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MN988519.1__QIG70619.1__EVB91_063__00048

Bact-Vir

MN988519.1__QIG70619.1__EVB91_063__00048

Identity

Accession:
MN988519 ↗
Kingdom:
phage

Quality

86.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhizobium_phage_RHph_I1_18

TaxID: 2509726

Cluster

View cluster (13 members)

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 medium residues 23-90
PDB
Domain cluster: representative
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1lmeA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.85 68.0 5.07e-01 88.2% 37.0%
3u04A00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.85 67.0 4.86e-01 89.7% 33.1%
3e3uA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.79 66.0 4.64e-01 89.7% 31.1%
3e0mC01 3.30.1060.10 Alpha Beta › 2-Layer Sandwich › Peptide Methionine Sulfoxide Reductase; Chain A › Peptide methionine sulphoxide reductase MsrA 0.57 50.0 3.82e-01 100.0% 75.6%
6c5cA01 3.40.50.1970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.54 46.0 3.50e-01 100.0% 56.0%
1m0wA04 3.40.50.1760 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glutathione synthase, substrate-binding domain superfamily, eukaryotic 0.52 43.0 3.58e-01 94.1% 71.3%
3zl8A02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.52 43.0 3.07e-01 95.6% 86.7%
4yo2A01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.52 42.0 4.17e-01 91.2% 94.4%
ECOD (20)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1877349 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.86 69.0 4.97e-01 89.7% 33.7%
4030761 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.85 68.0 5.00e-01 89.7% 35.6%
4256308 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.85 68.0 4.99e-01 89.7% 35.6%
140542 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.85 66.0 4.76e-01 89.7% 31.3%
4133607 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.84 66.0 4.93e-01 89.7% 35.6%
3693404 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.84 68.0 4.82e-01 89.7% 31.1%
2579249 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.83 69.0 5.12e-01 89.7% 37.7%
4224338 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.83 64.0 4.55e-01 89.7% 29.5%
3276058 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.82 65.0 4.77e-01 85.3% 34.7%
4628922 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.81 66.0 4.79e-01 89.7% 33.5%
3596563 289.1.1.0 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase 0.81 65.0 4.53e-01 86.8% 28.1%
3401134 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.79 64.0 4.56e-01 91.2% 31.2%
170021 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.79 66.0 4.64e-01 89.7% 31.1%
4999343 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.78 65.0 4.79e-01 89.7% 37.6%
3733993 109.4.1.102 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › WAPL 0.59 49.0 3.04e-01 94.1% 29.7%
4965650 7592.1.1.0 ↗ a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains 0.55 49.0 3.90e-01 100.0% 75.7%
3249058 4018.1.1.2 ↗ a+b two layers › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases › Inositol_P 0.54 46.0 3.32e-01 95.6% 37.0%
5074796 4143.1.1.1 ↗ a+b two layers › THUMP domain-like › THUMP domain-like › THUMP domain-like › THUMP 0.54 45.0 4.18e-01 97.1% 94.4%
3503970 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.53 41.0 2.66e-01 86.8% 24.6%
4981942 327.7.1.2 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › FKBP26_C 0.50 39.0 4.12e-01 98.5% 96.7%
D2 medium residues 91-191
PDB
Domain cluster: rep: MW015081.1__QPX48081.1__X__00116__D69-144
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01327.27 best Pep_deformylase 53.8 2.50e-14 89.1% 52.6%
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1lmeA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.95 79.0 6.60e-01 85.1% 57.1%
5mteA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.93 74.0 6.49e-01 81.2% 61.3%
3u04A00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.93 89.0 7.23e-01 100.0% 65.1%
3qu1A00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.92 88.0 7.17e-01 100.0% 62.5%
1lm4A00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.90 75.0 5.90e-01 87.1% 52.1%
1rl4B00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.89 85.0 7.16e-01 100.0% 64.7%
1zxzB00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.86 77.0 6.02e-01 93.1% 59.7%
3g5kA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.85 76.0 6.03e-01 93.1% 62.3%
1szzA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.85 76.0 6.18e-01 93.1% 61.4%
3e3uA00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.82 77.0 6.02e-01 100.0% 63.3%
1b9mA03 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.62 35.0 4.07e-01 75.2% 78.9%
1gutA00 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.60 33.0 3.87e-01 73.3% 77.6%
4hcsA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.58 32.0 3.75e-01 75.2% 79.1%
3fssA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 36.0 3.86e-01 79.2% 74.4%
1nr4C00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.55 31.0 3.61e-01 75.2% 80.3%
4fb5A02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.53 39.0 2.90e-01 76.2% 72.7%
1a41A01 3.90.15.10 Alpha Beta › Alpha-Beta Complex › Topoisomerase I; Chain A, domain 3 › Topoisomerase I; Chain A, domain 3 0.53 36.0 3.40e-01 77.2% 57.5%
3u4vA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 36.0 3.44e-01 73.3% 63.8%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4470382 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.95 91.0 7.24e-01 100.0% 65.0%
2121396 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.93 74.0 6.48e-01 81.2% 61.3%
3987299 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.93 73.0 6.44e-01 80.2% 60.0%
4256308 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.93 87.0 7.24e-01 98.0% 64.4%
2579249 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.93 77.0 6.43e-01 86.1% 62.3%
140542 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.93 88.0 7.06e-01 100.0% 65.4%
4224338 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.92 88.0 6.91e-01 100.0% 65.8%
3966296 289.1.1.0 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase 0.92 88.0 7.22e-01 100.0% 64.2%
4039287 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.92 87.0 7.12e-01 100.0% 61.8%
4133607 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.91 78.0 6.50e-01 89.1% 57.5%
4999343 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.91 78.0 6.43e-01 89.1% 56.4%
4030761 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.91 78.0 6.49e-01 89.1% 57.5%
4113678 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.91 75.0 5.97e-01 86.1% 53.8%
4220709 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.90 86.0 7.01e-01 100.0% 65.9%
167197 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.90 74.0 5.70e-01 86.1% 52.2%
4275485 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.90 85.0 6.95e-01 100.0% 64.1%
4420329 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.89 85.0 6.74e-01 100.0% 63.8%
4336204 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.89 77.0 6.09e-01 90.1% 58.4%
4096233 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.89 84.0 6.83e-01 100.0% 65.5%
4454013 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.89 76.0 6.08e-01 89.1% 56.1%
3427612 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.89 85.0 6.69e-01 100.0% 60.0%
4422867 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.88 84.0 6.61e-01 100.0% 57.9%
168447 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.88 84.0 6.67e-01 100.0% 60.9%
4086694 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.88 80.0 6.75e-01 93.1% 62.7%
4539518 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.88 84.0 6.57e-01 100.0% 66.8%
3693404 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.87 82.0 6.46e-01 100.0% 68.9%
3440362 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.87 78.0 6.08e-01 93.1% 60.0%
4325293 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.87 78.0 6.13e-01 93.1% 61.1%
4443928 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.86 81.0 6.38e-01 99.0% 65.8%
981342 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.86 81.0 6.48e-01 99.0% 59.9%
4165265 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.86 77.0 5.88e-01 93.1% 53.9%
3276058 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.85 76.0 6.19e-01 93.1% 60.6%
4628922 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.85 76.0 6.07e-01 93.1% 59.8%
3710708 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.85 76.0 5.81e-01 93.1% 50.7%
4220705 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.85 75.0 6.03e-01 93.1% 60.6%
1877349 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.84 75.0 6.14e-01 93.1% 61.5%
3596563 289.1.1.0 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase 0.84 75.0 5.68e-01 93.1% 56.7%
170021 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.82 77.0 6.02e-01 100.0% 63.3%
3401134 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.81 77.0 6.07e-01 100.0% 68.3%
3607053 289.1.1.1 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase › Pep_deformylase 0.79 75.0 5.46e-01 100.0% 73.5%
3383138 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.64 37.0 4.15e-01 74.3% 73.1%
3287981 2.1.1.94 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › TLP1_add_C 0.59 35.0 4.02e-01 71.3% 80.0%
4929364 896.1.1.0 ↗ a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related 0.54 35.0 4.10e-01 76.2% 100.0%
3342201 2.1.1.130 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DUF223 0.54 34.0 3.28e-01 72.3% 55.7%
3255946 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.53 34.0 3.74e-01 79.2% 82.5%
3619467 220.1.1.84 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_15 0.50 35.0 3.45e-01 77.2% 67.3%