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NC_053236.1__YP_010001790.1__J1763_gp81__00081

Bact-Vir

NC_053236.1__YP_010001790.1__J1763_gp81__00081

Identity

Accession:
NC_053236 ↗
Kingdom:
phage

Quality

78.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Stackebrandtviridae› Kroosvirus› Gordonia_phage_YorkOnyx

TaxID: 2762402

Cluster

View cluster (3 members)

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 15-75
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2dg7A00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.87 68.0 4.66e-01 82.0% 59.7%
1tj7A03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.86 54.0 5.08e-01 75.4% 54.9%
2h09A02 1.10.60.10 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › Iron dependent repressor, metal binding and dimerisation domain 0.85 55.0 5.79e-01 70.5% 73.2%
1dcnA03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.81 55.0 5.16e-01 78.7% 59.7%
2c5qA00 3.50.30.40 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › Ribonuclease E inhibitor RraA/RraA-like 0.79 56.0 3.68e-01 73.8% 99.6%
1tfeA02 1.10.286.20 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › 0.78 54.0 6.00e-01 78.7% 97.8%
3uoeA01 1.10.1530.10 Mainly Alpha › Orthogonal Bundle › Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 › Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel 0.76 57.0 5.01e-01 78.7% 77.0%
1dofA03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.76 43.0 4.49e-01 77.0% 60.7%
4m70B00 1.10.246.200 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › WPP domain 0.75 54.0 4.67e-01 90.2% 50.5%
3on4D00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.75 57.0 4.02e-01 82.0% 61.1%
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 0.73 57.0 4.73e-01 83.6% 79.6%
3triA02 1.10.3730.10 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › ProC C-terminal domain-like 0.72 65.0 5.44e-01 100.0% 85.4%
1ufhA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.72 62.0 4.65e-01 98.4% 41.9%
1rr7A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.71 49.0 5.40e-01 83.6% 97.8%
3mbhA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.71 61.0 3.85e-01 93.4% 75.8%
1nxuA01 1.10.1530.10 Mainly Alpha › Orthogonal Bundle › Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 › Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel 0.71 54.0 4.90e-01 80.3% 86.1%
4s1hA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.71 60.0 3.83e-01 93.4% 74.6%
3ousA00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.71 57.0 5.16e-01 86.9% 92.7%
2ddmB00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.70 59.0 3.84e-01 93.4% 77.5%
2ahrA02 1.10.3730.10 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › ProC C-terminal domain-like 0.70 63.0 5.20e-01 100.0% 83.0%
1yqgA02 1.10.3730.10 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › ProC C-terminal domain-like 0.70 62.0 5.04e-01 100.0% 77.9%
1a5yA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.70 49.0 3.14e-01 73.8% 51.1%
4jndA01 1.10.1740.220 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › 0.69 57.0 4.45e-01 90.2% 50.0%
7ue1B01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.69 50.0 3.79e-01 77.0% 35.4%
2no4A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.66 47.0 4.44e-01 83.6% 62.7%
2q0yA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.64 47.0 3.68e-01 85.2% 34.8%
6r1nA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.64 46.0 3.82e-01 75.4% 80.6%
2c5iT00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 46.0 3.90e-01 75.4% 52.1%
2c4eA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.61 52.0 3.29e-01 95.1% 61.2%
2w4sA00 1.10.10.1440 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › PHAX RNA-binding domain 0.59 45.0 4.08e-01 83.6% 86.0%
2w0gA00 1.20.58.610 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Cdc37, Hsp90 binding domain 0.59 50.0 4.03e-01 100.0% 51.9%
2da3A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.58 32.0 3.55e-01 96.7% 68.1%
3ibyD02 1.10.287.1770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.57 48.0 4.30e-01 91.8% 69.0%
4p3gD00 1.10.3450.40 Mainly Alpha › Orthogonal Bundle › Hyaluronidase domain-like › Signal recognition particle, SRP68 subunit, RNA-binding domain 0.57 44.0 3.10e-01 85.2% 59.0%
7s0rB01 1.20.81.20 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › 0.56 44.0 4.18e-01 91.8% 73.7%
2pjqA01 1.10.472.50 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › HD-domain/PDEase-like 0.56 46.0 4.17e-01 98.4% 89.9%
4o6kA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.55 41.0 3.22e-01 86.9% 36.8%
6dx5A00 3.90.70.80 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.52 44.0 3.29e-01 98.4% 74.6%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4621073 5054.1.1.6 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › TrkH 0.83 76.0 5.90e-01 100.0% 73.6%
4298932 103.1.1.6 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › RuvA_C 0.82 56.0 5.65e-01 82.0% 71.7%
1174242 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 0.82 64.0 6.49e-01 83.6% 85.2%
3925710 148.1.3.10 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_6 0.81 55.0 4.53e-01 72.1% 41.0%
4972595 102.1.1.0 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.81 61.0 5.04e-01 82.0% 46.7%
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 0.80 61.0 5.40e-01 80.3% 60.0%
3637647 4126.1.1.1 ↗ a/b three-layered sandwiches › beta-carbonic anhydrase-like › beta-carbonic anhydrase › beta-carbonic anhydrase › Pro_CA 0.79 59.0 4.10e-01 90.2% 25.9%
4641949 103.1.1.6 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › RuvA_C 0.79 48.0 5.19e-01 85.2% 74.0%
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 0.78 55.0 5.30e-01 73.8% 64.3%
3728568 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 0.78 58.0 5.91e-01 83.6% 80.0%
4679946 3869.1.1.1 ↗ alpha arrays › Mitochondrial 54S ribosomal protein L2 › Mitochondrial 54S ribosomal protein L2 › Mitochondrial 54S ribosomal protein L2 › Ribosomal_L27_C 0.78 57.0 3.83e-01 77.0% 22.0%
4411911 198.2.1.3 ↗ alpha arrays › Saposin-like › Bacteriocin AS-48-related › Bacteriocin AS-48-related › SseC 0.77 65.0 4.93e-01 95.1% 40.7%
4635506 230.3.1.1 ↗ a+b two layers › T-fold › Elongation factor Ts (EF-Ts), dimerisation domain › Elongation factor Ts (EF-Ts), dimerisation domain › EF_TS 0.77 55.0 4.16e-01 80.3% 32.9%
3279199 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 0.76 48.0 4.59e-01 72.1% 55.7%
3685821 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 0.76 69.0 5.52e-01 100.0% 80.9%
5055210 4009.1.1.0 ↗ alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins 0.75 53.0 5.21e-01 72.1% 67.7%
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 0.75 54.0 5.11e-01 77.0% 65.3%
4932779 5054.1.1.0 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels 0.75 69.0 5.86e-01 100.0% 81.1%
3165905 5054.1.1.6 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › TrkH 0.75 68.0 5.64e-01 100.0% 79.0%
3821344 5076.1.1.1 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Mitochondrial ADP/ATP carrier › Mitochondrial ADP/ATP carrier › Mito_carr 0.75 59.0 3.68e-01 88.5% 16.5%
3952706 101.1.4.0 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like 0.75 63.0 5.92e-01 93.4% 77.3%
4935458 5054.1.1.6 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › TrkH 0.74 68.0 5.79e-01 100.0% 87.4%
3909952 129.1.1.0 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like 0.74 68.0 4.22e-01 100.0% 53.4%
4296658 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.74 55.0 4.72e-01 82.0% 50.0%
3972061 5054.1.1.6 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › TrkH 0.74 67.0 5.56e-01 100.0% 79.0%
3881712 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 0.74 67.0 5.11e-01 100.0% 68.1%
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 0.74 67.0 5.42e-01 100.0% 81.8%
3270733 108.1.1.73 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_5+EF-hand_7 0.73 57.0 5.08e-01 83.6% 61.2%
3587414 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 0.73 66.0 5.43e-01 100.0% 87.6%
3255785 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 0.72 65.0 5.32e-01 100.0% 80.9%
4991198 2.1.1.359 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › HupF_HypC 0.72 50.0 4.14e-01 73.8% 39.1%
5028225 3352.1.1.0 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain 0.72 62.0 3.78e-01 98.4% 24.4%
3286823 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 0.72 65.0 5.16e-01 100.0% 73.3%
3925650 5076.1.1.1 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Mitochondrial ADP/ATP carrier › Mitochondrial ADP/ATP carrier › Mito_carr 0.71 57.0 3.67e-01 88.5% 38.9%
3344802 6158.1.1.0 ↗ alpha bundles › Nucleoporin p58/p45 helical region › Nucleoporin p58/p45 helical region › Nucleoporin p58/p45 helical region 0.69 52.0 5.13e-01 82.0% 76.9%
3291667 191.1.1.0 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.67 52.0 3.94e-01 85.2% 35.3%
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 0.66 58.0 5.06e-01 100.0% 88.4%
3741234 605.2.1.3 ↗ alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Seryl_tRNA_N 0.66 47.0 3.75e-01 75.4% 43.5%
4110549 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.65 47.0 3.76e-01 75.4% 43.6%
3518978 4009.1.1.0 ↗ alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins 0.64 55.0 4.87e-01 98.4% 72.2%
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 0.63 47.0 3.97e-01 83.6% 86.4%
3178200 524.1.1.0 ↗ alpha arrays › Ypt/Rab-GAP domain of gyp1p-like › Ypt/Rab-GAP domain of gyp1p › Ypt/Rab-GAP domain of gyp1p 0.59 50.0 3.63e-01 100.0% 38.4%
3518975 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 0.58 51.0 4.55e-01 100.0% 81.1%
3939608 631.1.1.1 ↗ alpha arrays › Glycolipid transfer protein, GLTP › Glycolipid transfer protein, GLTP › Glycolipid transfer protein, GLTP › GLTP 0.55 45.0 3.21e-01 98.4% 67.3%
3500138 564.1.1.0 ↗ alpha arrays › N-terminal, cytoplasmic domain of anti-sigma factors › N-terminal, cytoplasmic domain of anti-sigma factors › N-terminal, cytoplasmic domain of anti-sigma factors 0.53 37.0 3.75e-01 90.2% 73.3%
3712974 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.53 40.0 3.66e-01 83.6% 67.1%
2429119 219.1.1.15 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › OTU 0.51 44.0 3.25e-01 98.4% 74.6%