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NC_041929.1__YP_009601454.1__FDH46_gp149__00329

Bact-Vir

NC_041929.1__YP_009601454.1__FDH46_gp149__00329

Identity

Accession:
NC_041929 ↗
Kingdom:
phage

Quality

71.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Emdodecavirus› Sinorhizobium_phage_phiM7

TaxID: 1647403

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 30-86
PDB
Domain cluster: representative
CATH (37)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5dymA00 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 0.83 59.0 4.88e-01 75.4% 45.8%
3l7wA00 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 0.82 58.0 4.63e-01 75.4% 40.0%
3l9fA01 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 0.78 56.0 4.79e-01 75.4% 48.3%
2dqlA00 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 0.75 55.0 4.32e-01 77.2% 39.1%
2ab5B01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.61 44.0 3.53e-01 80.7% 51.6%
2pd0A01 3.30.2310.50 Alpha Beta › 2-Layer Sandwich › YaeB-like fold › Protein of unknown function (DUF3228), domain 1 0.58 43.0 3.56e-01 86.0% 55.8%
3v38A00 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.58 49.0 3.13e-01 100.0% 30.7%
1jqgA02 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.56 47.0 3.04e-01 100.0% 30.7%
2pgeA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.56 38.0 3.04e-01 84.2% 32.3%
1ckmA01 3.30.470.30 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme 0.56 44.0 3.33e-01 91.2% 96.8%
4l0mA00 3.40.50.1580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleoside phosphorylase domain 0.56 43.0 2.95e-01 100.0% 21.6%
3fcyA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.56 44.0 2.80e-01 89.5% 28.7%
1k8kA04 3.90.640.10 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › ATPase, substrate binding domain, subdomain 4 0.56 34.0 2.93e-01 73.7% 37.0%
1tkjA00 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.56 45.0 3.03e-01 100.0% 33.6%
2ab5A02 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.55 41.0 3.21e-01 82.5% 41.8%
2rs7A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.54 43.0 4.02e-01 93.0% 86.5%
1rtqA00 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.54 45.0 2.92e-01 100.0% 53.3%
1l7aA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.53 41.0 2.67e-01 89.5% 28.6%
2z17A00 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.53 39.0 3.44e-01 82.5% 55.3%
1t5rB00 2.70.240.10 Mainly Beta › Distorted Sandwich › Leukocidin-like › Leukocidin/porin MspA 0.53 44.0 2.94e-01 100.0% 81.5%
5zg8A02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.53 44.0 2.86e-01 100.0% 85.0%
2zo4A01 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.53 42.0 2.80e-01 89.5% 75.4%
3i6uA02 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.53 41.0 3.65e-01 87.7% 77.0%
2y1sA00 2.30.60.10 Mainly Beta › Roll › HIV-inactivating Protein, Cyanovirin-n › Cyanovirin-N 0.53 43.0 3.67e-01 100.0% 52.8%
1dq3A03 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.52 43.0 3.84e-01 96.5% 85.1%
1xfdA02 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 42.0 2.85e-01 96.5% 40.5%
1qlmA02 3.30.1030.10 Alpha Beta › 2-Layer Sandwich › Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 2 › Methenyltetrahydromethanopterin Cyclohydrolase; Chain A, domain 2 0.52 42.0 3.07e-01 100.0% 94.9%
1ocsA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.52 38.0 3.01e-01 82.5% 37.1%
6zj8D01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.51 36.0 3.00e-01 75.4% 66.7%
2xe4A02 2.130.10.120 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Prolyl oligopeptidase, N-terminal domain 0.51 39.0 2.47e-01 87.7% 22.4%
6f1uK02 3.90.1150.210 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › F-actin capping protein, beta subunit 0.51 41.0 3.20e-01 96.5% 60.0%
2kvtA00 3.30.730.30 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › YaiA protein 0.51 34.0 3.28e-01 80.7% 57.7%
3wuyA00 3.60.110.10 Alpha Beta › 4-Layer Sandwich › Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase › Carbon-nitrogen hydrolase 0.51 39.0 2.56e-01 89.5% 69.3%
3obqA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.50 40.0 3.15e-01 94.7% 58.2%
7rkbA01 3.90.420.10 Alpha Beta › Alpha-Beta Complex › Sulfite Oxidase; Chain A, domain 2 › Oxidoreductase, molybdopterin-binding domain 0.50 42.0 3.31e-01 98.2% 66.2%
2jovA01 3.10.530.10 Alpha Beta › Roll › CPE0013-like fold › CPE0013-like 0.50 38.0 3.55e-01 82.5% 98.6%
2qkpD00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.50 33.0 2.67e-01 80.7% 29.9%
ECOD (44)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4986012 101.1.2.14 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.90 65.0 4.22e-01 77.2% 20.5%
5035685 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.90 65.0 4.87e-01 75.4% 35.5%
4959599 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.89 64.0 4.98e-01 75.4% 38.6%
3587894 101.1.2.49 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR,Vir_act_alpha_C 0.88 63.0 4.31e-01 75.4% 24.6%
5041543 101.1.2.135 ↗ alpha arrays › HTH › HTH › winged helix domain › MarR_2 0.83 55.0 4.01e-01 73.7% 27.9%
5069274 101.1.2.135 ↗ alpha arrays › HTH › HTH › winged helix domain › MarR_2 0.82 56.0 4.38e-01 71.9% 35.7%
3330019 101.1.2.88 ↗ alpha arrays › HTH › HTH › winged helix domain › Dimerisation 0.82 57.0 4.49e-01 77.2% 36.5%
4978855 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.81 58.0 4.50e-01 75.4% 36.7%
4964954 101.1.2.136 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_20 0.81 59.0 4.48e-01 77.2% 37.5%
5025618 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.81 54.0 4.29e-01 71.9% 36.4%
5027566 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.80 57.0 4.99e-01 75.4% 51.8%
5062639 101.1.2.15 ↗ alpha arrays › HTH › HTH › winged helix domain › MarR 0.80 58.0 4.84e-01 77.2% 50.5%
141918 101.1.2.49 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR,Vir_act_alpha_C 0.78 56.0 3.93e-01 75.4% 25.3%
3286725 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.77 55.0 3.83e-01 75.4% 23.8%
3280086 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.77 57.0 3.90e-01 77.2% 36.1%
4944735 101.1.2.542 ↗ alpha arrays › HTH › HTH › winged helix domain › ATPase_2 0.77 57.0 4.31e-01 77.2% 37.6%
5058727 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.77 57.0 4.13e-01 77.2% 32.4%
5050784 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.77 56.0 4.78e-01 77.2% 50.0%
5070276 101.1.2.142 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_Crp_2 0.76 57.0 4.14e-01 78.9% 54.5%
5042462 101.1.2.31 ↗ alpha arrays › HTH › HTH › winged helix domain › TFIIE_alpha 0.75 49.0 3.47e-01 70.2% 23.0%
164542 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.75 55.0 4.32e-01 77.2% 39.1%
4957324 101.1.2.920 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_TbsP_C 0.74 54.0 4.21e-01 78.9% 39.2%
4998735 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.68 62.0 4.58e-01 98.2% 51.9%
4061942 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.66 50.0 3.91e-01 82.5% 49.6%
3933688 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.64 46.0 2.87e-01 77.2% 56.8%
3619358 5001.1.1.111 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1, 7TM_GPCR_Srw 0.64 45.0 2.82e-01 75.4% 57.5%
3425721 252.1.1.2 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD › DUF7028 0.62 42.0 3.94e-01 93.0% 54.7%
5012702 242.1.1.7 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.60 43.0 3.57e-01 80.7% 53.0%
3378706 211.1.1.0 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.59 41.0 3.81e-01 100.0% 55.0%
3499670 7579.1.1.6 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_1 0.58 49.0 3.08e-01 100.0% 41.5%
3606650 6132.1.1.0 ↗ alpha bundles › Nudix hydrolase N-terminal dimerization domain › Nudix hydrolase N-terminal dimerization domain › Nudix hydrolase N-terminal dimerization domain 0.58 46.0 3.88e-01 91.2% 84.8%
3930349 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.57 48.0 3.10e-01 100.0% 55.3%
3413834 2011.1.1.1 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M14 0.55 46.0 2.97e-01 100.0% 37.5%
3606814 896.1.1.0 ↗ 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 0.55 39.0 3.60e-01 96.5% 56.4%
4355868 71.1.1.2 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › LolA 0.55 46.0 3.29e-01 100.0% 76.4%
4928954 873.1.1.0 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain 0.55 45.0 3.57e-01 98.2% 70.8%
4606097 1.1.8.5 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › tRNA_Me_trans_C 0.54 35.0 3.13e-01 84.2% 45.2%
4018042 2011.1.1.6 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M20 0.54 44.0 2.89e-01 100.0% 46.1%
5034773 223.1.1.25 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_9 0.54 36.0 3.01e-01 71.9% 60.9%
3608583 330.1.1.22 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › PF26536 0.53 43.0 3.33e-01 100.0% 81.9%
3601659 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.53 43.0 3.30e-01 96.5% 56.7%
3721100 4161.1.1.0 ↗ beta complex topology › MOSC N-terminal domain-like › MOSC N-terminal domain-like › MOSC N-terminal domain-like 0.52 43.0 2.79e-01 100.0% 23.8%
3940239 3338.2.1.0 ↗ a+b two layers › Fragilysin-3 prodomain-like › Type II secretion chaperone CpaB › Type II secretion chaperone CpaB 0.51 38.0 3.21e-01 84.2% 59.6%
3802624 4246.1.1.2 ↗ a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 0.50 40.0 2.68e-01 98.2% 58.0%