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MW749006.1__QXN70532.1__AGENTSMITH_128__00126

Bact-Vir

MW749006.1__QXN70532.1__AGENTSMITH_128__00126

Identity

Accession:
MW749006 ↗
Kingdom:
phage

Quality

76.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Bacillus_phage_vB_BspM_AgentSmith

TaxID: 2836110

Cluster

View cluster (2 members)

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 high residues 297-491
PDB
Domain cluster: rep: MW735835.1__QTH80356.1__PA10_00156__00156__D313-410_469-520
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3872309 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 0.50 24.0 2.40e-01 100.0% 42.4%
D2 medium residues 1-70
PDB
Domain cluster: representative
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ynjJ02 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.63 40.0 4.25e-01 92.9% 74.2%
1qqgA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 40.0 3.54e-01 71.4% 45.6%
5i4dA02 2.40.50.110 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.61 42.0 4.15e-01 98.6% 67.1%
2o1uB01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.60 46.0 3.51e-01 82.9% 70.3%
3gd6A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.58 49.0 4.04e-01 100.0% 89.4%
1sgoA01 3.30.2280.10 Alpha Beta › 2-Layer Sandwich › copper amine oxidase-like fold › Hypothetical protein (hspc210) 0.58 35.0 3.01e-01 100.0% 38.0%
3qijB03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 37.0 3.53e-01 74.3% 56.2%
2gcjA01 2.30.29.150 Mainly Beta › Roll › PH-domain like › 0.55 38.0 3.22e-01 74.3% 64.9%
2elbA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 35.0 3.19e-01 70.0% 44.1%
1h4rA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 36.0 3.40e-01 70.0% 53.8%
3voqA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 39.0 3.32e-01 75.7% 47.4%
1pxfA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.54 42.0 3.67e-01 87.1% 84.7%
3wxmB02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.53 37.0 3.20e-01 74.3% 53.3%
1okeB02 3.30.67.10 Alpha Beta › 2-Layer Sandwich › Viral Envelope Glycoprotein; domain 2 › Viral Envelope Glycoprotein, domain 2 0.53 42.0 4.09e-01 100.0% 80.5%
2w9jA00 3.30.720.10 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Signal recognition particle alu RNA binding heterodimer, srp9/1 0.53 37.0 3.71e-01 74.3% 73.2%
1w0pA01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.52 41.0 3.16e-01 90.0% 36.7%
1e8oD00 3.30.720.10 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Signal recognition particle alu RNA binding heterodimer, srp9/1 0.52 36.0 3.54e-01 74.3% 67.1%
3r7wB02 3.30.450.190 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.52 37.0 3.26e-01 80.0% 83.1%
4m4zA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.51 29.0 3.49e-01 92.9% 85.1%
3mx7A00 2.40.128.180 Mainly Beta › Beta Barrel › Lipocalin › 0.51 36.0 3.38e-01 75.7% 75.6%
2nykA01 3.30.500.30 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › 0.51 41.0 3.28e-01 90.0% 87.2%
1w0pA03 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 40.0 3.05e-01 90.0% 34.2%
4fdtB00 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.51 44.0 2.78e-01 100.0% 62.4%
3j7yD01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.50 31.0 2.81e-01 95.7% 40.6%
1v73A00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.50 35.0 2.28e-01 72.9% 48.0%
ECOD (38)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3231587 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.66 45.0 4.14e-01 70.0% 58.9%
3719897 227.1.1.18 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › DUF7881_C 0.62 45.0 3.73e-01 97.1% 43.2%
4011458 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 44.0 3.29e-01 75.7% 34.5%
3909375 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.59 40.0 3.25e-01 81.4% 37.0%
4927858 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.58 30.0 3.32e-01 100.0% 60.0%
3620293 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 40.0 3.34e-01 77.1% 40.0%
4031110 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 39.0 3.26e-01 71.4% 46.4%
3933100 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.57 36.0 3.69e-01 98.6% 65.7%
4004179 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.56 39.0 2.78e-01 75.7% 22.2%
3486831 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.56 38.0 2.71e-01 81.4% 20.8%
3222225 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.56 38.0 3.97e-01 98.6% 78.5%
4679944 223.2.1.36 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Intu_longin_3 0.56 40.0 3.44e-01 78.6% 93.5%
4928233 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.56 39.0 3.20e-01 75.7% 83.6%
4341865 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.56 38.0 4.16e-01 87.1% 89.1%
3260733 220.1.1.158 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_LRR1 0.56 38.0 3.27e-01 71.4% 59.1%
3738905 884.1.1.1 ↗ a+b two layers › Hypothetical protein YjiA, C-terminal domain › Hypothetical protein YjiA, C-terminal domain › Hypothetical protein YjiA, C-terminal domain › CobW_C 0.55 38.0 3.45e-01 74.3% 51.0%
3205251 884.1.1.1 ↗ a+b two layers › Hypothetical protein YjiA, C-terminal domain › Hypothetical protein YjiA, C-terminal domain › Hypothetical protein YjiA, C-terminal domain › CobW_C 0.54 36.0 3.10e-01 74.3% 40.9%
4076629 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.54 38.0 2.64e-01 77.1% 19.3%
4110879 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.54 37.0 3.11e-01 81.4% 37.8%
3231448 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.54 37.0 2.94e-01 81.4% 30.9%
3500471 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.54 38.0 3.13e-01 81.4% 40.0%
3476139 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.54 37.0 3.21e-01 74.3% 43.5%
3701480 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.53 38.0 3.24e-01 87.1% 43.2%
3787887 896.1.1.2 ↗ a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › SRP14 0.52 35.0 3.51e-01 75.7% 67.1%
3533183 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.52 36.0 3.35e-01 77.1% 53.0%
3226947 220.1.1.7 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › IRS 0.52 38.0 3.36e-01 80.0% 51.4%
3565424 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.52 40.0 3.29e-01 81.4% 46.4%
3562988 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.52 39.0 3.20e-01 81.4% 43.0%
4179811 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.52 31.0 3.80e-01 100.0% 100.0%
3843072 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.52 39.0 2.68e-01 82.9% 81.0%
5002092 283.2.1.0 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like 0.51 33.0 3.03e-01 88.6% 51.1%
4952930 2.21.1.0 ↗ beta barrels › OB-fold › Small protein B (SmpB) › Small protein B (SmpB) 0.51 40.0 3.80e-01 92.9% 71.8%
3514660 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.51 36.0 3.28e-01 97.1% 56.7%
1100 10.1.1.32 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Sial-lect-inser 0.51 40.0 3.01e-01 90.0% 32.5%
3362766 386.1.1.4 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-BED 0.51 33.0 3.72e-01 94.3% 92.0%
3408937 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.51 35.0 3.37e-01 100.0% 62.5%
3209694 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.50 34.0 3.09e-01 97.1% 50.0%
4957557 3629.1.1.0 ↗ beta sandwiches › Tail sheath protein beta-sandwich domain › Tail sheath protein beta-sandwich domain › Tail sheath protein beta-sandwich domain 0.50 37.0 3.34e-01 84.3% 76.4%
D3 medium residues 71-154
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4mk6A00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.58 37.0 2.93e-01 85.7% 29.3%
2wv2A00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.52 43.0 2.76e-01 95.2% 37.0%
2fgyA01 1.20.120.1310 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Carboxysome Shell Carbonic Anhydrase, N-terminal helical domain 0.51 30.0 2.86e-01 91.7% 44.9%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3400609 320.4.1.1 ↗ a+b two layers › R3H domain-like › PUB domain › PUB domain › TIMELESS_C 0.71 31.0 2.91e-01 94.0% 34.0%
3218988 102.1.3.18 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › PAP/OAS1 substrate-binding domain › DUF7752 0.65 39.0 2.94e-01 75.0% 25.6%
4018260 141.1.1.8 ↗ alpha bundles › Terpenoid synthases › Terpenoid synthases › Terpenoid synthases › Terpene_syn_C_2 0.60 40.0 2.62e-01 100.0% 16.3%
2831995 5063.1.1.1 ↗ alpha bundles › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › PSI_PSAK 0.57 41.0 4.44e-01 82.1% 91.3%
4039355 2004.1.1.258 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA,AAA_2 0.57 49.0 3.25e-01 96.4% 45.7%
3288783 101.1.2.6 ↗ alpha arrays › HTH › HTH › winged helix domain › GntR 0.55 33.0 3.33e-01 96.4% 57.6%
3642551 4336.1.1.0 ↗ alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like 0.54 44.0 4.19e-01 100.0% 77.0%
3711596 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.54 39.0 3.21e-01 91.7% 40.6%
380466 4038.1.1.1 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Phage_portal 0.54 41.0 4.29e-01 91.7% 98.6%
3294780 3755.3.1.375 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › DUF4079 0.51 37.0 3.08e-01 77.4% 66.7%
4549262 2006.1.1.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like 0.51 43.0 3.05e-01 96.4% 58.5%
3598732 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.50 37.0 3.45e-01 83.3% 62.5%
D4 medium residues 155-263
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5es8A03 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.59 27.0 3.16e-01 72.5% 58.3%
3vprA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.57 41.0 3.77e-01 75.2% 92.4%
4dk4B00 1.10.4010.10 Mainly Alpha › Orthogonal Bundle › all-alpha NTP pyrophosphatase fold › Type II deoxyuridine triphosphatase 0.55 41.0 3.28e-01 78.0% 68.2%
3jvoA00 1.10.3230.30 Mainly Alpha › Orthogonal Bundle › Hypothetical protein yqbg › Phage gp6-like head-tail connector protein 0.54 38.0 4.05e-01 73.4% 84.4%
2xvtC00 1.10.150.510 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Receptor activity modifying family 0.53 29.0 3.32e-01 89.0% 72.2%
5k7fA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.52 37.0 3.52e-01 75.2% 92.8%
3fbzA01 1.20.58.800 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.50 34.0 3.50e-01 75.2% 73.5%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3505043 102.1.3.0 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › PAP/OAS1 substrate-binding domain 0.56 41.0 3.68e-01 77.1% 69.4%
1316591 160.1.1.3 ↗ alpha superhelices › C-terminal domain of alpha and beta subunits of F1 ATP synthase › C-terminal domain of alpha and beta subunits of F1 ATP synthase › C-terminal domain of alpha and beta subunits of F1 ATP synthase › T3SS_ATPase_C 0.54 25.0 2.87e-01 73.4% 58.2%
3385758 514.1.1.1 ↗ alpha bundles › YutG-like › YutG-like › YutG-like › PgpA 0.54 40.0 3.63e-01 78.0% 92.7%
3963928 514.1.1.1 ↗ alpha bundles › YutG-like › YutG-like › YutG-like › PgpA 0.53 39.0 3.48e-01 77.1% 83.9%
3210835 2498.1.1.102 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › PF30906 0.52 39.0 3.09e-01 81.7% 90.0%
4988663 101.1.2.30 ↗ alpha arrays › HTH › HTH › winged helix domain › TrmB 0.50 29.0 3.17e-01 93.6% 69.4%