RMLB1 - ECOLI - GREMLIN Contacts

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RMLB1 - dTDP-glucose 4,6-dehydratase 1

UniProt:	P37759	Sequences: MKILVTGGAGFIGSAVVRHIINNTQDSVVNVDKLTYAGNRESLADVSDSERYVFEHADICDAPAMARIFAQHQPDAVMHLAAESHVDRSITGPAAFIETNIVGTYVLLEAARNYWSALDSDKKNSFRFHHISTDEVYGDLPHPDEVNNTEELPLFTETTAYAPSSPYSASKASSDHLVRAWKRTYGLPTIVTNCSNNYGPYHFPEKLIPLVILNALEGKALPIYGKGDQIRDWLYVEDHARALYTVVTEGKAGETYNIGGHNEKKNIDVVLTICDLLDEIVPKEKSYREQITYVADRPGHDRRYAIDAEKIGRALGWKPQETFESGIRKTVEWYLSNTKWVDNVKSGAYQSWIEQNYEGRQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12412
Length:	361 (298)
Sequences:	49725 (34621)
Seq/√Len:	2005.5

ECOLI - RMLB1 RMLB2 GALE GM4D YBJS FCL HLDD RMLD YFCH YEEZ QOR2 ARNA YBJT
BACSU - YTCB GALE YFNG RMLB YFHF SPSK YTBQ YWNB YHFK YESF YHEG EPSC
HALSA - Q9HSV1 Q9HSU9 Q9HRD1 Q9HSE7 Q9HML4 Q9HS50 Q9HSQ3 Q9HNV3 Q9HPF1 Q9HR86
SULSO - Q97VN5 Q7LXE8 Q7LXG5 Q97XJ9 Q980W1 Q97XG1 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
8_G	30_N	3.296	1.00
272_T	324_E	3.071	1.00
242_A	258_I	2.815	1.00
19_H	241_R	2.743	1.00
254_E	310_K	2.597	1.00
2_K	27_S	2.553	1.00
98_E	102_V	2.542	1.00
76_A	247_V	2.473	1.00
66_A	113_N	2.417	1.00
92_G	95_A	2.404	1.00
256_Y	314_A	2.313	1.00
276_L	328_R	2.286	1.00
131_I	243_L	2.271	1.00
19_H	244_Y	2.229	1.00
275_D	324_E	2.157	1.00
19_H	23_N	2.151	1.00
127_R	188_P	2.143	1.00
241_R	320_Q	2.118	1.00
312_G	318_K	2.106	1.00
31_V	57_A	2.105	1.00
322_T	325_S	2.082	1.00
194_C	243_L	2.023	1.00
79_H	130_H	2.016	1.00
61_D	64_A	2.001	1.00
57_A	64_A	1.994	1.00
78_M	247_V	1.968	1.00
6_T	79_H	1.968	1.00
267_I	271_L	1.943	1.00
29_V	53_V	1.919	1.00
241_R	245_T	1.908	1.00
29_V	74_P	1.898	1.00
192_T	246_V	1.898	1.00
237_E	329_K	1.896	1.00
272_T	275_D	1.885	1.00
265_K	268_D	1.846	1.00
309_E	313_R	1.825	1.00
198_Y	326_G	1.824	1.00
4_L	74_P	1.813	1.00
23_N	244_Y	1.763	1.00
5_V	17_V	1.756	1.00
178_V	189_T	1.744	1.00
29_V	55_E	1.737	1.00
23_N	248_T	1.719	1.00
16_V	240_A	1.715	1.00
16_V	78_M	1.699	1.00
213_L	217_E	1.695	1.00
66_A	110_A	1.692	1.00
156_T	159_T	1.682	1.00
105_Y	177_L	1.681	1.00
60_C	98_E	1.670	1.00
235_Y	329_K	1.634	1.00
244_Y	248_T	1.583	1.00
27_S	53_V	1.581	1.00
19_H	22_N	1.567	1.00
172_A	176_H	1.560	1.00
16_V	80_L	1.555	1.00
132_S	136_V	1.541	1.00
62_A	109_E	1.541	1.00
102_V	105_Y	1.535	1.00
311_I	315_L	1.535	1.00
261_H	312_G	1.530	1.00
34_L	54_F	1.527	1.00
97_I	173_S	1.503	1.00
328_R	332_E	1.502	1.00
104_T	174_S	1.492	1.00
94_A	98_E	1.492	1.00
245_T	249_E	1.482	1.00
105_Y	109_E	1.453	1.00
272_T	276_L	1.447	1.00
18_R	201_Y	1.441	1.00
235_Y	326_G	1.429	1.00
194_C	239_H	1.428	1.00
161_Y	172_A	1.415	1.00
75_D	126_F	1.407	1.00
19_H	240_A	1.386	1.00
17_V	30_N	1.381	1.00
214_N	219_K	1.365	1.00
12_I	197_N	1.361	1.00
127_R	190_I	1.350	1.00
62_A	106_V	1.343	1.00
308_A	312_G	1.342	1.00
66_A	114_Y	1.341	1.00
321_E	329_K	1.340	1.00
78_M	243_L	1.335	1.00
195_S	306_I	1.335	1.00
268_D	271_L	1.317	1.00
77_V	111_A	1.313	1.00
64_A	67_R	1.310	1.00
192_T	243_L	1.308	1.00
131_I	194_C	1.288	1.00
3_I	26_D	1.286	1.00
130_H	174_S	1.280	1.00
2_K	29_V	1.277	1.00
80_L	131_I	1.273	1.00
234_L	239_H	1.270	1.00
167_Y	171_K	1.267	1.00
179_R	191_V	1.265	1.00
137_Y	257_N	1.259	1.00
62_A	66_A	1.258	1.00
236_V	240_A	1.244	1.00
325_S	328_R	1.239	1.00
230_I	263_E	1.237	1.00
8_G	17_V	1.226	1.00
23_N	26_D	1.220	1.00
19_H	237_E	1.215	1.00
100_N	170_S	1.215	1.00
220_A	292_T	1.208	1.00
232_D	261_H	1.207	1.00
70_A	114_Y	1.202	1.00
79_H	104_T	1.201	1.00
325_S	329_K	1.198	1.00
69_F	74_P	1.195	1.00
157_E	310_K	1.191	1.00
176_H	179_R	1.187	1.00
26_D	248_T	1.186	1.00
15_A	237_E	1.184	1.00
242_A	311_I	1.183	1.00
310_K	314_A	1.179	1.00
228_D	267_I	1.179	1.00
109_E	113_N	1.179	1.00
112_R	185_Y	1.168	1.00
188_P	252_A	1.158	1.00
109_E	112_R	1.157	1.00
20_I	244_Y	1.150	1.00
264_K	323_F	1.148	1.00
254_E	314_A	1.146	1.00
151_E	156_T	1.133	1.00
4_L	31_V	1.131	1.00
88_R	92_G	1.130	1.00
11_F	199_G	1.127	1.00
30_N	52_Y	1.126	1.00
177_L	180_A	1.125	1.00
111_A	128_F	1.124	1.00
108_L	181_W	1.117	1.00
259_G	306_I	1.110	1.00
182_K	189_T	1.108	1.00
21_I	52_Y	1.106	1.00
222_P	292_T	1.098	1.00
169_A	173_S	1.097	1.00
107_L	128_F	1.092	1.00
9_A	32_D	1.086	1.00
193_N	255_T	1.079	1.00
228_D	265_K	1.079	1.00
271_L	274_C	1.070	1.00
59_I	103_G	1.052	1.00
130_H	191_V	1.049	1.00
263_E	303_R	1.049	1.00
308_A	319_P	1.042	1.00
14_S	201_Y	1.041	1.00
38_G	42_S	1.039	1.00
179_R	255_T	1.036	1.00
235_Y	321_E	1.032	1.00
67_R	70_A	1.029	1.00
130_H	178_V	1.018	1.00
55_E	68_I	1.018	1.00
156_T	307_D	1.018	1.00
69_F	77_V	1.017	1.00
39_N	42_S	1.012	1.00
18_R	22_N	1.010	1.00
324_E	328_R	1.008	1.00
264_K	268_D	1.007	1.00
66_A	70_A	1.006	1.00
83_E	99_T	1.004	1.00
3_I	20_I	1.004	1.00
277_L	331_V	1.004	1.00
241_R	317_W	1.003	1.00
179_R	189_T	0.999	1.00
31_V	64_A	0.995	1.00
274_C	288_R	0.995	1.00
110_A	114_Y	0.993	1.00
21_I	51_R	0.991	1.00
276_L	331_V	0.985	1.00
190_I	246_V	0.983	1.00
179_R	183_R	0.980	1.00
108_L	128_F	0.976	1.00
241_R	321_E	0.974	1.00
80_L	243_L	0.972	1.00
245_T	315_L	0.969	1.00
59_I	81_A	0.966	1.00
110_A	113_N	0.965	1.00
63_P	67_R	0.963	1.00
230_I	303_R	0.962	1.00
263_E	305_A	0.957	1.00
128_F	178_V	0.956	1.00
259_G	308_A	0.944	1.00
245_T	248_T	0.943	1.00
276_L	324_E	0.943	1.00
256_Y	310_K	0.939	1.00
193_N	257_N	0.939	1.00
64_A	68_I	0.938	1.00
191_V	255_T	0.933	1.00
237_E	321_E	0.932	1.00
238_D	260_G	0.932	1.00
180_A	184_T	0.928	1.00
329_K	332_E	0.924	1.00
63_P	66_A	0.918	1.00
111_A	125_S	0.916	1.00
15_A	236_V	0.916	1.00
175_D	193_N	0.913	1.00
267_I	293_Y	0.909	1.00
151_E	159_T	0.908	1.00
230_I	265_K	0.907	1.00
112_R	187_L	0.905	1.00
242_A	317_W	0.904	1.00
31_V	68_I	0.898	1.00
3_I	76_A	0.898	1.00
99_T	103_G	0.897	1.00
220_A	290_Q	0.894	1.00
102_V	106_V	0.893	1.00
97_I	101_I	0.892	1.00
108_L	178_V	0.892	1.00
235_Y	238_D	0.887	1.00
6_T	107_L	0.884	1.00
31_V	65_M	0.880	1.00
197_N	239_H	0.876	1.00
2_K	75_D	0.875	1.00
65_M	110_A	0.873	1.00
332_E	335_L	0.871	1.00
35_T	56_H	0.869	1.00
115_W	125_S	0.868	1.00
192_T	258_I	0.868	1.00
40_R	56_H	0.863	1.00
62_A	113_N	0.863	1.00
290_Q	293_Y	0.859	1.00
69_F	114_Y	0.857	1.00
274_C	279_E	0.853	1.00
11_F	236_V	0.845	1.00
2_K	74_P	0.843	1.00
69_F	110_A	0.841	1.00
158_T	310_K	0.838	1.00
15_A	18_R	0.836	1.00
127_R	250_G	0.836	1.00
101_I	173_S	0.833	1.00
6_T	81_A	0.832	1.00
38_G	41_E	0.830	1.00
76_A	127_R	0.830	1.00
276_L	327_I	0.825	1.00
173_S	176_H	0.824	1.00
97_I	102_V	0.821	1.00
106_V	110_A	0.820	1.00
34_L	56_H	0.820	1.00
132_S	175_D	0.820	1.00
198_Y	235_Y	0.819	1.00
207_L	211_V	0.819	1.00
200_P	329_K	0.815	1.00
3_I	78_M	0.815	1.00
33_K	58_D	0.814	1.00
197_N	234_L	0.813	1.00
96_F	170_S	0.812	1.00
227_G	267_I	0.810	1.00
134_D	195_S	0.810	1.00
246_V	315_L	0.809	1.00
210_L	213_L	0.809	1.00
93_P	169_A	0.809	1.00
245_T	317_W	0.807	1.00
261_H	308_A	0.805	1.00
321_E	325_S	0.803	1.00
21_I	28_V	0.803	1.00
276_L	332_E	0.802	1.00
241_R	244_Y	0.800	1.00
60_C	99_T	0.799	1.00
309_E	312_G	0.799	1.00
129_H	192_T	0.795	1.00
29_V	73_Q	0.792	1.00
104_T	178_V	0.787	1.00
106_V	109_E	0.787	1.00
32_D	54_F	0.786	1.00
134_D	306_I	0.779	1.00
210_L	214_N	0.777	1.00
17_V	28_V	0.771	1.00
95_A	98_E	0.769	1.00
95_A	99_T	0.768	1.00
83_E	95_A	0.765	1.00
206_K	209_P	0.763	1.00
271_L	275_D	0.762	1.00
169_A	176_H	0.759	1.00
97_I	170_S	0.758	1.00
215_A	274_C	0.755	1.00
264_K	269_V	0.755	1.00
272_T	323_F	0.748	1.00
3_I	247_V	0.747	1.00
69_F	111_A	0.745	1.00
151_E	154_L	0.744	1.00
292_T	295_A	0.741	1.00
176_H	180_A	0.738	1.00
15_A	240_A	0.737	1.00
16_V	20_I	0.736	1.00
79_H	107_L	0.735	1.00
246_V	311_I	0.725	1.00
109_E	181_W	0.724	1.00
15_A	19_H	0.718	1.00
268_D	272_T	0.716	1.00
258_I	311_I	0.715	1.00
16_V	243_L	0.710	1.00
181_W	185_Y	0.706	1.00
262_N	322_T	0.705	1.00
12_I	239_H	0.703	1.00
126_F	188_P	0.700	1.00
83_E	96_F	0.692	1.00
26_D	75_D	0.686	1.00
136_V	175_D	0.685	1.00
289_E	293_Y	0.683	1.00
321_E	326_G	0.681	1.00
251_K	314_A	0.679	1.00
189_T	253_G	0.678	1.00
14_S	18_R	0.676	1.00
173_S	177_L	0.675	1.00
245_T	316_G	0.674	1.00
103_G	106_V	0.672	1.00
238_D	241_R	0.672	1.00
136_V	161_Y	0.672	1.00
49_S	52_Y	0.672	1.00
2_K	26_D	0.669	1.00
86_V	89_S	0.668	1.00
222_P	294_V	0.666	1.00
156_T	309_E	0.666	1.00
269_V	323_F	0.665	1.00
20_I	247_V	0.664	1.00
141_P	159_T	0.663	1.00
138_G	162_A	0.661	1.00
195_S	259_G	0.658	1.00
61_D	65_M	0.657	1.00
200_P	235_Y	0.656	1.00
112_R	181_W	0.654	1.00
104_T	108_L	0.650	1.00
108_L	177_L	0.647	1.00
212_I	216_L	0.646	1.00
218_G	279_E	0.646	1.00
297_R	300_H	0.644	1.00
238_D	320_Q	0.643	1.00
77_V	107_L	0.642	1.00
274_C	277_L	0.639	1.00
129_H	243_L	0.637	1.00
194_C	197_N	0.635	1.00
77_V	128_F	0.634	1.00
213_L	216_L	0.634	1.00
165_S	168_S	0.632	1.00
212_I	331_V	0.632	1.00
58_D	61_D	0.632	1.00
76_A	126_F	0.631	1.00
90_I	166_P	0.631	1.00
192_T	242_A	0.630	1.00
169_A	180_A	0.627	1.00
310_K	313_R	0.621	1.00
34_L	40_R	0.620	1.00
212_I	273_I	0.619	1.00
178_V	191_V	0.617	1.00
30_N	54_F	0.617	1.00
331_V	335_L	0.616	1.00
111_A	114_Y	0.615	1.00
15_A	201_Y	0.614	1.00
23_N	241_R	0.611	1.00
240_A	244_Y	0.611	1.00
112_R	186_G	0.608	1.00
4_L	68_I	0.608	1.00
174_S	178_V	0.603	1.00
230_I	305_A	0.602	1.00
135_E	168_S	0.601	1.00
272_T	327_I	0.597	1.00
16_V	244_Y	0.597	1.00
196_N	231_R	0.596	1.00
330_T	333_W	0.596	1.00
76_A	129_H	0.596	1.00
229_Q	266_N	0.595	1.00
97_I	169_A	0.592	1.00
188_P	250_G	0.591	1.00
70_A	73_Q	0.588	1.00
270_V	274_C	0.586	1.00
104_T	130_H	0.586	1.00
191_V	253_G	0.586	1.00
24_T	51_R	0.583	1.00
161_Y	176_H	0.583	1.00
4_L	69_F	0.582	1.00
65_M	106_V	0.581	1.00
9_A	34_L	0.581	1.00
290_Q	295_A	0.581	1.00
292_T	296_D	0.579	1.00
293_Y	296_D	0.578	1.00
215_A	221_L	0.578	1.00
26_D	76_A	0.577	1.00
23_N	245_T	0.575	1.00
68_I	74_P	0.574	1.00
17_V	21_I	0.573	1.00
129_H	247_V	0.573	1.00
289_E	292_T	0.570	1.00
18_R	237_E	0.570	1.00
295_A	298_P	0.567	1.00
82_A	100_N	0.566	1.00
294_V	297_R	0.564	1.00
27_S	51_R	0.562	1.00
89_S	96_F	0.561	1.00
200_P	237_E	0.558	1.00
4_L	77_V	0.556	1.00
170_S	174_S	0.556	1.00
5_V	20_I	0.555	1.00
157_E	311_I	0.555	1.00
29_V	68_I	0.553	1.00
133_T	136_V	0.553	1.00
264_K	272_T	0.552	1.00
268_D	324_E	0.551	1.00
279_E	289_E	0.550	1.00
177_L	181_W	0.549	1.00
114_Y	125_S	0.547	1.00
320_Q	325_S	0.546	1.00
215_A	273_I	0.544	1.00
87_D	90_I	0.542	1.00
55_E	64_A	0.542	1.00
244_Y	247_V	0.541	1.00
202_H	206_K	0.539	1.00
80_L	194_C	0.539	1.00
190_I	256_Y	0.539	1.00
129_H	246_V	0.538	1.00
273_I	327_I	0.538	1.00
226_K	293_Y	0.538	1.00
214_N	222_P	0.536	1.00
201_Y	333_W	0.535	1.00
133_T	171_K	0.534	1.00
79_H	128_F	0.534	1.00
311_I	319_P	0.532	1.00
166_P	169_A	0.530	1.00
153_P	156_T	0.530	1.00
4_L	57_A	0.529	1.00
114_Y	126_F	0.529	1.00
180_A	183_R	0.528	1.00
139_D	302_R	0.526	1.00
291_I	294_V	0.526	1.00
163_P	168_S	0.525	1.00
21_I	24_T	0.525	1.00
208_I	269_V	0.516	1.00
62_A	110_A	0.513	1.00
239_H	258_I	0.513	1.00
152_L	303_R	0.510	1.00
251_K	254_E	0.509	1.00
188_P	251_K	0.509	1.00
93_P	166_P	0.507	1.00
34_L	38_G	0.506	1.00
290_Q	294_V	0.505	1.00
141_P	152_L	0.505	1.00
111_A	187_L	0.504	1.00
216_L	335_L	0.504	1.00
38_G	43_L	0.503	1.00
131_I	192_T	0.503	1.00
132_S	191_V	0.503	1.00
136_V	193_N	0.502	1.00
9_A	30_N	0.501	1.00
199_G	236_V	0.500	1.00
209_P	213_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
1kewA	2	0.9972	100	0.221	Contact Map
2hunA	2	0.9086	100	0.235	Contact Map
1sb8A	2	0.867	100	0.237	Contact Map
3rufA	2	0.8532	100	0.24	Contact Map
1rpnA	4	0.8753	100	0.248	Contact Map
1r6dA	2	0.8781	100	0.254	Contact Map
4egbA	5	0.8532	100	0.256	Contact Map
1orrA	3	0.8809	100	0.256	Contact Map
1oc2A	2	0.9252	100	0.256	Contact Map
1rkxA	3	0.8947	100	0.257	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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