HLDD - ECOLI - GREMLIN Contacts

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HLDD - ADP-L-glycero-D-manno-heptose-6-epimerase

UniProt:	P67910	Sequences: MIIVTGGAGFIGSNIVKALNDKGITDILVVDNLKDGTKFVNLVDLNIADYMDKEDFLIQIMAGEEFGDVEAIFHEGACSSTTEWDGKYMMDNNYQYSKELLHYCLEREIPFLYASSAATYGGRTSDFIESREYEKPLNVYGYSKFLFDEYVRQILPEANSQIVGFRYFNVYGPREGHKGSMASVAFHLNTQLNNGESPKLFEGSENFKRDFVYVGDVADVNLWFLENGVSGIFNLGTGRAESFQAVADATLAYHKKGQIEYIPFPDKLKGRYQAFTQADLTNLRAAGYDKPFKTVAEGVTEYMAWLNRDA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10838
Length:	310 (284)
Sequences:	58864 (40996)
Seq/√Len:	2432.7

ECOLI - HLDD GM4D RMLB2 GALE RMLB1 YBJS FCL YFCH RMLD YEEZ QOR2 ARNA YBJT YRAR
BACSU - RMLB YFNG YTCB GALE SPSK YFHF YTBQ YESF YWNB YHFK YHEG EPSC
HALSA - Q9HSU9 Q9HSV1 Q9HRD1 Q9HSE7 Q9HML4 Q9HS50 Q9HSQ3 Q9HPF1 Q9HNV3 Q9HR86
SULSO - Q980W1 Q7LXG5 Q97VN5 Q97XJ9 Q97XG1 Q7LXE8 Q97UM3 Q7LX44 Q7LXE6 Q97XF9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_G	29_V	3.321	1.00
18_A	219_D	2.831	1.00
220_V	235_L	2.785	1.00
231_G	282_N	2.703	1.00
249_A	296_A	2.690	1.00
63_G	106_E	2.650	1.00
294_T	297_E	2.625	1.00
91_D	95_Q	2.411	1.00
71_A	225_L	2.402	1.00
252_A	296_A	2.381	1.00
284_R	290_K	2.303	1.00
114_A	221_N	2.276	1.00
281_T	285_A	2.256	1.00
30_V	54_E	2.217	1.00
5_T	74_H	2.198	1.00
73_F	225_L	2.150	1.00
58_I	61_M	2.142	1.00
74_H	113_Y	2.130	1.00
18_A	22_K	2.129	1.00
85_D	88_Y	2.115	1.00
54_E	61_M	2.089	1.00
171_Y	298_G	2.079	1.00
219_D	292_F	2.074	1.00
22_K	226_E	2.071	1.00
4_V	16_V	2.042	1.00
3_I	69_V	2.005	1.00
18_A	222_L	1.987	1.00
28_L	50_Y	1.895	1.00
244_Q	248_D	1.894	1.00
219_D	223_W	1.881	1.00
167_Y	221_N	1.840	1.00
129_E	132_E	1.837	1.00
28_L	69_V	1.833	1.00
253_Y	300_T	1.821	1.00
249_A	252_A	1.812	1.00
215_G	301_E	1.801	1.00
151_V	162_I	1.780	1.00
26_D	50_Y	1.769	1.00
242_S	245_A	1.757	1.00
165_F	224_F	1.732	1.00
190_T	194_N	1.727	1.00
15_I	218_A	1.724	1.00
66_F	69_V	1.719	1.00
15_I	73_F	1.693	1.00
57_L	91_D	1.676	1.00
115_S	119_T	1.655	1.00
33_L	51_M	1.651	1.00
238_G	284_R	1.642	1.00
28_L	52_D	1.629	1.00
59_Q	102_H	1.591	1.00
283_L	287_G	1.580	1.00
213_Y	301_E	1.573	1.00
11_I	170_V	1.573	1.00
245_A	248_D	1.553	1.00
98_K	102_H	1.540	1.00
18_A	21_D	1.532	1.00
98_K	150_Y	1.530	1.00
63_G	103_Y	1.524	1.00
249_A	253_Y	1.522	1.00
15_I	75_E	1.517	1.00
120_Y	234_N	1.508	1.00
130_S	282_N	1.507	1.00
140_Y	144_K	1.504	1.00
74_H	97_S	1.493	1.00
73_F	221_N	1.471	1.00
165_F	221_N	1.470	1.00
95_Q	98_K	1.457	1.00
28_L	67_G	1.456	1.00
22_K	222_L	1.431	1.00
222_L	226_E	1.423	1.00
167_Y	217_V	1.422	1.00
90_M	146_L	1.420	1.00
100_L	111_F	1.418	1.00
17_K	174_R	1.412	1.00
101_L	154_I	1.409	1.00
16_V	29_V	1.409	1.00
213_Y	298_G	1.404	1.00
134_E	145_F	1.396	1.00
18_A	218_A	1.385	1.00
214_V	218_A	1.383	1.00
87_K	91_D	1.383	1.00
280_L	284_R	1.374	1.00
223_W	227_N	1.372	1.00
145_F	149_E	1.363	1.00
110_P	161_Q	1.362	1.00
168_F	278_A	1.351	1.00
191_Q	196_E	1.351	1.00
104_C	109_I	1.345	1.00
93_N	143_S	1.339	1.00
72_I	104_C	1.335	1.00
293_K	301_E	1.333	1.00
114_A	167_Y	1.331	1.00
75_E	114_A	1.330	1.00
59_Q	99_E	1.330	1.00
297_E	300_T	1.323	1.00
97_S	147_F	1.310	1.00
149_E	152_R	1.299	1.00
212_V	217_V	1.288	1.00
63_G	107_R	1.286	1.00
197_S	262_I	1.267	1.00
199_K	262_I	1.254	1.00
210_D	238_G	1.251	1.00
297_E	301_E	1.250	1.00
166_R	232_I	1.241	1.00
129_E	279_D	1.221	1.00
102_H	106_E	1.219	1.00
102_H	105_L	1.215	1.00
24_I	226_E	1.206	1.00
8_A	31_D	1.204	1.00
7_G	16_V	1.194	1.00
20_N	49_D	1.172	1.00
197_S	260_E	1.169	1.00
19_L	222_L	1.160	1.00
280_L	291_P	1.159	1.00
166_R	234_N	1.154	1.00
61_M	64_E	1.153	1.00
56_F	96_Y	1.144	1.00
59_Q	63_G	1.140	1.00
208_K	240_A	1.139	1.00
104_C	111_F	1.137	1.00
213_Y	293_K	1.130	1.00
14_N	215_G	1.128	1.00
152_R	232_I	1.124	1.00
56_F	76_G	1.106	1.00
241_E	295_V	1.106	1.00
142_Y	146_L	1.106	1.00
113_Y	147_F	1.102	1.00
105_L	158_A	1.096	1.00
148_D	166_R	1.095	1.00
251_L	258_Q	1.093	1.00
17_K	21_D	1.093	1.00
244_Q	263_P	1.086	1.00
152_R	164_G	1.085	1.00
13_S	174_R	1.081	1.00
29_V	49_D	1.081	1.00
10_F	172_G	1.081	1.00
131_R	282_N	1.072	1.00
103_Y	107_R	1.070	1.00
171_Y	213_Y	1.061	1.00
3_I	30_V	1.059	1.00
206_N	244_Q	1.058	1.00
30_V	62_A	1.052	1.00
75_E	221_N	1.052	1.00
216_D	237_T	1.043	1.00
113_Y	151_V	1.040	1.00
20_N	48_A	1.035	1.00
213_Y	216_D	1.033	1.00
128_I	132_E	1.032	1.00
155_L	162_I	1.031	1.00
269_K	272_Y	1.025	1.00
105_L	160_S	1.021	1.00
112_L	165_F	1.018	1.00
101_L	111_F	1.012	1.00
18_A	215_G	1.007	1.00
92_N	96_Y	1.006	1.00
62_A	103_Y	0.999	1.00
50_Y	67_G	0.997	1.00
170_V	217_V	0.988	1.00
219_D	289_D	0.984	1.00
152_R	162_I	0.982	1.00
253_Y	303_M	0.978	1.00
113_Y	164_G	0.978	1.00
101_L	150_Y	0.973	1.00
240_A	275_F	0.969	1.00
220_V	283_L	0.966	1.00
296_A	300_T	0.965	1.00
60_I	63_G	0.960	1.00
10_F	214_V	0.959	1.00
150_Y	153_Q	0.958	1.00
14_N	214_V	0.955	1.00
60_I	64_E	0.951	1.00
125_S	129_E	0.950	1.00
161_Q	229_V	0.949	1.00
261_Y	265_P	0.948	1.00
111_F	151_V	0.940	1.00
236_G	278_A	0.935	1.00
5_T	76_G	0.931	1.00
115_S	148_D	0.930	1.00
253_Y	299_V	0.929	1.00
248_D	251_L	0.929	1.00
99_E	102_H	0.924	1.00
78_C	92_N	0.921	1.00
152_R	156_P	0.919	1.00
233_F	282_N	0.917	1.00
153_Q	157_E	0.910	1.00
261_Y	264_F	0.907	1.00
219_D	293_K	0.906	1.00
170_V	212_V	0.905	1.00
15_I	19_L	0.899	1.00
102_H	154_I	0.899	1.00
32_N	55_D	0.893	1.00
208_K	242_S	0.889	1.00
254_H	303_M	0.885	1.00
224_F	287_G	0.884	1.00
235_L	283_L	0.882	1.00
206_N	242_S	0.879	1.00
90_M	94_Y	0.879	1.00
220_V	289_D	0.878	1.00
70_E	110_P	0.878	1.00
163_V	224_F	0.873	1.00
95_Q	99_E	0.871	1.00
58_I	62_A	0.871	1.00
240_A	277_Q	0.870	1.00
224_F	283_L	0.867	1.00
101_L	151_V	0.864	1.00
33_L	36_G	0.863	1.00
164_G	232_I	0.852	1.00
20_N	27_I	0.852	1.00
24_I	70_E	0.850	1.00
282_N	285_A	0.849	1.00
268_L	272_Y	0.845	1.00
16_V	27_I	0.844	1.00
238_G	280_L	0.842	1.00
236_G	280_L	0.842	1.00
223_W	287_G	0.834	1.00
184_V	188_L	0.832	1.00
30_V	61_M	0.832	1.00
28_L	68_D	0.830	1.00
89_M	143_S	0.829	1.00
293_K	297_E	0.828	1.00
205_E	244_Q	0.825	1.00
241_E	245_A	0.821	1.00
117_A	168_F	0.821	1.00
5_T	100_L	0.821	1.00
262_I	265_P	0.821	1.00
264_F	267_K	0.818	1.00
223_W	226_E	0.810	1.00
183_S	186_F	0.810	1.00
248_D	252_A	0.809	1.00
59_Q	106_E	0.807	1.00
241_E	246_V	0.806	1.00
270_G	273_Q	0.803	1.00
31_D	51_M	0.803	1.00
103_Y	106_E	0.791	1.00
105_L	159_N	0.787	1.00
293_K	298_G	0.786	1.00
3_I	54_E	0.785	1.00
253_Y	296_A	0.785	1.00
258_Q	261_Y	0.782	1.00
14_N	18_A	0.782	1.00
165_F	235_L	0.781	1.00
14_N	17_K	0.778	1.00
268_L	271_R	0.778	1.00
90_M	95_Q	0.776	1.00
146_L	149_E	0.776	1.00
11_I	217_V	0.775	1.00
96_Y	99_E	0.773	1.00
90_M	143_S	0.767	1.00
57_L	92_N	0.767	1.00
125_S	132_E	0.767	1.00
14_N	218_A	0.762	1.00
239_R	294_T	0.761	1.00
33_L	53_K	0.759	1.00
215_G	293_K	0.758	1.00
15_I	221_N	0.755	1.00
210_D	237_T	0.752	1.00
34_K	53_K	0.750	1.00
105_L	154_I	0.750	1.00
55_D	58_I	0.747	1.00
65_E	68_D	0.746	1.00
136_P	141_G	0.745	1.00
119_T	148_D	0.743	1.00
130_S	283_L	0.743	1.00
2_I	24_I	0.740	1.00
281_T	284_R	0.737	1.00
99_E	103_Y	0.735	1.00
94_Y	146_L	0.733	1.00
173_P	301_E	0.725	1.00
223_W	288_Y	0.723	1.00
147_F	151_V	0.723	1.00
97_S	151_V	0.722	1.00
19_L	225_L	0.721	1.00
219_D	222_L	0.719	1.00
97_S	101_L	0.715	1.00
119_T	134_E	0.703	1.00
154_I	160_S	0.702	1.00
3_I	72_I	0.701	1.00
78_C	89_M	0.701	1.00
72_I	100_L	0.701	1.00
190_T	193_N	0.700	1.00
130_S	234_N	0.697	1.00
24_I	27_I	0.697	1.00
74_H	100_L	0.696	1.00
187_H	190_T	0.692	1.00
88_Y	91_D	0.692	1.00
223_W	289_D	0.691	1.00
78_C	93_N	0.687	1.00
208_K	275_F	0.685	1.00
65_E	69_V	0.685	1.00
173_P	213_Y	0.684	1.00
62_A	99_E	0.681	1.00
149_E	153_Q	0.676	1.00
246_V	295_V	0.673	1.00
154_I	158_A	0.672	1.00
86_G	142_Y	0.670	1.00
189_N	193_N	0.668	1.00
218_A	222_L	0.668	1.00
249_A	295_V	0.666	1.00
13_S	17_K	0.666	1.00
123_R	128_I	0.663	1.00
189_N	303_M	0.657	1.00
165_F	220_V	0.656	1.00
23_G	48_A	0.656	1.00
192_L	251_L	0.655	1.00
168_F	236_G	0.653	1.00
78_C	88_Y	0.652	1.00
187_H	191_Q	0.652	1.00
239_R	296_A	0.650	1.00
169_N	209_R	0.649	1.00
88_Y	92_N	0.647	1.00
116_S	119_T	0.644	1.00
72_I	111_F	0.641	1.00
260_E	263_P	0.640	1.00
284_R	291_P	0.639	1.00
124_T	132_E	0.639	1.00
146_L	150_Y	0.637	1.00
192_L	198_P	0.636	1.00
162_I	230_S	0.636	1.00
245_A	249_A	0.634	1.00
77_A	93_N	0.633	1.00
150_Y	154_I	0.629	1.00
8_A	33_L	0.628	1.00
26_D	48_A	0.628	1.00
151_V	164_G	0.627	1.00
97_S	113_Y	0.626	1.00
52_D	67_G	0.625	1.00
142_Y	149_E	0.623	1.00
22_K	219_D	0.619	1.00
93_N	140_Y	0.619	1.00
33_L	38_K	0.615	1.00
117_A	278_A	0.612	1.00
84_W	89_M	0.611	1.00
126_D	132_E	0.611	1.00
118_A	141_G	0.610	1.00
251_L	259_I	0.607	1.00
116_S	144_K	0.607	1.00
257_G	260_E	0.606	1.00
189_N	250_T	0.606	1.00
207_F	243_F	0.604	1.00
195_G	198_P	0.603	1.00
112_L	225_L	0.598	1.00
86_G	139_V	0.597	1.00
258_Q	264_F	0.596	1.00
251_L	257_G	0.595	1.00
65_E	107_R	0.595	1.00
46_N	49_D	0.590	1.00
24_I	71_A	0.589	1.00
2_I	71_A	0.589	1.00
167_Y	170_V	0.589	1.00
19_L	73_F	0.588	1.00
138_N	141_G	0.587	1.00
28_L	65_E	0.585	1.00
258_Q	265_P	0.584	1.00
229_V	233_F	0.584	1.00
71_A	112_L	0.584	1.00
142_Y	153_Q	0.582	1.00
254_H	257_G	0.580	1.00
199_K	264_F	0.580	1.00
258_Q	262_I	0.579	1.00
38_K	53_K	0.576	1.00
249_A	299_V	0.575	1.00
233_F	283_L	0.574	1.00
143_S	147_F	0.574	1.00
216_D	219_D	0.573	1.00
222_L	225_L	0.572	1.00
217_V	235_L	0.572	1.00
289_D	292_F	0.572	1.00
22_K	223_W	0.572	1.00
19_L	24_I	0.568	1.00
136_P	145_F	0.566	1.00
14_N	174_R	0.564	1.00
4_V	29_V	0.564	1.00
90_M	142_Y	0.562	1.00
66_F	72_I	0.561	1.00
112_L	224_F	0.560	1.00
259_I	264_F	0.560	1.00
168_F	210_D	0.556	1.00
52_D	66_F	0.554	1.00
3_I	66_F	0.554	1.00
173_P	215_G	0.552	1.00
74_H	111_F	0.551	1.00
139_V	142_Y	0.549	1.00
175_E	183_S	0.545	1.00
247_A	251_L	0.543	1.00
101_L	105_L	0.541	1.00
84_W	139_V	0.539	1.00
71_A	110_P	0.539	1.00
75_E	167_Y	0.538	1.00
15_I	222_L	0.534	1.00
171_Y	237_T	0.534	1.00
134_E	149_E	0.534	1.00
127_F	279_D	0.532	1.00
139_V	143_S	0.532	1.00
4_V	19_L	0.531	1.00
154_I	159_N	0.530	1.00
114_A	165_F	0.530	1.00
119_T	166_R	0.529	1.00
17_K	215_G	0.529	1.00
134_E	232_I	0.527	1.00
73_F	222_L	0.526	1.00
250_T	303_M	0.524	1.00
10_F	14_N	0.524	1.00
230_S	233_F	0.523	1.00
208_K	277_Q	0.523	1.00
121_G	135_K	0.521	1.00
153_Q	156_P	0.521	1.00
210_D	240_A	0.519	1.00
259_I	263_P	0.516	1.00
112_L	221_N	0.516	1.00
209_R	243_F	0.514	1.00
4_V	7_G	0.513	1.00
251_L	254_H	0.513	1.00
268_L	273_Q	0.512	1.00
192_L	250_T	0.512	1.00
29_V	51_M	0.511	1.00
227_N	233_F	0.510	1.00
140_Y	143_S	0.509	1.00
28_L	66_F	0.508	1.00
163_V	233_F	0.506	1.00
260_E	265_P	0.505	1.00
129_E	281_T	0.504	1.00
52_D	61_M	0.502	1.00
204_S	273_Q	0.502	1.00
16_V	20_N	0.501	1.00
110_P	228_G	0.500	1.00
115_S	164_G	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	0.9839	100	0.184	Contact Map
3rufA	2	0.971	100	0.189	Contact Map
3sxpA	3	0.9516	100	0.2	Contact Map
1rpnA	4	0.9839	100	0.202	Contact Map
1rkxA	3	0.9516	100	0.204	Contact Map
3m2pA	2	0.929	100	0.206	Contact Map
1oc2A	2	0.9742	100	0.207	Contact Map
2hunA	2	0.9742	100	0.211	Contact Map
1n7hA	4	0.9839	100	0.211	Contact Map
3slgA	4	0.9645	100	0.211	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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