Back to structures

NC_048678.1__YP_009835401.1__HWB33_gp09__00009

Bact-Vir

NC_048678.1__YP_009835401.1__HWB33_gp09__00009

Identity

Accession:
NC_048678 ↗
Kingdom:
phage

Quality

83.4 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 high residues 6-48
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ddmB00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.97 89.0 5.25e-01 97.7% 15.5%
1un8A02 1.25.40.340 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › DhaL domain 0.96 74.0 4.61e-01 81.4% 18.2%
3rm5B01 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.95 81.0 4.74e-01 95.3% 13.2%
1tfeA02 1.10.286.20 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › 0.93 75.0 7.39e-01 86.0% 82.2%
4h8aB01 1.10.1530.10 Mainly Alpha › Orthogonal Bundle › Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 › Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel 0.90 72.0 6.36e-01 86.0% 61.7%
1xrhD01 1.10.1530.10 Mainly Alpha › Orthogonal Bundle › Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 › Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel 0.89 80.0 5.79e-01 95.3% 69.9%
4jndA01 1.10.1740.220 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › 0.86 73.0 5.06e-01 95.3% 30.8%
1dofA03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.86 56.0 5.12e-01 76.7% 51.8%
1tj7A03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.86 68.0 5.69e-01 88.4% 52.1%
3on4D00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.86 76.0 4.90e-01 100.0% 23.8%
3ibyD02 1.10.287.1770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.86 68.0 5.36e-01 86.0% 70.2%
3jr7A01 3.40.50.10440 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Dihydroxyacetone kinase; domain 1 0.85 60.0 4.27e-01 74.4% 27.1%
1ss3A00 1.10.287.720 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Pollen allergen ole e 6 0.85 61.0 5.85e-01 81.4% 66.0%
2x9qB00 3.40.50.11710 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cyclodipeptide synthase 0.84 71.0 4.43e-01 100.0% 18.5%
3kp1E02 1.10.8.1000 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ornithine 4,5 aminomutase S component, alpha subunit-like 0.83 59.0 4.93e-01 74.4% 45.7%
1dcnA03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.83 65.0 5.46e-01 88.4% 51.4%
3l9wA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.83 72.0 4.82e-01 100.0% 26.4%
1yqgA02 1.10.3730.10 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › ProC C-terminal domain-like 0.82 70.0 5.17e-01 97.7% 37.2%
2irmA00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.82 71.0 4.16e-01 100.0% 15.9%
2zcuA02 3.90.25.10 Alpha Beta › Alpha-Beta Complex › UDP-galactose 4-epimerase; domain 1 › UDP-galactose 4-epimerase, domain 1 0.80 62.0 4.45e-01 83.7% 63.5%
1rr7A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.80 61.0 6.00e-01 95.3% 78.3%
3triA02 1.10.3730.10 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › ProC C-terminal domain-like 0.79 65.0 4.96e-01 100.0% 39.8%
3kksB00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.78 64.0 4.36e-01 97.7% 26.3%
3c3dA02 1.10.8.240 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › CofD-like domain 0.77 52.0 4.15e-01 74.4% 35.2%
1cukA03 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.77 57.0 5.48e-01 83.7% 70.8%
1c3cA03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.76 58.0 4.81e-01 88.4% 45.7%
2kjgA00 1.20.120.970 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.76 54.0 4.14e-01 79.1% 33.3%
5ts9B00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.75 66.0 4.46e-01 100.0% 27.3%
2ahrA02 1.10.3730.10 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › ProC C-terminal domain-like 0.73 59.0 4.58e-01 100.0% 38.7%
2g8lB01 1.10.8.380 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Uncharacterised protein PF01937, DUF89, domain 1 0.72 55.0 4.78e-01 88.4% 53.7%
4nleA03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.72 59.0 5.00e-01 95.3% 53.9%
7ue1B01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.72 56.0 3.92e-01 88.4% 29.2%
7s0rB01 1.20.81.20 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › 0.72 62.0 5.19e-01 100.0% 84.2%
2plrA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.71 62.0 3.92e-01 97.7% 41.5%
3l6gA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.70 51.0 3.52e-01 79.1% 22.7%
3keyA01 1.10.10.1080 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Stn1, N-terminal wHTH domain 0.70 56.0 4.54e-01 90.7% 80.5%
2q0yA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.70 55.0 3.97e-01 95.3% 29.0%
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.69 57.0 4.95e-01 93.0% 60.0%
4e6nA02 6.10.140.1010 Special › Helix non-globular › Helix Hairpins › 0.69 62.0 5.29e-01 97.7% 71.2%
2c5iT00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.69 62.0 4.76e-01 100.0% 48.9%
3cjlA00 3.10.20.850 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Protein of unknown function DUF3861 0.68 56.0 4.50e-01 100.0% 46.6%
1v9mA02 1.20.1690.10 Mainly Alpha › Up-down Bundle › V-type ATP synthase subunit C fold › V-type ATP synthase subunit C domain 0.67 51.0 3.98e-01 83.7% 89.1%
1wivA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.65 45.0 3.85e-01 74.4% 43.8%
4cfsA02 1.10.210.20 Mainly Alpha › Orthogonal Bundle › Uteroglobin › 0.60 49.0 4.28e-01 95.3% 91.4%
2o5nA02 3.30.500.30 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › 0.59 52.0 3.51e-01 100.0% 100.0%
2iexA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.57 46.0 4.37e-01 90.7% 74.5%
3l4aA00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.57 42.0 3.20e-01 88.4% 30.6%
6znjB01 3.40.50.10950 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 37.0 2.81e-01 93.0% 32.2%
ECOD (44)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4972595 102.1.1.0 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.95 80.0 5.74e-01 90.7% 36.2%
5067264 101.1.2.21 alpha arrays › HTH › HTH › winged helix domain › Fe_dep_repress 0.95 67.0 4.69e-01 76.7% 26.7%
2407303 2005.1.1.25 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › HIGH_NTase1 0.94 74.0 4.35e-01 83.7% 14.0%
3954850 268.2.1.1 a+b two layers › Sterol carrier protein-like › LytR-Cps2A-Psr (LCP) enzymes › LytR-Cps2A-Psr (LCP) enzymes › LytR_cpsA_psr 0.91 82.0 4.78e-01 100.0% 13.4%
4426344 101.35.1.4 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › RecX_HTH3 0.90 74.0 6.30e-01 90.7% 57.4%
3344802 6158.1.1.0 alpha bundles › Nucleoporin p58/p45 helical region › Nucleoporin p58/p45 helical region › Nucleoporin p58/p45 helical region 0.89 78.0 6.75e-01 100.0% 64.6%
4276746 192.1.1.40 alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain › VMA21 0.89 79.0 6.72e-01 100.0% 63.2%
4666964 4953.1.1.0 beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.89 70.0 5.74e-01 88.4% 49.3%
4116531 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 0.88 70.0 5.73e-01 88.4% 49.3%
3250429 129.1.1.36 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › ABA_GPCR 0.87 76.0 4.57e-01 100.0% 15.4%
3960202 3721.1.1.1 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 › VIT1 0.87 64.0 5.41e-01 79.1% 48.6%
3810884 621.1.1.3 alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Sey1_3HB 0.87 78.0 5.28e-01 100.0% 29.7%
3256442 3721.1.1.1 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 › VIT1 0.87 62.0 5.14e-01 76.7% 44.0%
4036926 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 0.87 68.0 5.63e-01 88.4% 49.3%
3962155 191.1.1.49 alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_C_13_2 0.86 76.0 6.06e-01 100.0% 51.8%
3970102 4953.1.1.0 beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.86 68.0 5.35e-01 88.4% 43.5%
4174632 2003.1.1.28 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › TrkA_N 0.86 76.0 4.81e-01 100.0% 20.5%
4636891 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 0.86 69.0 5.45e-01 88.4% 44.7%
4543015 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 0.85 66.0 5.35e-01 88.4% 46.3%
3688172 2004.1.1.73 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MMR_HSR1 0.84 74.0 4.18e-01 100.0% 10.1%
5079587 2006.1.4.2 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › PIN 0.84 71.0 4.77e-01 95.3% 26.7%
4597969 4953.1.1.0 beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.84 67.0 5.54e-01 88.4% 50.7%
3960067 191.1.1.49 alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_C_13_2 0.83 73.0 6.24e-01 100.0% 62.9%
1551401 3869.1.1.1 alpha arrays › Mitochondrial 54S ribosomal protein L2 › Mitochondrial 54S ribosomal protein L2 › Mitochondrial 54S ribosomal protein L2 › Ribosomal_L27_C 0.83 72.0 4.55e-01 100.0% 19.6%
3231906 397.7.1.4 few secondary structure elements › Toxic hairpin › Ribosome-inactivating protein luffin P1 › Ribosome-inactivating protein luffin P1 › C_tripleX 0.83 66.0 6.62e-01 93.0% 91.1%
1208317 142.1.1.3 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.83 75.0 5.41e-01 100.0% 65.5%
2392755 191.1.1.1 alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_C_1 0.82 70.0 5.65e-01 100.0% 51.2%
3346014 2003.1.5.66 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.80 71.0 4.23e-01 100.0% 16.9%
3174240 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.80 67.0 5.07e-01 100.0% 39.0%
3996384 3455.1.1.7 alpha arrays › WY-domain in RXLR effectors › WY-domain in RXLR effectors › WY-domain in RXLR effectors › COMM_HN 0.80 62.0 5.66e-01 88.4% 65.5%
5032477 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.80 67.0 4.99e-01 100.0% 37.3%
4979297 7064.1.1.1 alpha bundles › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › VIT1 0.80 71.0 4.61e-01 100.0% 75.4%
4298932 103.1.1.6 alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › RuvA_C 0.79 59.0 5.29e-01 86.0% 58.3%
5024787 7064.1.1.0 alpha bundles › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 0.79 69.0 4.75e-01 100.0% 40.7%
3188842 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.79 66.0 4.77e-01 100.0% 33.6%
5060609 632.8.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 0.78 70.0 5.77e-01 100.0% 73.3%
4136948 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.78 65.0 4.97e-01 100.0% 40.0%
4990523 129.1.1.15 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.77 61.0 4.82e-01 93.0% 41.1%
4956469 4953.1.1.2 beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › ADSL_C 0.77 60.0 5.02e-01 88.4% 49.3%
4987541 611.8.1.0 alpha bundles › N-cbl like › C-terminal domain of E3 ubiquitin-protein ligase ARIH1 › C-terminal domain of E3 ubiquitin-protein ligase ARIH1 0.76 68.0 4.97e-01 100.0% 39.1%
3498975 103.1.1.0 alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.75 55.0 5.45e-01 79.1% 80.0%
5039471 164.1.1.1 alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.72 64.0 5.01e-01 100.0% 48.9%
4991198 2.1.1.359 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › HupF_HypC 0.71 60.0 4.49e-01 100.0% 40.0%
4068539 602.1.1.1 alpha arrays › L-aspartase middle domain-like › L-aspartase middle domain-like › L-aspartase middle domain-like › Lyase_1 0.65 55.0 3.31e-01 100.0% 38.5%