YRDN - BACSU - GREMLIN Contacts

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YRDN - Probable tautomerase YrdN

UniProt:	P94502	Sequences: MPLLRFDLIEGRDQSSLKKLLDVAHNVVVEAFDVPQQDRYQIVHEHPENHMIIEDTGLGFNRTKNLVVLSVTSKSRPEEKKQKFYRLLAERLESECGIASTDLIVSIVENDNADWSFGLGEAQFLTGKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	129 (123)
Sequences:	819 (599)
Seq/√Len:	54.0

BACSU - YRDN YOLI YUSQ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_E	47_P	4.769	1.00
45_E	50_H	3.448	1.00
63_T	102_D	3.053	1.00
32_F	73_S	2.619	1.00
25_H	29_V	2.609	1.00
89_A	103_L	2.258	1.00
84_F	88_L	2.167	1.00
5_R	70_S	2.160	1.00
88_L	105_V	2.060	1.00
4_L	24_A	1.955	1.00
6_F	24_A	1.907	1.00
73_S	107_I	1.891	0.99
11_G	45_E	1.843	0.99
26_N	91_R	1.822	0.99
7_D	46_H	1.821	0.99
78_E	113_A	1.767	0.99
22_D	39_R	1.758	0.99
20_L	67_V	1.756	0.99
3_L	42_I	1.737	0.99
98_I	103_L	1.704	0.99
12_R	16_S	1.694	0.99
77_P	80_K	1.673	0.99
30_E	87_L	1.656	0.99
17_L	50_H	1.591	0.98
21_L	43_V	1.573	0.98
16_S	65_N	1.560	0.98
14_Q	49_N	1.557	0.98
60_F	119_L	1.532	0.98
87_L	91_R	1.483	0.97
86_R	90_E	1.459	0.97
21_L	41_Q	1.448	0.97
75_S	109_E	1.434	0.96
8_L	17_L	1.417	0.96
21_L	39_R	1.361	0.95
7_D	44_H	1.339	0.95
23_V	96_C	1.331	0.95
26_N	30_E	1.329	0.95
23_V	27_V	1.326	0.94
110_N	114_D	1.314	0.94
88_L	103_L	1.284	0.93
31_A	87_L	1.264	0.93
78_E	82_Q	1.256	0.93
30_E	91_R	1.235	0.92
101_T	119_L	1.223	0.92
68_V	104_I	1.223	0.92
12_R	65_N	1.200	0.91
19_K	23_V	1.194	0.91
74_K	112_N	1.147	0.89
83_K	86_R	1.144	0.89
70_S	108_V	1.118	0.88
90_E	94_S	1.098	0.87
18_K	52_I	1.093	0.86
87_L	90_E	1.083	0.86
26_N	94_S	1.067	0.85
74_K	121_E	1.054	0.84
81_K	114_D	1.049	0.84
26_N	36_Q	1.022	0.82
63_T	101_T	1.013	0.82
56_T	61_N	1.005	0.81
6_F	43_V	0.999	0.81
109_E	114_D	0.987	0.80
5_R	44_H	0.983	0.80
6_F	21_L	0.973	0.79
27_V	88_L	0.970	0.79
7_D	42_I	0.963	0.78
54_E	57_G	0.940	0.77
90_E	100_S	0.933	0.76
37_Q	54_E	0.927	0.76
116_S	120_G	0.919	0.75
93_E	100_S	0.915	0.75
17_L	45_E	0.915	0.75
66_L	104_I	0.914	0.75
11_G	16_S	0.906	0.74
20_L	92_L	0.902	0.74
53_I	66_L	0.890	0.73
93_E	99_A	0.889	0.73
24_A	69_L	0.884	0.72
24_A	43_V	0.882	0.72
23_V	91_R	0.878	0.72
23_V	95_E	0.871	0.71
92_L	96_C	0.870	0.71
8_L	43_V	0.849	0.69
69_L	92_L	0.848	0.69
48_E	64_K	0.844	0.69
72_T	85_Y	0.843	0.69
33_D	80_K	0.838	0.68
13_D	16_S	0.833	0.68
32_F	80_K	0.832	0.68
111_D	114_D	0.822	0.67
99_A	102_D	0.821	0.67
7_D	106_S	0.816	0.66
83_K	87_L	0.813	0.66
25_H	34_V	0.807	0.65
25_H	41_Q	0.803	0.65
85_Y	115_W	0.794	0.64
2_P	38_D	0.792	0.64
14_Q	47_P	0.792	0.64
34_V	84_F	0.791	0.64
51_M	66_L	0.785	0.63
20_L	98_I	0.783	0.63
27_V	91_R	0.782	0.63
57_G	73_S	0.775	0.62
54_E	62_R	0.768	0.61
91_R	94_S	0.759	0.60
27_V	84_F	0.758	0.60
89_A	105_V	0.758	0.60
13_D	17_L	0.756	0.60
6_F	69_L	0.746	0.59
4_L	69_L	0.730	0.57
19_K	95_E	0.730	0.57
38_D	117_F	0.729	0.57
29_V	37_Q	0.729	0.57
27_V	34_V	0.729	0.57
28_V	40_Y	0.728	0.57
70_S	106_S	0.723	0.57
71_V	84_F	0.723	0.57
60_F	101_T	0.721	0.57
69_L	75_S	0.721	0.57
8_L	67_V	0.705	0.55
37_Q	52_I	0.705	0.55
85_Y	120_G	0.701	0.54
72_T	108_V	0.693	0.54
46_H	50_H	0.691	0.53
117_F	123_Q	0.683	0.53
28_V	34_V	0.676	0.52
10_E	45_E	0.675	0.52
48_E	95_E	0.672	0.51
40_Y	104_I	0.660	0.50
95_E	100_S	0.656	0.50
39_R	55_D	0.651	0.49
85_Y	107_I	0.648	0.49
106_S	114_D	0.648	0.49
19_K	96_C	0.646	0.49
74_K	111_D	0.642	0.48
72_T	100_S	0.640	0.48
21_L	25_H	0.640	0.48
88_L	91_R	0.639	0.48
17_L	20_L	0.637	0.48
16_S	96_C	0.633	0.47
32_F	57_G	0.624	0.46
39_R	52_I	0.621	0.46
21_L	40_Y	0.621	0.46
97_G	103_L	0.606	0.44
39_R	62_R	0.600	0.44
26_N	95_E	0.596	0.43
25_H	84_F	0.595	0.43
46_H	70_S	0.592	0.43
106_S	110_N	0.590	0.43
105_V	109_E	0.588	0.42
18_K	86_R	0.586	0.42
2_P	120_G	0.585	0.42
4_L	75_S	0.583	0.42
21_L	52_I	0.580	0.42
41_Q	110_N	0.565	0.40
61_N	99_A	0.562	0.40
47_P	50_H	0.562	0.40
45_E	70_S	0.556	0.39
18_K	22_D	0.556	0.39
15_S	26_N	0.554	0.39
79_E	90_E	0.554	0.39
72_T	106_S	0.552	0.39
42_I	46_H	0.550	0.39
71_V	76_R	0.549	0.38
14_Q	83_K	0.546	0.38
24_A	75_S	0.544	0.38
93_E	96_C	0.542	0.38
49_N	53_I	0.537	0.37
23_V	69_L	0.536	0.37
64_K	94_S	0.532	0.37
91_R	95_E	0.531	0.37
69_L	103_L	0.531	0.37
42_I	51_M	0.531	0.37
29_V	41_Q	0.529	0.36
23_V	71_V	0.527	0.36
11_G	17_L	0.527	0.36
82_Q	114_D	0.520	0.36
19_K	97_G	0.518	0.35
31_A	83_K	0.512	0.35
58_L	118_G	0.512	0.35
42_I	56_T	0.509	0.35
117_F	120_G	0.509	0.35
63_T	99_A	0.508	0.34
16_S	45_E	0.503	0.34
83_K	94_S	0.500	0.34

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
2aalA	3	0.9922	100	0.401	Contact Map
4lhpA	3	0.9845	100	0.441	Contact Map
3c6vA	3	0.938	99.9	0.478	Contact Map
4jcuA	3	0.938	99.9	0.498	Contact Map
1mwwA	3	0.9225	99.9	0.509	Contact Map
1u9dA	3	0.8295	99.9	0.52	Contact Map
3e6qA	4	0.8837	99.9	0.52	Contact Map
4lkbF	4	0.9225	99.9	0.531	Contact Map
3fwtA	3	0.8682	99.9	0.545	Contact Map
3fwuA	3	0.8605	99.9	0.547	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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