YHFK - BACSU - GREMLIN Contacts

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YHFK - Uncharacterized sugar epimerase YhfK

UniProt:	O07609	Sequences: MKVFLIGANGQIGQRLVSLFQDNPDHSIRAMVRKEEQKASLEAAGAEAVLANLEGSPEEIAAAAKGCDAIIFTAGSGGSTGYDKTLLVDLDGAAKAIEAAAIAGIKRFIMVSALQAHNRENWNEALKPYYVAKHYADKILEASGLTYTIIRPGGLRNEPGTGTVSAAKDLERGFISRDDVAKTVIASLDEKNTENRAFDLTEGDTPIAEALKKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	214 (196)
Sequences:	62750 (42188)
Seq/√Len:	3013.5

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

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_A	30_A	3.199	1.00
19_L	182_K	2.505	1.00
87_L	91_D	2.472	1.00
31_M	51_A	2.351	1.00
69_A	188_L	2.299	1.00
72_F	110_M	2.257	1.00
183_T	200_L	2.249	1.00
107_R	146_T	2.215	1.00
55_G	59_E	2.062	1.00
19_L	185_I	2.026	1.00
4_F	67_C	1.978	1.00
61_A	102_I	1.965	1.00
111_V	184_V	1.960	1.00
29_R	67_C	1.928	1.00
51_A	59_E	1.928	1.00
29_R	47_E	1.871	1.00
19_L	24_P	1.849	1.00
152_P	184_V	1.811	1.00
81_G	84_K	1.805	1.00
5_L	17_V	1.799	1.00
29_R	49_V	1.791	1.00
9_N	32_V	1.756	1.00
93_A	136_A	1.742	1.00
140_L	147_Y	1.735	1.00
6_I	72_F	1.725	1.00
57_P	98_E	1.695	1.00
83_D	87_L	1.672	1.00
71_I	188_L	1.654	1.00
94_A	98_E	1.612	1.00
110_M	140_L	1.612	1.00
54_E	87_L	1.600	1.00
61_A	99_A	1.587	1.00
27_S	47_E	1.586	1.00
134_H	138_K	1.550	1.00
16_L	181_A	1.522	1.00
182_K	186_A	1.521	1.00
12_I	155_L	1.516	1.00
59_E	62_A	1.493	1.00
19_L	22_D	1.493	1.00
107_R	148_T	1.484	1.00
73_T	111_V	1.484	1.00
57_P	95_K	1.481	1.00
117_H	199_D	1.475	1.00
94_A	139_I	1.471	1.00
24_P	189_D	1.464	1.00
89_D	132_A	1.459	1.00
150_I	187_S	1.459	1.00
57_P	61_A	1.437	1.00
112_S	116_A	1.428	1.00
91_D	94_A	1.416	1.00
3_V	20_F	1.413	1.00
68_D	106_K	1.411	1.00
17_V	30_A	1.411	1.00
101_A	143_S	1.368	1.00
19_L	181_A	1.359	1.00
24_P	185_I	1.353	1.00
156_R	176_S	1.353	1.00
150_I	184_V	1.342	1.00
16_L	73_T	1.331	1.00
53_L	92_G	1.330	1.00
86_L	135_Y	1.330	1.00
90_L	135_Y	1.323	1.00
185_I	189_D	1.322	1.00
30_A	46_A	1.289	1.00
137_D	151_R	1.282	1.00
34_K	37_Q	1.282	1.00
16_L	71_I	1.280	1.00
15_R	178_D	1.276	1.00
3_V	26_H	1.276	1.00
112_S	137_D	1.274	1.00
3_V	69_A	1.270	1.00
111_V	152_P	1.255	1.00
34_K	48_A	1.218	1.00
151_R	197_A	1.215	1.00
173_G	203_G	1.203	1.00
61_A	103_A	1.201	1.00
186_A	190_E	1.198	1.00
19_L	178_D	1.198	1.00
70_I	100_A	1.184	1.00
21_Q	46_A	1.159	1.00
53_L	74_A	1.159	1.00
61_A	65_K	1.157	1.00
35_E	50_L	1.147	1.00
60_I	99_A	1.147	1.00
96_A	108_F	1.147	1.00
26_H	189_D	1.140	1.00
88_V	92_G	1.139	1.00
8_A	17_V	1.130	1.00
152_P	180_V	1.130	1.00
129_Y	133_K	1.125	1.00
131_V	135_Y	1.124	1.00
98_E	101_A	1.119	1.00
62_A	65_K	1.118	1.00
18_S	159_P	1.117	1.00
177_R	181_A	1.115	1.00
97_I	108_F	1.115	1.00
55_G	58_E	1.115	1.00
31_M	63_A	1.109	1.00
4_F	31_M	1.107	1.00
18_S	22_D	1.107	1.00
11_Q	157_N	1.104	1.00
176_S	179_D	1.100	1.00
91_D	95_K	1.098	1.00
71_I	184_V	1.092	1.00
100_A	108_F	1.092	1.00
70_I	96_A	1.092	1.00
109_I	150_I	1.078	1.00
20_F	185_I	1.069	1.00
86_L	90_L	1.068	1.00
72_F	93_A	1.044	1.00
100_A	105_I	1.043	1.00
6_I	96_A	1.043	1.00
21_Q	45_G	1.040	1.00
76_S	88_V	1.026	1.00
110_M	136_A	1.021	1.00
175_I	180_V	1.016	1.00
73_T	184_V	1.014	1.00
16_L	184_V	1.013	1.00
64_A	70_I	1.009	1.00
27_S	45_G	0.999	1.00
179_D	202_E	0.990	1.00
155_L	175_I	0.990	1.00
148_T	187_S	0.987	1.00
14_Q	18_S	0.986	1.00
58_E	62_A	0.973	1.00
146_T	194_E	0.972	1.00
65_K	103_A	0.969	1.00
155_L	180_V	0.968	1.00
83_D	91_D	0.961	1.00
15_R	18_S	0.955	1.00
110_M	149_I	0.955	1.00
58_E	61_A	0.954	1.00
151_R	199_D	0.951	1.00
35_E	39_A	0.941	1.00
20_F	188_L	0.941	1.00
98_E	102_I	0.936	1.00
64_A	99_A	0.934	1.00
95_K	98_E	0.928	1.00
11_Q	177_R	0.916	1.00
29_R	66_G	0.909	1.00
32_V	48_A	0.899	1.00
26_H	68_D	0.888	1.00
85_T	132_A	0.886	1.00
64_A	67_C	0.886	1.00
86_L	91_D	0.881	1.00
49_V	63_A	0.881	1.00
60_I	95_K	0.877	1.00
114_L	153_G	0.877	1.00
100_A	103_A	0.875	1.00
57_P	102_I	0.865	1.00
97_I	139_I	0.857	1.00
31_M	60_I	0.850	1.00
15_R	19_L	0.849	1.00
33_R	52_N	0.846	1.00
70_I	108_F	0.842	1.00
101_A	145_L	0.834	1.00
115_Q	130_Y	0.832	1.00
59_E	63_A	0.832	1.00
136_A	140_L	0.831	1.00
76_S	85_T	0.831	1.00
99_A	103_A	0.828	1.00
14_Q	159_P	0.819	1.00
182_K	185_I	0.814	1.00
108_F	140_L	0.813	1.00
17_V	28_I	0.811	1.00
6_I	74_A	0.807	1.00
64_A	100_A	0.797	1.00
31_M	59_E	0.797	1.00
106_K	146_T	0.796	1.00
34_K	50_L	0.794	1.00
76_S	84_K	0.794	1.00
21_Q	28_I	0.793	1.00
64_A	103_A	0.791	1.00
69_A	107_R	0.789	1.00
72_F	96_A	0.788	1.00
16_L	20_F	0.785	1.00
15_R	177_R	0.779	1.00
10_G	158_E	0.772	1.00
86_L	131_V	0.771	1.00
181_A	185_I	0.769	1.00
54_E	88_V	0.767	1.00
26_H	69_A	0.764	1.00
140_L	149_I	0.764	1.00
99_A	102_I	0.764	1.00
64_A	96_A	0.759	1.00
97_I	140_L	0.759	1.00
153_G	201_T	0.755	1.00
116_A	137_D	0.748	1.00
165_S	168_K	0.748	1.00
93_A	97_I	0.734	1.00
4_F	51_A	0.730	1.00
101_A	144_G	0.723	1.00
66_G	103_A	0.721	1.00
42_E	46_A	0.719	1.00
135_Y	138_K	0.719	1.00
15_R	181_A	0.718	1.00
55_G	60_I	0.709	1.00
93_A	140_L	0.707	1.00
152_P	155_L	0.704	1.00
113_A	116_A	0.702	1.00
52_N	55_G	0.700	1.00
84_K	87_L	0.698	1.00
116_A	151_R	0.696	1.00
95_K	99_A	0.686	1.00
149_I	197_A	0.686	1.00
34_K	39_A	0.673	1.00
5_L	20_F	0.673	1.00
186_A	189_D	0.668	1.00
3_V	71_I	0.667	1.00
51_A	63_A	0.665	1.00
173_G	202_E	0.664	1.00
147_Y	195_N	0.662	1.00
131_V	138_K	0.660	1.00
37_Q	40_S	0.660	1.00
10_G	14_Q	0.657	1.00
158_E	176_S	0.657	1.00
43_A	46_A	0.655	1.00
135_Y	139_I	0.651	1.00
30_A	48_A	0.648	1.00
4_F	64_A	0.645	1.00
12_I	180_V	0.644	1.00
86_L	132_A	0.640	1.00
3_V	188_L	0.640	1.00
89_D	133_K	0.638	1.00
191_K	194_E	0.634	1.00
98_E	139_I	0.634	1.00
84_K	88_V	0.632	1.00
107_R	191_K	0.630	1.00
20_F	26_H	0.628	1.00
37_Q	41_L	0.627	1.00
4_F	63_A	0.624	1.00
38_K	48_A	0.624	1.00
109_I	187_S	0.621	1.00
57_P	99_A	0.614	1.00
150_I	200_L	0.609	1.00
116_A	134_H	0.607	1.00
78_G	84_K	0.606	1.00
125_A	134_H	0.604	1.00
149_I	195_N	0.603	1.00
154_G	174_F	0.603	1.00
125_A	130_Y	0.597	1.00
18_S	178_D	0.591	1.00
54_E	84_K	0.589	1.00
82_Y	128_P	0.589	1.00
60_I	96_A	0.589	1.00
92_G	95_K	0.587	1.00
150_I	183_T	0.585	1.00
128_P	132_A	0.585	1.00
79_S	128_P	0.579	1.00
73_T	152_P	0.578	1.00
109_I	188_L	0.577	1.00
36_E	39_A	0.575	1.00
31_M	49_V	0.574	1.00
179_D	182_K	0.573	1.00
119_R	126_L	0.573	1.00
51_A	60_I	0.572	1.00
21_Q	43_A	0.569	1.00
75_G	89_D	0.568	1.00
137_D	149_I	0.560	1.00
117_H	151_R	0.558	1.00
69_A	109_I	0.554	1.00
112_S	149_I	0.553	1.00
76_S	89_D	0.550	1.00
153_G	173_G	0.548	1.00
9_N	34_K	0.546	1.00
127_K	130_Y	0.546	1.00
60_I	64_A	0.546	1.00
185_I	188_L	0.543	1.00
112_S	151_R	0.539	1.00
42_E	45_G	0.536	1.00
17_V	21_Q	0.535	1.00
38_K	41_L	0.535	1.00
29_R	63_A	0.534	1.00
128_P	131_V	0.534	1.00
78_G	81_G	0.531	1.00
82_Y	131_V	0.531	1.00
141_E	144_G	0.529	1.00
133_K	136_A	0.529	1.00
69_A	106_K	0.523	1.00
32_V	50_L	0.521	1.00
129_Y	132_A	0.520	1.00
164_V	167_A	0.516	1.00
85_T	128_P	0.511	1.00
63_A	67_C	0.511	1.00
71_I	111_V	0.511	1.00
131_V	134_H	0.507	1.00
93_A	110_M	0.507	1.00
89_D	129_Y	0.506	1.00
148_T	191_K	0.505	1.00
34_K	38_K	0.503	1.00
27_S	68_D	0.502	1.00
57_P	60_I	0.501	1.00
100_A	104_G	0.501	1.00
11_Q	15_R	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
2pzmA	2	0.9813	100	0.218	Contact Map
2x4gA	2	0.9346	100	0.223	Contact Map
1sb8A	2	0.9813	100	0.224	Contact Map
2c20A	2	0.9907	100	0.23	Contact Map
2c5aA	2	0.9813	100	0.231	Contact Map
3rufA	2	0.9907	100	0.232	Contact Map
3slgA	4	0.986	100	0.233	Contact Map
2bllA	2	0.9907	100	0.237	Contact Map
1gy8A	2	0.9907	100	0.237	Contact Map
1i24A	4	0.986	100	0.237	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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