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SR-VP_0-2_scaffold_141_2071242_prodigal-single.1__X__X__00397

Bact-Vir

SR-VP_0-2_scaffold_141_2071242_prodigal-single.1__X__X__00397

Identity

Kingdom:
phage

Quality

90.9 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 12-120
PDB
Domain cluster: representative
CATH (50)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2rrnA01 3.30.70.2040 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 46.0 5.22e-01 71.6% 91.6%
2dt9A02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.68 46.0 5.23e-01 70.6% 94.9%
2qmwA03 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.67 44.0 5.16e-01 71.6% 96.1%
3tupA02 3.30.70.380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ferrodoxin-fold anticodon-binding domain 0.67 47.0 5.02e-01 73.4% 90.6%
4ushA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 44.0 4.55e-01 70.6% 72.8%
2lqjA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.64 47.0 5.03e-01 88.1% 89.4%
1m55A00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.64 57.0 4.71e-01 98.2% 85.5%
3ce8A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 43.0 4.71e-01 70.6% 85.4%
6c6uN00 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.63 52.0 5.42e-01 93.6% 96.9%
4cyuA00 3.30.70.560 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK 0.63 54.0 4.85e-01 93.6% 96.8%
3mcnA01 3.30.70.560 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK 0.63 53.0 4.83e-01 92.7% 98.0%
2m9kA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.63 46.0 4.92e-01 94.5% 89.2%
1zavA01 3.30.70.1730 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein L10, N-terminal RNA-binding domain 0.63 46.0 4.36e-01 78.0% 80.7%
2cg8B02 3.30.70.560 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK 0.62 51.0 4.86e-01 89.9% 84.1%
3mgjA00 3.30.70.2690 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › LOR/SDH bifunctional enzyme, conserved domain 0.62 45.0 4.76e-01 83.5% 86.5%
1q2lA02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.61 43.0 3.44e-01 73.4% 83.5%
5yppA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.61 46.0 4.96e-01 94.5% 97.8%
1fnoA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 41.0 4.18e-01 70.6% 95.5%
2mq8A00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.60 41.0 4.14e-01 70.6% 84.8%
3n01A00 3.30.70.2470 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Protein-tyrosine phosphatase receptor IA-2 ectodomain 0.60 45.0 4.98e-01 83.5% 100.0%
6h8oA00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.59 45.0 4.85e-01 99.1% 92.6%
1r9wA00 3.40.1310.10 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.59 50.0 4.65e-01 99.1% 72.5%
2pd1A01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 41.0 4.30e-01 70.6% 90.5%
1r89A03 3.30.70.590 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Poly(A) polymerase predicted RNA binding domain 0.59 52.0 4.84e-01 96.3% 84.3%
2r7rA04 3.30.70.2480 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 48.0 4.24e-01 88.1% 62.4%
4bbyA05 3.30.300.330 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › 0.58 45.0 4.52e-01 81.7% 85.2%
1f08B00 3.40.1310.10 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.58 49.0 4.43e-01 98.2% 68.3%
6vh5C03 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.58 43.0 4.62e-01 98.2% 95.5%
5t0oA02 3.30.70.1430 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.57 47.0 4.89e-01 98.2% 95.1%
4er8A00 3.30.70.1290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Transposase IS200-like 0.57 50.0 4.36e-01 97.2% 77.0%
2qrrA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.56 39.0 4.13e-01 87.2% 80.4%
4mt1A02 3.30.70.1430 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.56 46.0 4.78e-01 98.2% 95.1%
2v50D07 3.30.70.1440 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.56 42.0 4.48e-01 80.7% 97.9%
2jgbA01 3.30.760.10 Alpha Beta › 2-Layer Sandwich › RNA Cap, Translation Initiation Factor Eif4e › RNA Cap, Translation Initiation Factor Eif4e 0.56 43.0 3.72e-01 89.0% 52.0%
1iujA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 38.0 3.94e-01 70.6% 90.2%
3ns6A00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.55 43.0 4.51e-01 87.2% 92.9%
2fmaA00 3.30.1490.140 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Amyloidogenic glycoprotein, copper-binding domain 0.55 30.0 3.69e-01 100.0% 93.2%
2hw0A00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.54 44.0 4.32e-01 97.2% 82.6%
2bvfA03 3.40.462.20 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › 0.54 47.0 3.86e-01 99.1% 68.6%
1q8bA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 39.0 4.17e-01 83.5% 90.3%
1pbuA00 3.30.70.1010 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Translation elongation factor EF1B, gamma chain, conserved domain 0.53 47.0 4.16e-01 99.1% 71.6%
1j2vA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 44.0 4.53e-01 100.0% 97.0%
3rjaA02 3.40.462.20 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › 0.53 47.0 3.74e-01 100.0% 65.1%
6wl5A01 3.20.80.10 Alpha Beta › Alpha-Beta Barrel › Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A › Regulatory factor, effector binding domain 0.52 45.0 4.14e-01 98.2% 85.2%
1p1lA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 43.0 4.49e-01 100.0% 97.1%
3nlcA01 3.30.70.2700 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 35.0 4.04e-01 87.2% 100.0%
2lu1A00 3.30.70.2370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 38.0 4.07e-01 76.1% 94.4%
3f44A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 45.0 3.69e-01 100.0% 94.8%
1tuwA00 3.30.70.1090 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel. 0.50 40.0 4.11e-01 89.0% 93.4%
5koxA02 3.30.70.2450 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.50 34.0 3.79e-01 88.1% 89.5%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5024024 304.16.1.1 ↗ a+b two layers › Alpha-beta plaits › eEF-1beta-like › eEF-1beta-like › EF1_GNE 0.69 48.0 5.14e-01 71.6% 87.2%
5030229 304.16.1.1 ↗ a+b two layers › Alpha-beta plaits › eEF-1beta-like › eEF-1beta-like › EF1_GNE 0.69 48.0 5.19e-01 71.6% 91.1%
4314849 304.16.1.1 ↗ a+b two layers › Alpha-beta plaits › eEF-1beta-like › eEF-1beta-like › EF1_GNE 0.69 47.0 5.26e-01 70.6% 92.9%
4048122 304.9.1.71 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › SNU71_RBD 0.69 47.0 4.45e-01 70.6% 65.4%
4978258 304.16.1.1 ↗ a+b two layers › Alpha-beta plaits › eEF-1beta-like › eEF-1beta-like › EF1_GNE 0.68 47.0 5.21e-01 87.2% 88.6%
4533171 304.18.1.1 ↗ a+b two layers › Alpha-beta plaits › Anticodon-binding domain of PheRS › Anticodon-binding domain of PheRS › FDX-ACB 0.68 48.0 4.96e-01 73.4% 81.9%
3970813 304.12.1.0 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 0.68 47.0 4.99e-01 70.6% 86.2%
4275789 304.18.1.1 ↗ a+b two layers › Alpha-beta plaits › Anticodon-binding domain of PheRS › Anticodon-binding domain of PheRS › FDX-ACB 0.68 48.0 5.17e-01 73.4% 93.5%
4983809 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.67 46.0 5.24e-01 70.6% 97.5%
4964918 304.59.1.1 ↗ a+b two layers › Alpha-beta plaits › MTH889-like › MTH889-like › DUF211 0.67 44.0 4.78e-01 71.6% 81.1%
3513861 304.162.1.0 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain 0.67 46.0 5.19e-01 85.3% 96.2%
3404732 304.9.1.95 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › DUF4780 0.67 46.0 5.23e-01 71.6% 98.8%
4965197 304.8.1.2 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT 0.65 44.0 4.98e-01 70.6% 93.8%
4959045 304.8.1.81 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › REP_ORF2-G2P 0.65 60.0 5.31e-01 99.1% 80.0%
5056848 256.1.1.1 ↗ a+b two layers › MTH1598-like › MTH1598-like › MTH1598-like › Archease 0.64 35.0 4.26e-01 100.0% 86.2%
5027887 256.1.1.1 ↗ a+b two layers › MTH1598-like › MTH1598-like › MTH1598-like › Archease 0.63 35.0 4.15e-01 100.0% 81.4%
4030911 304.8.1.2 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT 0.63 43.0 4.84e-01 71.6% 91.7%
5022932 304.130.1.1 ↗ a+b two layers › Alpha-beta plaits › Uncharacterized protein MK0293 N-terminal domain › Uncharacterized protein MK0293 N-terminal domain › Ni_insertion 0.63 43.0 4.74e-01 70.6% 89.4%
3285005 304.45.1.1 ↗ a+b two layers › Alpha-beta plaits › 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK › 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK › HPPK 0.63 54.0 4.67e-01 94.5% 97.6%
4511949 304.48.1.74 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Phage_GPA 0.62 57.0 4.37e-01 100.0% 78.3%
3845338 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.62 46.0 4.84e-01 83.5% 87.4%
4173640 304.55.1.27 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Phage_GPA 0.62 57.0 4.20e-01 100.0% 84.7%
4170426 304.8.1.70 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Phage_GPA 0.62 57.0 4.16e-01 100.0% 81.8%
4218099 304.55.1.1 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Gemini_AL1 0.62 56.0 5.22e-01 99.1% 91.9%
3949560 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.62 45.0 4.91e-01 92.7% 92.2%
4098707 304.159.1.1 ↗ a+b two layers › Alpha-beta plaits › Alpha-beta plait domain in NisB › Alpha-beta plait domain in NisB › Lant_dehydr_C 0.62 48.0 4.98e-01 89.0% 89.0%
3172782 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.62 45.0 5.02e-01 83.5% 98.8%
3675857 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.61 47.0 3.93e-01 94.5% 47.6%
4959915 256.1.1.1 ↗ a+b two layers › MTH1598-like › MTH1598-like › MTH1598-like › Archease 0.61 34.0 4.06e-01 100.0% 82.9%
5019384 304.39.1.0 ↗ a+b two layers › Alpha-beta plaits › Mechanosensitive channel protein MscS (YggB), C-terminal domain › Mechanosensitive channel protein MscS (YggB), C-terminal domain 0.61 44.0 4.70e-01 75.2% 89.5%
4443601 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.61 43.0 4.72e-01 86.2% 92.9%
3952812 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.60 46.0 4.97e-01 100.0% 98.9%
5017989 304.4.1.82 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › DUF3303 0.60 40.0 4.37e-01 70.6% 83.3%
3999424 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.60 47.0 4.77e-01 95.4% 84.5%
4988829 304.110.1.1 ↗ a+b two layers › Alpha-beta plaits › Acylphosphatase-like › Acylphosphatase-like › Acylphosphatase 0.60 45.0 4.56e-01 98.2% 80.0%
3941364 304.9.1.36 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_10 0.60 46.0 4.76e-01 87.2% 85.7%
4001719 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.59 45.0 4.77e-01 88.1% 92.6%
3279556 304.6.1.5 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › Cytokin-bind 0.59 44.0 3.44e-01 80.7% 48.0%
5005033 304.39.1.0 ↗ a+b two layers › Alpha-beta plaits › Mechanosensitive channel protein MscS (YggB), C-terminal domain › Mechanosensitive channel protein MscS (YggB), C-terminal domain 0.58 39.0 4.43e-01 76.1% 93.8%
5023983 304.130.1.1 ↗ a+b two layers › Alpha-beta plaits › Uncharacterized protein MK0293 N-terminal domain › Uncharacterized protein MK0293 N-terminal domain › Ni_insertion 0.58 39.0 4.10e-01 70.6% 82.0%
3597727 304.110.1.0 ↗ a+b two layers › Alpha-beta plaits › Acylphosphatase-like › Acylphosphatase-like 0.57 48.0 4.45e-01 93.6% 96.4%
4502232 304.162.1.1 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH 0.55 38.0 4.31e-01 73.4% 100.0%
3280543 210.1.3.5 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases › GATase_7 0.55 42.0 3.30e-01 83.5% 97.6%
4980881 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.54 40.0 4.37e-01 91.7% 100.0%
3319663 10.10.1.1 ↗ beta sandwiches › jelly-roll › Lipase/lipooxygenase domain (PLAT/LH2 domain) › Lipase/lipooxygenase domain (PLAT/LH2 domain) › PLAT 0.54 41.0 3.80e-01 81.7% 93.1%
1312366 304.28.1.1 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › ACR_tran 0.54 41.0 4.42e-01 83.5% 96.7%
4954583 210.1.3.5 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases › GATase_7 0.54 41.0 3.27e-01 83.5% 96.7%
3184500 304.7.1.0 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.53 35.0 3.94e-01 89.9% 90.0%
4682347 304.6.1.3 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.52 45.0 3.50e-01 100.0% 56.7%
3205744 304.6.1.3 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.52 45.0 3.43e-01 100.0% 63.5%
4051078 304.4.1.71 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › DUF4937 0.51 45.0 4.47e-01 99.1% 97.4%
4854269 304.4.1.7 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › Cyclase_polyket 0.51 40.0 4.09e-01 87.2% 88.5%
3280191 304.4.1.7 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › Cyclase_polyket 0.51 40.0 4.08e-01 88.1% 96.2%
4230728 304.4.1.70 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › PF29828 0.50 45.0 4.30e-01 100.0% 94.6%
4566039 304.4.1.4 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › ABM 0.50 39.0 4.03e-01 83.5% 94.0%