YWDF - BACSU - GREMLIN Contacts

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YWDF - Uncharacterized glycosyltransferase YwdF

UniProt:	P39614	Sequences: MKISIVIVTYNRIPALCELLESISRQTLMPYEIIIVNDAGESVVPVKALYPELPIAVINLEKNSGHVAARNAGVKEASGDCIMLCDDDDFFTPGHIEKMAKEIETADFVHSDAEIVSFEEKNGTRYPVSRKLFAYTADYEDMRVFSTYVPSGSMYRRFLHDEIGYFDADVHNYWDWDFYLRAAKDYRVKRVPCASVIYAFSDAGDNQSADLGAKRKQYLDRLSEKHGLGELPTKNFAVLLEEPEMKRREAKSEMVWDGEPVYSRLHRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	268 (219)
Sequences:	36250 (31256)
Seq/√Len:	2112.1

ECOLI - WCAA YIBD WCAE WBBL GTRB PGAC ARNC YAIP
BACSU - YWDF GGAA CGED EPSH YFNE GGAB EPSJ EPSE TUAG SPSA YDAM YKCC TAGF CSBB YKOT
HALSA - Q9HQP8 Q9HQP4 Q9HSC8 Q9HQP3 Q9HNK3 Q9HQQ6 Q9HR08 Q9HSB1
SULSO - Q7LXF7 Q97TZ0 Q97TY0 Q97X05 Q7LXG6 Q97YG5 Q97YN4 Q7LXY2 Q97W52 Q97YM4 Q97WK7 Q97UK7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
157_R	161_D	3.353	1.00
12_R	87_D	3.277	1.00
13_I	43_V	2.658	1.00
98_K	193_C	2.588	1.00
177_D	181_R	2.494	1.00
72_A	76_E	2.439	1.00
4_S	79_G	2.409	1.00
9_T	44_V	2.320	1.00
92_T	197_I	2.269	1.00
81_C	103_I	2.248	1.00
75_K	165_Y	2.215	1.00
37_N	59_N	2.187	1.00
27_T	97_E	2.185	1.00
32_E	56_A	2.162	1.00
36_V	73_G	2.090	1.00
18_E	199_A	2.085	1.00
64_S	68_A	2.071	1.00
45_P	48_A	2.030	1.00
7_I	33_I	2.012	1.00
17_C	21_E	2.009	1.00
6_V	73_G	1.995	1.00
91_F	95_H	1.914	1.00
11_N	41_E	1.903	1.00
3_I	100_A	1.877	1.00
70_R	86_D	1.860	1.00
45_P	59_N	1.843	1.00
102_E	191_V	1.837	1.00
68_A	168_A	1.834	1.00
4_S	32_E	1.820	1.00
99_M	154_M	1.820	1.00
83_M	154_M	1.808	1.00
18_E	90_F	1.808	1.00
58_I	76_E	1.806	1.00
102_E	189_K	1.768	1.00
60_L	72_A	1.743	1.00
28_L	100_A	1.743	1.00
95_H	99_M	1.727	1.00
17_C	50_Y	1.703	1.00
7_I	19_L	1.691	1.00
66_H	70_R	1.682	1.00
94_G	98_K	1.675	1.00
13_I	46_V	1.666	1.00
90_F	197_I	1.656	1.00
37_N	40_G	1.641	1.00
35_I	47_K	1.632	1.00
83_M	95_H	1.610	1.00
56_A	76_E	1.609	1.00
67_V	174_W	1.591	1.00
45_P	57_V	1.583	1.00
72_A	75_K	1.583	1.00
17_C	49_L	1.557	1.00
21_E	25_R	1.550	1.00
85_C	91_F	1.539	1.00
17_C	46_V	1.534	1.00
81_C	154_M	1.532	1.00
58_I	72_A	1.526	1.00
103_I	154_M	1.509	1.00
9_T	35_I	1.501	1.00
83_M	96_I	1.487	1.00
10_Y	63_N	1.478	1.00
21_E	50_Y	1.465	1.00
167_D	177_D	1.458	1.00
32_E	79_G	1.452	1.00
98_K	101_K	1.445	1.00
28_L	31_Y	1.416	1.00
48_A	59_N	1.415	1.00
9_T	12_R	1.403	1.00
97_E	101_K	1.388	1.00
162_E	185_D	1.386	1.00
3_I	96_I	1.382	1.00
158_F	162_E	1.348	1.00
61_E	64_S	1.343	1.00
70_R	84_L	1.337	1.00
22_S	91_F	1.330	1.00
153_S	179_Y	1.321	1.00
4_S	77_A	1.315	1.00
82_I	157_R	1.314	1.00
80_D	156_R	1.301	1.00
74_V	160_H	1.281	1.00
106_A	189_K	1.267	1.00
66_H	174_W	1.262	1.00
61_E	72_A	1.255	1.00
11_N	40_G	1.255	1.00
12_R	15_A	1.252	1.00
46_V	50_Y	1.250	1.00
90_F	199_A	1.246	1.00
20_L	33_I	1.236	1.00
159_L	182_A	1.228	1.00
107_D	187_R	1.227	1.00
38_D	63_N	1.225	1.00
77_A	157_R	1.223	1.00
74_V	84_L	1.202	1.00
9_T	87_D	1.177	1.00
36_V	69_A	1.166	1.00
19_L	85_C	1.165	1.00
83_M	91_F	1.156	1.00
100_A	104_E	1.139	1.00
32_E	78_S	1.128	1.00
158_F	161_D	1.124	1.00
37_N	45_P	1.118	1.00
94_G	97_E	1.109	1.00
102_E	105_T	1.090	1.00
101_K	105_T	1.090	1.00
3_I	154_M	1.084	1.00
4_S	34_I	1.081	1.00
116_V	197_I	1.078	1.00
25_R	93_P	1.070	1.00
106_A	109_V	1.061	1.00
8_V	69_A	1.057	1.00
110_H	188_V	1.055	1.00
201_S	204_G	1.039	1.00
60_L	69_A	1.036	1.00
33_I	55_I	1.031	1.00
156_R	159_L	1.031	1.00
22_S	90_F	1.030	1.00
98_K	191_V	1.027	1.00
60_L	64_S	1.014	1.00
107_D	156_R	1.002	1.00
70_R	174_W	0.996	1.00
23_I	85_C	0.992	1.00
160_H	178_F	0.983	1.00
74_V	82_I	0.977	1.00
21_E	24_S	0.975	1.00
114_E	197_I	0.969	1.00
66_H	205_D	0.966	1.00
109_V	112_D	0.966	1.00
27_T	94_G	0.961	1.00
47_K	57_V	0.957	1.00
68_A	72_A	0.953	1.00
99_M	111_S	0.952	1.00
56_A	78_S	0.950	1.00
46_V	49_L	0.934	1.00
81_C	100_A	0.934	1.00
95_H	195_S	0.918	1.00
24_S	50_Y	0.915	1.00
99_M	103_I	0.915	1.00
61_E	68_A	0.898	1.00
66_H	150_P	0.893	1.00
38_D	69_A	0.892	1.00
117_S	121_K	0.890	1.00
20_L	50_Y	0.889	1.00
43_V	46_V	0.884	1.00
98_K	102_E	0.881	1.00
24_S	55_I	0.880	1.00
66_H	86_D	0.874	1.00
5_I	83_M	0.869	1.00
67_V	71_N	0.868	1.00
151_S	196_V	0.862	1.00
15_A	199_A	0.854	1.00
163_I	185_D	0.852	1.00
5_I	23_I	0.845	1.00
150_P	166_F	0.845	1.00
19_L	22_S	0.839	1.00
38_D	65_G	0.838	1.00
9_T	47_K	0.838	1.00
31_Y	96_I	0.834	1.00
37_N	60_L	0.828	1.00
23_I	33_I	0.828	1.00
9_T	16_L	0.822	1.00
106_A	111_S	0.813	1.00
57_V	60_L	0.807	1.00
36_V	72_A	0.802	1.00
27_T	93_P	0.795	1.00
155_Y	179_Y	0.795	1.00
163_I	182_A	0.794	1.00
159_L	186_Y	0.792	1.00
150_P	153_S	0.792	1.00
84_L	166_F	0.786	1.00
218_Y	221_R	0.786	1.00
12_R	201_S	0.782	1.00
20_L	35_I	0.781	1.00
38_D	64_S	0.775	1.00
66_H	69_A	0.770	1.00
159_L	163_I	0.767	1.00
74_V	77_A	0.763	1.00
5_I	96_I	0.762	1.00
71_N	165_Y	0.762	1.00
64_S	69_A	0.760	1.00
214_K	218_Y	0.760	1.00
92_T	95_H	0.759	1.00
7_I	23_I	0.753	1.00
23_I	91_F	0.751	1.00
178_F	182_A	0.743	1.00
18_E	21_E	0.737	1.00
165_Y	178_F	0.736	1.00
34_I	73_G	0.733	1.00
28_L	96_I	0.733	1.00
216_K	220_D	0.728	1.00
28_L	97_E	0.727	1.00
69_A	72_A	0.725	1.00
24_S	53_L	0.719	1.00
213_A	217_Q	0.718	1.00
159_L	162_E	0.718	1.00
217_Q	221_R	0.717	1.00
13_I	17_C	0.713	1.00
141_D	144_V	0.713	1.00
92_T	195_S	0.711	1.00
48_A	57_V	0.708	1.00
103_I	111_S	0.706	1.00
108_F	189_K	0.692	1.00
34_I	56_A	0.688	1.00
8_V	87_D	0.688	1.00
114_E	194_A	0.686	1.00
113_A	152_G	0.685	1.00
71_N	168_A	0.685	1.00
112_D	190_R	0.685	1.00
24_S	54_P	0.683	1.00
80_D	158_F	0.683	1.00
16_L	87_D	0.683	1.00
204_G	207_Q	0.681	1.00
20_L	24_S	0.680	1.00
109_V	113_A	0.678	1.00
122_N	125_R	0.678	1.00
100_A	154_M	0.677	1.00
64_S	72_A	0.674	1.00
155_Y	178_F	0.671	1.00
77_A	82_I	0.670	1.00
118_F	122_N	0.669	1.00
83_M	152_G	0.669	1.00
160_H	165_Y	0.667	1.00
101_K	104_E	0.666	1.00
15_A	201_S	0.664	1.00
5_I	31_Y	0.662	1.00
95_H	152_G	0.661	1.00
34_I	76_E	0.660	1.00
89_D	198_Y	0.657	1.00
8_V	38_D	0.656	1.00
19_L	23_I	0.656	1.00
16_L	46_V	0.655	1.00
71_N	166_F	0.654	1.00
103_I	156_R	0.650	1.00
110_H	113_A	0.649	1.00
91_F	96_I	0.648	1.00
142_M	145_F	0.648	1.00
10_Y	38_D	0.647	1.00
183_A	188_V	0.643	1.00
217_Q	220_D	0.643	1.00
3_I	83_M	0.640	1.00
34_I	77_A	0.636	1.00
173_Y	176_W	0.634	1.00
8_V	70_R	0.633	1.00
74_V	165_Y	0.630	1.00
191_V	194_A	0.624	1.00
135_Y	138_D	0.622	1.00
215_R	218_Y	0.621	1.00
167_D	181_R	0.615	1.00
95_H	111_S	0.611	1.00
145_F	148_Y	0.602	1.00
4_S	78_S	0.601	1.00
48_A	60_L	0.597	1.00
219_L	223_S	0.596	1.00
117_S	120_E	0.596	1.00
81_C	156_R	0.594	1.00
39_A	63_N	0.591	1.00
151_S	198_Y	0.590	1.00
146_S	149_V	0.589	1.00
13_I	16_L	0.588	1.00
24_S	52_E	0.587	1.00
155_Y	160_H	0.586	1.00
111_S	195_S	0.586	1.00
214_K	217_Q	0.585	1.00
85_C	89_D	0.583	1.00
26_Q	97_E	0.581	1.00
13_I	42_S	0.581	1.00
19_L	88_D	0.579	1.00
31_Y	54_P	0.576	1.00
144_V	147_T	0.571	1.00
133_F	138_D	0.568	1.00
27_T	31_Y	0.568	1.00
86_D	174_W	0.565	1.00
98_K	195_S	0.565	1.00
35_I	55_I	0.562	1.00
26_Q	91_F	0.559	1.00
71_N	75_K	0.558	1.00
6_V	77_A	0.556	1.00
194_A	197_I	0.555	1.00
30_P	54_P	0.553	1.00
39_A	61_E	0.551	1.00
7_I	20_L	0.548	1.00
200_F	207_Q	0.548	1.00
215_R	219_L	0.547	1.00
207_Q	210_D	0.546	1.00
99_M	102_E	0.543	1.00
7_I	35_I	0.539	1.00
103_I	109_V	0.537	1.00
106_A	113_A	0.537	1.00
26_Q	96_I	0.535	1.00
49_L	52_E	0.534	1.00
109_V	156_R	0.533	1.00
38_D	86_D	0.533	1.00
48_A	51_P	0.531	1.00
106_A	112_D	0.530	1.00
161_D	165_Y	0.530	1.00
113_A	151_S	0.526	1.00
16_L	47_K	0.525	1.00
117_S	123_G	0.525	1.00
6_V	36_V	0.525	1.00
144_V	187_R	0.523	1.00
99_M	152_G	0.523	1.00
94_G	193_C	0.523	1.00
9_T	37_N	0.523	1.00
39_A	60_L	0.523	1.00
176_W	180_L	0.522	1.00
45_P	60_L	0.522	1.00
24_S	33_I	0.521	1.00
85_C	196_V	0.518	1.00
133_F	137_A	0.517	1.00
31_Y	79_G	0.517	1.00
92_T	194_A	0.516	1.00
106_A	110_H	0.514	1.00
130_R	133_F	0.513	1.00
100_A	103_I	0.513	1.00
213_A	218_Y	0.513	1.00
116_V	120_E	0.512	1.00
115_I	151_S	0.512	1.00
56_A	59_N	0.511	1.00
91_F	196_V	0.511	1.00
3_I	28_L	0.510	1.00
81_C	104_E	0.510	1.00
12_R	86_D	0.509	1.00
8_V	66_H	0.509	1.00
216_K	223_S	0.507	1.00
26_Q	94_G	0.506	1.00
155_Y	182_A	0.506	1.00
167_D	170_V	0.506	1.00
182_A	186_Y	0.502	1.00
47_K	50_Y	0.501	1.00
90_F	116_V	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
2d7iA	1	0.9963	100	0.264	Contact Map
1xhbA	1	0.9701	100	0.273	Contact Map
5ajoA	1	0.9925	100	0.281	Contact Map
3l7iA	4	0	100	0.305	Contact Map
3bcvA	2	0.6455	100	0.327	Contact Map
2z86A	2	0.9142	100	0.334	Contact Map
1qg8A	1	0.8134	100	0.342	Contact Map
4fixA	3	0.9851	100	0.389	Contact Map
4p02A	1	0.9366	100	0.425	Contact Map
2nxvA	4	0.8246	100	0.428	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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