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LacPavin_0818_WC40_scaffold_238879_prodigal-single.1__X__X__00413
Bact-VirLacPavin_0818_WC40_scaffold_238879_prodigal-single.1__X__X__00413
Identity
- Kingdom:
- phage
Quality
59.2
mean pLDDT
Cluster
Singleton — not in a non-trivial cluster
3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
high
residues 304-394
D2
medium
residues 1-92
Domain cluster:
representative
CATH (11)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2w9jA00 | 3.30.720.10 | Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Signal recognition particle alu RNA binding heterodimer, srp9/1 | 0.68 | 31.0 | 3.55e-01 | 83.7% | 56.3% |
| 1dc1A01 | 3.40.91.10 | Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › | 0.63 | 44.0 | 3.38e-01 | 93.5% | 30.6% |
| 2fhzA00 | 3.30.190.30 | Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › | 0.62 | 50.0 | 4.81e-01 | 87.0% | 93.4% |
| 1burS00 | 3.30.190.10 | Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribulose bisphosphate carboxylase, small subunit | 0.61 | 49.0 | 4.46e-01 | 87.0% | 73.2% |
| 1svdM00 | 3.30.190.10 | Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribulose bisphosphate carboxylase, small subunit | 0.61 | 48.0 | 4.55e-01 | 88.0% | 72.2% |
| 5mz2I00 | 3.30.190.10 | Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribulose bisphosphate carboxylase, small subunit | 0.57 | 47.0 | 4.14e-01 | 91.3% | 64.0% |
| 3gqcC04 | 3.30.1490.100 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain | 0.54 | 45.0 | 4.16e-01 | 93.5% | 90.0% |
| 7ovuA01 | 3.40.630.30 | Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) | 0.53 | 36.0 | 2.89e-01 | 70.7% | 36.8% |
| 3afhA02 | 3.90.800.10 | Alpha Beta › Alpha-Beta Complex › Glutamyl-tRNA Synthetase; domain 3 › Glutamyl-tRNA Synthetase; Domain 3 | 0.52 | 34.0 | 3.29e-01 | 84.8% | 56.7% |
| 3viuA04 | 3.90.650.10 | Alpha Beta › Alpha-Beta Complex › Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 › PurM-like C-terminal domain | 0.51 | 41.0 | 3.38e-01 | 95.7% | 46.8% |
| 2pq0A02 | 3.30.1240.10 | Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › | 0.51 | 41.0 | 4.03e-01 | 88.0% | 93.0% |
ECOD (10)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3483014 | 219.1.1.4 ↗ | a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C2 | 0.61 | 51.0 | 3.38e-01 | 91.3% | 46.5% |
| 3783849 | 219.1.1.3 ↗ | a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH | 0.52 | 42.0 | 2.66e-01 | 88.0% | 25.3% |
| 3582980 | 219.1.1.4 ↗ | a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C2 | 0.52 | 44.0 | 3.01e-01 | 93.5% | 41.8% |
| 5024617 | 4.15.1.2 ↗ | beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 | 0.52 | 42.0 | 4.20e-01 | 88.0% | 90.5% |
| 5058265 | 206.1.3.3 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › PPDK_N | 0.52 | 44.0 | 3.23e-01 | 95.7% | 78.5% |
| 3589020 | 2008.1.1.0 ↗ | a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like | 0.51 | 38.0 | 3.32e-01 | 80.4% | 96.7% |
| 3513788 | 886.1.1.2 ↗ | a+b duplicates or obligate multimers › Probable bacterial effector-binding domain › Probable bacterial effector-binding domain › Probable bacterial effector-binding domain › GyrI-like | 0.51 | 40.0 | 3.43e-01 | 87.0% | 82.6% |
| 4959045 | 304.8.1.81 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › REP_ORF2-G2P | 0.50 | 40.0 | 3.49e-01 | 89.1% | 98.0% |
| 4022883 | 2005.1.1.0 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains | 0.50 | 40.0 | 2.90e-01 | 87.0% | 45.6% |
| 3678932 | 221.1.1.99 ↗ | a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › UCH | 0.50 | 40.0 | 2.62e-01 | 91.3% | 23.5% |
D3
medium
residues 93-209
Domain cluster:
rep: NC_027397.1__YP_009153053.1__ACQ41_gp27__00027__D86-201
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF09250.17 best | Prim-Pol | 27.5 | 5.70e-06 | 96.6% | 51.3% |
CATH (26)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4cyuA00 | 3.30.70.560 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK | 0.69 | 50.0 | 4.58e-01 | 76.1% | 98.7% |
| 3h20A02 | 3.30.70.1790 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RepB DNA-primase, N-terminal domain | 0.67 | 52.0 | 5.51e-01 | 82.9% | 100.0% |
| 1rniA02 | 3.30.2250.10 | Alpha Beta › 2-Layer Sandwich › Prim-pol fold › Bifunctional DNA primase/polymerase domain | 0.64 | 56.0 | 5.70e-01 | 100.0% | 95.7% |
| 1z1dB00 | 3.40.1310.20 | Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › | 0.62 | 48.0 | 4.62e-01 | 80.3% | 74.0% |
| 2y1rK00 | 3.30.70.1950 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.62 | 43.0 | 4.74e-01 | 80.3% | 90.2% |
| 2pjyC00 | 2.10.60.10 | Mainly Beta › Ribbon › CD59 › CD59 | 0.62 | 34.0 | 3.97e-01 | 71.8% | 77.2% |
| 5fxdA03 | 3.40.462.10 | Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › FAD-linked oxidases, C-terminal domain | 0.61 | 47.0 | 3.78e-01 | 82.1% | 82.0% |
| 3jtnB00 | 3.30.70.1950 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.61 | 42.0 | 4.66e-01 | 78.6% | 91.1% |
| 1earA02 | 3.30.70.790 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain | 0.60 | 34.0 | 4.29e-01 | 81.2% | 95.7% |
| 2atzA00 | 3.90.920.20 | Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › HP0184-like | 0.59 | 47.0 | 4.10e-01 | 84.6% | 60.2% |
| 1gmuA01 | 3.30.70.790 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain | 0.58 | 33.0 | 4.11e-01 | 80.3% | 95.5% |
| 3tj8A02 | 3.30.70.790 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain | 0.58 | 35.0 | 4.17e-01 | 78.6% | 93.2% |
| 1darA05 | 3.30.70.240 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.58 | 38.0 | 4.28e-01 | 84.6% | 88.5% |
| 6lpnA03 | 3.30.70.2190 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.58 | 41.0 | 4.21e-01 | 74.4% | 100.0% |
| 4i68A00 | 3.30.70.1800 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.57 | 39.0 | 4.33e-01 | 78.6% | 91.1% |
| 1zpwX00 | 3.30.70.240 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.57 | 38.0 | 4.39e-01 | 77.8% | 97.6% |
| 3dfeA00 | 3.30.70.120 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.55 | 37.0 | 4.32e-01 | 82.1% | 97.6% |
| 1f0xA01 | 3.30.70.610 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › D-lactate dehydrogenase, cap domain, subdomain 1 | 0.55 | 39.0 | 4.17e-01 | 74.4% | 95.0% |
| 1g71A01 | 3.90.920.10 | Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain | 0.54 | 42.0 | 3.37e-01 | 82.1% | 48.7% |
| 3ce8A00 | 3.30.70.120 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.54 | 39.0 | 4.35e-01 | 79.5% | 96.6% |
| 5yppA00 | 3.30.70.260 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain | 0.54 | 38.0 | 4.22e-01 | 79.5% | 95.6% |
| 2dbbA02 | 3.30.70.920 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain | 0.53 | 37.0 | 4.09e-01 | 78.6% | 92.5% |
| 1sjqA00 | 3.30.70.330 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain | 0.52 | 36.0 | 4.06e-01 | 80.3% | 94.3% |
| 1jb3A00 | 2.40.50.120 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › | 0.51 | 37.0 | 3.62e-01 | 97.4% | 69.3% |
| 3euwA02 | 3.30.360.10 | Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 | 0.50 | 37.0 | 3.13e-01 | 78.6% | 97.2% |
| 2uuvB01 | 3.40.462.40 | Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › FAD-linked oxidase, cap domain/gating helix | 0.50 | 38.0 | 3.03e-01 | 81.2% | 66.3% |
ECOD (20)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4960053 | 862.1.1.3 ↗ | a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › Prim-Pol | 0.80 | 64.0 | 5.39e-01 | 83.8% | 68.6% |
| 3934530 | 304.9.1.0 ↗ | a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD | 0.63 | 43.0 | 4.78e-01 | 80.3% | 90.0% |
| 143128 | 304.55.1.4 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › T_Ag_DNA_bind | 0.60 | 46.0 | 4.62e-01 | 80.3% | 79.0% |
| 4979727 | 304.4.1.0 ↗ | a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel | 0.59 | 39.0 | 4.45e-01 | 70.1% | 92.9% |
| 4277197 | 304.11.1.0 ↗ | a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase | 0.59 | 35.0 | 4.37e-01 | 82.1% | 100.0% |
| 4220908 | 304.11.1.0 ↗ | a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase | 0.58 | 35.0 | 4.30e-01 | 82.1% | 100.0% |
| 4202472 | 304.11.1.0 ↗ | a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase | 0.57 | 35.0 | 4.26e-01 | 82.1% | 100.0% |
| 4998680 | 304.3.1.0 ↗ | a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain | 0.57 | 35.0 | 4.21e-01 | 79.5% | 100.0% |
| 432311 | 304.22.1.1 ↗ | a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain › UreE_C | 0.57 | 35.0 | 4.06e-01 | 81.2% | 88.7% |
| 3624909 | 382.1.1.0 ↗ | few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like | 0.55 | 33.0 | 3.37e-01 | 73.5% | 60.0% |
| 4227820 | 304.11.1.0 ↗ | a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase | 0.55 | 34.0 | 4.05e-01 | 80.3% | 100.0% |
| 4981048 | 304.4.1.1 ↗ | a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg | 0.54 | 36.0 | 4.18e-01 | 80.3% | 100.0% |
| 4153537 | 304.22.1.1 ↗ | a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain › UreE_C | 0.54 | 31.0 | 3.61e-01 | 76.9% | 82.5% |
| 5022444 | 304.24.1.0 ↗ | a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like | 0.52 | 32.0 | 3.73e-01 | 80.3% | 90.0% |
| 4297401 | 304.110.1.0 ↗ | a+b two layers › Alpha-beta plaits › Acylphosphatase-like › Acylphosphatase-like | 0.52 | 35.0 | 4.02e-01 | 78.6% | 100.0% |
| 3645145 | 304.110.1.3 ↗ | a+b two layers › Alpha-beta plaits › Acylphosphatase-like › Acylphosphatase-like › Prp3_C | 0.52 | 39.0 | 3.63e-01 | 79.5% | 82.8% |
| 4022998 | 304.110.1.0 ↗ | a+b two layers › Alpha-beta plaits › Acylphosphatase-like › Acylphosphatase-like | 0.51 | 39.0 | 3.78e-01 | 80.3% | 90.0% |
| 3604080 | 304.4.1.1 ↗ | a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg | 0.51 | 36.0 | 3.94e-01 | 79.5% | 93.5% |
| 5006559 | 304.4.1.1 ↗ | a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg | 0.50 | 43.0 | 4.13e-01 | 94.0% | 81.5% |
| 5044110 | 304.4.1.0 ↗ | a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel | 0.50 | 41.0 | 4.13e-01 | 94.0% | 90.4% |