RBSD - BACSU - GREMLIN Contacts

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RBSD - D-ribose pyranase

UniProt:	P36946	Sequences: MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEEFKLLTKDAKAVIRTGEFTPYANCILQAGVLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	131 (131)
Sequences:	854 (542)
Seq/√Len:	47.4

ECOLI - RBSD
BACSU - RBSD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_V	108_A	4.403	1.00
11_L	112_I	3.381	1.00
56_A	87_L	2.941	1.00
81_A	95_Y	2.813	1.00
66_K	94_E	2.633	1.00
50_A	53_D	2.596	1.00
68_I	126_Q	2.585	1.00
13_K	38_L	2.474	1.00
18_L	62_M	2.441	1.00
44_L	48_L	2.327	1.00
48_L	53_D	2.115	1.00
10_H	38_L	2.080	1.00
45_K	57_V	2.076	1.00
2_K	61_E	2.065	1.00
66_K	126_Q	1.984	0.99
80_N	121_A	1.943	0.99
13_K	17_D	1.848	0.99
14_I	110_A	1.761	0.99
65_E	126_Q	1.746	0.98
69_A	95_Y	1.730	0.98
69_A	73_I	1.653	0.98
9_S	39_K	1.633	0.98
67_V	88_F	1.598	0.97
44_L	54_T	1.595	0.97
33_V	39_K	1.549	0.97
12_A	16_A	1.542	0.97
29_A	117_F	1.541	0.97
25_V	101_F	1.512	0.96
67_V	93_I	1.501	0.96
23_K	126_Q	1.478	0.96
22_D	109_K	1.476	0.96
55_A	125_L	1.470	0.95
26_I	58_L	1.463	0.95
2_K	12_A	1.447	0.95
23_K	68_I	1.437	0.95
59_A	64_V	1.417	0.94
96_L	104_L	1.350	0.93
73_I	77_N	1.339	0.93
103_L	106_K	1.295	0.91
25_V	105_T	1.283	0.91
73_I	84_L	1.269	0.90
63_A	130_L	1.251	0.90
74_K	95_Y	1.250	0.90
24_I	110_A	1.249	0.90
31_L	101_F	1.229	0.89
25_V	31_L	1.190	0.87
71_A	75_A	1.176	0.87
35_D	109_K	1.175	0.87
73_I	95_Y	1.159	0.86
45_K	56_A	1.148	0.85
100_E	103_L	1.136	0.85
82_K	86_N	1.136	0.85
14_I	40_I	1.101	0.83
11_L	42_L	1.099	0.83
36_G	106_K	1.083	0.82
15_L	58_L	1.071	0.81
21_T	65_E	1.067	0.81
10_H	13_K	1.066	0.81
62_M	127_A	1.058	0.80
17_D	39_K	1.032	0.79
51_F	116_E	1.024	0.78
46_P	130_L	1.023	0.78
18_L	24_I	1.016	0.77
33_V	111_V	1.015	0.77
9_S	17_D	1.014	0.77
46_P	117_F	1.012	0.77
24_I	58_L	0.986	0.75
71_A	74_K	0.984	0.75
5_G	60_E	0.982	0.75
15_L	61_E	0.974	0.74
24_I	62_M	0.963	0.74
102_K	120_Y	0.960	0.73
63_A	128_G	0.958	0.73
105_T	111_V	0.953	0.73
81_A	85_E	0.950	0.73
23_K	124_I	0.949	0.72
53_D	56_A	0.947	0.72
52_Q	83_F	0.941	0.72
23_K	104_L	0.940	0.72
4_H	60_E	0.934	0.71
27_A	31_L	0.930	0.71
55_A	123_C	0.925	0.71
68_I	104_L	0.917	0.70
44_L	57_V	0.908	0.69
9_S	12_A	0.905	0.69
21_T	31_L	0.903	0.69
68_I	96_L	0.897	0.68
92_E	106_K	0.887	0.67
29_A	130_L	0.861	0.65
57_V	60_E	0.859	0.65
52_Q	80_N	0.853	0.64
55_A	84_L	0.847	0.64
31_L	105_T	0.840	0.63
24_I	40_I	0.836	0.63
14_I	24_I	0.828	0.62
19_G	33_V	0.808	0.60
58_L	112_I	0.798	0.59
40_I	110_A	0.796	0.59
54_T	114_T	0.785	0.58
112_I	130_L	0.769	0.56
31_L	111_V	0.762	0.56
77_N	118_T	0.761	0.55
77_N	83_F	0.747	0.54
65_E	111_V	0.747	0.54
69_A	123_C	0.747	0.54
85_E	90_E	0.746	0.54
9_S	43_S	0.744	0.54
29_A	46_P	0.743	0.54
80_N	83_F	0.737	0.53
10_H	40_I	0.720	0.51
71_A	95_Y	0.720	0.51
9_S	13_K	0.712	0.51
45_K	48_L	0.710	0.50
44_L	114_T	0.705	0.50
79_E	82_K	0.703	0.50
2_K	16_A	0.701	0.49
13_K	39_K	0.700	0.49
85_E	93_I	0.700	0.49
67_V	123_C	0.689	0.48
13_K	40_I	0.677	0.47
17_D	109_K	0.675	0.47
56_A	88_F	0.674	0.47
69_A	84_L	0.670	0.46
73_I	81_A	0.670	0.46
65_E	128_G	0.663	0.46
19_G	128_G	0.662	0.46
52_Q	87_L	0.658	0.45
72_E	98_H	0.657	0.45
50_A	56_A	0.649	0.44
55_A	59_A	0.648	0.44
39_K	67_V	0.641	0.43
19_G	43_S	0.641	0.43
52_Q	56_A	0.637	0.43
12_A	43_S	0.636	0.43
92_E	97_S	0.636	0.43
85_E	95_Y	0.634	0.43
11_L	15_L	0.633	0.43
39_K	43_S	0.632	0.43
8_N	43_S	0.630	0.42
18_L	127_A	0.628	0.42
15_L	129_V	0.627	0.42
78_Q	82_K	0.624	0.42
72_E	102_K	0.621	0.42
25_V	111_V	0.619	0.41
56_A	83_F	0.618	0.41
6_I	15_L	0.616	0.41
2_K	8_N	0.614	0.41
69_A	81_A	0.611	0.41
31_L	121_A	0.611	0.41
8_N	49_P	0.609	0.40
3_K	12_A	0.608	0.40
21_T	126_Q	0.606	0.40
4_H	61_E	0.600	0.40
19_G	119_P	0.597	0.39
45_K	53_D	0.597	0.39
47_G	116_E	0.596	0.39
24_I	112_I	0.588	0.38
27_A	121_A	0.585	0.38
3_K	63_A	0.582	0.38
57_V	61_E	0.581	0.38
84_L	123_C	0.578	0.37
11_L	130_L	0.577	0.37
96_L	106_K	0.573	0.37
117_F	130_L	0.571	0.37
66_K	92_E	0.562	0.36
6_I	130_L	0.561	0.36
19_G	27_A	0.559	0.36
86_N	92_E	0.558	0.36
18_L	112_I	0.558	0.36
70_A	98_H	0.557	0.35
96_L	107_D	0.552	0.35
61_E	64_V	0.552	0.35
31_L	116_E	0.551	0.35
9_S	16_A	0.546	0.35
15_L	130_L	0.542	0.34
16_A	58_L	0.539	0.34
74_K	79_E	0.539	0.34
31_L	65_E	0.534	0.33
48_L	61_E	0.533	0.33
70_A	131_F	0.533	0.33
39_K	80_N	0.532	0.33
101_F	105_T	0.530	0.33
106_K	109_K	0.524	0.33
30_G	122_N	0.523	0.32
79_E	112_I	0.522	0.32
64_V	67_V	0.518	0.32
27_A	111_V	0.516	0.32
23_K	107_D	0.513	0.32
98_H	102_K	0.512	0.32
27_A	131_F	0.511	0.31
7_L	29_A	0.509	0.31
59_A	62_M	0.506	0.31
71_A	97_S	0.504	0.31
25_V	93_I	0.504	0.31
15_L	62_M	0.502	0.31
32_P	102_K	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
1ogdA	5	1	100	0.152	Contact Map
3e7nA	6	1	100	0.162	Contact Map
3p12A	2	0.9695	100	0.162	Contact Map
2ob5A	2	0.9924	100	0.228	Contact Map
4a34A	5	0.9695	100	0.257	Contact Map
3mvkA	5	0.9618	100	0.259	Contact Map
2wcvA	7	0.9542	100	0.294	Contact Map
2wcuA	2	0.9695	100	0.316	Contact Map
3p9xA	2	0.8473	15.9	0.949	Contact Map
3qhpA	1	0.7481	14.4	0.95	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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