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NC_007917.1__YP_529615.1__CDBPCV119_gp64__00064

Bact-Vir

NC_007917.1__YP_529615.1__CDBPCV119_gp64__00064

Identity

Accession:
NC_007917 ↗
Kingdom:
phage

Quality

92.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Lubbockvirus› Clostridium_phage_phi_CD119

TaxID: 2883936

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 3-157
PDB
Domain cluster: rep: STL6-S73_scaffold_1_prodigal-single.1__X__X__00079__D1-144
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01507.26 best PAPS_reduct 31.8 2.00e-07 96.1% 57.1%
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1surA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.79 74.0 6.53e-01 100.0% 71.2%
7lhsB01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.78 72.0 6.56e-01 100.0% 75.9%
2goyA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.78 74.0 6.43e-01 100.0% 71.6%
4bwvA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.77 73.0 6.28e-01 100.0% 68.7%
2vxoA02 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.74 70.0 6.12e-01 100.0% 82.4%
1xngA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.72 64.0 5.43e-01 100.0% 59.9%
1zunA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.70 67.0 6.15e-01 100.0% 83.9%
7va8A01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.63 56.0 4.62e-01 94.2% 87.4%
4xfjB01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.61 55.0 5.37e-01 100.0% 93.1%
7zllA01 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.59 53.0 4.35e-01 97.4% 94.2%
3cgbA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.59 33.0 3.42e-01 75.5% 57.7%
3f4lA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 33.0 3.62e-01 84.5% 72.7%
4ru1A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.54 44.0 4.56e-01 87.7% 93.9%
3ia7A01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.54 47.0 4.08e-01 94.2% 88.0%
3gybA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.54 42.0 4.45e-01 89.7% 93.5%
3o9zA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.53 40.0 4.31e-01 87.1% 92.3%
4n03A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.53 48.0 4.65e-01 100.0% 98.9%
5l3sB02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 46.0 4.15e-01 94.2% 80.5%
2h3hB02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.53 44.0 4.40e-01 89.0% 93.0%
2wjwA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.52 45.0 4.52e-01 94.8% 97.5%
3klbA00 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.52 43.0 4.31e-01 89.0% 94.4%
3c3kA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.52 41.0 4.38e-01 85.2% 97.1%
1gudA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.52 38.0 4.03e-01 82.6% 84.9%
2iw1A01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.51 43.0 4.11e-01 91.6% 88.6%
4q3kB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 41.0 3.62e-01 88.4% 76.0%
3do6A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 44.0 3.53e-01 95.5% 72.9%
5fbhA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.50 43.0 4.12e-01 95.5% 89.8%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5083839 2005.1.1.14 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › PAPS_reduct 0.88 84.0 7.11e-01 100.0% 71.5%
3603161 2005.1.1.14 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › PAPS_reduct 0.83 79.0 6.44e-01 100.0% 58.1%
5051749 2005.1.1.14 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › PAPS_reduct 0.83 78.0 6.58e-01 100.0% 64.3%
5062204 2005.1.1.14 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › PAPS_reduct 0.82 73.0 6.41e-01 100.0% 67.0%
4163031 2005.1.1.14 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › PAPS_reduct 0.81 75.0 6.51e-01 100.0% 66.7%
4938182 2005.1.1.14 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › PAPS_reduct 0.80 76.0 5.97e-01 100.0% 69.3%
5038820 2005.1.1.14 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › PAPS_reduct 0.80 76.0 6.74e-01 99.4% 74.3%
5003321 2005.1.1.14 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › PAPS_reduct 0.80 76.0 6.05e-01 100.0% 55.8%
5082742 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.80 75.0 6.10e-01 100.0% 57.0%
5009871 2005.1.1.14 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › PAPS_reduct 0.80 67.0 6.03e-01 87.7% 76.1%
4005131 2005.1.1.14 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › PAPS_reduct 0.80 74.0 6.30e-01 100.0% 63.7%
3339632 2005.1.1.14 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › PAPS_reduct 0.78 74.0 6.19e-01 100.0% 64.8%
4052133 2005.1.1.14 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › PAPS_reduct 0.78 74.0 6.22e-01 100.0% 64.6%
1122392 2005.1.1.14 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › PAPS_reduct 0.77 73.0 6.28e-01 100.0% 68.7%
4971349 2005.1.1.27 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › QueC 0.75 70.0 5.72e-01 100.0% 64.8%
5049776 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.73 68.0 5.51e-01 100.0% 68.1%
None — 0.73 68.0 6.39e-01 100.0% 84.9%
5053982 2005.1.1.11 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ATP_bind_3 0.72 68.0 5.52e-01 100.0% 62.6%
3604378 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.72 68.0 5.56e-01 100.0% 60.8%
5024566 2005.1.1.11 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ATP_bind_3 0.72 67.0 6.30e-01 100.0% 84.9%
5069002 2005.1.1.11 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ATP_bind_3 0.72 67.0 5.50e-01 100.0% 60.7%
4982815 2005.1.1.11 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ATP_bind_3 0.72 67.0 5.23e-01 100.0% 56.5%
5015866 2005.1.1.14 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › PAPS_reduct 0.71 66.0 5.80e-01 100.0% 76.0%
3602090 2005.1.1.27 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › QueC 0.71 65.0 5.74e-01 100.0% 75.6%
3604580 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.70 60.0 6.01e-01 100.0% 90.0%
4099367 2005.1.1.11 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ATP_bind_3 0.68 62.0 5.55e-01 100.0% 70.7%
5073535 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.66 61.0 5.43e-01 100.0% 83.6%
5016836 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.61 57.0 5.17e-01 100.0% 84.9%
4486103 3008.1.1.0 ↗ a+b three layers › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 0.60 28.0 3.64e-01 71.0% 77.6%
3708155 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.54 27.0 3.42e-01 70.3% 82.4%
4945956 2004.1.1.43 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SRP54 0.53 46.0 4.18e-01 94.8% 81.0%
3743690 2006.1.4.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.53 39.0 3.74e-01 89.0% 66.9%
5049125 7550.1.1.0 ↗ a/b three-layered sandwiches › Tetrapyrrole methylase N-terminal domain › Tetrapyrrole methylase N-terminal domain › Tetrapyrrole methylase N-terminal domain 0.52 43.0 4.27e-01 89.0% 93.8%
4242923 7510.1.1.3 ↗ a/b three-layered sandwiches › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › FA_synthesis 0.51 40.0 3.97e-01 81.9% 85.0%
3284036 7577.1.1.3 ↗ a/b three-layered sandwiches › PLP-dependent transferases › PLP-dependent transferases › PLP-dependent transferases › Aminotran_5 0.51 44.0 3.37e-01 91.6% 53.9%
3288229 2007.1.2.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.50 42.0 4.29e-01 91.0% 100.0%
D2 high residues 171-232
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6fakA02 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.67 43.0 3.94e-01 91.9% 50.6%
4okvE00 6.10.140.1890 Special › Helix non-globular › Helix Hairpins › 0.65 50.0 4.99e-01 82.3% 80.0%
3k62A00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.65 51.0 3.15e-01 88.7% 21.3%
3o7iA00 1.10.3330.10 Mainly Alpha › Orthogonal Bundle › UraD-like › Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase 0.64 45.0 3.39e-01 80.6% 30.7%
1grjA01 1.10.287.180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Transcription elongation factor, GreA/GreB, N-terminal domain 0.63 51.0 4.86e-01 90.3% 74.3%
4m70B00 1.10.246.200 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › WPP domain 0.61 42.0 3.69e-01 74.2% 49.5%
3o39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.60 48.0 4.17e-01 93.5% 56.2%
2cufA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.59 50.0 4.78e-01 95.2% 87.5%
1np7A02 1.25.40.80 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.59 45.0 3.68e-01 83.9% 45.4%
2qm0A01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.59 48.0 3.20e-01 90.3% 44.8%
2hpgC00 3.40.190.170 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Bacterial extracellular solute-binding protein, family 7 0.54 46.0 2.99e-01 100.0% 82.1%
3cobC00 3.40.850.10 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain 0.53 44.0 2.80e-01 95.2% 17.6%
5lnkJ01 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.53 40.0 3.00e-01 85.5% 37.9%
4kh7B02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.52 43.0 3.53e-01 91.9% 48.3%
4bvxA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.50 34.0 3.04e-01 74.2% 45.7%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3739014 101.1.1.67 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Myb_DNA-bind_6 0.68 45.0 4.07e-01 83.9% 47.8%
4638004 192.29.1.1 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB_dom 0.68 58.0 5.60e-01 93.5% 88.6%
4000262 192.5.1.1 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1 0.66 56.0 4.90e-01 93.5% 63.3%
3790121 603.1.1.114 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › HR1 0.65 55.0 4.63e-01 93.5% 57.0%
3945039 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.63 43.0 2.76e-01 72.6% 48.5%
3676043 5076.2.1.10 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › PF29520 0.63 55.0 3.52e-01 98.4% 21.1%
3410408 3712.1.1.0 ↗ a+b complex topology › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 0.62 46.0 4.14e-01 85.5% 58.3%
5014330 148.1.3.402 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › Rad50_zn_hook 0.61 52.0 4.35e-01 95.2% 74.5%
3426106 101.1.1.3 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Myb_DNA-binding 0.61 41.0 3.77e-01 87.1% 53.8%
4501780 310.2.1.5 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › DUF842 0.60 46.0 3.76e-01 88.7% 42.4%
5002351 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.59 45.0 2.78e-01 83.9% 34.1%
3918122 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.58 43.0 2.66e-01 82.3% 66.6%
3439386 2004.1.1.26 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin 0.57 43.0 2.74e-01 83.9% 17.8%
4030648 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.54 42.0 3.40e-01 87.1% 69.5%
3923254 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 0.53 39.0 2.93e-01 82.3% 84.4%
4176207 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.51 42.0 3.21e-01 93.5% 37.3%
3895109 2004.1.1.130 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › NACHT 0.51 40.0 2.78e-01 87.1% 50.7%