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NC_013021.1__YP_003084152.1__PSS2_gp008__00008

Bact-Vir

NC_013021.1__YP_003084152.1__PSS2_gp008__00008

Identity

Accession:
NC_013021 ↗
Kingdom:
phage

Quality

86.2 mean pLDDT

Taxonomy

TaxID: 658401

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

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

D1 medium residues 30-85
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ngxA02 3.40.50.10860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Leucine Dehydrogenase, chain A, domain 1 0.70 46.0 4.06e-01 92.9% 45.2%
2h0aA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.68 43.0 3.42e-01 78.6% 32.1%
2e0gA00 3.30.300.180 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › DnaA, N-terminal domain 0.68 57.0 4.65e-01 100.0% 50.5%
4rkrB01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.65 43.0 3.23e-01 76.8% 29.2%
3prbA03 3.30.70.2210 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 53.0 4.91e-01 100.0% 73.0%
4hlnA02 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.63 50.0 3.32e-01 85.7% 27.0%
4i1tA02 3.30.70.2640 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Arenavirus RNA polymerase 0.63 52.0 4.69e-01 100.0% 71.4%
4hdtA00 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.60 48.0 3.11e-01 100.0% 16.5%
3gkuC02 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.60 51.0 4.47e-01 100.0% 69.7%
2ql8A00 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.60 49.0 3.85e-01 100.0% 46.4%
4eadA02 3.40.1030.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 › Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain 0.60 52.0 3.46e-01 100.0% 52.8%
2kzfA00 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.59 48.0 4.12e-01 100.0% 61.3%
6yubA02 3.40.250.10 Alpha Beta › 3-Layer(aba) Sandwich › Oxidized Rhodanese; domain 1 › Rhodanese-like domain 0.59 52.0 4.15e-01 100.0% 80.9%
3k4uE01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.59 45.0 3.47e-01 83.9% 45.9%
2yutA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.59 51.0 3.50e-01 100.0% 36.3%
5c3mC01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.59 49.0 3.54e-01 96.4% 41.3%
1qhhD01 3.30.160.800 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.59 48.0 4.33e-01 89.3% 80.3%
1alo006 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.58 45.0 3.67e-01 100.0% 41.3%
2pt7G01 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.58 48.0 4.39e-01 98.2% 89.7%
2dfwA02 3.30.750.24 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › STAS domain 0.58 42.0 3.84e-01 100.0% 54.8%
4eswA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.58 47.0 3.23e-01 98.2% 77.1%
2wabA02 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.58 48.0 3.35e-01 100.0% 64.5%
2heuB01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.57 43.0 3.20e-01 87.5% 57.0%
1s12A00 3.30.70.1490 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cysteine protease Prp 0.57 45.0 3.83e-01 96.4% 52.1%
2kdnA00 3.30.300.90 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › BolA-like 0.57 47.0 3.94e-01 100.0% 57.4%
4fdxB00 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.57 41.0 4.00e-01 82.1% 70.3%
8dqaA01 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.57 45.0 3.88e-01 94.6% 100.0%
3c6vA00 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.56 46.0 3.59e-01 100.0% 73.4%
4ab5B01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.56 46.0 3.69e-01 92.9% 48.7%
3zxsA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.56 48.0 3.50e-01 98.2% 48.1%
3up9A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.56 43.0 3.30e-01 87.5% 95.7%
3ja8601 3.30.1640.10 Alpha Beta › 2-Layer Sandwich › mini-chromosome maintenance (MCM) complex, chain A, domain 1 › mini-chromosome maintenance (MCM) complex, chain A, domain 1 0.55 47.0 3.90e-01 100.0% 88.6%
3hcwA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.55 42.0 3.32e-01 91.1% 37.1%
4dh4A00 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.55 44.0 3.71e-01 100.0% 88.6%
1ufvA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.55 46.0 3.34e-01 96.4% 72.7%
3m21F00 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.55 40.0 3.88e-01 83.9% 77.6%
1fvpA00 3.20.20.30 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Luciferase-like domain 0.55 46.0 3.12e-01 100.0% 54.5%
2bgiA02 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.54 44.0 3.38e-01 100.0% 48.7%
3m20A00 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.54 39.0 3.90e-01 83.9% 76.3%
6ogmD00 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.53 38.0 3.82e-01 83.9% 75.4%
2fm7A00 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.53 38.0 3.80e-01 83.9% 74.2%
7b3aA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.53 44.0 3.36e-01 100.0% 38.3%
1xmtA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.52 40.0 3.58e-01 98.2% 55.8%
1ufhA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.52 42.0 3.24e-01 100.0% 36.1%
3i8oA01 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.52 46.0 3.52e-01 100.0% 58.6%
3ctpA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.52 39.0 3.07e-01 96.4% 35.5%
1zhvA00 3.30.2130.10 Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like 0.51 41.0 3.29e-01 98.2% 72.4%
2g0iA00 3.30.70.1490 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cysteine protease Prp 0.51 43.0 3.47e-01 94.6% 87.4%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3302044 7512.1.1.0 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase 0.69 53.0 3.36e-01 82.1% 30.0%
5053188 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 0.69 55.0 5.09e-01 100.0% 69.3%
4663092 2484.1.1.40 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvX 0.67 58.0 4.26e-01 100.0% 61.9%
5027003 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 0.66 53.0 4.93e-01 100.0% 69.3%
5065518 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 0.66 55.0 5.31e-01 100.0% 83.1%
1521777 7523.1.1.16 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › DctP 0.66 48.0 3.77e-01 83.9% 35.8%
3588613 327.11.1.0 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.65 53.0 4.98e-01 96.4% 75.3%
5042709 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 0.65 52.0 4.95e-01 100.0% 75.7%
5004464 2008.1.1.78 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RE_endonuc 0.65 54.0 4.34e-01 100.0% 49.6%
3613496 2007.9.1.0 a/b three-layered sandwiches › Flavodoxin-like › Toll/Interleukin receptor TIR domain › Toll/Interleukin receptor TIR domain 0.65 52.0 3.70e-01 92.9% 41.1%
3549043 2005.1.1.36 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › SLC12 0.65 55.0 3.96e-01 98.2% 42.4%
5011481 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 0.65 54.0 5.04e-01 100.0% 74.7%
5078047 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 0.65 53.0 5.11e-01 100.0% 83.1%
4928951 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 0.65 51.0 4.84e-01 100.0% 74.3%
3549056 2005.1.1.36 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › SLC12 0.64 54.0 3.87e-01 98.2% 40.0%
5068376 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 0.64 51.0 4.99e-01 100.0% 81.5%
4933884 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 0.64 53.0 5.03e-01 100.0% 78.6%
4629797 327.11.1.2 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) › KhpA-B_KH 0.64 53.0 4.97e-01 100.0% 93.3%
4948030 327.7.1.0 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like 0.62 52.0 4.92e-01 100.0% 90.0%
4983265 327.7.1.0 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like 0.62 50.0 4.95e-01 100.0% 90.0%
4024234 2003.1.5.28 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › mRNA_G-N7_MeTrfase 0.62 51.0 3.15e-01 100.0% 14.3%
4426786 327.10.1.3 a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › DnaA_N 0.62 49.0 4.37e-01 100.0% 58.9%
5047209 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 0.62 51.0 4.77e-01 100.0% 76.0%
3446564 2005.1.1.3 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.62 52.0 3.95e-01 100.0% 49.0%
4220363 327.11.1.2 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) › KhpA-B_KH 0.61 50.0 4.59e-01 100.0% 70.0%
1144868 2008.1.1.66 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › ArenaCapSnatch 0.61 50.0 3.71e-01 100.0% 37.3%
4099491 2002.1.1.125 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM,SPASM 0.61 50.0 3.10e-01 94.6% 18.4%
2617704 7523.1.1.19 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › NMT1 0.60 42.0 3.61e-01 87.5% 42.6%
1734609 2003.1.1.20 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Epimerase 0.60 49.0 3.93e-01 92.9% 94.0%
3633643 2003.1.1.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.60 51.0 3.09e-01 100.0% 60.5%
5023294 327.11.1.1 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) › KH_2 0.60 49.0 4.41e-01 98.2% 65.9%
4229239 2484.1.1.85 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC_III 0.60 50.0 3.41e-01 100.0% 51.5%
5021647 2007.22.1.1 a/b three-layered sandwiches › Flavodoxin-like › Methyl-viologen reducing hydrogenase subunit D › Methyl-viologen reducing hydrogenase subunit D › FlpD 0.59 51.0 4.00e-01 100.0% 52.0%
4961052 2498.1.1.160 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_MA_2 0.59 41.0 2.72e-01 73.2% 36.4%
4995705 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.59 50.0 3.84e-01 100.0% 75.0%
5059354 2492.1.1.61 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › MOFRL 0.59 47.0 3.73e-01 94.6% 80.8%
3386442 327.11.1.0 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.58 47.0 4.36e-01 100.0% 73.8%
3535899 2003.1.1.3 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › adh_short 0.58 47.0 3.13e-01 94.6% 26.0%
3972482 2485.1.1.127 a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › DUF7088 0.57 42.0 3.22e-01 83.9% 32.7%
5579 306.8.1.1 a+b two layers › Glucose permease domain IIB-like › TM1457-like › TM1457-like › Peptidase_Prp 0.57 45.0 3.83e-01 96.4% 52.1%
3370560 2484.1.1.67 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.57 42.0 3.66e-01 83.9% 93.7%
9164 2003.1.1.26 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Glyco_hydro_4 0.57 48.0 3.50e-01 100.0% 39.1%
4953115 315.1.1.2 a+b two layers › Tautomerase/MIF-like › Tautomerase/MIF › Tautomerase/MIF › Tautomerase 0.56 42.0 4.16e-01 85.7% 78.3%
4478613 2007.5.1.0 a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase 0.56 45.0 3.17e-01 96.4% 59.5%
5016976 327.5.1.0 a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins 0.56 47.0 4.21e-01 98.2% 71.8%
4023223 192.4.1.0 alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.56 43.0 3.12e-01 85.7% 65.9%
3803366 2005.1.1.41 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_C 0.56 49.0 3.56e-01 100.0% 63.1%
4122147 315.1.1.2 a+b two layers › Tautomerase/MIF-like › Tautomerase/MIF › Tautomerase/MIF › Tautomerase 0.55 40.0 3.77e-01 85.7% 62.7%
2814166 315.1.1.2 a+b two layers › Tautomerase/MIF-like › Tautomerase/MIF › Tautomerase/MIF › Tautomerase 0.54 39.0 3.75e-01 83.9% 66.7%
3300901 2484.1.1.67 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.54 41.0 3.13e-01 91.1% 72.5%
3580315 2005.1.1.36 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › SLC12 0.52 44.0 3.24e-01 100.0% 38.2%
3321285 2005.1.1.41 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_C 0.52 42.0 2.90e-01 87.5% 65.6%
4991997 2005.1.1.13 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CTP_transf_like 0.52 46.0 3.44e-01 100.0% 85.0%
3284274 213.1.1.35 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_CG 0.52 42.0 3.73e-01 96.4% 60.7%
4104053 2007.1.2.11 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › Peripla_BP_4 0.52 41.0 2.98e-01 98.2% 59.0%