←Back to structures

NC_021803.1__YP_008242063.1__Phi13-2_gp038__00038

Bact-Vir

NC_021803.1__YP_008242063.1__Phi13-2_gp038__00038

Identity

Accession:
NC_021803 ↗
Kingdom:
phage

Quality

91.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pachyviridae› Baltivirus› Cellulophaga_phage_phi13:2

TaxID: 1328030

Cluster

View cluster (35 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 high residues 3-99
PDB
Domain cluster: rep: ON453897.1__WAK79106.1__X__00001__D3-93
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3wxmB02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.66 41.0 3.83e-01 82.5% 50.0%
5dynA01 3.40.50.11970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.59 36.0 3.57e-01 73.2% 55.7%
1zj8A03 3.30.413.10 Alpha Beta › 2-Layer Sandwich › Sulfite Reductase Hemoprotein; domain 1 › Sulfite Reductase Hemoprotein, domain 1 0.58 50.0 4.19e-01 100.0% 55.2%
1ig8A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.57 38.0 3.44e-01 81.4% 49.3%
1t6cA02 3.30.420.150 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Exopolyphosphatase. Domain 2 0.56 39.0 3.18e-01 71.1% 83.4%
2zgyA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.55 42.0 3.74e-01 80.4% 75.7%
4jn7A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.55 42.0 3.94e-01 100.0% 66.4%
3r07C00 3.30.390.50 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › CO dehydrogenase flavoprotein, C-terminal domain 0.54 35.0 3.63e-01 95.9% 70.5%
3qldA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.54 48.0 4.14e-01 100.0% 68.4%
1w0pA01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.53 33.0 2.76e-01 100.0% 33.3%
4abyD00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 37.0 2.61e-01 71.1% 37.3%
2qdeA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.53 42.0 3.80e-01 100.0% 61.0%
3u3gA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.53 37.0 3.38e-01 74.2% 75.7%
3iq2A00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.52 45.0 4.19e-01 93.8% 87.8%
6r2nA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.52 36.0 3.20e-01 81.4% 48.6%
1q48A00 3.90.1010.10 Alpha Beta › Alpha-Beta Complex › Sufe protein. Chain: A › 0.52 41.0 3.69e-01 83.5% 76.1%
3mkcA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.52 43.0 3.77e-01 100.0% 60.4%
3k6kA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 37.0 2.62e-01 74.2% 53.2%
4qmgC01 2.40.50.90 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.50 41.0 3.53e-01 89.7% 87.4%
2yysA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.50 41.0 3.05e-01 93.8% 85.6%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4096162 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.76 51.0 5.10e-01 100.0% 67.0%
5027780 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.67 41.0 5.00e-01 87.6% 100.0%
4144852 220.1.1.126 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Ycf4 0.63 36.0 3.54e-01 78.4% 50.0%
3255196 4970.1.1.28 ↗ 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 › SPC25 0.62 42.0 4.18e-01 81.4% 66.0%
3307236 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.61 38.0 3.59e-01 80.4% 50.0%
3291744 2484.1.1.4 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H 0.58 35.0 3.79e-01 78.4% 72.5%
3514516 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.55 33.0 3.18e-01 77.3% 49.1%
3509080 2484.8.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Separase pseudo-protease domain (PPD) › Separase pseudo-protease domain (PPD) 0.55 48.0 3.74e-01 100.0% 62.2%
3696592 2484.1.1.220 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27033 0.54 40.0 3.15e-01 80.4% 71.1%
3280772 2484.1.1.10 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TsaD 0.54 33.0 3.13e-01 78.4% 49.6%
3509199 633.23.1.4 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › Claudin_2 0.54 42.0 3.35e-01 83.5% 71.3%
3750853 330.1.1.18 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › DSRM_DHX29 0.54 39.0 3.63e-01 75.3% 75.8%
4013791 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.53 41.0 3.30e-01 83.5% 68.5%
4394739 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.53 31.0 3.57e-01 93.8% 78.6%
133860 218.1.1.1 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.53 40.0 3.87e-01 100.0% 69.9%
3492079 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.53 34.0 3.46e-01 74.2% 64.9%
4004698 2.1.1.135 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DUF3592 0.53 37.0 4.06e-01 100.0% 94.7%
5053329 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.53 44.0 4.14e-01 100.0% 75.0%
1174496 218.1.1.1 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.53 42.0 3.97e-01 100.0% 71.8%
4632081 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.51 41.0 3.77e-01 84.5% 87.2%
3692153 2484.1.1.220 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27033 0.51 40.0 3.16e-01 88.7% 99.1%
3995776 330.3.1.0 ↗ a+b two layers › dsRBD-like › Peptidyl-tRNA hydrolase domain-like › Peptidyl-tRNA hydrolase domain-like 0.51 37.0 3.91e-01 90.7% 83.3%
5011673 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.51 33.0 3.19e-01 99.0% 55.7%
4649167 2484.1.1.176 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Hexokinase_1+Hexokinase_2 0.51 40.0 2.59e-01 84.5% 36.8%
4198173 7579.1.1.13 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › DLH 0.51 37.0 2.82e-01 77.3% 51.7%
3745492 2484.1.1.176 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Hexokinase_1+Hexokinase_2 0.51 42.0 2.47e-01 91.8% 76.5%
4433752 5.1.3.35 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Neuraminidase 0.50 44.0 3.24e-01 100.0% 36.4%
3991950 2484.1.1.176 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Hexokinase_1+Hexokinase_2 0.50 40.0 2.53e-01 84.5% 89.2%
D2 high residues 112-221
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF13102.13 best Phage_int_SAM_5 32.5 1.30e-07 95.5% 76.2%
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3nrwA00 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.86 73.0 7.52e-01 99.1% 94.2%
2keyA00 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.78 64.0 6.42e-01 100.0% 85.7%
3hlzA02 1.20.120.1090 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.69 52.0 4.96e-01 79.1% 93.8%
1hyrC01 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.62 46.0 3.93e-01 77.3% 86.1%
2w02B01 1.10.150.640 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › AcsD, thumb domain, helical bundle 0.62 36.0 4.32e-01 92.7% 86.5%
1txuA01 1.10.246.120 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.60 47.0 5.03e-01 89.1% 95.7%
2vqgA00 1.10.10.1280 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Alpha-helical porin B/porin C 0.59 36.0 4.18e-01 98.2% 86.8%
2fefA01 1.20.1440.70 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › PA2201 N-terminal domain-like 0.56 47.0 4.49e-01 97.3% 77.6%
1v4aA03 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.56 44.0 3.98e-01 84.5% 77.8%
1yowA00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.55 47.0 3.77e-01 94.5% 79.6%
3q9oA02 3.90.1350.10 Alpha Beta › Alpha-Beta Complex › Exotoxin A, middle domain › Exotoxin A, middle domain 0.54 43.0 3.76e-01 86.4% 62.9%
6qumA04 1.10.1140.10 Mainly Alpha › Orthogonal Bundle › Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 › Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 0.53 40.0 3.66e-01 80.9% 73.8%
3au3A00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.52 37.0 2.74e-01 75.5% 50.2%
3ajfA00 1.20.1440.190 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Tenuivirus movement protein 0.52 39.0 4.15e-01 86.4% 95.7%
1gvnA00 1.10.8.130 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.51 32.0 3.49e-01 88.2% 77.0%
2d2mD00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.51 44.0 4.06e-01 97.3% 84.8%
1pz1A00 3.20.20.100 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › NADP-dependent oxidoreductase domain 0.51 39.0 2.80e-01 80.0% 34.6%
3hiuD00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.51 39.0 3.61e-01 83.6% 77.6%
5jrcA00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.50 36.0 3.07e-01 95.5% 45.2%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5061202 186.1.1.3 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_5 0.82 72.0 6.75e-01 97.3% 78.5%
5000879 186.1.1.4 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_4 0.82 67.0 6.67e-01 97.3% 82.6%
4954713 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.80 71.0 6.92e-01 98.2% 86.7%
134501 186.1.1.3 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_5 0.78 64.0 6.63e-01 100.0% 93.2%
5012907 3860.1.1.0 ↗ alpha bundles › Myosin VI lever arm › Myosin VI lever arm › Myosin VI lever arm 0.77 49.0 3.83e-01 86.4% 31.8%
3213226 3075.1.1.0 ↗ a+b two layers › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA 0.70 40.0 5.11e-01 91.8% 96.9%
3232510 3075.1.1.1 ↗ a+b two layers › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA › PFU 0.58 36.0 4.26e-01 93.6% 93.3%
3707191 109.4.1.451 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Iml2-TPR_39 0.57 39.0 2.76e-01 70.0% 30.4%
5047488 1075.1.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain › ABC2_membrane 0.56 43.0 3.38e-01 81.8% 72.0%
4491672 601.7.1.6 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › GlnD_UR_UTase 0.55 45.0 3.99e-01 88.2% 81.9%
3227034 5069.1.3.65 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › PF31020 0.55 47.0 4.65e-01 94.5% 90.4%
3864816 109.4.1.601 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PLU-1 0.55 35.0 3.35e-01 90.9% 54.6%
4409068 160.1.1.4 ↗ alpha superhelices › C-terminal domain of alpha and beta subunits of F1 ATP synthase › C-terminal domain of alpha and beta subunits of F1 ATP synthase › C-terminal domain of alpha and beta subunits of F1 ATP synthase › ATP-synt_VA_C 0.53 40.0 3.69e-01 80.9% 75.9%
4027904 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.53 42.0 4.22e-01 96.4% 84.5%
3525009 5051.1.1.10 ↗ alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › AA_permease_2 0.51 44.0 2.95e-01 95.5% 78.5%
3538928 4.1.1.358 ↗ beta barrels › SH3 › SH3 › SH3 › PLU-1 0.51 37.0 3.40e-01 75.5% 57.9%
3390793 4953.1.1.0 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.51 44.0 3.88e-01 94.5% 95.6%
3637143 109.4.1.356 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fungal_trans 0.50 44.0 2.91e-01 98.2% 24.9%
D3 high residues 240-427
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00589.28 best Phage_integrase 29.7 7.20e-07 93.1% 82.6%
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1aihA00 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.79 60.0 6.34e-01 96.3% 87.1%
4a8eA02 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.76 58.0 6.03e-01 85.1% 82.1%
1ae9A00 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.75 59.0 6.19e-01 84.6% 88.9%
5jk0B01 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.75 65.0 6.76e-01 94.1% 97.7%
3nkhA00 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.73 70.0 6.56e-01 100.0% 95.9%
1f44A01 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.73 67.0 6.63e-01 95.7% 96.4%
2a3vA02 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.69 63.0 6.06e-01 95.7% 93.8%
4c26A00 3.30.920.30 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Hypothetical protein. 0.60 21.0 3.40e-01 70.7% 84.8%
2x8xX01 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.58 20.0 3.06e-01 73.4% 73.7%
1j20A02 3.90.1260.10 Alpha Beta › Alpha-Beta Complex › Argininosuccinate synthetase, chain A, domain 2 › Argininosuccinate synthetase, chain A, domain 2 0.54 30.0 2.89e-01 88.8% 46.0%
6kf9G01 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 0.52 24.0 3.46e-01 74.5% 96.3%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5059725 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.79 70.0 7.15e-01 100.0% 95.0%
4940211 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.76 64.0 6.76e-01 95.7% 96.5%
5028306 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.74 67.0 6.85e-01 100.0% 98.3%
3983469 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.73 46.0 5.60e-01 71.3% 94.4%
3964171 101.1.8.1 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.73 63.0 6.54e-01 100.0% 96.6%
4592695 3121.1.1.1 ↗ a+b duplicates or obligate multimers › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain › POTRA 0.60 20.0 3.08e-01 89.4% 70.7%