YDAC - BACSU - GREMLIN Contacts

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YDAC - Uncharacterized methyltransferase YdaC

UniProt:	P96576	Sequences: MIAGYIMAAENQTLNQWTINQLGITRGDSILEVGFGPGYCMQQMLKREKDVHLHGIDVSEAMLKLAARRVKPKGVRLIQGSIETFPLPASFYDKVISVNNYTIWNDQTKGIKQIYRALKPGGKAAITMQPREADASPEKTKSFGRQMIADFKAAGFEDIDIQFKNIKPELSVCATAKKPAT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	181 (148)
Sequences:	23473 (18178)
Seq/√Len:	1494.2

ECOLI - UBIE TAM UBIG YJHP SMTA BIOC CMOA TEHB YAFE CMOB RLMA CFA
BACSU - YDAC YRHH YBAJ YODH MENG YXBB YCGJ YRRT YQEM YXJB
HALSA - Q9HND6 Q9HMT2 Q9HR81 ARSM Q9HRX3 Q9HR63 Q9HSK6 Q9HQ85
SULSO - Q97ZU8 Q97X57 Q97WT7 Q7LXN7 Q97YX4 Q97XD7 Q97WN4 Q97WH3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_S	52_H	2.599	1.00
60_E	79_Q	2.587	1.00
115_Y	156_F	2.489	1.00
35_F	55_G	2.388	1.00
54_H	78_I	2.253	1.00
54_H	92_Y	2.131	1.00
56_I	80_G	2.116	1.00
118_L	122_G	2.047	1.00
95_V	114_I	2.014	1.00
31_L	92_Y	2.009	1.00
42_Q	70_V	2.005	1.00
41_M	53_L	1.960	1.00
34_G	100_N	1.925	1.00
66_A	77_L	1.918	1.00
28_D	94_K	1.887	1.00
87_L	92_Y	1.862	1.00
95_V	118_L	1.814	1.00
52_H	76_R	1.809	1.00
93_D	119_K	1.783	1.00
25_T	28_D	1.782	1.00
113_Q	116_R	1.765	1.00
63_L	77_L	1.752	1.00
63_L	79_Q	1.752	1.00
114_I	124_A	1.749	1.00
106_D	109_K	1.690	1.00
29_S	54_H	1.641	1.00
108_T	150_D	1.629	1.00
108_T	153_A	1.626	1.00
60_E	64_K	1.613	1.00
33_V	114_I	1.611	1.00
100_N	104_W	1.593	1.00
80_G	86_P	1.530	1.00
33_V	82_I	1.530	1.00
108_T	112_K	1.507	1.00
35_F	41_M	1.495	1.00
54_H	76_R	1.474	1.00
107_Q	150_D	1.447	1.00
70_V	77_L	1.440	1.00
41_M	55_G	1.429	1.00
58_V	81_S	1.427	1.00
148_I	152_K	1.413	1.00
102_T	128_M	1.396	1.00
30_I	94_K	1.364	1.00
30_I	44_M	1.362	1.00
97_S	100_N	1.348	1.00
112_K	154_A	1.332	1.00
24_I	28_D	1.327	1.00
118_L	124_A	1.321	1.00
104_W	110_G	1.297	1.00
82_I	104_W	1.292	1.00
29_S	119_K	1.291	1.00
42_Q	69_R	1.279	1.00
29_S	92_Y	1.269	1.00
99_N	102_T	1.269	1.00
108_T	154_A	1.269	1.00
113_Q	117_A	1.264	1.00
65_L	68_R	1.222	1.00
88_P	91_F	1.212	1.00
78_I	87_L	1.202	1.00
29_S	93_D	1.199	1.00
57_D	63_L	1.195	1.00
82_I	100_N	1.192	1.00
29_S	91_F	1.174	1.00
89_A	116_R	1.167	1.00
111_I	151_F	1.166	1.00
45_L	74_G	1.160	1.00
118_L	156_F	1.156	1.00
32_E	35_F	1.150	1.00
55_G	77_L	1.142	1.00
54_H	87_L	1.123	1.00
85_F	117_A	1.112	1.00
115_Y	154_A	1.092	1.00
103_I	128_M	1.083	1.00
99_N	127_T	1.072	1.00
140_T	143_F	1.071	1.00
59_S	62_M	1.068	1.00
63_L	67_A	1.062	1.00
70_V	75_V	1.058	1.00
110_G	114_I	1.055	1.00
44_M	96_I	1.047	1.00
81_S	84_T	1.034	1.00
40_C	98_V	1.033	1.00
17_W	20_N	1.032	1.00
61_A	64_K	1.031	1.00
149_A	153_A	1.021	1.00
43_Q	47_R	1.020	1.00
85_F	113_Q	0.984	1.00
35_F	66_A	0.983	1.00
21_Q	162_Q	0.973	1.00
42_Q	46_K	0.972	1.00
101_Y	104_W	0.964	1.00
109_K	112_K	0.960	1.00
57_D	62_M	0.942	1.00
43_Q	46_K	0.940	1.00
41_M	77_L	0.938	1.00
40_C	96_I	0.936	1.00
28_D	51_V	0.928	1.00
99_N	103_I	0.928	1.00
98_V	127_T	0.926	1.00
64_K	67_A	0.886	1.00
37_P	62_M	0.879	1.00
27_G	51_V	0.872	1.00
31_L	95_V	0.870	1.00
17_W	21_Q	0.863	1.00
34_G	97_S	0.860	1.00
28_D	93_D	0.840	1.00
149_A	152_K	0.834	1.00
135_A	139_K	0.830	1.00
102_T	129_Q	0.825	1.00
86_P	113_Q	0.818	1.00
18_T	125_A	0.813	1.00
70_V	73_K	0.802	1.00
148_I	161_I	0.798	1.00
37_P	69_R	0.798	1.00
144_G	163_F	0.796	1.00
99_N	129_Q	0.794	1.00
35_F	63_L	0.791	1.00
94_K	123_K	0.784	1.00
24_I	27_G	0.781	1.00
101_Y	111_I	0.781	1.00
55_G	66_A	0.780	1.00
65_L	69_R	0.777	1.00
39_Y	43_Q	0.775	1.00
136_S	139_K	0.773	1.00
109_K	113_Q	0.771	1.00
42_Q	45_L	0.763	1.00
92_Y	117_A	0.761	1.00
95_V	117_A	0.760	1.00
135_A	140_T	0.756	1.00
97_S	126_I	0.740	1.00
87_L	117_A	0.738	1.00
67_A	70_V	0.730	1.00
31_L	117_A	0.726	1.00
134_D	137_P	0.725	1.00
111_I	154_A	0.725	1.00
137_P	141_K	0.724	1.00
33_V	95_V	0.724	1.00
111_I	147_M	0.722	1.00
64_K	68_R	0.721	1.00
39_Y	69_R	0.721	1.00
144_G	148_I	0.716	1.00
101_Y	110_G	0.714	1.00
17_W	162_Q	0.713	1.00
83_E	106_D	0.710	1.00
41_M	75_V	0.710	1.00
16_Q	43_Q	0.707	1.00
83_E	104_W	0.702	1.00
56_I	78_I	0.702	1.00
128_M	147_M	0.701	1.00
38_G	66_A	0.700	1.00
37_P	65_L	0.700	1.00
83_E	109_K	0.695	1.00
97_S	114_I	0.689	1.00
40_C	43_Q	0.688	1.00
84_T	109_K	0.687	1.00
61_A	65_L	0.687	1.00
67_A	77_L	0.686	1.00
146_Q	149_A	0.685	1.00
101_Y	126_I	0.684	1.00
19_I	47_R	0.681	1.00
158_D	161_I	0.677	1.00
67_A	71_K	0.673	1.00
130_P	163_F	0.664	1.00
30_I	96_I	0.654	1.00
137_P	140_T	0.653	1.00
80_G	85_F	0.652	1.00
97_S	104_W	0.651	1.00
139_K	142_S	0.649	1.00
16_Q	20_N	0.645	1.00
91_F	119_K	0.645	1.00
30_I	53_L	0.642	1.00
83_E	110_G	0.638	1.00
29_S	51_V	0.633	1.00
111_I	150_D	0.632	1.00
150_D	153_A	0.630	1.00
114_I	118_L	0.626	1.00
68_R	71_K	0.623	1.00
98_V	102_T	0.622	1.00
33_V	56_I	0.618	1.00
107_Q	110_G	0.614	1.00
138_E	141_K	0.613	1.00
68_R	72_P	0.613	1.00
56_I	85_F	0.610	1.00
130_P	144_G	0.599	1.00
45_L	53_L	0.596	1.00
26_R	50_D	0.596	1.00
138_E	142_S	0.595	1.00
126_I	151_F	0.592	1.00
35_F	57_D	0.589	1.00
84_T	113_Q	0.587	1.00
89_A	113_Q	0.585	1.00
90_S	120_P	0.581	1.00
124_A	156_F	0.577	1.00
137_P	143_F	0.570	1.00
87_L	91_F	0.567	1.00
40_C	44_M	0.558	1.00
73_K	76_R	0.555	1.00
97_S	124_A	0.554	1.00
35_F	77_L	0.551	1.00
31_L	56_I	0.550	1.00
150_D	154_A	0.545	1.00
50_D	74_G	0.544	1.00
132_E	137_P	0.542	1.00
38_G	77_L	0.537	1.00
146_Q	150_D	0.536	1.00
28_D	123_K	0.532	1.00
62_M	99_N	0.532	1.00
139_K	143_F	0.529	1.00
94_K	122_G	0.528	1.00
21_Q	160_D	0.523	1.00
69_R	72_P	0.516	1.00
42_Q	77_L	0.515	1.00
20_N	47_R	0.513	1.00
136_S	140_T	0.512	1.00
132_E	135_A	0.509	1.00
55_G	75_V	0.508	1.00
45_L	75_V	0.508	1.00
82_I	110_G	0.507	1.00
23_G	123_K	0.504	1.00
137_P	142_S	0.502	1.00
90_S	119_K	0.501	1.00
15_N	43_Q	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
2o57A	2	0.9945	100	0.365	Contact Map
3ujcA	1	0.9945	100	0.374	Contact Map
4obxA	2	0.9779	100	0.374	Contact Map
4krgA	1	0.989	100	0.376	Contact Map
4pneA	2	0.989	100	0.377	Contact Map
1vl5A	1	0.9171	100	0.378	Contact Map
4ineA	2	0.9945	100	0.378	Contact Map
4kriA	1	0.9945	100	0.379	Contact Map
3busA	1	0.9945	100	0.384	Contact Map
3bkxA	2	1	100	0.391	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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