RUVB - ECOLI - GREMLIN Contacts

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RUVB - Holliday junction ATP-dependent DNA helicase RuvB

UniProt:	P0A812	Sequences: MIEADRLISAGTTLPEDVADRAIRPKLLEEYVGQPQVRSQMEIFIKAAKLRGDALDHLLIFGPPGLGKTTLANIVANEMGVNLRTTSGPVLEKAGDLAAMLTNLEPHDVLFIDEIHRLSPVVEEVLYPAMEDYQLDIMIGEGPAARSIKIDLPPFTLIGATTRAGSLTSPLRDRFGIVQRLEFYQVPDLQYIVSRSARFMGLEMSDDGALEVARRARGTPRIANRLLRRVRDFAEVKHDGTISADIAAQALDMLNVDAEGFDYMDRKLLLAVIDKFFGGPVGLDNLAAAIGEERETIEDVLEPYLIQQGFLQRTPRGRMATTRAWNHFGITPPEMP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10924
Length:	336 (270)
Sequences:	17329 (9256)
Seq/√Len:	563.3

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
190_Q	210_L	4.707	1.00
21_R	25_P	4.110	1.00
185_Q	188_D	4.077	1.00
190_Q	194_S	3.681	1.00
18_V	82_N	3.489	1.00
35_P	188_D	3.177	1.00
186_V	214_R	3.140	1.00
16_E	84_R	2.875	1.00
243_S	246_I	2.698	1.00
186_V	213_A	2.622	1.00
194_S	206_D	2.605	1.00
189_L	213_A	2.534	1.00
191_Y	194_S	2.505	1.00
17_D	22_A	2.409	1.00
210_L	214_R	2.407	1.00
211_E	214_R	2.384	1.00
190_Q	209_A	2.382	1.00
194_S	209_A	2.258	1.00
241_T	244_A	2.208	1.00
105_E	154_P	2.201	1.00
244_A	248_A	2.189	1.00
42_E	46_K	2.113	1.00
119_S	171_L	2.007	1.00
193_V	224_N	1.949	1.00
111_F	160_A	1.934	1.00
186_V	190_Q	1.908	1.00
265_D	268_L	1.895	1.00
95_G	99_A	1.864	1.00
59_L	115_I	1.784	1.00
37_V	179_Q	1.719	1.00
245_D	249_Q	1.714	1.00
183_F	220_P	1.688	1.00
275_K	278_G	1.648	1.00
278_G	282_G	1.645	1.00
266_R	269_L	1.623	1.00
186_V	210_L	1.617	1.00
269_L	273_I	1.584	1.00
102_T	105_E	1.570	1.00
205_S	208_G	1.570	1.00
21_R	24_R	1.569	1.00
193_V	212_V	1.567	1.00
284_D	288_A	1.562	1.00
204_M	231_R	1.559	1.00
31_Y	74_I	1.544	1.00
115_I	159_G	1.543	1.00
193_V	209_A	1.530	1.00
289_A	293_E	1.516	1.00
220_P	223_A	1.514	1.00
297_I	300_V	1.476	1.00
280_P	284_D	1.469	1.00
186_V	217_R	1.457	1.00
287_A	291_G	1.455	1.00
195_R	199_F	1.452	1.00
275_K	279_G	1.447	1.00
211_E	215_R	1.437	1.00
276_F	280_P	1.434	1.00
60_I	181_L	1.425	1.00
89_P	135_L	1.410	1.00
281_V	285_N	1.405	1.00
298_E	302_E	1.383	1.00
285_N	289_A	1.380	1.00
230_V	234_A	1.376	1.00
35_P	191_Y	1.375	1.00
72_A	158_I	1.365	1.00
249_Q	252_D	1.353	1.00
246_I	250_A	1.347	1.00
28_L	77_N	1.344	1.00
29_E	42_E	1.322	1.00
31_Y	71_L	1.317	1.00
203_E	206_D	1.310	1.00
130_M	133_Y	1.303	1.00
238_H	246_I	1.302	1.00
128_P	131_E	1.298	1.00
270_L	274_D	1.294	1.00
18_V	21_R	1.294	1.00
268_L	272_V	1.286	1.00
277_F	281_V	1.270	1.00
288_A	292_E	1.261	1.00
271_A	275_K	1.260	1.00
249_Q	253_M	1.254	1.00
71_L	181_L	1.253	1.00
197_A	209_A	1.248	1.00
248_A	252_D	1.245	1.00
205_S	241_T	1.242	1.00
258_A	262_D	1.240	1.00
208_G	211_E	1.220	1.00
221_R	224_N	1.218	1.00
258_A	261_F	1.208	1.00
291_G	295_E	1.205	1.00
131_E	135_L	1.205	1.00
276_F	279_G	1.203	1.00
225_R	228_R	1.201	1.00
295_E	299_D	1.187	1.00
264_M	267_K	1.186	1.00
190_Q	213_A	1.186	1.00
273_I	276_F	1.185	1.00
279_G	282_G	1.184	1.00
187_P	190_Q	1.182	1.00
131_E	134_Q	1.179	1.00
35_P	39_S	1.163	1.00
267_K	271_A	1.159	1.00
73_N	85_T	1.151	1.00
253_M	257_D	1.141	1.00
281_V	284_D	1.140	1.00
266_R	273_I	1.138	1.00
61_F	180_R	1.138	1.00
187_P	191_Y	1.132	1.00
244_A	250_A	1.130	1.00
211_E	244_A	1.123	1.00
88_G	91_L	1.119	1.00
279_G	283_L	1.109	1.00
297_I	301_L	1.105	1.00
92_E	96_D	1.104	1.00
177_I	180_R	1.103	1.00
283_L	287_A	1.099	1.00
129_A	132_D	1.089	1.00
274_D	278_G	1.087	1.00
82_N	103_N	1.083	1.00
250_A	253_M	1.082	1.00
251_L	255_N	1.072	1.00
91_L	100_M	1.072	1.00
277_F	280_P	1.066	1.00
272_V	279_G	1.064	1.00
245_D	248_A	1.064	1.00
83_L	111_F	1.064	1.00
242_I	246_I	1.058	1.00
257_D	261_F	1.054	1.00
255_N	258_A	1.053	1.00
203_E	241_T	1.041	1.00
256_V	260_G	1.040	1.00
99_A	103_N	1.037	1.00
292_E	296_T	1.030	1.00
26_K	77_N	1.028	1.00
273_I	277_F	1.026	1.00
257_D	260_G	1.024	1.00
274_D	277_F	1.019	1.00
266_R	270_L	1.007	1.00
233_F	237_K	1.002	1.00
252_D	255_N	0.998	1.00
272_V	275_K	0.997	1.00
296_T	299_D	0.992	1.00
229_R	233_F	0.991	1.00
187_P	210_L	0.990	1.00
276_F	283_L	0.986	1.00
226_L	230_V	0.983	1.00
22_A	27_L	0.979	1.00
220_P	227_L	0.977	1.00
189_L	223_A	0.971	1.00
264_M	273_I	0.968	1.00
298_E	301_L	0.967	1.00
127_Y	130_M	0.966	1.00
207_D	244_A	0.964	1.00
220_P	230_V	0.962	1.00
252_D	256_V	0.961	1.00
234_A	238_H	0.960	1.00
265_D	269_L	0.957	1.00
99_A	102_T	0.950	1.00
228_R	232_D	0.948	1.00
27_L	30_E	0.948	1.00
40_Q	179_Q	0.947	1.00
36_Q	182_E	0.946	1.00
106_P	154_P	0.942	1.00
125_V	128_P	0.932	1.00
275_K	280_P	0.931	1.00
94_A	98_A	0.926	1.00
250_A	254_L	0.925	1.00
253_M	256_V	0.918	1.00
128_P	134_Q	0.916	1.00
132_D	135_L	0.916	1.00
273_I	280_P	0.910	1.00
264_M	268_L	0.907	1.00
212_V	227_L	0.906	1.00
282_G	285_N	0.906	1.00
286_L	290_I	0.902	1.00
270_L	273_I	0.894	1.00
284_D	287_A	0.893	1.00
188_D	191_Y	0.888	1.00
229_R	232_D	0.878	1.00
75_V	158_I	0.872	1.00
271_A	274_D	0.872	1.00
280_P	283_L	0.866	1.00
41_M	179_Q	0.865	1.00
76_A	83_L	0.864	1.00
283_L	294_R	0.862	1.00
250_A	257_D	0.858	1.00
87_S	90_V	0.856	1.00
82_N	108_D	0.856	1.00
287_A	290_I	0.855	1.00
128_P	133_Y	0.852	1.00
170_P	174_R	0.852	1.00
196_S	224_N	0.849	1.00
250_A	258_A	0.846	1.00
283_L	290_I	0.846	1.00
296_T	300_V	0.845	1.00
273_I	283_L	0.843	1.00
104_L	110_L	0.842	1.00
295_E	298_E	0.841	1.00
246_I	249_Q	0.839	1.00
268_L	273_I	0.837	1.00
124_E	127_Y	0.835	1.00
291_G	298_E	0.835	1.00
93_K	96_D	0.834	1.00
101_L	105_E	0.832	1.00
130_M	134_Q	0.829	1.00
17_D	21_R	0.829	1.00
225_R	232_D	0.829	1.00
272_V	276_F	0.827	1.00
268_L	271_A	0.827	1.00
31_Y	38_R	0.817	1.00
247_A	250_A	0.816	1.00
38_R	74_I	0.812	1.00
241_T	261_F	0.812	1.00
40_Q	43_I	0.810	1.00
283_L	286_L	0.809	1.00
291_G	294_R	0.808	1.00
204_M	209_A	0.806	1.00
280_P	290_I	0.806	1.00
159_G	175_F	0.806	1.00
211_E	248_A	0.802	1.00
230_V	233_F	0.800	1.00
269_L	272_V	0.798	1.00
196_S	199_F	0.797	1.00
286_L	289_A	0.794	1.00
280_P	287_A	0.794	1.00
226_L	229_R	0.792	1.00
255_N	259_E	0.788	1.00
193_V	223_A	0.788	1.00
265_D	272_V	0.788	1.00
292_E	295_E	0.787	1.00
269_L	276_F	0.783	1.00
92_E	121_V	0.782	1.00
232_D	236_V	0.781	1.00
264_M	269_L	0.781	1.00
244_A	257_D	0.775	1.00
267_K	270_L	0.773	1.00
221_R	228_R	0.770	1.00
123_E	129_A	0.770	1.00
243_S	250_A	0.769	1.00
224_N	228_R	0.767	1.00
115_I	157_L	0.766	1.00
282_G	286_L	0.759	1.00
112_I	157_L	0.759	1.00
73_N	83_L	0.757	1.00
287_A	294_R	0.756	1.00
96_D	99_A	0.756	1.00
262_D	265_D	0.756	1.00
86_T	112_I	0.754	1.00
58_L	179_Q	0.751	1.00
279_G	286_L	0.746	1.00
216_A	223_A	0.745	1.00
127_Y	131_E	0.743	1.00
224_N	227_L	0.742	1.00
84_R	103_N	0.740	1.00
206_D	210_L	0.739	1.00
76_A	109_V	0.738	1.00
39_S	237_K	0.737	1.00
20_D	80_G	0.737	1.00
87_S	91_L	0.736	1.00
285_N	288_A	0.732	1.00
251_L	258_A	0.732	1.00
257_D	262_D	0.729	1.00
228_R	247_A	0.725	1.00
20_D	23_I	0.723	1.00
38_R	42_E	0.715	1.00
81_V	107_H	0.714	1.00
84_R	108_D	0.713	1.00
256_V	259_E	0.712	1.00
254_L	257_D	0.710	1.00
34_Q	37_V	0.710	1.00
248_A	251_L	0.703	1.00
288_A	295_E	0.703	1.00
191_Y	195_R	0.700	1.00
127_Y	132_D	0.698	1.00
19_A	22_A	0.694	1.00
101_L	149_K	0.691	1.00
225_R	229_R	0.689	1.00
197_A	228_R	0.687	1.00
250_A	261_F	0.682	1.00
254_L	258_A	0.682	1.00
45_I	79_M	0.679	1.00
123_E	130_M	0.679	1.00
288_A	291_G	0.677	1.00
130_M	135_L	0.673	1.00
192_I	195_R	0.666	1.00
272_V	283_L	0.666	1.00
32_V	195_R	0.666	1.00
40_Q	253_M	0.666	1.00
162_T	165_G	0.657	1.00
251_L	261_F	0.656	1.00
265_D	273_I	0.654	1.00
290_I	293_E	0.652	1.00
231_R	234_A	0.648	1.00
190_Q	206_D	0.647	1.00
147_S	151_D	0.646	1.00
74_I	77_N	0.646	1.00
205_S	243_S	0.645	1.00
37_V	71_L	0.644	1.00
242_I	247_A	0.643	1.00
22_A	25_P	0.642	1.00
69_T	113_D	0.642	1.00
219_T	227_L	0.641	1.00
299_D	302_E	0.641	1.00
266_R	274_D	0.640	1.00
193_V	227_L	0.640	1.00
128_P	132_D	0.638	1.00
294_R	298_E	0.636	1.00
215_R	251_L	0.632	1.00
241_T	249_Q	0.630	1.00
247_A	258_A	0.626	1.00
41_M	75_V	0.626	1.00
283_L	300_V	0.626	1.00
116_H	162_T	0.624	1.00
290_I	294_R	0.624	1.00
129_A	134_Q	0.622	1.00
241_T	257_D	0.621	1.00
213_A	223_A	0.619	1.00
43_I	237_K	0.619	1.00
164_A	180_R	0.617	1.00
27_L	77_N	0.616	1.00
129_A	135_L	0.616	1.00
35_P	187_P	0.615	1.00
163_R	166_S	0.606	1.00
289_A	292_E	0.602	1.00
268_L	301_L	0.597	1.00
134_Q	149_K	0.594	1.00
223_A	228_R	0.593	1.00
225_R	230_V	0.591	1.00
279_G	301_L	0.588	1.00
265_D	283_L	0.588	1.00
235_E	239_D	0.583	1.00
61_F	164_A	0.583	1.00
251_L	257_D	0.580	1.00
294_R	297_I	0.580	1.00
286_L	291_G	0.579	1.00
113_D	118_L	0.575	1.00
243_S	249_Q	0.574	0.99
265_D	280_P	0.573	0.99
123_E	132_D	0.573	0.99
259_E	263_Y	0.573	0.99
220_P	226_L	0.572	0.99
30_E	195_R	0.572	0.99
221_R	230_V	0.571	0.99
93_K	98_A	0.570	0.99
246_I	257_D	0.569	0.99
96_D	112_I	0.568	0.99
194_S	210_L	0.568	0.99
245_D	261_F	0.568	0.99
242_I	248_A	0.565	0.99
124_E	128_P	0.564	0.99
40_Q	229_R	0.562	0.99
44_F	58_L	0.561	0.99
241_T	250_A	0.560	0.99
265_D	279_G	0.559	0.99
221_R	226_L	0.558	0.99
53_D	79_M	0.557	0.99
268_L	290_I	0.555	0.99
259_E	262_D	0.554	0.99
234_A	239_D	0.554	0.99
200_M	242_I	0.554	0.99
61_F	177_I	0.554	0.99
184_Y	189_L	0.554	0.99
190_Q	214_R	0.554	0.99
197_A	204_M	0.553	0.99
230_V	236_V	0.553	0.99
241_T	245_D	0.551	0.99
125_V	129_A	0.549	0.99
45_I	75_V	0.549	0.99
113_D	116_H	0.544	0.99
101_L	129_A	0.544	0.99
275_K	283_L	0.542	0.99
248_A	254_L	0.541	0.99
123_E	133_Y	0.540	0.99
87_S	92_E	0.537	0.99
122_V	133_Y	0.536	0.99
212_V	216_A	0.535	0.99
209_A	213_A	0.530	0.99
43_I	233_F	0.530	0.99
256_V	261_F	0.530	0.99
192_I	220_P	0.529	0.99
244_A	249_Q	0.528	0.99
237_K	240_G	0.527	0.99
279_G	285_N	0.526	0.99
266_R	276_F	0.526	0.99
244_A	254_L	0.526	0.99
290_I	297_I	0.525	0.99
30_E	199_F	0.524	0.99
276_F	286_L	0.524	0.99
242_I	254_L	0.524	0.99
28_L	45_I	0.524	0.99
280_P	294_R	0.523	0.99
246_I	258_A	0.522	0.99
216_A	219_T	0.517	0.99
69_T	85_T	0.516	0.99
24_R	82_N	0.513	0.99
279_G	284_D	0.510	0.99
227_L	230_V	0.509	0.99
125_V	131_E	0.507	0.99
228_R	231_R	0.507	0.99
223_A	227_L	0.507	0.99
284_D	294_R	0.506	0.99
246_I	251_L	0.505	0.99
194_S	198_R	0.504	0.99
292_E	300_V	0.501	0.99
221_R	231_R	0.501	0.99
241_T	246_I	0.500	0.99

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	0.9821	100	0.391	Contact Map
4rh7A	1	0.9137	100	0.422	Contact Map
1in4A	1	0.8869	100	0.484	Contact Map
4cr2J	1	0.7679	100	0.488	Contact Map
4akgA	2	0.8571	100	0.488	Contact Map
3b9pA	1	0.7381	100	0.496	Contact Map
2qp9X	1	0.7054	100	0.498	Contact Map
2zanA	1	0.747	100	0.501	Contact Map
1xwiA	1	0.7619	100	0.505	Contact Map
4cr2L	1	0.7619	100	0.507	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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