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NC_073367.1__YP_010751214.1__QDA03_gp89__00017

Bact-Vir

NC_073367.1__YP_010751214.1__QDA03_gp89__00017

Identity

Accession:
NC_073367 ↗
Kingdom:
phage

Quality

83.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Hodgkinviridae› Margaeryvirus› Microbacterium_phage_Terij

TaxID: 2686229

Cluster

Singleton — not in a non-trivial cluster

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 medium residues 46-131
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1x43A01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.71 48.0 5.45e-01 82.6% 96.8%
2ekhA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.70 47.0 4.84e-01 83.7% 73.8%
6my0A02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.69 44.0 4.92e-01 84.9% 84.6%
2dmoA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.68 45.0 4.94e-01 82.6% 85.3%
6uzjA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.68 47.0 5.29e-01 87.2% 98.4%
2pqhB00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.67 44.0 4.90e-01 81.4% 87.7%
1tg0A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.66 48.0 5.37e-01 87.2% 100.0%
2egcA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.66 45.0 4.82e-01 82.6% 81.3%
1y0mA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.66 44.0 5.01e-01 82.6% 96.7%
4cc2A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.65 45.0 5.03e-01 81.4% 96.8%
3m9qA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.64 50.0 5.40e-01 98.8% 100.0%
4iupA02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.63 48.0 5.17e-01 97.7% 97.2%
1igqB00 2.30.30.150 Mainly Beta › Roll › SH3 type barrels. › KorB, C-terminal domain 0.62 36.0 4.26e-01 83.7% 86.0%
2kxcA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.62 42.0 4.69e-01 81.4% 91.0%
2ke9A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.61 44.0 4.90e-01 82.6% 97.0%
2diqA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.61 40.0 3.83e-01 91.9% 57.0%
2l89A00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.61 45.0 4.21e-01 91.9% 63.0%
4fw1A02 2.30.30.10 Mainly Beta › Roll › SH3 type barrels. › Integrase, C-terminal domain superfamily, retroviral 0.60 37.0 4.37e-01 83.7% 96.3%
1khcA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.60 42.0 4.74e-01 94.2% 96.9%
3nmzD00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.60 49.0 4.95e-01 95.3% 90.5%
2gfuA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.60 46.0 3.94e-01 96.5% 52.2%
3oyyA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.58 40.0 4.44e-01 89.5% 93.9%
4ebgA00 3.10.450.560 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.56 34.0 3.28e-01 84.9% 52.6%
4me3A02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 39.0 3.78e-01 72.1% 93.8%
6p3qA02 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.56 49.0 4.09e-01 100.0% 84.8%
1uebA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.54 37.0 4.19e-01 90.7% 98.4%
2db9A01 3.90.70.200 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Plus-3 domain 0.54 45.0 3.93e-01 93.0% 83.5%
3upuA03 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.54 42.0 3.71e-01 87.2% 99.2%
2jxbA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.53 45.0 4.56e-01 98.8% 93.0%
3agjF01 2.30.30.870 Mainly Beta › Roll › SH3 type barrels. › Pelota, domain A 0.52 45.0 4.05e-01 100.0% 71.7%
3zugB02 2.40.30.30 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like 0.51 43.0 3.74e-01 98.8% 67.6%
1tj6A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.50 39.0 3.65e-01 87.2% 81.7%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4030603 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.71 50.0 5.50e-01 91.9% 92.6%
3243536 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.70 50.0 5.04e-01 94.2% 75.3%
3401559 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.69 48.0 5.43e-01 87.2% 96.9%
4104114 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.69 45.0 4.98e-01 82.6% 87.7%
4133335 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.68 44.0 5.07e-01 82.6% 95.0%
3542245 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.67 44.0 4.78e-01 82.6% 82.9%
3529708 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.66 45.0 4.76e-01 82.6% 80.0%
4550532 4.1.1.58 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_3 0.65 47.0 4.66e-01 82.6% 72.2%
3485667 4.1.1.99 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_10 0.64 51.0 5.46e-01 89.5% 98.7%
3541996 102.1.1.0 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.64 43.0 3.32e-01 83.7% 31.1%
3897602 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.64 49.0 4.76e-01 91.9% 74.7%
1144815 4.1.1.103 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_12 0.63 53.0 5.53e-01 100.0% 100.0%
3347795 4.1.1.94 ↗ beta barrels › SH3 › SH3 › SH3 › SAWADEE 0.63 48.0 4.96e-01 97.7% 87.5%
3441143 4.1.1.94 ↗ beta barrels › SH3 › SH3 › SH3 › SAWADEE 0.63 48.0 4.55e-01 97.7% 70.0%
3410370 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.62 46.0 4.97e-01 91.9% 97.1%
3570369 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.61 42.0 4.20e-01 90.7% 67.8%
3484620 4.1.1.92 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_9 0.61 49.0 4.78e-01 87.2% 85.3%
3677709 4.1.1.103 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_12 0.61 52.0 5.35e-01 95.3% 100.0%
3600862 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.61 45.0 4.63e-01 77.9% 100.0%
3715828 4.1.1.58 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_3 0.60 46.0 4.75e-01 82.6% 95.0%
3939982 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.57 43.0 3.99e-01 93.0% 62.7%
3733806 4.1.1.72 ↗ beta barrels › SH3 › SH3 › SH3 › Hva1_TUDOR 0.57 45.0 4.82e-01 97.7% 100.0%
3934278 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.56 45.0 4.14e-01 91.9% 66.1%
5016315 220.1.1.219 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › CheF-arch 0.56 43.0 3.80e-01 82.6% 79.2%
3898170 4.1.1.92 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_9 0.56 43.0 4.58e-01 84.9% 96.0%
4982529 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.56 32.0 3.88e-01 84.9% 96.0%
3931161 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 45.0 4.16e-01 93.0% 77.4%
3329012 4.18.1.1 ↗ beta barrels › SH3 › Plus3 › Plus3 › Plus-3 0.54 45.0 3.76e-01 93.0% 75.5%
4546371 220.1.1.219 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › CheF-arch 0.54 40.0 3.56e-01 77.9% 76.7%
3938484 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 45.0 4.03e-01 91.9% 66.7%
3254941 4.18.1.1 ↗ beta barrels › SH3 › Plus3 › Plus3 › Plus-3 0.53 45.0 3.94e-01 93.0% 85.4%
3391463 4.18.1.1 ↗ beta barrels › SH3 › Plus3 › Plus3 › Plus-3 0.53 45.0 3.99e-01 93.0% 82.4%
4173092 222.2.1.1 ↗ a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Insertion domain in thioesterase › Insertion domain in thioesterase › FAS1_thioest_ins 0.53 40.0 3.87e-01 86.0% 94.3%
3842362 1.1.5.76 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › CABIT 0.53 45.0 4.37e-01 97.7% 92.6%
5055689 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.53 34.0 3.63e-01 77.9% 76.0%
5080207 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.52 41.0 3.12e-01 83.7% 75.5%
3770801 4.1.1.248 ↗ beta barrels › SH3 › SH3 › SH3 › CABIT 0.52 44.0 4.30e-01 97.7% 91.6%
4962934 331.2.1.15 ↗ a+b two layers › TBP-like › Phosphoglucomutase, C-terminal domain › Phosphoglucomutase, C-terminal domain › DUF7845 0.52 44.0 3.72e-01 100.0% 81.9%
1174726 4028.1.1.1 ↗ beta barrels › Barrel domain in heme-dependent catalases › Barrel domain in heme-dependent catalases › Barrel domain in heme-dependent catalases › Catalase 0.52 37.0 3.20e-01 76.7% 47.2%
4955607 3435.1.1.0 ↗ a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC 0.52 36.0 2.75e-01 100.0% 29.3%
3507295 304.166.1.9 ↗ a+b two layers › Alpha-beta plaits › Nup54 ferredoxin-like domain › Nup54 ferredoxin-like domain › PF29949 0.51 34.0 3.28e-01 86.0% 59.0%
3651019 5.1.4.101 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › DUF1618 0.51 39.0 2.84e-01 86.0% 45.1%
4883912 4028.1.1.1 ↗ beta barrels › Barrel domain in heme-dependent catalases › Barrel domain in heme-dependent catalases › Barrel domain in heme-dependent catalases › Catalase 0.51 37.0 3.54e-01 76.7% 68.3%
3738161 4.18.1.1 ↗ beta barrels › SH3 › Plus3 › Plus3 › Plus-3 0.51 43.0 3.89e-01 97.7% 91.2%
3458138 375.1.1.131 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › DUF702 0.51 35.0 3.89e-01 73.3% 98.5%
4340770 4.1.1.248 ↗ beta barrels › SH3 › SH3 › SH3 › CABIT 0.51 43.0 4.18e-01 97.7% 93.7%
3486847 4.1.1.284 ↗ beta barrels › SH3 › SH3 › SH3 › SBNO 0.51 38.0 3.63e-01 86.0% 67.6%
D2 medium residues 132-198
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2wzfA01 1.10.1740.130 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › 0.67 45.0 3.93e-01 70.1% 60.6%
2csxA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.59 43.0 3.01e-01 77.6% 55.2%
7ecrA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.58 45.0 3.36e-01 86.6% 43.2%
1v1aA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.55 39.0 2.61e-01 76.1% 67.4%
4cswA01 2.60.120.650 Mainly Beta › Sandwich › Jelly Rolls › Cupin 0.53 39.0 2.84e-01 80.6% 77.4%
3sszA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.53 37.0 3.09e-01 76.1% 45.9%
1ei6A01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.53 42.0 2.84e-01 92.5% 83.6%
4h0pA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.52 41.0 3.06e-01 92.5% 50.5%
3qvoA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 37.0 2.74e-01 77.6% 92.3%
7ekqA01 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 0.51 38.0 2.81e-01 80.6% 70.0%
5o6uB00 3.30.70.2540 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › CRISPR-associated endoribonuclease Cas6/Csy4 0.50 37.0 2.83e-01 82.1% 47.8%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3600641 3456.1.1.0 ↗ extended segments › NADH-quinone oxidoreductase subunit A › NADH-quinone oxidoreductase subunit A › NADH-quinone oxidoreductase subunit A 0.53 38.0 3.48e-01 79.1% 91.6%
154280 2484.1.1.12 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Acetate_kinase 0.52 41.0 3.05e-01 92.5% 49.8%
4547229 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.51 35.0 2.74e-01 73.1% 54.8%