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NC_042016.1__YP_009612534.1__FDI43_gp04__00004

Bact-Vir

NC_042016.1__YP_009612534.1__FDI43_gp04__00004

Identity

Accession:
NC_042016 ↗
Kingdom:
phage

Quality

84.8 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 4-123
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF26571.1 best VldE 86.9 1.10e-24 89.2% 97.3%
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2vo9A01 3.30.1380.10 Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 › 0.68 64.0 6.21e-01 100.0% 96.2%
4lrjA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.65 37.0 4.53e-01 95.0% 90.4%
3havA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.62 34.0 3.91e-01 95.8% 73.0%
3lpxB02 3.30.1360.40 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.60 33.0 3.66e-01 72.5% 66.0%
1s9iB01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.60 36.0 4.03e-01 95.0% 76.3%
3ffrA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.60 36.0 3.73e-01 91.7% 62.3%
4o38A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.60 39.0 4.33e-01 94.2% 83.3%
6liuC02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.60 37.0 3.77e-01 92.5% 62.9%
3gkuA03 3.30.1370.50 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain 0.59 32.0 4.09e-01 79.2% 90.1%
2ppqA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.59 35.0 3.92e-01 95.8% 75.5%
3lzhA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.58 35.0 3.91e-01 95.8% 78.0%
3pgvA02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.57 45.0 4.91e-01 91.7% 98.0%
1vi7A01 3.30.230.30 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › Impact, N-terminal domain 0.55 39.0 3.80e-01 73.3% 69.6%
7xhzA01 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.54 47.0 4.70e-01 91.7% 98.4%
4h7wA00 3.90.1140.10 Alpha Beta › Alpha-Beta Complex › Cyclic Phosphodiesterase; Chain: A, › Cyclic phosphodiesterase 0.54 38.0 3.25e-01 70.8% 84.0%
3a2vD02 3.30.1020.10 Alpha Beta › 2-Layer Sandwich › Antioxidant, Horf6; Chain A, domain 2 › Antioxidant, Horf6; Chain A, domain2 0.53 29.0 3.22e-01 95.0% 63.2%
1crwG02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.53 44.0 3.97e-01 90.8% 98.8%
1bpeA04 3.30.210.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 3 › DNA polymerase, thumb domain 0.52 26.0 3.65e-01 87.5% 100.0%
3b59A01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.52 38.0 3.82e-01 76.7% 93.4%
1vkvA01 3.30.428.10 Alpha Beta › 2-Layer Sandwich › HIT family, subunit A › HIT-like 0.52 40.0 3.50e-01 98.3% 54.4%
3s0tA00 3.30.1690.10 Alpha Beta › 2-Layer Sandwich › TcpA-like pilin › TcpA-like pilin 0.51 46.0 4.02e-01 100.0% 95.6%
3b8xA02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.51 38.0 3.82e-01 92.5% 78.2%
3p24A01 2.40.128.470 Mainly Beta › Beta Barrel › Lipocalin › 0.50 38.0 3.56e-01 100.0% 62.7%
1st8A02 2.60.120.560 Mainly Beta › Sandwich › Jelly Rolls › Exo-inulinase; domain 1 0.50 37.0 3.18e-01 76.7% 92.6%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3990075 307.1.1.9 a+b two layers › Hedgehog/DD-peptidase › Hedgehog/DD-peptidase › Hedgehog/DD-peptidase › VldE 0.91 83.0 8.48e-01 95.8% 98.3%
3205223 307.1.1.9 a+b two layers › Hedgehog/DD-peptidase › Hedgehog/DD-peptidase › Hedgehog/DD-peptidase › VldE 0.88 80.0 8.25e-01 95.0% 100.0%
3953991 3012.1.1.12 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain › PF26571 0.87 82.0 7.69e-01 100.0% 83.6%
3960492 3012.1.1.0 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.87 75.0 7.53e-01 97.5% 89.2%
3959334 3012.1.1.12 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain › PF26571 0.86 75.0 7.38e-01 100.0% 85.9%
5011633 3012.1.1.0 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.81 49.0 5.27e-01 90.8% 70.2%
4959358 304.131.1.0 a+b two layers › Alpha-beta plaits › Phosphonoacetate hydrolase insertion domain › Phosphonoacetate hydrolase insertion domain 0.72 51.0 5.69e-01 89.2% 92.6%
3417366 312.1.1.19 a+b three layers › HIT-like › HIT-related › HIT-related › PF26216 0.71 41.0 3.91e-01 95.8% 49.3%
4162122 2006.1.1.7 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › S6PP 0.68 47.0 3.55e-01 91.7% 30.0%
None 0.68 64.0 5.95e-01 100.0% 86.5%
4977841 310.3.1.0 a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.67 43.0 5.12e-01 90.0% 97.5%
3968428 304.36.1.1 a+b two layers › Alpha-beta plaits › YajQ-like › YajQ-like › DUF520 0.65 44.0 4.99e-01 90.8% 93.3%
4995059 321.1.1.1 a+b two layers › Glutamine synthetase-like › Glutamine synthetase/guanido kinase › Glutamine synthetase/guanido kinase › Gln-synt_C 0.65 55.0 3.86e-01 89.2% 54.0%
3177556 314.1.1.2 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2b 0.64 54.0 3.70e-01 92.5% 85.0%
3265858 314.1.1.2 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2b 0.64 54.0 3.85e-01 92.5% 82.7%
4647064 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 0.63 27.0 3.74e-01 90.8% 80.0%
4027078 314.1.1.2 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2b 0.58 48.0 3.59e-01 92.5% 75.9%
4438218 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.56 43.0 4.46e-01 85.0% 87.3%
3976953 212.1.1.12 a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › UPF0029 0.55 39.0 3.83e-01 73.3% 69.6%
4032715 3012.1.1.0 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.55 48.0 4.75e-01 91.7% 96.8%
3708707 2006.1.1.37 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › S6PP+Hydrolase_3 0.55 47.0 3.47e-01 91.7% 37.7%
3988949 4070.1.1.2 alpha arrays › FtsH protease domain-like › FtsH protease domain-like › FtsH protease domain-like › Peptidase_M50 0.54 39.0 3.45e-01 75.0% 70.6%
4938623 881.1.1.45 a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like › PF26686 0.54 47.0 4.28e-01 93.3% 91.1%
2797934 304.113.1.1 a+b two layers › Alpha-beta plaits › Alpha subunit of glutamate synthase, insertion domain › Alpha subunit of glutamate synthase, insertion domain › GATase_2 0.53 46.0 4.73e-01 93.3% 96.6%
3491239 7523.1.1.2 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Transferrin 0.53 44.0 3.15e-01 90.8% 86.6%
4943581 328.4.1.0 a+b two layers › IF3-like › YhbY-like › YhbY-like 0.52 30.0 3.62e-01 95.0% 85.0%
4061362 327.4.1.1 a+b two layers › Alpha-lytic protease prodomain-like › YhbC-like, N-terminal domain › YhbC-like, N-terminal domain › RimP_N 0.52 41.0 4.41e-01 90.8% 100.0%
3588048 304.156.1.0 a+b two layers › Alpha-beta plaits › DNA translocase FtsK N-terminal domain › DNA translocase FtsK N-terminal domain 0.52 42.0 4.41e-01 90.0% 99.0%
3586949 2006.1.1.37 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › S6PP+Hydrolase_3 0.52 44.0 3.36e-01 92.5% 40.5%
5039911 328.4.1.1 a+b two layers › IF3-like › YhbY-like › YhbY-like › CRS1_YhbY 0.52 30.0 3.52e-01 95.0% 81.2%
4010106 3012.1.1.4 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain › Hydrolase_3 0.51 44.0 4.57e-01 90.8% 100.0%
3981523 2006.1.1.37 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › S6PP+Hydrolase_3 0.51 44.0 3.35e-01 91.7% 41.9%
3284610 213.1.1.0 a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.51 41.0 3.61e-01 87.5% 86.5%
2122949 2006.1.1.3 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Trehalose_PPase 0.51 45.0 3.52e-01 95.0% 57.0%
D2 high residues 147-187
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08230.17 best CW_7 43.1 4.00e-11 97.6% 95.0%
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1rr7A02 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.66 50.0 4.83e-01 100.0% 75.0%
3lmmC04 1.10.10.2340 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.64 53.0 4.26e-01 97.6% 59.8%
3tgnB02 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 0.63 52.0 4.65e-01 100.0% 71.4%
3dteA02 1.10.10.1030 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › IrrE, HTH domain 0.62 47.0 4.72e-01 92.7% 100.0%
2o8xA00 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 0.61 47.0 4.37e-01 97.6% 70.5%
3d5lB01 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 0.61 48.0 3.74e-01 95.1% 45.1%
4ha8A01 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 0.60 48.0 4.38e-01 100.0% 65.1%
1t0fA02 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 0.59 47.0 3.76e-01 100.0% 47.5%
2z99A01 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 0.59 47.0 3.86e-01 100.0% 46.0%
4u7bA02 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 0.57 44.0 4.47e-01 100.0% 100.0%
2pmyA00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.56 42.0 3.56e-01 78.0% 58.9%
1kq4A00 3.30.1360.170 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.55 47.0 3.03e-01 100.0% 85.7%
1zc6A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.50 39.0 2.75e-01 95.1% 25.6%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2036630 101.35.1.3 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › CW_7 0.96 89.0 7.97e-01 100.0% 75.9%
3222400 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.77 68.0 5.25e-01 100.0% 48.9%
3714702 4156.1.1.0 alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like 0.73 60.0 3.82e-01 100.0% 37.0%
4073499 101.35.1.0 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.70 57.0 5.79e-01 92.7% 97.5%
3466087 101.1.1.253 alpha arrays › HTH › HTH › Three-helical HTH › HTH_CLF_N 0.67 54.0 5.26e-01 100.0% 90.0%
3587439 101.1.1.2 alpha arrays › HTH › HTH › Three-helical HTH › HTH_AraC 0.66 54.0 5.09e-01 100.0% 81.8%
4158504 101.35.1.0 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.66 52.0 5.12e-01 100.0% 95.6%
3710980 101.35.1.0 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.65 50.0 4.94e-01 95.1% 93.3%
4928805 101.1.2.233 alpha arrays › HTH › HTH › winged helix domain › NirdL-like_HTH 0.64 52.0 4.45e-01 100.0% 56.0%
5042947 101.35.1.0 alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.63 52.0 4.97e-01 100.0% 84.0%
3737312 509.1.1.1 alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.62 48.0 4.18e-01 97.6% 53.3%
4939640 101.1.2.141 alpha arrays › HTH › HTH › winged helix domain › HTH_24 0.61 50.0 4.54e-01 100.0% 68.3%
5041744 2004.1.3.1 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR 0.60 48.0 3.37e-01 100.0% 25.6%
5060508 101.1.2.141 alpha arrays › HTH › HTH › winged helix domain › HTH_24 0.60 47.0 4.81e-01 100.0% 97.5%
3389326 101.1.2.383 alpha arrays › HTH › HTH › winged helix domain › HTH_69 0.60 48.0 4.53e-01 100.0% 74.5%
5013090 304.4.1.83 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › HTH_24 0.60 46.0 3.17e-01 100.0% 21.7%
4973736 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.59 48.0 4.12e-01 100.0% 68.0%
3948820 101.1.1.29 alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.58 48.0 3.89e-01 100.0% 48.9%
D3 medium residues 197-290
PDB
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF08230.17 best CW_7 51.7 8.10e-14 44.7% 97.5%
PF08230.17 CW_7 67.0 1.30e-18 41.5% 92.5%