T0414

Targets
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T0414

conserved protein of unknown function CA_C3497 from Clostridium acetobutylicum ATCC 824

Target type: Server only

Target sequence:

>T0414 CA_C3497, conserved protein of unknown function, Clostridium acetobutylicum ATCC 824, 140 residues
SNAMKPDIYENNREGILCVYKNEKWLVCIKNWKPDNDIEGIAHLEIHHSTDEQFILSAGKAILITAEKENDKFNIELTLMEKGKVYNVPAECWFYSITQKDTKMMYVQDSNCSMDNSDFCDLSKEEIEYIQTNARKLFEK

Structure:
Method: X-ray, res=1.53Å, R/Rfree=0.17/0.18
Determined by: MCSG
PDB ID: 3d0j

PyMOL of 3d0j

Domains:  PyMOL of domains

Single domain protein, but N-terminal segment 0-5 (pdb numbering) interacts with a symmetry mate, but does not form a swap. This region can be removed for evaluation.

To compute the weighted sum, GDT-TS for each domain was multiplied by the domain length, and this sum was divided by the sum of domain lengths. 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 weighted sum of domain GDT-TS scores and the whole chain GDT-TS score) are shown above the plot.

Structure classification:

Double-stranded β-helix fold.

CASP category:

Whole chain: Comparative modeling:hard.

Domain (with N-terminal segment pdb 0-5 removed): Comparative modeling:hard.

Closest templates:

2pa7.

Target sequence - PDB file inconsistencies:

T0414    3d0j.pdb    T0414.pdb    PyMOL    PyMOL of domains   

Residue change log: change 1, 77, 101, 102, 111, MSE to MET;

We suggest to evaluate this target as a single domain spanning whole chain. However, N-terminal segment (target 1-8, pdb 0-6) interacts with a symmetry mate, but does not form a swap. This segment can be removed for domain-based evaluation, resulting this domain definition:

1st domain: target 9-140 ; pdb 6-137

Sequence classification:

RmlC-like cupins superfamily in SCOP.

Comments:

This protein is a homolog of T0503.

Server predictions:

T0414:pdb 0-137:seq 3-140:CM_hard;   alignment

414_1:pdb 6-137:seq 9-140:CM_hard;   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 #
T0414 414_1 T0414 414_1 T0414 414_1 T0414 414_1
First score First Z-score Best score Best Z-score
1 Pcons_multi 59.96 51.51 63.33 62.12 53.28 63.48 1.85 1.73 1.51 1.81 1.64 1.51 59.96 54.47 63.33 62.12 56.38 63.48 1.43 1.59 1.19 1.39 1.57 1.20 Pcons_multi 1
2 Phyre_de_novo 58.88 49.34 67.31 61.55 51.58 67.37 1.72 1.42 1.88 1.74 1.41 1.88 58.88 49.58 68.71 61.55 51.64 68.77 1.31 0.96 1.74 1.33 0.97 1.74 Phyre_de_novo 2
3 LEE−SERVER 57.97 52.78 64.26 60.42 54.99 64.49 1.60 1.91 1.59 1.60 1.87 1.61 57.97 52.78 64.65 60.42 54.99 64.85 1.20 1.37 1.33 1.20 1.39 1.34 LEE−SERVER 3
4 Poing 56.34 48.73 67.47 58.52 50.57 67.66 1.40 1.34 1.90 1.37 1.28 1.91 56.34 48.73 67.47 58.52 51.58 67.66 1.01 0.85 1.61 0.98 0.96 1.63 Poing 4
5 Phragment 56.34 46.20 67.83 58.71 49.75 68.20 1.40 0.98 1.93 1.39 1.17 1.96 56.34 48.67 67.83 58.71 50.63 68.20 1.01 0.84 1.65 1.01 0.84 1.68 Phragment 5
6 Phyre2 56.16 48.43 67.36 58.52 50.44 67.38 1.37 1.30 1.89 1.37 1.26 1.89 56.16 50.48 67.36 58.52 51.20 67.38 0.98 1.07 1.60 0.98 0.91 1.60 Phyre2 6
7 SAM−T06−server 54.89 46.92 56.73 57.01 48.67 57.04 1.21 1.09 0.89 1.19 1.03 0.90 54.89 46.92 56.73 57.01 48.67 57.04 0.83 0.61 0.53 0.81 0.59 0.54 SAM−T06−server 7
8 Frankenstein 53.80 45.83 53.14 56.25 47.92 53.37 1.08 0.93 0.55 1.09 0.93 0.55 53.80 49.94 54.53 56.25 52.02 54.79 0.71 1.00 0.31 0.73 1.01 0.31 Frankenstein 8
9 Zhang−Server 53.08 41.85 60.76 55.30 43.56 61.31 0.98 0.37 1.27 0.98 0.35 1.31 56.34 47.52 65.06 58.71 49.49 65.46 1.01 0.69 1.37 1.01 0.69 1.40 Zhang−Server 9
10 HHpred4 52.90 45.29 48.29 55.11 47.16 48.68 0.96 0.86 0.10 0.95 0.82 0.11 52.90 45.29 48.29 55.11 47.16 48.68 0.60 0.40 -0.32 0.60 0.40 -0.32 HHpred4 10
11 3DShot2 52.54 45.17 55.26 54.73 47.03 55.42 0.92 0.84 0.75 0.91 0.81 0.75 52.54 45.17 55.26 54.73 47.03 55.42 0.56 0.39 0.38 0.55 0.38 0.37 3DShot2 11
12 mGenTHREADER 52.17 43.72 49.00 54.36 50.57 49.90 0.87 0.64 0.16 0.86 1.28 0.22 52.17 43.72 49.00 54.36 50.57 49.90 0.51 0.20 -0.25 0.51 0.83 -0.20 mGenTHREADER 12
13 keasar−server 51.81 47.34 54.90 54.17 49.49 55.23 0.82 1.14 0.72 0.84 1.13 0.73 52.54 47.34 54.90 54.73 49.56 55.23 0.56 0.67 0.34 0.55 0.70 0.35 keasar−server 13
14 MULTICOM−CMFR 51.09 45.53 53.18 52.84 47.03 53.37 0.73 0.89 0.56 0.68 0.81 0.55 51.09 45.53 53.18 52.84 47.03 53.37 0.39 0.43 0.17 0.34 0.38 0.16 MULTICOM−CMFR 14
15 METATASSER 50.91 43.90 56.51 53.22 45.90 56.72 0.71 0.66 0.87 0.72 0.66 0.87 56.34 47.52 62.69 58.33 49.12 62.88 1.01 0.69 1.13 0.96 0.65 1.14 METATASSER 15
16 BAKER−ROBETTA 50.00 44.69 59.84 52.27 46.59 60.22 0.59 0.77 1.18 0.61 0.75 1.20 50.18 46.26 61.33 52.27 47.92 61.71 0.28 0.53 0.99 0.27 0.49 1.02 BAKER−ROBETTA 16
17 MUProt 49.64 46.26 45.05 51.52 47.60 45.42 0.55 0.99 -0.21 0.52 0.88 -0.20 52.90 47.70 58.17 55.30 49.87 58.31 0.60 0.71 0.67 0.62 0.74 0.67 MUProt 17
18 MULTICOM−RANK 49.64 45.77 44.83 51.70 47.66 45.19 0.55 0.92 -0.23 0.54 0.89 -0.23 53.08 47.77 58.17 55.49 49.94 58.28 0.62 0.72 0.67 0.64 0.75 0.67 MULTICOM−RANK 18
19 MULTICOM−CLUSTER 49.64 45.77 44.83 51.70 47.66 45.19 0.55 0.92 -0.23 0.54 0.89 -0.23 49.64 45.77 48.27 51.70 47.66 48.37 0.21 0.46 -0.33 0.21 0.46 -0.35 MULTICOM−CLUSTER 19
20 MULTICOM−REFINE 49.46 44.14 44.90 51.52 47.35 45.26 0.53 0.70 -0.22 0.52 0.85 -0.22 53.08 47.52 57.66 55.30 49.49 57.79 0.62 0.69 0.62 0.62 0.69 0.61 MULTICOM−REFINE 20
21 circle 49.09 43.90 62.58 51.33 45.90 62.58 0.48 0.66 1.44 0.49 0.66 1.43 49.09 45.35 62.58 51.52 46.59 62.58 0.15 0.41 1.12 0.19 0.33 1.11 circle 21
22 fais−server 49.09 38.71 47.43 51.33 40.47 47.38 0.48 -0.07 0.02 0.49 -0.07 -0.02 49.09 41.06 47.43 51.33 42.93 47.38 0.15 -0.15 -0.41 0.16 -0.14 -0.46 fais−server 22
23 FAMSD 48.91 42.75 60.23 50.95 44.26 60.23 0.46 0.50 1.22 0.45 0.44 1.21 48.91 43.42 60.23 50.95 45.39 60.23 0.13 0.16 0.88 0.12 0.17 0.87 FAMSD 23
24 SAM−T08−server 48.73 41.73 62.91 50.95 43.62 63.05 0.43 0.36 1.47 0.45 0.35 1.47 51.45 44.20 62.91 53.79 46.21 63.05 0.43 0.26 1.15 0.44 0.28 1.16 SAM−T08−server 24
25 MUSTER 48.37 42.81 57.85 50.38 43.31 57.95 0.39 0.51 0.99 0.38 0.31 0.99 52.17 48.19 60.06 54.17 50.00 60.06 0.51 0.78 0.86 0.49 0.76 0.85 MUSTER 25
26 FFASsuboptimal 47.28 39.31 51.36 49.43 41.10 51.48 0.25 0.02 0.39 0.26 0.02 0.37 47.28 41.12 51.36 49.43 42.99 51.48 -0.07 -0.14 -0.01 -0.05 -0.13 -0.03 FFASsuboptimal 26
27 FOLDpro 47.10 40.82 47.93 49.24 42.68 48.24 0.23 0.23 0.06 0.24 0.23 0.06 47.10 41.18 48.97 49.24 42.68 48.98 -0.09 -0.13 -0.26 -0.07 -0.17 -0.29 FOLDpro 27
28 FALCON_CONSENSUS 46.92 42.69 44.88 49.05 44.63 44.95 0.21 0.49 -0.22 0.22 0.49 -0.25 52.72 48.01 58.70 54.92 50.00 58.78 0.58 0.75 0.73 0.57 0.76 0.72 FALCON_CONSENSUS 28
29 FALCON 46.92 42.69 44.88 49.05 44.63 44.95 0.21 0.49 -0.22 0.22 0.49 -0.25 52.72 48.01 58.70 54.92 50.00 58.78 0.58 0.75 0.73 0.57 0.76 0.72 FALCON 29
30 3Dpro 46.92 40.16 48.47 48.48 41.35 48.34 0.21 0.14 0.11 0.15 0.05 0.07 47.65 44.87 49.05 49.81 46.91 49.08 -0.02 0.35 -0.25 -0.01 0.37 -0.28 3Dpro 30
31 COMA 46.74 40.58 50.05 48.86 42.42 50.23 0.18 0.20 0.26 0.19 0.19 0.25 46.74 40.58 50.05 48.86 42.42 50.23 -0.13 -0.21 -0.15 -0.12 -0.20 -0.16 COMA 31
32 PS2−server 46.01 40.46 54.03 48.11 42.30 53.94 0.09 0.18 0.64 0.10 0.18 0.61 53.08 44.99 57.29 55.11 47.41 57.71 0.62 0.36 0.58 0.60 0.43 0.61 PS2−server 32
33 3D−JIGSAW_AEP 45.47 39.67 48.41 47.54 41.48 48.63 0.02 0.07 0.11 0.03 0.07 0.10 45.47 39.67 48.41 47.54 41.48 48.63 -0.28 -0.33 -0.31 -0.27 -0.32 -0.33 3D−JIGSAW_AEP 33
34 PSI 45.29 39.98 51.13 47.35 41.79 51.23 -0.00 0.11 0.36 0.01 0.11 0.35 56.52 50.60 58.90 59.09 52.90 59.16 1.03 1.09 0.75 1.05 1.13 0.76 PSI 34
35 HHpred2 44.38 37.14 50.33 46.59 39.02 50.43 -0.12 -0.29 0.29 -0.08 -0.26 0.27 44.38 37.14 50.33 46.59 39.02 50.43 -0.41 -0.65 -0.12 -0.38 -0.64 -0.14 HHpred2 35
36 forecast 44.20 39.49 52.98 46.21 41.29 52.93 -0.14 0.04 0.54 -0.13 0.04 0.51 44.20 39.49 52.98 46.21 41.29 52.93 -0.43 -0.35 0.15 -0.42 -0.35 0.12 forecast 36
37 mariner1 44.20 34.60 40.06 46.21 36.17 40.35 -0.14 -0.64 -0.67 -0.13 -0.64 -0.69 50.91 44.75 61.05 53.22 46.78 61.20 0.36 0.33 0.96 0.38 0.35 0.97 mariner1 37
38 3D−JIGSAW_V3 43.48 39.61 46.58 45.45 41.41 46.83 -0.23 0.06 -0.06 -0.22 0.06 -0.07 43.84 39.98 46.79 45.83 41.79 47.03 -0.47 -0.29 -0.48 -0.46 -0.28 -0.49 3D−JIGSAW_V3 38
39 GeneSilicoMetaServer 43.48 34.18 33.94 45.45 35.73 35.13 -0.23 -0.70 -1.25 -0.22 -0.70 -1.18 43.48 35.02 33.94 45.45 36.62 35.13 -0.51 -0.93 -1.77 -0.50 -0.94 -1.71 GeneSilicoMetaServer 39
40 COMA−M 43.12 38.89 40.10 45.08 40.66 40.11 -0.27 -0.04 -0.67 -0.27 -0.04 -0.71 44.75 41.37 44.39 46.59 43.06 44.48 -0.36 -0.11 -0.72 -0.38 -0.12 -0.75 COMA−M 40
41 FEIG 42.94 37.62 51.52 44.89 38.32 51.61 -0.30 -0.22 0.40 -0.29 -0.35 0.38 49.27 45.53 51.52 51.33 47.60 51.61 0.17 0.43 0.00 0.16 0.45 -0.02 FEIG 41
42 FUGUE_KM 41.85 35.69 42.50 43.75 37.31 42.68 -0.44 -0.49 -0.45 -0.43 -0.49 -0.46 41.85 35.69 42.50 43.75 37.31 42.68 -0.71 -0.84 -0.91 -0.70 -0.85 -0.94 FUGUE_KM 42
43 nFOLD3 41.30 33.27 32.68 43.18 34.78 33.86 -0.50 -0.83 -1.37 -0.50 -0.82 -1.30 53.26 45.41 54.00 55.30 47.10 54.29 0.64 0.42 0.25 0.62 0.39 0.25 nFOLD3 43
44 pro−sp3−TASSER 41.12 34.54 39.85 42.99 36.49 39.81 -0.53 -0.65 -0.69 -0.52 -0.60 -0.74 54.35 47.34 55.11 56.44 48.48 55.59 0.77 0.67 0.36 0.75 0.57 0.39 pro−sp3−TASSER 44
45 HHpred5 40.76 35.33 43.01 42.61 36.93 43.19 -0.57 -0.54 -0.40 -0.57 -0.54 -0.42 40.76 35.33 43.01 42.61 36.93 43.19 -0.84 -0.89 -0.86 -0.83 -0.90 -0.89 HHpred5 45
46 rehtnap 40.76 34.24 35.13 42.61 35.80 36.32 -0.57 -0.69 -1.14 -0.57 -0.69 -1.07 41.12 35.20 36.75 42.99 36.81 37.94 -0.79 -0.90 -1.49 -0.79 -0.92 -1.43 rehtnap 46
47 FFASstandard 40.40 35.81 40.20 42.23 37.44 41.41 -0.62 -0.47 -0.66 -0.61 -0.47 -0.59 46.74 44.44 42.89 48.86 46.47 43.72 -0.13 0.29 -0.87 -0.12 0.31 -0.83 FFASstandard 47
48 GS−MetaServer2 39.85 37.44 30.31 41.67 39.14 31.48 -0.69 -0.24 -1.59 -0.68 -0.24 -1.53 42.39 37.44 35.17 44.32 39.14 36.35 -0.64 -0.61 -1.65 -0.63 -0.62 -1.59 GS−MetaServer2 48
49 panther_server 39.31 36.17 32.43 40.91 38.13 32.82 -0.76 -0.42 -1.39 -0.77 -0.38 -1.40 47.10 40.94 49.03 48.48 42.55 49.24 -0.09 -0.16 -0.25 -0.16 -0.19 -0.26 panther_server 49
50 FFASflextemplate 39.31 34.00 37.30 41.10 35.54 38.49 -0.76 -0.73 -0.93 -0.75 -0.72 -0.86 39.31 34.00 38.13 41.10 35.54 39.33 -1.01 -1.06 -1.35 -1.00 -1.08 -1.28 FFASflextemplate 50
51 RAPTOR 38.23 33.03 40.84 39.96 34.53 40.84 -0.89 -0.86 -0.60 -0.89 -0.86 -0.64 51.27 45.71 59.84 53.60 47.79 60.13 0.41 0.46 0.84 0.42 0.48 0.86 RAPTOR 51
52 ACOMPMOD 37.68 31.64 37.41 39.39 33.08 37.64 -0.96 -1.06 -0.92 -0.96 -1.05 -0.94 47.83 42.87 42.21 50.00 44.82 42.40 -0.00 0.09 -0.94 0.01 0.10 -0.97 ACOMPMOD 52
53 CpHModels 37.50 31.46 33.20 39.20 32.89 34.38 -0.98 -1.08 -1.32 -0.98 -1.08 -1.25 37.50 31.46 33.20 39.20 32.89 34.38 -1.22 -1.39 -1.85 -1.22 -1.42 -1.79 CpHModels 53
54 GS−KudlatyPred 35.87 30.92 32.97 37.50 32.32 34.15 -1.19 -1.16 -1.34 -1.19 -1.15 -1.28 35.87 30.92 32.97 37.50 32.32 34.15 -1.41 -1.46 -1.87 -1.41 -1.49 -1.82 GS−KudlatyPred 54
55 Pcons_local 34.06 28.50 20.42 35.61 29.80 21.56 -1.42 -1.50 -2.51 -1.42 -1.49 -2.47 53.44 48.37 52.48 55.68 47.10 52.52 0.66 0.80 0.10 0.66 0.39 0.07 Pcons_local 55
56 SAM−T02−server 31.70 25.66 17.83 33.14 26.83 18.96 -1.72 -1.90 -2.76 -1.72 -1.88 -2.72 48.19 44.32 40.05 50.38 46.34 41.25 0.04 0.28 -1.16 0.06 0.29 -1.09 SAM−T02−server 56
57 MUFOLD−Server 30.62 25.00 33.21 32.01 26.26 33.35 -1.85 -1.99 -1.32 -1.86 -1.96 -1.35 30.62 25.54 33.25 32.01 26.70 33.39 -2.04 -2.16 -1.84 -2.04 -2.20 -1.89 MUFOLD−Server 57
58 MUFOLD−MD 20.47 17.63 33.28 21.40 18.43 33.32 -3.14 -3.02 -1.31 -3.15 -3.00 -1.36 20.83 17.63 33.28 21.97 18.43 33.32 -3.19 -3.18 -1.84 -3.18 -3.25 -1.90 MUFOLD−MD 58
59 RBO−Proteus 20.29 16.79 33.16 21.21 17.55 33.23 -3.16 -3.14 -1.32 -3.17 -3.12 -1.36 20.65 19.63 33.46 21.59 20.52 33.36 -3.21 -2.92 -1.82 -3.22 -2.99 -1.90 RBO−Proteus 59
60 BioSerf 19.75 17.75 30.81 20.27 18.18 31.09 -3.23 -3.00 -1.54 -3.29 -3.04 -1.57 19.75 17.75 30.81 20.27 18.18 31.09 -3.32 -3.16 -2.09 -3.37 -3.28 -2.13 BioSerf 60
61 Distill 18.12 17.21 27.51 18.94 17.99 27.47 -3.43 -3.08 -1.85 -3.45 -3.06 -1.91 21.01 17.39 28.39 21.59 20.96 28.37 -3.17 -3.21 -2.33 -3.22 -2.93 -2.41 Distill 61
62 LOOPP_Server 16.49 12.98 10.90 17.23 13.57 11.61 -3.64 -3.67 -3.41 -3.66 -3.65 -3.42 16.49 12.98 15.93 17.23 13.57 16.59 -3.71 -3.78 -3.59 -3.72 -3.87 -3.62 LOOPP_Server 62
63 RANDOM 14.57 12.49 14.57 15.51 13.18 15.51 -3.88 -3.74 -3.06 -3.87 -3.70 -3.05 14.57 12.49 14.57 15.51 13.18 15.51 -3.93 -3.85 -3.73 -3.92 -3.92 -3.73 RANDOM 63
64 Pushchino 13.04 10.75 11.56 13.64 11.24 12.04 -4.08 -3.99 -3.35 -4.10 -3.96 -3.38 13.04 10.75 11.56 13.64 11.24 12.04 -4.12 -4.07 -4.03 -4.13 -4.16 -4.09 Pushchino 64
65 huber−torda−server 11.96 10.99 9.30 12.50 11.49 9.91 -4.21 -3.95 -3.56 -4.23 -3.93 -3.58 15.94 13.04 18.69 15.72 14.58 18.86 -3.77 -3.77 -3.31 -3.89 -3.74 -3.39 huber−torda−server 65
66 schenk−torda−server 11.96 10.02 16.65 12.88 10.86 17.08 -4.21 -4.09 -2.87 -4.19 -4.01 -2.90 15.04 13.41 18.33 15.72 14.02 18.56 -3.88 -3.73 -3.35 -3.89 -3.81 -3.42 schenk−torda−server 66
67 OLGAFS 10.51 9.24 4.37 11.36 9.85 4.36 -4.40 -4.20 -4.02 -4.37 -4.15 -4.11 11.05 9.42 4.42 11.36 9.85 4.41 -4.35 -4.24 -4.75 -4.39 -4.34 -4.87 OLGAFS 67
68 BHAGEERATH                                     -3.88 -3.74 -3.06 -3.87 -3.70 -3.05                                     -3.93 -3.85 -3.73 -3.92 -3.92 -3.73 BHAGEERATH 68
69 Fiser−M4T                                     -3.88 -3.74 -3.06 -3.87 -3.70 -3.05                                     -3.93 -3.85 -3.73 -3.92 -3.92 -3.73 Fiser−M4T 69
70 Pcons_dot_net                                     -3.88 -3.74 -3.06 -3.87 -3.70 -3.05                                     -3.93 -3.85 -3.73 -3.92 -3.92 -3.73 Pcons_dot_net 70
71 YASARA                                     -3.88 -3.74 -3.06 -3.87 -3.70 -3.05                                     -3.93 -3.85 -3.73 -3.92 -3.92 -3.73 YASARA 71
72 mahmood−torda−server                                     -3.88 -3.74 -3.06 -3.87 -3.70 -3.05                                     -3.96 -3.68 -3.73 -3.98 -3.76 -3.73 mahmood−torda−server 72
73 pipe_int                                     -3.88 -3.74 -3.06 -3.87 -3.70 -3.05                                     -3.93 -3.85 -3.73 -3.92 -3.92 -3.73 pipe_int 73
74 test_http_server_01                                     -3.88 -3.74 -3.06 -3.87 -3.70 -3.05                                     -3.93 -3.85 -3.73 -3.92 -3.92 -3.73 test_http_server_01 74