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SR-VP_4-6_scaffold_141_476970_prodigal-single.1__X__X__00336

Bact-Vir

SR-VP_4-6_scaffold_141_476970_prodigal-single.1__X__X__00336

Identity

Kingdom:
phage

Quality

79.7 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 6-74
PDB
D2 high residues 78-241_254-269
PDB
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4r03A00 2.40.128.720 Mainly Beta › Beta Barrel › Lipocalin › 0.55 33.0 4.08e-01 95.0% 97.2%
4dduA07 2.60.510.20 Mainly Beta › Sandwich › EV matrix protein fold › 0.53 29.0 3.63e-01 100.0% 86.9%
3jvaA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.52 24.0 2.97e-01 84.4% 67.5%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1346676 3347.1.1.1 ↗ beta meanders › Uncharacterized protein BF3112 › Uncharacterized protein BF3112 › Uncharacterized protein BF3112 › DUF3836 0.55 33.0 4.08e-01 95.0% 97.2%
2841928 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.53 41.0 4.25e-01 80.0% 95.3%
3398694 4210.1.1.0 ↗ a+b two layers › WGR domain › WGR domain › WGR domain 0.53 30.0 3.79e-01 75.6% 94.3%
3705966 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.52 42.0 3.61e-01 85.0% 73.0%
3979319 5084.3.1.1 ↗ beta barrels › Outer membrane meander beta-barrels › Autotransporter › Autotransporter › Autotransporter 0.51 39.0 3.33e-01 78.9% 95.2%
D3 high residues 277-461
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1h2cA00 2.70.20.20 Mainly Beta › Distorted Sandwich › Topoisomerase I; domain 3 › Matrix protein VP40, N-terminal domain 0.54 34.0 3.98e-01 93.5% 91.1%
2g2sA00 3.30.1300.40 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 0.54 22.0 3.33e-01 72.4% 100.0%
2qz5A00 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.53 37.0 4.08e-01 71.4% 100.0%
1y8cA02 2.20.25.110 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › S-adenosyl-L-methionine-dependent methyltransferases 0.53 21.0 3.21e-01 76.2% 100.0%
3bp6B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 24.0 3.30e-01 72.4% 87.5%
2ffsA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.51 33.0 3.67e-01 76.8% 81.4%
3lq6A02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.51 27.0 3.25e-01 96.8% 77.2%
3d2uE01 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.51 35.0 3.57e-01 71.4% 97.9%
6gp1A00 3.30.1300.40 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 0.50 21.0 3.05e-01 71.9% 95.4%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5040130 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.63 30.0 4.22e-01 84.3% 92.2%
D4 high residues 495-585
PDB
Domain cluster: representative
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4l4qA02 3.30.300.340 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › S-adenosylmethionine synthetase, N-terminal domain 0.59 47.0 4.27e-01 89.0% 81.9%
3vseB02 3.30.750.80 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › RNA methyltransferase domain (HRMD) like 0.58 42.0 4.11e-01 94.5% 70.0%
3cniA00 3.40.1710.10 Alpha Beta › 3-Layer(aba) Sandwich › abc type-2 transporter like fold › abc type-2 transporter like domain 0.58 46.0 3.98e-01 86.8% 87.6%
2ob0C01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.57 45.0 3.77e-01 86.8% 72.2%
4ri1C00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.57 47.0 3.82e-01 91.2% 66.3%
3kxwA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.56 48.0 4.39e-01 96.7% 99.2%
1nslA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.56 45.0 3.70e-01 90.1% 65.3%
1vehA01 3.30.300.130 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › Fe-S cluster assembly (FSCA) 0.56 42.0 4.54e-01 85.7% 100.0%
5ktaA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.56 45.0 3.71e-01 91.2% 61.8%
2r7hB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.55 44.0 3.75e-01 89.0% 69.8%
3tthB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.55 45.0 3.75e-01 90.1% 81.1%
3gy9A00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.55 45.0 3.87e-01 91.2% 69.6%
1cm0A00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.55 44.0 3.71e-01 90.1% 68.5%
1mkyA03 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.54 42.0 4.30e-01 85.7% 88.9%
2ayaA00 3.30.300.150 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › DNA polymerase III, tau subunit, domain V 0.54 39.0 3.52e-01 80.2% 54.7%
3r96B00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.54 42.0 3.54e-01 89.0% 64.7%
1s7kA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.53 42.0 3.61e-01 89.0% 70.9%
5nfmA00 3.30.300.90 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › BolA-like 0.53 38.0 4.05e-01 79.1% 92.0%
3w5xA00 3.30.70.1350 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cation efflux protein, cytoplasmic domain 0.53 40.0 4.26e-01 83.5% 95.0%
3qb8A00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.53 42.0 3.40e-01 90.1% 75.1%
3fbuA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.53 42.0 3.49e-01 87.9% 96.4%
2oaiA00 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.52 33.0 3.46e-01 78.0% 70.0%
1d0nA02 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.52 42.0 4.02e-01 89.0% 75.5%
1hh2P04 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.52 35.0 3.88e-01 81.3% 94.1%
1x67A01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.52 42.0 3.78e-01 91.2% 81.2%
2zztA00 3.30.70.1350 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cation efflux protein, cytoplasmic domain 0.52 40.0 4.18e-01 85.7% 93.9%
4at7A02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.52 41.0 3.57e-01 89.0% 91.4%
3h4rA00 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.51 40.0 3.14e-01 86.8% 79.9%
2nqwA00 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.51 31.0 3.15e-01 78.0% 60.9%
4mfzA02 3.40.630.120 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › 0.51 40.0 3.48e-01 86.8% 100.0%
3ejxA02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.51 42.0 3.62e-01 91.2% 72.1%
7whfC02 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.50 39.0 3.79e-01 83.5% 87.0%
3s1sA01 3.90.1570.30 Alpha Beta › Alpha-Beta Complex › tt1808, chain A › 0.50 43.0 3.61e-01 100.0% 54.4%
2atrA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.50 42.0 3.77e-01 94.5% 65.6%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5064259 327.7.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.57 40.0 4.35e-01 82.4% 90.7%
4645686 327.6.1.3 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Fe-S cluster assembly (FSCA) domain-like › Fe-S cluster assembly (FSCA) domain-like › Germane 0.57 47.0 4.13e-01 94.5% 69.0%
4514947 1032.1.1.0 ↗ alpha arrays › Toxin A (TcdA) helical domain › Toxin A (TcdA) helical domain › Toxin A (TcdA) helical domain 0.57 49.0 2.78e-01 98.9% 12.6%
3971306 213.1.1.25 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_3 0.57 45.0 3.73e-01 90.1% 65.4%
5066183 327.7.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.56 43.0 4.55e-01 82.4% 95.0%
4960646 327.7.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like 0.56 46.0 4.33e-01 92.3% 99.1%
5076559 213.1.1.25 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_3 0.56 46.0 3.74e-01 91.2% 66.7%
5040914 213.1.1.25 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_3 0.56 47.0 3.76e-01 92.3% 63.8%
5061690 327.7.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.56 42.0 4.47e-01 83.5% 92.5%
4496745 217.2.1.1 ↗ a+b complex topology › FAD-binding domain-like › CorC/HlyC domain-like › CorC/HlyC domain-like › CorC_HlyC 0.56 32.0 3.28e-01 76.9% 56.7%
2098353 213.1.1.25 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_3 0.56 45.0 3.76e-01 91.2% 68.2%
5022436 327.7.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.56 43.0 4.50e-01 85.7% 97.6%
4174422 286.1.1.1 ↗ a+b complex topology › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › DAP_epimerase 0.56 44.0 3.96e-01 86.8% 87.7%
4116186 286.1.1.1 ↗ a+b complex topology › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › DAP_epimerase 0.55 44.0 3.50e-01 86.8% 65.8%
4086038 327.7.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.55 42.0 4.42e-01 82.4% 95.0%
3271043 286.1.1.1 ↗ a+b complex topology › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › DAP_epimerase 0.55 46.0 3.76e-01 97.8% 86.8%
4042899 286.1.1.1 ↗ a+b complex topology › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › DAP_epimerase 0.55 44.0 3.53e-01 87.9% 69.7%
4953632 217.2.1.1 ↗ a+b complex topology › FAD-binding domain-like › CorC/HlyC domain-like › CorC/HlyC domain-like › CorC_HlyC 0.55 32.0 3.30e-01 90.1% 60.0%
3855773 316.1.1.36 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › MTPAP-like_central 0.54 44.0 3.60e-01 90.1% 63.9%
3959452 327.5.1.6 ↗ a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-dom_DIP2-like 0.54 46.0 4.13e-01 95.6% 96.2%
3594151 2486.1.1.0 ↗ a/b three-layered sandwiches › ClpP/crotonase › ClpP/crotonase › ClpP/crotonase 0.54 42.0 3.04e-01 84.6% 68.8%
3588796 327.7.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.54 41.0 4.12e-01 82.4% 82.2%
5072460 327.7.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.54 43.0 4.44e-01 87.9% 95.3%
3646034 327.5.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins 0.54 46.0 4.02e-01 98.9% 94.7%
4971758 327.7.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.54 40.0 4.26e-01 81.3% 92.5%
5067906 327.7.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.54 43.0 4.35e-01 87.9% 96.7%
3419043 327.10.1.9 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › DnaA_N-like_STI 0.54 40.0 4.16e-01 82.4% 96.5%
5034898 327.7.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.54 43.0 4.39e-01 87.9% 95.3%
5078856 327.7.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like 0.54 42.0 4.25e-01 87.9% 93.3%
3511342 327.7.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like 0.53 42.0 4.22e-01 84.6% 88.9%
4955281 327.7.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › ZT_dimer 0.53 40.0 4.16e-01 81.3% 87.1%
3960051 327.5.1.3 ↗ a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-binding_C_2 0.53 42.0 4.05e-01 90.1% 99.1%
3974347 327.14.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › C-terminal domain of DNA Polymerase III subunit tau › C-terminal domain of DNA Polymerase III subunit tau › DNA_pol3_tau_5 0.53 38.0 3.66e-01 80.2% 64.5%
3270465 213.1.1.25 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_3 0.53 45.0 3.68e-01 97.8% 97.3%
2966282 224.1.1.2 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin 0.52 41.0 3.87e-01 85.7% 80.2%
5062497 213.1.1.25 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_3 0.52 41.0 3.47e-01 89.0% 66.5%
1313685 327.18.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › 40S ribosomal protein S7-A › 40S ribosomal protein S7-A › Ribosomal_S7e 0.52 38.0 3.78e-01 81.3% 84.0%
3289450 327.5.1.6 ↗ a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-dom_DIP2-like 0.51 40.0 3.77e-01 90.1% 90.8%
5021453 327.11.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.50 39.0 3.93e-01 86.8% 93.7%
4936367 2007.13.1.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Rossmann-like domains in magnesium chelatase catalytic subunit › Rossmann-like domains in magnesium chelatase catalytic subunit › CobN-Mg_chel 0.50 44.0 3.19e-01 98.9% 69.6%
3275431 224.1.1.0 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like 0.50 38.0 3.91e-01 82.4% 100.0%
4575341 286.1.1.1 ↗ a+b complex topology › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › Diaminopimelate epimerase-like › DAP_epimerase 0.50 42.0 3.62e-01 96.7% 61.0%