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SR-VP_2-4_scaffold_141_2548329_prodigal-single.1__X__X__00096

Bact-Vir

SR-VP_2-4_scaffold_141_2548329_prodigal-single.1__X__X__00096

Identity

Kingdom:
phage

Quality

86.9 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 5-109
PDB
CATH (47)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3l8hA00 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.79 67.0 5.54e-01 90.5% 89.3%
3bwvA01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.68 63.0 5.90e-01 98.1% 81.7%
3smvA01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.67 62.0 5.34e-01 98.1% 81.4%
1cqzB01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.65 55.0 5.06e-01 90.5% 82.2%
1x42A01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.65 60.0 5.28e-01 98.1% 83.6%
4axsA00 3.40.1160.10 Alpha Beta › 3-Layer(aba) Sandwich › Carbamate kinase › Acetylglutamate kinase-like 0.65 58.0 4.25e-01 100.0% 85.2%
2ah5A01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.65 61.0 5.42e-01 100.0% 84.7%
2i7nA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.65 46.0 4.10e-01 75.2% 82.6%
2amyA01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.64 53.0 4.84e-01 88.6% 79.7%
6jdbA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.62 43.0 3.88e-01 72.4% 96.1%
5djsA03 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.62 52.0 4.49e-01 92.4% 98.8%
3weeB02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.61 44.0 4.20e-01 75.2% 86.5%
2gfhA01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.61 56.0 4.80e-01 99.0% 76.9%
7d73A01 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 0.59 51.0 4.02e-01 97.1% 73.4%
2g7zA01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.59 44.0 3.93e-01 80.0% 85.8%
2pl1A00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.59 37.0 3.59e-01 79.0% 55.8%
2ggsA02 3.90.25.10 Alpha Beta › Alpha-Beta Complex › UDP-galactose 4-epimerase; domain 1 › UDP-galactose 4-epimerase, domain 1 0.59 31.0 3.61e-01 76.2% 73.5%
3ij3A01 3.40.220.10 Alpha Beta › 3-Layer(aba) Sandwich › Leucine Aminopeptidase, subunit E; domain 1 › Leucine Aminopeptidase, subunit E, domain 1 0.58 41.0 3.81e-01 72.4% 92.4%
4x9xA01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.58 44.0 3.93e-01 80.0% 89.3%
4i66A00 3.40.50.12140 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Domain of unknown function DUF4159 0.57 42.0 3.46e-01 78.1% 98.0%
2gupA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.57 47.0 3.89e-01 90.5% 86.9%
3nyiB01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.57 43.0 3.78e-01 80.0% 88.5%
2ivnA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.57 40.0 3.59e-01 74.3% 99.4%
4ymiB00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.57 48.0 3.96e-01 94.3% 71.7%
3h2gA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.57 42.0 3.16e-01 79.0% 72.8%
3pvsB01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.57 35.0 3.15e-01 74.3% 43.0%
3hdgA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.56 35.0 3.39e-01 79.0% 54.0%
2pg3A00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.56 46.0 3.65e-01 90.5% 60.9%
2yjgA02 3.40.50.11440 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › LarA, N-terminal domain 0.56 49.0 3.86e-01 100.0% 84.1%
2jjmA02 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.55 47.0 4.00e-01 95.2% 89.4%
1b93B00 3.40.50.1380 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Methylglyoxal synthase-like domain 0.55 46.0 4.06e-01 90.5% 66.2%
4do7A00 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.55 40.0 2.94e-01 77.1% 48.2%
3r64A01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.54 45.0 3.33e-01 90.5% 35.1%
7vo4B01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 40.0 3.11e-01 78.1% 76.9%
5jmuA00 3.20.20.370 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycoside hydrolase/deacetylase 0.54 44.0 3.52e-01 89.5% 77.7%
1vb5B02 3.40.50.10470 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Translation initiation factor eif-2b; domain 2 0.52 46.0 3.88e-01 100.0% 91.7%
3jr7A01 3.40.50.10440 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Dihydroxyacetone kinase; domain 1 0.52 39.0 3.78e-01 80.0% 78.8%
7c2xA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.52 46.0 3.44e-01 100.0% 72.1%
5tdeA03 3.40.50.261 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Succinyl-CoA synthetase domains 0.51 39.0 3.28e-01 81.0% 76.7%
2p9bA02 3.30.110.90 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Amidohydrolase 0.51 33.0 3.61e-01 79.0% 80.2%
1ez0B01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.51 45.0 3.22e-01 98.1% 41.0%
2e18A00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.51 45.0 3.42e-01 100.0% 85.2%
3h49B00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.51 43.0 3.21e-01 97.1% 65.9%
7uuim01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 45.0 3.95e-01 100.0% 77.8%
3moiA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.50 45.0 3.83e-01 100.0% 90.3%
3hj6A01 3.40.1190.30 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › 0.50 44.0 3.71e-01 100.0% 95.7%
4lg1B00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.50 45.0 3.60e-01 100.0% 55.4%
ECOD (57)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5040082 2006.1.1.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like 0.85 71.0 6.48e-01 88.6% 87.4%
5078078 2006.1.1.6 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Acid_phosphat_B 0.79 74.0 5.75e-01 98.1% 85.2%
5065644 2006.1.1.13 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Acid_PPase 0.78 66.0 5.62e-01 89.5% 85.9%
5029097 2006.1.1.10 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › NT5C 0.78 72.0 5.80e-01 98.1% 85.4%
4038162 2006.1.1.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like 0.77 71.0 5.79e-01 98.1% 86.5%
4092415 2006.1.1.12 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › PNK3P 0.77 65.0 5.75e-01 90.5% 89.3%
5057598 2006.1.1.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like 0.77 62.0 6.03e-01 84.8% 85.2%
5039917 2006.1.1.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like 0.76 70.0 5.55e-01 98.1% 81.4%
5074746 2006.1.1.18 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › HAD_2 0.76 70.0 5.77e-01 98.1% 80.9%
3743962 2006.1.1.28 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › APP1_cat 0.76 69.0 5.31e-01 98.1% 83.1%
3460476 2006.1.1.6 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Acid_phosphat_B 0.76 70.0 5.27e-01 99.0% 66.0%
4195491 2006.1.1.15 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase_like 0.75 69.0 5.50e-01 98.1% 85.6%
3395332 2006.1.1.36 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Put_Phosphatase 0.75 67.0 5.02e-01 95.2% 85.0%
3343247 2006.1.1.13 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Acid_PPase 0.74 63.0 5.21e-01 89.5% 65.1%
3187410 2006.1.1.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › NIF 0.74 63.0 4.86e-01 90.5% 80.9%
4942644 2006.1.1.15 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase_like 0.73 68.0 5.61e-01 100.0% 86.1%
3788157 2006.1.1.28 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › APP1_cat 0.73 67.0 4.88e-01 100.0% 75.9%
3613437 2006.1.1.33 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › HAD_SAK_2 0.71 59.0 5.13e-01 90.5% 70.6%
4001830 2006.1.1.16 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase_like,Hydrolase_6 0.68 64.0 5.51e-01 100.0% 82.6%
3427982 2006.1.1.52 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › PF28688 0.67 57.0 5.01e-01 90.5% 87.3%
3691951 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.66 47.0 3.92e-01 75.2% 98.4%
4886706 632.7.1.1 alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.64 48.0 4.07e-01 80.0% 97.8%
1698349 7512.1.1.33 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_41 0.62 53.0 4.28e-01 96.2% 84.8%
3490628 2484.1.1.7 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Ribosomal_S11 0.62 44.0 4.16e-01 75.2% 77.5%
4441419 2484.1.1.7 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Ribosomal_S11 0.61 43.0 4.16e-01 74.3% 80.8%
5003765 7516.1.1.24 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › NTP_transf_3 0.60 51.0 4.05e-01 92.4% 79.0%
4175121 2484.1.1.2 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.59 49.0 3.91e-01 92.4% 95.5%
5022353 7542.1.2.3 a/b three-layered sandwiches › Aconitase iron-sulfur domain › Aconitase iron-sulfur domain › Aconitase iron-sulfur domain II › AcnX_2nd 0.59 43.0 4.40e-01 84.8% 81.0%
4668786 2484.1.1.94 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HypF_C_2 0.59 44.0 3.29e-01 80.0% 98.2%
4680789 2484.1.1.8 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › ROK 0.58 48.0 3.95e-01 91.4% 89.0%
5074897 2002.1.1.0 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.58 46.0 3.20e-01 100.0% 26.3%
5073694 7516.1.1.0 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases 0.58 52.0 3.94e-01 100.0% 93.2%
4978361 2002.1.1.0 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.58 46.0 3.22e-01 100.0% 26.9%
4990562 7522.1.1.1 a/b three-layered sandwiches › TK C-terminal domain-like › TK C-terminal domain-like › TK C-terminal domain-like › Transketolase_C 0.57 43.0 3.91e-01 79.0% 82.1%
3648738 2003.1.2.165 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › GDP_Man_Dehyd 0.57 41.0 4.43e-01 85.7% 88.9%
4932648 2484.1.1.7 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Ribosomal_S11 0.57 40.0 3.65e-01 74.3% 70.7%
3466452 2484.1.1.10 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TsaD 0.57 50.0 3.81e-01 100.0% 97.3%
4980154 7516.1.1.2 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.56 50.0 4.09e-01 100.0% 91.5%
4358375 2484.1.1.10 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TsaD 0.56 49.0 3.89e-01 100.0% 98.3%
4000974 2004.1.1.73 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MMR_HSR1 0.56 42.0 3.64e-01 79.0% 94.4%
4986006 2484.1.1.333 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF1464 0.55 48.0 3.89e-01 97.1% 93.3%
4933350 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.55 41.0 3.89e-01 79.0% 93.0%
4061629 2006.1.3.8 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › Toprim_4,RecR_C 0.55 39.0 3.74e-01 74.3% 74.4%
3396302 7516.1.1.0 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases 0.55 48.0 3.55e-01 100.0% 79.0%
5061623 7516.1.1.26 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glyco_tranf_2_3 0.55 48.0 3.47e-01 100.0% 74.8%
5081219 2005.1.1.4 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Asn_synthase 0.55 45.0 3.47e-01 90.5% 60.0%
3626470 2003.1.1.72 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › GDP_Man_Dehyd 0.54 46.0 3.30e-01 92.4% 55.4%
4191640 2484.1.1.94 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HypF_C_2 0.54 43.0 3.25e-01 87.6% 100.0%
3967848 7579.1.1.10 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Thioesterase 0.54 40.0 3.04e-01 79.0% 85.8%
3182300 7579.1.1.6 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_1 0.54 41.0 2.97e-01 80.0% 60.3%
4370096 2484.1.1.10 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TsaD 0.53 46.0 3.74e-01 100.0% 95.9%
5054743 2003.1.7.2 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NagB/RpiA/CoA transferase-like › IF-2B 0.53 47.0 3.92e-01 100.0% 89.2%
5050772 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 38.0 3.48e-01 80.0% 89.3%
4481935 7543.1.1.2 a/b three-layered sandwiches › Methylglyoxal synthase-like › Methylglyoxal synthase-like › Methylglyoxal synthase-like › MGS 0.52 42.0 3.80e-01 92.4% 94.2%
5021540 7550.1.1.0 a/b three-layered sandwiches › Tetrapyrrole methylase N-terminal domain › Tetrapyrrole methylase N-terminal domain › Tetrapyrrole methylase N-terminal domain 0.51 39.0 4.01e-01 89.5% 87.0%
3651211 2003.1.1.153 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Epimerase, GDP_Man_Dehyd 0.51 45.0 2.99e-01 99.0% 34.9%
4656730 2005.1.1.11 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ATP_bind_3 0.50 44.0 3.36e-01 100.0% 78.1%
D2 high residues 121-164
PDB