RMLB2 - ECOLI - GREMLIN Contacts

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RMLB2 - dTDP-glucose 4,6-dehydratase 2

UniProt:	P27830	Sequences: MRKILITGGAGFIGSALVRYIINETSDAVVVVDKLTYAGNLMSLAPVAQSERFAFEKVDICDRAELARVFTEHQPDCVMHLAAESHVDRSIDGPAAFIETNIVGTYTLLEAARAYWNALTEDKKSAFRFHHISTDEVYGDLHSTDDFFTETTPYAPSSPYSASKASSDHLVRAWLRTYGLPTLITNCSNNYGPYHFPEKLIPLMILNALAGKSLPVYGNGQQIRDWLYVEDHARALYCVATTGKVGETYNIGGHNERKNLDVVETICELLEELAPNKPHGVAHYRDLITFVADRPGHDLRYAIDASKIARELGWLPQETFESGMRKTVQWYLANESWWKQVQDGSYQGERLGLKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11453
Length:	355 (298)
Sequences:	50384 (34883)
Seq/√Len:	2020.7

ECOLI - RMLB2 RMLB1 GM4D GALE YBJS HLDD FCL YFCH RMLD YEEZ QOR2 ARNA YBJT YRAR
BACSU - RMLB YFNG YTCB GALE SPSK YFHF YTBQ YESF YHFK YWNB YHEG EPSC
HALSA - Q9HSU9 Q9HSV1 Q9HS50 Q9HRD1 Q9HSE7 Q9HML4 Q9HNV3 Q9HSQ3 Q9HPF1 Q9HR86
SULSO - Q97VN5 Q980W1 Q7LXE8 Q97XG1 Q97XJ9 Q7LXG5 Q97UM3 Q7LX44 Q7LXE6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
265_T	321_E	3.100	1.00
9_G	31_V	3.044	1.00
235_A	251_I	2.751	1.00
3_K	28_A	2.654	1.00
20_Y	234_R	2.645	1.00
99_E	103_V	2.533	1.00
247_E	307_K	2.491	1.00
77_C	240_A	2.468	1.00
67_A	114_A	2.389	1.00
93_G	96_A	2.373	1.00
269_L	325_R	2.354	1.00
249_Y	311_E	2.291	1.00
20_Y	237_Y	2.249	1.00
132_I	236_L	2.242	1.00
20_Y	24_E	2.150	1.00
268_E	321_E	2.143	1.00
234_R	317_Q	2.063	1.00
128_R	181_P	2.063	1.00
32_V	58_V	2.052	1.00
319_T	322_S	2.035	1.00
309_A	315_L	2.005	1.00
149_T	152_T	1.998	1.00
62_D	65_E	1.997	1.00
187_C	236_L	1.945	1.00
260_L	264_E	1.937	1.00
58_V	65_E	1.934	1.00
265_T	268_E	1.915	1.00
185_T	239_V	1.910	1.00
79_M	240_A	1.907	1.00
80_H	131_H	1.907	1.00
30_V	54_A	1.907	1.00
3_K	30_V	1.889	1.00
234_R	238_C	1.887	1.00
230_E	326_K	1.880	1.00
30_V	75_P	1.878	1.00
24_E	237_Y	1.843	1.00
258_K	261_D	1.837	1.00
306_S	310_R	1.821	1.00
7_T	80_H	1.814	1.00
5_L	75_P	1.753	1.00
106_Y	170_L	1.746	1.00
30_V	56_E	1.744	1.00
171_V	182_T	1.726	1.00
191_Y	323_G	1.725	1.00
67_A	111_A	1.717	1.00
6_I	18_V	1.698	1.00
17_L	233_A	1.670	1.00
17_L	79_M	1.637	1.00
24_E	241_T	1.636	1.00
61_C	99_E	1.630	1.00
237_Y	241_T	1.618	1.00
228_Y	326_K	1.613	1.00
165_A	169_H	1.566	1.00
28_A	54_A	1.555	1.00
103_V	106_Y	1.543	1.00
17_L	81_L	1.540	1.00
206_L	210_A	1.538	1.00
98_I	166_S	1.533	1.00
308_I	312_L	1.532	1.00
254_H	309_A	1.528	1.00
20_Y	23_N	1.526	1.00
4_I	27_D	1.513	1.00
150_E	307_K	1.511	1.00
105_T	167_S	1.507	1.00
265_T	269_L	1.485	1.00
63_R	110_E	1.481	1.00
154_Y	165_A	1.467	1.00
106_Y	110_E	1.465	1.00
35_L	55_F	1.464	1.00
325_R	329_Q	1.461	1.00
113_R	178_Y	1.444	1.00
95_A	99_E	1.439	1.00
133_S	137_V	1.434	1.00
207_N	212_K	1.389	1.00
20_Y	233_A	1.389	1.00
76_D	127_F	1.389	1.00
19_R	194_Y	1.386	1.00
305_A	309_A	1.368	1.00
67_A	115_Y	1.368	1.00
13_I	190_N	1.365	1.00
187_C	232_H	1.365	1.00
63_R	107_T	1.362	1.00
228_Y	323_G	1.356	1.00
63_R	67_A	1.346	1.00
78_V	112_A	1.341	1.00
65_E	68_R	1.341	1.00
318_E	326_K	1.330	1.00
18_V	31_V	1.323	1.00
79_M	236_L	1.322	1.00
128_R	183_L	1.312	1.00
227_L	232_H	1.298	1.00
172_R	184_I	1.293	1.00
238_C	242_T	1.285	1.00
261_D	264_E	1.284	1.00
223_I	256_E	1.278	1.00
185_T	236_L	1.263	1.00
71_T	115_Y	1.253	1.00
81_L	132_I	1.244	1.00
188_S	303_I	1.237	1.00
9_G	18_V	1.233	1.00
169_H	172_R	1.229	1.00
131_H	167_S	1.224	1.00
322_S	326_K	1.220	1.00
307_K	311_E	1.218	1.00
20_Y	230_E	1.216	1.00
322_S	325_R	1.215	1.00
132_I	187_C	1.214	1.00
229_V	233_A	1.211	1.00
160_Y	164_K	1.200	1.00
148_F	152_T	1.200	1.00
24_E	27_D	1.192	1.00
110_E	113_R	1.190	1.00
235_A	308_I	1.190	1.00
70_F	75_P	1.187	1.00
80_H	105_T	1.175	1.00
247_E	311_E	1.164	1.00
149_T	304_D	1.164	1.00
225_D	254_H	1.159	1.00
181_P	245_V	1.151	1.00
110_E	114_A	1.150	1.00
138_Y	250_N	1.150	1.00
5_L	32_V	1.148	1.00
21_I	237_Y	1.144	1.00
27_D	241_T	1.144	1.00
89_R	93_G	1.143	1.00
101_N	163_S	1.142	1.00
175_L	182_T	1.137	1.00
16_A	230_E	1.135	1.00
267_C	273_L	1.134	1.00
213_S	289_T	1.133	1.00
221_Q	260_L	1.122	1.00
31_V	53_F	1.120	1.00
162_A	166_S	1.118	1.00
170_L	173_A	1.115	1.00
131_H	184_I	1.101	1.00
151_T	307_K	1.099	1.00
112_A	129_F	1.098	1.00
221_Q	258_K	1.097	1.00
4_I	21_I	1.094	1.00
257_R	320_F	1.094	1.00
143_S	149_T	1.092	1.00
252_G	303_I	1.091	1.00
215_P	289_T	1.073	1.00
172_R	248_T	1.069	1.00
108_L	129_F	1.066	1.00
264_E	267_C	1.066	1.00
60_I	104_G	1.058	1.00
257_R	261_D	1.047	1.00
111_A	115_Y	1.046	1.00
223_I	300_R	1.043	1.00
111_A	114_A	1.041	1.00
109_L	174_W	1.035	1.00
186_N	248_T	1.033	1.00
131_H	171_V	1.032	1.00
15_S	194_Y	1.026	1.00
256_E	300_R	1.020	1.00
270_L	328_V	1.018	1.00
183_L	239_V	1.014	1.00
321_E	325_R	1.013	1.00
70_F	78_V	1.009	1.00
60_I	82_A	1.008	1.00
22_I	53_F	1.007	1.00
12_F	192_G	1.006	1.00
10_A	33_D	1.006	1.00
305_A	316_P	1.006	1.00
68_R	71_T	1.000	1.00
84_E	100_T	0.999	1.00
256_E	302_A	0.998	1.00
4_I	77_C	0.997	1.00
172_R	182_T	0.993	1.00
22_I	52_R	0.991	1.00
172_R	176_R	0.983	1.00
234_R	318_E	0.981	1.00
228_Y	318_E	0.978	1.00
238_C	241_T	0.977	1.00
269_L	321_E	0.975	1.00
67_A	71_T	0.975	1.00
40_N	43_S	0.975	1.00
234_R	314_W	0.974	1.00
269_L	328_V	0.971	1.00
19_R	23_N	0.967	1.00
32_V	65_E	0.965	1.00
103_V	107_T	0.964	1.00
16_A	229_V	0.963	1.00
109_L	171_V	0.958	1.00
56_E	69_V	0.957	1.00
129_F	171_V	0.954	1.00
238_C	312_L	0.954	1.00
109_L	129_F	0.953	1.00
81_L	236_L	0.943	1.00
235_A	314_W	0.939	1.00
173_A	177_T	0.938	1.00
184_I	248_T	0.937	1.00
98_I	102_I	0.935	1.00
230_E	318_E	0.928	1.00
231_D	253_G	0.918	1.00
326_K	329_Q	0.906	1.00
329_Q	332_L	0.904	1.00
64_A	68_R	0.903	1.00
100_T	104_G	0.899	1.00
66_L	111_A	0.896	1.00
249_Y	307_K	0.890	1.00
143_S	152_T	0.890	1.00
168_D	186_N	0.890	1.00
65_E	69_V	0.889	1.00
223_I	258_K	0.888	1.00
64_A	67_A	0.884	1.00
186_N	250_N	0.883	1.00
32_V	69_V	0.880	1.00
41_L	57_K	0.879	1.00
102_I	166_S	0.876	1.00
4_I	79_M	0.876	1.00
36_T	57_K	0.874	1.00
203_L	206_L	0.874	1.00
252_G	305_A	0.872	1.00
32_V	66_L	0.871	1.00
3_K	76_D	0.870	1.00
113_R	180_L	0.868	1.00
185_T	251_I	0.868	1.00
70_F	115_Y	0.864	1.00
190_N	232_H	0.863	1.00
77_C	128_R	0.860	1.00
260_L	290_F	0.858	1.00
70_F	111_A	0.854	1.00
16_A	19_R	0.849	1.00
318_E	322_S	0.848	1.00
12_F	229_V	0.847	1.00
7_T	108_L	0.846	1.00
98_I	103_V	0.842	1.00
203_L	207_N	0.836	1.00
3_K	75_P	0.835	1.00
267_C	274_A	0.834	1.00
269_L	329_Q	0.833	1.00
63_R	114_A	0.833	1.00
166_S	169_H	0.832	1.00
228_Y	231_D	0.832	1.00
35_L	57_K	0.830	1.00
306_S	309_A	0.827	1.00
234_R	237_Y	0.826	1.00
267_C	272_E	0.825	1.00
174_W	178_Y	0.824	1.00
239_V	312_L	0.821	1.00
135_D	303_I	0.814	1.00
128_R	243_G	0.813	1.00
34_K	59_D	0.807	1.00
107_T	111_A	0.805	1.00
22_I	29_V	0.804	1.00
254_H	305_A	0.804	1.00
7_T	82_A	0.802	1.00
287_L	290_F	0.801	1.00
220_G	260_L	0.798	1.00
238_C	314_W	0.797	1.00
105_T	171_V	0.797	1.00
190_N	227_L	0.797	1.00
115_Y	125_S	0.796	1.00
33_D	55_F	0.792	1.00
135_D	188_S	0.791	1.00
80_H	108_L	0.789	1.00
269_L	324_M	0.786	1.00
96_A	99_E	0.785	1.00
84_E	96_A	0.783	1.00
107_T	110_E	0.782	1.00
61_C	100_T	0.777	1.00
169_H	173_A	0.775	1.00
191_Y	228_Y	0.773	1.00
30_V	74_Q	0.770	1.00
4_I	240_A	0.770	1.00
130_H	185_T	0.768	1.00
94_P	162_A	0.768	1.00
18_V	29_V	0.767	1.00
199_K	202_P	0.764	1.00
147_F	304_D	0.761	1.00
133_S	168_D	0.761	1.00
193_P	326_K	0.760	1.00
97_F	163_S	0.753	1.00
208_A	267_C	0.753	1.00
39_G	43_S	0.751	1.00
17_L	21_I	0.747	1.00
261_D	265_T	0.746	1.00
264_E	268_E	0.744	1.00
200_L	204_M	0.738	1.00
87_V	90_S	0.736	1.00
70_F	112_A	0.735	1.00
213_S	287_L	0.735	1.00
16_A	233_A	0.735	1.00
105_T	109_L	0.734	1.00
98_I	163_S	0.731	1.00
239_V	308_I	0.730	1.00
251_I	308_I	0.729	1.00
96_A	100_T	0.726	1.00
162_A	169_H	0.726	1.00
17_L	236_L	0.725	1.00
255_N	319_T	0.723	1.00
231_D	234_R	0.721	1.00
115_Y	126_A	0.720	1.00
265_T	320_F	0.716	1.00
137_V	154_Y	0.715	1.00
16_A	20_Y	0.710	1.00
257_R	262_V	0.707	1.00
126_A	181_P	0.706	1.00
110_E	174_W	0.704	1.00
318_E	323_G	0.704	1.00
15_S	19_R	0.701	1.00
193_P	228_Y	0.698	1.00
112_A	126_A	0.697	1.00
166_S	170_L	0.693	1.00
13_I	232_H	0.692	1.00
78_V	129_F	0.692	1.00
286_D	290_F	0.690	1.00
150_E	308_I	0.689	1.00
262_V	320_F	0.686	1.00
84_E	97_F	0.685	1.00
215_P	291_V	0.684	1.00
127_F	181_P	0.679	1.00
113_R	174_W	0.678	1.00
109_L	170_L	0.677	1.00
142_H	152_T	0.677	1.00
50_S	53_F	0.676	1.00
289_T	292_A	0.675	1.00
205_I	209_L	0.672	1.00
244_K	311_E	0.670	1.00
238_C	313_G	0.667	1.00
231_D	317_Q	0.663	1.00
223_I	302_A	0.662	1.00
91_I	159_P	0.661	1.00
21_I	240_A	0.659	1.00
188_S	252_G	0.658	1.00
62_D	66_L	0.657	1.00
149_T	306_S	0.656	1.00
206_L	209_L	0.653	1.00
158_S	161_S	0.652	1.00
307_K	310_R	0.650	1.00
137_V	168_D	0.649	1.00
147_F	302_A	0.648	1.00
142_H	146_D	0.648	1.00
146_D	152_T	0.647	1.00
16_A	194_Y	0.647	1.00
112_A	125_S	0.645	1.00
185_T	235_A	0.642	1.00
77_C	127_F	0.639	1.00
104_G	107_T	0.637	1.00
182_T	246_G	0.637	1.00
327_T	330_W	0.637	1.00
27_D	76_D	0.635	1.00
130_H	236_L	0.633	1.00
39_G	42_M	0.628	1.00
162_A	173_A	0.626	1.00
78_V	108_L	0.622	1.00
167_S	171_V	0.621	1.00
233_A	237_Y	0.621	1.00
17_L	237_Y	0.621	1.00
150_E	250_N	0.616	1.00
3_K	27_D	0.615	1.00
294_R	297_H	0.614	1.00
27_D	77_C	0.614	1.00
211_G	272_E	0.613	1.00
139_G	155_A	0.612	1.00
59_D	62_D	0.612	1.00
187_C	190_N	0.611	1.00
154_Y	169_H	0.610	1.00
24_E	234_R	0.609	1.00
257_R	265_T	0.606	1.00
271_E	274_A	0.604	1.00
88_D	91_I	0.604	1.00
90_S	97_F	0.601	1.00
290_F	293_D	0.600	1.00
328_V	332_L	0.599	1.00
184_I	246_G	0.599	1.00
66_L	107_T	0.597	1.00
6_I	21_I	0.595	1.00
267_C	270_L	0.593	1.00
56_E	65_E	0.592	1.00
5_L	69_V	0.591	1.00
189_N	224_R	0.589	1.00
24_E	238_C	0.588	1.00
19_R	230_E	0.587	1.00
207_N	215_P	0.585	1.00
10_A	35_L	0.585	1.00
141_L	148_F	0.584	1.00
113_R	179_G	0.584	1.00
288_I	291_V	0.584	1.00
5_L	70_F	0.584	1.00
159_P	162_A	0.583	1.00
202_P	206_L	0.582	1.00
63_R	111_A	0.581	1.00
18_V	22_I	0.580	1.00
265_T	324_M	0.580	1.00
83_A	101_N	0.578	1.00
98_I	162_A	0.578	1.00
31_V	55_F	0.576	1.00
156_P	161_S	0.576	1.00
71_T	74_Q	0.576	1.00
25_T	52_R	0.575	1.00
317_Q	322_S	0.572	1.00
163_S	167_S	0.568	1.00
146_D	300_R	0.566	1.00
205_I	266_I	0.566	1.00
77_C	130_H	0.565	1.00
206_L	212_K	0.563	1.00
205_I	328_V	0.562	1.00
171_V	184_I	0.561	1.00
143_S	146_D	0.559	1.00
35_L	41_L	0.558	1.00
130_H	240_A	0.557	1.00
208_A	214_L	0.556	1.00
130_H	239_V	0.556	1.00
222_Q	259_N	0.551	1.00
105_T	131_H	0.548	1.00
112_A	115_Y	0.547	1.00
136_E	161_S	0.546	1.00
183_L	249_Y	0.545	1.00
298_D	301_Y	0.544	1.00
263_V	267_C	0.543	1.00
5_L	78_V	0.542	1.00
3_K	74_Q	0.542	1.00
156_P	165_A	0.538	1.00
193_P	230_E	0.536	1.00
80_H	129_F	0.536	1.00
28_A	52_R	0.535	1.00
112_A	127_F	0.532	1.00
237_Y	240_A	0.530	1.00
195_H	199_K	0.529	1.00
154_Y	248_T	0.529	1.00
201_I	262_V	0.528	1.00
308_I	316_P	0.527	1.00
181_P	244_K	0.525	1.00
266_I	324_M	0.524	1.00
172_R	175_L	0.524	1.00
292_A	295_P	0.524	1.00
291_V	294_R	0.520	1.00
134_T	137_V	0.520	1.00
137_V	186_N	0.519	1.00
25_T	29_V	0.518	1.00
35_L	39_G	0.518	1.00
22_I	25_T	0.517	1.00
198_E	201_I	0.514	1.00
95_A	106_Y	0.513	1.00
261_D	321_E	0.513	1.00
159_P	163_S	0.513	1.00
170_L	174_W	0.511	1.00
194_Y	330_W	0.510	1.00
134_T	164_K	0.510	1.00
30_V	69_V	0.508	1.00
173_A	176_R	0.507	1.00
94_P	159_P	0.505	1.00
249_Y	308_I	0.505	1.00
205_I	270_L	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
1sb8A	2	0.8845	100	0.218	Contact Map
3rufA	2	0.8704	100	0.223	Contact Map
1orrA	3	0.8732	100	0.227	Contact Map
1rpnA	4	0.893	100	0.228	Contact Map
2hunA	2	0.9239	100	0.229	Contact Map
1rkxA	3	0.9183	100	0.233	Contact Map
1oc2A	2	0.9268	100	0.236	Contact Map
2z1mA	4	0.9268	100	0.237	Contact Map
2q1sA	2	0.8761	100	0.238	Contact Map
4egbA	5	0.8732	100	0.239	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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