YSDA - BACSU - GREMLIN Contacts

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YSDA - Uncharacterized protein YsdA

UniProt:	P94519	Sequences: MIIAAYLVLINLCGFWVMGIDKRKAQQHKWRISEDRLWLIAIVFGALGVWLGMQTFRHKTKHASFKYGVPLLLVIEAILIAIYYSPFDL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	89 (80)
Sequences:	1074 (928)
Seq/√Len:	103.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_G	56_F	3.175	1.00
17_V	40_I	3.070	1.00
46_A	76_E	2.972	1.00
14_G	49_V	2.859	1.00
15_F	55_T	2.800	1.00
18_M	49_V	2.716	1.00
14_G	40_I	2.355	1.00
20_I	24_K	2.238	1.00
41_A	49_V	1.959	1.00
72_L	76_E	1.895	1.00
23_R	27_Q	1.762	1.00
38_W	69_V	1.713	1.00
14_G	18_M	1.702	1.00
46_A	72_L	1.691	1.00
68_G	72_L	1.651	1.00
33_S	36_R	1.651	1.00
49_V	69_V	1.622	1.00
38_W	64_S	1.557	1.00
6_Y	44_F	1.488	1.00
54_Q	66_K	1.445	1.00
39_L	43_V	1.397	1.00
6_Y	10_I	1.372	1.00
38_W	72_L	1.327	0.99
10_I	43_V	1.325	0.99
16_W	20_I	1.321	0.99
19_G	23_R	1.320	0.99
63_A	67_Y	1.299	0.99
50_W	69_V	1.297	0.99
18_M	38_W	1.290	0.99
7_L	76_E	1.282	0.99
20_I	32_I	1.279	0.99
23_R	26_Q	1.177	0.99
24_K	32_I	1.145	0.98
50_W	73_L	1.133	0.98
52_G	56_F	1.069	0.97
46_A	73_L	1.068	0.97
63_A	66_K	1.048	0.97
53_M	69_V	1.033	0.97
19_G	52_G	0.965	0.95
69_V	72_L	0.926	0.94
73_L	76_E	0.919	0.94
24_K	29_K	0.901	0.93
53_M	70_P	0.897	0.93
46_A	69_V	0.886	0.92
23_R	29_K	0.885	0.92
15_F	56_F	0.876	0.92
64_S	69_V	0.869	0.92
17_V	32_I	0.862	0.91
42_I	72_L	0.848	0.91
46_A	70_P	0.828	0.89
18_M	69_V	0.826	0.89
20_I	74_V	0.816	0.89
78_I	82_I	0.813	0.89
22_K	31_R	0.811	0.88
6_Y	43_V	0.796	0.88
10_I	13_C	0.796	0.88
57_R	60_T	0.792	0.87
53_M	62_H	0.787	0.87
7_L	11_N	0.786	0.87
67_Y	71_L	0.785	0.87
21_D	58_H	0.772	0.86
11_N	47_L	0.765	0.85
53_M	68_G	0.758	0.85
22_K	58_H	0.738	0.83
41_A	69_V	0.733	0.83
61_K	66_K	0.732	0.83
20_I	43_V	0.716	0.81
37_L	49_V	0.709	0.81
18_M	41_A	0.706	0.80
69_V	73_L	0.704	0.80
22_K	65_F	0.703	0.80
40_I	44_F	0.691	0.79
50_W	54_Q	0.681	0.78
41_A	72_L	0.654	0.75
25_A	58_H	0.654	0.75
74_V	78_I	0.653	0.75
58_H	65_F	0.641	0.74
30_W	64_S	0.638	0.73
14_G	17_V	0.637	0.73
31_R	65_F	0.636	0.73
35_D	82_I	0.632	0.73
31_R	58_H	0.632	0.73
50_W	66_K	0.627	0.72
62_H	68_G	0.627	0.72
15_F	52_G	0.627	0.72
56_F	60_T	0.622	0.72
71_L	75_I	0.620	0.71
28_H	61_K	0.619	0.71
38_W	41_A	0.608	0.70
41_A	65_F	0.607	0.70
18_M	52_G	0.605	0.69
56_F	62_H	0.605	0.69
22_K	25_A	0.595	0.68
42_I	75_I	0.590	0.68
54_Q	57_R	0.584	0.67
21_D	31_R	0.584	0.67
21_D	25_A	0.580	0.66
20_I	39_L	0.579	0.66
71_L	74_V	0.574	0.65
46_A	53_M	0.574	0.65
21_D	65_F	0.572	0.65
55_T	80_I	0.568	0.65
14_G	44_F	0.567	0.64
48_G	52_G	0.566	0.64
16_W	83_Y	0.562	0.64
15_F	20_I	0.562	0.64
10_I	51_L	0.562	0.64
16_W	26_Q	0.560	0.64
25_A	31_R	0.553	0.63
12_L	78_I	0.539	0.61
8_V	11_N	0.538	0.60
35_D	39_L	0.535	0.60
75_I	82_I	0.528	0.59
15_F	19_G	0.528	0.59
77_A	81_A	0.525	0.59
22_K	34_E	0.515	0.57
38_W	68_G	0.514	0.57
4_A	8_V	0.513	0.57
18_M	62_H	0.509	0.56
7_L	80_I	0.500	0.55

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
4cofA	3	0.2135	8.8	0.922	Contact Map
2ks1B	1	0.4045	5.5	0.929	Contact Map
4pypA	1	0.9438	4.7	0.931	Contact Map
4l6rA	1	0.9775	4.6	0.931	Contact Map
4zw9A	1	0.9326	4.3	0.932	Contact Map
2yiuB	1	0.2809	3.5	0.935	Contact Map
4j05A	3	0.9888	3	0.938	Contact Map
1fftB	1	0.764	2.8	0.938	Contact Map
2l2tA	2	0.4045	2.6	0.94	Contact Map
3wdoA	1	1	2.6	0.94	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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