RHO - BACSU - GREMLIN Contacts

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RHO - Transcription termination factor Rho

UniProt:	Q03222	Sequences: MKDVSISSLENMKLKELYELARHYKISYYSKLTKKELIFAILKANAEQEDLLFMEGVLEIIQSEGFGFLRPINYSPSSEDIYISASQIRRFDLRNGDKVSGKVRPPKENERYYGLLHVEAVNGDDPESAKERVHFPALTPLYPDRQMVLETKPNFLSTRIMDMMAPVGFGQRGLIVAPPKAGKTMLLKEIANSITANQPEAELIVLLIDERPEEVTDIERSVAGDVVSSTFDEVPENHIKVAELVLERAMRLVEHKKDVIILMDSITRLARAYNLVIPPSGRTLSGGIDPAAFHRPKRFFGAARNIEEGGSLTILATALVDTGSRMDDVIYEEFKGTGNMELHLDRSLAERRIFPAIDIRRSGTRKEELLVPKEHLDRLWSIRKTMSDSPDFAEKFMRKMKKTKTNQEFFDILNQEWKQANLSSARR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	427 (361)
Sequences:	7938 (2627)
Seq/√Len:	138.3

ECOLI - RHO ATPA FLII ATPB
BACSU - RHO ATPA FLII ATPB
HALSA - VATB VATA
SULSO - VATB VATA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
120_A	124_D	8.351	1.00
169_F	258_D	5.722	1.00
206_L	245_V	5.024	1.00
345_D	358_D	4.937	1.00
160_I	357_I	3.977	1.00
117_H	127_E	3.320	1.00
72_I	84_S	3.210	1.00
112_Y	255_H	3.041	1.00
167_V	315_L	3.011	1.00
202_E	257_K	3.009	1.00
246_L	316_A	2.910	1.00
112_Y	257_K	2.778	1.00
152_K	169_F	2.709	1.00
104_R	107_K	2.619	1.00
348_L	353_I	2.610	1.00
371_V	376_L	2.524	1.00
204_I	249_A	2.501	1.00
216_T	220_R	2.468	1.00
54_M	84_S	2.402	1.00
381_S	384_K	2.355	1.00
411_D	415_Q	2.319	1.00
227_V	248_R	2.312	1.00
390_P	393_A	2.246	1.00
373_K	377_D	2.222	1.00
56_G	101_G	2.211	1.00
60_I	74_Y	2.203	1.00
249_A	312_L	2.186	1.00
164_M	382_I	2.160	1.00
119_E	248_R	2.124	1.00
416_E	419_Q	2.078	1.00
250_M	302_A	2.067	1.00
113_Y	130_K	2.067	1.00
202_E	225_D	2.058	1.00
326_M	343_H	2.036	1.00
178_P	181_A	2.030	1.00
155_F	162_D	2.023	1.00
225_D	248_R	1.984	1.00
381_S	411_D	1.950	1.00
253_V	306_I	1.909	1.00
147_M	201_A	1.895	1.00
393_A	397_M	1.894	1.00
173_G	315_L	1.878	1.00
107_K	132_R	1.853	1.00
403_T	414_N	1.838	1.00
219_E	226_V	1.832	1.00
251_R	255_H	1.794	1.00
202_E	252_L	1.763	1.00
352_R	380_W	1.760	1.00
173_G	340_M	1.747	1.00
161_M	342_L	1.745	1.00
372_P	375_H	1.735	1.00
133_V	251_R	1.729	1.00
258_D	311_S	1.727	1.00
167_V	342_L	1.724	1.00
411_D	414_N	1.714	1.00
242_A	299_F	1.699	1.00
204_I	248_R	1.661	1.00
152_K	305_N	1.655	1.00
243_E	273_Y	1.654	1.00
139_T	142_Y	1.648	1.00
368_E	376_L	1.638	1.00
166_P	367_E	1.633	1.00
133_V	137_A	1.627	1.00
376_L	380_W	1.609	1.00
206_L	263_M	1.600	1.00
139_T	143_P	1.568	1.00
117_H	125_D	1.566	1.00
331_Y	343_H	1.565	1.00
133_V	247_E	1.558	1.00
318_A	334_F	1.557	1.00
174_L	338_G	1.547	1.00
221_S	369_L	1.535	1.00
145_R	307_E	1.521	1.00
388_D	409_F	1.499	1.00
154_N	201_A	1.486	1.00
146_Q	375_H	1.481	1.00
90_R	93_L	1.474	1.00
109_N	132_R	1.451	1.00
161_M	190_I	1.451	1.00
273_Y	295_R	1.433	1.00
351_R	393_A	1.432	1.00
129_A	132_R	1.421	1.00
367_E	379_L	1.420	1.00
208_I	241_V	1.416	1.00
300_F	337_T	1.416	1.00
259_V	312_L	1.409	1.00
384_K	408_E	1.408	1.00
149_L	168_G	1.401	1.00
233_E	237_N	1.394	1.00
66_F	84_S	1.391	1.00
388_D	391_D	1.391	1.00
112_Y	251_R	1.383	1.00
328_D	331_Y	1.382	1.00
296_P	334_F	1.372	1.00
59_E	100_S	1.365	1.00
119_E	227_V	1.357	1.00
106_P	135_F	1.356	1.00
147_M	308_E	1.353	1.00
145_R	308_E	1.353	1.00
396_F	413_L	1.334	1.00
361_R	390_P	1.313	1.00
108_E	248_R	1.301	1.00
138_L	142_Y	1.289	1.00
156_L	167_V	1.287	1.00
191_A	262_L	1.285	1.00
220_R	307_E	1.278	1.00
347_S	350_E	1.278	1.00
207_L	215_V	1.272	1.00
108_E	244_L	1.270	1.00
266_I	334_F	1.267	1.00
277_I	284_L	1.267	1.00
246_L	303_A	1.252	1.00
300_F	334_F	1.250	1.00
155_F	189_E	1.242	1.00
118_V	219_E	1.238	1.00
381_S	385_T	1.236	1.00
267_T	271_R	1.232	1.00
165_A	342_L	1.229	1.00
58_L	99_V	1.228	1.00
407_Q	411_D	1.227	1.00
104_R	132_R	1.224	1.00
167_V	313_T	1.222	1.00
153_P	370_L	1.217	1.00
246_L	312_L	1.216	1.00
208_I	263_M	1.214	1.00
114_G	248_R	1.211	1.00
366_K	370_L	1.197	1.00
392_F	409_F	1.195	1.00
358_D	361_R	1.194	1.00
138_L	143_P	1.192	1.00
371_V	379_L	1.179	1.00
177_A	181_A	1.160	0.99
134_H	137_A	1.146	0.99
68_F	71_P	1.144	0.99
147_M	150_E	1.141	0.99
380_W	383_R	1.136	0.99
111_R	114_G	1.136	0.99
158_T	161_M	1.120	0.99
113_Y	128_S	1.116	0.99
256_K	309_G	1.114	0.99
320_V	331_Y	1.106	0.99
206_L	261_I	1.106	0.99
86_S	90_R	1.102	0.99
55_E	58_L	1.101	0.99
121_V	244_L	1.099	0.99
133_V	254_E	1.093	0.99
367_E	371_V	1.091	0.99
350_E	361_R	1.091	0.99
323_G	327_D	1.086	0.99
53_F	56_G	1.086	0.99
203_L	224_G	1.078	0.99
167_V	173_G	1.078	0.99
117_H	126_P	1.077	0.99
306_I	309_G	1.074	0.99
243_E	295_R	1.069	0.99
178_P	346_R	1.067	0.99
94_R	97_D	1.063	0.99
191_A	224_G	1.057	0.99
60_I	66_F	1.050	0.99
254_E	306_I	1.048	0.99
246_L	261_I	1.041	0.99
115_L	202_E	1.038	0.99
120_A	233_E	1.037	0.99
197_N	258_D	1.037	0.99
161_M	165_A	1.034	0.99
204_I	227_V	1.034	0.99
210_E	214_E	1.031	0.99
158_T	186_L	1.028	0.99
212_P	230_T	1.021	0.99
88_I	237_N	1.020	0.99
271_R	321_D	1.020	0.99
139_T	308_E	1.013	0.98
415_Q	418_K	1.009	0.98
296_P	337_T	1.009	0.98
392_F	396_F	1.008	0.98
351_R	419_Q	1.006	0.98
294_H	297_K	1.004	0.98
211_R	214_E	0.998	0.98
205_V	224_G	0.987	0.98
305_N	311_S	0.980	0.98
156_L	162_D	0.980	0.98
384_K	388_D	0.977	0.98
210_E	268_R	0.973	0.98
115_L	225_D	0.972	0.98
255_H	259_V	0.969	0.98
201_A	260_I	0.967	0.98
260_I	315_L	0.964	0.98
178_P	332_E	0.963	0.98
251_R	254_E	0.962	0.98
165_A	363_G	0.962	0.98
270_A	330_I	0.954	0.98
271_R	333_E	0.951	0.98
62_Q	66_F	0.949	0.98
204_I	225_D	0.948	0.98
121_V	126_P	0.948	0.98
323_G	346_R	0.945	0.98
245_V	261_I	0.942	0.98
147_M	307_E	0.942	0.98
121_V	237_N	0.926	0.97
67_G	100_S	0.923	0.97
169_F	311_S	0.922	0.97
303_A	314_I	0.919	0.97
178_P	323_G	0.916	0.97
191_A	205_V	0.913	0.97
147_M	305_N	0.906	0.97
166_P	371_V	0.904	0.97
229_S	238_H	0.903	0.97
404_K	408_E	0.902	0.97
340_M	365_R	0.901	0.97
138_L	141_L	0.900	0.97
262_L	317_T	0.895	0.97
266_I	300_F	0.895	0.97
253_V	312_L	0.890	0.97
197_N	257_K	0.886	0.96
239_I	273_Y	0.885	0.96
191_A	203_L	0.883	0.96
137_A	254_E	0.879	0.96
324_S	332_E	0.878	0.96
351_R	418_K	0.875	0.96
130_K	135_F	0.873	0.96
296_P	333_E	0.872	0.96
269_L	299_F	0.870	0.96
238_H	275_L	0.867	0.96
253_V	259_V	0.866	0.96
161_M	186_L	0.861	0.96
320_V	328_D	0.859	0.96
121_V	233_E	0.852	0.96
131_E	134_H	0.850	0.96
66_F	69_L	0.849	0.96
154_N	194_I	0.848	0.95
194_I	260_I	0.845	0.95
203_L	206_L	0.844	0.95
343_H	361_R	0.843	0.95
106_P	244_L	0.842	0.95
173_G	342_L	0.842	0.95
65_G	68_F	0.840	0.95
208_I	242_A	0.840	0.95
59_E	71_P	0.834	0.95
347_S	390_P	0.834	0.95
269_L	295_R	0.824	0.95
59_E	62_Q	0.823	0.95
61_I	98_K	0.821	0.95
283_T	288_I	0.821	0.95
217_D	369_L	0.818	0.95
166_P	375_H	0.815	0.94
397_M	406_N	0.812	0.94
403_T	413_L	0.807	0.94
88_I	124_D	0.807	0.94
113_Y	129_A	0.804	0.94
163_M	166_P	0.802	0.94
371_V	375_H	0.802	0.94
358_D	390_P	0.801	0.94
326_M	331_Y	0.801	0.94
185_M	188_K	0.794	0.94
153_P	166_P	0.793	0.94
56_G	103_V	0.793	0.94
147_M	309_G	0.791	0.93
408_E	417_W	0.789	0.93
217_D	221_S	0.785	0.93
53_F	81_I	0.784	0.93
204_I	245_V	0.782	0.93
61_I	67_G	0.780	0.93
77_S	83_I	0.776	0.93
248_R	252_L	0.774	0.93
109_N	129_A	0.771	0.93
292_A	295_R	0.771	0.93
78_S	83_I	0.770	0.93
102_K	119_E	0.768	0.92
158_T	189_E	0.768	0.92
202_E	259_V	0.767	0.92
61_I	100_S	0.767	0.92
124_D	128_S	0.765	0.92
195_T	258_D	0.765	0.92
187_L	262_L	0.765	0.92
211_R	268_R	0.765	0.92
62_Q	69_L	0.764	0.92
149_L	366_K	0.762	0.92
347_S	391_D	0.762	0.92
179_P	271_R	0.762	0.92
271_R	288_I	0.761	0.92
187_L	218_I	0.758	0.92
162_D	193_S	0.758	0.92
148_V	369_L	0.757	0.92
115_L	257_K	0.756	0.92
377_D	380_W	0.756	0.92
386_M	390_P	0.754	0.92
178_P	324_S	0.752	0.92
129_A	136_P	0.751	0.92
113_Y	125_D	0.750	0.92
131_E	251_R	0.749	0.92
168_G	370_L	0.747	0.91
59_E	69_L	0.747	0.91
176_V	331_Y	0.747	0.91
332_E	335_K	0.746	0.91
243_E	269_L	0.745	0.91
229_S	233_E	0.744	0.91
60_I	97_D	0.744	0.91
83_I	280_S	0.743	0.91
77_S	95_N	0.743	0.91
56_G	60_I	0.740	0.91
288_I	324_S	0.740	0.91
114_G	225_D	0.739	0.91
115_L	118_V	0.737	0.91
282_R	291_A	0.736	0.91
57_V	61_I	0.735	0.91
145_R	169_F	0.734	0.91
215_V	228_S	0.732	0.91
343_H	346_R	0.732	0.91
73_N	87_Q	0.731	0.90
192_N	219_E	0.731	0.90
128_S	131_E	0.730	0.90
137_A	142_Y	0.724	0.90
87_Q	122_N	0.723	0.90
130_K	134_H	0.723	0.90
112_Y	252_L	0.720	0.90
106_P	240_K	0.718	0.90
225_D	252_L	0.718	0.90
56_G	61_I	0.714	0.89
137_A	143_P	0.712	0.89
164_M	359_I	0.711	0.89
388_D	392_F	0.711	0.89
239_I	276_V	0.710	0.89
366_K	371_V	0.709	0.89
239_I	295_R	0.706	0.89
234_V	237_N	0.703	0.89
130_K	133_V	0.701	0.89
141_L	145_R	0.701	0.89
353_I	417_W	0.700	0.89
179_P	337_T	0.699	0.88
146_Q	149_L	0.698	0.88
261_I	303_A	0.698	0.88
113_Y	131_E	0.698	0.88
179_P	335_K	0.697	0.88
326_M	361_R	0.696	0.88
191_A	223_A	0.695	0.88
279_P	290_P	0.694	0.88
404_K	407_Q	0.690	0.88
368_E	383_R	0.690	0.88
265_S	317_T	0.689	0.88
62_Q	65_G	0.686	0.88
322_T	328_D	0.682	0.87
164_M	379_L	0.681	0.87
56_G	68_F	0.679	0.87
114_G	119_E	0.678	0.87
168_G	366_K	0.678	0.87
182_G	264_D	0.678	0.87
406_N	409_F	0.677	0.87
275_L	290_P	0.675	0.87
282_R	304_R	0.675	0.87
277_I	291_A	0.670	0.86
279_P	283_T	0.669	0.86
88_I	234_V	0.668	0.86
87_Q	237_N	0.667	0.86
395_K	399_K	0.665	0.86
52_L	56_G	0.665	0.86
277_I	290_P	0.664	0.86
209_D	238_H	0.663	0.86
203_L	262_L	0.662	0.86
395_K	398_R	0.661	0.86
374_E	378_R	0.661	0.86
56_G	66_F	0.660	0.85
131_E	255_H	0.659	0.85
345_D	361_R	0.658	0.85
205_V	215_V	0.655	0.85
270_A	296_P	0.654	0.85
70_R	97_D	0.653	0.85
375_H	379_L	0.652	0.85
178_P	287_G	0.650	0.85
120_A	126_P	0.649	0.84
133_V	136_P	0.648	0.84
53_F	60_I	0.646	0.84
162_D	194_I	0.645	0.84
108_E	111_R	0.645	0.84
103_V	106_P	0.644	0.84
51_L	55_E	0.638	0.83
385_T	388_D	0.636	0.83
280_S	291_A	0.635	0.83
156_L	315_L	0.635	0.83
367_E	375_H	0.634	0.83
65_G	69_L	0.634	0.83
179_P	336_G	0.632	0.83
285_S	289_D	0.631	0.83
273_Y	276_V	0.628	0.83
175_I	391_D	0.627	0.82
285_S	333_E	0.626	0.82
246_L	263_M	0.624	0.82
263_M	299_F	0.624	0.82
69_L	97_D	0.623	0.82
110_E	247_E	0.623	0.82
161_M	167_V	0.623	0.82
353_I	419_Q	0.623	0.82
60_I	80_D	0.620	0.82
188_K	217_D	0.620	0.82
237_N	240_K	0.617	0.81
102_K	117_H	0.616	0.81
121_V	124_D	0.615	0.81
146_Q	351_R	0.611	0.81
269_L	273_Y	0.608	0.80
52_L	55_E	0.606	0.80
394_E	400_M	0.605	0.80
256_K	308_E	0.602	0.80
252_L	257_K	0.601	0.80
152_K	258_D	0.599	0.79
183_K	264_D	0.597	0.79
180_K	275_L	0.596	0.79
132_R	373_K	0.596	0.79
176_V	338_G	0.596	0.79
116_L	127_E	0.596	0.79
285_S	409_F	0.595	0.79
85_A	280_S	0.592	0.79
55_E	100_S	0.592	0.79
106_P	162_D	0.592	0.79
76_P	83_I	0.590	0.78
389_S	393_A	0.590	0.78
175_I	315_L	0.589	0.78
69_L	81_I	0.589	0.78
118_V	126_P	0.589	0.78
385_T	411_D	0.589	0.78
119_E	122_N	0.588	0.78
327_D	334_F	0.587	0.78
59_E	65_G	0.586	0.78
241_V	245_V	0.586	0.78
239_I	269_L	0.586	0.78
352_R	384_K	0.582	0.78
70_R	92_D	0.582	0.78
156_L	161_M	0.582	0.78
197_N	223_A	0.580	0.77
377_D	381_S	0.580	0.77
156_L	303_A	0.579	0.77
88_I	122_N	0.579	0.77
110_E	114_G	0.579	0.77
184_T	264_D	0.577	0.77
56_G	162_D	0.576	0.77
221_S	247_E	0.574	0.77
168_G	365_R	0.574	0.77
244_L	247_E	0.574	0.77
75_S	280_S	0.574	0.77
189_E	193_S	0.574	0.77
321_D	327_D	0.573	0.76
266_I	316_A	0.573	0.76
346_R	350_E	0.572	0.76
360_R	386_M	0.572	0.76
105_P	164_M	0.572	0.76
55_E	59_E	0.572	0.76
122_N	125_D	0.572	0.76
87_Q	106_P	0.571	0.76
58_L	84_S	0.571	0.76
378_R	381_S	0.569	0.76
153_P	366_K	0.569	0.76
258_D	305_N	0.568	0.76
205_V	222_V	0.567	0.76
62_Q	67_G	0.567	0.76
183_K	210_E	0.566	0.76
402_K	405_T	0.565	0.75
375_H	378_R	0.565	0.75
116_L	119_E	0.565	0.75
137_A	141_L	0.563	0.75
322_T	332_E	0.563	0.75
54_M	103_V	0.561	0.75
107_K	112_Y	0.560	0.75
148_V	162_D	0.560	0.75
112_Y	125_D	0.560	0.75
150_E	309_G	0.560	0.75
190_I	193_S	0.559	0.75
157_S	186_L	0.558	0.75
59_E	70_R	0.558	0.75
207_L	210_E	0.558	0.75
401_K	404_K	0.557	0.74
368_E	371_V	0.557	0.74
162_D	166_P	0.556	0.74
183_K	268_R	0.556	0.74
82_Y	99_V	0.556	0.74
190_I	260_I	0.552	0.74
262_L	271_R	0.552	0.74
181_A	346_R	0.552	0.74
215_V	230_T	0.550	0.73
300_F	314_I	0.549	0.73
129_A	133_V	0.548	0.73
322_T	330_I	0.548	0.73
124_D	255_H	0.547	0.73
205_V	218_I	0.547	0.73
91_F	107_K	0.546	0.73
119_E	123_G	0.545	0.73
56_G	59_E	0.543	0.73
320_V	327_D	0.543	0.73
266_I	299_F	0.542	0.72
243_E	280_S	0.540	0.72
250_M	253_V	0.540	0.72
83_I	175_I	0.539	0.72
196_A	223_A	0.539	0.72
386_M	416_E	0.539	0.72
110_E	133_V	0.538	0.72
283_T	290_P	0.537	0.72
274_N	330_I	0.537	0.72
206_L	209_D	0.536	0.72
179_P	333_E	0.535	0.71
336_G	363_G	0.535	0.71
162_D	240_K	0.534	0.71
388_D	410_F	0.534	0.71
185_M	189_E	0.533	0.71
334_F	338_G	0.533	0.71
51_L	54_M	0.533	0.71
89_R	92_D	0.531	0.71
73_N	240_K	0.531	0.71
277_I	289_D	0.531	0.71
242_A	263_M	0.531	0.71
72_I	77_S	0.530	0.71
74_Y	77_S	0.530	0.71
67_G	71_P	0.529	0.71
163_M	410_F	0.528	0.70
333_E	400_M	0.528	0.70
348_L	356_A	0.527	0.70
404_K	410_F	0.526	0.70
66_F	70_R	0.526	0.70
229_S	237_N	0.526	0.70
246_L	250_M	0.525	0.70
247_E	250_M	0.525	0.70
145_R	150_E	0.524	0.70
389_S	413_L	0.524	0.70
156_L	176_V	0.522	0.70
171_Q	365_R	0.522	0.70
286_G	333_E	0.520	0.69
392_F	397_M	0.520	0.69
53_F	65_G	0.518	0.69
127_E	157_S	0.518	0.69
116_L	123_G	0.516	0.69
58_L	121_V	0.516	0.69
80_D	309_G	0.511	0.68
382_I	417_W	0.511	0.68
275_L	288_I	0.510	0.68
215_V	226_V	0.509	0.68
214_E	217_D	0.509	0.68
155_F	195_T	0.509	0.68
205_V	295_R	0.508	0.68
61_I	68_F	0.508	0.68
203_L	260_I	0.506	0.67
182_G	210_E	0.505	0.67
158_T	193_S	0.505	0.67
389_S	396_F	0.505	0.67
163_M	375_H	0.501	0.66
247_E	251_R	0.500	0.66
169_F	294_H	0.500	0.66

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
3oaaA	2	0.897	100	0.189	Contact Map
2qe7A	1	0.8899	100	0.19	Contact Map
2c61A	2	0.8525	100	0.196	Contact Map
1fx0A	1	0.897	100	0.198	Contact Map
2ck3A	1	0.904	100	0.199	Contact Map
3j9tA	1	0.8876	100	0.199	Contact Map
3vr4D	1	0.9016	100	0.202	Contact Map
3mfyA	1	0.726	100	0.203	Contact Map
3gqbB	1	0.904	100	0.203	Contact Map
3gqbA	1	0.8923	100	0.208	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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