RBSD - ECOLI - GREMLIN Contacts

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RBSD - D-ribose pyranase

UniProt:	P04982	Sequences: MKKGTVLNSDISSVISRLGHTDTLVVCDAGLPIPKSTTRIDMALTQGVPSFMQVLGVVTNEMQVEAAIIAEEIKHHNPQLHETLLTHLEQLQKHQGNTIEIRYTTHEQFKQQTAESQAVIRSGECSPYANIILCAGVTF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10817
Length:	139 (131)
Sequences:	860 (540)
Seq/√Len:	47.2

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	116_S	4.334	1.00
11_I	120_I	3.291	1.00
56_G	87_H	3.231	1.00
81_H	103_Y	2.691	1.00
66_A	102_R	2.627	1.00
50_S	53_Q	2.587	1.00
68_I	134_C	2.569	1.00
13_S	38_T	2.466	1.00
18_L	62_M	2.428	1.00
44_L	48_V	2.284	1.00
48_V	53_Q	2.121	1.00
45_T	57_V	2.063	1.00
2_K	61_E	2.062	1.00
10_D	38_T	2.016	0.99
66_A	134_C	1.987	0.99
67_A	88_L	1.863	0.99
80_L	129_A	1.861	0.99
13_S	17_R	1.842	0.99
69_I	103_Y	1.817	0.99
14_V	118_A	1.753	0.98
69_I	73_I	1.722	0.98
65_E	134_C	1.664	0.98
9_S	39_R	1.636	0.98
33_I	39_R	1.599	0.97
44_L	54_V	1.562	0.97
67_A	101_I	1.550	0.97
29_A	125_C	1.544	0.97
22_D	117_Q	1.515	0.96
55_L	133_L	1.507	0.96
26_V	58_V	1.493	0.96
12_S	16_S	1.492	0.96
25_V	109_F	1.482	0.96
23_T	134_C	1.478	0.96
23_T	68_I	1.430	0.95
2_K	12_S	1.421	0.94
59_T	64_V	1.372	0.93
104_T	112_Q	1.310	0.92
74_K	103_Y	1.305	0.92
63_Q	138_T	1.261	0.90
73_I	77_N	1.252	0.90
25_V	113_T	1.252	0.90
24_L	118_A	1.243	0.89
73_I	103_Y	1.228	0.89
111_Q	114_A	1.223	0.89
71_E	75_H	1.208	0.88
31_L	109_F	1.204	0.88
25_V	31_L	1.197	0.88
82_E	86_T	1.194	0.87
73_I	84_L	1.184	0.87
45_T	56_G	1.175	0.87
35_K	117_Q	1.159	0.86
14_V	40_I	1.136	0.85
108_Q	111_Q	1.120	0.84
11_I	42_M	1.111	0.83
15_I	58_V	1.090	0.82
36_S	114_A	1.087	0.82
18_L	24_L	1.071	0.81
62_M	135_A	1.058	0.80
10_D	13_S	1.056	0.80
51_F	124_E	1.045	0.79
21_T	65_E	1.043	0.79
33_I	119_V	1.023	0.78
15_I	61_E	1.022	0.78
46_Q	125_C	1.012	0.77
55_L	84_L	1.010	0.77
24_L	58_V	1.010	0.77
9_S	17_R	1.000	0.76
17_R	39_R	0.991	0.76
55_L	131_I	0.990	0.75
46_Q	138_T	0.988	0.75
68_I	104_T	0.977	0.74
5_T	60_N	0.973	0.74
71_E	74_K	0.959	0.73
110_K	128_Y	0.950	0.72
68_I	112_Q	0.944	0.72
23_T	132_I	0.938	0.71
4_G	60_N	0.937	0.71
63_Q	136_G	0.935	0.71
113_T	119_V	0.930	0.71
24_L	62_M	0.929	0.71
52_M	83_T	0.927	0.71
27_C	31_L	0.918	0.70
85_L	103_Y	0.918	0.70
21_T	31_L	0.916	0.70
44_L	57_V	0.908	0.69
100_E	114_A	0.903	0.68
53_Q	56_G	0.903	0.68
23_T	112_Q	0.871	0.66
57_V	60_N	0.869	0.66
52_M	80_L	0.856	0.64
9_S	12_S	0.853	0.64
31_L	113_T	0.840	0.63
85_L	101_I	0.839	0.63
24_L	40_I	0.839	0.63
58_V	120_I	0.829	0.62
19_G	33_I	0.824	0.61
29_A	138_T	0.822	0.61
40_I	118_A	0.807	0.60
14_V	24_L	0.802	0.59
79_Q	82_E	0.787	0.58
73_I	81_H	0.785	0.58
80_L	83_T	0.778	0.57
69_I	131_I	0.773	0.56
65_E	119_V	0.751	0.54
31_L	119_V	0.748	0.54
9_S	43_A	0.745	0.54
71_E	103_Y	0.741	0.53
77_N	126_S	0.739	0.53
9_S	13_S	0.735	0.53
10_D	40_I	0.731	0.52
2_K	16_S	0.728	0.52
52_M	87_H	0.725	0.52
54_V	122_S	0.724	0.52
120_I	138_T	0.722	0.51
29_A	46_Q	0.716	0.51
67_A	131_I	0.704	0.50
45_T	48_V	0.699	0.49
13_S	39_R	0.697	0.49
44_L	122_S	0.696	0.49
13_S	40_I	0.692	0.48
77_N	83_T	0.675	0.47
17_R	117_Q	0.672	0.46
18_L	135_A	0.660	0.45
52_M	56_G	0.654	0.45
19_G	136_G	0.648	0.44
72_E	106_H	0.647	0.44
84_L	131_I	0.643	0.44
56_G	83_T	0.641	0.43
81_H	85_L	0.640	0.43
19_G	43_A	0.640	0.43
59_T	97_N	0.639	0.43
6_V	15_I	0.638	0.43
11_I	15_I	0.638	0.43
8_N	43_A	0.637	0.43
39_R	43_A	0.635	0.43
50_S	56_G	0.628	0.42
65_E	136_G	0.623	0.42
31_L	129_A	0.623	0.42
15_I	137_V	0.620	0.41
12_S	43_A	0.617	0.41
72_E	110_K	0.615	0.41
2_K	8_N	0.614	0.41
39_R	67_A	0.613	0.41
27_C	129_A	0.612	0.41
19_G	127_P	0.608	0.40
8_N	49_P	0.606	0.40
56_G	88_L	0.605	0.40
55_L	59_T	0.604	0.40
3_K	12_S	0.602	0.40
79_Q	98_T	0.601	0.39
24_L	120_I	0.599	0.39
47_G	124_E	0.594	0.39
21_T	134_C	0.592	0.39
25_V	119_V	0.589	0.38
3_K	63_Q	0.588	0.38
61_E	64_V	0.584	0.38
45_T	53_Q	0.584	0.38
74_K	79_Q	0.579	0.37
69_I	81_H	0.576	0.37
69_I	84_L	0.575	0.37
114_A	117_Q	0.573	0.37
6_V	138_T	0.571	0.37
11_I	138_T	0.570	0.37
104_T	115_E	0.568	0.36
57_V	61_E	0.561	0.36
66_A	100_E	0.560	0.36
4_G	61_E	0.560	0.36
19_G	27_C	0.557	0.35
70_A	106_H	0.555	0.35
31_L	124_E	0.555	0.35
23_T	115_E	0.554	0.35
64_V	88_L	0.553	0.35
86_T	100_E	0.552	0.35
31_L	65_E	0.551	0.35
16_S	58_V	0.551	0.35
9_S	16_S	0.550	0.35
102_R	112_Q	0.539	0.34
79_Q	120_I	0.533	0.33
30_G	130_N	0.532	0.33
18_L	120_I	0.529	0.33
67_A	99_I	0.527	0.33
33_I	36_S	0.522	0.32
15_I	138_T	0.522	0.32
15_I	62_M	0.520	0.32
32_P	127_P	0.520	0.32
39_R	80_L	0.518	0.32
7_L	29_A	0.517	0.32
125_C	138_T	0.516	0.32
48_V	61_E	0.514	0.32
70_A	139_F	0.511	0.31
104_T	114_A	0.510	0.31
109_F	113_T	0.507	0.31
100_E	105_T	0.504	0.31
75_H	111_Q	0.504	0.31
106_H	110_K	0.503	0.31
113_T	116_S	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
3e7nA	6	1	100	0.168	Contact Map
1ogdA	5	0.9424	100	0.18	Contact Map
3p12A	2	0.9209	100	0.191	Contact Map
2ob5A	2	0.9712	100	0.247	Contact Map
3mvkA	5	0.9496	100	0.278	Contact Map
4a34A	5	0.9424	100	0.28	Contact Map
2wcvA	7	0.9281	100	0.314	Contact Map
2wcuA	2	0.9424	100	0.331	Contact Map
3oy2A	2	0.9712	21.1	0.948	Contact Map
1wzuA	1	0.4101	15.9	0.951	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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