RHO - ECOLI - GREMLIN Contacts

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RHO - Transcription termination factor Rho

UniProt:	P0AG30	Sequences: MNLTELKNTPVSELITLGENMGLENLARMRKQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRVFPAIDYNRSGTRKEELLTTQEELQKMWILRKIIHPMGEIDAMEFLINKLAMTKTNDDFFEMMKRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10845
Length:	419 (350)
Sequences:	7781 (2563)
Seq/√Len:	137.0

ECOLI - RHO FLII ATPB ATPA
BACSU - RHO FLII ATPA 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
118_E	122_D	8.385	1.00
170_R	259_D	5.762	1.00
207_L	246_V	5.063	1.00
346_S	359_D	4.810	1.00
161_V	358_I	4.253	1.00
70_S	82_S	3.149	1.00
168_I	316_I	3.102	1.00
115_K	125_E	3.067	1.00
110_Y	256_H	3.055	1.00
203_V	258_K	3.055	1.00
247_I	317_A	2.985	1.00
153_S	170_R	2.952	1.00
102_R	105_K	2.792	1.00
110_Y	258_K	2.754	1.00
205_M	250_A	2.634	1.00
349_I	354_V	2.602	1.00
217_T	221_R	2.598	1.00
372_T	377_L	2.575	1.00
391_G	394_D	2.500	1.00
382_I	385_K	2.433	1.00
105_K	136_L	2.425	1.00
250_A	313_L	2.302	1.00
374_Q	378_Q	2.298	1.00
137_T	141_A	2.251	1.00
251_K	303_A	2.232	1.00
111_F	134_E	2.205	1.00
394_D	398_F	2.189	1.00
117_N	249_K	2.170	1.00
165_A	383_L	2.153	1.00
327_M	344_H	2.112	1.00
145_L	202_C	2.109	1.00
156_D	163_D	2.101	1.00
226_E	249_K	2.084	1.00
203_V	226_E	2.076	1.00
254_V	307_V	2.070	1.00
228_V	249_K	2.066	1.00
137_T	248_E	2.033	1.00
179_P	182_A	2.018	1.00
137_T	252_R	1.996	1.00
174_G	316_I	1.884	1.00
168_I	343_L	1.873	1.00
162_L	343_L	1.869	1.00
57_I	72_Y	1.846	1.00
373_T	376_E	1.831	1.00
353_R	381_W	1.830	1.00
203_V	253_L	1.816	1.00
174_G	341_M	1.814	1.00
220_Q	227_V	1.804	1.00
167_P	368_E	1.764	1.00
107_G	136_L	1.758	1.00
243_A	300_F	1.756	1.00
252_R	256_H	1.748	1.00
259_D	312_S	1.711	1.00
153_S	306_N	1.665	1.00
104_P	139_L	1.654	1.00
244_E	274_Y	1.650	1.00
175_L	339_G	1.649	1.00
369_E	377_L	1.641	1.00
332_Y	344_H	1.616	1.00
377_L	381_W	1.603	1.00
205_M	249_K	1.600	1.00
222_L	370_L	1.585	1.00
115_K	123_K	1.568	1.00
207_L	264_L	1.566	1.00
88_R	91_L	1.560	1.00
155_E	202_C	1.557	1.00
209_I	242_V	1.536	1.00
260_V	313_L	1.534	1.00
382_I	386_I	1.534	1.00
319_A	335_F	1.531	1.00
137_T	255_E	1.514	1.00
368_E	380_M	1.508	1.00
102_R	136_L	1.488	1.00
133_F	136_L	1.476	1.00
162_L	191_I	1.474	1.00
274_Y	296_R	1.432	1.00
352_K	394_D	1.426	1.00
301_F	338_T	1.425	1.00
297_P	335_F	1.425	1.00
234_E	238_R	1.422	1.00
110_Y	252_R	1.392	1.00
112_A	249_K	1.391	1.00
208_L	216_V	1.387	1.00
144_R	376_E	1.380	1.00
115_K	128_R	1.364	1.00
166_S	343_L	1.361	1.00
106_E	245_M	1.354	1.00
247_I	304_A	1.345	1.00
329_E	332_Y	1.344	1.00
117_N	228_V	1.331	1.00
115_K	129_N	1.305	1.00
267_I	335_F	1.294	1.00
278_V	285_L	1.292	1.00
348_K	351_E	1.288	1.00
111_F	132_L	1.287	1.00
192_A	263_L	1.287	1.00
106_E	249_K	1.282	1.00
159_A	162_L	1.282	1.00
157_L	168_I	1.280	1.00
116_V	220_Q	1.279	1.00
389_P	392_E	1.277	1.00
359_D	362_R	1.272	1.00
209_I	264_L	1.257	1.00
141_A	255_E	1.248	1.00
268_T	272_R	1.247	1.00
381_W	384_R	1.235	1.00
247_I	313_L	1.228	1.00
143_S	170_R	1.222	1.00
372_T	380_M	1.222	1.00
221_R	308_E	1.219	1.00
107_G	133_F	1.217	1.00
168_I	314_T	1.215	1.00
123_K	129_N	1.213	1.00
351_E	362_R	1.207	1.00
301_F	335_F	1.204	1.00
207_L	262_I	1.198	1.00
62_F	65_L	1.194	1.00
321_I	332_Y	1.190	1.00
367_K	371_L	1.187	1.00
156_D	190_N	1.172	0.99
162_L	166_S	1.162	0.99
154_T	371_L	1.162	0.99
119_V	245_M	1.159	0.99
255_E	307_V	1.155	0.99
362_R	391_G	1.155	0.99
86_I	238_R	1.144	0.99
178_A	182_A	1.131	0.99
118_E	234_E	1.127	0.99
368_E	372_T	1.124	0.99
130_K	133_F	1.121	0.99
92_R	95_D	1.120	0.99
257_K	310_G	1.115	0.99
113_L	203_V	1.114	0.99
111_F	133_F	1.109	0.99
297_P	338_T	1.102	0.99
168_I	174_G	1.099	0.99
247_I	262_I	1.097	0.99
84_S	88_R	1.093	0.99
109_R	112_A	1.092	0.99
205_M	228_V	1.090	0.99
198_N	259_D	1.089	0.99
135_N	252_R	1.079	0.99
393_I	397_E	1.077	0.99
63_G	66_R	1.075	0.99
244_E	296_R	1.072	0.99
192_A	225_G	1.071	0.99
211_E	215_E	1.071	0.99
54_V	58_L	1.070	0.99
306_N	312_S	1.061	0.99
272_R	322_D	1.056	0.99
212_R	215_E	1.055	0.99
162_L	187_L	1.053	0.99
213_P	231_T	1.050	0.99
295_H	298_K	1.049	0.99
113_L	226_E	1.048	0.99
179_P	347_R	1.048	0.99
159_A	187_L	1.041	0.99
204_L	225_G	1.027	0.99
307_V	310_G	1.023	0.99
179_P	333_E	1.019	0.99
272_R	334_E	1.013	0.98
148_E	308_E	1.006	0.98
192_A	204_L	1.002	0.98
137_T	309_E	0.997	0.98
111_F	131_I	0.992	0.98
66_R	95_D	0.992	0.98
166_S	364_G	0.990	0.98
55_L	60_D	0.987	0.98
53_G	57_I	0.981	0.98
211_E	269_R	0.981	0.98
56_E	60_D	0.979	0.98
325_S	328_D	0.975	0.98
192_A	206_V	0.974	0.98
261_I	316_I	0.973	0.98
57_I	60_D	0.970	0.98
119_V	238_R	0.962	0.98
209_I	243_A	0.961	0.98
202_C	261_I	0.961	0.98
256_H	260_V	0.958	0.98
64_F	67_S	0.954	0.98
157_L	163_D	0.944	0.98
297_P	334_E	0.944	0.98
321_I	329_E	0.942	0.97
155_E	195_I	0.931	0.97
304_A	315_I	0.930	0.97
148_E	309_E	0.929	0.97
119_V	234_E	0.929	0.97
263_L	318_T	0.928	0.97
205_M	226_E	0.926	0.97
167_P	372_T	0.921	0.97
270_L	300_F	0.920	0.97
407_K	410_D	0.919	0.97
198_N	258_K	0.919	0.97
151_N	370_L	0.917	0.97
119_V	124_P	0.915	0.97
239_H	276_T	0.914	0.97
240_V	274_Y	0.911	0.97
246_V	262_I	0.906	0.97
62_F	66_R	0.905	0.97
67_S	70_S	0.904	0.97
154_T	167_P	0.903	0.97
324_G	329_E	0.903	0.97
139_L	245_M	0.900	0.97
164_L	167_P	0.895	0.97
254_V	260_V	0.886	0.96
153_S	259_D	0.883	0.96
112_A	226_E	0.882	0.96
145_L	148_E	0.882	0.96
271_A	331_I	0.878	0.96
188_L	219_M	0.873	0.96
122_D	130_K	0.867	0.96
348_K	391_G	0.867	0.96
113_L	116_V	0.866	0.96
389_P	393_I	0.863	0.96
230_S	239_H	0.857	0.96
252_R	255_E	0.856	0.96
341_M	366_R	0.855	0.96
196_A	259_D	0.852	0.95
150_G	310_G	0.849	0.95
284_V	289_V	0.849	0.95
344_H	362_R	0.849	0.95
206_V	225_G	0.848	0.95
257_K	309_E	0.846	0.95
81_V	281_S	0.845	0.95
105_K	138_P	0.845	0.95
385_K	389_P	0.842	0.95
272_R	289_V	0.841	0.95
167_P	376_E	0.839	0.95
254_V	313_L	0.838	0.95
195_I	261_I	0.832	0.95
115_K	124_P	0.832	0.95
267_I	301_F	0.832	0.95
170_R	312_S	0.829	0.95
174_G	343_L	0.829	0.95
204_L	207_L	0.828	0.95
104_P	245_M	0.827	0.95
240_V	277_V	0.824	0.95
333_E	336_K	0.824	0.95
327_M	332_Y	0.823	0.95
75_G	81_V	0.821	0.94
53_G	62_F	0.820	0.94
132_L	135_N	0.816	0.94
112_A	117_N	0.816	0.94
177_V	332_Y	0.815	0.94
395_A	398_F	0.811	0.94
110_Y	253_L	0.810	0.94
150_G	306_N	0.809	0.94
55_L	58_L	0.809	0.94
270_L	296_R	0.803	0.94
128_R	131_I	0.802	0.94
57_I	63_G	0.800	0.94
64_F	98_S	0.795	0.93
180_P	272_R	0.793	0.93
283_K	292_N	0.793	0.93
390_M	394_D	0.792	0.93
157_L	400_I	0.790	0.93
126_N	129_N	0.787	0.93
204_L	263_L	0.786	0.93
104_P	241_Q	0.783	0.93
266_S	318_T	0.782	0.93
378_Q	381_W	0.782	0.93
193_Q	220_Q	0.782	0.93
186_M	189_Q	0.781	0.93
157_L	316_I	0.781	0.93
244_E	270_L	0.780	0.93
165_A	380_M	0.777	0.93
327_M	362_R	0.777	0.93
169_G	371_L	0.776	0.93
61_G	64_F	0.775	0.93
262_I	304_A	0.774	0.93
179_P	325_S	0.774	0.93
188_L	263_L	0.771	0.92
57_I	62_F	0.769	0.92
125_E	129_N	0.768	0.92
218_E	370_L	0.767	0.92
180_P	336_K	0.765	0.92
346_S	362_R	0.765	0.92
405_M	409_N	0.763	0.92
179_P	288_G	0.756	0.92
212_R	269_R	0.755	0.92
76_P	81_V	0.748	0.91
163_D	194_S	0.746	0.91
159_A	190_N	0.746	0.91
205_M	246_V	0.742	0.91
372_T	376_E	0.742	0.91
131_I	134_E	0.738	0.91
169_G	367_K	0.737	0.91
359_D	391_G	0.737	0.91
165_A	360_Y	0.736	0.91
75_G	93_T	0.734	0.90
116_V	124_P	0.734	0.90
293_A	296_R	0.734	0.90
192_A	224_K	0.734	0.90
369_E	384_R	0.732	0.90
240_V	296_R	0.732	0.90
280_A	284_V	0.731	0.90
344_H	347_R	0.729	0.90
56_E	99_G	0.728	0.90
216_V	229_A	0.726	0.90
53_G	58_L	0.725	0.90
104_P	163_D	0.724	0.90
53_G	56_E	0.724	0.90
180_P	338_T	0.722	0.90
118_E	124_P	0.722	0.90
238_R	241_Q	0.719	0.90
395_A	401_N	0.718	0.89
264_L	300_F	0.718	0.89
402_K	405_M	0.716	0.89
368_E	376_E	0.716	0.89
59_Q	62_F	0.715	0.89
86_I	235_P	0.712	0.89
123_K	128_R	0.711	0.89
113_L	258_K	0.710	0.89
325_S	347_R	0.710	0.89
283_K	305_R	0.708	0.89
230_S	234_E	0.705	0.89
115_K	130_K	0.704	0.89
117_N	131_I	0.701	0.88
60_D	65_L	0.701	0.88
235_P	238_R	0.700	0.88
203_V	260_V	0.700	0.88
85_Q	238_R	0.698	0.88
183_G	265_D	0.696	0.88
103_P	138_P	0.696	0.88
162_L	168_I	0.694	0.88
86_I	122_D	0.694	0.88
71_S	85_Q	0.689	0.87
240_V	270_L	0.687	0.87
59_Q	65_L	0.684	0.87
247_I	264_L	0.683	0.87
210_D	239_H	0.682	0.87
157_L	162_L	0.681	0.87
108_E	248_E	0.680	0.87
348_K	392_E	0.677	0.87
53_G	60_D	0.676	0.86
393_I	398_F	0.676	0.86
280_A	291_A	0.676	0.86
58_L	64_F	0.674	0.86
249_K	253_L	0.673	0.86
100_K	117_N	0.673	0.86
218_E	222_L	0.670	0.86
278_V	291_A	0.670	0.86
270_L	274_Y	0.667	0.86
123_K	130_K	0.667	0.86
367_K	372_T	0.663	0.85
353_R	385_K	0.663	0.85
115_K	126_N	0.662	0.85
226_E	253_L	0.661	0.85
163_D	167_P	0.661	0.85
276_T	291_A	0.660	0.85
376_E	380_M	0.660	0.85
387_I	391_G	0.654	0.85
286_T	334_E	0.654	0.85
259_D	306_N	0.653	0.85
176_I	343_L	0.647	0.84
156_D	196_A	0.647	0.84
278_V	292_N	0.647	0.84
135_N	256_H	0.647	0.84
206_V	216_V	0.645	0.84
271_A	297_P	0.644	0.84
378_Q	382_I	0.643	0.84
181_K	276_T	0.641	0.83
58_L	62_F	0.641	0.83
401_N	405_M	0.641	0.83
242_V	246_V	0.637	0.83
386_I	389_P	0.637	0.83
184_K	211_E	0.634	0.83
177_V	339_G	0.633	0.83
361_N	387_I	0.632	0.83
106_E	109_R	0.629	0.82
274_Y	277_V	0.624	0.82
163_D	195_I	0.624	0.82
53_G	99_G	0.623	0.82
83_P	281_S	0.622	0.82
400_I	410_D	0.622	0.82
101_I	104_P	0.622	0.82
396_M	399_L	0.621	0.82
154_T	367_K	0.617	0.81
245_M	248_E	0.614	0.81
190_N	194_S	0.613	0.81
189_Q	218_E	0.612	0.81
85_Q	120_N	0.612	0.81
337_G	342_E	0.608	0.80
80_Y	97_I	0.606	0.80
321_I	328_D	0.605	0.80
56_E	98_S	0.605	0.80
172_Q	366_R	0.605	0.80
347_R	351_E	0.604	0.80
114_L	125_E	0.603	0.80
147_M	359_D	0.603	0.80
184_K	269_R	0.602	0.79
180_P	337_G	0.601	0.79
185_T	265_D	0.601	0.79
206_V	223_V	0.599	0.79
56_E	64_F	0.599	0.79
124_P	234_E	0.598	0.79
284_V	291_A	0.598	0.79
251_K	254_V	0.596	0.79
110_Y	134_E	0.596	0.79
108_E	112_A	0.595	0.79
140_H	244_E	0.595	0.79
184_K	265_D	0.594	0.79
133_F	252_R	0.594	0.79
281_S	292_N	0.593	0.78
55_L	62_F	0.593	0.78
286_T	290_D	0.593	0.78
55_L	59_Q	0.592	0.78
125_E	130_K	0.592	0.78
369_E	372_T	0.591	0.78
53_G	61_G	0.590	0.78
208_L	211_E	0.590	0.78
328_D	335_F	0.589	0.78
144_R	307_V	0.587	0.78
158_T	187_L	0.587	0.78
123_K	126_N	0.586	0.78
138_P	141_A	0.585	0.78
100_K	115_K	0.585	0.78
322_D	328_D	0.584	0.77
375_E	379_K	0.583	0.77
112_A	133_F	0.582	0.77
148_E	152_G	0.580	0.77
73_L	281_S	0.576	0.76
122_D	132_L	0.575	0.76
253_L	258_K	0.574	0.76
247_I	251_K	0.574	0.76
207_L	210_D	0.572	0.76
335_F	339_G	0.570	0.76
263_L	272_R	0.569	0.76
153_S	310_G	0.569	0.76
55_L	61_G	0.566	0.75
180_P	334_E	0.566	0.75
138_P	248_E	0.560	0.74
125_E	128_R	0.560	0.74
189_Q	229_A	0.560	0.74
169_G	366_R	0.560	0.74
243_A	264_L	0.560	0.74
206_V	219_M	0.559	0.74
81_V	176_I	0.557	0.74
239_H	251_K	0.557	0.74
74_A	81_V	0.557	0.74
150_G	307_V	0.557	0.74
248_E	251_K	0.556	0.74
83_P	395_A	0.556	0.74
379_K	382_I	0.555	0.74
260_V	276_T	0.555	0.74
85_Q	104_P	0.554	0.74
334_E	399_L	0.553	0.74
53_G	63_G	0.553	0.74
159_A	194_S	0.552	0.73
120_N	238_R	0.550	0.73
58_L	66_R	0.549	0.73
180_P	401_N	0.549	0.73
216_V	231_T	0.547	0.73
176_I	332_Y	0.547	0.73
103_P	165_A	0.546	0.73
390_M	397_E	0.546	0.73
72_Y	75_G	0.546	0.73
53_G	64_F	0.545	0.72
180_P	324_G	0.544	0.72
267_I	300_F	0.543	0.72
63_G	67_S	0.542	0.72
267_I	317_A	0.542	0.72
111_F	135_N	0.542	0.72
148_E	153_S	0.541	0.72
289_V	395_A	0.541	0.72
167_P	364_G	0.540	0.72
183_G	211_E	0.540	0.72
146_R	149_R	0.539	0.72
294_L	297_P	0.538	0.72
83_P	277_V	0.538	0.72
275_N	331_I	0.538	0.72
146_R	163_D	0.538	0.72
398_F	407_K	0.537	0.71
182_A	347_R	0.537	0.71
191_I	261_I	0.537	0.71
374_Q	377_L	0.537	0.71
163_D	241_Q	0.536	0.71
376_E	379_K	0.536	0.71
71_S	215_E	0.536	0.71
298_K	313_L	0.535	0.71
230_S	238_R	0.528	0.70
134_E	137_T	0.528	0.70
272_R	287_G	0.528	0.70
191_I	194_S	0.528	0.70
142_N	299_R	0.526	0.70
400_I	404_A	0.522	0.69
159_A	165_A	0.522	0.69
278_V	290_D	0.521	0.69
196_A	224_K	0.521	0.69
71_S	241_Q	0.521	0.69
186_M	190_N	0.520	0.69
151_N	222_L	0.520	0.69
116_V	408_T	0.520	0.69
286_T	328_D	0.519	0.69
98_S	118_E	0.519	0.69
215_E	269_R	0.518	0.69
329_E	333_E	0.516	0.68
78_D	310_G	0.516	0.68
197_Y	224_K	0.516	0.68
169_G	172_Q	0.516	0.68
125_E	158_T	0.515	0.68
157_L	304_A	0.515	0.68
354_V	391_G	0.514	0.68
337_G	364_G	0.513	0.68
223_V	229_A	0.512	0.68
321_I	327_M	0.511	0.68
334_E	395_A	0.510	0.67
152_G	310_G	0.510	0.67
56_E	61_G	0.510	0.67
105_K	110_Y	0.510	0.67
179_P	321_I	0.510	0.67
334_E	337_G	0.509	0.67
403_L	406_T	0.508	0.67
204_L	261_I	0.508	0.67
384_R	387_I	0.508	0.67
55_L	63_G	0.506	0.67
193_Q	331_I	0.505	0.67
192_A	223_V	0.504	0.67
135_N	150_G	0.504	0.67
254_V	259_D	0.503	0.66
301_F	315_I	0.502	0.66
215_E	218_E	0.502	0.66
120_N	399_L	0.502	0.66
129_N	133_F	0.501	0.66
379_K	386_I	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	0.9045	100	0.2	Contact Map
2qe7A	1	0.8974	100	0.202	Contact Map
1fx0A	1	0.9045	100	0.209	Contact Map
2c61A	2	0.852	100	0.21	Contact Map
3l0oA	2	0.9761	100	0.21	Contact Map
3gqbB	1	0.9069	100	0.211	Contact Map
2ck3A	1	0.9117	100	0.212	Contact Map
3vr4D	1	0.9021	100	0.212	Contact Map
3j9tA	1	0.8926	100	0.213	Contact Map
3mfyA	1	0.7327	100	0.213	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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