GM4D - ECOLI - GREMLIN Contacts

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GM4D - GDP-mannose 4,6-dehydratase

UniProt:	P0AC88	Sequences: MSKVALITGVTGQDGSYLAEFLLEKGYEVHGIKRRASSFNTERVDHIYQDPHTCNPKFHLHYGDLSDTSNLTRILREVQPDEVYNLGAMSHVAVSFESPEYTADVDAMGTLRLLEAIRFLGLEKKTRFYQASTSELYGLVQEIPQKETTPFYPRSPYAVAKLYAYWITVNYRESYGMYACNGILFNHESPRRGETFVTRKITRAIANIAQGLESCLYLGNMDSLRDWGHAKDYVKMQWMMLQQEQPEDFVIATGVQYSVRQFVEMAAAQLGIKLRFEGTGVEEKGIVVSVTGHDAPGVKPGDVIIAVDPRYFRPAEVETLLGDPTKAHEKLGWKPEITLREMVSEMVANDLEAAKKHSLLKSHGYDVAIALES	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11787
Length:	373 (300)
Sequences:	43871 (30575)
Seq/√Len:	1765.3

ECOLI - GM4D RMLB2 RMLB1 GALE YBJS HLDD FCL YFCH RMLD YEEZ QOR2 YBJT ARNA
BACSU - RMLB YFNG GALE YTCB SPSK YFHF YTBQ YESF EPSC YWNB YHFK YHEG
HALSA - Q9HSV1 Q9HSU9 Q9HRD1 Q9HML4 Q9HSE7 Q9HS50 Q9HNV3 Q9HSQ3 Q9HPF1 Q9HR86
SULSO - Q97VN5 Q980W1 Q7LXG5 Q97XJ9 Q97XG1 Q7LXE8 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
10_V	31_G	3.283	1.00
265_M	340_R	2.939	1.00
4_V	28_E	2.815	1.00
247_E	326_K	2.697	1.00
21_F	235_K	2.626	1.00
249_F	330_K	2.608	1.00
72_T	119_F	2.558	1.00
236_M	251_I	2.535	1.00
338_T	341_E	2.396	1.00
104_D	108_M	2.332	1.00
82_E	241_L	2.307	1.00
32_I	63_G	2.256	1.00
235_K	336_E	2.240	1.00
63_G	70_N	2.237	1.00
268_A	340_R	2.214	1.00
98_S	101_Y	2.188	1.00
21_F	25_K	2.146	1.00
328_H	334_K	2.136	1.00
188_E	342_M	2.121	1.00
127_R	178_Y	2.111	1.00
131_A	237_Q	2.078	1.00
184_L	237_Q	2.028	1.00
84_Y	241_L	2.027	1.00
269_Q	344_S	2.024	1.00
67_D	70_N	2.012	1.00
182_G	240_M	1.984	1.00
325_T	329_E	1.958	1.00
235_K	239_M	1.957	1.00
260_R	264_E	1.947	1.00
7_I	19_A	1.935	1.00
21_F	238_W	1.915	1.00
231_K	345_E	1.914	1.00
30_H	59_H	1.873	1.00
8_T	85_N	1.872	1.00
66_S	104_D	1.819	1.00
25_K	242_Q	1.802	1.00
258_S	261_Q	1.771	1.00
18_L	234_V	1.771	1.00
168_T	179_A	1.756	1.00
229_H	345_E	1.754	1.00
85_N	130_Q	1.742	1.00
4_V	30_H	1.738	1.00
30_H	78_V	1.706	1.00
30_H	61_H	1.703	1.00
18_L	84_Y	1.699	1.00
18_L	86_L	1.652	1.00
72_T	116_A	1.651	1.00
265_M	268_A	1.649	1.00
28_E	59_H	1.649	1.00
35_R	60_L	1.630	1.00
20_E	191_R	1.622	1.00
327_A	331_L	1.615	1.00
254_G	328_H	1.596	1.00
348_A	352_E	1.577	1.00
68_T	115_E	1.573	1.00
344_S	348_A	1.553	1.00
110_T	164_A	1.548	1.00
21_F	24_E	1.531	1.00
324_P	328_H	1.523	1.00
207_N	212_L	1.491	1.00
5_A	27_Y	1.488	1.00
111_L	167_I	1.449	1.00
206_A	210_Q	1.449	1.00
59_H	78_V	1.448	1.00
260_R	278_G	1.447	1.00
25_K	238_W	1.435	1.00
73_R	77_E	1.429	1.00
146_K	149_T	1.403	1.00
111_L	115_E	1.402	1.00
72_T	120_L	1.402	1.00
229_H	342_M	1.401	1.00
81_D	123_E	1.396	1.00
185_F	322_G	1.390	1.00
238_W	242_Q	1.384	1.00
162_L	166_W	1.372	1.00
14_D	187_H	1.369	1.00
132_S	136_L	1.369	1.00
70_N	73_R	1.367	1.00
84_Y	237_Q	1.359	1.00
108_M	111_L	1.355	1.00
68_T	112_R	1.350	1.00
261_Q	264_E	1.348	1.00
224_L	256_Q	1.348	1.00
130_Q	164_A	1.326	1.00
341_E	344_S	1.325	1.00
19_A	31_G	1.323	1.00
147_E	326_K	1.323	1.00
85_N	110_T	1.318	1.00
137_Y	250_V	1.305	1.00
182_G	237_Q	1.305	1.00
31_G	58_F	1.302	1.00
86_L	131_A	1.299	1.00
83_V	117_I	1.298	1.00
106_D	160_A	1.297	1.00
142_E	146_K	1.293	1.00
341_E	345_E	1.292	1.00
265_M	269_Q	1.291	1.00
151_F	162_L	1.288	1.00
247_E	330_K	1.283	1.00
27_Y	242_Q	1.277	1.00
117_I	128_F	1.274	1.00
21_F	234_V	1.272	1.00
100_E	104_D	1.269	1.00
157_Y	161_K	1.266	1.00
239_M	243_Q	1.266	1.00
115_E	118_R	1.264	1.00
127_R	180_C	1.261	1.00
68_T	72_T	1.256	1.00
226_D	254_G	1.251	1.00
230_A	234_V	1.250	1.00
10_V	19_A	1.244	1.00
113_L	128_F	1.241	1.00
6_L	78_V	1.224	1.00
337_I	345_E	1.223	1.00
228_G	233_Y	1.222	1.00
75_L	83_V	1.219	1.00
216_L	277_E	1.217	1.00
65_L	109_G	1.207	1.00
103_A	163_Y	1.203	1.00
172_R	179_A	1.198	1.00
114_L	171_Y	1.192	1.00
73_R	76_R	1.185	1.00
183_I	248_D	1.176	1.00
131_A	184_L	1.164	1.00
222_D	260_R	1.161	1.00
166_W	169_V	1.158	1.00
21_F	231_K	1.157	1.00
115_E	119_F	1.149	1.00
184_L	233_Y	1.147	1.00
118_R	175_Y	1.145	1.00
324_P	335_P	1.141	1.00
86_L	237_Q	1.133	1.00
222_D	258_S	1.122	1.00
11_T	33_K	1.117	1.00
257_Y	339_L	1.116	1.00
326_K	330_K	1.113	1.00
267_A	273_K	1.112	1.00
5_A	22_L	1.112	1.00
76_R	120_L	1.111	1.00
130_Q	181_N	1.109	1.00
32_I	71_L	1.104	1.00
142_E	149_T	1.099	1.00
16_S	191_R	1.084	1.00
229_H	337_I	1.083	1.00
264_E	267_A	1.083	1.00
169_V	181_N	1.078	1.00
20_E	24_E	1.078	1.00
269_Q	347_V	1.067	1.00
23_L	58_F	1.066	1.00
17_Y	231_K	1.061	1.00
128_F	168_T	1.059	1.00
165_Y	183_I	1.057	1.00
252_A	322_G	1.056	1.00
146_K	323_D	1.049	1.00
340_R	344_S	1.045	1.00
6_L	32_I	1.040	1.00
4_V	78_V	1.040	1.00
72_T	76_R	1.036	1.00
61_H	74_I	1.034	1.00
32_I	70_N	1.032	1.00
23_L	57_K	1.032	1.00
61_H	78_V	1.027	1.00
114_L	128_F	1.021	1.00
117_I	122_L	1.016	1.00
345_E	348_A	1.015	1.00
148_T	326_K	1.007	1.00
130_Q	168_T	1.007	1.00
183_I	250_V	1.002	1.00
200_K	204_A	0.997	1.00
270_L	347_V	0.996	1.00
71_L	116_A	0.994	1.00
180_C	240_M	0.989	1.00
118_R	177_M	0.989	1.00
61_H	77_E	0.986	1.00
199_R	202_T	0.985	1.00
32_I	74_I	0.978	1.00
70_N	74_I	0.976	1.00
65_L	87_G	0.976	1.00
236_M	327_A	0.971	1.00
231_K	337_I	0.967	1.00
68_T	119_F	0.964	1.00
89_M	105_V	0.963	1.00
235_K	337_I	0.959	1.00
75_L	120_L	0.959	1.00
348_A	351_L	0.958	1.00
4_V	81_D	0.951	1.00
214_S	275_R	0.950	1.00
105_V	109_G	0.949	1.00
22_L	238_W	0.946	1.00
116_A	120_L	0.944	1.00
188_E	229_H	0.934	1.00
190_P	345_E	0.932	1.00
169_V	248_D	0.930	1.00
240_M	327_A	0.930	1.00
169_V	173_E	0.929	1.00
239_M	242_Q	0.928	1.00
232_D	253_T	0.927	1.00
69_S	73_R	0.924	1.00
170_N	174_S	0.919	1.00
34_R	64_D	0.918	1.00
159_V	163_Y	0.916	1.00
123_E	178_Y	0.908	1.00
187_H	233_Y	0.907	1.00
69_S	72_T	0.907	1.00
129_Y	182_G	0.902	1.00
5_A	82_E	0.893	1.00
280_G	283_E	0.888	1.00
75_L	78_V	0.883	1.00
18_L	22_L	0.882	1.00
167_I	170_N	0.882	1.00
249_F	326_K	0.881	1.00
23_L	29_V	0.881	1.00
114_L	167_I	0.880	1.00
337_I	341_E	0.879	1.00
13_Q	230_A	0.878	1.00
203_R	206_A	0.877	1.00
132_S	165_Y	0.877	1.00
269_Q	343_V	0.871	1.00
108_M	112_R	0.868	1.00
35_R	62_Y	0.860	1.00
267_A	274_L	0.859	1.00
114_L	168_T	0.858	1.00
116_A	119_F	0.851	1.00
269_Q	340_R	0.846	1.00
325_T	328_H	0.845	1.00
107_A	163_Y	0.844	1.00
5_A	84_Y	0.842	1.00
251_I	327_A	0.841	1.00
74_I	78_V	0.833	1.00
4_V	27_Y	0.831	1.00
54_C	58_F	0.828	1.00
252_A	324_P	0.825	1.00
245_Q	330_K	0.823	1.00
94_V	98_S	0.821	1.00
221_M	260_R	0.817	1.00
30_H	77_E	0.816	1.00
75_L	116_A	0.814	1.00
181_N	248_D	0.813	1.00
75_L	117_I	0.811	1.00
103_A	107_A	0.809	1.00
257_Y	261_Q	0.809	1.00
35_R	38_S	0.807	1.00
200_K	203_R	0.807	1.00
187_H	228_G	0.806	1.00
171_Y	175_Y	0.806	1.00
66_S	105_V	0.802	1.00
19_A	29_V	0.799	1.00
110_T	168_T	0.799	1.00
145_Q	149_T	0.798	1.00
115_E	171_Y	0.796	1.00
33_K	60_L	0.795	1.00
17_Y	230_A	0.791	1.00
282_E	285_G	0.791	1.00
229_H	232_D	0.789	1.00
134_S	185_F	0.788	1.00
203_R	207_N	0.788	1.00
5_A	241_L	0.786	1.00
182_G	251_I	0.776	1.00
96_F	156_P	0.776	1.00
103_A	108_M	0.776	1.00
13_Q	189_S	0.769	1.00
8_T	113_L	0.766	1.00
85_N	113_L	0.765	1.00
264_E	268_A	0.760	1.00
236_M	333_W	0.760	1.00
262_F	339_L	0.760	1.00
235_K	333_W	0.759	1.00
8_T	87_G	0.757	1.00
18_L	237_Q	0.756	1.00
326_K	329_E	0.756	1.00
239_M	332_G	0.755	1.00
267_A	272_I	0.754	1.00
214_S	277_E	0.751	1.00
136_L	165_Y	0.744	1.00
257_Y	262_F	0.743	1.00
36_A	62_Y	0.741	1.00
269_Q	348_A	0.737	1.00
169_V	179_A	0.737	1.00
135_E	158_A	0.737	1.00
27_Y	81_D	0.735	1.00
118_R	171_Y	0.726	1.00
118_R	176_G	0.724	1.00
337_I	342_M	0.724	1.00
224_L	258_S	0.723	1.00
166_W	170_N	0.715	1.00
232_D	336_E	0.714	1.00
235_K	238_W	0.713	1.00
239_M	331_L	0.711	1.00
265_M	339_L	0.709	1.00
14_D	233_Y	0.707	1.00
206_A	209_A	0.707	1.00
201_I	204_A	0.706	1.00
136_L	151_F	0.705	1.00
164_A	168_T	0.705	1.00
26_G	29_V	0.704	1.00
101_Y	104_D	0.702	1.00
17_Y	234_V	0.701	1.00
6_L	83_V	0.700	1.00
159_V	166_W	0.700	1.00
256_Q	321_L	0.697	1.00
261_Q	265_M	0.697	1.00
22_L	241_L	0.696	1.00
255_V	338_T	0.695	1.00
44_V	47_I	0.694	1.00
83_V	128_F	0.692	1.00
110_T	114_L	0.691	1.00
194_E	197_V	0.690	1.00
134_S	322_G	0.688	1.00
182_G	236_M	0.686	1.00
83_V	113_L	0.685	1.00
101_Y	105_V	0.683	1.00
55_N	58_F	0.683	1.00
159_V	170_N	0.680	1.00
254_G	324_P	0.679	1.00
179_A	246_P	0.678	1.00
25_K	235_K	0.678	1.00
103_A	160_A	0.678	1.00
190_P	229_H	0.677	1.00
240_M	331_L	0.673	1.00
27_Y	82_E	0.668	1.00
17_Y	20_E	0.667	1.00
95_S	102_T	0.667	1.00
127_R	244_E	0.665	1.00
129_Y	241_L	0.665	1.00
59_H	77_E	0.663	1.00
346_M	349_N	0.661	1.00
184_L	187_H	0.661	1.00
17_Y	21_F	0.660	1.00
11_T	35_R	0.657	1.00
28_E	57_K	0.655	1.00
140_V	145_Q	0.654	1.00
112_R	116_A	0.652	1.00
20_E	46_H	0.651	1.00
112_R	115_E	0.651	1.00
226_D	253_T	0.651	1.00
89_M	102_T	0.650	1.00
129_Y	237_Q	0.650	1.00
151_F	166_W	0.646	1.00
102_T	160_A	0.645	1.00
20_E	231_K	0.643	1.00
109_G	112_R	0.643	1.00
147_E	327_A	0.643	1.00
7_I	22_L	0.642	1.00
239_M	333_W	0.642	1.00
223_S	259_V	0.639	1.00
234_V	238_W	0.637	1.00
153_P	158_A	0.635	1.00
267_A	276_F	0.634	1.00
88_A	106_D	0.633	1.00
67_D	71_L	0.630	1.00
202_T	206_A	0.629	1.00
163_Y	167_I	0.628	1.00
71_L	112_R	0.628	1.00
99_P	159_V	0.626	1.00
68_T	116_A	0.624	1.00
86_L	184_L	0.621	1.00
328_H	335_P	0.619	1.00
89_M	106_D	0.617	1.00
267_A	270_L	0.617	1.00
6_L	74_I	0.617	1.00
89_M	101_Y	0.617	1.00
347_V	351_L	0.616	1.00
163_Y	166_W	0.614	1.00
82_E	127_R	0.611	1.00
30_H	74_I	0.610	1.00
324_P	333_W	0.610	1.00
6_L	63_G	0.607	1.00
16_S	20_E	0.606	1.00
18_L	238_W	0.604	1.00
106_D	157_Y	0.601	1.00
178_Y	245_Q	0.601	1.00
17_Y	191_R	0.599	1.00
153_P	162_L	0.595	1.00
22_L	27_Y	0.595	1.00
204_A	207_N	0.591	1.00
168_T	181_N	0.590	1.00
144_P	323_D	0.590	1.00
257_Y	265_M	0.589	1.00
265_M	343_V	0.589	1.00
209_A	212_L	0.584	1.00
279_T	282_E	0.582	1.00
61_H	70_N	0.581	1.00
190_P	231_K	0.580	1.00
141_Q	149_T	0.579	1.00
103_A	159_V	0.579	1.00
211_G	272_I	0.577	1.00
266_A	343_V	0.574	1.00
63_G	74_I	0.573	1.00
274_L	277_E	0.569	1.00
65_L	105_V	0.568	1.00
22_L	84_Y	0.566	1.00
84_Y	238_W	0.564	1.00
74_I	77_E	0.564	1.00
285_G	288_V	0.564	1.00
185_F	252_A	0.563	1.00
133_T	161_K	0.563	1.00
186_N	225_R	0.560	1.00
19_A	58_F	0.559	1.00
100_E	111_L	0.559	1.00
232_D	235_K	0.558	1.00
82_E	123_E	0.555	1.00
75_L	113_L	0.555	1.00
54_C	57_K	0.555	1.00
147_E	250_V	0.554	1.00
167_I	171_Y	0.552	1.00
85_N	128_F	0.549	1.00
6_L	75_L	0.549	1.00
13_Q	17_Y	0.548	1.00
64_D	67_D	0.548	1.00
82_E	129_Y	0.547	1.00
117_I	120_L	0.545	1.00
31_G	60_L	0.544	1.00
151_F	248_D	0.544	1.00
202_T	205_I	0.542	1.00
133_T	136_L	0.541	1.00
266_A	347_V	0.541	1.00
155_S	158_A	0.540	1.00
327_A	330_K	0.538	1.00
170_N	173_E	0.538	1.00
23_L	55_N	0.538	1.00
261_Q	340_R	0.535	1.00
216_L	279_T	0.533	1.00
256_Q	319_T	0.533	1.00
255_V	340_R	0.531	1.00
279_T	284_K	0.530	1.00
273_K	276_F	0.529	1.00
143_I	149_T	0.528	1.00
214_S	217_Y	0.523	1.00
188_E	253_T	0.523	1.00
139_L	154_R	0.522	1.00
156_P	160_A	0.518	1.00
117_I	177_M	0.518	1.00
113_L	117_I	0.516	1.00
172_R	178_Y	0.515	1.00
249_F	327_A	0.515	1.00
193_G	197_V	0.515	1.00
284_K	287_V	0.513	1.00
172_R	246_P	0.513	1.00
33_K	37_S	0.511	1.00
275_R	278_G	0.511	1.00
243_Q	249_F	0.510	1.00
228_G	232_D	0.507	1.00
165_Y	181_N	0.506	1.00
186_N	227_W	0.504	1.00
284_K	288_V	0.504	1.00
82_E	242_Q	0.504	1.00
172_R	177_M	0.503	1.00
238_W	241_L	0.501	1.00
71_L	75_L	0.501	1.00
132_S	181_N	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
1db3A	2	0.8981	100	0.234	Contact Map
1rpnA	4	0.8579	100	0.246	Contact Map
1t2aA	4	0.9062	100	0.251	Contact Map
2z1mA	4	0.9169	100	0.254	Contact Map
1orrA	3	0.8338	100	0.267	Contact Map
3rufA	2	0.8499	100	0.267	Contact Map
1sb8A	2	0.8633	100	0.268	Contact Map
1n7hA	4	0.882	100	0.268	Contact Map
1rkxA	3	0.8686	100	0.272	Contact Map
2c20A	2	0.8365	100	0.274	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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