←Back to structures

NC_019421.1__YP_006990540.1__D863_gp62__00062

Bact-Vir

NC_019421.1__YP_006990540.1__D863_gp62__00062

Identity

Accession:
NC_019421 ↗
Kingdom:
phage

Quality

73.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Colneyvirus› Clostridium_phage_phiMMP02

TaxID: 1204534

Cluster

View cluster (4 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 52-105
PDB
Domain cluster: rep: OP310984.1__UXD83619.1__NP274_00212__00212__D3-72
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3eM02 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 0.85 76.0 7.01e-01 100.0% 77.9%
2jqzA00 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.78 68.0 5.11e-01 98.1% 98.5%
3gp4B00 1.10.1660.10 Mainly Alpha › Orthogonal Bundle › Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 › 0.74 46.0 3.43e-01 74.1% 25.4%
2ed8A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.67 48.0 4.11e-01 100.0% 47.7%
2ww8A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.67 49.0 3.88e-01 100.0% 39.6%
2edyA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.67 47.0 3.83e-01 100.0% 39.8%
3eipA00 3.10.50.20 Alpha Beta › Roll › Chitinase A; domain 3 › Cloacin immunity protein 0.65 54.0 4.80e-01 98.1% 97.6%
8h68A01 2.60.120.590 Mainly Beta › Sandwich › Jelly Rolls › Alpha-ketoglutarate-dependent dioxygenase AlkB-like 0.65 46.0 3.04e-01 100.0% 18.6%
1uasA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.64 43.0 3.62e-01 96.3% 42.0%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.64 49.0 4.60e-01 100.0% 68.2%
2iw3A03 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.61 42.0 2.85e-01 72.2% 32.9%
5jzxD02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.60 42.0 3.12e-01 100.0% 28.1%
4avaA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.60 45.0 3.35e-01 100.0% 31.2%
5utkA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 46.0 3.98e-01 100.0% 55.4%
4dqnA01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.57 42.0 3.08e-01 81.5% 81.6%
7neaA01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.57 42.0 3.27e-01 79.6% 87.6%
3qt2B03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 43.0 3.58e-01 85.2% 64.3%
1aw8B00 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.55 47.0 3.95e-01 100.0% 56.0%
4eq3A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 49.0 3.84e-01 100.0% 49.1%
3ougA00 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.54 46.0 3.70e-01 100.0% 48.1%
4pofA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.54 44.0 4.55e-01 100.0% 96.0%
4n0rA03 2.60.40.3950 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 48.0 3.76e-01 100.0% 48.2%
5u3fB01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.54 45.0 3.44e-01 98.1% 97.1%
3bpnC03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 48.0 3.91e-01 100.0% 59.4%
3lzqA00 2.60.40.2480 Mainly Beta › Sandwich › Immunoglobulin-like › Periplasmic metal-binding protein Tp34-type 0.54 49.0 3.46e-01 100.0% 35.0%
2mtzA01 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.54 37.0 3.82e-01 72.2% 92.0%
5ce8A01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.54 44.0 3.41e-01 90.7% 96.7%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.54 45.0 3.85e-01 100.0% 56.5%
8bs9A01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.54 47.0 2.94e-01 100.0% 23.3%
4a6fA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 44.0 3.72e-01 100.0% 81.0%
3puaA01 2.60.120.650 Mainly Beta › Sandwich › Jelly Rolls › Cupin 0.53 41.0 2.68e-01 88.9% 31.5%
2k2dA00 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.53 35.0 3.70e-01 94.4% 78.7%
2hn1A01 3.30.460.20 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › CorA soluble domain-like 0.53 42.0 3.35e-01 100.0% 88.7%
5c8qB02 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.53 40.0 4.33e-01 83.3% 97.8%
4avrA00 2.40.40.10 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › RlpA-like domain 0.52 46.0 3.78e-01 96.3% 58.5%
1qxfA00 2.20.25.100 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › Ribosomal protein S27 0.52 43.0 4.24e-01 100.0% 89.7%
3in6A02 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 45.0 3.52e-01 100.0% 45.3%
3cjmA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.52 46.0 2.97e-01 100.0% 79.2%
1bw3A00 2.40.40.10 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › RlpA-like domain 0.52 46.0 3.52e-01 100.0% 47.2%
1ln0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.52 44.0 3.79e-01 100.0% 65.2%
1ghpA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.52 44.0 2.87e-01 98.1% 85.2%
3r7wC02 3.30.450.190 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.52 40.0 3.34e-01 90.7% 90.7%
6bn3A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.51 45.0 2.91e-01 100.0% 82.4%
4ecnA02 2.60.40.3540 Mainly Beta › Sandwich › Immunoglobulin-like › Domain of unknown function DUF4458 0.51 45.0 3.48e-01 100.0% 51.6%
4iajA00 3.30.1490.390 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Protein of unknown function DUF4649 0.51 40.0 3.70e-01 100.0% 65.8%
4e9kA00 2.60.120.1350 Mainly Beta › Sandwich › Jelly Rolls › Protein of unknown function DUF4465 0.51 41.0 2.71e-01 100.0% 20.4%
1zc1A01 2.40.40.50 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › Ubiquitin fusion degradation protein UFD1, N-terminal domain 0.50 43.0 3.51e-01 100.0% 51.5%
6nhsA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.50 44.0 2.87e-01 100.0% 84.1%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3587703 101.1.14.0 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases 0.88 75.0 7.80e-01 96.3% 100.0%
3058113 101.1.14.0 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases 0.86 73.0 7.44e-01 100.0% 94.2%
2876 101.1.14.2 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › I-HmuI_NUMOD-like 0.85 76.0 6.98e-01 100.0% 76.8%
4384880 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.84 74.0 6.31e-01 96.3% 62.4%
4414927 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.83 76.0 6.98e-01 100.0% 81.2%
3171408 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.81 70.0 7.23e-01 92.6% 100.0%
5041000 11.1.4.23 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › CarboxypepD_reg 0.68 48.0 4.03e-01 100.0% 44.4%
5055044 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.68 49.0 4.37e-01 100.0% 54.7%
3624908 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.67 58.0 4.99e-01 100.0% 77.8%
4970102 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.67 48.0 4.02e-01 100.0% 45.6%
5055294 10.4.1.0 ↗ beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain 0.67 49.0 4.17e-01 98.1% 49.4%
3276203 223.1.1.13 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_3 0.65 49.0 3.76e-01 83.3% 65.4%
4957982 11.1.4.27 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › fn3_3 0.64 47.0 3.68e-01 100.0% 37.4%
3400352 379.1.1.0 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors 0.63 44.0 4.45e-01 96.3% 74.1%
4961190 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.62 46.0 3.82e-01 100.0% 45.3%
3389022 379.1.1.0 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors 0.62 47.0 4.86e-01 100.0% 88.0%
3278973 375.1.1.185 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Zn_ribbon_8 0.62 42.0 4.77e-01 92.6% 97.5%
3240617 101.15.1.0 ↗ alpha arrays › HTH › LysM domain › LysM domain 0.61 43.0 4.20e-01 74.1% 90.0%
3956578 2492.1.1.1 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › dCMP_cyt_deam_1 0.61 55.0 3.88e-01 100.0% 77.4%
3238303 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.61 53.0 4.22e-01 100.0% 62.7%
5021979 223.1.1.13 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_3 0.61 45.0 3.68e-01 85.2% 81.7%
3518250 822.2.1.0 ↗ a+b two layers › GYF/BRK domain-like › BRK domain-like › BRK domain-like 0.60 38.0 4.21e-01 96.3% 87.5%
3983134 223.1.1.113 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PF30408 0.59 43.0 3.65e-01 81.5% 61.0%
4008034 223.1.1.113 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PF30408 0.59 43.0 3.14e-01 81.5% 35.9%
3371515 2007.1.19.2 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › FabD/lysophospholipase-like › Patatin 0.59 48.0 3.00e-01 100.0% 42.5%
4259798 4020.1.1.0 ↗ a+b two layers › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes 0.58 43.0 3.08e-01 79.6% 67.3%
5047755 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.58 50.0 3.72e-01 98.1% 49.3%
4974400 4121.1.1.1 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.58 47.0 3.13e-01 98.1% 44.8%
4986404 4008.1.1.0 ↗ 0.58 41.0 4.26e-01 92.6% 82.0%
4566976 375.14.2.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) › Rubredoxin-like domain in leucyl-tRNA synthetase (LS2) 0.58 39.0 4.27e-01 100.0% 95.0%
5029740 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 48.0 3.96e-01 100.0% 52.6%
1392732 221.1.1.4 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.57 41.0 3.41e-01 83.3% 79.1%
4958145 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.57 41.0 2.76e-01 83.3% 36.1%
3289555 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 48.0 3.52e-01 100.0% 37.0%
5019917 223.1.1.13 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_3 0.55 40.0 3.16e-01 85.2% 67.1%
3494162 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 48.0 3.78e-01 100.0% 49.6%
4607892 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.54 37.0 4.06e-01 98.1% 95.0%
4946668 4020.1.1.1 ↗ a+b two layers › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › Aminotran_4 0.54 45.0 3.26e-01 96.3% 82.5%
3235407 11.2.1.52 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2_nem 0.54 45.0 3.33e-01 100.0% 35.2%
3992138 11.2.1.52 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2_nem 0.54 43.0 3.35e-01 100.0% 98.0%
4945087 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.53 40.0 3.22e-01 96.3% 41.9%
4600774 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.53 43.0 4.34e-01 92.6% 100.0%
3785593 304.112.1.0 ↗ a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain 0.53 45.0 3.89e-01 100.0% 96.7%
3320938 4020.1.1.1 ↗ a+b two layers › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › Aminotran_4 0.53 44.0 3.24e-01 100.0% 82.4%
3176457 4139.1.1.1 ↗ a+b two layers › AMMECR1-like › AMMECR1-like › AMMECR1-like › AMMECR1 0.52 45.0 3.87e-01 100.0% 71.1%
4944154 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.52 37.0 2.97e-01 79.6% 53.6%
3496147 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.52 45.0 3.72e-01 100.0% 73.0%
5032187 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.52 43.0 4.35e-01 96.3% 94.5%
3727369 4139.1.1.1 ↗ a+b two layers › AMMECR1-like › AMMECR1-like › AMMECR1-like › AMMECR1 0.52 42.0 4.03e-01 100.0% 76.9%
221869 235.1.1.16 ↗ a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Peptidase_U40 0.51 41.0 3.01e-01 100.0% 30.4%
4937954 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 44.0 3.56e-01 100.0% 53.6%
77927 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.51 44.0 3.73e-01 100.0% 66.0%
3579303 4020.1.1.1 ↗ a+b two layers › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › Aminotran_4 0.51 39.0 2.90e-01 90.7% 77.1%
4990637 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.51 44.0 3.84e-01 100.0% 67.5%
4505111 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.50 43.0 4.32e-01 98.1% 100.0%
3508278 4139.1.1.1 ↗ a+b two layers › AMMECR1-like › AMMECR1-like › AMMECR1-like › AMMECR1 0.50 43.0 3.63e-01 100.0% 66.3%