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NC_070781.1__YP_010651148.1__PP453_gp020__00020

Bact-Vir

NC_070781.1__YP_010651148.1__PP453_gp020__00020

Identity

Accession:
NC_070781 ↗
Kingdom:
phage

Quality

70.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Stanwilliamsviridae› Tomasvirus› Streptomyces_phage_Tomas

TaxID: 2914443

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 3-67
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6abqB00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.64 44.0 3.76e-01 72.3% 88.7%
2iieA01 4.10.520.10 Few Secondary Structures › Irregular › HU Protein; Chain A › IHF-like DNA-binding proteins 0.62 43.0 3.67e-01 72.3% 54.6%
8ctsB01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.57 41.0 3.75e-01 75.4% 59.8%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4420382 5051.1.1.18 ↗ alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Spore_permease 0.85 58.0 3.56e-01 75.4% 13.1%
3498339 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.85 69.0 6.18e-01 84.6% 97.6%
3439843 101.1.1.270 ↗ alpha arrays › HTH › HTH › Three-helical HTH › A_thal_3526 0.81 56.0 5.00e-01 70.8% 74.1%
5070097 4070.1.1.2 ↗ alpha arrays › FtsH protease domain-like › FtsH protease domain-like › FtsH protease domain-like › Peptidase_M50 0.77 56.0 3.75e-01 80.0% 20.6%
3983978 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.70 47.0 3.34e-01 70.8% 23.9%
3268481 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.63 51.0 5.00e-01 87.7% 87.1%
D2 medium residues 73-123
PDB
Domain cluster: representative
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1whuA00 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.81 69.0 5.47e-01 96.1% 66.3%
4ye6A02 1.10.10.2420 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.78 66.0 6.39e-01 96.1% 98.3%
3lcnB00 1.10.340.40 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain 0.74 65.0 5.28e-01 100.0% 55.7%
4nmyA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.73 63.0 4.24e-01 100.0% 72.1%
7ccmB01 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.71 60.0 4.38e-01 96.1% 51.0%
1xg7A02 1.10.340.30 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2 0.69 59.0 4.35e-01 100.0% 41.3%
4s3mB02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.68 58.0 4.63e-01 98.0% 61.3%
3er9B01 1.20.1270.320 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Poxvirus poly(A) polymerase, N domain 0.68 46.0 3.63e-01 70.6% 41.5%
2yqzA02 1.10.8.900 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.67 46.0 4.21e-01 70.6% 97.1%
2khmA01 1.10.10.1350 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Spidroin domain, C-terminal domain 0.67 55.0 4.50e-01 100.0% 64.8%
2zxyA00 1.10.760.10 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain 0.66 57.0 4.86e-01 100.0% 90.7%
6tmfT00 1.10.60.20 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › Ribosomal protein S17 0.65 56.0 5.26e-01 100.0% 84.4%
2q00B00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.65 44.0 3.43e-01 72.5% 91.0%
2kjgA00 1.20.120.970 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.64 54.0 4.47e-01 100.0% 55.6%
4usaA02 1.10.150.120 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › [2Fe-2S]-binding domain 0.64 53.0 4.22e-01 100.0% 44.5%
3tjmA02 1.10.1470.20 Mainly Alpha › Orthogonal Bundle › Protein Yjbj; Chain: A; › Fatty acid synthase; domain 2 0.63 50.0 4.19e-01 90.2% 64.4%
1ij5A03 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.63 47.0 3.57e-01 84.3% 34.4%
1x9fC00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.62 51.0 3.81e-01 100.0% 91.9%
1h1oA02 1.10.760.10 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain 0.61 51.0 4.48e-01 100.0% 85.7%
3e3rB01 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.61 49.0 4.28e-01 96.1% 78.8%
4dccA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.60 50.0 4.49e-01 96.1% 83.8%
2e1qC10 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.59 47.0 3.54e-01 96.1% 35.9%
2x43S00 6.10.140.1430 Special › Helix non-globular › Helix Hairpins › 0.56 40.0 3.78e-01 80.4% 95.5%
2l09A01 1.10.8.550 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Proto-chlorophyllide reductase 57 kD subunit B 0.56 37.0 3.70e-01 70.6% 67.3%
1fcdC01 1.10.760.10 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain 0.55 43.0 3.98e-01 100.0% 98.7%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.52 37.0 3.22e-01 74.5% 53.9%
3nzpB03 1.20.58.930 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.52 42.0 3.80e-01 100.0% 84.8%
1x4oA00 1.10.10.790 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Surp module 0.52 41.0 3.76e-01 100.0% 76.9%
4ga4A01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.52 45.0 4.16e-01 100.0% 77.6%
7odyC01 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.52 42.0 3.56e-01 94.1% 62.0%
2ntxA01 1.20.58.2010 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › PRONE domain, subdomain 1 0.52 42.0 2.90e-01 100.0% 76.2%
1z8sA02 6.10.140.360 Special › Helix non-globular › Helix Hairpins › 0.51 34.0 3.57e-01 70.6% 92.9%
3lynB00 1.20.150.10 Mainly Alpha › Up-down Bundle › Lysin › Fertilization protein 0.51 40.0 3.18e-01 96.1% 94.4%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3839206 101.11.1.1 ↗ alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase 0.85 73.0 6.27e-01 96.1% 78.8%
3427512 101.1.17.0 ↗ alpha arrays › HTH › HTH › FF domain 0.83 74.0 6.85e-01 100.0% 83.1%
3483536 5059.1.1.0 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter 0.79 54.0 4.09e-01 72.5% 35.0%
4595954 101.11.1.0 ↗ alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 0.74 63.0 5.46e-01 100.0% 81.2%
4934319 101.1.2.947 ↗ alpha arrays › HTH › HTH › winged helix domain › PF27234 0.74 62.0 5.83e-01 96.1% 82.5%
3989754 592.2.1.0 ↗ alpha arrays › PWI domain-like › YugE-like › YugE-like 0.72 62.0 5.64e-01 100.0% 87.1%
4255518 4973.1.1.0 ↗ alpha bundles › helical domain in DNA primase DnaG catalytic core › helical domain in DNA primase DnaG catalytic core › helical domain in DNA primase DnaG catalytic core 0.72 59.0 5.28e-01 100.0% 71.2%
4978129 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.71 59.0 3.47e-01 94.1% 11.7%
3573598 101.1.2.154 ↗ alpha arrays › HTH › HTH › winged helix domain › CDT1_C 0.71 61.0 4.82e-01 100.0% 58.2%
5009771 2.21.1.5 ↗ beta barrels › OB-fold › Small protein B (SmpB) › Small protein B (SmpB) › PF27234 0.71 59.0 4.19e-01 100.0% 34.1%
3264673 101.1.2.498 ↗ alpha arrays › HTH › HTH › winged helix domain › PF25870 0.70 60.0 4.52e-01 100.0% 72.3%
4501322 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.69 57.0 3.81e-01 100.0% 29.6%
4600245 3640.1.1.1 ↗ alpha duplicates or obligate multimers › Minor ampullate fibroin 1 C-terminal domain › Minor ampullate fibroin 1 C-terminal domain › Minor ampullate fibroin 1 C-terminal domain › Spidroin_MaSp 0.69 51.0 4.51e-01 82.4% 70.9%
3928650 101.1.1.315 ↗ alpha arrays › HTH › HTH › Three-helical HTH › CCD_aECM 0.66 52.0 5.02e-01 94.1% 91.7%
4062718 130.1.1.3 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Rho_N 0.65 43.0 4.35e-01 74.5% 70.0%
4927979 192.4.1.0 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.64 57.0 5.41e-01 100.0% 88.3%
None — 0.64 53.0 4.70e-01 100.0% 64.0%
4097522 601.25.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › TrmE connector domain › TrmE connector domain › MnmE_helical 0.64 44.0 3.17e-01 74.5% 67.1%
3744474 109.54.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13 › C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13 › Utp12 0.63 53.0 4.27e-01 98.0% 49.0%
3626359 101.1.1.315 ↗ alpha arrays › HTH › HTH › Three-helical HTH › CCD_aECM 0.62 50.0 4.95e-01 94.1% 100.0%
4540906 101.1.4.82 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › DUF3603 0.60 42.0 3.48e-01 72.5% 42.6%
3401277 110.1.1.28 ↗ alpha arrays › DEATH domain › DEATH domain › DEATH domain › Dredd_2nd 0.60 40.0 3.37e-01 72.5% 95.0%
5058985 7064.1.1.1 ↗ alpha bundles › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › VIT1 0.59 47.0 3.53e-01 100.0% 51.9%
3991367 101.1.2.558 ↗ alpha arrays › HTH › HTH › winged helix domain › CCD_aECM 0.58 45.0 4.51e-01 96.1% 96.4%
5030095 192.4.1.0 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.58 48.0 4.35e-01 100.0% 72.0%
3797372 106.1.1.1 ↗ alpha arrays › Globin-like › Globin-like › Globin-like › Globin 0.58 47.0 3.43e-01 100.0% 39.4%
3913395 110.1.1.0 ↗ alpha arrays › DEATH domain › DEATH domain › DEATH domain 0.57 40.0 3.46e-01 74.5% 94.1%
3360431 4030.1.1.0 ↗ alpha bundles › alpha-helical domain in subunits of heterodimeric actin filament capping protein Capz › alpha-helical domain in subunits of heterodimeric actin filament capping protein Capz › alpha-helical domain in subunits of heterodimeric actin filament capping protein Capz 0.56 45.0 4.27e-01 100.0% 76.9%
3883722 110.1.1.0 ↗ alpha arrays › DEATH domain › DEATH domain › DEATH domain 0.56 42.0 3.50e-01 82.4% 76.8%
4329065 4953.1.1.0 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.55 44.0 3.91e-01 100.0% 75.3%
4994581 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.54 37.0 2.52e-01 72.5% 20.0%
5061373 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.51 36.0 3.08e-01 74.5% 44.7%
5059273 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.51 35.0 3.03e-01 72.5% 43.5%