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KJ746502.1__AID18322.1__PPF1_09__00009

Bact-Vir

KJ746502.1__AID18322.1__PPF1_09__00009

Identity

Accession:
KJ746502 ↗
Kingdom:
phage

Quality

74.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhizobium_phage_vB_RleM_PPF1

TaxID: 1498228

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 3-69
PDB
Domain cluster: rep: MW980061.1__QXV73597.1__X__00063__D3-66
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3anwA02 3.40.5.50 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.79 57.0 6.15e-01 95.5% 87.9%
2lsmA00 3.40.5.70 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › DNA packaging chaperone protein FI, C-terminal beta-strand domain 0.77 56.0 5.86e-01 88.1% 83.6%
2e9xB01 3.40.5.50 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.75 53.0 5.42e-01 91.0% 75.8%
2hjqA01 3.40.5.20 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › YqbF domain 0.71 46.0 5.31e-01 89.6% 97.8%
2e9xD02 3.40.5.60 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.70 53.0 5.57e-01 88.1% 90.0%
6rawN02 3.40.5.60 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.68 48.0 5.17e-01 88.1% 89.1%
3vwdA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.57 40.0 2.94e-01 74.6% 92.3%
1vc9A01 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.55 38.0 3.19e-01 73.1% 90.2%
3ga8A00 3.10.20.860 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.55 33.0 3.34e-01 92.5% 58.2%
1gaxA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.54 41.0 2.73e-01 85.1% 92.3%
1y71A00 2.30.30.430 Mainly Beta › Roll › SH3 type barrels. › Kinase associated protein B domain 0.54 33.0 2.86e-01 82.1% 36.7%
4qmaA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.52 42.0 3.27e-01 88.1% 45.5%
2zewB00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.51 40.0 3.21e-01 89.6% 66.7%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5010674 4076.3.1.11 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › PF25865 0.92 58.0 6.45e-01 91.0% 80.0%
5000438 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.88 59.0 5.88e-01 89.6% 67.1%
4981952 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.84 58.0 6.72e-01 91.0% 96.0%
4935547 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.83 58.0 6.63e-01 88.1% 96.0%
3716713 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.83 57.0 6.54e-01 88.1% 96.0%
5042275 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.82 57.0 6.32e-01 88.1% 89.1%
4956454 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.82 54.0 5.95e-01 91.0% 83.6%
4994655 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 57.0 6.54e-01 88.1% 98.0%
5015232 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 57.0 6.25e-01 91.0% 89.1%
5011186 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 56.0 5.90e-01 89.6% 80.0%
4946969 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.79 57.0 6.51e-01 89.6% 100.0%
4932084 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.79 56.0 6.41e-01 91.0% 100.0%
4932061 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.78 51.0 6.13e-01 86.6% 100.0%
5024995 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.78 55.0 6.11e-01 91.0% 92.5%
4967982 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.78 50.0 5.98e-01 85.1% 100.0%
4030073 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.77 59.0 4.34e-01 91.0% 34.2%
4939413 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.77 55.0 6.25e-01 86.6% 100.0%
218750 4076.3.1.1 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Packaging_FI 0.77 56.0 5.86e-01 88.1% 83.6%
4230268 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.76 50.0 6.02e-01 85.1% 100.0%
3600426 4076.3.1.3 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › SLD5_C 0.76 55.0 6.01e-01 88.1% 92.7%
4025462 4076.1.1.1 ↗ a+b two layers › L9 N-domain-like › L9 N-domain-like › L9 N-domain-like › Ribosomal_L9_N 0.76 58.0 6.11e-01 100.0% 88.3%
4536596 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.76 50.0 5.87e-01 88.1% 95.8%
4641420 4076.4.1.1 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain › PriS_C 0.73 50.0 4.47e-01 89.6% 52.2%
4976498 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.73 56.0 5.88e-01 91.0% 90.0%
5009 4076.3.1.2 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › YqbF 0.71 46.0 5.21e-01 89.6% 91.8%
4025149 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.70 54.0 5.64e-01 88.1% 93.3%
4128951 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.64 47.0 3.06e-01 79.1% 90.3%
3896872 3529.1.1.1 ↗ beta sandwiches › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Vault 0.61 49.0 4.85e-01 89.6% 82.9%
3601134 4076.1.1.0 ↗ a+b two layers › L9 N-domain-like › L9 N-domain-like › L9 N-domain-like 0.61 56.0 5.59e-01 100.0% 95.7%
3861853 376.1.2.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_1 0.56 27.0 2.67e-01 85.1% 37.1%
3544841 10.12.1.1 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.55 43.0 3.53e-01 89.6% 54.1%
3599253 3167.1.1.0 ↗ a+b two layers › 40S ribosomal protein rpS21 (S21e) › 40S ribosomal protein rpS21 (S21e) › 40S ribosomal protein rpS21 (S21e) 0.55 33.0 3.18e-01 80.6% 50.0%
5065691 304.51.1.0 ↗ a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related 0.54 44.0 3.65e-01 89.6% 93.3%
4559415 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.53 40.0 2.52e-01 86.6% 87.8%
3848483 4.1.1.248 ↗ beta barrels › SH3 › SH3 › SH3 › CABIT 0.53 44.0 3.93e-01 94.0% 84.7%
3903397 102.1.1.124 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › CABIT 0.53 41.0 3.92e-01 85.1% 87.5%
3530890 2004.1.1.402 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › CABIT 0.53 41.0 3.79e-01 85.1% 86.4%
4594837 275.1.1.0 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase 0.51 38.0 3.68e-01 85.1% 85.0%
3973128 10.12.1.0 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.51 41.0 2.93e-01 88.1% 32.5%