RHLB - ECOLI - GREMLIN Contacts

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RHLB - ATP-dependent RNA helicase RhlB

UniProt:	P0A8J8	Sequences: MSKTHLTEQKFSDFALHPKVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTSTFHYLLSHPAIADRKVNQPRALIMAPTRELAVQIHADAEPLAEATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMYDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEQMNNAEYIEVEPEQKTGHRIKEELFYPSNEEKMRLLQTLIEEEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILDEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEEYALNLPAIETYIGHSIPVSKYNPDALMTDLPKPLRLTRPRTGNGPRRTGAPRNRRRSG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10844
Length:	421 (341)
Sequences:	57117 (33559)
Seq/√Len:	1817.3

ECOLI - RHLB DEAD SRMB RHLE RECQ DBPA RECG YFJK YEJH RAPA LHR
BACSU - CSHA DBPA CSHB RECG RECQ RECS YFML YPRA COMFA YQHH YWQA
HALSA - Q9HN80 HELS Q9HNB2 RAD25 Q9HMW5 Q9HQA5 O51997 O52003
SULSO - Q981C8 HELX HELS Q97WT0 Q980C0 Q97X74 Q97X64 Q97ZF9 Q97Y93 Q97WW1 Q97YC4 Q97ZF3 Q97ZV2 Q97YQ4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
67_T	87_A	3.724	1.00
64_L	104_A	3.552	1.00
284_G	307_L	3.292	1.00
301_E	306_D	2.929	1.00
43_T	195_M	2.853	1.00
101_H	105_E	2.813	1.00
284_G	301_E	2.764	1.00
273_W	277_A	2.658	1.00
300_D	304_R	2.636	1.00
273_W	285_L	2.633	1.00
273_W	283_V	2.535	1.00
297_R	301_E	2.529	1.00
114_K	136_D	2.494	1.00
248_Q	279_D	2.473	1.00
116_G	135_V	2.419	1.00
259_A	327_H	2.386	1.00
266_K	289_D	2.380	1.00
270_E	285_L	2.318	1.00
44_L	69_H	2.309	1.00
91_A	100_I	2.248	1.00
282_R	308_D	2.242	1.00
167_A	196_L	2.176	1.00
263_A	269_C	2.155	1.00
101_H	117_L	2.145	1.00
63_F	197_F	2.142	1.00
275_H	279_D	2.139	1.00
257_D	326_T	2.138	1.00
296_L	300_D	2.113	1.00
263_A	272_I	2.028	1.00
177_K	180_R	2.009	1.00
284_G	298_I	2.007	1.00
291_A	294_K	1.935	1.00
140_G	145_L	1.905	1.00
246_L	249_T	1.893	1.00
258_R	324_A	1.882	1.00
87_A	161_V	1.841	1.00
37_A	41_P	1.841	1.00
86_R	160_Q	1.823	1.00
176_I	179_I	1.819	1.00
176_I	180_R	1.814	1.00
178_D	181_W	1.786	1.00
85_P	160_Q	1.780	1.00
233_E	344_I	1.730	1.00
70_Y	161_V	1.711	1.00
101_H	115_L	1.693	1.00
244_M	275_H	1.693	1.00
35_I	51_G	1.683	1.00
248_Q	252_E	1.677	1.00
43_T	66_S	1.667	1.00
269_C	285_L	1.666	1.00
98_V	102_A	1.664	1.00
344_I	356_S	1.654	1.00
246_L	250_L	1.650	1.00
116_G	130_V	1.639	1.00
39_A	62_A	1.638	1.00
47_R	217_E	1.630	1.00
263_A	311_V	1.630	1.00
98_V	296_L	1.622	1.00
328_V	347_T	1.619	1.00
276_L	311_V	1.609	1.00
269_C	287_T	1.597	1.00
103_D	321_H	1.597	1.00
330_N	344_I	1.594	1.00
208_L	213_M	1.593	1.00
204_R	207_E	1.563	1.00
268_R	332_D	1.557	1.00
252_E	279_D	1.554	1.00
63_F	163_V	1.554	1.00
327_H	357_I	1.553	1.00
272_I	331_Y	1.537	1.00
103_D	106_P	1.534	1.00
277_A	283_V	1.513	1.00
294_K	297_R	1.507	1.00
208_L	212_Q	1.499	1.00
268_R	271_E	1.492	1.00
148_Y	153_H	1.487	1.00
312_A	316_A	1.466	1.00
175_F	179_I	1.456	1.00
177_K	181_W	1.447	1.00
123_G	126_K	1.445	1.00
265_T	268_R	1.425	1.00
316_A	320_L	1.424	1.00
43_T	49_V	1.417	1.00
208_L	214_N	1.413	1.00
206_R	210_F	1.413	1.00
104_A	137_I	1.407	1.00
71_L	87_A	1.405	1.00
234_E	355_H	1.403	1.00
41_P	45_A	1.397	1.00
51_G	197_F	1.392	1.00
259_A	329_F	1.372	1.00
125_D	129_K	1.364	1.00
232_K	355_H	1.363	1.00
290_V	298_I	1.357	1.00
247_L	329_F	1.356	1.00
42_L	49_V	1.350	1.00
99_Q	321_H	1.347	1.00
298_I	310_L	1.318	1.00
168_D	318_R	1.316	1.00
179_I	182_L	1.309	1.00
294_K	298_I	1.299	1.00
250_L	253_E	1.298	1.00
88_L	159_I	1.297	1.00
208_L	211_E	1.295	1.00
104_A	115_L	1.286	1.00
71_L	136_D	1.285	1.00
301_E	307_L	1.285	1.00
96_L	319_G	1.284	1.00
70_Y	160_Q	1.281	1.00
53_A	57_T	1.275	1.00
175_F	180_R	1.268	1.00
124_Y	128_L	1.266	1.00
68_F	72_L	1.266	1.00
162_V	194_N	1.257	1.00
259_A	309_I	1.253	1.00
209_A	213_M	1.253	1.00
180_R	184_R	1.240	1.00
102_A	106_P	1.240	1.00
281_H	309_I	1.240	1.00
258_R	305_G	1.240	1.00
273_W	311_V	1.237	1.00
67_T	161_V	1.237	1.00
68_F	108_A	1.236	1.00
183_F	186_M	1.234	1.00
324_A	352_A	1.231	1.00
209_A	212_Q	1.212	1.00
40_L	44_L	1.211	1.00
29_F	61_M	1.206	1.00
211_E	214_N	1.206	1.00
42_L	217_E	1.201	1.00
205_V	208_L	1.200	1.00
91_A	97_A	1.195	1.00
269_C	273_W	1.191	1.00
228_G	231_I	1.190	1.00
85_P	158_A	1.184	1.00
97_A	117_L	1.174	1.00
181_W	184_R	1.173	1.00
215_N	218_Y	1.169	1.00
245_R	248_Q	1.164	1.00
84_Q	158_A	1.164	1.00
67_T	163_V	1.147	1.00
86_R	136_D	1.137	1.00
216_A	220_E	1.128	1.00
70_Y	193_L	1.124	1.00
250_L	329_F	1.115	1.00
135_V	138_L	1.112	1.00
290_V	294_K	1.111	1.00
303_T	324_A	1.111	1.00
146_I	181_W	1.110	1.00
336_D	339_D	1.110	1.00
333_L	358_S	1.109	1.00
302_F	310_L	1.107	1.00
368_L	372_E	1.102	1.00
39_A	51_G	1.102	1.00
101_H	139_I	1.100	1.00
298_I	301_E	1.093	1.00
330_N	343_R	1.089	1.00
300_D	303_T	1.084	1.00
175_F	178_D	1.082	1.00
34_P	38_L	1.080	1.00
330_N	358_S	1.079	1.00
275_H	278_A	1.078	1.00
38_L	42_L	1.075	1.00
247_L	331_Y	1.074	1.00
248_Q	275_H	1.072	1.00
244_M	248_Q	1.071	1.00
269_C	311_V	1.069	1.00
233_E	340_Y	1.060	1.00
102_A	105_E	1.059	1.00
90_M	140_G	1.057	1.00
298_I	307_L	1.055	1.00
40_L	65_T	1.050	1.00
297_R	300_D	1.044	1.00
204_R	208_L	1.037	1.00
60_T	100_I	1.036	1.00
243_K	246_L	1.033	1.00
69_H	72_L	1.029	1.00
161_V	195_M	1.025	1.00
54_Q	57_T	1.024	1.00
52_Q	220_E	1.022	1.00
287_T	290_V	1.020	1.00
305_G	308_D	1.016	1.00
116_G	138_L	1.013	1.00
27_K	106_P	1.010	1.00
127_Q	130_V	1.007	1.00
364_Y	368_L	1.005	1.00
305_G	324_A	1.003	1.00
242_E	245_R	0.997	1.00
181_W	185_R	0.997	1.00
97_A	139_I	0.994	1.00
49_V	195_M	0.988	1.00
261_I	329_F	0.986	1.00
169_R	172_D	0.979	1.00
272_I	311_V	0.977	1.00
244_M	331_Y	0.977	1.00
327_H	355_H	0.973	1.00
169_R	318_R	0.971	1.00
286_L	315_V	0.971	1.00
334_P	340_Y	0.968	1.00
34_P	37_A	0.966	1.00
226_K	229_H	0.965	1.00
244_M	279_D	0.961	1.00
210_F	214_N	0.961	1.00
292_Q	296_L	0.951	1.00
146_I	178_D	0.951	1.00
61_M	103_D	0.950	1.00
206_R	218_Y	0.946	1.00
180_R	211_E	0.943	1.00
270_E	287_T	0.937	1.00
249_T	253_E	0.936	1.00
286_L	316_A	0.934	1.00
104_A	139_I	0.929	1.00
370_A	374_Y	0.925	1.00
179_I	186_M	0.923	1.00
42_L	45_A	0.922	1.00
317_A	339_D	0.918	1.00
31_N	37_A	0.918	1.00
274_G	277_A	0.916	1.00
96_L	99_Q	0.915	1.00
90_M	145_L	0.908	1.00
26_K	109_E	0.898	1.00
125_D	128_L	0.894	1.00
221_V	224_E	0.893	1.00
179_I	183_F	0.892	1.00
218_Y	222_E	0.891	1.00
372_E	376_G	0.886	1.00
236_F	246_L	0.883	1.00
251_I	259_A	0.879	1.00
228_G	233_E	0.878	1.00
274_G	278_A	0.875	1.00
256_P	308_D	0.872	1.00
209_A	214_N	0.872	1.00
176_I	183_F	0.871	1.00
356_S	360_A	0.868	1.00
268_R	331_Y	0.867	1.00
354_G	357_I	0.862	1.00
267_H	271_E	0.859	1.00
293_K	297_R	0.858	1.00
67_T	137_I	0.858	1.00
262_F	343_R	0.856	1.00
257_D	327_H	0.852	1.00
367_N	370_A	0.849	1.00
182_L	186_M	0.849	1.00
249_T	252_E	0.846	1.00
216_A	221_V	0.840	1.00
178_D	182_L	0.840	1.00
281_H	308_D	0.836	1.00
160_Q	192_R	0.836	1.00
206_R	209_A	0.835	1.00
98_V	117_L	0.833	1.00
220_E	223_P	0.832	1.00
62_A	66_S	0.829	1.00
38_L	41_P	0.828	1.00
71_L	113_L	0.826	1.00
234_E	237_Y	0.826	1.00
122_D	126_K	0.822	1.00
365_A	369_P	0.812	1.00
161_V	193_L	0.811	1.00
369_P	372_E	0.808	1.00
250_L	357_I	0.807	1.00
127_Q	131_L	0.806	1.00
302_F	325_V	0.804	1.00
299_L	303_T	0.792	1.00
142_T	164_L	0.792	1.00
143_G	146_I	0.791	1.00
252_E	281_H	0.791	1.00
207_E	210_F	0.791	1.00
277_A	282_R	0.787	1.00
370_A	373_T	0.785	1.00
65_T	68_F	0.785	1.00
261_I	309_I	0.784	1.00
207_E	211_E	0.783	1.00
225_Q	228_G	0.781	1.00
256_P	259_A	0.780	1.00
180_R	183_F	0.778	1.00
119_Y	122_D	0.778	1.00
314_D	339_D	0.778	1.00
229_H	233_E	0.777	1.00
258_R	326_T	0.777	1.00
89_I	104_A	0.777	1.00
243_K	250_L	0.775	1.00
66_S	161_V	0.773	1.00
35_I	38_L	0.772	1.00
198_S	201_L	0.772	1.00
108_A	111_T	0.770	1.00
122_D	127_Q	0.770	1.00
257_D	352_A	0.769	1.00
87_A	163_V	0.767	1.00
98_V	101_H	0.765	1.00
147_D	151_Q	0.764	1.00
113_L	136_D	0.764	1.00
357_I	361_C	0.764	1.00
51_G	62_A	0.762	1.00
140_G	144_R	0.761	1.00
217_E	220_E	0.759	1.00
368_L	371_I	0.759	1.00
86_R	158_A	0.758	1.00
217_E	221_V	0.758	1.00
261_I	311_V	0.756	1.00
232_K	353_S	0.755	1.00
270_E	274_G	0.755	1.00
162_V	183_F	0.754	1.00
205_V	209_A	0.753	1.00
177_K	184_R	0.741	1.00
245_R	249_T	0.741	1.00
184_R	213_M	0.737	1.00
146_I	150_K	0.736	1.00
243_K	332_D	0.732	1.00
271_E	275_H	0.732	1.00
55_T	199_A	0.730	1.00
210_F	213_M	0.728	1.00
227_T	230_R	0.727	1.00
375_I	378_S	0.727	1.00
177_K	183_F	0.726	1.00
244_M	247_L	0.725	1.00
126_K	129_K	0.725	1.00
261_I	331_Y	0.721	1.00
126_K	130_V	0.721	1.00
87_A	137_I	0.718	1.00
258_R	308_D	0.716	1.00
88_L	162_V	0.714	1.00
63_F	100_I	0.711	1.00
51_G	195_M	0.710	1.00
103_D	107_L	0.709	1.00
325_V	347_T	0.708	1.00
243_K	247_L	0.708	1.00
233_E	237_Y	0.707	1.00
216_A	219_I	0.706	1.00
150_K	181_W	0.706	1.00
42_L	47_R	0.703	1.00
162_V	186_M	0.702	1.00
202_S	205_V	0.701	1.00
245_R	275_H	0.700	1.00
122_D	130_V	0.699	1.00
156_L	159_I	0.698	1.00
35_I	222_E	0.698	1.00
371_I	375_I	0.698	1.00
230_R	233_E	0.697	1.00
64_L	108_A	0.696	1.00
366_L	370_A	0.694	1.00
41_P	44_L	0.694	1.00
32_C	40_L	0.693	1.00
228_G	232_K	0.691	1.00
67_T	104_A	0.690	1.00
177_K	182_L	0.688	1.00
163_V	195_M	0.687	1.00
326_T	352_A	0.685	1.00
266_K	270_E	0.685	1.00
53_A	62_A	0.684	1.00
61_M	65_T	0.682	1.00
130_V	135_V	0.681	1.00
98_V	300_D	0.680	1.00
250_L	327_H	0.679	1.00
67_T	89_I	0.678	1.00
89_I	100_I	0.677	1.00
105_E	109_E	0.676	1.00
262_F	316_A	0.675	1.00
98_V	119_Y	0.672	1.00
282_R	307_L	0.671	1.00
178_D	185_R	0.670	1.00
247_L	251_I	0.668	1.00
261_I	272_I	0.668	1.00
149_A	185_R	0.664	1.00
358_S	361_C	0.662	1.00
239_S	242_E	0.661	1.00
244_M	271_E	0.660	1.00
264_N	332_D	0.658	1.00
231_I	236_F	0.656	1.00
175_F	183_F	0.655	1.00
182_L	185_R	0.653	1.00
372_E	375_I	0.653	1.00
374_Y	378_S	0.650	1.00
216_A	222_E	0.649	1.00
215_N	219_I	0.647	1.00
102_A	303_T	0.647	1.00
330_N	334_P	0.647	1.00
344_I	358_S	0.646	1.00
138_L	159_I	0.644	1.00
363_E	366_L	0.641	1.00
168_D	342_H	0.639	1.00
285_L	290_V	0.638	1.00
260_I	325_V	0.638	1.00
243_K	248_Q	0.634	1.00
301_E	305_G	0.634	1.00
247_L	261_I	0.633	1.00
244_M	250_L	0.631	1.00
170_M	175_F	0.631	1.00
295_R	299_L	0.630	1.00
203_Y	207_E	0.630	1.00
247_L	272_I	0.628	1.00
40_L	66_S	0.627	1.00
200_T	342_H	0.625	1.00
226_K	230_R	0.624	1.00
48_D	196_L	0.622	1.00
314_D	343_R	0.622	1.00
183_F	187_P	0.618	1.00
114_K	134_G	0.618	1.00
46_G	70_Y	0.615	1.00
97_A	119_Y	0.615	1.00
144_R	147_D	0.614	1.00
46_G	193_L	0.614	1.00
118_A	127_Q	0.613	1.00
61_M	107_L	0.613	1.00
303_T	323_P	0.613	1.00
371_I	374_Y	0.612	1.00
369_P	373_T	0.610	1.00
260_I	347_T	0.608	1.00
180_R	187_P	0.607	1.00
354_G	358_S	0.606	1.00
373_T	377_H	0.605	1.00
229_H	232_K	0.605	1.00
71_L	137_I	0.604	1.00
354_G	361_C	0.603	1.00
263_A	331_Y	0.602	1.00
132_E	135_V	0.602	1.00
88_L	140_G	0.601	1.00
177_K	186_M	0.598	1.00
374_Y	377_H	0.598	1.00
264_N	335_D	0.598	1.00
187_P	191_Q	0.597	1.00
260_I	312_A	0.595	1.00
227_T	233_E	0.593	1.00
234_E	357_I	0.591	1.00
154_I	157_G	0.591	1.00
220_E	224_E	0.590	1.00
128_L	153_H	0.588	1.00
286_L	299_L	0.587	1.00
40_L	62_A	0.587	1.00
100_I	139_I	0.586	1.00
184_R	187_P	0.584	1.00
84_Q	136_D	0.584	1.00
175_F	182_L	0.583	1.00
271_E	274_G	0.581	1.00
229_H	234_E	0.581	1.00
365_A	368_L	0.581	1.00
124_Y	151_Q	0.580	1.00
368_L	378_S	0.579	1.00
55_T	345_G	0.577	1.00
299_L	322_I	0.575	1.00
117_L	122_D	0.574	1.00
176_I	186_M	0.574	1.00
286_L	290_V	0.573	1.00
163_V	197_F	0.571	1.00
273_W	276_L	0.571	1.00
355_H	358_S	0.571	1.00
232_K	235_L	0.570	1.00
199_A	345_G	0.569	1.00
367_N	371_I	0.568	1.00
188_P	191_Q	0.567	1.00
326_T	354_G	0.567	1.00
226_K	231_I	0.566	1.00
102_A	296_L	0.566	1.00
100_I	103_D	0.562	1.00
270_E	273_W	0.562	1.00
282_R	301_E	0.562	1.00
218_Y	221_V	0.561	1.00
262_F	328_V	0.561	1.00
180_R	186_M	0.557	1.00
231_I	235_L	0.557	1.00
124_Y	127_Q	0.555	1.00
215_N	221_V	0.553	1.00
330_N	333_L	0.553	1.00
47_R	193_L	0.548	1.00
299_L	302_F	0.548	1.00
372_E	378_S	0.548	1.00
235_L	360_A	0.545	1.00
63_F	195_M	0.544	1.00
102_A	300_D	0.544	1.00
227_T	231_I	0.544	1.00
219_I	222_E	0.541	1.00
25_E	30_H	0.538	1.00
235_L	238_P	0.538	1.00
39_A	43_T	0.537	1.00
231_I	348_G	0.537	1.00
104_A	108_A	0.533	1.00
364_Y	367_N	0.532	1.00
52_Q	201_L	0.530	1.00
270_E	289_D	0.529	1.00
33_T	350_A	0.528	1.00
293_K	296_L	0.527	1.00
178_D	183_F	0.527	1.00
117_L	120_G	0.525	1.00
148_Y	151_Q	0.522	1.00
286_L	298_I	0.521	1.00
148_Y	152_N	0.517	1.00
176_I	184_R	0.516	1.00
48_D	193_L	0.516	1.00
205_V	212_Q	0.515	1.00
167_A	201_L	0.514	1.00
176_I	181_W	0.514	1.00
48_D	194_N	0.513	1.00
179_I	185_R	0.513	1.00
187_P	192_R	0.513	1.00
114_K	135_V	0.512	1.00
266_K	269_C	0.511	1.00
345_G	348_G	0.511	1.00
32_C	37_A	0.510	1.00
204_R	209_A	0.509	1.00
264_N	268_R	0.508	1.00
284_G	308_D	0.508	1.00
179_I	187_P	0.508	1.00
292_Q	295_R	0.507	1.00
89_I	139_I	0.506	1.00
230_R	353_S	0.506	1.00
118_A	138_L	0.505	1.00
106_P	109_E	0.505	1.00
245_R	279_D	0.502	1.00
228_G	235_L	0.502	1.00
176_I	185_R	0.501	1.00
303_T	322_I	0.501	1.00
373_T	376_G	0.500	1.00
366_L	369_P	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
4pxaA	1	0.9287	100	0.23	Contact Map
4nhoA	1	0.9145	100	0.243	Contact Map
2db3A	1	0.9121	100	0.247	Contact Map
4c9bA	1	0.9002	100	0.248	Contact Map
4d25A	1	0.9192	100	0.253	Contact Map
4ljyA	1	0.9501	100	0.256	Contact Map
3eiqA	1	0.8551	100	0.26	Contact Map
1s2mA	1	0.8955	100	0.263	Contact Map
4ct4B	1	0.8955	100	0.268	Contact Map
4kbfA	2	0.867	100	0.272	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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