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NC_021559.1__YP_008130132.1__PRAG_00206__00199

Bact-Vir

NC_021559.1__YP_008130132.1__PRAG_00206__00199

Identity

Accession:
NC_021559 ↗
Kingdom:
phage

Quality

86.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Kyanoviridae› Ronodorvirus› Prochlorococcus_phage_P-SSM3

TaxID: 536453

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

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

D1 high residues 3-54
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7r97A01 1.10.1520.10 Mainly Alpha › Orthogonal Bundle › Ribonuclease iii, N-terminal Endonuclease Domain; Chain A › Ribonuclease III domain 0.70 59.0 4.34e-01 100.0% 72.3%
7dfeA01 1.10.274.60 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain 0.70 52.0 3.89e-01 80.8% 84.3%
3h2zA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.67 55.0 3.82e-01 92.3% 94.3%
4dbgB02 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.66 55.0 5.29e-01 100.0% 86.9%
3vs8H00 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.66 48.0 2.94e-01 82.7% 47.9%
3ne5B04 6.10.140.730 Special › Helix non-globular › Helix Hairpins › 0.65 40.0 4.06e-01 98.1% 62.7%
1s8nA02 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 0.65 47.0 4.59e-01 78.8% 84.5%
1ngnA00 1.10.340.30 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2 0.63 53.0 3.93e-01 98.1% 38.9%
1j09A04 1.10.8.70 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Glutamate-tRNA synthetase, class I, anticodon-binding domain 1 0.62 49.0 5.04e-01 90.4% 97.9%
3k6hA01 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.62 49.0 3.41e-01 86.5% 51.5%
6wshA02 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 0.62 46.0 4.57e-01 82.7% 83.6%
1qo0D02 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 0.61 46.0 4.87e-01 82.7% 97.8%
3s84A02 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.61 52.0 3.79e-01 100.0% 79.0%
1zv1A00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.60 46.0 4.51e-01 92.3% 79.7%
1lzwA00 3.30.1390.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L30; Chain: A, › Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS 0.59 45.0 3.83e-01 86.5% 75.8%
2jaqA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.58 39.0 2.73e-01 71.2% 27.0%
1puzA00 1.10.150.250 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Flavinator of succinate dehydrogenase 0.56 43.0 3.91e-01 92.3% 92.7%
7w5lA01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.55 43.0 2.85e-01 90.4% 32.7%
2w9mB01 1.10.150.110 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DNA polymerase beta, N-terminal domain-like 0.55 41.0 3.53e-01 80.8% 89.5%
1ctfA00 3.30.1390.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L30; Chain: A, › Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS 0.55 40.0 3.71e-01 80.8% 85.3%
1z72A00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.51 41.0 2.80e-01 94.2% 59.7%
4fqnC00 1.20.1160.20 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › 0.50 42.0 3.65e-01 98.1% 60.0%
1tjoB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.50 42.0 3.03e-01 98.1% 77.7%
2qytA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.50 43.0 3.51e-01 98.1% 70.3%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3928496 143.1.1.0 ↗ alpha arrays › PABP domain-like › PABC(PABP) domain › PABC(PABP) domain 0.83 74.0 7.05e-01 100.0% 91.7%
3888185 103.1.1.52 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › UBA_N4BP1_C 0.78 63.0 6.38e-01 100.0% 96.0%
3260787 143.1.1.1 ↗ alpha arrays › PABP domain-like › PABC(PABP) domain › PABC(PABP) domain › PABP 0.76 64.0 5.79e-01 100.0% 81.3%
3878202 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.74 50.0 4.29e-01 71.2% 47.1%
3410442 190.1.1.0 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box 0.74 51.0 3.86e-01 73.1% 33.6%
3730979 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.74 61.0 6.09e-01 100.0% 90.9%
4025966 103.4.1.2 ↗ alpha arrays › RuvA-C › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › TFIIS_M 0.73 62.0 5.03e-01 96.2% 81.0%
3788827 103.4.1.0 ↗ alpha arrays › RuvA-C › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein 0.73 56.0 5.26e-01 84.6% 83.1%
3170390 3721.1.1.0 ↗ alpha bundles › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › Protein regulator of cytokinesis 1 (PRC1) dimerization domain 0.72 53.0 4.82e-01 78.8% 64.3%
4489811 103.17.1.0 ↗ alpha arrays › RuvA-C › HMG-CoA reductase flap domain › HMG-CoA reductase flap domain 0.71 58.0 5.95e-01 100.0% 100.0%
4156650 3254.1.1.1 ↗ alpha arrays › helical domain in flagellar biosynthesis protein flhA › helical domain in flagellar biosynthesis protein flhA › helical domain in flagellar biosynthesis protein flhA › FHIPEP 0.70 60.0 5.09e-01 100.0% 61.1%
3579615 103.1.1.3 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › CRAL_TRIO_N 0.69 59.0 5.06e-01 100.0% 60.0%
4846309 2004.1.1.7 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran,BCA_ABC_TP_C 0.69 52.0 3.38e-01 82.7% 26.5%
3697200 4049.1.1.2 ↗ alpha superhelices › alpha-helical domain in siroheme synthase middle domains-like › alpha-helical domain in siroheme synthase middle domains-like › alpha-helical domain in siroheme synthase middle domains-like › Sirohm_synth_C 0.69 58.0 5.20e-01 98.1% 82.7%
5006371 4049.1.1.0 ↗ alpha superhelices › alpha-helical domain in siroheme synthase middle domains-like › alpha-helical domain in siroheme synthase middle domains-like › alpha-helical domain in siroheme synthase middle domains-like 0.67 58.0 5.58e-01 100.0% 100.0%
3239423 190.1.1.0 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box 0.67 47.0 4.92e-01 75.0% 97.8%
3588971 6026.1.1.0 ↗ alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain 0.67 45.0 4.06e-01 71.2% 50.7%
4997861 4953.1.1.4 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › ASL_C2 0.66 53.0 4.58e-01 100.0% 61.1%
4031456 162.1.1.1 ↗ alpha bundles › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PRD 0.66 52.0 4.31e-01 98.1% 88.2%
3289310 103.12.1.1 ↗ alpha arrays › RuvA-C › ANTAR domain › ANTAR domain › ANTAR 0.65 47.0 4.65e-01 76.9% 89.1%
3701737 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.65 55.0 5.08e-01 100.0% 75.7%
3618000 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.65 48.0 4.15e-01 80.8% 67.1%
4024642 185.2.1.1 ↗ alpha superhelices › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin-like › PfEMP1 core intracellular domain › PfEMP1 core intracellular domain › ATS 0.65 53.0 5.26e-01 98.1% 100.0%
5046317 213.1.1.29 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_9 0.63 46.0 3.54e-01 82.7% 53.8%
3513428 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.62 53.0 3.26e-01 100.0% 37.2%
3702895 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.61 49.0 4.90e-01 100.0% 90.9%
4042981 4953.1.1.4 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › ASL_C2 0.61 48.0 4.23e-01 92.3% 63.5%
3620069 633.1.1.0 ↗ alpha bundles › Bromodomain-like › Bromodomain › Bromodomain 0.60 48.0 4.08e-01 100.0% 61.0%
4605697 516.1.1.1 ↗ alpha arrays › YgfY-like (DUP399, Pfam03937) › YgfY-like (DUP399, Pfam03937) › YgfY-like (DUP399, Pfam03937) › Sdh5 0.59 48.0 4.27e-01 100.0% 90.6%
3654606 1128.1.1.1 ↗ alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.58 44.0 3.97e-01 84.6% 76.0%
3597591 1128.1.1.0 ↗ alpha bundles › LYR protein › LYR protein › LYR protein 0.57 43.0 3.92e-01 82.7% 81.4%
5070467 632.2.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains 0.56 43.0 4.09e-01 86.5% 69.2%
3485616 1128.1.1.1 ↗ alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.56 42.0 4.06e-01 88.5% 90.8%
4941976 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.56 48.0 3.84e-01 100.0% 87.3%
3941103 103.1.1.14 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › UBA_4 0.54 41.0 3.99e-01 88.5% 95.4%
3414016 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.53 35.0 2.79e-01 71.2% 60.0%