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NC_011398.1__YP_002290879.1__phiCD27_gp03__00003

Bact-Vir

NC_011398.1__YP_002290879.1__phiCD27_gp03__00003

Identity

Accession:
NC_011398 ↗
Kingdom:
phage

Quality

82.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Colneyvirus› Clostridioides_phage_phiCD27

TaxID: 2849704

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 32-109
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3l9fA02 6.10.140.1570 Special › Helix non-globular › Helix Hairpins › 0.56 44.0 4.40e-01 85.9% 85.2%
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 0.56 38.0 3.70e-01 85.9% 61.5%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3977737 3831.1.1.1 ↗ alpha bundles › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › LprI 0.56 44.0 3.92e-01 91.0% 58.3%
4973230 1079.1.1.0 ↗ alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA 0.53 39.0 2.88e-01 79.5% 69.1%
3714843 592.6.1.0 ↗ alpha arrays › PWI domain-like › Pre-mRNA-splicing helicase BRR2 plug domain › Pre-mRNA-splicing helicase BRR2 plug domain 0.52 33.0 3.08e-01 80.8% 49.0%
3686051 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.52 29.0 3.10e-01 78.2% 58.6%
3289474 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.52 37.0 3.52e-01 87.2% 61.1%
3859306 109.4.1.898 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_leprecan 0.52 38.0 3.13e-01 84.6% 48.6%
142262 191.1.1.17 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_C_13 0.51 39.0 3.49e-01 98.7% 56.6%
3742281 1009.1.1.1 ↗ alpha duplicates or obligate multimers › Taz1 dimerization domain › Taz1 dimerization domain › Taz1 dimerization domain › PF31211 0.51 38.0 3.62e-01 94.9% 68.9%
D2 medium residues 110-227
PDB
Domain cluster: rep: MW512570.1__QVW56605.1__X__00003__D116-221
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1af6A00 2.40.170.10 Mainly Beta › Beta Barrel › Maltoporin; Chain A › Porin, LamB type 0.57 45.0 3.11e-01 84.7% 83.8%
2jmuA01 2.40.320.10 Mainly Beta › Beta Barrel › Hypothetical Protein Pfu-838710-001 › Hypothetical Protein Pfu-838710-001 0.56 41.0 3.38e-01 75.4% 81.7%
2imjD01 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.56 38.0 3.61e-01 70.3% 78.2%
2ebkA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.56 41.0 4.07e-01 81.4% 71.9%
2qkdA01 2.20.25.420 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › ZPR1, zinc finger domain 0.53 23.0 3.42e-01 83.9% 95.8%
3r1kA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.53 39.0 3.83e-01 78.8% 85.0%
2wjsA01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.53 40.0 3.47e-01 78.0% 91.4%
5n1tA03 3.90.760.10 Alpha Beta › Alpha-Beta Complex › Flavocytochrome C Sulfide Dehydrogenase; Chain A Domain 3 › Flavocytochrome c sulphide dehydrogenase, flavin-binding domain 0.53 29.0 3.53e-01 75.4% 85.9%
3ebtA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 37.0 3.63e-01 72.9% 95.4%
4jhyA00 3.30.530.80 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › 0.53 42.0 3.83e-01 84.7% 78.2%
1iicA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.52 38.0 3.36e-01 75.4% 69.9%
3hpeA00 2.40.128.110 Mainly Beta › Beta Barrel › Lipocalin › Lipid/polyisoprenoid-binding, YceI-like 0.52 45.0 4.12e-01 98.3% 95.1%
2a15A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 36.0 3.48e-01 71.2% 97.0%
4r1kB00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 38.0 3.63e-01 78.0% 98.5%
4e6fA00 3.30.530.80 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › 0.50 39.0 3.41e-01 80.5% 76.0%
4iedA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.50 34.0 2.74e-01 70.3% 62.8%
2jd4A02 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.50 38.0 3.32e-01 78.8% 88.1%
1pz7A00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.50 38.0 3.26e-01 78.8% 87.8%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3559952 71.2.1.4 ↗ beta meanders › Lipoprotein localization factors LolAB › PA1994-like › PA1994-like › CATIP_N 0.55 40.0 3.20e-01 76.3% 68.3%
3254046 243.1.1.9 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › DUF1348 0.55 37.0 3.44e-01 70.3% 72.1%
3400954 5.1.4.8 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › CNH 0.55 40.0 2.93e-01 76.3% 78.1%
5044200 289.1.1.0 ↗ a+b complex topology › Peptide deformylase › Peptide deformylase › Peptide deformylase 0.54 39.0 3.48e-01 74.6% 73.9%
4629131 9.29.1.1 ↗ beta barrels › Lipocalins/Streptavidin › VirK › VirK › VirK 0.53 43.0 4.28e-01 91.5% 83.7%
3658408 4325.1.1.13 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF4371 0.53 26.0 3.08e-01 75.4% 66.7%
3217155 243.1.1.97 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › DUF5382_N 0.53 38.0 3.47e-01 72.9% 85.3%
3744079 243.1.1.18 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › SnoaL_2 0.53 39.0 3.84e-01 76.3% 99.2%
3362578 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.52 39.0 3.43e-01 78.8% 71.7%
3830390 5.1.3.65 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › DUF295 0.52 40.0 2.96e-01 81.4% 98.1%
4014154 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.52 36.0 3.33e-01 70.3% 75.2%
3283292 243.1.1.18 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › SnoaL_2 0.52 37.0 3.65e-01 75.4% 98.5%
3275455 4210.1.1.0 ↗ a+b two layers › WGR domain › WGR domain › WGR domain 0.51 36.0 3.64e-01 74.6% 71.7%
4995758 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.50 32.0 3.67e-01 96.6% 89.4%
3010621 9.13.1.5 ↗ beta barrels › Lipocalins/Streptavidin › AOC barrel-like › AOC barrel-like › AOC_like 0.50 38.0 3.58e-01 80.5% 84.5%
3649104 844.1.1.5 ↗ beta barrels › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › DUF3527 0.50 39.0 3.05e-01 82.2% 40.4%
D3 medium residues 250-313
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3e56A00 6.20.180.10 Special › Other non-globular › Ubiquitin-like (UB roll) › 0.51 38.0 3.70e-01 100.0% 73.3%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3164784 4038.1.1.8 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Abc1-like 0.51 41.0 2.77e-01 100.0% 20.7%
3944936 4038.1.1.8 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Abc1-like 0.50 42.0 2.80e-01 100.0% 21.0%
3367888 101.15.1.5 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM3_LYK4_5 0.50 35.0 3.48e-01 76.6% 72.9%
D4 medium residues 407-497
PDB
Domain cluster: representative
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2kp8A00 1.20.5.170 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.72 44.0 4.99e-01 84.6% 79.2%
2gx5C00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.62 42.0 3.51e-01 70.3% 77.0%
7ae2A01 1.20.120.580 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › bsu32300-like 0.56 33.0 2.82e-01 71.4% 38.7%
4hteA02 1.20.58.1740 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 38.0 3.49e-01 80.2% 53.8%
8a1gC01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.56 44.0 3.49e-01 83.5% 95.0%
4g3vA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.54 39.0 3.24e-01 74.7% 51.2%
2a1fC00 3.40.1160.10 Alpha Beta › 3-Layer(aba) Sandwich › Carbamate kinase › Acetylglutamate kinase-like 0.51 38.0 2.93e-01 83.5% 88.6%
3thxB04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.50 39.0 3.51e-01 87.9% 59.4%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3294636 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.77 45.0 4.09e-01 73.6% 46.1%
4886353 4958.1.1.2 ↗ a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_4 0.55 47.0 3.96e-01 95.6% 73.8%
4521765 604.29.1.1 ↗ alpha bundles › Spectrin repeat-like › Trehalose-6-phosphate phosphatase N-terminal helical bundle › Trehalose-6-phosphate phosphatase N-terminal helical bundle › T6PP_N 0.54 38.0 3.39e-01 71.4% 96.8%
3990912 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.54 47.0 3.29e-01 100.0% 52.9%
4360452 4958.1.1.1 ↗ a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5,RNA_pol_Rpb1_4 0.53 45.0 3.67e-01 94.5% 76.0%