RUVB - BACSU - GREMLIN Contacts

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RUVB - Holliday junction ATP-dependent DNA helicase RuvB

UniProt:	O32055	Sequences: MDERLVSSEADNHESVIEQSLRPQNLAQYIGQHKVKENLRVFIDAAKMRQETLDHVLLYGPPGLGKTTLASIVANEMGVELRTTSGPAIERPGDLAAILTALEPGDVLFIDEIHRLHRSIEEVLYPAMEDFCLDIVIGKGPSARSVRLDLPPFTLVGATTRVGLLTAPLRDRFGVMSRLEYYTQEELADIVTRTADVFEVEIDKPSALEIARRSRGTPRVANRLLRRVRDFAQVLGDSRITEDISQNALERLQVDRLGLDHIDHKLLMGMIEKFNGGPVGLDTISATIGEESHTIEDVYEPYLLQIGFIQRTPRGRIVTPAVYHHFQMEAPRYD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	334 (267)
Sequences:	15420 (8464)
Seq/√Len:	518.0

ECOLI - RUVB RARA DPO3X FTSH RAVA YEHL
BACSU - RUVB YRVN DPO3X YJOB FTSH YEAC YPLP SP5K
HALSA - RFCS RFCL CDCH PAN2 PAN1 Q9HPG1 Q9HNK6 Q9HHW2 Q9HPV0 Q9HSH7 Q9HPU1 Q9HN59 CDC69 CDC61
SULSO - RFCL RFCS Q97ZJ7 Q97W74 PAN Q97V06 Q97ZZ9 Q980U9 Q97W25

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
188_A	208_L	4.591	1.00
19_Q	23_P	4.436	1.00
183_T	186_E	3.995	1.00
16_V	80_E	3.527	1.00
188_A	192_T	3.377	1.00
184_Q	212_R	3.053	1.00
33_H	186_E	2.684	1.00
189_D	192_T	2.679	1.00
15_S	20_S	2.635	1.00
192_T	204_K	2.552	1.00
187_L	211_A	2.429	1.00
242_E	246_Q	2.411	1.00
208_L	212_R	2.402	1.00
239_R	242_E	2.378	1.00
184_Q	211_A	2.339	1.00
188_A	207_A	2.324	1.00
209_E	212_R	2.230	1.00
109_F	158_A	2.101	1.00
117_H	169_L	2.084	1.00
191_V	222_N	2.054	1.00
241_T	244_I	2.043	1.00
57_L	113_I	1.964	1.00
243_D	247_N	1.956	1.00
181_Y	218_P	1.923	1.00
93_G	97_A	1.856	1.00
302_Y	305_Q	1.850	1.00
192_T	207_A	1.814	1.00
100_T	103_E	1.808	1.00
184_Q	188_A	1.716	1.00
268_M	272_E	1.693	1.00
276_G	280_G	1.690	1.00
128_M	131_F	1.687	1.00
191_V	207_A	1.680	1.00
263_D	266_L	1.670	1.00
264_H	267_L	1.669	1.00
282_D	286_A	1.662	1.00
218_P	221_A	1.648	1.00
113_I	157_G	1.646	1.00
103_E	132_C	1.642	1.00
285_S	289_G	1.630	1.00
40_R	44_D	1.609	1.00
295_I	298_V	1.603	1.00
191_V	210_I	1.593	1.00
202_I	229_R	1.582	1.00
301_P	305_Q	1.563	1.00
267_L	271_I	1.551	1.00
293_H	297_D	1.545	1.00
87_P	123_V	1.539	1.00
273_K	276_G	1.531	1.00
296_E	300_E	1.525	1.00
240_I	244_I	1.497	1.00
286_A	290_E	1.495	1.00
247_N	251_R	1.495	1.00
19_Q	22_R	1.481	1.00
195_A	207_A	1.424	1.00
184_Q	215_R	1.421	1.00
270_M	277_G	1.419	1.00
297_D	301_P	1.415	1.00
70_A	156_V	1.412	1.00
58_L	179_L	1.409	1.00
203_D	206_S	1.407	1.00
223_R	226_R	1.397	1.00
226_R	230_D	1.397	1.00
274_F	278_P	1.393	1.00
273_K	277_G	1.372	1.00
184_Q	208_L	1.352	1.00
92_P	96_A	1.343	1.00
278_P	282_D	1.339	1.00
193_R	197_V	1.334	1.00
16_V	19_Q	1.299	1.00
26_L	75_N	1.296	1.00
35_V	177_S	1.294	1.00
263_D	267_L	1.286	1.00
279_V	283_T	1.280	1.00
69_L	179_L	1.270	1.00
126_P	129_E	1.268	1.00
281_L	285_S	1.260	1.00
185_E	208_L	1.258	1.00
294_T	297_D	1.257	1.00
33_H	37_E	1.257	1.00
246_Q	250_E	1.254	1.00
287_T	291_E	1.253	1.00
254_V	258_G	1.250	1.00
265_K	269_G	1.249	1.00
243_D	246_Q	1.245	1.00
27_A	40_R	1.242	1.00
99_L	103_E	1.242	1.00
185_E	189_D	1.241	1.00
299_Y	303_L	1.238	1.00
299_Y	302_Y	1.238	1.00
219_R	222_N	1.212	1.00
277_G	280_G	1.208	1.00
209_E	213_R	1.206	1.00
275_N	279_V	1.195	1.00
255_D	259_L	1.193	1.00
274_F	277_G	1.186	1.00
110_I	155_L	1.183	1.00
266_L	270_M	1.169	1.00
201_E	204_K	1.167	1.00
252_L	255_D	1.166	1.00
228_V	232_A	1.163	1.00
29_Y	72_I	1.161	1.00
232_A	236_G	1.158	1.00
271_I	274_F	1.158	1.00
224_L	228_V	1.156	1.00
81_L	109_F	1.156	1.00
38_N	177_S	1.139	1.00
279_V	282_D	1.137	1.00
282_D	285_S	1.136	1.00
74_A	107_V	1.136	1.00
265_K	268_M	1.131	1.00
129_E	133_L	1.130	1.00
296_E	299_Y	1.127	1.00
20_S	25_N	1.125	1.00
242_E	248_A	1.122	1.00
264_H	268_M	1.119	1.00
45_A	56_V	1.117	1.00
33_H	189_D	1.112	1.00
293_H	296_E	1.111	1.00
206_S	209_E	1.103	1.00
294_T	298_V	1.102	1.00
283_T	287_T	1.096	1.00
270_M	274_F	1.093	1.00
272_E	276_G	1.091	1.00
86_G	89_I	1.089	1.00
59_Y	178_R	1.087	1.00
85_S	88_A	1.084	1.00
99_L	127_A	1.083	1.00
89_I	98_I	1.081	1.00
264_H	271_I	1.073	1.00
266_L	271_I	1.068	1.00
129_E	132_C	1.063	1.00
256_R	260_D	1.059	1.00
128_M	132_C	1.058	1.00
104_P	152_P	1.056	1.00
250_E	253_Q	1.053	1.00
269_G	273_K	1.048	1.00
301_P	304_L	1.030	1.00
248_A	255_D	1.028	1.00
247_N	250_E	1.025	1.00
168_P	172_R	1.018	1.00
251_R	255_D	1.009	1.00
284_I	287_T	1.003	1.00
125_Y	128_M	1.001	1.00
198_F	240_I	1.000	1.00
244_I	248_A	0.998	1.00
255_D	258_G	0.994	1.00
250_E	254_V	0.994	1.00
25_N	28_Q	0.977	1.00
283_T	286_A	0.974	1.00
29_Y	69_L	0.973	1.00
39_L	177_S	0.969	1.00
280_G	283_T	0.968	1.00
38_N	41_V	0.968	1.00
281_L	284_I	0.968	1.00
277_G	281_L	0.962	1.00
245_S	248_A	0.960	1.00
97_A	101_A	0.956	1.00
253_Q	256_R	0.954	1.00
227_R	230_D	0.947	1.00
230_D	234_V	0.946	1.00
126_P	130_D	0.937	1.00
237_D	241_T	0.935	1.00
126_P	131_F	0.931	1.00
248_A	252_L	0.928	1.00
175_V	178_R	0.925	1.00
188_A	211_A	0.922	1.00
289_G	293_H	0.920	1.00
127_A	130_D	0.919	1.00
288_I	292_S	0.917	1.00
97_A	100_T	0.916	1.00
252_L	256_R	0.912	1.00
223_R	228_V	0.910	1.00
185_E	188_A	0.910	1.00
256_R	259_L	0.901	1.00
239_R	259_L	0.901	1.00
94_D	97_A	0.890	1.00
122_E	125_Y	0.887	1.00
157_G	173_F	0.886	1.00
298_V	301_P	0.880	1.00
74_A	81_L	0.875	1.00
223_R	230_D	0.871	1.00
37_E	235_L	0.867	1.00
231_F	235_L	0.860	1.00
16_V	82_R	0.857	1.00
268_M	271_I	0.854	1.00
80_E	106_D	0.852	1.00
269_G	272_E	0.850	1.00
90_E	94_D	0.849	1.00
270_M	281_L	0.844	1.00
272_E	275_N	0.838	1.00
290_E	293_H	0.838	1.00
249_L	256_R	0.837	1.00
292_S	296_E	0.832	1.00
241_T	248_A	0.832	1.00
128_M	133_L	0.825	1.00
299_Y	305_Q	0.822	1.00
286_A	293_H	0.822	1.00
284_I	288_I	0.819	1.00
120_I	123_V	0.818	1.00
275_N	278_P	0.818	1.00
130_D	133_L	0.816	1.00
39_L	73_V	0.814	1.00
24_Q	75_N	0.814	1.00
73_V	156_V	0.812	1.00
203_D	239_R	0.804	1.00
252_L	259_L	0.804	1.00
253_Q	257_L	0.803	1.00
248_A	251_R	0.802	1.00
71_S	83_T	0.802	1.00
194_T	222_N	0.792	1.00
38_N	227_R	0.791	1.00
125_Y	130_D	0.791	1.00
280_G	284_I	0.789	1.00
204_K	208_L	0.787	1.00
248_A	256_R	0.786	1.00
259_L	262_I	0.782	1.00
190_I	193_R	0.782	1.00
34_K	180_E	0.782	1.00
210_I	225_L	0.778	1.00
223_R	227_R	0.778	1.00
161_R	164_L	0.776	1.00
285_S	292_S	0.776	1.00
218_P	225_L	0.775	1.00
289_G	292_S	0.774	1.00
300_E	303_L	0.773	1.00
85_S	89_I	0.764	1.00
300_E	304_L	0.763	1.00
237_D	244_I	0.762	1.00
36_K	72_I	0.759	1.00
244_I	247_N	0.758	1.00
290_E	294_T	0.758	1.00
270_M	273_K	0.758	1.00
202_I	207_A	0.756	1.00
38_N	251_R	0.756	1.00
278_P	281_L	0.756	1.00
226_R	229_R	0.755	1.00
219_R	226_R	0.752	1.00
249_L	253_Q	0.747	1.00
102_L	108_L	0.744	1.00
251_R	254_V	0.743	1.00
85_S	90_E	0.742	1.00
28_Q	193_R	0.737	1.00
195_A	225_L	0.737	1.00
248_A	259_L	0.736	1.00
213_R	249_L	0.736	1.00
267_L	274_F	0.733	1.00
263_D	277_G	0.729	1.00
80_E	101_A	0.727	1.00
287_T	290_E	0.726	1.00
271_I	281_L	0.725	1.00
273_K	284_I	0.725	1.00
123_V	126_P	0.722	1.00
77_M	154_T	0.722	1.00
292_S	295_I	0.721	1.00
266_L	299_Y	0.716	1.00
71_S	81_L	0.716	1.00
292_S	299_Y	0.714	1.00
291_E	295_I	0.714	1.00
285_S	288_I	0.712	1.00
296_E	301_P	0.710	1.00
263_D	270_M	0.710	1.00
267_L	270_M	0.710	1.00
210_I	214_S	0.703	1.00
295_I	301_P	0.702	1.00
289_G	296_E	0.702	1.00
221_A	226_R	0.702	1.00
20_S	23_P	0.695	1.00
271_I	275_N	0.693	1.00
57_L	162_V	0.692	1.00
189_D	193_R	0.692	1.00
298_V	305_Q	0.691	1.00
26_L	43_I	0.686	1.00
59_Y	162_V	0.682	1.00
295_I	299_Y	0.677	1.00
35_V	69_L	0.677	1.00
263_D	271_I	0.676	1.00
227_R	231_F	0.675	1.00
186_E	189_D	0.675	1.00
297_D	302_Y	0.673	1.00
232_A	238_S	0.673	1.00
209_E	242_E	0.672	1.00
126_P	132_C	0.672	1.00
246_Q	249_L	0.671	1.00
266_L	269_G	0.671	1.00
85_S	91_R	0.669	1.00
29_Y	36_K	0.669	1.00
114_H	159_T	0.668	1.00
201_E	239_R	0.664	1.00
194_T	197_V	0.660	1.00
248_A	273_K	0.660	1.00
233_Q	237_D	0.654	1.00
297_D	300_E	0.653	1.00
232_A	237_D	0.652	1.00
67_T	111_D	0.651	1.00
244_I	255_D	0.650	1.00
285_S	290_E	0.647	1.00
266_L	288_I	0.647	1.00
214_S	221_A	0.646	1.00
218_P	228_V	0.646	1.00
228_V	234_V	0.644	1.00
261_H	265_K	0.640	1.00
236_G	244_I	0.638	1.00
114_H	160_T	0.632	1.00
123_V	131_F	0.631	1.00
32_Q	35_V	0.630	1.00
242_E	255_D	0.627	1.00
286_A	304_L	0.627	1.00
232_A	235_L	0.625	1.00
235_L	238_S	0.623	1.00
218_P	222_N	0.619	1.00
222_N	225_L	0.619	1.00
297_D	303_L	0.619	1.00
235_L	247_N	0.617	1.00
123_V	129_E	0.611	1.00
41_V	231_F	0.609	1.00
284_I	299_Y	0.606	1.00
192_T	208_L	0.603	1.00
289_G	299_Y	0.601	1.00
162_V	178_R	0.595	0.99
281_L	292_S	0.595	0.99
91_R	94_D	0.594	0.99
241_T	247_N	0.590	0.99
299_Y	304_L	0.588	0.99
182_Y	218_P	0.587	0.99
125_Y	129_E	0.587	0.99
90_E	119_S	0.586	0.99
291_E	298_V	0.585	0.99
86_G	90_E	0.583	0.99
219_R	228_V	0.582	0.99
298_V	302_Y	0.582	0.99
290_E	301_P	0.582	0.99
254_V	257_L	0.578	0.99
294_T	299_Y	0.577	0.99
43_I	77_M	0.574	0.99
297_D	305_Q	0.574	0.99
233_Q	236_G	0.573	0.99
273_K	278_P	0.572	0.99
242_E	247_N	0.571	0.99
262_I	265_K	0.571	0.99
224_L	227_R	0.570	0.99
258_G	261_H	0.570	0.99
225_L	229_R	0.569	0.99
288_I	291_E	0.569	0.99
191_V	221_A	0.568	0.99
294_T	305_Q	0.566	0.99
294_T	302_Y	0.565	0.99
263_D	278_P	0.565	0.99
296_E	302_Y	0.564	0.99
295_I	302_Y	0.558	0.99
270_M	288_I	0.556	0.99
125_Y	133_L	0.554	0.99
249_L	252_L	0.554	0.99
36_K	40_R	0.553	0.99
70_A	109_F	0.552	0.99
18_E	78_G	0.551	0.99
271_I	278_P	0.551	0.99
229_R	232_A	0.550	0.99
256_R	271_I	0.550	0.99
93_G	96_A	0.550	0.99
191_V	225_L	0.549	0.99
126_P	133_L	0.548	0.99
80_E	86_G	0.548	0.99
294_T	301_P	0.547	0.99
284_I	289_G	0.546	0.99
296_E	303_L	0.545	0.99
276_G	279_V	0.543	0.99
242_E	249_L	0.540	0.99
95_L	98_I	0.535	0.99
243_D	248_A	0.535	0.99
242_E	252_L	0.534	0.99
182_Y	187_L	0.533	0.99
256_R	261_H	0.531	0.99
111_D	116_L	0.530	0.99
124_L	132_C	0.529	0.99
285_S	303_L	0.526	0.99
42_F	56_V	0.526	0.99
112_E	160_T	0.526	0.99
267_L	281_L	0.524	0.99
257_L	261_H	0.521	0.99
17_I	20_S	0.518	0.99
280_G	285_S	0.517	0.99
231_F	236_G	0.517	0.99
280_G	287_T	0.516	0.99
290_E	302_Y	0.516	0.99
18_E	21_L	0.513	0.98
224_L	230_D	0.513	0.98
121_E	125_Y	0.513	0.98
34_K	37_E	0.513	0.98
127_A	131_F	0.510	0.98
257_L	260_D	0.509	0.98
275_N	283_T	0.509	0.98
258_G	262_I	0.508	0.98
243_D	259_L	0.504	0.98
124_L	128_M	0.504	0.98
79_V	90_E	0.504	0.98
284_I	296_E	0.502	0.98
205_P	242_E	0.501	0.98
245_S	249_L	0.501	0.98
278_P	292_S	0.500	0.98

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
3vkgA	2	0.9731	100	0.41	Contact Map
4rh7A	1	0.9132	100	0.429	Contact Map
1in4A	1	0.8922	100	0.491	Contact Map
4akgA	2	0.8533	100	0.494	Contact Map
1qvrA	3	0.8713	100	0.511	Contact Map
1sxjD	1	0.8383	100	0.515	Contact Map
1hqcA	1	0.9341	100	0.515	Contact Map
4cr2J	1	0.7665	100	0.517	Contact Map
2qp9X	1	0.7096	100	0.52	Contact Map
4ciuA	1	0.8413	100	0.524	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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