←Back to structures

NC_028762.1__YP_009195525.1__AVT59_gp107__00107

Bact-Vir

NC_028762.1__YP_009195525.1__AVT59_gp107__00107

Identity

Accession:
NC_028762 ↗
Kingdom:
phage

Quality

96.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Straboviridae› Bragavirus› Proteus_phage_vB_PmiM_Pm5461

TaxID: 1636250

Cluster

View cluster (8 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 2-70
PDB
Domain cluster: representative
CATH (55)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5mj6A03 2.60.40.1910 Mainly Beta › Sandwich › Immunoglobulin-like › 0.74 51.0 4.91e-01 88.4% 62.5%
3weeA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.70 54.0 4.05e-01 87.0% 65.6%
2dbbA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.69 48.0 4.39e-01 73.9% 81.7%
3mfiA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.68 48.0 4.04e-01 73.9% 55.5%
4a4yA01 2.60.200.50 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.66 46.0 4.03e-01 72.5% 98.0%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.66 46.0 3.99e-01 73.9% 56.9%
2v3sA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.65 44.0 4.03e-01 71.0% 96.9%
1jx4A04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.65 46.0 4.11e-01 73.9% 59.2%
1unnC00 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.65 44.0 3.87e-01 72.5% 48.6%
3nkgA00 2.60.120.790 Mainly Beta › Sandwich › Jelly Rolls › 0.64 56.0 4.19e-01 97.1% 41.8%
6julA02 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.64 45.0 4.07e-01 73.9% 59.4%
2jvuA00 2.60.40.2290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.64 44.0 3.92e-01 72.5% 50.0%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.62 52.0 4.10e-01 100.0% 41.3%
3rj2X00 2.60.120.1150 Mainly Beta › Sandwich › Jelly Rolls › 0.62 56.0 4.50e-01 100.0% 65.4%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.62 53.0 4.89e-01 100.0% 73.4%
1i1gA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.62 43.0 4.23e-01 73.9% 96.1%
3b8fB00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.61 53.0 4.24e-01 100.0% 52.1%
2hlcA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.61 48.0 4.27e-01 98.6% 58.7%
3loiA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.60 44.0 3.41e-01 95.7% 33.8%
4llgM00 3.10.20.510 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNA polymerase inhibitor 0.59 39.0 4.32e-01 72.5% 94.0%
1ca1A02 2.60.60.20 Mainly Beta › Sandwich › Lipoxygenase-1 › PLAT/LH2 domain 0.59 51.0 4.31e-01 100.0% 65.0%
3liuA01 2.60.40.3160 Mainly Beta › Sandwich › Immunoglobulin-like › 0.59 54.0 4.44e-01 100.0% 87.3%
3bh1A03 3.40.140.40 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Domain of unknown function (DUF1846), C-terminal subdomain 0.59 52.0 4.08e-01 100.0% 83.6%
2orzA01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.57 49.0 3.87e-01 100.0% 44.8%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.57 39.0 3.82e-01 72.5% 71.1%
4lplA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.57 49.0 3.96e-01 100.0% 48.6%
3wqbA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.57 48.0 3.73e-01 98.6% 63.3%
1r9fA01 3.30.390.180 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › RNA silencing suppressor P19 0.57 49.0 4.23e-01 97.1% 77.1%
2z8lA01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.57 48.0 4.15e-01 100.0% 82.1%
1uyvA01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.56 46.0 3.14e-01 92.8% 63.0%
7c2fB01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.56 42.0 3.96e-01 81.2% 73.3%
3bn6A00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.56 49.0 3.79e-01 100.0% 44.3%
1rfeA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 46.0 3.74e-01 97.1% 73.5%
1txkA01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.54 47.0 3.00e-01 100.0% 31.3%
1wv4B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 46.0 3.58e-01 97.1% 53.2%
1vl7A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 45.0 3.71e-01 97.1% 56.3%
7ylrA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.53 37.0 3.27e-01 72.5% 65.7%
2htdB00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 45.0 3.80e-01 97.1% 74.2%
2fhqA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 45.0 3.70e-01 97.1% 73.3%
2mv2A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.53 46.0 3.66e-01 100.0% 70.9%
3gasB02 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 45.0 3.45e-01 97.1% 66.7%
3in6A02 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 45.0 3.88e-01 98.6% 89.7%
2dk6A01 3.30.720.50 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.53 29.0 2.67e-01 71.0% 37.2%
1wmhA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.53 47.0 4.43e-01 100.0% 100.0%
6z9cA01 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.53 45.0 3.84e-01 100.0% 60.7%
4b7lA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 41.0 3.66e-01 100.0% 59.0%
2aq6A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 44.0 3.57e-01 97.1% 49.0%
4uzgA01 2.60.40.740 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 43.0 3.45e-01 97.1% 58.3%
6rptC00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 46.0 3.92e-01 100.0% 61.6%
2fg9A01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 43.0 3.41e-01 97.1% 49.7%
3rhaA00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.51 36.0 2.26e-01 75.4% 67.3%
2bkfA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.51 45.0 4.25e-01 100.0% 98.8%
3mb5A01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.51 34.0 3.52e-01 100.0% 75.8%
1qltA03 3.40.462.10 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › FAD-linked oxidases, C-terminal domain 0.51 37.0 2.64e-01 79.7% 23.8%
4iauA01 2.60.20.10 Mainly Beta › Sandwich › Gamma-B Crystallin; domain 1 › Crystallins 0.50 45.0 4.36e-01 100.0% 91.0%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3217608 284.1.2.1 ↗ a+b two layers › FKBP-like › FKBP-like › Conserved carboxy-terminal domain of oxidative-stress-responsive kinase 1-like kinases › OSR1_C 0.69 47.0 4.18e-01 71.0% 96.0%
394175 302.1.1.1 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.68 48.0 4.00e-01 73.9% 53.7%
3988557 2003.1.5.12 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › N6_N4_Mtase 0.66 52.0 3.53e-01 88.4% 30.4%
3969006 3115.6.1.2 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › PF28597 0.66 42.0 4.73e-01 72.5% 97.8%
3216210 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.66 45.0 5.02e-01 72.5% 98.0%
3615237 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.65 55.0 3.47e-01 94.2% 20.6%
3972526 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.64 46.0 4.65e-01 76.8% 95.7%
5081134 3986.2.1.0 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.64 48.0 5.06e-01 100.0% 95.0%
2323826 4187.2.1.1 ↗ a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 › NAGPA 0.62 42.0 4.07e-01 71.0% 64.1%
3744271 3662.1.1.3 ↗ a+b two layers › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › PAC4 0.62 41.0 3.43e-01 100.0% 39.2%
5025706 304.6.1.1 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › FAD-oxidase_C 0.61 42.0 2.92e-01 72.5% 36.7%
4654177 1119.1.1.1 ↗ a+b complex topology › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › BioW 0.61 43.0 2.98e-01 73.9% 21.6%
4078508 302.1.1.1 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.60 42.0 3.69e-01 76.8% 53.9%
4962335 3115.5.1.1 ↗ a+b two layers › GP2-like › phenylacetate-CoA oxygenase subunit PaaB › phenylacetate-CoA oxygenase subunit PaaB › PaaB 0.59 42.0 4.28e-01 73.9% 80.0%
3285401 3986.2.1.0 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.59 46.0 4.54e-01 100.0% 81.3%
4026734 2003.1.5.73 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.59 51.0 3.50e-01 100.0% 57.3%
3649476 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.58 49.0 3.19e-01 100.0% 28.0%
3784003 302.1.1.0 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.57 42.0 3.28e-01 79.7% 92.9%
3790561 210.2.1.1 ↗ a+b four layers › Ntn/PP2C › Protein serine/threonine phosphatase 2C, catalytic domain › Protein serine/threonine phosphatase 2C, catalytic domain › PP2C 0.57 47.0 3.25e-01 100.0% 58.8%
3717721 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.56 51.0 3.40e-01 100.0% 68.7%
3467990 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.56 46.0 2.75e-01 100.0% 16.5%
3517068 3115.1.1.6 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › DUF4494 0.56 38.0 3.88e-01 72.5% 87.7%
3788749 6109.1.1.0 ↗ a+b two layers › N-terminal domain of chitin biosynthesis protein CHS6 › N-terminal domain of chitin biosynthesis protein CHS6 › N-terminal domain of chitin biosynthesis protein CHS6 0.55 47.0 3.79e-01 100.0% 48.7%
3461676 10.32.1.212 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › GUB_WAK_bind 0.55 46.0 3.44e-01 100.0% 41.5%
3501768 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.54 38.0 3.81e-01 72.5% 71.4%
3579804 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 41.0 3.68e-01 100.0% 57.0%
5053865 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.54 39.0 3.66e-01 78.3% 96.7%
3228120 11.1.1.408 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF281 0.53 38.0 3.35e-01 73.9% 59.2%
4031235 3986.2.1.2 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd › DUF2922 0.53 42.0 4.27e-01 92.8% 97.1%
5005349 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.53 44.0 2.74e-01 98.6% 14.1%
3594014 2007.2.3.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II 0.52 42.0 3.00e-01 91.3% 91.3%
3589173 11.24.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › N-terminal Ig-like domain in baseplate protein ORF48 › N-terminal Ig-like domain in baseplate protein ORF48 › BppU_N 0.52 45.0 3.82e-01 100.0% 58.3%
3395224 11.1.1.179 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.52 38.0 3.47e-01 100.0% 57.9%
3289401 274.1.1.0 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.52 42.0 3.55e-01 95.7% 75.4%
5040531 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.52 43.0 3.61e-01 94.2% 61.6%
3261440 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.52 35.0 3.59e-01 73.9% 75.4%
3772640 10.21.1.1 ↗ beta sandwiches › jelly-roll › Jelly-roll domain in ADAMTS13 › Jelly-roll domain in ADAMTS13 › ADAMTS_spacer1 0.51 44.0 3.71e-01 100.0% 58.4%
3182274 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.51 45.0 3.16e-01 100.0% 42.1%
362818 221.1.1.17 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Stap_Strp_tox_C 0.51 43.0 3.68e-01 100.0% 56.8%
3277542 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.50 43.0 3.42e-01 100.0% 75.5%