_Y	216_L	0.943	1.00
241_W	244_Y	0.940	1.00
236_L	239_I	0.936	1.00
230_L	233_F	0.936	1.00
327_N	332_W	0.932	1.00
11_R	62_H	0.929	1.00
278_E	282_R	0.926	1.00
263_I	266_I	0.916	1.00
132_Y	139_N	0.914	1.00
249_K	256_Q	0.914	1.00
311_M	315_G	0.912	1.00
260_D	263_I	0.905	1.00
80_Q	85_I	0.903	1.00
82_I	86_A	0.901	1.00
228_R	232_P	0.900	1.00
274_Y	306_S	0.897	1.00
232_P	239_I	0.892	1.00
133_P	140_D	0.892	1.00
258_D	261_M	0.889	1.00
201_I	205_Q	0.888	1.00
240_F	243_R	0.884	1.00
248_A	308_A	0.881	1.00
253_T	257_I	0.879	1.00
54_T	106_D	0.875	1.00
232_P	236_L	0.875	1.00
291_S	297_A	0.873	1.00
229_E	233_F	0.868	1.00
7_K	177_E	0.868	1.00
290_A	293_F	0.866	1.00
324_K	327_N	0.866	1.00
227_E	233_F	0.865	1.00
317_A	321_P	0.863	1.00
8_Y	177_E	0.857	1.00
310_D	313_S	0.857	1.00
200_A	203_I	0.856	1.00
308_A	316_V	0.854	1.00
309_Y	320_E	0.852	1.00
75_D	78_K	0.852	1.00
263_I	269_N	0.851	1.00
262_L	269_N	0.851	1.00
108_V	134_I	0.843	1.00
284_F	290_A	0.841	1.00
249_K	252_A	0.840	1.00
265_W	270_I	0.836	1.00
300_G	305_L	0.835	1.00
319_A	322_E	0.834	1.00
17_E	169_I	0.833	1.00
293_F	300_G	0.832	1.00
254_S	257_I	0.829	1.00
316_V	321_P	0.827	1.00
273_Q	293_F	0.827	1.00
256_Q	262_L	0.826	1.00
287_L	293_F	0.826	1.00
20_D	24_K	0.825	1.00
44_L	153_A	0.818	1.00
43_V	156_I	0.817	1.00
303_D	306_S	0.815	1.00
73_A	78_K	0.813	1.00
239_I	244_Y	0.813	1.00
200_A	204_L	0.811	1.00
315_G	319_A	0.809	1.00
239_I	243_R	0.808	1.00
83_K	87_E	0.806	1.00
216_L	223_A	0.802	1.00
261_M	269_N	0.800	1.00
259_Y	267_S	0.799	1.00
166_L	197_A	0.796	1.00
167_R	190_I	0.795	1.00
323_K	327_N	0.795	1.00
221_S	224_K	0.787	1.00
264_R	267_S	0.785	1.00
312_M	315_G	0.784	1.00
317_A	320_E	0.782	1.00
313_S	319_A	0.779	1.00
261_M	264_R	0.773	1.00
260_D	265_W	0.772	1.00
312_M	319_A	0.771	1.00
136_M	141_P	0.769	1.00
259_Y	269_N	0.769	1.00
313_S	317_A	0.767	1.00
233_F	240_F	0.764	1.00
318_F	321_P	0.764	1.00
305_L	309_Y	0.763	1.00
173_I	177_E	0.762	1.00
285_D	288_S	0.762	1.00
174_C	181_C	0.761	1.00
230_L	234_E	0.759	1.00
231_D	237_R	0.758	1.00
252_A	308_A	0.757	1.00
25_Q	32_S	0.757	1.00
287_L	294_L	0.753	1.00
309_Y	313_S	0.753	1.00
7_K	10_P	0.753	1.00
269_N	308_A	0.751	1.00
301_D	304_L	0.750	1.00
237_R	240_F	0.749	1.00
326_P	329_K	0.749	1.00
164_Y	167_R	0.746	1.00
25_Q	156_I	0.742	1.00
182_D	215_T	0.741	1.00
290_A	297_A	0.740	1.00
312_M	317_A	0.739	1.00
314_S	318_F	0.735	1.00
218_L	223_A	0.735	1.00
259_Y	270_I	0.734	1.00
25_Q	31_E	0.734	1.00
234_E	244_Y	0.732	1.00
310_D	314_S	0.731	1.00
235_T	239_I	0.730	1.00
173_I	201_I	0.727	1.00
262_L	267_S	0.725	1.00
263_I	271_P	0.724	1.00
242_A	246_W	0.724	1.00
238_D	242_A	0.724	1.00
236_L	240_F	0.718	1.00
166_L	170_L	0.715	1.00
253_T	256_Q	0.714	1.00
54_T	70_E	0.712	1.00
313_S	316_V	0.711	1.00
283_A	292_I	0.710	1.00
228_R	236_L	0.708	1.00
258_D	265_W	0.706	1.00
229_E	239_I	0.705	1.00
231_D	242_A	0.705	1.00
205_Q	208_G	0.701	0.99
325_K	332_W	0.700	0.99
241_W	246_W	0.700	0.99
229_E	232_P	0.697	0.99
73_A	111_I	0.693	0.99
288_S	297_A	0.693	0.99
227_E	234_E	0.689	0.99
136_M	140_D	0.688	0.99
71_M	105_L	0.687	0.99
46_H	155_M	0.687	0.99
148_E	151_N	0.685	0.99
170_L	204_L	0.683	0.99
258_D	267_S	0.682	0.99
296_R	303_D	0.680	0.99
281_W	314_S	0.680	0.99
183_D	187_N	0.679	0.99
274_Y	281_W	0.677	0.99
277_I	283_A	0.675	0.99
284_F	295_K	0.674	0.99
82_I	111_I	0.673	0.99
289_R	295_K	0.672	0.99
306_S	312_M	0.672	0.99
291_S	296_R	0.672	0.99
292_I	295_K	0.670	0.99
168_R	171_K	0.670	0.99
86_A	126_L	0.669	0.99
283_A	297_A	0.668	0.99
242_A	245_A	0.667	0.99
252_A	256_Q	0.666	0.99
133_P	139_N	0.665	0.99
165_P	168_R	0.664	0.99
134_I	140_D	0.663	0.99
104_L	137_T	0.662	0.99
266_I	269_N	0.662	0.99
20_D	23_K	0.661	0.99
73_A	77_R	0.656	0.99
281_W	284_F	0.655	0.99
294_L	298_K	0.655	0.99
200_A	205_Q	0.654	0.99
192_S	223_A	0.654	0.99
249_K	255_A	0.650	0.99
15_D	172_K	0.650	0.99
229_E	244_Y	0.648	0.99
312_M	318_F	0.647	0.99
325_K	330_P	0.644	0.99
233_F	242_A	0.644	0.99
295_K	298_K	0.643	0.99
66_F	102_L	0.640	0.99
238_D	246_W	0.638	0.99
235_T	244_Y	0.638	0.99
91_V	94_S	0.634	0.99
67_E	88_K	0.632	0.99
134_I	137_T	0.629	0.99
289_R	307_Y	0.629	0.99
8_Y	176_A	0.628	0.99
282_R	288_S	0.627	0.99
227_E	242_A	0.625	0.99
250_N	257_I	0.624	0.99
251_A	256_Q	0.617	0.99
263_I	270_I	0.617	0.99
274_Y	279_D	0.616	0.99
308_A	315_G	0.614	0.99
286_A	295_K	0.613	0.99
259_Y	271_P	0.613	0.99
216_L	224_K	0.611	0.99
27_Q	30_I	0.610	0.99
309_Y	321_P	0.610	0.99
261_M	267_S	0.609	0.99
247_Q	250_N	0.609	0.99
248_A	257_I	0.609	0.99
284_F	292_I	0.603	0.98
133_P	136_M	0.601	0.98
79_L	112_N	0.601	0.98
132_Y	137_T	0.600	0.98
57_A	135_I	0.599	0.98
24_K	27_Q	0.597	0.98
308_A	311_M	0.595	0.98
283_A	293_F	0.594	0.98
275_D	279_D	0.592	0.98
199_Y	203_I	0.591	0.98
232_P	235_T	0.591	0.98
22_A	30_I	0.591	0.98
237_R	242_A	0.590	0.98
77_R	85_I	0.590	0.98
212_G	215_T	0.588	0.98
329_K	332_W	0.588	0.98
259_Y	266_I	0.586	0.98
111_I	120_I	0.583	0.98
220_E	225_R	0.583	0.98
324_K	332_W	0.582	0.98
163_K	167_R	0.581	0.98
179_I	208_G	0.581	0.98
311_M	314_S	0.579	0.98
258_D	262_L	0.577	0.98
255_A	265_W	0.576	0.98
265_W	272_I	0.574	0.98
286_A	289_R	0.573	0.98
276_N	287_L	0.572	0.98
234_E	239_I	0.571	0.98
164_Y	168_R	0.568	0.98
227_E	235_T	0.568	0.98
110_G	113_V	0.567	0.98
105_L	123_I	0.566	0.98
306_S	314_S	0.562	0.98
223_A	226_K	0.562	0.98
232_P	242_A	0.560	0.98
234_E	238_D	0.560	0.98
51_V	158_L	0.559	0.98
81_D	85_I	0.559	0.98
250_N	253_T	0.559	0.98
170_L	200_A	0.558	0.97
64_Y	133_P	0.557	0.97
180_I	183_D	0.556	0.97
218_L	221_S	0.556	0.97
32_S	39_N	0.555	0.97
238_D	244_Y	0.553	0.97
315_G	320_E	0.553	0.97
279_D	306_S	0.552	0.97
219_V	225_R	0.551	0.97
236_L	269_N	0.547	0.97
38_S	64_Y	0.544	0.97
314_S	317_A	0.541	0.97
330_P	333_K	0.540	0.97
211_Y	218_L	0.539	0.97
199_Y	204_L	0.539	0.97
283_A	288_S	0.538	0.97
230_L	243_R	0.536	0.97
194_E	198_R	0.536	0.97
90_A	126_L	0.533	0.97
288_S	293_F	0.532	0.97
184_E	187_N	0.532	0.97
227_E	232_P	0.530	0.97
72_N	75_D	0.529	0.97
282_R	294_L	0.527	0.96
310_D	315_G	0.527	0.96
66_F	100_G	0.524	0.96
237_R	244_Y	0.522	0.96
189_I	203_I	0.522	0.96
281_W	293_F	0.522	0.96
229_E	243_R	0.520	0.96
81_D	86_A	0.520	0.96
218_L	224_K	0.518	0.96
231_D	236_L	0.515	0.96
229_E	235_T	0.514	0.96
252_A	255_A	0.513	0.96
132_Y	140_D	0.512	0.96
128_E	152_K	0.512	0.96
100_G	133_P	0.510	0.96
128_E	148_E	0.507	0.96
110_G	121_Q	0.507	0.96
283_A	291_S	0.506	0.96
227_E	239_I	0.505	0.96
231_D	235_T	0.504	0.95
189_I	200_A	0.504	0.95
159_S	162_G	0.504	0.95
260_D	270_I	0.503	0.95
137_T	141_P	0.503	0.95
188_Y	192_S	0.501	0.95
266_I	272_I	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
4rh7A	1	0.9506	100	0.442	Contact Map
2chqA	3	0.7457	100	0.537	Contact Map
1sxjD	1	0.7407	100	0.539	Contact Map
1sxjA	1	0.879	100	0.54	Contact Map
1iqpA	5	0.7531	100	0.542	Contact Map
1sxjC	1	0.7531	100	0.547	Contact Map
1sxjE	1	0.721	100	0.565	Contact Map
3vkgA	2	0.9383	100	0.568	Contact Map
3u61B	3	0.7432	100	0.587	Contact Map
1sxjB	1	0.7457	100	0.587	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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