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MG948468.1__AVJ51820.1__Vid5_gp65__00065

Bact-Vir

MG948468.1__AVJ51820.1__Vid5_gp65__00065

Identity

Accession:
MG948468 ↗
Kingdom:
phage

Quality

67.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vidquintavirus› Pantoea_phage_vB_PagS_Vid5

TaxID: 2099652

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 high residues 3-87
PDB
Domain cluster: representative
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1s2oA02 3.90.1070.10 Alpha Beta › Alpha-Beta Complex › Hypothetical Protein Ta0175; Chain: A, domain 2 › 0.66 38.0 4.17e-01 100.0% 69.0%
1wz9A02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.63 46.0 3.89e-01 77.6% 73.9%
4zk3A02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.62 44.0 3.85e-01 74.1% 72.4%
3ndaA02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.62 45.0 3.92e-01 77.6% 73.5%
1xkiA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.62 45.0 3.90e-01 83.5% 50.8%
4h61A00 3.10.450.580 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Mediator complex, subunit Med6 0.61 46.0 3.94e-01 81.2% 66.4%
1attA01 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.60 46.0 3.87e-01 81.2% 74.3%
3nraA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.60 38.0 3.11e-01 96.5% 34.4%
1l7aA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.59 48.0 3.27e-01 89.4% 42.1%
2nlvA00 3.30.310.110 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › XisI-like 0.58 48.0 4.42e-01 100.0% 69.6%
2fpnA01 3.30.2030.10 Alpha Beta › 2-Layer Sandwich › TBP-like › YwmB-like 0.57 49.0 4.25e-01 100.0% 60.0%
3qkgA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.57 47.0 3.84e-01 91.8% 90.2%
1q40D00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.56 44.0 3.48e-01 84.7% 93.7%
2rh0A01 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 28.0 3.18e-01 70.6% 60.9%
2psoB02 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.55 49.0 3.88e-01 100.0% 73.0%
2nvmA00 3.30.310.110 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › XisI-like 0.55 45.0 4.27e-01 100.0% 76.0%
2e3nA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.54 46.0 3.48e-01 100.0% 63.2%
3fo5B00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.54 45.0 3.39e-01 96.5% 57.9%
3mswA00 2.40.128.720 Mainly Beta › Beta Barrel › Lipocalin › 0.52 47.0 3.95e-01 97.6% 71.2%
3ecrB03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.52 41.0 3.93e-01 88.2% 85.3%
3jb9H00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.52 32.0 3.39e-01 71.8% 69.7%
3c0wA01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.51 36.0 3.26e-01 72.9% 65.8%
1e8oA00 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 0.51 32.0 3.37e-01 71.8% 70.3%
4r03A00 2.40.128.720 Mainly Beta › Beta Barrel › Lipocalin › 0.51 44.0 4.07e-01 94.1% 75.2%
2c4iA01 2.40.128.30 Mainly Beta › Beta Barrel › Lipocalin › Avidin-like 0.51 42.0 3.89e-01 95.3% 89.0%
1tkjA00 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.51 43.0 2.97e-01 90.6% 83.8%
1ew3A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.51 40.0 3.36e-01 88.2% 88.7%
2xskA00 2.60.40.2420 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 40.0 3.87e-01 85.9% 97.9%
4fnvA02 2.70.98.70 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.51 44.0 3.14e-01 100.0% 74.1%
4qjvA01 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.51 30.0 3.00e-01 95.3% 53.9%
4opmA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.50 38.0 2.72e-01 84.7% 56.5%
1vwxr00 3.30.390.110 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.50 41.0 3.68e-01 92.9% 72.0%
3a7rA02 3.30.390.50 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › CO dehydrogenase flavoprotein, C-terminal domain 0.50 43.0 4.26e-01 100.0% 95.5%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4975431 331.3.1.0 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.69 56.0 5.49e-01 100.0% 82.2%
3743072 3435.1.1.2 ↗ a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC › CENP-N 0.68 60.0 5.08e-01 100.0% 66.9%
4941979 5104.1.1.1 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.64 34.0 3.03e-01 100.0% 34.2%
3710638 881.1.1.0 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.64 57.0 4.50e-01 100.0% 94.3%
3221750 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.63 40.0 3.80e-01 100.0% 54.0%
3874376 897.1.1.1 ↗ a+b two layers › Acidic mitochondrial matrix protein p32-like › Acidic mitochondrial matrix protein p32 › Acidic mitochondrial matrix protein p32 › MAM33 0.62 48.0 3.60e-01 81.2% 52.9%
3990077 330.7.1.0 ↗ a+b two layers › dsRBD-like › PI-Pfui intein middle domain › PI-Pfui intein middle domain 0.62 44.0 4.16e-01 96.5% 62.0%
5075730 3435.1.1.0 ↗ a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC 0.62 55.0 5.01e-01 100.0% 77.4%
4138832 304.8.1.2 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT 0.62 40.0 4.00e-01 100.0% 62.9%
4243367 3561.1.1.0 ↗ a+b complex topology › Mediator of RNA polymerase II transcription subunit 17 › Mediator of RNA polymerase II transcription subunit 17 › Mediator of RNA polymerase II transcription subunit 17 0.60 54.0 3.37e-01 96.5% 26.4%
3807906 331.3.1.43 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › PDF2_C 0.59 51.0 3.89e-01 100.0% 66.5%
4023222 7556.1.1.0 ↗ a/b three-layered sandwiches › Fe-only hydrogenase › Fe-only hydrogenase › Fe-only hydrogenase 0.59 41.0 2.68e-01 97.6% 16.7%
3790608 708.1.1.0 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain 0.57 47.0 4.39e-01 91.8% 88.2%
5011595 330.10.1.1 ↗ a+b two layers › dsRBD-like › Heterocyclase TruD C-terminal domain › Heterocyclase TruD C-terminal domain › YcaO 0.56 43.0 3.80e-01 85.9% 54.6%
3413965 5.1.4.463 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_NWD2_C 0.56 43.0 2.76e-01 82.4% 21.5%
2096018 330.17.1.1 ↗ a+b two layers › dsRBD-like › Anti-CRISPR protein AcrIIA4 › Anti-CRISPR protein AcrIIA4 › AcrIIA4 0.56 48.0 4.83e-01 100.0% 95.4%
4247396 304.8.1.2 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT 0.56 39.0 3.15e-01 100.0% 36.5%
3670595 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.55 43.0 4.22e-01 95.3% 76.8%
3802643 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.55 43.0 4.15e-01 96.5% 74.7%
3640668 719.1.1.2 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain › XLF 0.55 38.0 3.37e-01 71.8% 93.6%
4946684 2004.1.1.308 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_21 0.55 45.0 3.01e-01 90.6% 34.3%
3381295 4018.1.1.1 ↗ a+b two layers › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases › FBPase 0.55 48.0 4.10e-01 98.8% 62.9%
4009433 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.55 41.0 2.67e-01 78.8% 20.3%
3286318 1.1.5.8 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.54 40.0 3.22e-01 78.8% 70.0%
3600787 2008.6.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Acetyl-CoA carboxylase AC4 and AC5 domains › Acetyl-CoA carboxylase AC4 and AC5 domains 0.53 47.0 3.42e-01 98.8% 59.2%
5018154 873.1.1.19 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › MetOD1 0.53 42.0 3.64e-01 83.5% 57.7%
3592743 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.53 42.0 4.38e-01 92.9% 93.8%
5006953 873.1.1.12 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › PF27313 0.53 39.0 3.70e-01 84.7% 66.0%
3600343 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.53 44.0 2.81e-01 90.6% 60.9%
3704303 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.52 44.0 3.73e-01 96.5% 91.3%
4954535 310.3.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.52 46.0 4.45e-01 97.6% 89.5%
3514202 2008.6.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Acetyl-CoA carboxylase AC4 and AC5 domains › Acetyl-CoA carboxylase AC4 and AC5 domains › ACC_central 0.52 42.0 3.17e-01 89.4% 96.7%
3262017 2008.6.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Acetyl-CoA carboxylase AC4 and AC5 domains › Acetyl-CoA carboxylase AC4 and AC5 domains › ACC_central 0.52 42.0 3.20e-01 90.6% 98.1%
4927237 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.51 35.0 2.93e-01 70.6% 46.9%
5012803 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.51 35.0 2.92e-01 70.6% 46.2%
4582428 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.51 35.0 3.08e-01 70.6% 55.2%
1498250 12.3.1.14 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › Hepar_II_III 0.51 44.0 3.13e-01 100.0% 73.3%
5023066 1.1.5.44 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › SecDF_P1_head 0.51 37.0 3.35e-01 77.6% 83.3%
3170444 2008.6.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Acetyl-CoA carboxylase AC4 and AC5 domains › Acetyl-CoA carboxylase AC4 and AC5 domains › ACC_central 0.51 41.0 3.16e-01 89.4% 99.5%