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NC_048664.1__YP_009833472.1__HWB19_gp093__00093

Bact-Vir

NC_048664.1__YP_009833472.1__HWB19_gp093__00093

Identity

Accession:
NC_048664 ↗
Kingdom:
phage

Quality

43.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Grimontviridae› Privateervirus› Cronobacter_phage_vB_CsaP_009

TaxID: 2699738

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 432-567
PDB
D2 high residues 1358-1499
PDB
D3 medium residues 1035-1111
PDB
D4 medium residues 1112-1174
PDB
D5 medium residues 1175-1242
PDB
Domain cluster: representative
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3bgeA01 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.65 53.0 4.74e-01 91.2% 63.5%
2y1eA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.64 49.0 4.57e-01 85.3% 80.5%
2q9rA01 1.20.1590.10 Mainly Alpha › Up-down Bundle › YP_001051499.1 fold like › YP_001051499.1 domain like 0.63 50.0 3.68e-01 89.7% 93.8%
3a06B03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.62 49.0 4.54e-01 88.2% 80.7%
5jazA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.62 49.0 4.51e-01 88.2% 81.3%
3iieB03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.61 46.0 4.39e-01 85.3% 76.5%
3p42A02 6.10.250.2280 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.59 40.0 4.02e-01 91.2% 68.6%
7oq4Z01 1.20.120.950 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Uncharacterised protein DUF5062 0.58 47.0 4.16e-01 88.2% 71.4%
1m4rB00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.58 45.0 3.61e-01 85.3% 57.4%
1lm3B00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.58 46.0 4.04e-01 89.7% 73.6%
2fu2A00 1.20.1440.50 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like 0.58 45.0 4.35e-01 91.2% 78.2%
4m70I00 1.20.5.4130 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.57 48.0 4.24e-01 100.0% 79.6%
1aepA00 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.56 46.0 3.67e-01 95.6% 52.9%
1a41A02 1.20.120.380 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Type 1-topoisomerase catalytic fragment, domain 2 0.56 42.0 3.88e-01 83.8% 68.1%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.56 46.0 4.05e-01 95.6% 72.7%
1a7eA00 1.20.120.50 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hemerythrin-like 0.56 43.0 3.73e-01 89.7% 95.8%
4q8gA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.55 48.0 3.11e-01 100.0% 35.8%
2ajrA01 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.55 46.0 3.14e-01 95.6% 83.0%
3a98A02 1.20.1270.350 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Dedicator of cytokinesis N-terminal subdomain 0.55 41.0 3.93e-01 85.3% 86.2%
2wl8C00 1.20.120.900 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Pex19, mPTS binding domain 0.55 37.0 3.26e-01 70.6% 60.6%
4od4A02 1.20.120.1780 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › UbiA prenyltransferase 0.55 46.0 3.92e-01 97.1% 68.1%
1tedA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.54 45.0 3.56e-01 94.1% 90.6%
3zssA02 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.54 42.0 4.06e-01 89.7% 77.2%
1sr2A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.54 42.0 3.69e-01 92.6% 54.3%
4mtdD01 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 0.53 41.0 3.80e-01 85.3% 83.0%
2vl7A02 1.10.275.30 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › 0.53 42.0 3.62e-01 88.2% 60.0%
4boqA00 3.90.70.80 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.51 45.0 3.35e-01 100.0% 45.1%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3607124 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.73 59.0 5.27e-01 88.2% 69.5%
3464709 632.15.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) › GAUT_1 0.65 51.0 4.55e-01 88.2% 82.0%
3211172 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.65 55.0 3.67e-01 97.1% 90.7%
4144086 166.1.1.1 ↗ alpha superhelices › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › DXPR_C 0.64 48.0 4.32e-01 83.8% 68.0%
4201591 166.1.1.1 ↗ alpha superhelices › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › DXPR_C 0.62 48.0 4.33e-01 88.2% 68.0%
5013248 601.3.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain › Hpt 0.62 51.0 4.24e-01 94.1% 59.2%
5057835 610.3.1.1 ↗ alpha arrays › ERP29 C domain-like › GatB/GatE C-terminal domain › GatB/GatE C-terminal domain › GatB_Yqey 0.61 46.0 3.50e-01 83.8% 32.9%
3978907 601.3.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain 0.60 49.0 4.47e-01 92.6% 67.8%
3962361 138.1.1.0 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain 0.60 50.0 3.75e-01 97.1% 91.4%
5041402 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.60 35.0 3.65e-01 72.1% 61.5%
5040017 601.3.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain › Hpt 0.60 48.0 4.21e-01 92.6% 58.2%
3603451 601.7.2.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › HEPN domain in CRISPR-associated protein Csx1 0.59 46.0 4.03e-01 91.2% 87.0%
3971690 601.3.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain 0.59 47.0 3.99e-01 92.6% 57.6%
4025168 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.57 44.0 4.20e-01 91.2% 84.7%
4955523 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.57 46.0 3.86e-01 88.2% 75.7%
4164998 166.1.1.1 ↗ alpha superhelices › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › DXPR_C 0.56 46.0 4.13e-01 100.0% 64.0%
3275451 633.12.1.0 ↗ alpha bundles › Bromodomain-like › Ta0600-like › Ta0600-like 0.56 45.0 3.97e-01 89.7% 63.8%
54604 601.14.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Hemerythrin › Hemerythrin 0.56 43.0 3.74e-01 89.7% 95.8%
4478129 166.1.1.1 ↗ alpha superhelices › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › DXPR_C 0.56 46.0 4.29e-01 100.0% 74.4%
5075040 601.14.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Hemerythrin › Hemerythrin 0.55 45.0 3.84e-01 89.7% 63.6%
4264118 601.14.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Hemerythrin › Hemerythrin › Hemerythrin 0.55 45.0 3.99e-01 97.1% 68.2%
5071060 632.15.1.4 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) › HSP70 0.55 44.0 4.09e-01 95.6% 78.9%
5016324 601.3.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain 0.55 43.0 3.98e-01 91.2% 80.0%
4360723 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.54 43.0 4.07e-01 94.1% 83.3%
4973140 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.54 41.0 4.07e-01 88.2% 86.7%
3980912 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.53 44.0 3.82e-01 97.1% 70.4%
5009867 601.7.1.2 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN 0.53 41.0 3.66e-01 92.6% 88.2%
D6 medium residues 1243-1300
PDB
Domain cluster: representative
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ykhA00 6.10.140.200 Special › Helix non-globular › Helix Hairpins › 0.92 64.0 5.30e-01 72.4% 44.2%
1wpaA01 6.10.140.340 Special › Helix non-globular › Helix Hairpins › 0.85 60.0 4.95e-01 74.1% 43.4%
2p18A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.84 55.0 3.41e-01 70.7% 13.8%
6xj1A01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.79 56.0 3.64e-01 75.9% 18.8%
6t0bc01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.79 59.0 5.35e-01 81.0% 69.2%
2y4tA02 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.78 52.0 5.46e-01 75.9% 76.9%
1zpyA00 6.10.140.1960 Special › Helix non-globular › Helix Hairpins › 0.77 54.0 4.67e-01 79.3% 47.3%
3ripA02 1.20.120.1900 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Gamma-tubulin complex, C-terminal domain 0.77 60.0 3.81e-01 84.5% 52.0%
3ehfD01 1.20.5.1930 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.75 54.0 5.29e-01 79.3% 71.4%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.73 60.0 5.46e-01 91.4% 67.5%
1xzzA00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.73 50.0 3.36e-01 70.7% 19.0%
3fppA03 6.10.140.1990 Special › Helix non-globular › Helix Hairpins › 0.72 62.0 5.49e-01 100.0% 71.6%
3ehfB01 6.10.250.2870 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.72 59.0 4.89e-01 91.4% 67.3%
2b5dX01 3.20.110.10 Alpha Beta › Alpha-Beta Barrel › 7-stranded beta/alpha barrel › Glycoside hydrolase 38, N terminal domain 0.69 59.0 3.55e-01 94.8% 24.0%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.68 57.0 4.98e-01 100.0% 62.2%
8fbnB01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.66 49.0 3.29e-01 100.0% 20.7%
3nyjA00 1.20.120.770 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Amyloid precursor protein, E2 domain 0.62 51.0 3.74e-01 100.0% 32.6%
1lvfB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 46.0 3.98e-01 93.1% 52.9%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3219759 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.80 69.0 5.28e-01 98.3% 42.2%
3323862 611.9.1.4 ↗ alpha bundles › N-cbl like › Resistance protein (Rx) N-terminal domain › Resistance protein (Rx) N-terminal domain › Rx_N 0.80 63.0 5.59e-01 84.5% 61.3%
4094257 150.3.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › Hormone_1 0.79 59.0 4.55e-01 81.0% 38.5%
3535346 2004.1.1.184 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11 0.78 58.0 3.37e-01 79.3% 10.1%
4563128 4992.1.1.29 ↗ extended segments › RelB-like › RelB-like › RelB-like › DUF5373 0.76 63.0 4.62e-01 87.9% 84.3%
4034092 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.75 56.0 5.13e-01 79.3% 84.0%
3797789 5001.1.1.63 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srab 0.75 64.0 4.14e-01 100.0% 21.1%
4043561 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.75 61.0 4.89e-01 91.4% 46.4%
4596031 109.4.1.3089 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MSP1_C 0.74 64.0 4.00e-01 100.0% 21.5%
3623065 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.72 51.0 3.16e-01 74.1% 23.2%
3500901 4177.1.1.2 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.71 61.0 4.30e-01 100.0% 31.1%
8997 2002.3.1.3 ↗ a/b barrels › TIM beta/alpha-barrel › Glycoside hydrolase/deacetylase › Glycoside hydrolase/deacetylase › Glyco_hydro_57 0.69 59.0 3.55e-01 94.8% 24.0%
3766182 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.69 59.0 4.51e-01 100.0% 44.8%
3580368 4163.1.1.1 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like › Sld5 0.69 61.0 4.53e-01 98.3% 46.9%
3503725 4177.1.1.2 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.68 58.0 4.09e-01 100.0% 29.5%
3937465 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.68 62.0 4.12e-01 100.0% 50.2%
4028874 4177.1.1.1 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › FCH 0.68 57.0 3.64e-01 100.0% 18.7%
4464045 4177.1.1.66 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › ATG17_like 0.66 60.0 3.89e-01 100.0% 81.2%
4649114 3559.1.1.1 ↗ a+b complex topology › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 › Med22 0.66 54.0 4.62e-01 100.0% 55.0%
3634960 603.1.1.5 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › Syntaxin-6_N 0.65 55.0 4.56e-01 100.0% 52.7%
3578025 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 0.63 55.0 4.38e-01 100.0% 61.7%
D7 medium residues 1301-1355
PDB