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SR-VP_4-6_scaffold_141_476970_prodigal-single.1__X__X__00130

Bact-Vir

SR-VP_4-6_scaffold_141_476970_prodigal-single.1__X__X__00130

Identity

Kingdom:
phage

Quality

94.1 mean pLDDT

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 4-161_225-268
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02739.23 best 5_3_exonuc_N 62.4 5.90e-17 86.1% 88.4%
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3zdbA01 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.91 64.0 7.26e-01 78.2% 91.7%
1tfrA01 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.82 77.0 7.71e-01 100.0% 97.1%
1xo1A02 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.82 62.0 7.01e-01 86.1% 98.7%
5v07Z01 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.72 55.0 5.51e-01 78.2% 83.0%
2q5cA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.63 29.0 3.98e-01 77.2% 86.6%
2n3zA00 3.40.50.11230 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.63 27.0 3.70e-01 76.7% 77.8%
1duvG01 3.40.50.1370 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Aspartate/ornithine carbamoyltransferase 0.59 31.0 3.51e-01 76.7% 65.3%
4gywA05 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.59 36.0 3.99e-01 78.2% 75.2%
7oo1A02 3.40.1380.20 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate Kinase; Chain: A, domain 1 › Pyruvate kinase, C-terminal domain 0.58 29.0 3.75e-01 78.2% 82.2%
2l82A00 3.40.50.11230 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.58 37.0 4.10e-01 78.2% 79.0%
3milB00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.57 39.0 3.69e-01 87.6% 57.6%
2omkA00 3.40.50.10240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Thiamin pyrophosphokinase, catalytic domain 0.57 37.0 3.62e-01 78.2% 59.5%
2bmuB00 3.40.1160.10 Alpha Beta › 3-Layer(aba) Sandwich › Carbamate kinase › Acetylglutamate kinase-like 0.57 43.0 4.16e-01 78.2% 98.2%
1a3wA01 3.40.1380.20 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate Kinase; Chain: A, domain 1 › Pyruvate kinase, C-terminal domain 0.56 30.0 3.37e-01 78.2% 65.8%
4yo7A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.55 36.0 4.02e-01 71.3% 83.3%
2qv7A01 3.40.50.10330 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Probable inorganic polyphosphate/atp-NAD kinase; domain 1 0.55 34.0 3.95e-01 78.2% 85.5%
2vg0A00 3.40.1180.10 Alpha Beta › 3-Layer(aba) Sandwich › Undecaprenyl pyrophosphate synthetase › Decaprenyl diphosphate synthase-like 0.55 41.0 3.99e-01 78.2% 98.2%
4y9tA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.54 37.0 3.90e-01 71.3% 77.3%
2etvA01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.54 32.0 3.76e-01 76.7% 81.2%
2vk2A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.53 35.0 3.88e-01 72.8% 81.8%
5g5tA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.52 32.0 3.54e-01 78.2% 75.2%
2vdvE01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.52 34.0 3.55e-01 78.2% 69.4%
2zosB01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.52 38.0 4.28e-01 76.7% 98.7%
2qtlA03 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.51 38.0 4.23e-01 75.2% 98.7%
1u7nA00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.50 38.0 3.21e-01 76.7% 93.4%
1hv9A01 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.50 38.0 3.65e-01 76.2% 96.9%
2i33B00 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.50 37.0 3.53e-01 75.2% 65.7%
4ru1A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.50 34.0 3.94e-01 72.3% 94.6%
ECOD (53)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4040391 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.88 68.0 7.19e-01 78.2% 95.6%
4238071 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.88 67.0 7.26e-01 78.2% 95.4%
3831671 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.88 67.0 6.89e-01 78.2% 95.4%
4157264 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.87 67.0 7.14e-01 78.2% 93.3%
3387660 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.87 65.0 7.16e-01 78.2% 91.2%
3942272 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.87 67.0 7.29e-01 78.2% 96.5%
4995752 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.86 65.0 7.26e-01 78.2% 94.5%
2074443 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.86 66.0 7.13e-01 78.2% 92.0%
4031817 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.86 66.0 7.19e-01 78.2% 94.7%
4125023 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.85 66.0 7.18e-01 78.2% 92.9%
4029535 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.85 66.0 6.98e-01 78.2% 95.0%
3283240 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.85 65.0 6.70e-01 78.2% 90.3%
3261281 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.85 65.0 7.20e-01 78.2% 94.0%
3969358 2006.1.4.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.85 65.0 7.27e-01 78.2% 98.1%
3293941 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.84 70.0 6.95e-01 85.6% 95.2%
4355422 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.83 69.0 7.43e-01 88.1% 98.3%
4322588 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.83 70.0 7.44e-01 86.6% 100.0%
3964138 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.83 70.0 7.46e-01 87.1% 99.4%
3838580 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.82 65.0 6.89e-01 80.7% 95.0%
3710018 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.82 69.0 6.74e-01 86.1% 96.7%
4324598 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.81 68.0 7.12e-01 87.6% 93.5%
3942445 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.81 70.0 7.34e-01 88.6% 97.8%
3593819 2006.1.4.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.81 68.0 6.76e-01 87.1% 99.0%
4299585 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.81 70.0 7.34e-01 89.1% 98.4%
3596146 2006.1.4.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.81 62.0 6.19e-01 78.2% 92.6%
3808902 2006.1.4.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.76 54.0 5.78e-01 78.2% 82.2%
3913336 2006.1.4.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.75 54.0 5.69e-01 78.2% 80.5%
4136793 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.75 72.0 7.11e-01 100.0% 96.7%
3428426 2006.1.4.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.73 56.0 5.58e-01 78.2% 82.9%
4002931 2006.1.4.6 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › Fcf1 0.72 37.0 4.70e-01 78.2% 82.5%
3581443 2006.1.4.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.71 60.0 5.14e-01 87.1% 91.1%
3683988 2006.1.4.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.71 54.0 5.34e-01 78.2% 83.6%
3472483 2006.1.4.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.70 59.0 5.02e-01 87.1% 86.1%
3937112 2006.1.4.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.70 59.0 5.37e-01 88.1% 90.0%
4020826 2006.1.4.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.70 57.0 5.25e-01 85.1% 86.3%
3274669 2006.1.4.6 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › Fcf1 0.69 44.0 4.93e-01 78.2% 80.0%
4001799 2006.1.4.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.69 59.0 5.37e-01 88.6% 90.3%
3525340 2006.1.4.6 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › Fcf1 0.69 43.0 4.88e-01 78.2% 80.6%
3170744 2006.1.4.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.64 58.0 5.05e-01 95.0% 89.8%
3482158 2006.1.4.6 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › Fcf1 0.64 43.0 4.73e-01 78.2% 81.2%
3660261 2006.1.4.7 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › NYN_YacP 0.63 43.0 4.60e-01 100.0% 78.9%
4478290 7512.1.1.30 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_4 0.57 36.0 4.04e-01 78.2% 80.0%
3388330 2003.1.1.28 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › TrkA_N 0.57 32.0 3.81e-01 78.2% 80.7%
3837240 2005.1.1.3 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.56 41.0 4.37e-01 78.2% 86.3%
5056029 7534.1.1.1 a/b three-layered sandwiches › Undecaprenyl diphosphate synthase › Undecaprenyl diphosphate synthase › Undecaprenyl diphosphate synthase › Prenyltransf 0.55 42.0 4.05e-01 78.2% 95.7%
5063561 2007.1.16.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Iron-sulphur enzyme Dph2 0.55 29.0 3.89e-01 75.2% 100.0%
3798806 7534.1.1.0 a/b three-layered sandwiches › Undecaprenyl diphosphate synthase › Undecaprenyl diphosphate synthase › Undecaprenyl diphosphate synthase 0.55 41.0 3.93e-01 76.7% 93.0%
5011611 2006.1.4.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.55 41.0 4.15e-01 76.7% 95.5%
3954412 2007.1.4.2 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Phosphofructokinase N-terminal domain › DAGK_cat 0.54 31.0 3.81e-01 76.7% 87.7%
3785527 7514.1.1.3 a/b three-layered sandwiches › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › NAD_binding_6 0.54 39.0 4.19e-01 75.2% 96.1%
3951025 2007.1.2.11 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › Peripla_BP_4 0.53 36.0 3.98e-01 83.2% 85.6%
5025521 323.1.1.3 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.52 33.0 3.69e-01 94.1% 78.8%
5001367 2003.1.9.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.50 36.0 3.47e-01 78.2% 62.1%
D2 high residues 166-223
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5hmlA02 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.86 77.0 6.78e-01 94.8% 86.3%
3zdbA02 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.82 73.0 6.33e-01 100.0% 79.8%
5k97A02 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.66 57.0 5.43e-01 100.0% 92.6%
2k85A00 1.10.10.440 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain 0.52 36.0 3.54e-01 77.6% 67.7%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2074406 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.88 82.0 6.54e-01 100.0% 68.9%
4995753 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.85 79.0 6.06e-01 100.0% 59.7%
None 0.85 78.0 6.61e-01 100.0% 80.0%
3964109 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.85 78.0 7.08e-01 100.0% 94.7%
4343577 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.85 76.0 4.89e-01 98.3% 28.6%
4030601 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.84 77.0 6.02e-01 100.0% 61.7%
3283743 102.1.1.0 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.84 77.0 4.67e-01 100.0% 21.2%
4644646 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.83 76.0 6.62e-01 100.0% 82.4%
4237116 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.83 76.0 6.79e-01 100.0% 88.7%
3956065 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.83 76.0 6.75e-01 100.0% 93.8%
4440292 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.83 76.0 5.98e-01 100.0% 59.1%
4030950 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.83 76.0 5.97e-01 100.0% 61.7%
3593817 102.1.1.0 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.83 75.0 6.71e-01 100.0% 90.0%
4364220 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.82 74.0 5.77e-01 100.0% 61.7%
3610020 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.81 73.0 6.41e-01 100.0% 84.7%
4341259 102.1.1.4 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › 5_3_exonuc 0.80 72.0 6.59e-01 100.0% 93.3%
3941508 148.1.3.57 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › DUF5375 0.54 38.0 3.26e-01 74.1% 88.4%