RHMD - ECOLI - GREMLIN Contacts

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RHMD - L-rhamnonate dehydratase

UniProt:	P77215	Sequences: MTLPKIKQVRAWFTGGATAEKGAGGGDYHDQGANHWIDDHIATPMSKYRDYEQSRQSFGINVLGTLVVEVEAENGQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLSATLYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMGFIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGEDFWLMLDCWMSQDVNYATKLAHACAPYNLKWIEECLPPQQYESYRELKRNAPVGMMVTSGEHHGTLQSFRTLSETGIDIMQPDVGWCGGLTTLVEIAAIAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTMRPQFDPILLNEPVPVNGRIHKSVLDKPGFGVELNRDCNLKRPYSH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14085
Length:	401 (335)
Sequences:	11693 (6779)
Seq/√Len:	370.4

ECOLI - RHMD GUDD GUDX RSPA DGOD AEEP MENC
BACSU - YITF GUDD AEEP MENC
HALSA - Q9HS20 Q9HP25 Q9HQN7
SULSO - GAD Q97VG1 Q97YL9 ARAD Q97YR3 Q97UK8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
103_K	114_Q	3.715	1.00
163_E	374_R	3.562	1.00
263_K	293_D	3.367	1.00
228_D	231_Y	3.171	1.00
107_D	110_L	3.034	1.00
260_R	264_R	3.026	1.00
255_Q	258_S	2.836	1.00
76_Q	143_L	2.826	1.00
68_V	135_C	2.823	1.00
71_E	77_T	2.788	1.00
285_R	289_E	2.734	1.00
72_A	143_L	2.552	1.00
69_E	77_T	2.523	1.00
261_E	264_R	2.428	1.00
281_L	307_T	2.340	1.00
90_F	94_K	2.336	1.00
237_H	240_A	2.324	1.00
180_G	212_K	2.305	1.00
365_L	388_E	2.251	1.00
137_D	306_T	2.241	1.00
236_A	247_I	2.237	1.00
237_H	265_N	2.226	1.00
261_E	265_N	2.217	1.00
72_A	76_Q	2.206	1.00
288_S	320_Q	2.150	1.00
109_K	310_E	2.139	1.00
302_C	311_I	2.129	1.00
218_W	245_K	2.069	1.00
207_A	242_Y	2.047	1.00
57_S	81_V	1.996	1.00
69_E	79_F	1.978	1.00
76_Q	147_V	1.976	1.00
236_A	266_A	1.974	1.00
180_G	184_G	1.958	1.00
208_D	211_E	1.953	1.00
145_G	152_V	1.938	1.00
74_N	147_V	1.933	1.00
165_Q	188_T	1.930	1.00
294_I	321_L	1.900	1.00
111_I	140_L	1.898	1.00
176_A	212_K	1.893	1.00
70_V	140_L	1.889	1.00
238_A	241_P	1.884	1.00
235_L	239_C	1.848	1.00
289_E	318_R	1.848	1.00
82_S	135_C	1.834	1.00
240_A	267_P	1.830	1.00
371_V	378_S	1.819	1.00
233_T	265_N	1.793	1.00
284_F	311_I	1.786	1.00
151_P	154_K	1.774	1.00
150_L	154_K	1.765	1.00
103_K	110_L	1.764	1.00
203_A	238_A	1.748	1.00
89_C	93_E	1.746	1.00
314_I	318_R	1.722	1.00
204_A	207_A	1.718	1.00
251_L	262_L	1.704	1.00
313_A	316_K	1.660	1.00
183_G	217_F	1.628	1.00
76_Q	146_K	1.606	1.00
230_N	261_E	1.596	1.00
229_V	261_E	1.593	1.00
288_S	314_I	1.584	1.00
287_L	292_I	1.567	1.00
95_H	127_G	1.563	1.00
122_Y	282_Q	1.540	1.00
163_E	378_S	1.536	1.00
87_M	90_F	1.517	1.00
72_A	147_V	1.515	1.00
198_G	201_K	1.515	1.00
146_K	388_E	1.506	1.00
137_D	141_W	1.491	1.00
309_V	313_A	1.491	1.00
97_N	101_E	1.477	1.00
233_T	261_E	1.464	1.00
229_V	262_L	1.464	1.00
152_V	385_F	1.462	1.00
106_S	147_V	1.452	1.00
188_T	220_M	1.450	1.00
285_R	314_I	1.421	1.00
240_A	268_V	1.420	1.00
207_A	241_P	1.419	1.00
181_F	185_K	1.418	1.00
103_K	111_I	1.399	1.00
229_V	258_S	1.387	1.00
307_T	310_E	1.387	1.00
288_S	318_R	1.382	1.00
73_E	105_V	1.379	1.00
207_A	211_E	1.376	1.00
283_S	286_T	1.360	1.00
200_R	204_A	1.335	1.00
201_K	204_A	1.332	1.00
221_L	244_L	1.326	1.00
142_D	146_K	1.323	1.00
203_A	207_A	1.321	1.00
159_A	162_D	1.310	1.00
54_S	59_G	1.309	1.00
94_K	98_R	1.305	1.00
144_F	148_V	1.299	1.00
234_K	238_A	1.296	1.00
273_T	294_I	1.295	1.00
110_L	114_Q	1.293	1.00
234_K	237_H	1.288	1.00
145_G	155_L	1.285	1.00
251_L	258_S	1.283	1.00
180_G	183_G	1.281	1.00
150_L	155_L	1.273	1.00
220_M	245_K	1.268	1.00
286_T	289_E	1.265	1.00
250_C	272_V	1.258	1.00
115_M	133_I	1.253	1.00
165_Q	374_R	1.250	1.00
254_Q	283_S	1.250	1.00
203_A	242_Y	1.249	1.00
178_E	181_F	1.245	1.00
138_L	305_L	1.242	1.00
233_T	262_L	1.240	1.00
220_M	246_W	1.233	1.00
67_V	79_F	1.229	1.00
284_F	295_M	1.222	1.00
366_N	382_K	1.219	1.00
260_R	291_G	1.213	1.00
190_W	217_F	1.210	1.00
177_K	180_G	1.205	1.00
106_S	144_F	1.199	1.00
209_M	213_C	1.195	1.00
263_K	290_T	1.191	1.00
113_D	117_S	1.187	1.00
104_C	107_D	1.184	1.00
274_S	287_L	1.177	1.00
281_L	314_I	1.177	1.00
193_H	224_W	1.158	1.00
231_Y	234_K	1.154	1.00
310_E	313_A	1.147	1.00
95_H	98_R	1.138	1.00
109_K	309_V	1.131	1.00
237_H	267_P	1.126	1.00
271_M	342_P	1.126	1.00
87_M	92_V	1.124	1.00
176_A	180_G	1.121	1.00
203_A	241_P	1.121	1.00
310_E	316_K	1.119	1.00
167_Y	170_G	1.117	1.00
250_C	262_L	1.115	1.00
206_V	242_Y	1.104	1.00
213_C	219_L	1.104	1.00
313_A	317_S	1.101	1.00
280_T	283_S	1.101	1.00
177_K	181_F	1.099	1.00
273_T	296_Q	1.091	1.00
141_W	306_T	1.090	1.00
299_V	308_L	1.090	1.00
295_M	315_A	1.086	1.00
223_C	247_I	1.085	1.00
106_S	148_V	1.080	1.00
179_M	213_C	1.071	1.00
232_A	236_A	1.070	1.00
227_Q	235_L	1.067	1.00
210_R	214_G	1.057	1.00
173_P	176_A	1.037	1.00
290_T	320_Q	1.028	1.00
262_L	272_V	1.027	1.00
96_L	136_V	1.025	1.00
227_Q	232_A	1.022	1.00
285_R	318_R	1.021	1.00
331_S	334_A	1.017	1.00
176_A	213_C	1.005	1.00
206_V	221_L	1.004	1.00
206_V	210_R	1.004	1.00
108_I	144_F	0.998	1.00
215_E	243_N	0.993	1.00
314_I	317_S	0.992	1.00
249_E	296_Q	0.990	1.00
179_M	190_W	0.989	1.00
210_R	219_L	0.986	1.00
192_P	209_M	0.986	1.00
148_V	155_L	0.982	1.00
268_V	271_M	0.976	1.00
204_A	208_D	0.971	1.00
302_C	308_L	0.967	1.00
288_S	295_M	0.967	1.00
152_V	305_L	0.962	1.00
340_N	349_T	0.961	1.00
176_A	211_E	0.957	1.00
111_I	114_Q	0.954	1.00
190_W	218_W	0.952	1.00
194_D	198_G	0.944	1.00
154_K	381_D	0.943	1.00
99_F	114_Q	0.942	1.00
182_I	185_K	0.939	1.00
144_F	155_L	0.938	1.00
256_Y	291_G	0.935	1.00
309_V	338_F	0.934	1.00
339_T	344_S	0.928	1.00
103_K	107_D	0.924	1.00
70_V	78_G	0.921	1.00
213_C	217_F	0.920	1.00
111_I	115_M	0.919	1.00
281_L	310_E	0.917	1.00
292_I	295_M	0.910	1.00
79_F	358_P	0.905	1.00
189_H	220_M	0.905	1.00
156_L	309_V	0.905	1.00
298_D	325_H	0.902	1.00
208_D	212_K	0.900	1.00
112_H	116_L	0.900	1.00
112_H	115_M	0.900	1.00
382_K	388_E	0.900	1.00
264_R	290_T	0.898	1.00
183_G	190_W	0.898	1.00
203_A	206_V	0.897	1.00
87_M	91_I	0.896	1.00
52_E	59_G	0.894	1.00
374_R	378_S	0.891	1.00
112_H	137_D	0.891	1.00
230_N	234_K	0.891	1.00
71_E	75_G	0.886	1.00
251_L	259_Y	0.885	1.00
207_A	210_R	0.884	1.00
166_F	169_T	0.878	1.00
279_G	283_S	0.877	1.00
378_S	381_D	0.873	1.00
181_F	184_G	0.871	1.00
360_F	363_I	0.866	1.00
356_M	360_F	0.866	1.00
210_R	216_D	0.865	1.00
232_A	251_L	0.864	1.00
201_K	205_M	0.862	1.00
229_V	251_L	0.858	1.00
153_Y	379_V	0.857	1.00
152_V	156_L	0.855	1.00
341_T	379_V	0.853	1.00
223_C	227_Q	0.852	1.00
274_S	292_I	0.852	1.00
91_I	95_H	0.849	1.00
206_V	239_C	0.846	1.00
179_M	182_I	0.843	1.00
370_P	375_I	0.842	1.00
94_K	97_N	0.842	1.00
275_G	298_D	0.835	1.00
105_V	144_F	0.832	1.00
278_H	284_F	0.832	1.00
105_V	140_L	0.829	1.00
297_P	308_L	0.827	1.00
99_F	103_K	0.826	1.00
308_L	339_T	0.820	1.00
258_S	261_E	0.819	1.00
233_T	266_A	0.817	1.00
316_K	345_E	0.816	1.00
227_Q	247_I	0.815	1.00
124_G	127_G	0.813	1.00
194_D	197_A	0.810	1.00
357_R	360_F	0.806	1.00
100_I	103_K	0.804	1.00
71_E	79_F	0.803	1.00
261_E	290_T	0.801	1.00
257_E	286_T	0.801	1.00
259_Y	272_V	0.798	1.00
141_W	305_L	0.796	1.00
89_C	92_V	0.794	1.00
78_G	142_D	0.794	1.00
98_R	101_E	0.791	1.00
229_V	233_T	0.789	1.00
305_L	309_V	0.789	1.00
179_M	209_M	0.785	1.00
333_H	358_P	0.784	1.00
240_A	266_A	0.783	1.00
202_D	205_M	0.781	1.00
244_L	268_V	0.779	1.00
116_L	307_T	0.779	1.00
309_V	342_P	0.777	1.00
257_E	260_R	0.775	1.00
259_Y	274_S	0.774	1.00
163_E	372_N	0.771	1.00
338_F	344_S	0.762	1.00
176_A	208_D	0.762	1.00
55_R	67_V	0.760	1.00
256_Y	287_L	0.757	1.00
168_A	187_P	0.756	1.00
152_V	155_L	0.751	1.00
70_V	100_I	0.750	1.00
256_Y	286_T	0.749	1.00
199_I	235_L	0.748	1.00
297_P	312_A	0.748	1.00
149_G	383_P	0.747	1.00
96_L	115_M	0.744	1.00
223_C	236_A	0.744	1.00
195_G	199_I	0.744	1.00
197_A	201_K	0.744	1.00
168_A	182_I	0.740	1.00
278_H	287_L	0.738	1.00
259_Y	262_L	0.736	1.00
93_E	97_N	0.736	1.00
72_A	105_V	0.736	1.00
105_V	147_V	0.735	1.00
148_V	151_P	0.733	1.00
232_A	262_L	0.732	1.00
312_A	316_K	0.731	1.00
263_K	272_V	0.728	1.00
278_H	283_S	0.727	1.00
371_V	374_R	0.726	1.00
113_D	116_L	0.726	1.00
262_L	266_A	0.723	1.00
369_V	378_S	0.720	1.00
109_K	306_T	0.719	1.00
114_Q	117_S	0.719	1.00
312_A	322_V	0.719	1.00
282_Q	286_T	0.717	1.00
295_M	320_Q	0.716	1.00
200_R	238_A	0.715	1.00
156_L	305_L	0.714	1.00
194_D	212_K	0.712	1.00
210_R	243_N	0.712	1.00
154_K	159_A	0.712	1.00
233_T	237_H	0.709	0.99
281_L	311_I	0.708	0.99
105_V	143_L	0.708	0.99
52_E	100_I	0.705	0.99
78_G	146_K	0.704	0.99
282_Q	285_R	0.703	0.99
92_V	136_V	0.702	0.99
358_P	362_P	0.702	0.99
202_D	227_Q	0.700	0.99
366_N	388_E	0.700	0.99
334_A	337_T	0.698	0.99
145_G	150_L	0.695	0.99
183_G	186_M	0.695	0.99
141_W	152_V	0.694	0.99
112_H	306_T	0.691	0.99
196_D	202_D	0.686	0.99
167_Y	171_A	0.686	0.99
198_G	202_D	0.686	0.99
113_D	310_E	0.685	0.99
197_A	200_R	0.682	0.99
297_P	322_V	0.680	0.99
168_A	171_A	0.680	0.99
159_A	381_D	0.674	0.99
78_G	139_A	0.674	0.99
144_F	147_V	0.673	0.99
284_F	320_Q	0.672	0.99
108_I	140_L	0.672	0.99
210_R	213_C	0.672	0.99
109_K	113_D	0.671	0.99
145_G	383_P	0.671	0.99
188_T	372_N	0.668	0.99
323_V	340_N	0.668	0.99
178_E	182_I	0.668	0.99
312_A	338_F	0.660	0.99
77_T	146_K	0.659	0.99
199_I	203_A	0.659	0.99
296_Q	325_H	0.657	0.99
77_T	388_E	0.655	0.99
169_T	202_D	0.655	0.99
202_D	207_A	0.653	0.99
92_V	97_N	0.651	0.99
81_V	330_Y	0.650	0.99
179_M	212_K	0.647	0.99
88_G	91_I	0.646	0.99
141_W	156_L	0.643	0.99
108_I	111_I	0.641	0.99
176_A	179_M	0.641	0.99
95_H	99_F	0.640	0.99
51_Y	178_E	0.640	0.99
73_E	76_Q	0.640	0.99
235_L	238_A	0.636	0.99
171_A	209_M	0.636	0.99
90_F	95_H	0.636	0.99
71_E	74_N	0.636	0.99
150_L	158_G	0.634	0.99
143_L	147_V	0.632	0.99
295_M	311_I	0.630	0.99
299_V	305_L	0.630	0.99
284_F	315_A	0.627	0.99
205_M	208_D	0.622	0.99
170_G	182_I	0.621	0.99
315_A	320_Q	0.620	0.99
163_E	371_V	0.620	0.99
233_T	251_L	0.619	0.99
352_D	355_T	0.619	0.99
206_V	213_C	0.617	0.99
100_I	136_V	0.617	0.99
355_T	358_P	0.616	0.99
133_I	304_G	0.615	0.99
210_R	242_Y	0.614	0.99
68_V	92_V	0.614	0.99
202_D	210_R	0.612	0.98
335_V	385_F	0.612	0.98
205_M	209_M	0.611	0.98
107_D	154_K	0.609	0.98
188_T	218_W	0.604	0.98
161_R	164_I	0.603	0.98
338_F	342_P	0.602	0.98
249_E	275_G	0.602	0.98
183_G	213_C	0.602	0.98
292_I	320_Q	0.601	0.98
189_H	193_H	0.600	0.98
151_P	155_L	0.600	0.98
116_L	133_I	0.599	0.98
80_A	135_C	0.597	0.98
108_I	306_T	0.596	0.98
174_D	177_K	0.596	0.98
266_A	272_V	0.595	0.98
82_S	131_N	0.594	0.98
194_D	201_K	0.592	0.98
100_I	111_I	0.591	0.98
189_H	218_W	0.590	0.98
74_N	105_V	0.588	0.98
127_G	304_G	0.588	0.98
263_K	291_G	0.587	0.98
179_M	183_G	0.586	0.98
312_A	343_F	0.584	0.98
104_C	154_K	0.583	0.98
281_L	285_R	0.583	0.98
197_A	205_M	0.583	0.98
183_G	212_K	0.582	0.98
110_L	113_D	0.582	0.98
260_R	290_T	0.575	0.98
49_R	52_E	0.572	0.98
214_G	217_F	0.571	0.98
202_D	206_V	0.569	0.98
162_D	381_D	0.567	0.98
203_A	210_R	0.567	0.98
96_L	100_I	0.567	0.98
245_K	271_M	0.566	0.98
249_E	277_H	0.563	0.97
67_V	358_P	0.562	0.97
283_S	291_G	0.561	0.97
72_A	75_G	0.560	0.97
308_L	324_P	0.556	0.97
145_G	148_V	0.553	0.97
105_V	108_I	0.553	0.97
166_F	170_G	0.552	0.97
236_A	239_C	0.552	0.97
375_I	378_S	0.552	0.97
146_K	382_K	0.552	0.97
335_V	339_T	0.551	0.97
339_T	342_P	0.550	0.97
166_F	375_I	0.547	0.97
194_D	210_R	0.546	0.97
340_N	345_E	0.546	0.97
203_A	235_L	0.544	0.97
343_F	346_F	0.543	0.97
175_L	179_M	0.542	0.97
192_P	206_V	0.542	0.97
284_F	297_P	0.542	0.97
140_L	144_F	0.541	0.97
172_R	176_A	0.541	0.97
146_K	385_F	0.541	0.97
153_Y	381_D	0.538	0.97
337_T	340_N	0.538	0.97
210_R	215_E	0.538	0.97
326_G	329_V	0.538	0.97
340_N	346_F	0.537	0.97
194_D	202_D	0.537	0.97
249_E	276_E	0.537	0.97
108_I	155_L	0.536	0.97
177_K	212_K	0.536	0.97
188_T	193_H	0.536	0.97
99_F	118_A	0.535	0.97
91_I	94_K	0.535	0.97
195_G	198_G	0.535	0.97
259_Y	292_I	0.534	0.96
291_G	320_Q	0.534	0.96
175_L	205_M	0.533	0.96
154_K	157_G	0.531	0.96
80_A	139_A	0.531	0.96
334_A	339_T	0.529	0.96
205_M	212_K	0.527	0.96
91_I	128_L	0.526	0.96
334_A	387_V	0.526	0.96
236_A	262_L	0.526	0.96
234_K	265_N	0.525	0.96
83_T	300_G	0.524	0.96
66_L	89_C	0.524	0.96
97_N	136_V	0.523	0.96
206_V	349_T	0.523	0.96
55_R	69_E	0.522	0.96
244_L	247_I	0.521	0.96
315_A	322_V	0.518	0.96
345_E	348_M	0.517	0.96
206_V	209_M	0.517	0.96
255_Q	319_G	0.516	0.96
165_Q	218_W	0.516	0.96
339_T	343_F	0.514	0.96
259_Y	291_G	0.513	0.96
122_Y	129_V	0.513	0.96
366_N	369_V	0.512	0.96
234_K	243_N	0.512	0.96
246_W	323_V	0.507	0.95
188_T	216_D	0.505	0.95
321_L	347_L	0.505	0.95
225_M	253_P	0.504	0.95
101_E	104_C	0.504	0.95
316_K	344_S	0.504	0.95
225_M	277_H	0.503	0.95
157_G	162_D	0.503	0.95
194_D	206_V	0.503	0.95
194_D	203_A	0.502	0.95
138_L	385_F	0.502	0.95
195_G	202_D	0.500	0.95
327_S	330_Y	0.500	0.95

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
3dgbA	5	0.8853	100	0.235	Contact Map
3s5sA	2	0.8653	100	0.236	Contact Map
3ekgA	5	0.9252	100	0.239	Contact Map
3fcpA	5	0.8504	100	0.239	Contact Map
3cyjA	5	0.8778	100	0.239	Contact Map
1wufA	2	0.8728	100	0.241	Contact Map
3i4kA	4	0.8803	100	0.242	Contact Map
1wueA	2	0.8778	100	0.242	Contact Map
1sjdA	5	0.8678	100	0.242	Contact Map
2p3zA	5	0.9651	100	0.243	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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