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NC_041929.1__YP_009601150.1__FDH46_gp025__00025

Bact-Vir

NC_041929.1__YP_009601150.1__FDH46_gp025__00025

Identity

Accession:
NC_041929 ↗
Kingdom:
phage

Quality

70.3 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 high residues 13-64
PDB
Domain cluster: representative
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2xe4A01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.73 47.0 2.82e-01 73.1% 9.5%
3n91A02 2.40.128.420 Mainly Beta › Beta Barrel › Lipocalin › 0.68 47.0 3.49e-01 73.1% 65.4%
3j7aZ00 3.30.1230.20 Alpha Beta › 2-Layer Sandwich › Hypothetical Cytosolic Protein; Chain: A; › Ribosomal protein S21 0.67 54.0 4.93e-01 92.3% 73.6%
2xzmZ00 3.30.1230.20 Alpha Beta › 2-Layer Sandwich › Hypothetical Cytosolic Protein; Chain: A; › Ribosomal protein S21 0.67 54.0 4.47e-01 92.3% 54.6%
2vw9B00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.66 47.0 3.82e-01 76.9% 88.6%
5ek8A01 2.60.40.3330 Mainly Beta › Sandwich › Immunoglobulin-like › 0.65 45.0 3.44e-01 73.1% 78.6%
2hdwA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.65 45.0 2.92e-01 73.1% 45.7%
2d42A02 3.10.450.380 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.65 44.0 4.17e-01 73.1% 58.5%
4bgjA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.63 47.0 3.72e-01 100.0% 37.3%
2ab5B01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.63 45.0 3.46e-01 78.8% 55.5%
4wksC02 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.62 43.0 3.93e-01 75.0% 97.3%
2i5tA00 3.10.490.10 Alpha Beta › Roll › Hypothetical upf0131 protein ytfp › Gamma-glutamyl cyclotransferase-like 0.62 42.0 3.01e-01 71.2% 63.9%
1fs7A01 1.10.1130.10 Mainly Alpha › Orthogonal Bundle › Flavocytochrome C3; Chain A, domain 2 › Flavocytochrome C3; Chain A 0.62 49.0 3.03e-01 88.5% 39.7%
6nvxB02 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.62 45.0 4.04e-01 80.8% 96.1%
1fm2B03 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.61 43.0 4.08e-01 76.9% 97.0%
5iryA05 2.60.40.60 Mainly Beta › Sandwich › Immunoglobulin-like › Cadherins 0.60 41.0 3.50e-01 71.2% 100.0%
2k5qA00 2.40.50.480 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Protein of unknown function DUF1093 0.60 41.0 3.31e-01 73.1% 39.0%
2k4zA01 2.60.300.12 Mainly Beta › Sandwich › Hypothetical Protein Aq_1857; Chain: A; › HesB-like domain 0.59 42.0 3.28e-01 75.0% 40.7%
3cetB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.59 40.0 3.22e-01 71.2% 87.3%
1nqzA00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.59 42.0 3.08e-01 80.8% 71.3%
3n77A00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.58 46.0 3.44e-01 90.4% 96.5%
1dw9A02 3.30.1160.10 Alpha Beta › 2-Layer Sandwich › Cyanate Lyase; Chain: A, domain 2 › Cyanate lyase, C-terminal domain 0.58 40.0 3.71e-01 73.1% 61.8%
1cp9B02 2.30.120.10 Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region 0.58 41.0 3.79e-01 78.8% 94.5%
1gcbA01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.57 43.0 2.52e-01 100.0% 10.2%
8in8C01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.57 40.0 2.63e-01 75.0% 31.7%
5ib9A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.57 48.0 3.07e-01 100.0% 66.3%
7sxqA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.57 43.0 2.80e-01 84.6% 17.7%
5iu1B00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.57 38.0 3.09e-01 71.2% 89.3%
2v79A00 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 0.56 42.0 3.28e-01 80.8% 81.7%
1se8A02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 44.0 3.47e-01 86.5% 83.8%
4gs5A01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.56 37.0 2.51e-01 73.1% 14.8%
5iroD00 2.60.40.3530 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 40.0 3.20e-01 76.9% 76.5%
7r5mA01 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.55 43.0 2.88e-01 88.5% 83.0%
3cjlA00 3.10.20.850 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Protein of unknown function DUF3861 0.54 36.0 3.14e-01 73.1% 40.9%
5odnC00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.54 42.0 3.46e-01 88.5% 53.9%
2nrqA00 3.30.1440.10 Alpha Beta › 2-Layer Sandwich › 50s Ribosomal Protein L5; Chain: A, › Ribosomal protein L5 0.54 36.0 2.77e-01 73.1% 40.1%
2v8qA01 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.53 36.0 3.03e-01 71.2% 60.7%
4dzdA02 3.30.70.1210 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Crispr-associated protein; domain 2 0.53 36.0 2.80e-01 71.2% 66.7%
5xc5A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 41.0 2.90e-01 88.5% 86.2%
2qsqB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 35.0 2.85e-01 73.1% 95.4%
3r0aA00 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 0.51 36.0 2.83e-01 76.9% 51.7%
2jkgA00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.51 41.0 2.87e-01 88.5% 73.3%
1xttB00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 39.0 2.64e-01 86.5% 44.2%
3iuzA00 3.10.180.50 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 0.51 35.0 2.19e-01 73.1% 25.0%
2od5A00 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 0.50 42.0 3.56e-01 96.2% 85.7%
ECOD (53)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3484504 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.72 47.0 4.19e-01 71.2% 46.7%
3487873 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.72 59.0 5.64e-01 90.4% 83.3%
3743393 59.1.4.2 ↗ beta complex topology › triple barrel › triple barrel › TFIID subunits TAF1-TAF7 › DUF3591 0.71 50.0 2.95e-01 75.0% 9.6%
4033072 101.1.9.32 ↗ alpha arrays › HTH › HTH › Putative DNA-binding domain › ANT 0.71 48.0 4.11e-01 71.2% 84.7%
3588288 101.1.9.32 ↗ alpha arrays › HTH › HTH › Putative DNA-binding domain › ANT 0.69 48.0 3.46e-01 73.1% 46.0%
5010647 1075.1.1.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain 0.69 48.0 3.17e-01 75.0% 18.7%
3709549 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.69 56.0 4.01e-01 94.2% 86.1%
3391162 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.66 49.0 3.11e-01 78.8% 73.7%
4833007 3167.1.1.1 ↗ a+b two layers › 40S ribosomal protein rpS21 (S21e) › 40S ribosomal protein rpS21 (S21e) › 40S ribosomal protein rpS21 (S21e) › Ribosomal_S21e 0.66 53.0 4.58e-01 92.3% 60.2%
3591474 4106.1.1.1 ↗ few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.65 46.0 3.05e-01 75.0% 29.5%
5080275 101.1.2.914 ↗ alpha arrays › HTH › HTH › winged helix domain › DUF6015 0.65 47.0 3.59e-01 76.9% 47.5%
4980535 101.1.2.914 ↗ alpha arrays › HTH › HTH › winged helix domain › DUF6015 0.65 47.0 3.92e-01 78.8% 62.1%
4595166 5076.2.1.0 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ 0.65 40.0 2.67e-01 76.9% 14.2%
3717300 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.65 48.0 2.80e-01 80.8% 16.6%
4012111 812.2.1.0 ↗ a+b duplicates or obligate multimers › MinE-like › Cyanase C-terminal domain › Cyanase C-terminal domain 0.63 44.0 4.10e-01 73.1% 66.7%
3218156 389.1.1.145 ↗ few secondary structure elements › EGF-like › EGF-related › EGF/Laminin › PF29138 0.62 39.0 4.15e-01 78.8% 73.3%
4944536 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.61 42.0 3.94e-01 73.1% 81.5%
4234844 7527.1.1.1 ↗ a/b three-layered sandwiches › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE 0.61 43.0 2.76e-01 75.0% 69.0%
3608304 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.61 44.0 3.46e-01 76.9% 70.9%
3717203 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.61 41.0 2.82e-01 71.2% 80.5%
3517917 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.60 47.0 4.43e-01 86.5% 83.1%
3633076 1.1.1.30 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › PF30863 0.60 42.0 3.34e-01 75.0% 41.0%
3512923 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.60 43.0 3.17e-01 76.9% 45.0%
4262649 812.2.1.1 ↗ a+b duplicates or obligate multimers › MinE-like › Cyanase C-terminal domain › Cyanase C-terminal domain › Cyanate_lyase 0.60 41.0 3.56e-01 71.2% 52.5%
3810414 812.2.1.1 ↗ a+b duplicates or obligate multimers › MinE-like › Cyanase C-terminal domain › Cyanase C-terminal domain › Cyanate_lyase 0.59 41.0 3.57e-01 71.2% 52.5%
3303720 3336.1.1.1 ↗ alpha complex topology › plant-specific ROP nucleotide exchanger (PRONE) domain › plant-specific ROP nucleotide exchanger (PRONE) domain › plant-specific ROP nucleotide exchanger (PRONE) domain › PRONE 0.59 38.0 2.29e-01 73.1% 8.5%
3818469 2484.1.1.67 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.59 41.0 3.16e-01 75.0% 52.0%
3592269 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.58 48.0 3.61e-01 94.2% 92.6%
7696 812.2.1.1 ↗ a+b duplicates or obligate multimers › MinE-like › Cyanase C-terminal domain › Cyanase C-terminal domain › Cyanate_lyase 0.58 40.0 3.67e-01 73.1% 60.0%
3351840 284.1.3.2 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › OSR1_C 0.58 39.0 3.59e-01 71.2% 94.2%
5045478 7527.1.1.1 ↗ a/b three-layered sandwiches › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE 0.58 41.0 2.66e-01 76.9% 47.8%
3779781 109.4.1.1812 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RYDR_ITPR, RIH_assoc 0.58 50.0 2.71e-01 100.0% 9.9%
3951280 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.57 48.0 2.92e-01 100.0% 87.3%
4443502 109.4.1.116 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RIH_assoc 0.57 49.0 2.82e-01 100.0% 18.3%
3602516 7527.1.1.1 ↗ a/b three-layered sandwiches › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE 0.57 41.0 2.62e-01 76.9% 45.3%
4978825 101.1.2.30 ↗ alpha arrays › HTH › HTH › winged helix domain › TrmB 0.56 41.0 3.18e-01 80.8% 54.2%
4833097 2484.1.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.56 43.0 3.32e-01 84.6% 57.4%
4971747 101.1.2.30 ↗ alpha arrays › HTH › HTH › winged helix domain › TrmB 0.56 42.0 3.38e-01 84.6% 60.0%
5082809 101.1.2.30 ↗ alpha arrays › HTH › HTH › winged helix domain › TrmB 0.55 40.0 3.24e-01 80.8% 61.9%
3194847 3343.1.1.2 ↗ alpha complex topology › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › GCP_C_terminal,GCP_N_terminal 0.54 39.0 2.21e-01 78.8% 9.9%
2559786 3256.1.1.0 ↗ a+b two layers › DUF2233 N-terminal domain › DUF2233 N-terminal domain › DUF2233 N-terminal domain 0.54 33.0 3.52e-01 76.9% 68.9%
4890002 2003.1.5.81 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.54 38.0 2.78e-01 76.9% 41.9%
4045000 7527.1.1.1 ↗ a/b three-layered sandwiches › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE 0.54 39.0 2.52e-01 76.9% 68.8%
3740624 101.1.2.111 ↗ alpha arrays › HTH › HTH › winged helix domain › RQC 0.53 40.0 3.08e-01 82.7% 69.6%
3270195 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.53 37.0 2.89e-01 71.2% 74.8%
3303587 207.1.1.55 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_1,LRR_8 0.53 37.0 2.37e-01 73.1% 24.2%
3252037 109.3.1.20 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank_2,Ank_4 0.52 36.0 2.49e-01 73.1% 28.6%
4426017 2004.1.1.19 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.52 42.0 2.82e-01 90.4% 70.2%
4880598 3070.2.1.0 ↗ a+b complex topology › N0 domain in phage tail proteins and secretins-like › TonB-dependent receptor plug domain › TonB-dependent receptor plug domain 0.52 32.0 3.25e-01 71.2% 61.2%
3517620 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 0.51 42.0 2.60e-01 92.3% 29.7%
3450430 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.51 40.0 2.89e-01 92.3% 69.1%
3830346 207.1.1.137 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_1, LRR_4, LRR_8 0.51 35.0 2.13e-01 73.1% 9.9%
3173410 2004.1.1.19 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.50 42.0 2.74e-01 92.3% 63.6%