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NC_053249.1__YP_010002900.1__J1776_gp62__00062

Bact-Vir

NC_053249.1__YP_010002900.1__J1776_gp62__00062

Identity

Accession:
NC_053249 ↗
Kingdom:
phage

Quality

66.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Stackebrandtviridae› Zitchvirus› Gordonia_phage_Verity

TaxID: 2591211

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 43-79_91-148
PDB
Domain cluster: representative
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vyfA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.80 41.0 3.59e-01 74.7% 36.3%
2rcqA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.76 39.0 3.37e-01 74.7% 34.0%
1o8vA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.76 39.0 3.40e-01 74.7% 36.1%
4ok4A02 2.70.98.70 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.74 63.0 4.15e-01 90.5% 51.8%
1k8kD01 3.30.1460.20 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.73 51.0 4.33e-01 71.6% 62.3%
8bddA02 2.70.98.70 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.69 59.0 3.91e-01 90.5% 51.4%
2p4bB02 3.30.200.100 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › MucB/RseB, C-terminal domain 0.69 48.0 4.75e-01 71.6% 84.7%
1xkiA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.68 39.0 3.52e-01 91.6% 42.2%
4azpA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.66 38.0 3.39e-01 71.6% 41.0%
2yfoA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.66 45.0 4.57e-01 70.5% 99.0%
2xn2A03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.65 45.0 4.56e-01 71.6% 99.0%
2giaB00 2.30.31.40 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › 0.64 39.0 3.36e-01 74.7% 40.4%
1uxbA00 2.60.90.10 Mainly Beta › Sandwich › Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) › Adenovirus pIV-related, attachment domain 0.64 44.0 3.51e-01 70.5% 99.5%
1yqfB00 3.10.280.10 Alpha Beta › Roll › Mitochondrial Matrix Protein; Chain A › Mitochondrial glycoprotein 0.64 37.0 2.97e-01 74.7% 31.1%
5gv0A00 2.40.160.110 Mainly Beta › Beta Barrel › Porin › 0.63 42.0 3.46e-01 74.7% 39.5%
3mi6B03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.62 42.0 4.14e-01 70.5% 99.0%
2nvnA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.62 36.0 3.29e-01 71.6% 45.8%
4yrdA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.62 43.0 3.97e-01 71.6% 89.1%
1mdcA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.61 37.0 3.32e-01 86.3% 43.5%
3w9kA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.60 39.0 3.42e-01 89.5% 45.9%
1lfoA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.59 34.0 3.08e-01 88.4% 42.5%
1j0hA04 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.59 40.0 4.28e-01 70.5% 100.0%
2w4yA00 2.40.160.220 Mainly Beta › Beta Barrel › Porin › 0.59 44.0 4.05e-01 87.4% 61.5%
1mbyA00 2.40.50.930 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.59 32.0 3.64e-01 81.1% 69.3%
3kd4A03 2.60.120.1130 Mainly Beta › Sandwich › Jelly Rolls › 0.58 46.0 4.06e-01 84.2% 87.6%
3tu3A00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.56 39.0 3.68e-01 73.7% 68.1%
1xn5A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.56 40.0 3.52e-01 95.8% 51.4%
4qi3A00 2.60.40.1210 Mainly Beta › Sandwich › Immunoglobulin-like › Cellobiose dehydrogenase, cytochrome domain 0.55 45.0 3.54e-01 90.5% 94.7%
3p51A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.54 37.0 3.26e-01 87.4% 45.5%
2qziA00 3.40.1720.10 Alpha Beta › 3-Layer(aba) Sandwich › Streptococcus thermophilus LMG 18311 protein like › Streptococcus thermophilus LMG 18311 protein like 0.54 46.0 4.57e-01 90.5% 94.1%
6phxA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.54 44.0 4.43e-01 86.3% 98.9%
3v8uA02 2.40.160.90 Mainly Beta › Beta Barrel › Porin › 0.53 37.0 2.99e-01 76.8% 39.1%
2giaA00 2.30.31.40 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › 0.51 34.0 2.86e-01 72.6% 41.6%
2pmlX01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.50 34.0 3.23e-01 70.5% 79.8%
1epaA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.50 42.0 3.49e-01 89.5% 77.5%
ECOD (43)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5014009 11.1.1.53 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DOMON 0.72 50.0 4.13e-01 70.5% 68.1%
3225336 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.69 39.0 3.33e-01 72.6% 36.6%
3165921 881.4.1.1 ↗ a+b three layers › Mog1p/PsbP-like › C-terminal domain in sigma-E factor regulatory protein rseB › C-terminal domain in sigma-E factor regulatory protein rseB › MucB_RseB_C 0.69 48.0 4.85e-01 71.6% 84.2%
2774000 881.4.1.1 ↗ a+b three layers › Mog1p/PsbP-like › C-terminal domain in sigma-E factor regulatory protein rseB › C-terminal domain in sigma-E factor regulatory protein rseB › MucB_RseB_C 0.68 47.0 4.59e-01 71.6% 83.5%
3468140 304.8.1.45 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › bHLH-TF_ACT-like_plant 0.67 47.0 4.81e-01 71.6% 77.8%
3367441 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.67 46.0 4.60e-01 71.6% 72.7%
1952891 9.1.1.9 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › CpeT 0.66 39.0 3.47e-01 74.7% 41.9%
5014277 274.1.1.0 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.66 36.0 3.81e-01 86.3% 58.8%
3367922 304.8.1.45 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › bHLH-TF_ACT-like_plant 0.65 46.0 4.60e-01 71.6% 75.8%
5043414 4252.1.1.0 ↗ beta barrels › AttH-like › AttH-like › AttH-like 0.65 42.0 3.64e-01 88.4% 45.9%
3670765 11.1.1.53 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DOMON 0.64 49.0 4.05e-01 81.1% 64.1%
3953302 331.2.1.1 ↗ a+b two layers › TBP-like › Phosphoglucomutase, C-terminal domain › Phosphoglucomutase, C-terminal domain › PGM_PMM_IV 0.64 41.0 3.98e-01 89.5% 58.7%
4970968 331.10.2.0 ↗ a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase 0.64 38.0 3.62e-01 87.4% 50.4%
3514856 1181.1.1.0 ↗ 0.64 44.0 4.94e-01 71.6% 90.7%
3663259 881.1.1.1 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like › PsbP 0.64 47.0 4.17e-01 77.9% 89.6%
3981185 241.1.1.25 ↗ a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone › PF27378 0.63 45.0 4.23e-01 74.7% 68.7%
4942135 9.2.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Avidin/Streptavidin › Avidin/Streptavidin 0.62 36.0 3.31e-01 72.6% 43.5%
3999005 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.62 39.0 4.58e-01 70.5% 92.3%
5792 295.1.1.6 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › DUF1818 0.62 36.0 3.28e-01 71.6% 45.5%
820 9.1.1.1 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › Lipocalin 0.61 37.0 3.32e-01 86.3% 43.5%
5038486 881.1.1.0 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.61 50.0 3.96e-01 89.5% 82.0%
1066273 331.3.1.12 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › STK_08120-like 0.60 39.0 3.42e-01 89.5% 45.9%
3191832 12.3.1.36 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › DUF5127 0.60 54.0 3.83e-01 98.9% 70.2%
1148074 3400.1.1.1 ↗ a+b complex topology › Membrane-associated protein VP24 › Membrane-associated protein VP24 › Membrane-associated protein VP24 › Filo_VP24 0.60 36.0 2.68e-01 85.3% 25.7%
3884325 12.5.1.2 ↗ beta sandwiches › Glycosyl hydrolase domain-like › ZU5/Nup98-C/GAIN-B autoproteolytic domain-related › ZU5/Nup98-C/GAIN-B autoproteolytic domain-related › GPS 0.59 41.0 3.32e-01 71.6% 80.5%
3421867 2003.1.2.15 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3 0.59 42.0 3.02e-01 73.7% 77.3%
5046458 844.1.1.2 ↗ beta barrels › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › LOR 0.57 34.0 2.81e-01 86.3% 32.0%
3639368 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.57 46.0 4.39e-01 85.3% 96.4%
3251123 319.1.1.3 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › CS 0.57 40.0 3.92e-01 71.6% 85.0%
3278459 881.1.1.33 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like › PF26056 0.57 45.0 3.68e-01 86.3% 74.9%
3456369 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 0.56 38.0 2.98e-01 75.8% 35.1%
3963158 4252.1.1.0 ↗ beta barrels › AttH-like › AttH-like › AttH-like 0.56 40.0 3.41e-01 73.7% 53.8%
4113246 220.1.1.153 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_TRF2_HOY1 0.55 40.0 3.48e-01 74.7% 60.7%
3108766 9.1.1.1 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › Lipocalin 0.55 38.0 3.32e-01 71.6% 52.5%
3615896 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 0.54 35.0 2.68e-01 71.6% 31.0%
3789660 897.1.1.0 ↗ a+b two layers › Acidic mitochondrial matrix protein p32-like › Acidic mitochondrial matrix protein p32 › Acidic mitochondrial matrix protein p32 0.54 35.0 2.69e-01 71.6% 31.8%
5071561 4252.1.1.12 ↗ beta barrels › AttH-like › AttH-like › AttH-like › DUF7064 0.54 39.0 3.20e-01 88.4% 42.4%
4027918 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 0.54 35.0 2.89e-01 73.7% 38.7%
5014493 331.3.1.12 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › STK_08120-like 0.52 41.0 3.02e-01 88.4% 34.3%
3743718 319.1.1.3 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › CS 0.52 41.0 3.39e-01 83.2% 55.6%
3316079 220.1.1.183 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_RDR2 0.51 37.0 3.14e-01 75.8% 60.7%
3907054 319.1.1.3 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › CS 0.50 36.0 3.57e-01 74.7% 82.0%
3584281 12.3.1.13 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › Glyco_hydro_38C 0.50 46.0 3.23e-01 100.0% 78.6%