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NC_029065.1__YP_009222763.1__VCM_00182__00165

Bact-Vir

NC_029065.1__YP_009222763.1__VCM_00182__00165

Identity

Accession:
NC_029065 ↗
Kingdom:
phage

Quality

82.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vandenendeviridae› Kremarvirus› Pseudomonas_phage_VCM

TaxID: 1729937

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 medium residues 4-65
PDB
Domain cluster: representative
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4m70I00 1.20.5.4130 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.80 56.0 4.63e-01 74.2% 85.2%
1iuqA01 1.10.1200.50 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Glycerol-3-phosphate acyltransferase, alpha helical bundle, N-terminal 0.79 60.0 5.60e-01 80.6% 68.4%
2l37A00 6.10.250.890 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.79 53.0 6.02e-01 77.4% 100.0%
3ez0C00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.75 54.0 3.73e-01 77.4% 25.5%
5u1xA01 1.10.287.940 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › atp-gated p2x4 ion channel 0.74 51.0 5.68e-01 72.6% 100.0%
2lqxA00 6.10.250.1700 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.73 46.0 5.27e-01 85.5% 97.6%
3godB02 1.20.120.920 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain 0.73 63.0 4.44e-01 100.0% 62.5%
7wboA01 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.73 49.0 3.54e-01 71.0% 27.8%
1oksA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.72 46.0 4.97e-01 71.0% 77.4%
2ffjA01 1.10.8.380 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Uncharacterised protein PF01937, DUF89, domain 1 0.71 46.0 4.85e-01 88.7% 75.0%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.70 52.0 4.00e-01 79.0% 84.3%
3h0dB02 1.10.1200.150 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Transcriptional repressor of class III stress genes, C-terminal domain 0.70 51.0 4.71e-01 79.0% 95.1%
3rm5B02 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.68 49.0 3.34e-01 75.8% 21.4%
3kkbA00 1.20.120.880 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Histidine kinase (KinB), sensor domain 0.68 48.0 3.86e-01 75.8% 88.9%
1o9gA02 1.10.287.540 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.68 44.0 5.16e-01 75.8% 95.3%
1m56C01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.67 48.0 4.65e-01 74.2% 91.3%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.67 48.0 4.51e-01 75.8% 62.2%
4r42A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.67 52.0 3.63e-01 82.3% 71.1%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 45.0 4.33e-01 74.2% 60.3%
7vevA01 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.66 47.0 3.10e-01 74.2% 85.5%
1nt2B02 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.66 47.0 4.66e-01 75.8% 71.6%
1wkbA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.65 49.0 3.92e-01 80.6% 49.6%
1d2mA03 6.10.140.240 Special › Helix non-globular › Helix Hairpins › 0.65 47.0 4.66e-01 82.3% 72.7%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 42.0 4.03e-01 71.0% 55.4%
1vf6C00 1.10.287.650 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › L27 domain 0.65 44.0 4.75e-01 72.6% 90.2%
3dkqA02 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.65 45.0 5.00e-01 72.6% 100.0%
1zhcA00 6.10.280.50 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 49.0 4.59e-01 82.3% 86.8%
3behB01 1.20.120.540 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels 0.64 48.0 3.97e-01 83.9% 90.6%
5jxxA02 1.20.1180.10 Mainly Alpha › Up-down Bundle › Udp N-acetylglucosamine O-acyltransferase; Domain 2 › Udp N-acetylglucosamine O-acyltransferase, C-terminal domain 0.62 41.0 4.05e-01 72.6% 63.6%
7tzoA01 1.10.1070.11 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › Phosphatidylinositol 3-/4-kinase, catalytic domain 0.61 42.0 3.07e-01 72.6% 25.9%
4z7xB00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.60 43.0 3.02e-01 79.0% 23.1%
3vkgA14 6.10.140.1060 Special › Helix non-globular › Helix Hairpins › 0.60 42.0 3.91e-01 74.2% 73.8%
3a8pA02 6.10.140.680 Special › Helix non-globular › Helix Hairpins › 0.59 49.0 4.00e-01 90.3% 83.3%
ECOD (32)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3576658 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.91 65.0 6.86e-01 75.8% 83.6%
4927311 5069.1.3.1 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › Sdh_cyt 0.85 64.0 5.15e-01 79.0% 45.5%
3697355 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.84 63.0 4.57e-01 79.0% 32.3%
3649999 109.4.1.927 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › ARM_LIN 0.83 65.0 4.37e-01 82.3% 34.1%
4933188 5069.1.3.1 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › Sdh_cyt 0.82 63.0 5.36e-01 80.6% 52.6%
4992050 5069.1.3.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits 0.82 61.0 4.86e-01 77.4% 41.7%
4956171 5069.1.3.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits 0.82 62.0 5.34e-01 80.6% 52.6%
3410128 5041.1.1.0 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C 0.78 55.0 5.46e-01 75.8% 70.8%
3839762 1008.1.1.0 ↗ alpha bundles › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain 0.77 57.0 5.08e-01 77.4% 56.5%
3586032 605.1.1.237 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › Patched 0.74 56.0 4.70e-01 82.3% 78.1%
4025205 601.19.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein 0.73 61.0 4.55e-01 91.9% 68.7%
3857011 4095.1.1.1 ↗ alpha bundles › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › DNA_ligase_A_N 0.72 56.0 4.39e-01 96.8% 40.0%
57654 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.72 48.0 5.12e-01 82.3% 79.6%
3491670 614.1.1.0 ↗ alpha duplicates or obligate multimers › L27 domain › L27 domain › L27 domain 0.71 51.0 5.33e-01 77.4% 89.1%
3692552 5071.3.1.0 ↗ alpha bundles › cytochrome bc1 complex 11 kDa protein-like › DUF465 › DUF465 0.71 53.0 5.24e-01 79.0% 84.6%
5044958 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.71 51.0 4.66e-01 75.8% 75.0%
3435812 3711.1.1.0 ↗ alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein 0.70 53.0 4.21e-01 80.6% 63.2%
3860451 108.1.1.68 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › TPGS1_C 0.70 51.0 4.93e-01 77.4% 84.3%
3430353 4163.1.2.1 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF2 C-terminal domain-like › Sld5 0.68 46.0 3.63e-01 71.0% 60.0%
5048061 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.67 50.0 5.27e-01 77.4% 98.2%
1159562 2498.1.1.99 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › PF29194 0.67 54.0 3.20e-01 88.7% 26.6%
3572303 601.1.2.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.67 51.0 4.07e-01 83.9% 48.5%
3234609 192.6.1.10 ↗ alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain › WHEP-TRS 0.66 45.0 4.92e-01 72.6% 86.0%
4048828 377.1.1.11 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › RecO_C 0.64 53.0 3.99e-01 91.9% 48.1%
4014352 109.1.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C 0.63 52.0 3.71e-01 91.9% 35.9%
2035563 614.1.1.1 ↗ alpha duplicates or obligate multimers › L27 domain › L27 domain › L27 domain › L27 0.61 45.0 4.56e-01 80.6% 88.1%
3197359 109.4.1.191 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_7 0.61 52.0 3.18e-01 96.8% 20.5%
4000385 5054.1.1.59 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans, Ion_trans_2 0.61 47.0 3.11e-01 83.9% 70.7%
3611066 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.61 44.0 4.29e-01 79.0% 84.3%
3613445 7563.1.1.2 ↗ a/b three-layered sandwiches › MCP/YpsA-related › MCP/YpsA-related › MCP/YpsA-related › Lysine_decarbox 0.60 51.0 3.40e-01 98.4% 57.8%
3399433 3826.1.1.39 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › WHEP-TRS 0.55 48.0 4.66e-01 98.4% 100.0%
4290511 7572.1.1.1 ↗ a/b three-layered sandwiches › Phosphofructokinase C-terminal domain › Phosphofructokinase C-terminal domain › Phosphofructokinase C-terminal domain › PFK 0.54 45.0 3.48e-01 98.4% 78.1%