RFCS - HALSA - GREMLIN Contacts

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RFCS - Replication factor C small subunit

UniProt:	Q9HN27	Sequences: MTDAAGGRQEIWVEKYRPERLEDVVGHPDITERLQSYVDRDDLPHLLFAGPAGTGKTASSVSIAKELYGDDWQDNFLELNASDERGIDVVRDRIKDFARSSFGGHNYRVIFLDEADALTDDAQSALRRTMEQFSNNTRFILSCNYSSKIIDPIQSRCAVFRFAQLGDDAVAAHLREIAETEGLEHTDDGIDALVYAADGDMRRAINALQAASATGDSVNEETVYAITATARPEEIETMVTEALGGDFAAARATLDDLLTNRGLAGGDIIDQVHRSVWEFDVEEAAAVRLLDRLGEADYRIAEGANERVQLEALLASVALNAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	322 (281)
Sequences:	21623 (13172)
Seq/√Len:	785.8

ECOLI - DPO3X RARA RUVB HOLB
BACSU - DPO3X YRVN RUVB HOLB YEAC YJOB YPLP
HALSA - RFCS Q9HN59 RFCL Q9HPV0 Q9HPG1 PAN1 Q9HNK6 Q9HSH7 PAN2
SULSO - RFCS RFCL Q97W74 Q97ZJ7 Q97V06 PAN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
171_A	191_D	4.015	1.00
14_E	18_P	3.752	1.00
28_P	169_A	3.274	1.00
171_A	175_R	3.245	1.00
166_G	169_A	3.045	1.00
11_I	75_N	2.799	1.00
175_R	190_I	2.444	1.00
167_D	195_Y	2.293	1.00
170_V	194_V	2.285	1.00
171_A	190_I	2.272	1.00
175_R	187_D	2.178	1.00
209_Q	213_A	2.081	1.00
167_D	194_V	2.042	1.00
287_V	291_D	2.030	1.00
288_R	292_R	1.963	1.00
172_A	175_R	1.954	1.00
273_H	277_W	1.946	1.00
290_L	294_G	1.918	1.00
291_D	295_E	1.902	1.00
186_T	189_G	1.902	1.00
59_S	162_F	1.868	1.00
272_V	276_V	1.857	1.00
220_E	224_Y	1.833	1.00
176_E	180_T	1.811	1.00
191_D	195_Y	1.810	1.00
283_E	287_V	1.798	1.00
240_T	244_G	1.790	1.00
48_F	162_F	1.746	1.00
252_A	256_D	1.746	1.00
217_S	220_E	1.711	1.00
282_E	285_A	1.704	1.00
267_D	271_Q	1.702	1.00
24_V	59_S	1.687	1.00
249_A	253_T	1.650	1.00
287_V	290_L	1.635	1.00
164_Q	201_M	1.625	1.00
137_T	145_Y	1.613	1.00
216_D	220_E	1.601	1.00
147_S	150_I	1.599	1.00
266_G	270_D	1.596	1.00
85_R	88_D	1.595	1.00
84_E	88_D	1.593	1.00
246_D	249_A	1.591	1.00
24_V	62_S	1.577	1.00
138_R	145_Y	1.557	1.00
92_D	96_D	1.549	1.00
223_V	227_T	1.546	1.00
221_E	225_A	1.544	1.00
264_A	268_I	1.533	1.00
167_D	191_D	1.522	1.00
221_E	224_Y	1.509	1.00
222_T	227_T	1.502	1.00
178_A	190_I	1.502	1.00
82_S	125_A	1.494	1.00
220_E	223_V	1.489	1.00
224_Y	227_T	1.487	1.00
185_H	190_I	1.485	1.00
256_D	260_N	1.480	1.00
210_A	213_A	1.476	1.00
167_D	171_A	1.471	1.00
292_R	296_A	1.460	1.00
20_R	23_D	1.456	1.00
265_G	269_I	1.437	1.00
47_L	115_A	1.427	1.00
269_I	272_V	1.426	1.00
30_I	160_F	1.421	1.00
222_T	226_I	1.410	1.00
14_E	17_R	1.408	1.00
262_G	265_G	1.406	1.00
99_R	103_G	1.403	1.00
95_K	98_A	1.402	1.00
49_A	159_V	1.398	1.00
289_L	292_R	1.392	1.00
173_H	201_M	1.391	1.00
210_A	214_T	1.383	1.00
286_A	290_L	1.381	1.00
173_H	176_E	1.374	1.00
294_G	297_D	1.373	1.00
28_P	172_A	1.365	1.00
87_I	91_R	1.355	1.00
234_E	238_M	1.345	1.00
265_G	268_I	1.342	1.00
22_E	35_Q	1.317	1.00
241_E	245_G	1.301	1.00
192_A	195_Y	1.299	1.00
269_I	273_H	1.298	1.00
222_T	225_A	1.296	1.00
111_F	142_S	1.293	1.00
216_D	219_N	1.292	1.00
64_A	109_V	1.287	1.00
84_E	87_I	1.284	1.00
197_A	204_A	1.280	1.00
165_L	201_M	1.273	1.00
269_I	276_V	1.260	1.00
174_L	205_I	1.260	1.00
223_V	226_I	1.258	1.00
277_W	280_D	1.258	1.00
274_R	278_E	1.256	1.00
27_H	30_I	1.255	1.00
184_E	217_S	1.251	1.00
281_V	285_A	1.247	1.00
209_Q	214_T	1.241	1.00
96_D	99_R	1.232	1.00
268_I	272_V	1.232	1.00
275_S	278_E	1.227	1.00
253_T	257_L	1.225	1.00
236_E	240_T	1.217	1.00
49_A	161_R	1.211	1.00
251_R	255_D	1.210	1.00
174_L	204_A	1.209	1.00
219_N	222_T	1.203	1.00
76_F	111_F	1.203	1.00
293_L	296_A	1.196	1.00
254_L	258_L	1.191	1.00
220_E	226_I	1.189	1.00
286_A	293_L	1.189	1.00
231_R	234_E	1.182	1.00
95_K	99_R	1.180	1.00
168_D	171_A	1.179	1.00
172_A	176_E	1.175	1.00
262_G	266_G	1.172	1.00
189_G	192_A	1.170	1.00
61_V	78_E	1.164	1.00
24_V	31_T	1.160	1.00
265_G	272_V	1.157	1.00
169_A	172_A	1.152	1.00
171_A	194_V	1.148	1.00
288_R	291_D	1.143	1.00
255_D	258_L	1.137	1.00
293_L	297_D	1.136	1.00
239_V	243_L	1.133	1.00
253_T	256_D	1.131	1.00
245_G	249_A	1.130	1.00
220_E	227_T	1.127	1.00
228_A	231_R	1.125	1.00
285_A	288_R	1.117	1.00
232_P	236_E	1.116	1.00
168_D	172_A	1.112	1.00
273_H	276_V	1.099	1.00
190_I	194_V	1.099	1.00
31_T	35_Q	1.079	1.00
174_L	190_I	1.076	1.00
266_G	269_I	1.066	1.00
248_A	252_A	1.062	1.00
99_R	104_G	1.062	1.00
242_A	275_S	1.059	1.00
35_Q	39_D	1.058	1.00
86_G	89_V	1.055	1.00
271_Q	275_S	1.052	1.00
291_D	294_G	1.039	1.00
282_E	286_A	1.038	1.00
96_D	100_S	1.037	1.00
219_N	225_A	1.030	1.00
85_R	119_T	1.027	1.00
249_A	252_A	1.020	1.00
276_V	280_D	1.015	1.00
178_A	185_H	1.012	1.00
278_E	281_V	1.007	1.00
88_D	92_D	1.006	1.00
230_A	233_E	1.004	1.00
167_D	198_D	0.996	1.00
216_D	224_Y	0.985	1.00
57_T	113_D	0.978	1.00
228_A	232_P	0.977	1.00
19_E	65_K	0.976	1.00
284_A	288_R	0.975	1.00
184_E	187_D	0.975	1.00
229_T	232_P	0.970	1.00
250_A	254_L	0.969	1.00
264_A	267_D	0.969	1.00
175_R	179_E	0.965	1.00
204_A	207_A	0.962	1.00
193_L	208_L	0.961	1.00
219_N	223_V	0.961	1.00
250_A	253_T	0.961	1.00
98_A	129_T	0.959	1.00
251_R	254_L	0.957	1.00
204_A	208_L	0.957	1.00
63_I	140_I	0.955	1.00
247_F	251_R	0.953	1.00
271_Q	274_R	0.953	1.00
247_F	250_A	0.952	1.00
11_I	14_E	0.951	1.00
140_I	143_C	0.949	1.00
265_G	276_V	0.949	1.00
256_D	261_R	0.949	1.00
250_A	258_L	0.948	1.00
47_L	157_C	0.936	1.00
209_Q	212_S	0.930	1.00
92_D	95_K	0.927	1.00
270_D	274_R	0.926	1.00
194_V	204_A	0.922	1.00
139_F	142_S	0.920	1.00
170_V	204_A	0.916	1.00
168_D	191_D	0.916	1.00
87_I	121_D	0.916	1.00
254_L	257_L	0.913	1.00
177_I	205_I	0.907	1.00
233_E	237_T	0.906	1.00
60_S	140_I	0.903	1.00
268_I	276_V	0.903	1.00
240_T	243_L	0.902	1.00
276_V	279_F	0.901	1.00
272_V	275_S	0.900	1.00
93_R	97_F	0.896	1.00
139_F	145_Y	0.896	1.00
187_D	191_D	0.894	1.00
219_N	226_I	0.886	1.00
280_D	283_E	0.881	1.00
263_L	267_D	0.880	1.00
258_L	262_G	0.879	1.00
185_H	212_S	0.873	1.00
141_L	144_N	0.872	1.00
238_M	245_G	0.869	1.00
152_P	156_R	0.869	1.00
251_R	257_L	0.868	1.00
218_V	224_Y	0.867	1.00
154_Q	159_V	0.865	1.00
217_S	222_T	0.860	1.00
115_A	147_S	0.860	1.00
15_K	20_R	0.857	1.00
286_A	289_L	0.852	1.00
177_I	180_T	0.846	1.00
192_A	196_A	0.845	1.00
217_S	223_V	0.841	1.00
220_E	225_A	0.841	1.00
239_V	242_A	0.837	1.00
146_S	159_V	0.837	1.00
292_R	295_E	0.829	1.00
34_L	63_I	0.828	1.00
49_A	146_S	0.825	1.00
262_G	269_I	0.823	1.00
231_R	238_M	0.823	1.00
290_L	293_L	0.822	1.00
285_A	289_L	0.815	1.00
28_P	32_E	0.812	1.00
17_R	75_N	0.804	1.00
29_D	163_A	0.800	1.00
219_N	227_T	0.797	1.00
170_V	201_M	0.797	1.00
255_D	260_N	0.796	1.00
237_T	241_E	0.796	1.00
138_R	141_L	0.794	1.00
248_A	251_R	0.793	1.00
183_L	212_S	0.788	1.00
251_R	258_L	0.787	1.00
237_T	240_T	0.786	1.00
218_V	223_V	0.785	1.00
21_L	65_K	0.783	1.00
264_A	272_V	0.779	1.00
228_A	235_I	0.775	1.00
287_V	293_L	0.774	1.00
141_L	145_Y	0.773	1.00
265_G	273_H	0.771	1.00
81_A	84_E	0.770	1.00
197_A	200_D	0.769	1.00
80_N	83_D	0.767	1.00
291_D	296_A	0.767	1.00
146_S	161_R	0.766	1.00
217_S	221_E	0.766	1.00
233_E	236_E	0.766	1.00
164_Q	198_D	0.763	1.00
32_E	35_Q	0.762	1.00
217_S	225_A	0.760	1.00
236_E	239_V	0.752	1.00
216_D	221_E	0.746	1.00
218_V	227_T	0.733	1.00
282_E	290_L	0.731	1.00
15_K	18_P	0.731	1.00
90_V	94_I	0.728	1.00
67_L	74_D	0.728	1.00
218_V	222_T	0.724	1.00
75_N	100_S	0.724	1.00
219_N	224_Y	0.719	1.00
243_L	247_F	0.718	1.00
46_L	160_F	0.715	1.00
33_R	36_S	0.714	1.00
235_I	239_V	0.708	1.00
242_A	245_G	0.705	1.00
258_L	263_L	0.705	1.00
102_F	134_S	0.703	1.00
261_R	269_I	0.701	1.00
269_I	282_E	0.696	1.00
174_L	208_L	0.694	1.00
230_A	234_E	0.693	1.00
136_N	145_Y	0.689	1.00
211_A	215_G	0.687	1.00
216_D	222_T	0.686	1.00
15_K	181_E	0.685	1.00
201_M	204_A	0.685	1.00
221_E	227_T	0.684	1.00
19_E	23_D	0.683	1.00
125_A	129_T	0.680	1.00
75_N	82_S	0.679	1.00
77_L	108_R	0.679	1.00
231_R	235_I	0.677	1.00
178_A	208_L	0.674	1.00
193_L	204_A	0.672	1.00
25_V	173_H	0.671	1.00
267_D	270_D	0.669	1.00
174_L	193_L	0.669	1.00
118_L	122_A	0.667	1.00
241_E	246_D	0.667	1.00
275_S	279_F	0.666	1.00
188_D	191_D	0.659	1.00
54_T	162_F	0.656	1.00
232_P	235_I	0.656	1.00
233_E	240_T	0.655	1.00
36_S	39_D	0.653	1.00
115_A	141_L	0.653	1.00
115_A	149_I	0.652	1.00
241_E	249_A	0.652	1.00
75_N	106_N	0.650	1.00
235_I	238_M	0.646	1.00
40_R	45_H	0.646	1.00
119_T	122_A	0.644	1.00
142_S	145_Y	0.643	1.00
218_V	225_A	0.640	1.00
186_T	217_S	0.640	1.00
170_V	174_L	0.634	1.00
85_R	121_D	0.632	1.00
171_A	187_D	0.631	1.00
89_V	92_D	0.630	1.00
193_L	207_A	0.630	1.00
51_P	54_T	0.623	1.00
128_R	132_Q	0.623	1.00
165_L	169_A	0.623	1.00
268_I	271_Q	0.622	1.00
85_R	93_R	0.622	1.00
274_R	277_W	0.622	1.00
216_D	223_V	0.620	1.00
185_H	189_G	0.616	1.00
75_N	79_L	0.616	1.00
94_I	98_A	0.614	1.00
229_T	233_E	0.612	1.00
261_R	265_G	0.610	1.00
93_R	98_A	0.608	1.00
178_A	183_L	0.602	1.00
216_D	227_T	0.602	1.00
242_A	247_F	0.601	1.00
290_L	297_D	0.600	1.00
260_N	263_L	0.599	1.00
139_F	143_C	0.597	1.00
232_P	238_M	0.596	1.00
31_T	59_S	0.593	1.00
279_F	283_E	0.592	1.00
246_D	250_A	0.586	1.00
250_A	257_L	0.586	1.00
231_R	263_L	0.582	1.00
216_D	226_I	0.580	1.00
94_I	97_F	0.580	1.00
238_M	242_A	0.579	1.00
282_E	287_V	0.577	1.00
268_I	273_H	0.577	1.00
277_W	281_V	0.577	1.00
261_R	268_I	0.576	1.00
140_I	144_N	0.575	1.00
231_R	242_A	0.574	1.00
281_V	286_A	0.574	1.00
217_S	226_I	0.572	1.00
91_R	95_K	0.570	1.00
138_R	142_S	0.570	1.00
272_V	279_F	0.568	1.00
229_T	236_E	0.568	1.00
261_R	264_A	0.568	1.00
241_E	247_F	0.567	1.00
23_D	176_E	0.566	1.00
286_A	297_D	0.564	1.00
115_A	139_F	0.563	1.00
235_I	267_D	0.563	1.00
79_L	82_S	0.562	1.00
263_L	266_G	0.560	1.00
16_Y	181_E	0.558	1.00
270_D	273_H	0.555	1.00
99_R	102_F	0.554	1.00
79_L	112_L	0.550	1.00
84_E	97_F	0.550	1.00
264_A	276_V	0.550	1.00
243_L	246_D	0.547	1.00
20_R	66_E	0.546	1.00
252_A	255_D	0.544	1.00
245_G	248_A	0.543	1.00
107_Y	138_R	0.543	1.00
77_L	93_R	0.543	1.00
235_I	240_T	0.542	1.00
138_R	144_N	0.540	1.00
25_V	176_E	0.540	1.00
240_T	246_D	0.539	1.00
262_G	276_V	0.536	1.00
32_E	36_S	0.536	1.00
131_E	155_S	0.535	1.00
124_S	127_R	0.535	1.00
139_F	144_N	0.534	1.00
202_R	205_I	0.533	1.00
58_A	202_R	0.532	1.00
140_I	145_Y	0.531	1.00
173_H	177_I	0.531	1.00
76_F	82_S	0.530	1.00
289_L	297_D	0.530	1.00
38_V	63_I	0.529	1.00
234_E	237_T	0.528	1.00
16_Y	180_T	0.528	1.00
283_E	286_A	0.527	1.00
234_E	243_L	0.526	1.00
279_F	282_E	0.526	1.00
74_D	107_Y	0.523	1.00
260_N	264_A	0.518	1.00
239_V	274_R	0.517	1.00
272_V	280_D	0.516	1.00
101_S	104_G	0.515	1.00
282_E	289_L	0.514	1.00
211_A	214_T	0.514	1.00
175_R	178_A	0.512	1.00
47_L	146_S	0.512	1.00
192_A	220_E	0.510	1.00
264_A	269_I	0.509	1.00
215_G	220_E	0.506	1.00
131_E	152_P	0.505	1.00
67_L	138_R	0.505	1.00
280_D	284_A	0.503	1.00
200_D	208_L	0.502	1.00
269_I	275_S	0.500	1.00

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
2chqA	3	0.9689	100	0.357	Contact Map
1iqpA	5	0.9969	100	0.358	Contact Map
1sxjC	1	0.9752	100	0.366	Contact Map
1sxjD	1	0.9596	100	0.366	Contact Map
1sxjB	1	0.9658	100	0.425	Contact Map
1sxjE	1	0.9348	100	0.435	Contact Map
3u61B	3	0.9565	100	0.454	Contact Map
3pvsA	4	0.941	100	0.456	Contact Map
3vkgA	2	0.972	100	0.465	Contact Map
1jr3A	3	0.9689	100	0.465	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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