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SR-VP_0-2_scaffold_141_4556078_prodigal-single.1__X__X__00335

Bact-Vir

SR-VP_0-2_scaffold_141_4556078_prodigal-single.1__X__X__00335

Identity

Kingdom:
phage

Quality

92.1 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 medium residues 31-194
PDB
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2bmbA02 3.20.20.20 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Dihydropteroate synthase-like 0.67 52.0 4.14e-01 81.1% 95.3%
3qqwC01 3.20.20.60 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Phosphoenolpyruvate-binding domains 0.64 50.0 4.33e-01 82.9% 94.3%
7mpyA01 3.20.20.20 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Dihydropteroate synthase-like 0.62 49.0 4.31e-01 83.5% 95.9%
5d84A02 3.40.50.1100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.61 38.0 4.48e-01 72.6% 91.0%
2jbmA02 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.59 43.0 4.51e-01 74.4% 100.0%
2b7nA02 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.59 42.0 4.43e-01 73.2% 99.3%
3o63A00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.59 47.0 4.30e-01 84.1% 95.3%
1piiA02 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.58 45.0 4.27e-01 80.5% 99.5%
3a0uA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.58 33.0 3.80e-01 78.0% 77.4%
1dxyA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.57 35.0 3.82e-01 78.0% 72.9%
3snkA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.57 34.0 3.92e-01 78.0% 79.8%
1mb3A00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.57 32.0 3.71e-01 78.0% 75.2%
5x5jA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.57 32.0 3.71e-01 78.0% 74.6%
2qxyA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.57 32.0 3.73e-01 78.7% 75.6%
3rd5A00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.56 39.0 3.36e-01 70.1% 87.7%
1tdjA01 3.40.50.1100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.56 43.0 3.90e-01 80.5% 78.9%
6bmaA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.55 45.0 3.91e-01 87.2% 75.7%
4e4yA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.54 40.0 3.56e-01 78.0% 81.8%
2gn0B01 3.40.50.1100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.53 41.0 3.67e-01 79.9% 75.8%
3c3mA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.52 30.0 3.39e-01 71.3% 73.2%
5f5nA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 37.0 3.09e-01 72.6% 92.4%
3r1iB00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 39.0 3.43e-01 78.7% 78.5%
3mw8A02 3.40.50.10090 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 34.0 3.88e-01 73.8% 91.6%
1w25A01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.51 36.0 3.90e-01 78.7% 84.4%
2hlzA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.51 46.0 3.80e-01 98.8% 92.6%
4eexA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 36.0 3.85e-01 72.0% 95.0%
3e8xA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 39.0 3.57e-01 79.3% 77.1%
1vb3A03 3.40.50.1100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 36.0 3.83e-01 73.2% 95.2%
2jb9B00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.51 35.0 4.00e-01 78.0% 95.9%
6ontA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.51 35.0 4.01e-01 78.7% 96.7%
3lteD00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.50 35.0 3.93e-01 77.4% 93.5%
2oqrA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.50 24.0 3.27e-01 74.4% 90.0%
2rjnA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.50 36.0 3.91e-01 78.7% 89.6%
ECOD (26)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4610054 7555.1.1.2 a/b three-layered sandwiches › Alpha-2,3/8-sialyltransferase CstII-related › Alpha-2,3/8-sialyltransferase CstII-related › Alpha-2,3/8-sialyltransferase CstII-related › MptE-like 0.84 79.0 6.11e-01 98.2% 54.2%
3838380 7555.1.1.2 a/b three-layered sandwiches › Alpha-2,3/8-sialyltransferase CstII-related › Alpha-2,3/8-sialyltransferase CstII-related › Alpha-2,3/8-sialyltransferase CstII-related › MptE-like 0.83 76.0 6.18e-01 95.7% 56.1%
4325819 7555.1.1.2 a/b three-layered sandwiches › Alpha-2,3/8-sialyltransferase CstII-related › Alpha-2,3/8-sialyltransferase CstII-related › Alpha-2,3/8-sialyltransferase CstII-related › MptE-like 0.78 72.0 6.10e-01 98.2% 62.4%
5016816 7555.1.1.2 a/b three-layered sandwiches › Alpha-2,3/8-sialyltransferase CstII-related › Alpha-2,3/8-sialyltransferase CstII-related › Alpha-2,3/8-sialyltransferase CstII-related › MptE-like 0.76 72.0 6.26e-01 100.0% 75.3%
4965044 7555.1.1.2 a/b three-layered sandwiches › Alpha-2,3/8-sialyltransferase CstII-related › Alpha-2,3/8-sialyltransferase CstII-related › Alpha-2,3/8-sialyltransferase CstII-related › MptE-like 0.72 67.0 6.12e-01 100.0% 78.1%
4033332 7512.1.1.15 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyphos_transf 0.61 46.0 4.22e-01 79.3% 87.9%
5016726 7512.1.1.107 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › DUF354 0.59 45.0 4.33e-01 79.3% 84.9%
3649553 2002.1.1.97 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › TMP-TENI 0.58 46.0 4.08e-01 83.5% 86.8%
4939118 2007.1.3.1 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › Response_reg 0.57 33.0 3.79e-01 79.3% 76.7%
4103302 2007.1.3.58 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › PF29701 0.57 34.0 3.93e-01 78.7% 80.8%
5035309 7543.1.1.2 a/b three-layered sandwiches › Methylglyoxal synthase-like › Methylglyoxal synthase-like › Methylglyoxal synthase-like › MGS 0.56 34.0 3.12e-01 79.9% 46.2%
2814431 7586.1.1.1 a/b three-layered sandwiches › Rossmann-like domain in prismane-like proteins › Rossmann-like domain in prismane-like proteins › Rossmann-like domain in prismane-like proteins › Prismane 0.55 36.0 3.51e-01 87.2% 59.4%
4123668 7586.1.1.1 a/b three-layered sandwiches › Rossmann-like domain in prismane-like proteins › Rossmann-like domain in prismane-like proteins › Rossmann-like domain in prismane-like proteins › Prismane 0.54 38.0 3.73e-01 73.2% 96.2%
4987917 2002.3.1.2 a/b barrels › TIM beta/alpha-barrel › Glycoside hydrolase/deacetylase › Glycoside hydrolase/deacetylase › Polysacc_deac_1 0.53 41.0 3.68e-01 81.7% 85.5%
4343693 2003.1.1.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.52 37.0 3.69e-01 74.4% 68.6%
3652115 2003.1.5.27 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › NAS 0.52 37.0 2.54e-01 72.0% 41.0%
5046403 2003.1.1.20 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Epimerase 0.51 39.0 3.10e-01 78.0% 89.8%
3980630 2007.1.3.1 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › Response_reg 0.51 35.0 3.84e-01 77.4% 86.9%
168853 2003.1.1.67 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › NAD_binding_10 0.51 39.0 3.57e-01 78.7% 77.0%
5053982 2005.1.1.11 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › ATP_bind_3 0.51 37.0 3.11e-01 74.4% 61.1%
4037133 2003.1.5.15 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › FtsJ 0.51 36.0 3.37e-01 72.6% 93.1%
3739337 2003.1.5.15 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › FtsJ 0.51 40.0 3.44e-01 82.3% 91.0%
4991110 2003.1.5.69 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › GCD14 0.50 34.0 3.42e-01 75.0% 65.9%
3256900 2003.1.1.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.50 36.0 3.64e-01 74.4% 74.4%
4978872 2003.1.11.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Formate/glycerate dehydrogenase catalytic domain-like 0.50 36.0 3.89e-01 78.7% 88.8%
4034184 2007.1.3.1 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › Response_reg 0.50 35.0 3.83e-01 78.0% 88.5%
D2 medium residues 195-279
PDB
Domain cluster: representative
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7febA03 3.40.50.12790 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › FHIPEP family, domain 4 0.60 51.0 5.02e-01 96.5% 94.6%
3gzaA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.57 49.0 3.30e-01 96.5% 55.1%
1hzdA01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.56 49.0 3.73e-01 98.8% 72.8%
3h8lA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.56 46.0 3.91e-01 94.1% 74.8%
3s28A03 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.56 46.0 3.23e-01 94.1% 42.6%
2zgyA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 45.0 3.83e-01 88.2% 97.1%
3axiA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.55 49.0 3.14e-01 100.0% 86.8%
2dt5A02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 37.0 3.26e-01 97.6% 43.5%
7qjnA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.55 48.0 3.41e-01 100.0% 89.4%
3p9dG03 3.50.7.10 Alpha Beta › 3-Layer(bba) Sandwich › GroEL › GroEL 0.55 49.0 4.01e-01 100.0% 83.3%
3wg9A02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 37.0 3.26e-01 97.6% 43.6%
1avaA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.54 48.0 3.22e-01 100.0% 89.9%
1dciA01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.54 48.0 3.63e-01 100.0% 62.3%
2a35A00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.54 48.0 3.63e-01 100.0% 59.6%
3iplB01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.54 40.0 2.69e-01 80.0% 21.7%
3p3vA00 3.40.35.10 Alpha Beta › 3-Layer(aba) Sandwich › Fructose Permease › Phosphotransferase system, sorbose subfamily IIB component 0.54 37.0 3.04e-01 74.1% 37.9%
1peaA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.53 41.0 3.17e-01 92.9% 36.5%
2gk4A00 3.40.50.10300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › CoaB-like 0.53 44.0 3.30e-01 92.9% 35.4%
3uesB01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.53 44.0 3.00e-01 94.1% 53.9%
2jrjA00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.53 28.0 3.41e-01 77.6% 82.7%
5fc1A01 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.52 44.0 2.93e-01 100.0% 33.9%
3lfjB00 3.40.35.10 Alpha Beta › 3-Layer(aba) Sandwich › Fructose Permease › Phosphotransferase system, sorbose subfamily IIB component 0.52 37.0 3.04e-01 76.5% 92.8%
4xpqA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.51 44.0 3.12e-01 100.0% 68.8%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3386000 7555.1.1.2 a/b three-layered sandwiches › Alpha-2,3/8-sialyltransferase CstII-related › Alpha-2,3/8-sialyltransferase CstII-related › Alpha-2,3/8-sialyltransferase CstII-related › MptE-like 0.78 69.0 4.70e-01 96.5% 35.2%
5064407 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.63 38.0 2.70e-01 78.8% 20.1%
3944717 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.61 54.0 3.84e-01 97.6% 74.0%
4964292 2003.1.1.12 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › DapB_N 0.61 40.0 3.32e-01 97.6% 37.3%
4464625 7512.1.1.0 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase 0.60 52.0 3.11e-01 97.6% 15.2%
4944916 2003.1.2.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.57 49.0 3.91e-01 94.1% 70.6%
3671742 376.1.1.8 few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › U-box 0.56 32.0 3.91e-01 89.4% 89.1%
3598301 376.1.1.0 few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.55 38.0 3.75e-01 70.6% 83.3%
1879027 244.1.1.6 a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C › Amino_oxidase 0.54 38.0 2.49e-01 72.9% 48.3%
4961001 2008.1.1.107 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NERD 0.54 46.0 3.74e-01 100.0% 48.2%
4882187 2002.1.1.51 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Alpha_L_fucos 0.54 47.0 3.15e-01 98.8% 58.9%
5025231 2003.1.1.51 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › DFP 0.54 45.0 3.49e-01 94.1% 41.2%
3943457 2007.1.5.5 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › ATC-like › AroM 0.54 40.0 3.68e-01 81.2% 95.7%
4199672 2492.1.1.0 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.53 30.0 2.99e-01 88.2% 48.4%
4660343 2003.1.1.32 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › CoA_binding 0.53 39.0 3.32e-01 94.1% 47.9%
4948746 7555.1.1.2 a/b three-layered sandwiches › Alpha-2,3/8-sialyltransferase CstII-related › Alpha-2,3/8-sialyltransferase CstII-related › Alpha-2,3/8-sialyltransferase CstII-related › MptE-like 0.53 44.0 3.26e-01 95.3% 76.7%
3513491 2498.1.1.1 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M10 0.52 34.0 2.59e-01 71.8% 26.7%
4943951 3110.1.1.0 a/b three-layered sandwiches › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain 0.51 37.0 3.26e-01 78.8% 56.4%
3977040 2484.1.1.175 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FGGY_N+FGGY_C 0.51 43.0 2.72e-01 96.5% 91.5%
3801081 2498.1.1.1 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M10 0.50 38.0 2.82e-01 80.0% 83.3%
4170393 314.1.1.9 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_His 0.50 43.0 2.95e-01 100.0% 54.9%