T0388

Targets
387 388 389 390
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443 444 445 446
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511 512 513 514

T0388

probable glutathione peroxidase 8 (GPX8) Homo sapiens

Target type: Server only

Target sequence:

>T0388 LOC493869A, Homo sapiens, 174 residues
ENLYFQSMINSFYAFEVKDAKGRTVSLEKYKGKVSLVVNVASDCQLTDRNYLGLKELHKEFGPSHFSVLAFPCNQFGESEPRPSKEVESFARKNYGVTFPIFHKIKILGSEGEPAFRFLVDSSKKEPRWNFWKYLVNPEGQVVKFWRPEEPIEVIRPDIAALVRQVIIKKKEDL

Structure:
Method: X-ray, res=2.0Å, R/Rfree=0.17/0.20
Determined by: SGC
PDB ID: 3cyn

PyMOL of 3cyn

Domains:  PyMOL of domains

Single domain protein. N-terminal segment (36-43 in PDB numbering) extends away from the domain and may be removed for domain-based evaluation.

Each point represents first server model. Green, gray and black points are top 10, bottom 25% and the rest of prediction models. Blue line is the best-fit slope line (intersection 0) to the top 10 server models. Red line is the diagonal. Slope and root mean square y-x distance for the top 10 models (average difference between the domain GDT-TS scores and the whole chain GDT-TS score) are shown above the plot.

Structure classification:

Thioredoxin-like fold.

CASP category:

Comparative modeling:easy.

Closest templates:

2p31

Target sequence - PDB file inconsistencies:

None, except that PDB sequence is numbered starting from 36, which creates a 35-residue offset in numbers.

T0388    3cyn.pdb    T0388.pdb    PyMOL    PyMOL of domains   

We suggest to evaluate this target as a single domain spanning whole chain. However, N-terminal segment (target 1-8, pdb 36-43) extends away and may be removed, resulting in this domain definition:

1st domain: target 9-174 ; pdb 44-209

Sequence classification:

Glutathione peroxidase (GSHPx) in Pfam.

Server predictions:

T0388:pdb 36-209:seq 1-174:CM_easy;   alignment

388_1:pdb 44-209:seq 9-174:CM_easy;   alignment

click on a score in the table below to display the model in PyMOL

# GROUP ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ TS ↓ TR ↓ CS ↓ ↓ GROUP #
T0388 388_1 T0388 388_1 T0388 388_1 T0388 388_1
First score First Z-score Best score Best Z-score
1 pro−sp3−TASSER 89.66 85.63 91.31 93.07 84.04 92.33 1.53 1.44 1.37 1.49 0.20 1.34 91.24 87.12 92.16 93.83 90.16 93.24 1.96 1.55 1.47 1.65 1.28 1.45 pro−sp3−TASSER 1
2 Zhang−Server 88.51 86.21 91.24 91.87 89.66 91.95 1.25 1.57 1.36 1.20 1.34 1.27 88.65 86.21 91.24 92.02 89.66 92.09 1.19 1.30 1.27 1.10 1.15 1.19 Zhang−Server 2
3 MULTICOM−RANK 87.50 85.30 88.61 90.81 88.50 89.93 1.01 1.36 0.91 0.95 1.11 0.91 87.50 85.30 88.61 90.81 88.50 89.93 0.84 1.05 0.72 0.74 0.85 0.70 MULTICOM−RANK 3
4 YASARA 87.50 84.82 88.80 90.36 89.46 90.10 1.01 1.26 0.94 0.85 1.30 0.94 87.50 84.82 88.80 90.36 89.46 90.10 0.84 0.92 0.76 0.61 1.10 0.74 YASARA 4
5 FAMSD 87.36 85.63 87.45 90.96 88.15 88.56 0.98 1.44 0.71 0.99 1.04 0.66 87.36 85.63 87.45 90.96 88.15 88.56 0.80 1.14 0.47 0.79 0.76 0.39 FAMSD 5
6 MUSTER 87.36 84.67 88.59 90.81 89.41 90.04 0.98 1.23 0.91 0.95 1.29 0.93 87.36 84.67 88.59 90.81 89.41 90.04 0.80 0.88 0.71 0.74 1.09 0.73 MUSTER 6
7 Phyre_de_novo 87.36 84.48 87.81 90.06 87.15 89.05 0.98 1.18 0.77 0.77 0.83 0.75 87.36 84.48 87.81 90.06 87.15 89.05 0.80 0.83 0.55 0.52 0.49 0.50 Phyre_de_novo 7
8 MUProt 87.21 83.76 89.42 90.96 87.35 90.40 0.94 1.02 1.05 0.99 0.87 0.99 87.21 83.76 89.42 90.96 87.35 90.40 0.76 0.63 0.89 0.79 0.55 0.81 MUProt 8
9 MULTICOM−CMFR 87.21 83.19 89.19 90.51 86.60 90.35 0.94 0.90 1.01 0.88 0.72 0.98 87.21 83.62 89.19 90.51 87.15 90.35 0.76 0.59 0.84 0.65 0.49 0.80 MULTICOM−CMFR 9
10 fais−server 87.21 81.18 88.28 90.06 85.34 89.33 0.94 0.45 0.85 0.77 0.46 0.80 87.21 81.18 88.28 90.06 85.84 89.33 0.76 -0.08 0.65 0.52 0.15 0.57 fais−server 10
11 Phyre2 87.07 84.19 87.81 90.06 86.95 89.26 0.91 1.12 0.77 0.77 0.79 0.79 87.07 84.19 87.81 90.06 86.95 89.26 0.72 0.75 0.55 0.52 0.44 0.55 Phyre2 11
12 Poing 87.07 80.17 87.78 90.21 87.70 89.17 0.91 0.23 0.77 0.81 0.94 0.77 87.07 80.17 87.78 90.21 87.70 89.17 0.72 -0.36 0.54 0.56 0.64 0.53 Poing 12
13 Phragment 86.92 80.03 86.89 90.06 85.14 88.74 0.87 0.20 0.62 0.77 0.42 0.69 86.92 82.47 86.89 90.06 85.14 88.74 0.67 0.27 0.36 0.52 -0.03 0.43 Phragment 13
14 METATASSER 86.64 83.19 87.10 90.36 86.75 88.48 0.81 0.90 0.65 0.85 0.75 0.65 86.64 83.33 87.10 90.36 87.90 88.48 0.59 0.51 0.40 0.61 0.69 0.38 METATASSER 14
15 HHpred4 86.49 77.97 88.78 90.21 81.28 89.82 0.77 -0.26 0.94 0.81 -0.36 0.89 86.49 77.97 88.78 90.21 81.28 89.82 0.54 -0.96 0.75 0.56 -1.04 0.68 HHpred4 15
16 HHpred5 86.49 77.97 88.78 90.21 81.28 89.82 0.77 -0.26 0.94 0.81 -0.36 0.89 86.49 77.97 88.78 90.21 81.28 89.82 0.54 -0.96 0.75 0.56 -1.04 0.68 HHpred5 16
17 PS2−server 86.49 77.68 87.53 90.06 86.45 89.06 0.77 -0.32 0.73 0.77 0.69 0.75 86.49 81.47 87.53 90.06 86.45 89.06 0.54 -0.00 0.49 0.52 0.31 0.51 PS2−server 17
18 MULTICOM−REFINE 86.35 80.32 88.99 90.06 83.73 89.96 0.74 0.26 0.97 0.77 0.13 0.91 86.64 82.23 88.99 90.51 85.89 89.96 0.59 0.21 0.80 0.65 0.17 0.71 MULTICOM−REFINE 18
19 BAKER−ROBETTA 86.21 79.89 89.68 90.06 89.16 90.72 0.71 0.17 1.09 0.77 1.24 1.05 89.51 86.25 92.17 93.67 90.26 93.23 1.45 1.31 1.47 1.60 1.31 1.45 BAKER−ROBETTA 19
20 RAPTOR 86.21 79.69 87.71 90.21 88.50 88.99 0.71 0.12 0.76 0.81 1.11 0.74 86.21 81.70 87.71 90.21 88.50 88.99 0.46 0.06 0.53 0.56 0.85 0.49 RAPTOR 20
21 SAM−T06−server 86.21 79.50 90.04 89.16 86.04 90.38 0.71 0.08 1.15 0.56 0.61 0.99 86.21 79.50 90.04 89.16 86.04 90.38 0.46 -0.54 1.02 0.25 0.20 0.80 SAM−T06−server 21
22 SAM−T08−server 85.92 83.43 88.66 89.46 86.85 89.51 0.64 0.95 0.92 0.63 0.77 0.83 85.92 83.43 88.66 89.46 86.85 89.51 0.37 0.54 0.73 0.34 0.42 0.61 SAM−T08−server 22
23 3D−JIGSAW_V3 85.49 83.38 88.41 89.61 87.40 89.60 0.54 0.94 0.88 0.67 0.88 0.85 85.63 83.38 88.96 89.76 87.40 90.08 0.28 0.52 0.79 0.43 0.56 0.74 3D−JIGSAW_V3 23
24 BioSerf 85.49 80.51 86.57 88.70 82.28 87.96 0.54 0.31 0.56 0.45 -0.16 0.55 85.49 80.51 86.57 88.70 82.28 87.96 0.24 -0.27 0.29 0.11 -0.78 0.26 BioSerf 24
25 HHpred2 85.49 76.96 87.10 89.16 80.22 88.10 0.54 -0.48 0.65 0.56 -0.58 0.58 85.49 76.96 87.10 89.16 80.22 88.10 0.24 -1.24 0.40 0.25 -1.32 0.29 HHpred2 25
26 MULTICOM−CLUSTER 85.34 77.49 86.52 88.86 83.94 87.56 0.50 -0.36 0.55 0.49 0.18 0.48 87.36 84.29 89.51 90.81 87.60 90.40 0.80 0.77 0.91 0.74 0.61 0.81 MULTICOM−CLUSTER 26
27 Fiser−M4T 85.20 84.63 85.00 89.31 88.70 87.45 0.47 1.22 0.30 0.60 1.15 0.46 85.20 84.63 85.00 89.31 88.70 87.45 0.16 0.87 -0.04 0.30 0.90 0.14 Fiser−M4T 27
28 FFASsuboptimal 85.06 84.48 85.14 89.16 88.55 87.60 0.43 1.18 0.32 0.56 1.12 0.49 85.06 84.48 85.14 89.16 88.55 87.60 0.11 0.83 -0.01 0.25 0.86 0.18 FFASsuboptimal 28
29 FFASstandard 84.91 84.15 85.02 89.01 88.20 87.47 0.40 1.11 0.30 0.52 1.05 0.46 85.06 84.48 85.14 89.16 88.55 87.60 0.11 0.83 -0.01 0.25 0.86 0.18 FFASstandard 29
30 CpHModels 84.77 83.14 82.94 88.86 87.15 85.38 0.36 0.89 -0.06 0.49 0.83 0.09 84.77 83.14 82.94 88.86 87.15 85.38 0.03 0.46 -0.48 0.16 0.49 -0.32 CpHModels 30
31 FFASflextemplate 84.63 81.47 82.47 88.70 85.39 84.90 0.33 0.52 -0.14 0.45 0.47 0.00 85.06 84.48 85.14 89.16 88.55 87.60 0.11 0.83 -0.01 0.25 0.86 0.18 FFASflextemplate 31
32 LEE−SERVER 84.34 79.93 86.20 88.25 83.64 87.81 0.26 0.18 0.50 0.34 0.12 0.52 85.78 81.56 88.03 89.61 85.44 89.56 0.33 0.02 0.60 0.39 0.05 0.62 LEE−SERVER 32
33 GS−KudlatyPred 84.19 77.68 83.86 87.20 80.37 85.21 0.23 -0.32 0.10 0.09 -0.55 0.06 84.19 77.68 83.86 87.20 80.37 85.21 -0.15 -1.04 -0.28 -0.33 -1.28 -0.36 GS−KudlatyPred 33
34 FEIG 84.19 74.42 87.15 87.50 85.89 87.87 0.23 -1.04 0.66 0.17 0.58 0.54 87.36 82.66 90.61 91.11 85.89 91.59 0.80 0.32 1.14 0.83 0.17 1.08 FEIG 34
35 COMA−M 83.48 80.80 82.46 86.75 84.54 84.22 0.06 0.37 -0.14 -0.01 0.30 -0.12 84.48 80.80 84.13 87.95 84.54 85.67 -0.06 -0.19 -0.22 -0.11 -0.19 -0.26 COMA−M 35
36 3DShot2 83.05 81.42 82.02 86.14 84.74 83.33 -0.04 0.51 -0.21 -0.16 0.34 -0.28 83.05 81.42 82.02 86.14 84.74 83.33 -0.49 -0.02 -0.67 -0.65 -0.14 -0.79 3DShot2 36
37 Frankenstein 83.05 77.39 83.35 87.05 81.22 85.79 -0.04 -0.38 0.01 0.06 -0.38 0.16 86.21 85.63 86.64 90.36 89.76 89.10 0.46 1.14 0.30 0.61 1.18 0.51 Frankenstein 37
38 GS−MetaServer2 82.90 80.80 81.71 86.90 84.69 84.14 -0.08 0.37 -0.27 0.02 0.33 -0.14 82.90 80.80 81.71 86.90 84.69 84.14 -0.53 -0.19 -0.73 -0.42 -0.15 -0.60 GS−MetaServer2 38
39 keasar−server 82.90 78.97 82.71 86.75 82.63 84.02 -0.08 -0.03 -0.09 -0.01 -0.09 -0.16 87.21 84.82 89.60 90.81 86.60 90.42 0.76 0.92 0.93 0.74 0.35 0.81 keasar−server 39
40 3D−JIGSAW_AEP 82.33 76.72 84.81 86.30 80.42 85.95 -0.21 -0.53 0.26 -0.12 -0.54 0.19 85.92 81.85 88.88 90.06 85.79 90.02 0.37 0.10 0.77 0.52 0.14 0.72 3D−JIGSAW_AEP 40
41 3Dpro 82.18 80.17 82.40 85.84 83.73 83.49 -0.25 0.23 -0.15 -0.23 0.13 -0.25 82.18 80.46 82.40 85.84 84.04 83.49 -0.75 -0.28 -0.59 -0.74 -0.32 -0.75 3Dpro 41
42 GeneSilicoMetaServer 82.04 78.59 81.06 85.99 82.38 83.50 -0.28 -0.12 -0.38 -0.19 -0.14 -0.25 85.63 80.27 84.88 89.76 83.43 87.33 0.28 -0.33 -0.07 0.43 -0.48 0.12 GeneSilicoMetaServer 42
43 mGenTHREADER 81.61 79.79 80.55 85.54 83.64 82.98 -0.39 0.15 -0.46 -0.30 0.12 -0.34 81.61 79.79 80.55 85.54 83.64 82.98 -0.92 -0.46 -0.98 -0.83 -0.42 -0.86 mGenTHREADER 43
44 Pcons_local 81.03 79.89 79.25 84.94 83.73 81.67 -0.52 0.17 -0.68 -0.44 0.13 -0.58 85.20 84.44 85.08 89.31 88.50 87.53 0.16 0.81 -0.03 0.30 0.85 0.16 Pcons_local 44
45 Pcons_dot_net 81.03 79.89 79.25 84.94 83.73 81.67 -0.52 0.17 -0.68 -0.44 0.13 -0.58 85.20 84.44 85.08 89.31 88.50 87.53 0.16 0.81 -0.03 0.30 0.85 0.16 Pcons_dot_net 45
46 Pcons_multi 81.03 79.89 79.25 84.94 83.73 81.67 -0.52 0.17 -0.68 -0.44 0.13 -0.58 87.79 86.16 89.25 91.42 89.71 90.34 0.93 1.29 0.85 0.93 1.16 0.79 Pcons_multi 46
47 COMA 80.17 72.13 79.26 83.43 75.00 81.10 -0.73 -1.55 -0.68 -0.80 -1.64 -0.68 83.05 80.84 84.13 86.75 84.54 85.67 -0.49 -0.18 -0.22 -0.47 -0.19 -0.26 COMA 47
48 panther_server 80.17 70.02 75.91 83.28 72.64 77.08 -0.73 -2.01 -1.25 -0.84 -2.13 -1.41 80.60 78.02 78.96 83.58 81.98 80.77 -1.22 -0.95 -1.31 -1.42 -0.86 -1.36 panther_server 48
49 rehtnap 78.88 77.16 79.07 82.38 75.15 81.34 -1.03 -0.43 -0.71 -1.05 -1.61 -0.64 78.88 77.16 79.07 82.38 80.52 81.34 -1.74 -1.19 -1.29 -1.77 -1.24 -1.23 rehtnap 49
50 SAM−T02−server 78.16 75.48 73.65 81.48 78.67 75.70 -1.20 -0.81 -1.64 -1.27 -0.90 -1.66 85.06 84.48 85.14 89.16 88.55 87.59 0.11 0.83 -0.01 0.25 0.86 0.17 SAM−T02−server 50
51 forecast 78.16 72.17 77.53 81.93 75.65 78.96 -1.20 -1.54 -0.98 -1.16 -1.51 -1.07 78.16 72.17 77.53 81.93 75.65 78.96 -1.95 -2.56 -1.61 -1.91 -2.51 -1.77 forecast 51
52 ACOMPMOD 77.44 75.53 74.80 81.17 79.17 77.20 -1.38 -0.79 -1.44 -1.34 -0.79 -1.39 77.44 75.53 74.80 81.17 79.17 77.20 -2.17 -1.64 -2.19 -2.14 -1.59 -2.17 ACOMPMOD 52
53 FALCON_CONSENSUS 77.16 75.43 75.11 80.87 79.07 77.51 -1.44 -0.82 -1.39 -1.41 -0.81 -1.33 77.16 75.43 75.11 80.87 79.07 77.51 -2.25 -1.66 -2.12 -2.22 -1.62 -2.10 FALCON_CONSENSUS 53
54 FALCON 77.16 75.43 75.11 80.87 79.07 77.51 -1.44 -0.82 -1.39 -1.41 -0.81 -1.33 77.16 75.43 75.11 80.87 79.07 77.51 -2.25 -1.66 -2.12 -2.22 -1.62 -2.10 FALCON 54
55 FUGUE_KM 75.86 68.49 72.42 79.52 71.79 74.81 -1.75 -2.35 -1.85 -1.73 -2.30 -1.82 75.86 68.49 72.42 79.52 71.79 74.81 -2.64 -3.57 -2.69 -2.63 -3.52 -2.71 FUGUE_KM 55
56 nFOLD3 75.43 71.69 73.94 78.92 75.00 76.20 -1.85 -1.64 -1.59 -1.87 -1.64 -1.57 85.06 84.48 85.14 89.16 88.55 87.60 0.11 0.83 -0.01 0.25 0.86 0.18 nFOLD3 56
57 Distill 75.00 72.51 68.11 78.31 75.70 69.49 -1.95 -1.46 -2.58 -2.02 -1.50 -2.77 76.29 73.99 72.30 79.67 77.26 73.82 -2.51 -2.06 -2.71 -2.58 -2.09 -2.93 Distill 57
58 circle 74.86 72.46 74.02 78.31 75.80 76.27 -1.99 -1.47 -1.57 -2.02 -1.48 -1.55 85.49 82.04 84.60 89.61 85.99 87.05 0.24 0.15 -0.13 0.39 0.19 0.05 circle 58
59 MUFOLD−Server 68.10 65.52 66.17 71.23 68.52 67.73 -3.59 -3.01 -2.91 -3.70 -2.97 -3.09 68.97 65.52 66.79 71.99 69.08 68.29 -4.71 -4.39 -3.87 -4.88 -4.23 -4.18 MUFOLD−Server 59
60 PSI 49.28 42.96 49.69 51.66 45.03 50.99 -8.06 -7.99 -5.72 -8.35 -7.75 -6.10 78.45 75.43 77.39 81.78 79.07 78.80 -1.87 -1.66 -1.64 -1.95 -1.62 -1.81 PSI 60
61 OLGAFS 49.14 44.06 41.86 51.51 46.19 43.96 -8.09 -7.75 -7.05 -8.39 -7.52 -7.37 74.28 71.31 66.84 77.26 74.15 69.03 -3.12 -2.80 -3.86 -3.30 -2.91 -4.01 OLGAFS 61
62 mariner1 48.85 41.86 46.06 51.20 43.88 47.04 -8.16 -8.24 -6.34 -8.46 -7.99 -6.81 53.30 48.42 52.52 55.87 50.75 53.68 -9.40 -9.09 -6.88 -9.69 -9.03 -7.47 mariner1 62
63 FOLDpro 45.12 37.26 44.54 47.29 38.85 45.84 -9.05 -9.25 -6.60 -9.39 -9.01 -7.03 45.12 37.26 44.54 47.29 38.85 45.84 -11.85 -12.16 -8.56 -12.25 -12.14 -9.24 FOLDpro 63
64 MUFOLD−MD 21.70 18.63 39.98 22.74 19.53 40.84 -14.61 -13.37 -7.37 -15.22 -12.95 -7.93 21.70 18.63 40.65 22.74 19.53 41.41 -18.86 -17.28 -9.38 -19.59 -17.19 -10.24 MUFOLD−MD 64
65 RBO−Proteus 21.26 18.87 41.39 21.99 19.48 42.09 -14.71 -13.32 -7.13 -15.40 -12.96 -7.71 22.70 19.44 41.39 23.80 20.38 42.09 -18.56 -17.06 -9.22 -19.27 -16.97 -10.08 RBO−Proteus 65
66 RANDOM 13.34 11.53 13.34 14.28 12.57 14.28 -16.59 -14.94 -11.91 -17.23 -14.37 -12.71 13.34 11.53 13.34 14.28 12.57 14.28 -21.37 -19.24 -15.12 -22.11 -19.01 -16.35 RANDOM 66
67 schenk−torda−server 9.77 8.48 11.26 10.54 9.19 11.31 -17.44 -15.61 -12.26 -18.12 -15.06 -13.25 12.21 11.11 13.28 12.80 11.65 13.79 -21.71 -19.35 -15.14 -22.55 -19.25 -16.46 schenk−torda−server 67
68 BHAGEERATH                                     -16.59 -14.94 -11.91 -17.23 -14.37 -12.71                                     -21.37 -19.24 -15.12 -22.11 -19.01 -16.35 BHAGEERATH 68
69 LOOPP_Server                                     -16.59 -14.94 -11.91 -17.23 -14.37 -12.71                                     -21.37 -19.24 -15.12 -22.11 -19.01 -16.35 LOOPP_Server 69
70 Pushchino                                     -16.59 -14.94 -11.91 -17.23 -14.37 -12.71                                     -21.37 -19.24 -15.12 -22.11 -19.01 -16.35 Pushchino 70
71 huber−torda−server                                     -16.59 -14.94 -11.91 -17.23 -14.37 -12.71                                     -21.37 -19.24 -15.12 -22.11 -19.01 -16.35 huber−torda−server 71
72 mahmood−torda−server                                     -16.59 -14.94 -11.91 -17.23 -14.37 -12.71                                     -21.37 -19.24 -15.12 -22.11 -19.01 -16.35 mahmood−torda−server 72
73 pipe_int                                     -16.59 -14.94 -11.91 -17.23 -14.37 -12.71                                     -21.37 -19.24 -15.12 -22.11 -19.01 -16.35 pipe_int 73
74 test_http_server_01                                     -16.59 -14.94 -11.91 -17.23 -14.37 -12.71                                     -21.37 -19.24 -15.12 -22.11 -19.01 -16.35 test_http_server_01 74