T0408

X-ray Targets
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T0408

carboxymuconolactone decarboxylase family protein possibly involved in oxygen detoxification from Methanococcus jannaschii

Target type: Server only

Target sequence:

>T0408 Hypothetical protein MJ0742, Methanococcus jannaschii, 104 residues
MKNEVFFGEGMKVVKEKYPDLYDIIVKLNDTVFTGKTLDYKTQKLIAIGIVASRCDEVAIEKQMKSAMKELGITKEEIADVLRVVLLTSGMPAFTKAMKILEKL

Structure:
Method: X-ray, res=1.75Å, R/Rfree=0.17/0.20
Determined by: JCSG
PDB ID: 3d7i

3d7i_A cartoon
Cartoon diagram of 408: 3d7i chain A

PyMOL of 3d7i

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

AhpD-like fold.

CASP category:

Comparative modeling:medium.

Closest templates:

2cwq, 2ouw, 3bey.

Target sequence - PDB file inconsistencies:

T0408    3d7i.pdb    T0408.pdb    PyMOL    PyMOL of domains    

T0408    1 MKNEVFFGEGMKVVKEKYPDLYDIIVKLNDTVFTGKTLDYKTQKLIAIGIVASRCDEVAIEKQMKSAMKELGITKEEIADVLRVVLLTSGMPAFTKAMKILEKL 104
           ~~~~~~~|||||||:::|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3d7iA    8 -------GEGMKVVAAAYPDLYDIIVKLNDTVFTGKTLDYKTQKLIAIGIVASRCDEVAIEKQMKSAMKELGITKEEIADVLRVVLLTSGMPAFTKAMKILEKL 104

Residue change log: change 15 A to K; change 16 A to E; change 17 A to K; change 11, 64, 68, 91, 98, MSE to MET;

Single domain protein: target 8-104 ; pdb 8-104

Sequence classification:

Carboxymuconolactone decarboxylase family CMD in Pfam.

Server predictions:

T0408:pdb 8-104:seq 8-104:CM_medium;   alignment

distribution of first scores
First models for T0408: Gaussian kernel density estimation for GDT-TS scores of the first server models, plotted at various bandwidths (=standard deviations). The GDT-TS scores are shown as a spectrum along the horizontal axis: each bar represents first server model. The bars are colored green, gray and black for top 10, bottom 25% and the rest of servers. The family of curves with varying bandwidth is shown. Bandwidth varies from 0.3 to 8.2 GDT-TS % units with a step of 0.1, which corresponds to the color ramp from magenta through blue to cyan. Thicker curves: red, yellow-framed brown and black, correspond to bandwidths 1, 2 and 4 respectively.

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 ↓ ↓ GROUP #
T0408 T0408 T0408 T0408
First score First Z-score Best score Best Z-score
1 METATASSER 84.02 80.93 83.98 1.92 2.17 1.94 84.02 80.93 83.98 1.92 2.23 1.87 METATASSER 1
2 Zhang−Server 82.22 77.75 86.09 1.70 1.84 2.16 82.22 77.75 86.09 1.59 1.72 2.17 Zhang−Server 2
3 MULTICOM−REFINE 80.67 76.38 81.76 1.50 1.69 1.71 81.70 77.06 82.00 1.49 1.60 1.59 MULTICOM−REFINE 3
4 MULTICOM−RANK 78.61 72.42 80.79 1.24 1.27 1.61 85.05 79.90 81.98 2.11 2.06 1.58 MULTICOM−RANK 4
5 MULTICOM−CLUSTER 78.61 72.42 80.79 1.24 1.27 1.61 81.96 74.06 81.98 1.54 1.12 1.58 MULTICOM−CLUSTER 5
6 MUProt 78.35 73.37 81.28 1.21 1.37 1.66 78.61 73.97 81.37 0.93 1.11 1.50 MUProt 6
7 HHpred2 78.35 71.48 77.49 1.21 1.17 1.27 78.35 71.48 77.49 0.88 0.71 0.94 HHpred2 7
8 FAMSD 77.83 73.54 74.46 1.14 1.39 0.96 77.83 73.54 74.46 0.78 1.04 0.51 FAMSD 8
9 panther_server 77.83 64.09 71.81 1.14 0.38 0.69 77.83 64.09 71.81 0.78 -0.48 0.13 panther_server 9
10 circle 77.58 72.42 74.07 1.11 1.27 0.92 77.58 73.37 74.11 0.74 1.01 0.46 circle 10
11 nFOLD3 76.55 73.45 72.40 0.98 1.38 0.75 76.55 73.45 72.40 0.55 1.02 0.22 nFOLD3 11
12 GS−KudlatyPred 76.03 71.05 74.49 0.92 1.12 0.97 76.03 71.05 74.49 0.45 0.64 0.52 GS−KudlatyPred 12
13 3DShot2 76.03 67.10 64.86 0.92 0.70 -0.02 76.03 67.10 64.86 0.45 0.00 -0.86 3DShot2 13
14 Pcons_multi 75.26 69.76 74.09 0.82 0.98 0.93 75.26 69.76 74.09 0.31 0.43 0.46 Pcons_multi 14
15 MUFOLD−Server 75.26 69.42 66.44 0.82 0.95 0.14 76.03 71.48 68.64 0.45 0.71 -0.32 MUFOLD−Server 15
16 pro−sp3−TASSER 74.74 65.64 77.34 0.76 0.55 1.26 82.99 80.07 84.24 1.73 2.09 1.91 pro−sp3−TASSER 16
17 LEE−SERVER 74.48 66.24 76.28 0.72 0.61 1.15 75.52 70.19 76.28 0.36 0.50 0.77 LEE−SERVER 17
18 MULTICOM−CMFR 74.48 62.80 74.39 0.72 0.24 0.96 79.38 75.43 82.27 1.07 1.34 1.63 MULTICOM−CMFR 18
19 BAKER−ROBETTA 72.68 65.46 67.49 0.50 0.53 0.25 73.20 66.32 70.13 -0.07 -0.12 -0.11 BAKER−ROBETTA 19
20 FALCON 72.68 63.40 70.51 0.50 0.31 0.56 77.06 64.00 73.05 0.64 -0.49 0.31 FALCON 20
21 Fiser−M4T 72.42 64.86 70.11 0.47 0.46 0.52 72.42 64.86 70.11 -0.21 -0.36 -0.11 Fiser−M4T 21
22 COMA 72.42 51.12 64.77 0.47 -1.00 -0.03 72.42 67.95 66.99 -0.21 0.14 -0.55 COMA 22
23 CpHModels 71.91 64.43 59.59 0.40 0.42 -0.56 71.91 64.43 59.59 -0.31 -0.42 -1.61 CpHModels 23
24 keasar−server 71.91 62.63 70.19 0.40 0.22 0.53 72.68 65.29 70.42 -0.16 -0.29 -0.06 keasar−server 24
25 PSI 71.65 61.00 66.55 0.37 0.05 0.15 78.09 71.56 77.06 0.83 0.72 0.88 PSI 25
26 MUSTER 71.39 62.97 71.91 0.34 0.26 0.70 80.67 73.97 75.98 1.31 1.11 0.73 MUSTER 26
27 Pcons_local 71.13 61.51 65.53 0.30 0.11 0.05 76.29 66.32 71.07 0.50 -0.12 0.03 Pcons_local 27
28 Pcons_dot_net 71.13 61.51 65.53 0.30 0.11 0.05 73.20 66.32 70.13 -0.07 -0.12 -0.11 Pcons_dot_net 28
29 rehtnap 70.88 64.86 59.04 0.27 0.46 -0.62 71.91 64.86 63.01 -0.31 -0.36 -1.12 rehtnap 29
30 FUGUE_KM 70.88 60.57 66.73 0.27 0.00 0.17 70.88 62.54 66.73 -0.50 -0.73 -0.59 FUGUE_KM 30
31 COMA−M 70.36 67.95 66.99 0.21 0.79 0.20 73.45 70.53 66.99 -0.02 0.56 -0.55 COMA−M 31
32 pipe_int 70.36 63.83 67.20 0.21 0.35 0.22 70.36 66.41 70.14 -0.59 -0.11 -0.10 pipe_int 32
33 mGenTHREADER 69.84 62.97 65.69 0.14 0.26 0.06 69.84 62.97 65.69 -0.69 -0.66 -0.74 mGenTHREADER 33
34 ACOMPMOD 69.84 54.55 70.70 0.14 -0.64 0.58 69.84 64.17 70.70 -0.69 -0.47 -0.02 ACOMPMOD 34
35 HHpred4 69.07 52.92 59.97 0.04 -0.81 -0.52 69.07 52.92 59.97 -0.83 -2.27 -1.55 HHpred4 35
36 3D−JIGSAW_V3 68.81 61.60 62.40 0.01 0.11 -0.27 69.07 61.60 62.50 -0.83 -0.88 -1.19 3D−JIGSAW_V3 36
37 forecast 68.56 60.14 68.38 -0.02 -0.04 0.34 68.56 60.14 68.38 -0.92 -1.11 -0.36 forecast 37
38 GeneSilicoMetaServer 68.56 59.79 56.34 -0.02 -0.08 -0.90 76.55 67.61 68.39 0.55 0.09 -0.35 GeneSilicoMetaServer 38
39 RAPTOR 68.56 53.78 69.44 -0.02 -0.72 0.45 74.48 66.75 76.17 0.17 -0.05 0.76 RAPTOR 39
40 3Dpro 68.04 63.23 59.62 -0.08 0.29 -0.56 68.04 63.23 59.62 -1.02 -0.62 -1.60 3Dpro 40
41 huber−torda−server 67.78 50.77 56.95 -0.12 -1.04 -0.83 67.78 61.08 67.01 -1.07 -0.96 -0.55 huber−torda−server 41
42 YASARA 67.53 61.68 58.96 -0.15 0.12 -0.63 68.81 61.68 58.96 -0.88 -0.87 -1.70 YASARA 42
43 SAM−T08−server 67.27 63.49 77.13 -0.18 0.32 1.24 67.27 63.49 77.13 -1.16 -0.58 0.89 SAM−T08−server 43
44 FFASflextemplate 67.27 60.74 56.02 -0.18 0.02 -0.93 67.27 60.74 56.02 -1.16 -1.02 -2.12 FFASflextemplate 44
45 Frankenstein 66.75 64.00 41.59 -0.25 0.37 -2.41 77.83 65.29 77.36 0.78 -0.29 0.93 Frankenstein 45
46 FFASstandard 66.75 61.77 57.74 -0.25 0.13 -0.75 78.09 64.00 75.95 0.83 -0.49 0.72 FFASstandard 46
47 FFASsuboptimal 66.75 61.77 57.74 -0.25 0.13 -0.75 67.27 61.77 57.74 -1.16 -0.85 -1.87 FFASsuboptimal 47
48 HHpred5 66.24 61.60 57.90 -0.31 0.11 -0.74 66.24 61.60 57.90 -1.35 -0.88 -1.85 HHpred5 48
49 Phyre_de_novo 64.69 50.09 64.36 -0.51 -1.11 -0.07 77.06 72.25 76.31 0.64 0.83 0.78 Phyre_de_novo 49
50 fais−server 64.17 54.04 55.84 -0.57 -0.69 -0.95 71.65 66.06 69.76 -0.35 -0.16 -0.16 fais−server 50
51 PS2−server 63.66 54.21 66.17 -0.63 -0.67 0.11 75.52 71.56 75.75 0.36 0.72 0.70 PS2−server 51
52 3D−JIGSAW_AEP 63.14 59.71 63.69 -0.70 -0.09 -0.14 65.72 60.74 64.23 -1.45 -1.02 -0.95 3D−JIGSAW_AEP 52
53 Poing 63.14 54.73 47.51 -0.70 -0.62 -1.80 77.06 72.08 76.31 0.64 0.80 0.78 Poing 53
54 Phyre2 63.14 54.73 47.52 -0.70 -0.62 -1.80 77.06 72.25 76.31 0.64 0.83 0.78 Phyre2 54
55 Phragment 63.14 54.73 47.54 -0.70 -0.62 -1.80 77.06 72.25 76.31 0.64 0.83 0.78 Phragment 55
56 GS−MetaServer2 63.14 54.38 50.29 -0.70 -0.65 -1.52 71.13 63.06 64.32 -0.45 -0.64 -0.93 GS−MetaServer2 56
57 SAM−T02−server 60.57 51.29 46.42 -1.02 -0.98 -1.92 75.26 70.62 67.34 0.31 0.57 -0.50 SAM−T02−server 57
58 Pushchino 58.25 52.75 49.23 -1.31 -0.83 -1.63 58.25 52.75 49.23 -2.82 -2.30 -3.09 Pushchino 58
59 RBO−Proteus 53.35 44.07 63.83 -1.93 -1.75 -0.13 53.35 44.07 63.83 -3.72 -3.70 -1.00 RBO−Proteus 59
60 FALCON_CONSENSUS 52.84 44.76 63.89 -1.99 -1.68 -0.12 61.34 53.35 73.05 -2.25 -2.20 0.31 FALCON_CONSENSUS 60
61 MUFOLD−MD 49.74 42.01 66.89 -2.38 -1.97 0.19 49.74 42.01 66.89 -4.39 -4.03 -0.57 MUFOLD−MD 61
62 BioSerf 48.71 30.67 65.58 -2.51 -3.18 0.05 48.71 30.67 65.58 -4.58 -5.85 -0.75 BioSerf 62
63 mariner1 48.20 42.01 21.77 -2.58 -1.97 -4.45 62.89 57.73 54.43 -1.97 -1.50 -2.35 mariner1 63
64 FEIG 46.91 32.22 56.60 -2.74 -3.02 -0.87 78.35 72.68 77.70 0.88 0.90 0.97 FEIG 64
65 FOLDpro 39.95 32.73 38.86 -3.61 -2.96 -2.69 68.04 63.23 59.62 -1.02 -0.62 -1.60 FOLDpro 65
66 SAM−T06−server 37.89 36.51 48.98 -3.87 -2.56 -1.65 61.08 55.16 49.49 -2.30 -1.91 -3.05 SAM−T06−server 66
67 LOOPP_Server 31.19 25.17 12.06 -4.71 -3.77 -5.44 61.08 51.55 58.21 -2.30 -2.49 -1.81 LOOPP_Server 67
68 Distill 29.38 20.96 12.45 -4.94 -4.22 -5.40 29.38 21.56 17.98 -8.13 -7.31 -7.54 Distill 68
69 RANDOM 25.86 21.86 25.86 -5.38 -4.12 -4.03 25.86 21.86 25.86 -8.78 -7.26 -6.42 RANDOM 69
70 mahmood−torda−server 22.68 16.15 13.09 -5.78 -4.73 -5.34 22.68 18.99 17.39 -9.37 -7.73 -7.63 mahmood−torda−server 70
71 schenk−torda−server 21.65 18.56 0.41 -5.91 -4.47 -6.64 26.29 21.13 9.57 -8.70 -7.38 -8.74 schenk−torda−server 71
72 OLGAFS 19.59 16.50 -11.68 -6.17 -4.69 -7.88 76.55 71.56 72.08 0.55 0.72 0.17 OLGAFS 72
73 BHAGEERATH                   -5.38 -4.12 -4.03                   -8.78 -7.26 -6.42 BHAGEERATH 73
74 test_http_server_01                   -5.38 -4.12 -4.03                   -8.78 -7.26 -6.42 test_http_server_01 74