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CG_2015-01t_scaffold_1_prodigal-single.1__X__X__00301

Bact-Vir

CG_2015-01t_scaffold_1_prodigal-single.1__X__X__00301

Identity

Kingdom:
phage

Quality

91.6 mean pLDDT

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 7-70
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01327.27 best Pep_deformylase 35.1 1.40e-08 96.9% 34.6%
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1rl4B00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.86 73.0 5.28e-01 100.0% 36.5%
3qu1A00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.84 78.0 5.58e-01 100.0% 38.7%
3u04A00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.83 77.0 5.48e-01 100.0% 41.3%
5mteA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.83 72.0 5.51e-01 100.0% 43.8%
1lmeA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.83 74.0 5.45e-01 100.0% 40.3%
1lm4A00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.82 75.0 5.25e-01 100.0% 42.6%
3g5kA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.82 75.0 5.26e-01 100.0% 46.4%
1zxzB00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.81 75.0 5.20e-01 100.0% 44.0%
1szzA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.80 73.0 5.26e-01 100.0% 43.9%
3e3uA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.80 73.0 5.06e-01 100.0% 37.8%
4ixoA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.65 46.0 3.70e-01 73.4% 82.4%
2basA03 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.63 45.0 3.68e-01 75.0% 42.2%
3zduA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.61 52.0 3.66e-01 96.9% 51.2%
3is5F02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.60 52.0 3.79e-01 96.9% 60.9%
2a90A01 3.30.720.50 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.59 44.0 3.86e-01 81.2% 55.1%
5bk7H01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.57 42.0 3.42e-01 100.0% 40.3%
2xr1A03 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.56 49.0 3.25e-01 100.0% 45.3%
4trtA01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.53 42.0 3.47e-01 87.5% 70.5%
5hsqA02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.52 39.0 3.23e-01 84.4% 46.5%
3l4eA00 3.40.50.880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain 0.52 38.0 2.67e-01 78.1% 68.8%
1u17A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.51 36.0 2.68e-01 75.0% 73.5%
ECOD (48)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4999343 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.91 84.0 6.06e-01 100.0% 40.6%
3987299 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.88 76.0 5.86e-01 100.0% 44.4%
4086694 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.87 80.0 5.89e-01 100.0% 42.0%
4030761 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.85 78.0 5.62e-01 100.0% 39.4%
4133607 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.84 76.0 5.54e-01 100.0% 39.4%
3309735 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.84 78.0 6.01e-01 100.0% 51.9%
167197 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.84 76.0 5.23e-01 100.0% 43.9%
3427612 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.83 77.0 5.39e-01 100.0% 36.2%
3966296 289.1.1.0 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase 0.83 78.0 5.57e-01 100.0% 39.4%
4039287 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.83 78.0 5.52e-01 100.0% 38.2%
140542 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.83 77.0 5.42e-01 100.0% 42.5%
3693404 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.83 77.0 5.32e-01 100.0% 36.8%
4470382 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.83 77.0 5.39e-01 100.0% 42.2%
2121396 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.83 73.0 5.57e-01 100.0% 44.5%
168447 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.83 76.0 5.34e-01 100.0% 36.4%
4256308 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.83 77.0 5.56e-01 100.0% 40.6%
2579249 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.82 76.0 5.54e-01 100.0% 47.2%
4275485 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.82 76.0 5.44e-01 100.0% 37.6%
4096233 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.82 76.0 5.40e-01 100.0% 40.2%
4325293 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.82 76.0 5.29e-01 100.0% 41.6%
4113678 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.82 74.0 5.27e-01 100.0% 44.0%
4220709 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.82 75.0 5.39e-01 100.0% 40.0%
1877349 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.82 75.0 5.39e-01 100.0% 42.0%
4420329 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.82 75.0 5.27e-01 100.0% 39.5%
3440362 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.82 75.0 5.22e-01 100.0% 44.2%
3336542 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.82 75.0 6.06e-01 100.0% 73.0%
3401134 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.81 75.0 5.20e-01 100.0% 45.0%
4224338 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.81 74.0 5.16e-01 100.0% 41.6%
4628922 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.80 74.0 5.22e-01 100.0% 42.5%
3276058 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.80 74.0 5.28e-01 100.0% 44.7%
4454013 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.80 72.0 5.18e-01 100.0% 44.4%
170021 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.80 73.0 5.06e-01 100.0% 37.8%
4422867 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.79 72.0 5.06e-01 100.0% 35.3%
4165265 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.79 72.0 4.96e-01 100.0% 38.7%
3596563 289.1.1.0 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase 0.79 70.0 4.78e-01 100.0% 29.5%
3607053 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.79 70.0 4.60e-01 100.0% 25.3%
4336204 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.78 71.0 5.00e-01 100.0% 47.6%
3710708 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.76 68.0 4.73e-01 100.0% 33.2%
4539518 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.75 67.0 4.75e-01 100.0% 42.6%
4220705 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.74 66.0 4.77e-01 100.0% 43.3%
3329408 3887.2.1.0 a+b two layers › Yeast killer toxin-like › Antifungal protein ginkbilobin-2 › Antifungal protein ginkbilobin-2 0.69 48.0 4.54e-01 71.9% 86.7%
3427650 331.2.1.0 a+b two layers › TBP-like › Phosphoglucomutase, C-terminal domain › Phosphoglucomutase, C-terminal domain 0.56 40.0 3.15e-01 75.0% 91.4%
5000172 2003.1.10.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › PreATP-grasp domain 0.56 39.0 3.44e-01 73.4% 68.4%
4270851 73.1.1.1 beta sandwiches › SMAD/FHA domain › SMAD/FHA domain › SMAD/FHA domain › FHA 0.56 37.0 3.20e-01 70.3% 56.9%
5080337 4312.1.1.3 a+b two layers › RelE-like › RelE-like › RelE-like › ParE_toxin 0.55 38.0 3.41e-01 71.9% 82.0%
3339917 376.1.1.1 few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-C3HC4 0.54 38.0 3.61e-01 76.6% 87.5%
3965422 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.53 38.0 3.47e-01 79.7% 93.7%
4838661 223.1.1.0 a+b three layers › Profilin-like › sensor domains › sensor domains 0.52 38.0 3.35e-01 84.4% 55.0%
D2 high residues 73-172
PDB
Domain cluster: representative
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF01327.27 best Pep_deformylase 53.9 2.30e-14 75.0% 40.4%
PF02810.22 SEC-C 23.1 7.40e-05 14.0% 73.7%
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1rl4B00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.91 65.0 5.42e-01 73.0% 48.1%
1lmeA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.91 64.0 5.36e-01 72.0% 48.1%
3qu1A00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.89 62.0 5.01e-01 71.0% 42.9%
3u04A00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.87 60.0 4.88e-01 71.0% 42.4%
1szzA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.86 61.0 5.00e-01 73.0% 43.9%
3g5kA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.86 61.0 4.84e-01 73.0% 41.0%
1lm4A00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.85 67.0 5.30e-01 82.0% 47.4%
1zxzB00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.84 66.0 5.14e-01 81.0% 50.3%
3e3uA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.82 58.0 4.57e-01 73.0% 40.8%
5umsA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 32.0 3.21e-01 82.0% 61.8%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4086694 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.91 64.0 5.40e-01 72.0% 49.3%
4133607 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.91 64.0 5.26e-01 72.0% 46.3%
2579249 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.90 63.0 5.20e-01 71.0% 45.9%
4030761 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.90 63.0 5.24e-01 72.0% 46.3%
3427612 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.89 64.0 5.00e-01 73.0% 40.5%
4325293 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.89 63.0 5.00e-01 73.0% 41.1%
4420329 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.89 63.0 4.99e-01 73.0% 40.5%
4999343 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.89 63.0 5.16e-01 73.0% 46.1%
4224338 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.88 63.0 4.91e-01 73.0% 39.5%
4039287 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.88 61.0 4.97e-01 71.0% 42.4%
4256308 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.88 61.0 5.07e-01 71.0% 45.0%
4220709 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.88 62.0 5.02e-01 72.0% 43.5%
4275485 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.88 63.0 5.07e-01 73.0% 44.1%
168447 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.87 63.0 4.97e-01 74.0% 41.3%
4096233 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.87 62.0 4.99e-01 73.0% 42.5%
3401134 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.87 62.0 4.85e-01 73.0% 39.7%
4470382 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.87 60.0 4.80e-01 71.0% 40.6%
981342 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.87 62.0 4.92e-01 73.0% 41.2%
3693404 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.86 61.0 4.81e-01 73.0% 48.9%
4454013 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.86 67.0 5.32e-01 80.0% 48.9%
3966296 289.1.1.0 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase 0.86 60.0 4.91e-01 71.0% 44.2%
140542 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.86 60.0 4.76e-01 71.0% 40.8%
4113678 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.84 68.0 5.40e-01 84.0% 49.5%
3276058 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.84 60.0 4.85e-01 74.0% 42.9%
3440362 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.83 65.0 5.09e-01 81.0% 50.5%
4443928 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.83 58.0 4.61e-01 73.0% 47.9%
3710708 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.73 63.0 4.89e-01 92.0% 55.6%
3596563 289.1.1.0 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase 0.73 63.0 4.80e-01 91.0% 63.8%
3607053 289.1.1.1 a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.70 65.0 4.77e-01 99.0% 59.6%