YQFW - BACSU - GREMLIN Contacts

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YQFW - Putative nucleotidase YqfW

UniProt:	P54480	Sequences: MLRLGIDIDGTITAQDTFVPYLNRSFNLSISLNDMTDYDLTKLLNITQEEFWDWMNQNEAIIYKEALLAQHAKQSLDLLKEEHKLIYITARRTHLTDITYEWFDRQNIHYDHIELVGGHHKVEAVKNHNIDLFFEDHHGNAMMIAKEAGIPVILFNSPYNQLPIDSNIIRVNNWLEAVQWMNNNKHHLIRVNN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	193 (171)
Sequences:	727 (608)
Seq/√Len:	46.5

BACSU - YQFW 53DR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
3_R	84_K	5.267	1.00
78_L	178_V	5.254	1.00
156_N	161_Q	5.076	1.00
64_K	105_R	3.445	1.00
5_G	130_I	3.391	1.00
156_N	172_N	2.787	1.00
6_I	76_L	2.784	1.00
23_N	29_S	2.698	1.00
160_N	170_R	2.682	1.00
75_S	178_V	2.634	1.00
64_K	101_E	2.554	1.00
47_T	50_E	2.424	1.00
71_H	175_L	2.305	1.00
156_N	170_R	2.264	1.00
96_T	100_Y	2.253	1.00
73_K	77_D	2.183	1.00
20_P	24_R	2.174	1.00
53_D	57_Q	2.139	1.00
5_G	88_I	2.118	1.00
89_T	115_L	2.110	1.00
71_H	75_S	2.029	0.99
79_L	181_M	1.848	0.99
12_I	76_L	1.829	0.99
76_L	85_L	1.786	0.99
78_L	81_E	1.730	0.98
97_D	101_E	1.716	0.98
5_G	128_H	1.689	0.98
153_I	180_W	1.683	0.98
6_I	134_F	1.502	0.96
141_A	152_V	1.498	0.96
15_Q	66_A	1.417	0.94
134_F	153_I	1.408	0.94
153_I	177_A	1.403	0.94
80_K	111_D	1.378	0.93
27_N	129_N	1.378	0.93
75_S	78_L	1.374	0.93
74_Q	175_L	1.357	0.93
16_D	67_L	1.348	0.92
172_N	176_E	1.344	0.92
88_I	130_I	1.334	0.92
8_I	99_T	1.334	0.92
138_H	141_A	1.326	0.92
141_A	168_I	1.301	0.91
63_Y	95_L	1.300	0.91
17_T	65_E	1.282	0.90
132_L	181_M	1.264	0.90
62_I	159_Y	1.263	0.90
18_F	22_L	1.263	0.90
10_G	15_Q	1.261	0.90
141_A	154_L	1.260	0.90
37_D	42_K	1.255	0.89
91_R	99_T	1.255	0.89
10_G	135_E	1.237	0.89
145_A	167_N	1.232	0.89
93_T	96_T	1.206	0.88
61_I	98_I	1.204	0.87
22_L	51_F	1.201	0.87
49_E	53_D	1.196	0.87
105_R	166_S	1.194	0.87
87_Y	109_H	1.182	0.86
135_E	144_I	1.177	0.86
12_I	87_Y	1.169	0.86
23_N	28_L	1.168	0.86
132_L	151_P	1.149	0.85
11_T	69_A	1.148	0.85
120_H	143_M	1.142	0.84
173_N	176_E	1.136	0.84
18_F	158_P	1.122	0.83
14_A	69_A	1.102	0.82
175_L	179_Q	1.095	0.82
4_L	79_L	1.089	0.82
83_H	132_L	1.080	0.81
134_F	177_A	1.074	0.81
78_L	82_E	1.073	0.81
151_P	169_I	1.069	0.80
10_G	140_N	1.068	0.80
155_F	177_A	1.057	0.80
4_L	7_D	1.053	0.79
8_I	87_Y	1.039	0.78
77_D	81_E	1.039	0.78
42_K	153_I	1.037	0.78
79_L	168_I	1.033	0.78
138_H	163_P	1.016	0.77
63_Y	99_T	1.011	0.76
78_L	105_R	0.986	0.75
144_I	150_I	0.986	0.75
88_I	128_H	0.965	0.73
117_G	170_R	0.961	0.73
23_N	31_S	0.952	0.72
169_I	180_W	0.942	0.71
11_T	14_A	0.931	0.70
176_E	179_Q	0.931	0.70
13_T	157_S	0.924	0.70
101_E	104_D	0.919	0.69
71_H	80_K	0.916	0.69
38_Y	141_A	0.902	0.68
153_I	171_V	0.902	0.68
154_L	163_P	0.896	0.67
49_E	106_Q	0.896	0.67
132_L	152_V	0.892	0.67
3_R	130_I	0.889	0.67
18_F	88_I	0.883	0.66
115_L	119_H	0.875	0.65
107_N	172_N	0.871	0.65
25_S	57_Q	0.869	0.65
154_L	170_R	0.856	0.64
40_L	109_H	0.850	0.63
72_A	174_W	0.845	0.63
12_I	38_Y	0.836	0.62
27_N	101_E	0.836	0.62
49_E	153_I	0.836	0.62
24_R	28_L	0.835	0.62
70_Q	78_L	0.834	0.62
10_G	159_Y	0.831	0.61
68_L	106_Q	0.825	0.61
85_L	145_A	0.825	0.61
8_I	91_R	0.814	0.60
63_Y	174_W	0.806	0.59
12_I	143_M	0.805	0.59
71_H	173_N	0.799	0.58
10_G	133_F	0.791	0.58
91_R	127_N	0.789	0.57
19_V	35_M	0.786	0.57
87_Y	102_W	0.785	0.57
89_T	132_L	0.781	0.57
36_T	43_L	0.766	0.55
80_K	85_L	0.761	0.55
68_L	73_K	0.760	0.55
11_T	133_F	0.759	0.54
8_I	150_I	0.755	0.54
135_E	152_V	0.752	0.54
41_T	48_Q	0.752	0.54
102_W	158_P	0.750	0.54
5_G	133_F	0.750	0.54
101_E	147_E	0.742	0.53
100_Y	104_D	0.740	0.53
103_F	108_I	0.724	0.51
102_W	115_L	0.719	0.51
55_M	89_T	0.718	0.50
14_A	148_A	0.715	0.50
138_H	154_L	0.711	0.50
100_Y	181_M	0.711	0.50
85_L	138_H	0.710	0.50
88_I	140_N	0.706	0.49
11_T	66_A	0.702	0.49
43_L	46_I	0.698	0.48
16_D	52_W	0.697	0.48
97_D	163_P	0.692	0.48
5_G	159_Y	0.690	0.48
18_F	21_Y	0.688	0.47
86_I	128_H	0.687	0.47
141_A	145_A	0.686	0.47
19_V	55_M	0.686	0.47
30_I	35_M	0.681	0.47
35_M	92_R	0.675	0.46
88_I	133_F	0.675	0.46
67_L	176_E	0.674	0.46
16_D	53_D	0.670	0.46
108_I	113_I	0.669	0.46
10_G	157_S	0.669	0.46
4_L	106_Q	0.668	0.45
29_S	68_L	0.664	0.45
171_V	175_L	0.663	0.45
6_I	109_H	0.657	0.44
89_T	139_G	0.656	0.44
60_A	127_N	0.650	0.44
87_Y	135_E	0.648	0.44
66_A	102_W	0.647	0.43
20_P	172_N	0.644	0.43
3_R	86_I	0.637	0.42
10_G	69_A	0.637	0.42
119_H	170_R	0.636	0.42
147_E	155_F	0.633	0.42
38_Y	137_H	0.632	0.42
13_T	63_Y	0.632	0.42
12_I	138_H	0.631	0.42
42_K	143_M	0.630	0.42
171_V	180_W	0.629	0.42
135_E	157_S	0.624	0.41
50_E	53_D	0.616	0.40
11_T	63_Y	0.610	0.40
129_N	179_Q	0.610	0.40
67_L	74_Q	0.610	0.40
52_W	70_Q	0.608	0.40
44_L	96_T	0.607	0.40
24_R	162_L	0.606	0.40
8_I	13_T	0.606	0.40
27_N	111_D	0.604	0.39
8_I	130_I	0.599	0.39
27_N	179_Q	0.596	0.39
139_G	142_M	0.593	0.38
27_N	86_I	0.593	0.38
35_M	132_L	0.590	0.38
166_S	169_I	0.586	0.38
87_Y	133_F	0.584	0.37
145_A	168_I	0.584	0.37
21_Y	54_W	0.582	0.37
83_H	112_H	0.581	0.37
16_D	106_Q	0.578	0.37
56_N	82_E	0.578	0.37
11_T	87_Y	0.573	0.36
81_E	105_R	0.572	0.36
48_Q	105_R	0.571	0.36
89_T	122_V	0.570	0.36
96_T	103_F	0.569	0.36
39_D	156_N	0.566	0.36
55_M	71_H	0.564	0.36
48_Q	58_N	0.563	0.36
133_F	144_I	0.563	0.36
31_S	34_D	0.561	0.35
89_T	116_V	0.561	0.35
9_D	136_D	0.560	0.35
114_E	144_I	0.554	0.35
62_I	170_R	0.554	0.35
28_L	128_H	0.553	0.35
84_K	106_Q	0.549	0.34
113_I	116_V	0.548	0.34
53_D	145_A	0.547	0.34
60_A	85_L	0.547	0.34
53_D	67_L	0.546	0.34
57_Q	129_N	0.544	0.34
4_L	12_I	0.543	0.34
49_E	56_N	0.538	0.33
89_T	110_Y	0.537	0.33
87_Y	134_F	0.537	0.33
94_H	113_I	0.533	0.33
79_L	115_L	0.532	0.33
159_Y	170_R	0.531	0.33
106_Q	173_N	0.530	0.33
68_L	102_W	0.528	0.32
53_D	81_E	0.527	0.32
6_I	138_H	0.526	0.32
5_G	91_R	0.525	0.32
76_L	97_D	0.525	0.32
173_N	179_Q	0.525	0.32
127_N	179_Q	0.524	0.32
135_E	141_A	0.524	0.32
76_L	80_K	0.519	0.32
110_Y	137_H	0.519	0.32
73_K	163_P	0.517	0.31
103_F	119_H	0.517	0.31
68_L	171_V	0.516	0.31
5_G	121_K	0.515	0.31
28_L	45_N	0.513	0.31
24_R	36_T	0.513	0.31
91_R	130_I	0.513	0.31
99_T	174_W	0.512	0.31
35_M	158_P	0.510	0.31
74_Q	147_E	0.507	0.31
142_M	168_I	0.505	0.30
89_T	103_F	0.504	0.30
13_T	102_W	0.504	0.30
13_T	144_I	0.503	0.30
89_T	96_T	0.501	0.30
79_L	89_T	0.501	0.30
50_E	113_I	0.500	0.30

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
3bwvA	2	0.8394	99.8	0.633	Contact Map
4mumA	2	0.9016	99.7	0.67	Contact Map
4l57A	2	0.9119	99.7	0.677	Contact Map
2b82A	4	0.8601	99.6	0.698	Contact Map
2zg6A	2	0.8756	99.5	0.727	Contact Map
2obbA	2	0.6114	99.5	0.73	Contact Map
2om6A	2	0.9482	99.4	0.731	Contact Map
3sd7A	1	0.9171	99.4	0.735	Contact Map
2go7A	2	0.9016	99.4	0.74	Contact Map
3kzxA	1	0.886	99.4	0.744	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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