Back to structures

NC_028882.1__YP_009206113.1__AVT15_gp053__00148

Bact-Vir

NC_028882.1__YP_009206113.1__AVT15_gp053__00148

Identity

Accession:
NC_028882 ↗
Kingdom:
phage

Quality

89.7 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 4-59
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3i3lA02 3.30.390.160 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.73 55.0 4.23e-01 96.4% 36.8%
2kvtA00 3.30.730.30 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › YaiA protein 0.72 57.0 5.29e-01 96.4% 69.0%
2y7bA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.66 48.0 3.67e-01 83.9% 32.8%
1nf3C00 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.66 54.0 4.28e-01 94.6% 57.7%
3ro6C01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.66 54.0 4.42e-01 92.9% 98.1%
2oq1A03 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.64 45.0 3.72e-01 96.4% 42.0%
6cngA03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.63 56.0 4.25e-01 100.0% 93.0%
2n3gA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.63 48.0 4.47e-01 94.6% 65.3%
2f9wA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.62 49.0 3.76e-01 100.0% 37.4%
3wasA00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.62 46.0 2.87e-01 85.7% 25.7%
4e19A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.60 53.0 4.04e-01 100.0% 50.4%
4indA01 2.60.120.1320 Mainly Beta › Sandwich › Jelly Rolls › 0.59 43.0 3.20e-01 76.8% 93.2%
4d6wA03 2.30.29.130 Mainly Beta › Roll › PH-domain like › 0.58 43.0 3.65e-01 82.1% 47.4%
3ddmA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.58 48.0 3.76e-01 94.6% 88.8%
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 47.0 4.41e-01 94.6% 76.1%
1erzA00 3.60.110.10 Alpha Beta › 4-Layer Sandwich › Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase › Carbon-nitrogen hydrolase 0.57 47.0 3.09e-01 100.0% 63.0%
2k75A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.57 42.0 3.53e-01 91.1% 44.7%
4c89C00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.57 43.0 2.69e-01 85.7% 78.2%
1bf5A04 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.57 49.0 3.95e-01 100.0% 63.7%
4rgyA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.56 45.0 3.09e-01 96.4% 23.6%
1mixA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 37.0 3.31e-01 83.9% 43.0%
1wp0A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.55 45.0 3.37e-01 96.4% 86.3%
6zj8D01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.55 34.0 2.74e-01 92.9% 29.8%
1cx8A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.55 44.0 2.87e-01 94.6% 97.1%
5cxxB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 43.0 2.89e-01 96.4% 23.0%
5aj3P00 3.30.1320.10 Alpha Beta › 2-Layer Sandwich › S16 Ribosomal Protein; Chain: A; › Ribosomal protein S16 0.54 45.0 3.69e-01 100.0% 57.3%
4kcaA03 2.40.128.10 Mainly Beta › Beta Barrel › Lipocalin › 0.54 34.0 2.96e-01 71.4% 36.1%
3bxpB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 39.0 2.71e-01 87.5% 100.0%
3fm2A00 3.40.1570.10 Alpha Beta › 3-Layer(aba) Sandwich › Heme iron utilization protein-like fold › HemS/ChuS/ChuX like domains 0.53 46.0 3.54e-01 100.0% 49.6%
1qlmA02 3.30.1030.10 Alpha Beta › 2-Layer Sandwich › Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 2 › Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 2 0.52 40.0 2.94e-01 94.6% 85.4%
1wqsA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.52 39.0 3.21e-01 82.1% 86.4%
3p06A00 3.30.230.110 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.52 43.0 3.02e-01 96.4% 56.2%
4i1sB00 4.10.80.340 Few Secondary Structures › Irregular › Rhinovirus 14, subunit 4 › 0.51 36.0 3.67e-01 100.0% 84.6%
3qt2A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 41.0 3.47e-01 100.0% 92.0%
3o2iA00 3.30.70.2710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 37.0 3.16e-01 78.6% 50.5%
3icsA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.51 34.0 2.31e-01 71.4% 16.3%
6gp1A00 3.30.1300.40 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 0.51 34.0 3.28e-01 71.4% 58.5%
4id2A00 2.40.128.510 Mainly Beta › Beta Barrel › Lipocalin › Protein of unknown function DUF4738 0.50 39.0 3.13e-01 94.6% 75.0%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4929236 3604.1.1.1 a+b two layers › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Ni_insertion 0.77 50.0 4.70e-01 71.4% 54.3%
4524698 3604.1.1.1 a+b two layers › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Ni_insertion 0.75 50.0 4.81e-01 71.4% 60.0%
4960997 3604.1.1.1 a+b two layers › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Ni_insertion 0.72 49.0 4.61e-01 73.2% 57.1%
119245 252.3.1.1 a+b two layers › DNA-binding domain › Uncharacterized protein yaiA › Uncharacterized protein yaiA › YaiA 0.72 57.0 5.29e-01 96.4% 69.0%
4975236 3604.1.1.1 a+b two layers › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Ni_insertion 0.71 44.0 4.25e-01 71.4% 53.8%
4935912 3604.1.1.1 a+b two layers › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Ni_insertion 0.70 47.0 4.40e-01 73.2% 55.7%
4982570 3604.1.1.1 a+b two layers › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Ni_insertion 0.70 46.0 4.37e-01 71.4% 55.7%
5031772 3604.1.1.1 a+b two layers › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Ni_insertion 0.69 47.0 4.31e-01 71.4% 57.3%
1807411 101.1.2.215 alpha arrays › HTH › HTH › winged helix domain › CmlS_C 0.69 53.0 4.16e-01 96.4% 38.1%
4514946 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.68 58.0 4.06e-01 100.0% 33.3%
5055744 5.1.3.40 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Arylsulfotran_2 0.67 56.0 3.42e-01 94.6% 32.4%
4998648 4312.1.1.0 a+b two layers › RelE-like › RelE-like › RelE-like 0.64 50.0 4.17e-01 83.9% 51.6%
4932428 65.1.1.0 beta sandwiches › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases 0.64 55.0 5.15e-01 100.0% 90.0%
5053359 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.64 41.0 3.69e-01 71.4% 46.3%
3902357 7.1.1.1 beta barrels › PDZ domain › PDZ domain › PDZ domain › PDZ 0.64 51.0 4.00e-01 94.6% 52.6%
4024732 295.1.1.40 a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › Microp_apicomplexa_10 0.63 51.0 4.55e-01 89.3% 62.5%
4020571 2004.1.1.162 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Rad51 0.62 44.0 2.83e-01 76.8% 17.9%
3718687 220.1.1.175 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_31 0.62 53.0 3.96e-01 100.0% 64.0%
4534897 3234.1.1.2 a+b two layers › GerBC protein › GerBC protein › GerBC protein › Spore_GerAC, Spore_GerAC_N 0.62 50.0 3.19e-01 98.2% 41.8%
3192520 2004.1.1.146 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ATPase 0.61 47.0 2.99e-01 83.9% 17.8%
3586665 295.1.1.0 a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.60 45.0 4.62e-01 87.5% 85.5%
4213862 246.1.1.1 a+b four layers › Carbon-nitrogen hydrolase-like › Carbon-nitrogen hydrolase › Carbon-nitrogen hydrolase › CN_hydrolase 0.59 51.0 3.34e-01 100.0% 66.9%
3250857 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 50.0 4.41e-01 100.0% 95.6%
4927462 2484.1.1.59 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › NurA 0.59 51.0 3.31e-01 100.0% 27.8%
3788285 395.1.1.4 few secondary structure elements › Midkine-related › Midkine-related › Midkine-related › Flocculin_t3 0.59 44.0 4.63e-01 82.1% 94.0%
139759 218.1.1.1 a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.58 46.0 3.86e-01 94.6% 85.0%
3738197 277.1.1.1 a+b two layers › PX domain › PX domain › PX domain › PX 0.58 45.0 3.44e-01 94.6% 72.7%
3913820 5.1.4.13 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › FG-GAP 0.58 44.0 2.79e-01 89.3% 25.3%
3739022 246.1.1.1 a+b four layers › Carbon-nitrogen hydrolase-like › Carbon-nitrogen hydrolase › Carbon-nitrogen hydrolase › CN_hydrolase 0.58 48.0 3.17e-01 100.0% 71.2%
3396736 65.1.1.0 beta sandwiches › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases 0.58 48.0 4.68e-01 100.0% 86.2%
3598422 222.1.1.0 a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase 0.57 37.0 3.18e-01 71.4% 38.0%
319085 208.1.1.8 beta duplicates or obligate multimers › Single-stranded left-handed beta-helix › Trimeric LpxA-like enzymes › Trimeric LpxA-like enzymes › B_solenoid_ydck 0.57 44.0 2.86e-01 92.9% 17.9%
3217119 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.57 47.0 2.99e-01 100.0% 20.9%
4014945 65.1.1.0 beta sandwiches › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases 0.57 46.0 4.39e-01 100.0% 87.1%
3572103 220.1.1.74 beta barrels › PH domain-like › PH domain-like › PH domain-like › PIG-H 0.56 47.0 3.66e-01 98.2% 41.5%
4951490 223.1.1.14 a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.56 36.0 3.04e-01 71.4% 36.0%
5029482 295.1.1.0 a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.56 44.0 4.06e-01 92.9% 73.8%
3250206 65.1.1.0 beta sandwiches › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases 0.55 45.0 4.20e-01 100.0% 88.0%
4971602 316.1.1.45 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › DUF4269 0.55 37.0 2.80e-01 71.4% 26.4%
3744517 277.1.1.1 a+b two layers › PX domain › PX domain › PX domain › PX 0.55 43.0 3.56e-01 94.6% 77.5%
3250605 277.1.1.1 a+b two layers › PX domain › PX domain › PX domain › PX 0.55 43.0 3.49e-01 94.6% 72.0%
3522960 277.1.1.1 a+b two layers › PX domain › PX domain › PX domain › PX 0.54 42.0 3.27e-01 92.9% 70.3%
3411134 5.1.4.12 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Sema 0.54 43.0 2.60e-01 98.2% 45.0%
5072529 512.1.1.1 a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.54 43.0 3.83e-01 96.4% 72.2%
3599634 4261.1.1.4 a+b two layers › TrkA C-terminal domain-like › TrkA C-terminal domain-like › TrkA C-terminal domain-like › Slowpoke_C 0.53 36.0 2.99e-01 96.4% 38.5%
3624183 206.1.1.20 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › PK_Tyr_Ser-Thr 0.53 45.0 2.80e-01 98.2% 47.6%
3997550 1.1.1.1 beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp 0.53 34.0 2.59e-01 71.4% 23.9%
4966168 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.53 40.0 2.53e-01 92.9% 14.2%
4493573 4964.1.1.2 alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › RNA_pol 0.53 41.0 2.93e-01 92.9% 37.0%
5073695 512.1.1.1 a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.52 40.0 3.52e-01 94.6% 63.0%
3598159 224.1.1.0 a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like 0.52 41.0 3.25e-01 91.1% 53.5%
3799677 7026.1.1.0 beta meanders › N-terminal region of lipid transporter Vps13 › N-terminal region of lipid transporter Vps13 › N-terminal region of lipid transporter Vps13 0.52 41.0 2.72e-01 92.9% 37.9%
4025365 220.1.1.74 beta barrels › PH domain-like › PH domain-like › PH domain-like › PIG-H 0.52 40.0 3.44e-01 100.0% 49.1%
5013239 220.1.1.219 beta barrels › PH domain-like › PH domain-like › PH domain-like › CheF-arch 0.51 40.0 3.33e-01 98.2% 46.4%
5076310 316.1.1.2 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.51 35.0 2.62e-01 71.4% 25.2%
3889863 277.1.1.1 a+b two layers › PX domain › PX domain › PX domain › PX 0.50 40.0 3.31e-01 94.6% 93.3%