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LacPavin_0818_WC40_scaffold_354720_prodigal-single.1__X__X__00197

Bact-Vir

LacPavin_0818_WC40_scaffold_354720_prodigal-single.1__X__X__00197

Identity

Kingdom:
phage

Quality

76.1 mean pLDDT

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 22-115
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3b34A02 3.30.2010.30 Alpha Beta › 2-Layer Sandwich › Zincin-like › 0.65 51.0 5.30e-01 97.9% 91.8%
5zi7A02 3.30.2010.30 Alpha Beta › 2-Layer Sandwich › Zincin-like › 0.64 49.0 5.19e-01 97.9% 91.8%
3c6vA00 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.61 36.0 3.16e-01 78.7% 37.8%
4gs5A02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.59 31.0 3.02e-01 78.7% 44.8%
6ogmD00 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.59 35.0 4.27e-01 85.1% 93.4%
4cthA02 1.10.1380.10 Mainly Alpha › Orthogonal Bundle › Neutral endopeptidase; domain 2 › Neutral endopeptidase , domain2 0.58 41.0 2.76e-01 73.4% 32.9%
1akoA00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.57 39.0 2.86e-01 71.3% 54.5%
5jenA01 3.30.565.40 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Fervidobacterium nodosum Rt17-B1 like 0.57 41.0 3.98e-01 78.7% 100.0%
6lkvA01 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.56 36.0 3.24e-01 87.2% 45.1%
2xczA00 3.30.429.10 Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor 0.56 36.0 3.38e-01 86.2% 52.6%
4fvaC00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.54 37.0 2.76e-01 72.3% 47.0%
4isbB02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.53 31.0 3.06e-01 73.4% 49.5%
3kxwA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.52 31.0 2.85e-01 75.5% 43.5%
4xeaA01 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.52 37.0 2.81e-01 74.5% 83.5%
1qsmD00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.51 40.0 3.45e-01 86.2% 90.1%
4s39A02 3.30.413.10 Alpha Beta › 2-Layer Sandwich › Sulfite Reductase Hemoprotein; domain 1 › Sulfite Reductase Hemoprotein, domain 1 0.51 40.0 3.77e-01 87.2% 81.9%
1vkcA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.51 37.0 3.24e-01 76.6% 88.5%
1atnD00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.51 35.0 2.64e-01 72.3% 38.4%
1j72A01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.50 29.0 2.82e-01 78.7% 47.7%
3ihlB00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.50 39.0 2.96e-01 84.0% 87.8%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3730197 327.7.1.1 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.59 34.0 3.53e-01 86.2% 60.0%
4951792 2498.1.1.9 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M1 0.59 52.0 3.77e-01 96.8% 73.3%
3225023 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 0.57 36.0 3.52e-01 72.3% 56.2%
3933457 2498.1.1.9 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M1 0.56 46.0 3.44e-01 88.3% 70.4%
3293421 2484.1.1.72 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › YqgF 0.56 39.0 3.14e-01 81.9% 35.8%
3743593 59.1.1.0 beta complex topology › triple barrel › triple barrel › Rap30/74 interaction domains-like 0.55 38.0 4.10e-01 71.3% 100.0%
3885821 327.7.1.1 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.55 33.0 3.30e-01 72.3% 56.8%
4976057 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 0.53 33.0 3.24e-01 78.7% 57.0%
5039752 327.7.1.1 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.53 31.0 3.21e-01 75.5% 60.0%
5051070 316.1.1.2 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.52 38.0 3.23e-01 75.5% 61.9%
4947038 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 0.52 30.0 3.43e-01 83.0% 77.1%
5082956 213.1.1.1 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.52 41.0 3.61e-01 89.4% 94.0%
3212579 219.1.1.0 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.51 43.0 3.04e-01 92.6% 44.3%
5014698 327.7.1.1 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.50 29.0 2.98e-01 75.5% 56.7%
3175551 213.1.1.0 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.50 40.0 3.19e-01 87.2% 91.5%
3588796 327.7.1.1 a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.50 29.0 3.01e-01 75.5% 57.8%
D2 medium residues 116-184
PDB
Domain cluster: representative
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1y56B01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.68 46.0 3.22e-01 81.2% 21.5%
4akgA08 1.10.472.130 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Dynein motor, AAA2 domain, small subdomain 0.66 49.0 3.73e-01 78.3% 41.7%
2j82A00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.63 55.0 3.91e-01 100.0% 36.7%
7x4eA01 1.10.1220.160 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant › DNA sulphur modification protein DndE 0.63 37.0 3.20e-01 100.0% 37.4%
3mnlB00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.62 52.0 3.96e-01 97.1% 63.7%
1t6jA03 1.10.274.20 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Phenylalanine ammonia-lyase 1; domain 3 0.62 45.0 3.97e-01 78.3% 55.3%
2no4A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.61 49.0 4.85e-01 98.6% 80.0%
7sk7A01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.61 51.0 3.48e-01 92.8% 41.9%
3on2A00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.61 52.0 3.90e-01 100.0% 62.6%
1dpgA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.60 50.0 3.36e-01 97.1% 89.0%
2jfrA00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.60 53.0 3.70e-01 100.0% 31.2%
2c61A00 3.40.50.12240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.60 45.0 2.78e-01 81.2% 66.8%
4od4A02 1.20.120.1780 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › UbiA prenyltransferase 0.58 50.0 4.24e-01 97.1% 95.0%
3bk2A03 3.10.20.580 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.58 48.0 4.40e-01 100.0% 68.7%
2nx4C00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.57 48.0 3.60e-01 95.7% 58.8%
4oa3A00 3.10.310.50 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › 0.57 47.0 3.88e-01 98.6% 68.8%
3djcB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 39.0 3.69e-01 97.1% 58.0%
2kptA00 3.10.310.50 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › 0.56 42.0 3.41e-01 92.8% 39.9%
1qv9A02 6.10.140.120 Special › Helix non-globular › Helix Hairpins › 0.55 45.0 3.98e-01 89.9% 65.0%
1gqeA01 1.20.58.410 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Release factor 0.55 43.0 3.69e-01 85.5% 85.8%
1y1xB00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.54 45.0 3.43e-01 94.2% 81.0%
1l8sA00 1.20.90.10 Mainly Alpha › Up-down Bundle › Phospholipase A2 › Phospholipase A2 domain 0.53 46.0 3.84e-01 97.1% 68.5%
1u8vA01 1.10.3140.10 Mainly Alpha › Orthogonal Bundle › 4-hydroxybutyryl-coa dehydratase, domain 1 › 4-hydroxybutyryl-coa dehydratase, domain 1 0.53 40.0 3.26e-01 84.1% 56.6%
3zt9A00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.53 44.0 3.29e-01 97.1% 43.8%
3ty4B00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.53 43.0 2.85e-01 98.6% 24.4%
2ap1A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.52 41.0 3.42e-01 92.8% 81.3%
2z5bA00 3.30.230.100 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.52 41.0 3.43e-01 98.6% 48.8%
1ig8A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 39.0 3.25e-01 98.6% 44.0%
1x9mA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.51 40.0 2.84e-01 98.6% 26.5%
3t91B00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.51 44.0 3.11e-01 97.1% 39.3%
6jpaE00 1.20.140.150 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › 0.51 43.0 3.27e-01 94.2% 53.8%
3flkA00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.50 42.0 2.77e-01 100.0% 76.0%
2wsiA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.50 44.0 2.94e-01 100.0% 91.9%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3632302 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.72 56.0 5.36e-01 84.1% 88.7%
3398509 5076.1.1.1 alpha complex topology › Mitochondrial ADP/ATP carrier-like › Mitochondrial ADP/ATP carrier › Mitochondrial ADP/ATP carrier › Mito_carr 0.67 57.0 3.70e-01 94.2% 41.0%
3580090 5067.1.1.0 alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain 0.64 45.0 3.70e-01 73.9% 73.1%
3282974 5051.1.1.3 alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › SSF 0.64 57.0 3.37e-01 100.0% 68.4%
5069510 3542.1.1.2 alpha arrays › Presenilin family intramembrane aspartate proteases › Presenilin family intramembrane aspartate proteases › Presenilin family intramembrane aspartate proteases › SPP 0.64 54.0 3.69e-01 94.2% 98.4%
3516872 4006.1.1.4 alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › TraG_N 0.62 48.0 3.55e-01 87.0% 90.0%
5082167 632.22.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.61 45.0 4.12e-01 78.3% 73.3%
3624956 3105.1.1.0 a+b three layers › thylakoid acid phosphatase domain-related › thylakoid acid phosphatase domain-related › thylakoid acid phosphatase domain-related 0.60 51.0 3.89e-01 100.0% 93.9%
3533264 109.3.1.460 alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › PF28421 0.60 51.0 3.81e-01 100.0% 87.4%
4352248 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.60 46.0 3.22e-01 85.5% 30.4%
3366945 109.54.1.0 alpha superhelices › Repetitive alpha hairpins › C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13 › C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13 0.59 40.0 2.60e-01 71.0% 15.4%
5009781 131.1.1.0 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like 0.59 40.0 3.38e-01 79.7% 40.0%
3467149 601.1.2.0 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.59 47.0 3.86e-01 85.5% 63.2%
4940509 2498.1.1.0 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.59 49.0 4.43e-01 95.7% 74.0%
3231673 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.59 51.0 5.00e-01 95.7% 88.0%
5034929 633.23.1.0 alpha bundles › Bromodomain-like › Claudin › Claudin 0.59 45.0 3.23e-01 82.6% 57.9%
3909519 601.1.2.122 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › PF28421 0.59 49.0 3.69e-01 98.6% 86.8%
1710393 3068.2.1.1 a+b complex topology › Flagellar protein FlgA N-terminal domain-like › RNase J C-terminal domain › RNase J C-terminal domain › RNase_J_C 0.58 48.0 4.42e-01 100.0% 70.1%
3927546 601.21.1.1 alpha bundles › Four-helical up-and-down bundle › FAD-dependent thiol oxidase › FAD-dependent thiol oxidase › Evr1_Alr 0.58 46.0 3.11e-01 89.9% 72.9%
5060704 371.1.1.5 few secondary structure elements › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 › DUF1353 0.57 42.0 3.73e-01 82.6% 65.5%
4944772 3355.1.1.2 alpha complex topology › dicarboxylate/sodium symporter › dicarboxylate/sodium symporter › dicarboxylate/sodium symporter › CitMHS 0.57 46.0 2.98e-01 100.0% 26.8%
3700820 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.57 48.0 4.43e-01 92.8% 87.8%
3946553 3226.1.1.1 alpha complex topology › Uracil Transporter UraA › Uracil Transporter UraA › Uracil Transporter UraA › Xan_ur_permease 0.57 48.0 2.99e-01 97.1% 66.1%
3498294 148.1.3.40 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › ORC5_lid 0.55 48.0 4.23e-01 100.0% 78.1%
3392118 304.107.1.0 a+b two layers › Alpha-beta plaits › Aminomethyltransferase folate-binding domain › Aminomethyltransferase folate-binding domain 0.55 48.0 2.82e-01 97.1% 29.0%
3200574 601.1.2.81 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Serinc 0.55 45.0 3.76e-01 89.9% 86.7%
5023646 2003.6.1.5 a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › Phos_pyr_kin 0.55 44.0 3.17e-01 94.2% 71.1%
3938192 633.22.1.0 alpha bundles › Bromodomain-like › Vitamin K epoxide reductase (VKOR) › Vitamin K epoxide reductase (VKOR) 0.54 42.0 3.23e-01 84.1% 65.0%
3248749 216.1.1.0 a+b two layers › UBC-like › UBC-like › UBC-like 0.54 46.0 4.00e-01 95.7% 62.7%
4015841 7516.1.1.0 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases 0.54 48.0 3.17e-01 100.0% 51.6%
4952580 2003.6.1.5 a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › Phos_pyr_kin 0.54 43.0 3.09e-01 94.2% 68.8%
4978955 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.53 42.0 3.48e-01 94.2% 46.9%
5030821 3542.1.1.0 alpha arrays › Presenilin family intramembrane aspartate proteases › Presenilin family intramembrane aspartate proteases › Presenilin family intramembrane aspartate proteases 0.53 44.0 3.10e-01 100.0% 44.2%
3167596 3662.1.1.2 a+b two layers › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › POC3_POC4 0.53 44.0 3.37e-01 97.1% 54.2%
4978002 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 40.0 3.28e-01 91.3% 86.7%
4255608 195.1.1.1 alpha complex topology › NusB-like › NusB-like › NusB-like › NusB 0.51 41.0 3.35e-01 98.6% 71.1%