T0481

Targets
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T0481

DinB-like protein (NP_389123.1) from Bacillus subtilis

Target type: Server only

Target sequence:

>T0481 NP_389123.1, Bacillus subtilis, 154 residues
MCQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQNKQEETETDLNVLAKTYTEKTVAILEQLTEEQLDREIDLTSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELPFYQQRM

Structure:
Method: X-ray, res=2.3Å, R/Rfree=0.22/0.27
Determined by: JCSG
PDB ID: 3dka

3dka_A cartoon
Cartoon diagram of 481: 3dka chain A

PyMOL of 3dka

Domains:  PyMOL of domains

Single domain protein.

Structure classification:

DinB/YfiT-like putative metalloenzymes.

CASP category:

Comparative modeling:medium.

Closest templates:

2qe9.

Target sequence - PDB file inconsistencies:

T0481    3dka.pdb    T0481.pdb    PyMOL    PyMOL of domains    

T0481    1 MCQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQNKQEETETDLNVLAKTYTEKTVAILEQLTEEQLDREIDLTSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELPFYQQRM 154
           ~~~~|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||~~~~|||||||||||||||||||||||||||||||||~~~|||||||||||||||||||||||||||||||||||||||||||||
3dkaA    5 ----NQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQN----TETDLNVLAKTYTEKTVAILEQLTEEQLDREID---AFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELPFYQQRM 154

Residue change log: change 39, 125, 142, 154, MSE to MET;

Single domain protein: target 5-69, 74-106, 110-154 ; pdb 5-69, 74-106, 110-154

Sequence classification:

DinB family (PF05163) in Pfam.

Comments:

This protein is a close homolog of T0406:

Server predictions:

T0481:pdb 5-154:seq 5-154:CM_medium;   alignment

distribution of first scores
First models for T0481: 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 #
T0481 T0481 T0481 T0481
First score First Z-score Best score Best Z-score
1 LEE−SERVER 72.73 65.27 70.03 1.44 2.31 1.70 72.73 66.14 71.89 1.63 2.40 2.06 LEE−SERVER 1
2 pro−sp3−TASSER 71.15 58.10 71.49 1.23 1.30 1.92 73.25 63.23 72.90 1.72 1.90 2.24 pro−sp3−TASSER 2
3 Pcons_multi 70.98 56.82 69.29 1.21 1.12 1.59 73.25 62.30 70.63 1.72 1.74 1.83 Pcons_multi 3
4 FEIG 69.93 60.96 65.12 1.08 1.70 0.97 73.25 66.61 69.14 1.72 2.48 1.56 FEIG 4
5 METATASSER 69.93 60.55 67.35 1.08 1.65 1.30 69.93 60.55 68.14 1.13 1.44 1.38 METATASSER 5
6 RAPTOR 69.93 57.69 67.64 1.08 1.24 1.35 70.98 62.35 68.14 1.32 1.75 1.38 RAPTOR 6
7 MULTICOM−CMFR 69.23 52.62 65.37 0.99 0.53 1.01 69.23 56.18 67.33 1.01 0.68 1.23 MULTICOM−CMFR 7
8 MULTICOM−CLUSTER 68.36 58.68 67.28 0.87 1.38 1.29 68.36 58.68 67.28 0.86 1.11 1.22 MULTICOM−CLUSTER 8
9 Phyre_de_novo 67.66 58.68 68.03 0.78 1.38 1.41 67.66 58.68 68.03 0.73 1.11 1.36 Phyre_de_novo 9
10 MULTICOM−RANK 67.31 54.49 66.44 0.74 0.79 1.17 68.36 54.49 66.96 0.86 0.39 1.17 MULTICOM−RANK 10
11 CpHModels 66.96 54.95 59.58 0.69 0.86 0.15 66.96 54.95 59.58 0.61 0.47 -0.17 CpHModels 11
12 Zhang−Server 66.08 50.41 64.61 0.58 0.22 0.90 70.11 60.78 65.77 1.17 1.48 0.95 Zhang−Server 12
13 SAM−T08−server 65.73 52.51 67.97 0.53 0.51 1.40 65.73 54.78 67.97 0.39 0.44 1.35 SAM−T08−server 13
14 MULTICOM−REFINE 65.21 49.71 63.07 0.46 0.12 0.67 66.26 52.16 64.67 0.48 -0.01 0.75 MULTICOM−REFINE 14
15 Frankenstein 64.86 55.77 63.66 0.42 0.97 0.76 64.86 55.77 63.66 0.24 0.61 0.57 Frankenstein 15
16 MUProt 64.86 50.17 63.18 0.42 0.18 0.69 65.56 51.63 63.18 0.36 -0.10 0.48 MUProt 16
17 3DShot2 64.86 48.13 58.84 0.42 -0.10 0.04 64.86 48.13 58.84 0.24 -0.70 -0.30 3DShot2 17
18 BioSerf 64.86 46.15 59.16 0.42 -0.38 0.09 64.86 46.15 59.16 0.24 -1.04 -0.25 BioSerf 18
19 Pcons_dot_net 64.51 48.78 59.56 0.37 -0.01 0.15 64.51 49.18 63.56 0.17 -0.52 0.55 Pcons_dot_net 19
20 GS−KudlatyPred 64.34 51.17 62.41 0.35 0.32 0.57 65.39 52.68 62.41 0.33 0.08 0.34 GS−KudlatyPred 20
21 3Dpro 64.16 51.05 59.36 0.33 0.31 0.12 64.16 51.05 59.36 0.11 -0.20 -0.21 3Dpro 21
22 Poing 64.16 49.59 60.23 0.33 0.10 0.25 64.16 49.59 60.23 0.11 -0.45 -0.05 Poing 22
23 Phragment 63.99 50.00 59.79 0.30 0.16 0.18 63.99 50.00 59.88 0.08 -0.38 -0.12 Phragment 23
24 Phyre2 63.99 49.77 60.07 0.30 0.13 0.22 63.99 49.77 60.07 0.08 -0.42 -0.08 Phyre2 24
25 HHpred2 62.94 55.36 53.72 0.17 0.91 -0.72 62.94 55.36 53.72 -0.10 0.54 -1.23 HHpred2 25
26 3D−JIGSAW_AEP 62.94 48.95 61.87 0.17 0.01 0.49 63.99 49.88 63.30 0.08 -0.40 0.50 3D−JIGSAW_AEP 26
27 mGenTHREADER 62.59 55.13 54.34 0.12 0.88 -0.63 62.59 55.13 54.34 -0.17 0.50 -1.12 mGenTHREADER 27
28 HHpred4 62.59 50.93 55.23 0.12 0.29 -0.49 62.59 50.93 55.23 -0.17 -0.22 -0.96 HHpred4 28
29 HHpred5 62.59 50.93 55.23 0.12 0.29 -0.49 62.59 50.93 55.23 -0.17 -0.22 -0.96 HHpred5 29
30 Pcons_local 62.24 51.05 56.38 0.08 0.31 -0.32 64.51 55.59 59.56 0.17 0.58 -0.17 Pcons_local 30
31 MUSTER 62.24 47.20 59.81 0.08 -0.23 0.19 65.21 50.06 62.10 0.30 -0.37 0.29 MUSTER 31
32 BAKER−ROBETTA 62.24 46.62 63.56 0.08 -0.32 0.74 62.24 50.52 63.56 -0.23 -0.29 0.55 BAKER−ROBETTA 32
33 PS2−server 62.06 44.64 55.79 0.05 -0.59 -0.41 62.59 53.50 59.39 -0.17 0.22 -0.21 PS2−server 33
34 panther_server 61.89 48.02 51.55 0.03 -0.12 -1.04 61.89 49.13 56.81 -0.29 -0.53 -0.67 panther_server 34
35 keasar−server 61.89 47.61 61.13 0.03 -0.18 0.38 61.89 47.96 61.26 -0.29 -0.73 0.13 keasar−server 35
36 COMA−M 61.89 44.23 62.37 0.03 -0.65 0.57 66.26 51.11 64.34 0.48 -0.19 0.69 COMA−M 36
37 PSI 61.71 57.75 55.83 0.01 1.25 -0.41 63.64 57.75 62.07 0.02 0.95 0.28 PSI 37
38 pipe_int 61.71 45.22 62.23 0.01 -0.51 0.54 61.71 45.22 62.23 -0.32 -1.20 0.31 pipe_int 38
39 FAMSD 61.36 47.03 59.83 -0.04 -0.26 0.19 61.89 53.38 59.83 -0.29 0.20 -0.13 FAMSD 39
40 fais−server 61.19 44.52 56.77 -0.06 -0.61 -0.27 62.76 55.13 56.77 -0.14 0.50 -0.68 fais−server 40
41 GeneSilicoMetaServer 61.01 47.49 54.50 -0.08 -0.19 -0.60 61.01 47.84 54.52 -0.45 -0.75 -1.09 GeneSilicoMetaServer 41
42 3D−JIGSAW_V3 61.01 45.75 60.81 -0.08 -0.44 0.33 63.46 54.02 65.14 -0.01 0.31 0.84 3D−JIGSAW_V3 42
43 MUFOLD−Server 60.84 52.10 58.13 -0.11 0.46 -0.06 62.24 52.56 59.31 -0.23 0.06 -0.22 MUFOLD−Server 43
44 FFASflextemplate 60.66 46.80 56.25 -0.13 -0.29 -0.34 60.66 48.43 56.25 -0.51 -0.65 -0.77 FFASflextemplate 44
45 FFASsuboptimal 60.66 46.80 56.25 -0.13 -0.29 -0.34 61.71 48.08 57.88 -0.32 -0.71 -0.48 FFASsuboptimal 45
46 COMA 60.66 46.10 59.80 -0.13 -0.39 0.18 60.66 46.33 64.34 -0.51 -1.01 0.69 COMA 46
47 FUGUE_KM 60.49 45.69 53.58 -0.15 -0.45 -0.74 60.49 49.01 53.58 -0.54 -0.55 -1.26 FUGUE_KM 47
48 nFOLD3 60.31 45.45 58.39 -0.17 -0.48 -0.03 62.41 51.92 58.39 -0.20 -0.05 -0.39 nFOLD3 48
49 circle 60.14 52.21 59.03 -0.20 0.47 0.07 61.01 52.21 59.09 -0.45 0.00 -0.26 circle 49
50 FFASstandard 60.14 46.27 55.91 -0.20 -0.37 -0.39 62.94 57.92 57.86 -0.10 0.98 -0.48 FFASstandard 50
51 LOOPP_Server 59.27 50.06 52.63 -0.31 0.17 -0.88 59.79 51.52 55.27 -0.66 -0.12 -0.95 LOOPP_Server 51
52 SAM−T06−server 58.92 45.92 63.47 -0.36 -0.41 0.73 62.24 51.28 63.47 -0.23 -0.16 0.53 SAM−T06−server 52
53 Pushchino 58.92 43.24 51.53 -0.36 -0.79 -1.04 58.92 43.24 51.53 -0.82 -1.54 -1.63 Pushchino 53
54 GS−MetaServer2 58.39 46.97 50.42 -0.42 -0.27 -1.21 64.16 53.79 60.47 0.11 0.27 -0.01 GS−MetaServer2 54
55 forecast 58.39 42.54 61.16 -0.42 -0.89 0.39 59.62 43.06 62.11 -0.69 -1.58 0.29 forecast 55
56 rehtnap 58.22 48.08 47.77 -0.45 -0.11 -1.60 58.22 48.08 47.77 -0.94 -0.71 -2.31 rehtnap 56
57 SAM−T02−server 58.22 43.41 50.84 -0.45 -0.77 -1.15 61.01 54.08 56.24 -0.45 0.32 -0.78 SAM−T02−server 57
58 ACOMPMOD 54.90 48.48 50.61 -0.88 -0.05 -1.18 60.14 48.48 54.90 -0.60 -0.64 -1.02 ACOMPMOD 58
59 FOLDpro 48.95 32.40 39.51 -1.65 -2.32 -2.83 64.51 50.64 60.31 0.17 -0.27 -0.04 FOLDpro 59
60 RBO−Proteus 26.22 22.96 41.88 -4.61 -3.65 -2.48 29.37 26.81 41.88 -6.05 -4.37 -3.38 RBO−Proteus 60
61 Distill 25.70 20.57 31.78 -4.67 -3.98 -3.98 26.22 21.68 33.42 -6.61 -5.26 -4.91 Distill 61
62 MUFOLD−MD 24.13 21.27 37.48 -4.88 -3.89 -3.13 24.48 22.67 38.89 -6.92 -5.09 -3.92 MUFOLD−MD 62
63 FALCON_CONSENSUS 22.20 19.87 33.97 -5.13 -4.08 -3.65 25.00 21.39 35.16 -6.83 -5.31 -4.60 FALCON_CONSENSUS 63
64 FALCON 20.98 17.72 33.51 -5.29 -4.38 -3.72 58.74 52.45 55.42 -0.85 0.04 -0.92 FALCON 64
65 RANDOM 19.49 16.60 19.49 -5.48 -4.54 -5.80 19.49 16.60 19.49 -7.80 -6.13 -7.44 RANDOM 65
66 schenk−torda−server 17.66 14.63 18.14 -5.72 -4.82 -6.00 17.66 14.63 18.14 -8.13 -6.47 -7.68 schenk−torda−server 66
67 mariner1 16.43 12.59 16.07 -5.88 -5.11 -6.31 20.80 19.64 26.56 -7.57 -5.61 -6.16 mariner1 67
68 mahmood−torda−server 15.91 13.58 20.11 -5.95 -4.97 -5.71 15.91 13.75 20.11 -8.44 -6.62 -7.32 mahmood−torda−server 68
69 OLGAFS 15.21 14.63 -14.77 -6.04 -4.82 -10.89 15.38 14.80 -14.67 -8.53 -6.44 -13.63 OLGAFS 69
70 BHAGEERATH                   -5.48 -4.54 -5.80                   -7.80 -6.13 -7.44 BHAGEERATH 70
71 Fiser−M4T                   -5.48 -4.54 -5.80                   -7.80 -6.13 -7.44 Fiser−M4T 71
72 YASARA                   -5.48 -4.54 -5.80                   -7.80 -6.13 -7.44 YASARA 72
73 huber−torda−server                   -5.48 -4.54 -5.80                   -7.80 -6.13 -7.44 huber−torda−server 73
74 test_http_server_01                   -5.48 -4.54 -5.80                   -7.80 -6.13 -7.44 test_http_server_01 74