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KR063281.1__AKJ72603.1__GMA2_65__00065

Bact-Vir

KR063281.1__AKJ72603.1__GMA2_65__00065

Identity

Accession:
KR063281 ↗
Kingdom:
phage

Quality

83.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Gimaduovirus› Gordonia_phage_GMA2

TaxID: 1647283

Cluster

View cluster (5 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 4-162
PDB
Domain cluster: representative
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ep4A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.77 72.0 7.15e-01 99.4% 96.4%
3bzcA03 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.76 59.0 6.54e-01 96.9% 100.0%
4ktwA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.70 64.0 6.42e-01 98.1% 100.0%
1sz2B01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.67 49.0 5.47e-01 100.0% 99.2%
5f7pA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.66 49.0 5.48e-01 96.9% 100.0%
2derB01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.64 45.0 4.17e-01 100.0% 57.1%
4wnyA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.63 40.0 4.37e-01 97.5% 76.5%
5if3B00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.63 45.0 4.06e-01 72.3% 66.0%
3fojA00 3.40.250.10 Alpha Beta › 3-Layer(aba) Sandwich › Oxidized Rhodanese; domain 1 › Rhodanese-like domain 0.62 34.0 4.19e-01 84.3% 84.8%
2cx6A00 3.30.370.10 Alpha Beta › 2-Layer Sandwich › Barnase; Chain D › Barstar-like 0.62 36.0 4.57e-01 70.4% 100.0%
2vgnA02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.62 47.0 5.14e-01 99.4% 97.6%
6uqjA02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.61 46.0 3.53e-01 78.0% 85.5%
3b48F00 3.40.50.510 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphotransferase system, mannose-type IIA component 0.60 43.0 4.68e-01 100.0% 87.4%
7y11A01 3.40.525.10 Alpha Beta › 3-Layer(aba) Sandwich › Phosphatidylinositol Transfer Protein Sec14p › CRAL-TRIO lipid binding domain 0.55 45.0 4.15e-01 86.2% 88.5%
2btoA01 3.40.50.1440 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Tubulin/FtsZ, GTPase domain 0.55 50.0 4.26e-01 100.0% 90.5%
1ej0A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.54 40.0 3.87e-01 75.5% 79.4%
6aeoB01 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.54 41.0 4.42e-01 88.7% 93.3%
3gffA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 43.0 3.46e-01 84.3% 62.0%
6dntA02 3.90.25.10 Alpha Beta › Alpha-Beta Complex › UDP-galactose 4-epimerase; domain 1 › UDP-galactose 4-epimerase, domain 1 0.54 26.0 3.03e-01 80.5% 62.0%
4lnuB01 3.40.50.1440 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Tubulin/FtsZ, GTPase domain 0.54 49.0 4.20e-01 100.0% 91.1%
1oizA02 3.40.525.10 Alpha Beta › 3-Layer(aba) Sandwich › Phosphatidylinositol Transfer Protein Sec14p › CRAL-TRIO lipid binding domain 0.54 42.0 3.98e-01 83.0% 82.4%
6h99A02 3.40.250.10 Alpha Beta › 3-Layer(aba) Sandwich › Oxidized Rhodanese; domain 1 › Rhodanese-like domain 0.54 40.0 4.03e-01 89.9% 77.4%
2wabA02 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.53 48.0 4.36e-01 100.0% 97.2%
4h08A00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.53 48.0 4.49e-01 100.0% 88.0%
1dnpA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.53 39.0 4.30e-01 97.5% 94.6%
1hxhA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 47.0 4.06e-01 100.0% 89.3%
4zkdA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 47.0 4.08e-01 100.0% 94.0%
2x9qB00 3.40.50.11710 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cyclodipeptide synthase 0.52 46.0 4.12e-01 100.0% 68.9%
6yubA02 3.40.250.10 Alpha Beta › 3-Layer(aba) Sandwich › Oxidized Rhodanese; domain 1 › Rhodanese-like domain 0.52 33.0 3.76e-01 76.7% 87.0%
5tdeA03 3.40.50.261 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Succinyl-CoA synthetase domains 0.52 45.0 4.29e-01 100.0% 79.9%
2efjA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.52 36.0 3.29e-01 72.3% 62.6%
2rbgA00 3.40.50.11100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 35.0 3.89e-01 96.9% 88.7%
1bxkA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 47.0 4.00e-01 100.0% 96.4%
1x6vB03 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.51 41.0 3.64e-01 86.2% 88.0%
6hcdD00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.51 37.0 4.00e-01 94.3% 90.4%
5ktkA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 46.0 3.34e-01 100.0% 52.0%
2g9zA02 3.40.50.10240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Thiamin pyrophosphokinase, catalytic domain 0.51 36.0 3.50e-01 71.7% 100.0%
4gicA01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.51 35.0 3.67e-01 95.0% 77.8%
1f21A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.51 41.0 4.26e-01 89.3% 91.4%
6uqyB01 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.51 45.0 3.79e-01 98.1% 100.0%
4yhbA02 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.50 36.0 3.88e-01 72.3% 87.9%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5029161 2484.1.1.330 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF460 0.79 58.0 5.95e-01 100.0% 78.1%
3308941 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.78 74.0 6.70e-01 100.0% 83.9%
5067783 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.72 40.0 4.69e-01 98.1% 76.1%
3953223 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.71 43.0 5.37e-01 76.7% 96.0%
4267061 2484.1.1.40 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvX 0.71 58.0 6.22e-01 98.1% 100.0%
3288652 2484.1.1.40 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvX 0.66 58.0 5.75e-01 100.0% 90.3%
3438965 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.66 39.0 4.75e-01 100.0% 93.0%
4604367 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.64 39.0 4.25e-01 97.5% 71.1%
5005020 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.63 39.0 4.13e-01 95.6% 68.6%
4963302 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.62 40.0 4.23e-01 96.2% 72.9%
5042296 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.62 38.0 4.07e-01 96.2% 70.9%
3583171 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.61 45.0 4.45e-01 74.2% 92.7%
4931828 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.61 38.0 4.05e-01 95.6% 69.3%
4001806 2005.1.1.36 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › SLC12 0.61 44.0 4.31e-01 74.2% 86.3%
3959101 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.61 37.0 4.03e-01 94.3% 71.1%
3362218 2005.1.1.36 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › SLC12 0.61 45.0 4.41e-01 76.1% 86.5%
4345567 2484.1.1.8 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › ROK 0.59 42.0 4.55e-01 97.5% 86.7%
3959532 2005.1.1.18 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › NAD_synthase 0.58 41.0 4.03e-01 100.0% 66.3%
3479417 2005.1.1.36 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › SLC12 0.58 41.0 4.31e-01 71.7% 100.0%
3243588 2484.1.1.200 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FTH 0.57 53.0 4.16e-01 100.0% 63.4%
3263189 2007.2.5.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Rhodanese/Cell cycle control phosphatase 0.56 42.0 4.08e-01 90.6% 67.6%
3955549 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.56 33.0 3.74e-01 96.9% 75.8%
3355734 2484.1.1.67 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.55 37.0 4.44e-01 71.7% 100.0%
5002880 2004.1.1.641 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF6079 0.55 39.0 2.99e-01 73.0% 33.1%
3348352 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.54 40.0 3.88e-01 76.1% 79.4%
3779769 2003.1.6.6 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Tubulin nucleotide-binding domain-like › Misat_Tub_SegII+Tubulin_3 0.54 50.0 4.08e-01 100.0% 94.7%
4933955 7592.1.1.6 ↗ a/b three-layered sandwiches › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › CARF (CRISPR-associated Rossmann fold) domains › Csa3_N 0.54 41.0 4.27e-01 97.5% 84.7%
3976298 7579.1.1.9 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Esterase 0.54 44.0 3.62e-01 87.4% 78.6%
5012303 2003.1.6.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Tubulin nucleotide-binding domain-like 0.53 46.0 4.80e-01 100.0% 98.7%
3976110 2004.1.1.641 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF6079 0.53 38.0 3.08e-01 73.0% 49.5%
None — 0.53 43.0 3.86e-01 88.7% 94.0%
3218178 2484.1.1.4 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H 0.52 42.0 4.30e-01 89.3% 89.3%
4221376 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.52 39.0 4.24e-01 85.5% 96.2%
3587056 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.52 48.0 4.79e-01 99.4% 99.4%
3730885 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.52 37.0 3.01e-01 72.3% 46.4%
4991997 2005.1.1.13 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CTP_transf_like 0.51 37.0 3.92e-01 94.3% 83.6%
3446564 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.51 37.0 3.91e-01 74.8% 93.1%
3412825 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.51 47.0 3.36e-01 100.0% 84.7%
5024526 2005.1.1.14 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › PAPS_reduct 0.51 43.0 3.68e-01 90.6% 80.0%
2391911 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.51 37.0 4.00e-01 94.3% 90.4%
4948408 300.1.1.8 ↗ a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease › PLDc_2 0.51 41.0 3.26e-01 98.1% 42.2%
4933889 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.50 38.0 4.08e-01 96.2% 94.0%