YTKD - BACSU - GREMLIN Contacts

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YTKD - Putative 8-oxo-dGTP diphosphatase YtkD

UniProt:	O35013	Sequences: MYEFKDYYQNTVQLSFDDQPFSDSPKHVWVICRFGGKWLLTEHEDRGYEFPGGKVEPMECAEEAALREVKEETGARVKSLKYLGQYKVLGKEKVIVKNIYFADIEKLEKQADYFETKGPVLFHELPENLSRNKKFSFIMKDSVLPISLKKLKESGWIE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	158 (136)
Sequences:	337 (289)
Seq/√Len:	24.8

BACSU - YTKD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
42_E	117_K	4.463	1.00
84_G	99_I	3.347	1.00
85_Q	98_N	3.203	1.00
48_Y	122_F	2.942	1.00
39_L	104_I	2.594	0.99
99_I	147_S	2.572	0.99
13_Q	87_K	2.439	0.98
113_Y	119_P	2.325	0.98
29_W	144_L	2.288	0.98
30_V	65_A	2.194	0.97
110_Q	113_Y	2.145	0.96
48_Y	120_V	2.140	0.96
51_P	73_T	2.136	0.96
62_E	80_L	2.028	0.95
60_C	63_E	1.991	0.95
42_E	118_G	1.953	0.94
43_H	46_R	1.806	0.91
108_E	111_A	1.801	0.91
50_F	119_P	1.797	0.91
62_E	66_L	1.755	0.90
37_K	123_H	1.718	0.89
33_R	38_W	1.710	0.89
84_G	147_S	1.707	0.89
39_L	119_P	1.697	0.88
11_T	89_L	1.693	0.88
135_F	139_M	1.610	0.85
34_F	121_L	1.593	0.85
65_A	102_A	1.592	0.85
55_V	61_A	1.534	0.83
92_E	105_E	1.503	0.81
38_W	139_M	1.498	0.81
47_G	141_D	1.497	0.81
55_V	64_A	1.476	0.80
61_A	98_N	1.458	0.79
78_K	105_E	1.436	0.78
27_H	97_K	1.432	0.78
28_V	136_S	1.418	0.77
28_V	64_A	1.375	0.75
83_L	94_V	1.345	0.73
73_T	88_V	1.331	0.72
28_V	61_A	1.307	0.71
27_H	136_S	1.304	0.71
40_L	50_F	1.288	0.70
90_G	100_Y	1.287	0.70
142_S	146_I	1.282	0.70
21_F	139_M	1.272	0.69
69_V	77_V	1.262	0.68
36_G	78_K	1.239	0.67
100_Y	120_V	1.231	0.66
13_Q	127_E	1.197	0.64
125_L	147_S	1.191	0.64
97_K	136_S	1.166	0.62
46_R	52_G	1.135	0.60
122_F	135_F	1.129	0.59
129_L	142_S	1.109	0.58
29_W	52_G	1.106	0.58
25_P	98_N	1.092	0.57
47_G	97_K	1.088	0.57
76_R	105_E	1.069	0.55
28_V	55_V	1.068	0.55
142_S	145_P	1.066	0.55
76_R	106_K	1.023	0.52
14_L	27_H	1.018	0.52
95_I	99_I	1.001	0.50
50_F	116_T	0.989	0.49
136_S	141_D	0.980	0.49
91_K	100_Y	0.967	0.48
27_H	41_T	0.966	0.48
103_D	121_L	0.961	0.47
47_G	136_S	0.947	0.46
15_S	18_D	0.942	0.46
70_K	110_Q	0.941	0.46
41_T	136_S	0.941	0.46
16_F	120_V	0.938	0.46
110_Q	114_F	0.933	0.45
79_S	105_E	0.926	0.45
92_E	145_P	0.921	0.45
31_I	142_S	0.911	0.44
46_R	86_Y	0.910	0.44
110_Q	119_P	0.907	0.44
76_R	109_K	0.906	0.44
24_S	103_D	0.903	0.43
51_P	136_S	0.885	0.42
33_R	103_D	0.880	0.42
77_V	80_L	0.876	0.41
41_T	116_T	0.873	0.41
22_S	55_V	0.871	0.41
78_K	103_D	0.868	0.41
49_E	86_Y	0.864	0.41
35_G	58_M	0.860	0.40
27_H	47_G	0.854	0.40
29_W	95_I	0.853	0.40
31_I	129_L	0.830	0.38
67_R	71_E	0.816	0.37
84_G	143_V	0.806	0.37
41_T	98_N	0.802	0.36
14_L	55_V	0.770	0.34
36_G	123_H	0.770	0.34
77_V	106_K	0.769	0.34
130_S	147_S	0.767	0.34
125_L	142_S	0.766	0.34
44_E	76_R	0.764	0.34
31_I	143_V	0.760	0.34
24_S	94_V	0.757	0.33
43_H	49_E	0.756	0.33
75_A	78_K	0.755	0.33
61_A	64_A	0.754	0.33
67_R	72_E	0.754	0.33
58_M	93_K	0.752	0.33
135_F	143_V	0.751	0.33
61_A	100_Y	0.745	0.33
126_P	144_L	0.745	0.33
29_W	97_K	0.744	0.33
144_L	147_S	0.733	0.32
133_K	142_S	0.733	0.32
48_Y	91_K	0.731	0.32
38_W	101_F	0.722	0.31
40_L	93_K	0.720	0.31
123_H	134_K	0.720	0.31
23_D	35_G	0.717	0.31
87_K	133_K	0.712	0.31
38_W	88_V	0.710	0.30
41_T	73_T	0.708	0.30
27_H	88_V	0.703	0.30
103_D	134_K	0.702	0.30
19_Q	127_E	0.699	0.30
34_F	104_I	0.699	0.30
58_M	62_E	0.694	0.29
63_E	81_K	0.691	0.29
43_H	86_Y	0.691	0.29
76_R	79_S	0.687	0.29
130_S	142_S	0.683	0.29
49_E	52_G	0.681	0.29
81_K	100_Y	0.679	0.29
30_V	110_Q	0.673	0.28
50_F	137_F	0.673	0.28
47_G	54_K	0.669	0.28
42_E	131_R	0.667	0.28
30_V	101_F	0.667	0.28
88_V	118_G	0.667	0.28
47_G	64_A	0.665	0.28
18_D	104_I	0.662	0.28
96_V	100_Y	0.662	0.28
87_K	129_L	0.655	0.27
92_E	95_I	0.654	0.27
25_P	102_A	0.650	0.27
125_L	129_L	0.645	0.27
46_R	49_E	0.643	0.27
13_Q	89_L	0.642	0.26
11_T	146_I	0.636	0.26
32_C	69_V	0.635	0.26
47_G	77_V	0.627	0.26
63_E	111_A	0.625	0.26
14_L	32_C	0.621	0.25
13_Q	79_S	0.617	0.25
75_A	104_I	0.613	0.25
41_T	51_P	0.613	0.25
25_P	69_V	0.610	0.25
51_P	88_V	0.610	0.25
35_G	123_H	0.609	0.25
126_P	143_V	0.607	0.25
60_C	64_A	0.604	0.24
58_M	103_D	0.603	0.24
139_M	143_V	0.600	0.24
13_Q	42_E	0.600	0.24
39_L	107_L	0.595	0.24
25_P	85_Q	0.595	0.24
54_K	97_K	0.594	0.24
83_L	103_D	0.594	0.24
33_R	101_F	0.590	0.24
88_V	97_K	0.588	0.24
63_E	105_E	0.573	0.23
21_F	143_V	0.572	0.23
13_Q	37_K	0.570	0.23
100_Y	134_K	0.570	0.23
83_L	100_Y	0.569	0.23
11_T	57_P	0.569	0.23
27_H	140_K	0.567	0.22
40_L	48_Y	0.563	0.22
33_R	80_L	0.562	0.22
37_K	131_R	0.559	0.22
41_T	95_I	0.556	0.22
50_F	113_Y	0.552	0.22
18_D	123_H	0.550	0.22
65_A	80_L	0.546	0.21
90_G	93_K	0.545	0.21
54_K	118_G	0.543	0.21
90_G	102_A	0.539	0.21
20_P	75_A	0.535	0.21
13_Q	94_V	0.535	0.21
31_I	70_K	0.528	0.21
50_F	118_G	0.524	0.20
77_V	114_F	0.521	0.20
89_L	114_F	0.521	0.20
33_R	42_E	0.510	0.20
117_K	133_K	0.509	0.20
23_D	123_H	0.507	0.20
135_F	147_S	0.507	0.20
34_F	107_L	0.507	0.20
130_S	133_K	0.506	0.20
143_V	147_S	0.505	0.19
135_F	140_K	0.504	0.19
32_C	44_E	0.504	0.19
111_A	142_S	0.500	0.19

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
4jzuA	1	0.9937	99.9	0.555	Contact Map
4jzsA	1	0.9937	99.9	0.582	Contact Map
1vhzA	2	0.9684	99.7	0.698	Contact Map
2yvpA	2	0.943	99.7	0.705	Contact Map
2w4eA	2	0.8101	99.7	0.705	Contact Map
2dscA	2	0.8987	99.6	0.713	Contact Map
3i7uA	4	0.8101	99.6	0.714	Contact Map
3q91A	2	0.7722	99.6	0.715	Contact Map
4kg3A	1	0.8481	99.6	0.715	Contact Map
3o6zA	2	0.943	99.6	0.717	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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