YFML - BACSU - GREMLIN Contacts

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YFML - Probable ATP-dependent RNA helicase YfmL

UniProt:	O34750	Sequences: MTQTWPFLHNAQSFIQENWNASGFQKPTPVQEQAAQLIMDGKDVIAESPTGTGKTLAYALPVLERIKPEQKHPQAVILAPSRELVMQIFQVIQDWKAGSELRAASLIGGANVKKQVEKLKKHPHIIVGTPGRVFELIKAKKLKMHEVKTIVLDETDQLVLPEHRETMKQIIKTTLRDRQLLCFSATLKKETEDVLRELAQEPEVLKVQRSKAEAGKVKHQYLICDQRDKVKLLQKLSRLEGMQALVFVRDIGNLSVYAEKLAYHHVELGVLHSEAKKMERAKIIATFEDGEFPLLLATDIAARGLDIENLPYVIHADIPDEDGYVHRSGRTGRAGKEGNVLSLVTKLEESKLKKMAKKLGVELSEAVYAGGKLKTK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	376 (323)
Sequences:	71480 (44449)
Seq/√Len:	2473.2

ECOLI - DEAD RECQ DBPA RHLE SRMB RECG RHLB YFJK YEJH RAPA LHR CAS3
BACSU - YFML CSHA DBPA RECQ RECG CSHB RECS YPRA COMFA YQHH YWQA
HALSA - HELS Q9HN80 RAD25 Q9HNB2 Q9HQA5 Q9HMW5 O51997 O52003
SULSO - Q981C8 HELX HELS Q97WT0 Q980C0 Q97X64 Q97X74 Q97WW1 Q97Y93 Q97ZF9 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
62_V	75_A	3.594	1.00
59_A	92_I	3.165	1.00
269_G	292_F	3.017	1.00
286_T	291_E	2.857	1.00
89_F	93_Q	2.758	1.00
258_A	262_A	2.748	1.00
267_E	293_P	2.634	1.00
269_G	286_T	2.574	1.00
38_I	181_L	2.526	1.00
258_A	270_V	2.500	1.00
251_I	274_E	2.500	1.00
155_T	182_C	2.497	1.00
102_R	124_H	2.480	1.00
285_A	289_D	2.406	1.00
282_K	286_T	2.346	1.00
258_A	268_L	2.338	1.00
248_V	257_Y	2.278	1.00
255_S	270_V	2.277	1.00
58_Y	183_F	2.261	1.00
244_A	312_Y	2.242	1.00
242_M	311_P	2.239	1.00
232_L	237_S	2.235	1.00
104_A	123_P	2.215	1.00
39_M	64_E	2.179	1.00
164_R	167_M	2.129	1.00
248_V	254_L	2.120	1.00
73_P	148_K	2.030	1.00
281_A	285_A	2.023	1.00
89_F	105_S	2.004	1.00
248_V	296_L	2.000	1.00
79_A	88_I	1.989	1.00
32_E	36_Q	1.969	1.00
165_E	168_K	1.932	1.00
269_G	283_I	1.931	1.00
232_L	235_K	1.841	1.00
243_Q	309_N	1.824	1.00
74_Q	148_K	1.817	1.00
276_K	279_E	1.803	1.00
254_L	270_V	1.795	1.00
48_S	52_T	1.768	1.00
261_L	296_L	1.734	1.00
315_H	328_S	1.715	1.00
234_Q	238_R	1.693	1.00
128_G	133_V	1.677	1.00
166_T	169_Q	1.676	1.00
250_D	253_N	1.672	1.00
86_M	281_A	1.664	1.00
91_V	306_D	1.664	1.00
167_M	170_I	1.664	1.00
164_R	168_K	1.653	1.00
313_V	331_T	1.646	1.00
55_T	88_I	1.642	1.00
163_H	167_M	1.624	1.00
75_A	149_T	1.612	1.00
231_K	234_Q	1.611	1.00
91_V	94_D	1.600	1.00
38_I	61_P	1.592	1.00
156_D	303_R	1.587	1.00
219_H	328_S	1.577	1.00
328_S	340_V	1.576	1.00
258_A	296_L	1.575	1.00
192_E	196_R	1.574	1.00
86_M	90_Q	1.574	1.00
235_K	239_L	1.561	1.00
34_A	57_A	1.527	1.00
89_F	103_A	1.524	1.00
254_L	272_H	1.523	1.00
165_E	169_Q	1.502	1.00
191_T	195_L	1.498	1.00
65_R	149_T	1.492	1.00
191_T	194_V	1.492	1.00
301_A	305_L	1.485	1.00
312_Y	341_L	1.474	1.00
58_Y	151_V	1.460	1.00
297_A	301_A	1.457	1.00
279_E	282_K	1.456	1.00
30_V	46_A	1.451	1.00
234_Q	237_S	1.450	1.00
208_Q	211_K	1.434	1.00
234_Q	264_H	1.432	1.00
56_L	91_V	1.430	1.00
220_Q	339_N	1.400	1.00
84_L	304_G	1.392	1.00
157_Q	303_R	1.391	1.00
232_L	236_L	1.383	1.00
254_L	258_A	1.374	1.00
111_N	114_K	1.370	1.00
36_Q	40_D	1.366	1.00
272_H	275_A	1.366	1.00
104_A	118_K	1.361	1.00
87_Q	306_D	1.360	1.00
230_V	237_S	1.353	1.00
76_V	147_V	1.352	1.00
275_A	283_I	1.342	1.00
37_L	44_V	1.331	1.00
235_K	238_R	1.330	1.00
163_H	166_T	1.314	1.00
113_K	117_E	1.314	1.00
262_A	268_L	1.309	1.00
220_Q	223_I	1.307	1.00
66_I	75_A	1.300	1.00
117_E	121_K	1.298	1.00
194_V	199_A	1.293	1.00
257_Y	316_A	1.292	1.00
38_I	44_V	1.287	1.00
283_I	295_L	1.272	1.00
253_N	317_D	1.270	1.00
92_I	125_I	1.267	1.00
279_E	283_I	1.261	1.00
136_L	141_K	1.253	1.00
209_R	212_A	1.241	1.00
253_N	256_V	1.237	1.00
254_L	296_L	1.234	1.00
315_H	327_R	1.226	1.00
244_A	314_I	1.224	1.00
226_Q	229_K	1.222	1.00
163_H	168_K	1.220	1.00
286_T	292_F	1.199	1.00
42_K	203_E	1.197	1.00
150_I	180_L	1.196	1.00
46_A	183_F	1.194	1.00
231_K	235_K	1.191	1.00
90_Q	94_D	1.189	1.00
195_L	199_A	1.184	1.00
218_K	339_N	1.183	1.00
244_A	294_L	1.180	1.00
275_A	279_E	1.176	1.00
290_G	293_P	1.173	1.00
243_Q	290_G	1.150	1.00
63_L	67_K	1.146	1.00
282_K	285_A	1.131	1.00
194_V	198_L	1.125	1.00
92_I	127_V	1.124	1.00
230_V	260_K	1.124	1.00
35_A	39_M	1.122	1.00
260_K	264_H	1.120	1.00
29_P	33_Q	1.115	1.00
195_L	198_L	1.112	1.00
199_A	202_P	1.106	1.00
194_V	197_E	1.103	1.00
89_F	127_V	1.102	1.00
283_I	286_T	1.096	1.00
206_K	210_S	1.093	1.00
74_Q	124_H	1.093	1.00
65_R	148_K	1.092	1.00
163_H	170_I	1.089	1.00
166_T	170_I	1.085	1.00
287_F	295_L	1.084	1.00
277_K	281_A	1.084	1.00
34_A	46_A	1.082	1.00
271_L	300_I	1.074	1.00
112_V	116_V	1.069	1.00
92_I	103_A	1.064	1.00
219_H	223_I	1.063	1.00
230_V	234_Q	1.062	1.00
79_A	85_V	1.061	1.00
149_T	181_L	1.061	1.00
311_P	336_K	1.052	1.00
285_A	288_E	1.050	1.00
65_R	179_Q	1.044	1.00
167_M	171_I	1.039	1.00
260_K	263_Y	1.038	1.00
302_A	323_G	1.037	1.00
283_I	292_F	1.034	1.00
288_E	309_N	1.033	1.00
33_Q	37_L	1.031	1.00
309_N	336_K	1.031	1.00
44_V	181_L	1.027	1.00
168_K	172_K	1.024	1.00
266_V	293_P	1.010	1.00
73_P	146_E	1.007	1.00
232_L	239_L	1.005	1.00
257_Y	296_L	1.003	1.00
90_Q	93_Q	1.003	1.00
62_V	149_T	1.003	1.00
208_Q	212_A	1.000	1.00
85_V	105_S	0.998	1.00
24_F	56_L	0.998	1.00
118_K	121_K	0.996	1.00
219_H	324_Y	0.994	1.00
63_L	96_K	0.994	1.00
47_E	206_K	0.979	1.00
252_G	256_V	0.978	1.00
62_V	151_V	0.973	1.00
212_A	215_G	0.972	1.00
48_S	57_A	0.969	1.00
37_L	40_D	0.969	1.00
35_A	60_L	0.965	1.00
123_P	126_I	0.962	1.00
78_L	128_G	0.962	1.00
49_P	52_T	0.959	1.00
57_A	61_P	0.952	1.00
233_L	236_L	0.945	1.00
207_V	210_S	0.944	1.00
115_Q	118_K	0.944	1.00
319_P	324_Y	0.940	1.00
74_Q	146_E	0.939	1.00
193_D	197_E	0.936	1.00
76_V	150_I	0.936	1.00
237_S	264_H	0.934	1.00
246_V	314_I	0.933	1.00
290_G	309_N	0.933	1.00
266_V	294_L	0.927	1.00
191_T	198_L	0.925	1.00
259_E	262_A	0.924	1.00
207_V	211_K	0.922	1.00
169_Q	172_K	0.921	1.00
117_E	120_K	0.918	1.00
315_H	342_S	0.918	1.00
209_R	213_E	0.918	1.00
66_I	124_H	0.915	1.00
204_V	208_Q	0.908	1.00
116_V	120_K	0.907	1.00
256_V	260_K	0.906	1.00
210_S	213_E	0.906	1.00
203_E	208_Q	0.904	1.00
134_F	169_Q	0.903	1.00
214_A	217_V	0.902	1.00
29_P	32_E	0.896	1.00
85_V	127_V	0.896	1.00
230_V	239_L	0.894	1.00
84_L	87_Q	0.893	1.00
316_A	319_P	0.893	1.00
72_H	146_E	0.891	1.00
188_K	191_T	0.890	1.00
91_V	95_W	0.885	1.00
194_V	200_Q	0.881	1.00
259_E	263_Y	0.881	1.00
318_I	342_S	0.879	1.00
278_M	282_K	0.876	1.00
164_R	170_I	0.875	1.00
169_Q	173_T	0.871	1.00
105_S	108_G	0.870	1.00
171_I	174_T	0.863	1.00
271_L	301_A	0.862	1.00
33_Q	36_Q	0.860	1.00
310_L	331_T	0.857	1.00
302_A	327_R	0.857	1.00
204_V	210_S	0.854	1.00
242_M	312_Y	0.852	1.00
26_K	32_E	0.849	1.00
104_A	126_I	0.848	1.00
255_S	272_H	0.848	1.00
36_Q	39_M	0.848	1.00
86_M	105_S	0.846	1.00
64_E	67_K	0.845	1.00
246_V	296_L	0.845	1.00
107_I	110_A	0.841	1.00
128_G	132_R	0.840	1.00
163_H	171_I	0.840	1.00
253_N	316_A	0.839	1.00
203_E	207_V	0.837	1.00
284_I	288_E	0.836	1.00
184_S	187_L	0.835	1.00
299_D	323_G	0.834	1.00
280_R	284_I	0.834	1.00
251_I	255_S	0.828	1.00
192_E	195_L	0.826	1.00
203_E	206_K	0.820	1.00
247_F	327_R	0.817	1.00
206_K	209_R	0.812	1.00
287_F	310_L	0.812	1.00
201_E	204_V	0.808	1.00
77_I	88_I	0.804	1.00
78_L	133_V	0.798	1.00
243_Q	311_P	0.796	1.00
205_L	208_Q	0.792	1.00
149_T	179_Q	0.792	1.00
60_L	63_L	0.789	1.00
108_G	111_N	0.785	1.00
340_V	344_V	0.782	1.00
157_Q	160_L	0.779	1.00
208_Q	213_E	0.778	1.00
131_G	134_F	0.776	1.00
61_P	149_T	0.771	1.00
37_L	203_E	0.771	1.00
135_E	139_A	0.770	1.00
241_G	293_P	0.766	1.00
168_K	197_E	0.765	1.00
234_Q	260_K	0.762	1.00
110_A	115_Q	0.759	1.00
88_I	127_V	0.759	1.00
50_T	185_A	0.756	1.00
191_T	199_A	0.753	1.00
213_E	216_K	0.752	1.00
164_R	171_I	0.752	1.00
164_R	169_Q	0.752	1.00
105_S	110_A	0.748	1.00
216_K	219_H	0.747	1.00
160_L	164_R	0.746	1.00
205_L	209_R	0.744	1.00
218_K	337_E	0.743	1.00
165_E	170_I	0.743	1.00
103_A	106_L	0.743	1.00
255_S	258_A	0.742	1.00
233_L	237_S	0.742	1.00
90_Q	281_A	0.741	1.00
134_F	166_T	0.738	1.00
255_S	259_E	0.733	1.00
75_A	151_V	0.733	1.00
246_V	257_Y	0.724	1.00
148_K	178_R	0.718	1.00
206_K	211_K	0.717	1.00
76_V	128_G	0.716	1.00
113_K	116_V	0.716	1.00
236_L	239_L	0.714	1.00
130_P	152_L	0.713	1.00
211_K	214_A	0.712	1.00
267_E	292_F	0.710	1.00
162_E	165_E	0.709	1.00
30_V	33_Q	0.707	1.00
35_A	61_P	0.705	1.00
168_K	171_I	0.704	1.00
101_L	124_H	0.703	1.00
62_V	125_I	0.701	1.00
347_L	350_S	0.700	1.00
22_S	94_D	0.696	1.00
110_A	114_K	0.696	1.00
126_I	147_V	0.695	1.00
86_M	89_F	0.693	1.00
151_V	181_L	0.688	1.00
58_Y	88_I	0.687	1.00
192_E	199_A	0.686	1.00
242_M	336_K	0.686	1.00
77_I	127_V	0.684	1.00
118_K	123_P	0.684	1.00
96_K	99_S	0.682	1.00
203_E	210_S	0.681	1.00
243_Q	293_P	0.679	1.00
219_H	222_L	0.679	1.00
62_V	92_I	0.674	1.00
234_Q	239_L	0.673	1.00
46_A	181_L	0.673	1.00
42_K	179_Q	0.672	1.00
114_K	118_K	0.670	1.00
151_V	183_F	0.668	1.00
116_V	119_L	0.667	1.00
30_V	208_Q	0.666	1.00
271_L	275_A	0.664	1.00
110_A	118_K	0.664	1.00
256_V	259_E	0.662	1.00
41_G	44_V	0.661	1.00
246_V	294_L	0.659	1.00
312_Y	339_N	0.659	1.00
114_K	117_E	0.657	1.00
270_V	275_A	0.656	1.00
35_A	57_A	0.655	1.00
284_I	287_F	0.655	1.00
27_P	35_A	0.653	1.00
229_K	232_L	0.650	1.00
191_T	197_E	0.649	1.00
170_I	174_T	0.647	1.00
46_A	57_A	0.643	1.00
58_Y	77_I	0.638	1.00
193_D	196_R	0.638	1.00
251_I	272_H	0.635	1.00
341_L	345_T	0.635	1.00
206_K	212_A	0.635	1.00
204_V	207_V	0.634	1.00
245_L	310_L	0.634	1.00
77_I	92_I	0.632	1.00
219_H	224_C	0.630	1.00
342_S	345_T	0.630	1.00
102_R	122_H	0.628	1.00
144_M	147_V	0.626	1.00
72_H	124_H	0.626	1.00
214_A	219_H	0.625	1.00
203_E	209_R	0.624	1.00
186_T	326_H	0.623	1.00
107_I	111_N	0.623	1.00
245_L	307_I	0.622	1.00
249_R	317_D	0.621	1.00
241_G	244_A	0.621	1.00
205_L	211_K	0.618	1.00
196_R	199_A	0.618	1.00
228_D	231_K	0.611	1.00
134_F	138_K	0.610	1.00
325_V	328_S	0.610	1.00
82_R	109_G	0.608	1.00
156_D	326_H	0.607	1.00
86_M	285_A	0.607	1.00
177_D	180_L	0.606	1.00
220_Q	224_C	0.605	1.00
267_E	286_T	0.604	1.00
230_V	236_L	0.602	1.00
62_V	77_I	0.602	1.00
163_H	169_Q	0.600	1.00
78_L	130_P	0.599	1.00
217_V	222_L	0.599	1.00
202_P	205_L	0.598	1.00
338_G	341_L	0.598	1.00
230_V	235_K	0.598	1.00
205_L	210_S	0.597	1.00
43_D	179_Q	0.596	1.00
220_Q	225_D	0.596	1.00
201_E	205_L	0.592	1.00
162_E	166_T	0.592	1.00
286_T	290_G	0.592	1.00
56_L	95_W	0.591	1.00
167_M	174_T	0.589	1.00
231_K	239_L	0.588	1.00
194_V	201_E	0.582	1.00
262_A	267_E	0.581	1.00
192_E	204_V	0.579	1.00
142_L	145_H	0.575	1.00
197_E	202_P	0.575	1.00
132_R	135_E	0.575	1.00
185_A	329_G	0.573	1.00
202_P	207_V	0.573	1.00
205_L	212_A	0.572	1.00
175_L	178_R	0.571	1.00
247_F	301_A	0.569	1.00
215_G	219_H	0.564	1.00
299_D	327_R	0.562	1.00
75_A	125_I	0.560	1.00
255_S	274_E	0.560	1.00
245_L	297_A	0.560	1.00
160_L	163_H	0.557	1.00
338_G	345_T	0.557	1.00
27_P	60_L	0.557	1.00
39_M	65_R	0.557	1.00
273_S	280_R	0.556	1.00
66_I	101_L	0.554	1.00
218_K	221_Y	0.554	1.00
192_E	197_E	0.552	1.00
44_V	205_L	0.551	1.00
60_L	64_E	0.550	1.00
81_S	303_R	0.548	1.00
278_M	281_A	0.547	1.00
137_I	173_T	0.547	1.00
243_Q	287_F	0.546	1.00
196_R	200_Q	0.546	1.00
86_M	107_I	0.545	1.00
271_L	280_R	0.543	1.00
56_L	60_L	0.542	1.00
225_D	228_D	0.542	1.00
195_L	202_P	0.541	1.00
81_S	84_L	0.541	1.00
136_L	140_K	0.539	1.00
271_L	297_A	0.539	1.00
150_I	177_D	0.538	1.00
251_I	254_L	0.538	1.00
166_T	173_T	0.537	1.00
102_R	105_S	0.536	1.00
280_R	300_I	0.536	1.00
168_K	174_T	0.533	1.00
202_P	206_K	0.532	1.00
269_G	293_P	0.532	1.00
50_T	329_G	0.530	1.00
329_G	332_G	0.530	1.00
160_L	165_E	0.527	1.00
43_D	180_L	0.525	1.00
212_A	216_K	0.525	1.00
41_G	179_Q	0.525	1.00
132_R	136_L	0.523	1.00
247_F	313_V	0.522	1.00
233_L	239_L	0.521	1.00
170_I	173_T	0.519	1.00
284_I	307_I	0.519	1.00
249_R	253_N	0.519	1.00
47_E	187_L	0.519	1.00
115_Q	119_L	0.518	1.00
246_V	316_A	0.517	1.00
92_I	96_K	0.517	1.00
250_D	254_L	0.514	1.00
338_G	342_S	0.514	1.00
102_R	123_P	0.513	1.00
269_G	295_L	0.513	1.00
230_V	233_L	0.513	1.00
59_A	96_K	0.512	1.00
136_L	139_A	0.512	1.00
162_E	167_M	0.511	1.00
90_Q	288_E	0.508	1.00
30_V	48_S	0.508	1.00
249_R	320_D	0.507	1.00
271_L	284_I	0.507	1.00
90_Q	285_A	0.507	1.00
34_A	38_I	0.506	1.00
165_E	171_I	0.505	1.00
217_V	220_Q	0.504	1.00
195_L	200_Q	0.503	1.00
286_T	289_D	0.502	1.00
311_P	338_G	0.501	1.00
245_L	331_T	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	0.9947	100	0.163	Contact Map
2db3A	1	0.984	100	0.177	Contact Map
4d25A	1	0.984	100	0.191	Contact Map
4nhoA	1	0.9654	100	0.191	Contact Map
4c9bA	1	0.9867	100	0.194	Contact Map
4ljyA	1	0.9947	100	0.202	Contact Map
3eiqA	1	0.9362	100	0.203	Contact Map
4w7sA	2	0.9973	100	0.21	Contact Map
2i4iA	1	0.9814	100	0.213	Contact Map
1s2mA	1	0.9894	100	0.215	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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