←Back to structures

YP_010772096.1

Arc-Vir

NC_074639__YP_010772096.1__QIT36-gp013__00013

Identity

Accession:
NC_074639 ↗
Protein ID:
YP_010772096.1 ↗
Kingdom:
archaea

Quality

90.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Nakonvirales› Ekchuahviridae› Kukulkanvirus› Methanophagales_virus_GBV301

TaxID: 2999280

Cluster

View cluster (25 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 3-104_164-211
PDB
Domain cluster: rep: IMGVR_UViG_3300021495_000001-3300021495-Ga0190352_1000003117__D1-101_192-218
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00149.34 best Metallophos 24.8 3.70e-05 86.7% 42.8%
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6gitA02 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.72 67.0 5.03e-01 100.0% 94.5%
3floA02 3.60.21.60 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › 0.71 64.0 5.35e-01 94.7% 91.3%
1fjmB00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.64 58.0 4.62e-01 96.7% 83.7%
2a22B00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.64 60.0 5.40e-01 100.0% 90.1%
5w8mA00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.63 59.0 5.34e-01 100.0% 93.9%
8d89A01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.63 52.0 3.94e-01 90.0% 87.4%
1auiA00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.63 57.0 4.17e-01 97.3% 67.5%
2wqpA01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.62 53.0 4.35e-01 91.3% 93.0%
2jepB00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.57 52.0 3.91e-01 100.0% 94.2%
1h65B00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.56 42.0 3.50e-01 76.7% 68.0%
5tcgA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.56 51.0 4.32e-01 100.0% 92.4%
2ahuA01 3.40.1080.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaconate Coenzyme A-transferase › Glutaconate Coenzyme A-transferase 0.55 49.0 4.04e-01 97.3% 82.8%
3bleA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.54 48.0 3.90e-01 100.0% 98.7%
4k3zA00 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.54 46.0 3.61e-01 90.7% 78.1%
1ezwA00 3.20.20.30 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Luciferase-like domain 0.54 49.0 3.78e-01 100.0% 96.8%
3ha2A00 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.54 39.0 3.81e-01 74.7% 86.8%
2clsA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 37.0 3.48e-01 88.0% 57.5%
3aptA00 3.20.20.220 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › 0.54 48.0 3.93e-01 100.0% 92.8%
2iw0A01 3.20.20.370 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycoside hydrolase/deacetylase 0.54 48.0 4.28e-01 100.0% 82.3%
3elbA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.54 41.0 4.30e-01 97.3% 89.1%
3milB00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.53 44.0 3.80e-01 90.0% 92.4%
3qxbA00 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.53 47.0 3.83e-01 100.0% 96.0%
3oqvA00 3.40.50.11710 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cyclodipeptide synthase 0.52 48.0 4.25e-01 99.3% 99.5%
4gxtA01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.52 44.0 3.85e-01 90.0% 87.0%
3elbA02 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.52 42.0 4.07e-01 97.3% 77.0%
1gnlA03 3.40.50.2030 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.52 39.0 3.90e-01 99.3% 76.2%
3a21B01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.52 46.0 3.77e-01 100.0% 91.1%
2x0kA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.52 44.0 4.16e-01 97.3% 75.8%
3glvA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.51 39.0 4.26e-01 98.0% 99.2%
6lcjD01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.51 45.0 3.70e-01 99.3% 97.3%
1dnpA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.50 40.0 4.30e-01 97.3% 100.0%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4995790 246.2.1.0 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases 0.83 75.0 5.95e-01 94.7% 95.7%
5058976 246.2.1.1 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos 0.70 66.0 5.19e-01 100.0% 94.1%
3363628 246.2.1.1 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos 0.67 52.0 4.27e-01 81.3% 91.1%
2388236 246.2.1.9 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos_2 0.62 58.0 5.29e-01 100.0% 91.3%
4028099 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.61 39.0 4.46e-01 91.3% 89.5%
5032065 2008.1.1.7 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › ERCC4 0.58 38.0 4.00e-01 91.3% 71.4%
4464495 2003.1.5.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › DNA_methylase 0.57 47.0 3.56e-01 88.0% 96.3%
4564490 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.57 51.0 3.48e-01 100.0% 44.8%
5062741 2002.1.1.44 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › TatD_DNase 0.56 47.0 3.94e-01 91.3% 94.8%
3653415 2002.1.1.90 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › MTHFR 0.56 42.0 3.74e-01 78.0% 62.3%
5043600 2002.3.1.2 ↗ a/b barrels › TIM beta/alpha-barrel › Glycoside hydrolase/deacetylase › Glycoside hydrolase/deacetylase › Polysacc_deac_1 0.55 49.0 4.36e-01 100.0% 91.1%
3438965 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.55 36.0 4.25e-01 72.7% 100.0%
145700 2003.1.1.3 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › adh_short 0.54 48.0 3.98e-01 100.0% 92.2%
4961722 2002.1.1.16 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Bac_luciferase 0.54 48.0 3.71e-01 100.0% 97.5%
4209604 2002.1.1.348 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › DUF6259 0.54 49.0 3.76e-01 100.0% 83.8%
4991997 2005.1.1.13 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CTP_transf_like 0.53 42.0 4.35e-01 96.7% 90.0%
3449542 2006.1.6.9 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › Copine 0.53 41.0 3.46e-01 83.3% 94.4%
4978071 2002.1.1.16 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Bac_luciferase 0.53 47.0 3.77e-01 100.0% 97.4%
3270427 2005.1.1.13 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CTP_transf_like 0.52 42.0 3.97e-01 97.3% 69.7%
4324516 7512.1.1.0 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase 0.52 39.0 3.43e-01 90.7% 52.0%
3706111 2005.1.1.13 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CTP_transf_like 0.52 42.0 4.11e-01 97.3% 80.0%
4286526 7570.1.1.1 ↗ a/b three-layered sandwiches › MurD-like peptide ligases, peptide-binding domain › MurD-like peptide ligases, peptide-binding domain › MurD-like peptide ligases, peptide-binding domain › Mur_ligase_C 0.52 40.0 4.22e-01 92.0% 91.9%
4413280 2005.1.1.13 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CTP_transf_like 0.51 40.0 4.08e-01 98.0% 83.3%
3743251 2005.1.1.13 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CTP_transf_like 0.51 41.0 4.10e-01 97.3% 83.2%
3955549 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.51 38.0 4.15e-01 97.3% 98.3%
3788819 2005.1.1.13 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CTP_transf_like 0.50 41.0 4.13e-01 97.3% 85.8%
5053002 2002.1.1.56 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Dus 0.50 45.0 3.55e-01 100.0% 70.8%
D2 medium residues 105-163
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3e0jA01 3.60.21.50 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › 0.85 77.0 4.80e-01 100.0% 29.1%
1s3lA00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.77 60.0 4.31e-01 100.0% 30.3%
2kknA00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.71 58.0 4.28e-01 100.0% 34.4%
2wddA01 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.63 55.0 3.52e-01 100.0% 34.8%
4dapA02 3.40.1350.60 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.61 51.0 3.95e-01 100.0% 60.5%
3sftA00 3.40.50.180 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Methylesterase CheB, C-terminal domain 0.59 42.0 3.02e-01 76.3% 47.6%
2ynmC03 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.58 39.0 3.17e-01 74.6% 34.1%
1xoiA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.58 45.0 2.79e-01 94.9% 34.9%
3kl7A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.57 48.0 3.36e-01 100.0% 36.8%
1wueA02 3.20.20.120 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Enolase-like C-terminal domain 0.57 47.0 3.29e-01 98.3% 55.9%
1sz2B01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 43.0 3.61e-01 91.5% 78.3%
2ph7A02 3.40.50.10670 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › af2093 domain 0.56 47.0 4.09e-01 98.3% 89.6%
1wp9A02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.56 41.0 3.17e-01 83.1% 69.1%
2c4mA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.55 43.0 2.66e-01 94.9% 33.9%
3hdjA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 42.0 3.15e-01 88.1% 30.4%
4jn7A02 3.20.20.120 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Enolase-like C-terminal domain 0.53 43.0 2.92e-01 98.3% 42.8%
5ha4A02 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.53 44.0 3.54e-01 100.0% 45.6%
4c0kA02 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.52 40.0 2.86e-01 86.4% 61.6%
3c1aA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 42.0 3.18e-01 100.0% 70.4%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5080277 246.2.1.1 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos 0.91 85.0 5.42e-01 100.0% 30.3%
3212577 246.2.1.7 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › DNA_pol_E_B 0.86 78.0 4.84e-01 100.0% 30.2%
3931546 246.2.1.7 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › DNA_pol_E_B 0.85 77.0 4.83e-01 100.0% 31.7%
3739917 246.2.1.7 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › DNA_pol_E_B 0.84 76.0 4.70e-01 100.0% 29.2%
3783068 246.2.1.7 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › DNA_pol_E_B 0.84 76.0 4.68e-01 100.0% 29.8%
4945908 246.2.1.9 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos_2 0.81 65.0 4.64e-01 100.0% 30.9%
3602674 2008.1.1.114 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF4143 0.68 57.0 4.95e-01 100.0% 64.0%
5083835 246.2.1.1 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos 0.67 58.0 3.64e-01 100.0% 42.1%
4937850 2008.1.1.114 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF4143 0.65 56.0 4.58e-01 100.0% 51.3%
4026895 246.2.1.7 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › DNA_pol_E_B 0.65 54.0 3.45e-01 100.0% 28.2%
4959341 2008.1.1.152 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF2130 0.60 51.0 4.10e-01 100.0% 52.0%
5011639 246.2.1.0 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases 0.58 49.0 3.74e-01 100.0% 38.7%
5061175 7512.1.1.30 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_4 0.58 48.0 3.58e-01 100.0% 62.9%
3706394 7507.1.1.1 ↗ a/b three-layered sandwiches › Glutaminase/Asparaginase C-terminal domain › Glutaminase/Asparaginase C-terminal domain › Glutaminase/Asparaginase C-terminal domain › Asparaginase_C 0.57 48.0 3.76e-01 94.9% 47.7%
4175432 246.1.1.1 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Carbon-nitrogen hydrolase › Carbon-nitrogen hydrolase › CN_hydrolase 0.56 46.0 3.05e-01 96.6% 37.5%
4041544 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 41.0 2.93e-01 79.7% 78.4%
1717299 7512.1.1.2 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Phosphorylase 0.55 43.0 2.68e-01 94.9% 35.6%
5062584 3008.1.1.2 ↗ a+b three layers › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › DUF5915 0.54 36.0 3.35e-01 71.2% 71.8%
5001378 7512.1.1.30 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_4 0.54 43.0 3.00e-01 94.9% 26.1%
4982881 7512.1.1.30 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_4 0.53 44.0 3.31e-01 100.0% 65.3%
5077468 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.51 43.0 3.02e-01 100.0% 55.8%