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NC_019519.1__YP_007006548.1__F406_gp025__00092

Bact-Vir

NC_019519.1__YP_007006548.1__F406_gp025__00092

Identity

Accession:
NC_019519 ↗
Kingdom:
phage

Quality

85.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Schmittlotzvirus› Agrobacterium_phage_7-7-1

TaxID: 1161931

Cluster

View cluster (7 members)

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 medium residues 2-67
PDB
Domain cluster: rep: OM621816.1__UNA00758.1__ZHS_2__00002__D2-79
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2fm8B00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.56 44.0 3.70e-01 90.9% 82.4%
1to6A02 3.90.1510.10 Alpha Beta › Alpha-Beta Complex › Glycerate kinase, domain 2 › Glycerate kinase, domain 2 0.54 38.0 2.73e-01 77.3% 90.4%
3evzA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.54 41.0 3.17e-01 86.4% 99.4%
3dtdD00 2.60.40.1880 Mainly Beta › Sandwich › Immunoglobulin-like › Invasion associated locus B (IalB) protein 0.53 43.0 3.43e-01 90.9% 51.0%
3l9fA01 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 0.51 27.0 2.47e-01 71.2% 33.7%
1kfqA01 3.40.120.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 › Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 0.51 40.0 3.00e-01 93.9% 63.8%
3o27B00 2.10.260.10 Mainly Beta › Ribbon › Pemi-like Protein 1; Chain: D › 0.50 34.0 3.60e-01 95.5% 82.5%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4947865 1.1.3.0 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB 0.54 38.0 4.12e-01 98.5% 98.0%
4542856 2003.1.5.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › DNA_methylase 0.53 43.0 2.77e-01 97.0% 96.3%
3205634 630.1.1.0 ↗ a+b complex topology › RuBisCo LSMT C-terminal, substrate-binding domain › RuBisCo LSMT C-terminal, substrate-binding domain › RuBisCo LSMT C-terminal, substrate-binding domain 0.53 38.0 2.88e-01 78.8% 88.1%
4666593 241.1.1.2 ↗ a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone › Autophagy_act_C 0.52 38.0 2.95e-01 78.8% 43.4%
5069260 1.1.3.0 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB 0.52 36.0 3.86e-01 98.5% 96.0%
5031154 1.1.3.0 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB 0.51 35.0 3.69e-01 100.0% 80.0%
5062781 1.1.3.0 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB 0.51 34.0 3.73e-01 95.5% 100.0%
4944882 1.1.3.2 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB › MazE_antitoxin 0.51 36.0 3.91e-01 100.0% 100.0%
4993826 1.1.3.0 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB 0.51 34.0 3.67e-01 74.2% 95.8%
3946755 605.1.1.26 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › DUF2058 0.51 35.0 2.99e-01 100.0% 42.6%
4967714 1.1.3.2 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB › MazE_antitoxin 0.50 33.0 3.46e-01 100.0% 76.7%
4994587 1.1.3.0 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB 0.50 33.0 3.22e-01 100.0% 57.5%
D2 medium residues 80-110
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2qqpD00 6.10.140.650 Special › Helix non-globular › Helix Hairpins › 0.80 63.0 6.04e-01 100.0% 85.0%
1mjtB01 3.90.340.10 Alpha Beta › Alpha-Beta Complex › Nitric Oxide Synthase; Chain A, domain 1 › Nitric Oxide Synthase; Chain A, domain 1 0.79 59.0 3.85e-01 100.0% 19.4%
1ynbA00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.78 63.0 4.04e-01 100.0% 32.3%
1n69B00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.78 58.0 4.22e-01 83.9% 31.2%
2f4lA03 3.10.28.20 Alpha Beta › Roll › Endonuclease I-creI › Acetamidase/Formamidase-like domains 0.78 67.0 4.97e-01 100.0% 41.2%
5cbgA00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.77 62.0 4.45e-01 100.0% 30.4%
3ousA00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.76 62.0 4.70e-01 100.0% 37.8%
3fbzA01 1.20.58.800 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 65.0 4.60e-01 100.0% 90.2%
2bpoA04 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.75 64.0 4.04e-01 100.0% 19.8%
3lcvB01 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.74 57.0 4.95e-01 96.8% 56.1%
1ufhA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.73 59.0 3.84e-01 100.0% 20.6%
4d3pA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.69 53.0 3.60e-01 100.0% 44.2%
1m4rB00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.69 55.0 3.66e-01 96.8% 85.8%
1rykA00 1.10.1470.10 Mainly Alpha › Orthogonal Bundle › Protein Yjbj; Chain: A; › YjbJ 0.69 53.0 4.24e-01 93.5% 43.5%
3d8lA00 1.10.8.940 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Uncharacterised protein, phage p2 ORF12 0.67 58.0 4.15e-01 100.0% 48.4%
1lzwA00 3.30.1390.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L30; Chain: A, › Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS 0.67 50.0 3.77e-01 100.0% 31.9%
6fjxA01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.66 53.0 3.12e-01 93.5% 66.4%
3um7A03 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 46.0 3.55e-01 100.0% 32.0%
3l4aA00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.63 54.0 3.66e-01 96.8% 57.0%
1ctfA00 3.30.1390.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L30; Chain: A, › Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS 0.62 47.0 3.94e-01 96.8% 42.6%
3bs3A00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.52 39.0 3.29e-01 87.1% 51.7%
2vqaC01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.52 36.0 2.35e-01 87.1% 13.0%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4464956 4337.1.1.0 ↗ a+b two layers › DNA mismatch repair protein MutL dimerization subdomain › DNA mismatch repair protein MutL dimerization subdomain › DNA mismatch repair protein MutL dimerization subdomain 0.89 75.0 5.23e-01 100.0% 31.3%
3825234 2004.1.1.153 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_2 0.87 71.0 4.29e-01 100.0% 14.9%
3394326 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.85 73.0 4.13e-01 100.0% 9.8%
3665480 109.4.1.1559 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Tic110 0.81 67.0 3.88e-01 100.0% 11.1%
3589629 307.1.1.3 ↗ a+b two layers › Hedgehog/DD-peptidase › Hedgehog/DD-peptidase › Hedgehog/DD-peptidase › VanY 0.80 67.0 4.08e-01 100.0% 16.6%
4941372 5054.1.1.0 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels 0.78 64.0 4.79e-01 100.0% 37.6%
4984680 3962.1.1.1 ↗ alpha arrays › N-terminal helical domain in restriction-modification system methylation subunit-like › N-terminal helical domain in restriction-modification system methylation subunit › N-terminal helical domain in restriction-modification system methylation subunit › HsdM_N 0.77 63.0 3.98e-01 100.0% 18.2%
4978574 230.1.1.5 ↗ a+b two layers › T-fold › Tetrahydrobiopterin biosynthesis enzymes-like › Tetrahydrobiopterin biosynthesis enzymes-like › GCHY-1 0.76 60.0 3.89e-01 100.0% 19.4%
4038683 103.1.1.5 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › FmrO 0.75 59.0 5.00e-01 96.8% 53.3%
1634610 2498.5.1.0 ↗ mixed a+b and a/b › Zincin-like › GroEL-intermediate domain like › GroEL-intermediate domain like 0.75 56.0 4.80e-01 87.1% 48.2%
3923696 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.75 63.0 4.60e-01 100.0% 35.6%
3552352 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.74 62.0 4.64e-01 100.0% 37.6%
4936146 101.35.1.0 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.74 60.0 5.18e-01 100.0% 56.4%
3799156 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.73 56.0 4.44e-01 96.8% 43.2%
4025313 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 0.71 56.0 4.60e-01 100.0% 45.7%
4929489 101.1.2.897 ↗ alpha arrays › HTH › HTH › winged helix domain › Zn_ribbon_2 0.64 53.0 4.38e-01 100.0% 49.2%
4023942 308.1.1.1 ↗ a+b two layers › ClpS-like › ClpS-related › ClpS-related › Ribosomal_L12 0.61 45.0 3.70e-01 96.8% 37.5%
2968637 1.1.2.2 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › RNA_pol_Rpb1_2 0.56 44.0 2.99e-01 100.0% 32.9%