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NC_042099.1__YP_009622105.1__FDJ24_gp44__00044

Bact-Vir

NC_042099.1__YP_009622105.1__FDJ24_gp44__00044

Identity

Accession:
NC_042099 ↗
Kingdom:
phage

Quality

84.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Dismasvirus› Microbacterium_phage_Dismas

TaxID: 2065199

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 high residues 13-57
PDB
Domain cluster: representative
CATH (47)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6my0A02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.83 74.0 6.55e-01 100.0% 70.8%
1wgsA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.78 68.0 4.85e-01 100.0% 39.1%
3j7aF03 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.77 68.0 5.84e-01 100.0% 67.6%
2eqkA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.77 68.0 5.81e-01 100.0% 63.0%
5kcoA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.76 66.0 6.05e-01 100.0% 79.7%
2gfaB01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.75 64.0 5.84e-01 100.0% 77.4%
4ytlA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.74 64.0 6.23e-01 100.0% 88.0%
4ii1A01 2.30.30.1190 Mainly Beta › Roll › SH3 type barrels. › 0.73 64.0 5.30e-01 100.0% 88.7%
1ex4B02 2.30.30.10 Mainly Beta › Roll › SH3 type barrels. › Integrase, C-terminal domain superfamily, retroviral 0.72 62.0 5.69e-01 100.0% 74.6%
4b9wA02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.71 61.0 5.76e-01 100.0% 82.1%
6ghmC02 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.70 61.0 5.47e-01 100.0% 87.5%
2eczA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.70 60.0 5.23e-01 100.0% 78.6%
3h8zA02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.70 59.0 5.33e-01 100.0% 68.8%
1udlA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.68 58.0 4.61e-01 100.0% 54.1%
2egeA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.68 56.0 4.92e-01 100.0% 81.3%
2pqhB00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.67 57.0 5.16e-01 100.0% 81.5%
4x9cD00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.66 57.0 5.22e-01 100.0% 75.0%
3i35A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.66 56.0 5.27e-01 100.0% 96.5%
6c6sD02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.66 55.0 5.12e-01 100.0% 78.3%
7afrX02 2.30.30.180 Mainly Beta › Roll › SH3 type barrels. › Ribosome maturation factor RimP, C-terminal domain 0.66 56.0 5.22e-01 100.0% 80.0%
3q5zA02 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.66 53.0 4.12e-01 100.0% 66.1%
4zciA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.66 46.0 3.59e-01 75.6% 85.1%
1ug1A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.64 50.0 4.26e-01 100.0% 62.0%
1kq1H00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.62 51.0 4.64e-01 100.0% 68.2%
4h75A00 2.80.10.70 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › Spindlin/Ssty 0.62 47.0 3.32e-01 100.0% 26.1%
3na2A00 3.40.1570.20 Alpha Beta › 3-Layer(aba) Sandwich › Heme iron utilization protein-like fold › 0.61 49.0 3.67e-01 100.0% 58.7%
4m4zA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.61 49.0 4.90e-01 100.0% 100.0%
2dmoA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.61 48.0 4.42e-01 100.0% 77.9%
3pg7A02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 48.0 3.84e-01 97.8% 54.5%
1uirA01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.60 47.0 4.61e-01 93.3% 94.2%
1inlC02 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.60 47.0 4.33e-01 93.3% 76.6%
2k3aA01 3.90.1720.10 Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › endopeptidase domain like (from Nostoc punctiforme) 0.60 50.0 4.00e-01 100.0% 53.0%
2htdB00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.60 44.0 3.33e-01 84.4% 91.1%
4jrnA02 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.59 44.0 3.42e-01 100.0% 67.4%
2cmgA01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.59 45.0 4.41e-01 88.9% 92.2%
7u32F02 2.30.30.10 Mainly Beta › Roll › SH3 type barrels. › Integrase, C-terminal domain superfamily, retroviral 0.59 46.0 4.55e-01 100.0% 96.1%
1onfA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.58 49.0 3.74e-01 100.0% 97.5%
4k17B01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 50.0 3.81e-01 100.0% 60.4%
2diqA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.58 45.0 3.79e-01 100.0% 45.0%
1iy9A02 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.58 47.0 4.58e-01 97.8% 92.3%
3o4fC01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.57 45.0 4.44e-01 97.8% 94.1%
2i2lA01 2.10.70.50 Mainly Beta › Ribbon › Complement Module; domain 1 › 0.54 42.0 4.13e-01 95.6% 98.1%
3bs1A00 2.40.50.1020 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › LytTr DNA-binding domain 0.54 41.0 3.42e-01 97.8% 47.6%
2pmaA01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.53 40.0 3.21e-01 95.6% 43.0%
4g54A01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.53 41.0 3.23e-01 100.0% 38.4%
3zs6A02 3.90.76.10 Alpha Beta › Alpha-Beta Complex › Dipeptide-binding Protein; domain 1 › Dipeptide-binding Protein; Domain 1 0.51 42.0 3.16e-01 97.8% 96.7%
3in6A02 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.51 39.0 3.15e-01 100.0% 43.6%
ECOD (71)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4025829 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.86 78.0 7.24e-01 100.0% 85.5%
3507146 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.85 77.0 6.13e-01 100.0% 57.6%
3836457 4.1.1.20 ↗ beta barrels › SH3 › SH3 › SH3 › BAH 0.85 76.0 5.19e-01 100.0% 48.0%
3741680 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.83 74.0 6.94e-01 100.0% 87.3%
5050716 4.11.1.2 ↗ beta barrels › SH3 › LexA/Signal peptidase › LexA/Signal peptidase › Peptidase_S26 0.81 72.0 5.05e-01 100.0% 41.5%
3176265 4.11.1.1 ↗ beta barrels › SH3 › LexA/Signal peptidase › LexA/Signal peptidase › Peptidase_S24 0.81 69.0 4.79e-01 100.0% 39.4%
3488114 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.80 71.0 5.17e-01 100.0% 40.8%
5017073 4.11.1.0 ↗ beta barrels › SH3 › LexA/Signal peptidase › LexA/Signal peptidase 0.80 70.0 4.85e-01 100.0% 32.7%
4999430 4.11.1.0 ↗ beta barrels › SH3 › LexA/Signal peptidase › LexA/Signal peptidase 0.80 71.0 5.16e-01 100.0% 39.2%
3629536 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.80 70.0 5.50e-01 100.0% 52.6%
4093836 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.80 71.0 6.43e-01 100.0% 81.7%
4981578 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.78 60.0 4.57e-01 84.4% 58.1%
3549321 4.11.1.5 ↗ beta barrels › SH3 › LexA/Signal peptidase › LexA/Signal peptidase › Peptidase_S24, PF31032 0.77 65.0 4.50e-01 100.0% 37.5%
3486271 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.76 69.0 5.41e-01 100.0% 51.1%
3226827 4.1.1.133 ↗ beta barrels › SH3 › SH3 › SH3 › SMN_YG-box 0.76 68.0 5.13e-01 100.0% 47.6%
3768347 4.1.1.230 ↗ beta barrels › SH3 › SH3 › SH3 › DUF7030 0.76 65.0 5.84e-01 100.0% 87.7%
3475965 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.75 65.0 6.53e-01 100.0% 97.8%
4642857 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.75 64.0 5.38e-01 100.0% 78.8%
3568329 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.75 65.0 5.93e-01 100.0% 83.3%
3464886 4.1.1.42 ↗ beta barrels › SH3 › SH3 › SH3 › Agenet 0.75 66.0 5.99e-01 100.0% 83.3%
3449268 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.75 66.0 5.32e-01 100.0% 54.1%
4956443 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.74 65.0 5.91e-01 100.0% 81.7%
3826746 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.74 65.0 5.38e-01 100.0% 57.5%
3612184 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.74 63.0 5.81e-01 100.0% 73.3%
3502388 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.73 64.0 5.43e-01 100.0% 61.3%
3570700 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.73 62.0 4.67e-01 100.0% 40.9%
3514970 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.73 64.0 5.08e-01 100.0% 51.1%
3395948 4.1.1.43 ↗ beta barrels › SH3 › SH3 › SH3 › SMN_Tudor 0.73 64.0 6.05e-01 100.0% 83.6%
3925408 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.72 63.0 6.10e-01 100.0% 90.0%
3571064 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.72 62.0 5.09e-01 100.0% 54.1%
3389161 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.72 61.0 4.84e-01 100.0% 46.3%
3231675 4.1.1.92 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_9 0.71 61.0 5.34e-01 100.0% 78.6%
2581331 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.71 61.0 5.24e-01 100.0% 85.3%
3274551 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.71 62.0 5.29e-01 100.0% 61.3%
3914833 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.71 61.0 5.35e-01 100.0% 78.6%
3723101 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.71 60.0 5.57e-01 100.0% 96.7%
3522910 4.1.1.92 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_9 0.71 61.0 5.21e-01 100.0% 73.3%
3744277 4.1.1.33 ↗ beta barrels › SH3 › SH3 › SH3 › Myosin_N 0.71 61.0 5.95e-01 100.0% 90.0%
3356591 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.71 63.0 4.89e-01 100.0% 48.4%
3317400 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.71 63.0 4.39e-01 100.0% 32.9%
3797970 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.70 59.0 4.85e-01 100.0% 62.2%
3769245 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.70 59.0 5.12e-01 100.0% 73.3%
2866962 4.31.1.1 ↗ beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.70 58.0 4.54e-01 100.0% 51.9%
2893010 4.1.1.8 ↗ beta barrels › SH3 › SH3 › SH3 › IN_DBD_C 0.70 60.0 5.71e-01 100.0% 85.2%
3929784 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.70 61.0 5.95e-01 100.0% 96.0%
2575643 4.1.1.8 ↗ beta barrels › SH3 › SH3 › SH3 › IN_DBD_C 0.70 59.0 5.16e-01 100.0% 63.8%
3523046 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.68 58.0 4.81e-01 100.0% 61.2%
3774692 4.1.1.31 ↗ beta barrels › SH3 › SH3 › SH3 › Spin-Ssty 0.68 58.0 4.88e-01 100.0% 70.0%
3936496 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.67 54.0 4.42e-01 100.0% 48.0%
3731599 2003.1.2.16 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3,NAD_binding_8 0.66 57.0 3.49e-01 97.8% 52.5%
3665882 4.1.1.42 ↗ beta barrels › SH3 › SH3 › SH3 › Agenet 0.63 48.0 3.73e-01 100.0% 35.6%
3477189 375.14.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) 0.63 48.0 4.87e-01 97.8% 91.1%
3425088 145.1.1.3 ↗ alpha arrays › F-box domain › F-box domain › F-box domain › F-box-like 0.63 48.0 4.38e-01 86.7% 75.4%
3924149 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.63 48.0 4.79e-01 100.0% 88.0%
4937731 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.62 49.0 4.66e-01 100.0% 78.3%
540 4.1.1.8 ↗ beta barrels › SH3 › SH3 › SH3 › IN_DBD_C 0.62 48.0 4.77e-01 100.0% 91.7%
3769507 4.1.1.31 ↗ beta barrels › SH3 › SH3 › SH3 › Spin-Ssty 0.60 49.0 4.40e-01 100.0% 68.6%
4424609 4.8.1.5 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.59 50.0 4.78e-01 95.6% 90.6%
3236689 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.59 45.0 4.44e-01 100.0% 81.8%
3411714 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.59 46.0 4.21e-01 100.0% 65.7%
3978877 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.58 47.0 3.92e-01 100.0% 55.6%
3970112 4167.1.1.0 ↗ beta complex topology › Flagellar hook protein flgE D1 domain › Flagellar hook protein flgE D1 domain › Flagellar hook protein flgE D1 domain 0.58 48.0 3.32e-01 93.3% 31.7%
5045214 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.58 45.0 4.11e-01 100.0% 65.7%
3567457 4.1.1.92 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_9 0.56 44.0 4.02e-01 100.0% 74.3%
3886102 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.56 43.0 3.23e-01 97.8% 63.3%
3885695 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.56 43.0 3.82e-01 100.0% 65.0%
4995694 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.55 43.0 4.20e-01 100.0% 89.1%
3168302 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.55 44.0 2.58e-01 95.6% 14.5%
3775000 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.53 40.0 3.03e-01 95.6% 62.1%
3287636 304.136.1.1 ↗ a+b two layers › Alpha-beta plaits › Oligo-peptide binding protein (OPPA) insertion domain › Oligo-peptide binding protein (OPPA) insertion domain › SBP_bac_5 0.52 43.0 3.40e-01 97.8% 100.0%
4281130 212.1.1.14 ↗ a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › CbiD 0.52 41.0 2.96e-01 100.0% 56.6%