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NC_029058.1__YP_009222239.1__AXJ15_gp001__00001

Bact-Vir

NC_029058.1__YP_009222239.1__AXJ15_gp001__00001

Identity

Accession:
NC_029058 ↗
Kingdom:
phage

Quality

81.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Herelleviridae› Hopescreekvirus› Lactobacillus_phage_LfeInf

TaxID: 1567484

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 1-36_102-140
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2mpcA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.66 50.0 4.78e-01 82.7% 94.4%
1wj7A01 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.65 39.0 4.30e-01 73.3% 75.0%
3lcvB01 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.62 39.0 4.36e-01 73.3% 84.2%
1v66A00 1.10.720.30 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › SAP domain 0.58 46.0 4.87e-01 93.3% 100.0%
2el7A02 1.10.240.10 Mainly Alpha › Orthogonal Bundle › Tyrosyl-Transfer RNA Synthetase › Tyrosyl-Transfer RNA Synthetase 0.58 49.0 4.63e-01 100.0% 76.6%
7bqiA01 1.20.58.900 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › RUN domain 0.57 46.0 3.83e-01 94.7% 92.1%
3hzrA02 1.10.240.10 Mainly Alpha › Orthogonal Bundle › Tyrosyl-Transfer RNA Synthetase › Tyrosyl-Transfer RNA Synthetase 0.57 50.0 4.41e-01 100.0% 82.9%
3dxlA02 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.56 48.0 3.90e-01 100.0% 82.9%
2ms7A00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.56 43.0 3.98e-01 88.0% 91.2%
3fxdB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 33.0 3.71e-01 100.0% 77.6%
2kjgA00 1.20.120.970 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.55 38.0 3.50e-01 73.3% 55.6%
3hw5B00 3.40.91.90 Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain 0.55 44.0 3.37e-01 89.3% 92.8%
2e6oA00 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.54 41.0 3.91e-01 100.0% 70.1%
4hdrA01 1.10.1610.10 Mainly Alpha › Orthogonal Bundle › 5,6-Dimethylbenzimidazole Phosphoribosyltransferase; Chain: A; domain 1 › Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (CobT), small domain 0.54 31.0 3.37e-01 72.0% 67.2%
6jrpA01 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.53 39.0 4.23e-01 100.0% 98.4%
2p11A02 1.10.286.50 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › 0.53 41.0 4.13e-01 84.0% 91.9%
1zq3P00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.52 36.0 3.71e-01 72.0% 92.6%
1z0pA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 34.0 3.47e-01 76.0% 69.9%
3ck6C02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.51 37.0 3.15e-01 76.0% 47.9%
1ryuA00 1.10.150.60 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › ARID DNA-binding domain 0.51 40.0 3.58e-01 92.0% 84.2%
2fh5A01 3.30.450.60 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.50 37.0 3.17e-01 78.7% 81.1%
3c7jA02 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.50 42.0 3.51e-01 98.7% 98.6%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3663702 143.1.1.5 ↗ alpha arrays › PABP domain-like › PABC(PABP) domain › PABC(PABP) domain › VIN3_C 0.67 45.0 4.64e-01 82.7% 74.3%
3368018 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.60 47.0 4.90e-01 86.7% 100.0%
4517001 632.3.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Phosphoprotein XD domain › Phosphoprotein XD domain 0.60 38.0 4.48e-01 80.0% 98.0%
3778682 150.1.1.24 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Prominin 0.59 42.0 3.48e-01 76.0% 90.7%
3393892 130.1.1.1 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › SAP 0.59 44.0 4.53e-01 80.0% 88.6%
4615565 101.1.1.249 ↗ alpha arrays › HTH › HTH › Three-helical HTH › SGIII 0.59 34.0 3.28e-01 98.7% 50.6%
2986816 563.1.1.0 ↗ alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase 0.59 36.0 2.74e-01 77.3% 26.0%
4094168 547.1.1.1 ↗ alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.59 38.0 3.45e-01 100.0% 49.0%
4473504 304.136.1.3 ↗ a+b two layers › Alpha-beta plaits › Oligo-peptide binding protein (OPPA) insertion domain › Oligo-peptide binding protein (OPPA) insertion domain › SGIII 0.59 34.0 3.22e-01 98.7% 47.8%
3777242 3919.1.1.2 ↗ alpha duplicates or obligate multimers › N-terminal domain of COMMD9 › N-terminal domain of COMMD9 › N-terminal domain of COMMD9 › COMM_HN 0.57 38.0 3.22e-01 78.7% 42.5%
4962283 604.4.1.0 ↗ alpha bundles › Spectrin repeat-like › Alpha-hemoglobin stabilizing protein AHSP › Alpha-hemoglobin stabilizing protein AHSP 0.57 39.0 3.85e-01 73.3% 66.3%
3218104 601.1.2.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.57 43.0 3.66e-01 81.3% 80.8%
169889 130.1.1.1 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › SAP 0.56 42.0 3.74e-01 82.7% 61.4%
3599601 633.24.1.0 ↗ alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain 0.56 44.0 3.80e-01 100.0% 54.2%
3734131 130.1.1.1 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › SAP 0.55 43.0 4.50e-01 85.3% 98.5%
5046799 10.13.1.10 ↗ beta sandwiches › jelly-roll › Calcium ATPase, transduction domain A › Calcium ATPase, transduction domain A › Cation_ATPase_C 0.55 46.0 2.74e-01 92.0% 20.6%
3928597 633.21.1.0 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.55 40.0 3.30e-01 77.3% 81.4%
3794285 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.55 46.0 4.61e-01 94.7% 98.7%
3313893 604.14.1.4 ↗ alpha bundles › Spectrin repeat-like › PPK N-terminal domain-like › PPK N-terminal domain-like › DUF4110 0.55 37.0 3.40e-01 100.0% 50.5%
3987991 5086.1.1.94 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HB_LcnD 0.54 41.0 2.98e-01 85.3% 29.0%
3594525 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.54 35.0 3.18e-01 100.0% 50.0%
5048341 4156.1.1.0 ↗ alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like 0.52 40.0 3.75e-01 86.7% 66.0%
3993655 1008.1.1.0 ↗ alpha bundles › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain 0.52 39.0 3.09e-01 80.0% 40.7%
3939577 7516.1.1.33 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › DUF273 0.52 45.0 3.29e-01 98.7% 62.3%
5016166 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.51 39.0 2.86e-01 80.0% 37.4%
3651135 3788.1.1.20 ↗ alpha bundles › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › VIN3_C 0.51 35.0 3.52e-01 81.3% 72.0%
3896752 632.3.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Phosphoprotein XD domain › Phosphoprotein XD domain 0.51 36.0 3.81e-01 88.0% 95.0%
5015200 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.50 42.0 2.87e-01 98.7% 34.7%
D2 medium residues 37-101
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1d1lA00 3.30.240.10 Alpha Beta › 2-Layer Sandwich › CRO Repressor › CRO Repressor 0.57 45.0 4.67e-01 96.9% 91.8%
4anjA06 1.20.5.4820 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.55 39.0 3.26e-01 73.8% 68.1%
1dp7P00 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 0.50 42.0 4.04e-01 100.0% 82.9%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3685510 108.1.1.29 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_7 0.62 47.0 3.84e-01 84.6% 80.8%
3219373 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.57 46.0 4.37e-01 89.2% 92.5%
3250467 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.55 41.0 3.91e-01 83.1% 90.0%
2773953 108.1.1.67 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_PLCG2 0.52 38.0 3.57e-01 83.1% 79.1%
5029778 101.1.2.43 ↗ alpha arrays › HTH › HTH › winged helix domain › Pox_D5 0.51 44.0 3.97e-01 100.0% 71.1%
4878203 7581.1.1.16 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › FAE1_CUT1_RppA 0.51 40.0 2.90e-01 92.3% 87.4%