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NC_071013.1__YP_010676519.1__PQD69_gp053__00053

Bact-Vir

NC_071013.1__YP_010676519.1__PQD69_gp053__00053

Identity

Accession:
NC_071013 ↗
Kingdom:
phage

Quality

86.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Carnodivirus› Carnobacterium_phage_cd4

TaxID: 2849246

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 9-74
PDB
Domain cluster: representative
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ei5A03 2.40.128.50 Mainly Beta › Beta Barrel › Lipocalin › 0.70 54.0 4.66e-01 83.3% 95.1%
2j7qA00 3.90.70.120 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.67 58.0 4.03e-01 100.0% 41.1%
4r3dA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.66 49.0 3.96e-01 100.0% 39.4%
2f5tX02 2.30.30.690 Mainly Beta › Roll › SH3 type barrels. › 0.64 56.0 5.11e-01 100.0% 94.4%
7oo1A01 2.40.33.10 Mainly Beta › Beta Barrel › M1 Pyruvate Kinase; Domain 3 › PK beta-barrel domain-like 0.62 46.0 4.44e-01 92.4% 68.8%
2qmiA02 2.40.128.210 Mainly Beta › Beta Barrel › Lipocalin › Pab87 octamerisation domain 0.62 46.0 4.08e-01 81.8% 86.0%
1n4kA01 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.61 42.0 3.35e-01 74.2% 100.0%
3gg8C03 2.40.33.10 Mainly Beta › Beta Barrel › M1 Pyruvate Kinase; Domain 3 › PK beta-barrel domain-like 0.60 53.0 4.70e-01 100.0% 93.8%
3zx7A02 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.59 41.0 3.30e-01 74.2% 95.6%
8eq1A01 2.40.33.10 Mainly Beta › Beta Barrel › M1 Pyruvate Kinase; Domain 3 › PK beta-barrel domain-like 0.59 50.0 4.59e-01 95.5% 100.0%
1yzbA01 3.90.70.40 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.58 49.0 4.10e-01 100.0% 58.9%
3qtgA02 2.40.33.10 Mainly Beta › Beta Barrel › M1 Pyruvate Kinase; Domain 3 › PK beta-barrel domain-like 0.58 51.0 4.58e-01 100.0% 91.5%
3fanA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.58 36.0 3.50e-01 74.2% 56.2%
7r6yA01 2.40.33.10 Mainly Beta › Beta Barrel › M1 Pyruvate Kinase; Domain 3 › PK beta-barrel domain-like 0.57 49.0 4.39e-01 95.5% 100.0%
3cpxA02 2.40.30.40 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Peptidase M42, domain 2 0.57 47.0 4.84e-01 100.0% 100.0%
3n6rA03 3.30.700.30 Alpha Beta › 2-Layer Sandwich › Glycoprotein, Type 4 Pilin › 0.57 46.0 3.80e-01 95.5% 81.2%
3fqmA01 2.20.25.210 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › Hepatitis C NS5A, domain 1B 0.57 42.0 4.40e-01 95.5% 88.5%
1h30A01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.56 47.0 3.43e-01 100.0% 58.7%
2greF02 2.40.30.40 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Peptidase M42, domain 2 0.56 46.0 4.48e-01 98.5% 100.0%
1maiA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 42.0 3.57e-01 84.8% 82.4%
1xa6A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.55 39.0 3.42e-01 74.2% 51.9%
1ljoA00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.54 44.0 4.27e-01 93.9% 94.7%
4l69A01 2.40.240.20 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Hypothetical PUA domain-like; domain 1 0.53 36.0 3.60e-01 71.2% 91.2%
4wjmA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.53 37.0 2.43e-01 74.2% 27.9%
1u7bA00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.53 37.0 2.64e-01 77.3% 38.6%
3c12A01 2.30.30.910 Mainly Beta › Roll › SH3 type barrels. › 0.53 37.0 4.04e-01 81.8% 100.0%
1vpkA01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.53 34.0 2.80e-01 80.3% 35.8%
4mxtA00 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.52 42.0 3.16e-01 92.4% 80.2%
6muwB00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.52 44.0 3.14e-01 100.0% 82.5%
3ossC00 2.30.30.830 Mainly Beta › Roll › SH3 type barrels. › 0.52 37.0 3.72e-01 77.3% 90.8%
1vpkA02 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.52 37.0 3.13e-01 80.3% 77.3%
6ptrB01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.51 31.0 2.67e-01 80.3% 35.4%
1mbmA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.51 33.0 3.23e-01 74.2% 56.6%
4gdxB00 3.60.20.40 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Gamma-glutamyltranspeptidase, small (S) subunit 0.50 38.0 2.87e-01 86.4% 96.3%
2p84A01 2.60.430.10 Mainly Beta › Sandwich › YopX-like fold › YopX-like domain 0.50 35.0 3.66e-01 77.3% 98.3%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4168024 6.1.1.0 ↗ beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil 0.61 44.0 3.58e-01 78.8% 97.9%
3369217 3459.1.1.3 ↗ beta sandwiches › Fas apoptotic inhibitory molecule › Fas apoptotic inhibitory molecule › Fas apoptotic inhibitory molecule › DUF868 0.60 43.0 3.67e-01 77.3% 100.0%
3244902 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.57 49.0 3.68e-01 100.0% 58.3%
3826272 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.57 48.0 3.14e-01 100.0% 27.8%
1124180 3794.1.1.1 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit › PCC_BT 0.57 46.0 3.78e-01 95.5% 80.0%
5056156 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.55 45.0 4.35e-01 93.9% 98.7%
3821077 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.55 46.0 2.93e-01 100.0% 38.9%
3463325 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.54 41.0 2.88e-01 87.9% 32.9%
143428 227.1.1.6 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_C 0.52 37.0 3.21e-01 78.8% 78.3%
3590631 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.52 45.0 3.05e-01 100.0% 41.9%
426904 227.1.1.8 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.52 38.0 3.26e-01 83.3% 78.0%
3625965 4184.1.1.2 ↗ beta barrels › MFPT repeat › MFPT repeat › MFPT repeat › MFP2b 0.52 43.0 3.91e-01 100.0% 84.2%
3251867 227.1.1.11 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.51 38.0 3.21e-01 83.3% 78.5%
4030418 227.1.1.6 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_C 0.51 37.0 3.03e-01 80.3% 72.9%
4372908 227.1.1.0 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.51 37.0 3.13e-01 80.3% 72.8%
4948360 227.1.1.6 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_C 0.51 36.0 3.03e-01 77.3% 74.4%
5081486 3425.2.1.0 ↗ a+b three layers › Two-component system yycF/yycG regulatory protein yycH-like › YycH C-terminal domain › YycH C-terminal domain 0.51 37.0 2.61e-01 81.8% 96.4%
3932751 227.1.1.0 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.51 36.0 3.04e-01 78.8% 74.6%
3883683 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.50 40.0 3.59e-01 92.4% 77.0%
5028024 227.1.1.6 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_C 0.50 36.0 3.02e-01 78.8% 74.6%
309454 227.1.1.0 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.50 36.0 3.00e-01 78.8% 72.7%
3558235 227.1.1.11 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.50 37.0 3.09e-01 83.3% 79.3%
3754881 11.1.1.29 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › TIG 0.50 39.0 3.66e-01 90.9% 83.3%
D2 high residues 80-140
PDB
Domain cluster: rep: NC_071083.1__YP_010683437.1__PQF09_gp43__00043__D112-175
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ol0B00 6.20.90.30 Special › Other non-globular › SH3 type barrels. › 0.82 51.0 6.05e-01 80.3% 95.1%
1ybiA01 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.71 60.0 4.52e-01 91.8% 60.1%
2vseA04 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.71 64.0 4.81e-01 100.0% 92.3%
6lf2B01 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.69 62.0 4.90e-01 100.0% 96.8%
2zuoA08 2.30.30.620 Mainly Beta › Roll › SH3 type barrels. › 0.55 41.0 4.23e-01 80.3% 87.9%
6qcbA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.53 40.0 3.48e-01 82.0% 97.9%
1mppA01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.53 45.0 3.31e-01 100.0% 97.8%
1wkrA01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.52 44.0 3.27e-01 100.0% 93.5%
3vkwA01 3.30.450.420 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.51 36.0 2.78e-01 95.1% 30.7%
7tbdB01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.51 43.0 3.22e-01 98.4% 100.0%
1qs8A01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.51 43.0 3.19e-01 100.0% 94.9%
4c0dB00 2.30.30.1020 Mainly Beta › Roll › SH3 type barrels. › CCR4-NOT complex subunit 2/3/5, C-terminal domain 0.50 35.0 2.44e-01 72.1% 35.1%
1b5fC00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.50 42.0 2.92e-01 100.0% 68.9%
ECOD (20)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3890187 6.1.1.8 ↗ beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil › AbfB 0.75 68.0 4.91e-01 100.0% 89.1%
2708873 6.1.1.0 ↗ beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil 0.69 62.0 4.82e-01 100.0% 91.6%
3587970 11.1.4.36 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › SpaA 0.68 58.0 4.59e-01 100.0% 46.4%
4853186 2002.1.1.128 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › NAPRTase 0.62 43.0 2.77e-01 73.8% 23.0%
3265984 3529.1.1.0 ↗ beta sandwiches › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain 0.60 36.0 4.29e-01 80.3% 90.0%
3610326 3529.1.1.0 ↗ beta sandwiches › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain 0.59 35.0 4.14e-01 80.3% 87.5%
3595896 3529.1.1.0 ↗ beta sandwiches › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain 0.58 36.0 4.07e-01 77.0% 84.4%
3384823 1.1.1.28 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp, TAXi_C, TAXi_N 0.56 46.0 2.93e-01 100.0% 48.7%
1546151 1.1.1.1 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp 0.55 41.0 3.54e-01 82.0% 98.0%
3883684 355.1.1.9 ↗ few secondary structure elements › Trefoil/Plexin domain-like › Trefoil/Plexin domain-like › Trefoil/Plexin domain-like › PSI_PlexinA-B 0.54 35.0 3.66e-01 75.4% 72.7%
1171642 1.1.1.27 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp, TAXi_N 0.53 45.0 3.27e-01 100.0% 94.1%
3331374 1.1.1.28 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp, TAXi_C, TAXi_N 0.53 45.0 2.83e-01 100.0% 47.6%
3600630 3529.1.1.0 ↗ beta sandwiches › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain 0.53 40.0 3.80e-01 82.0% 94.7%
3824081 1.1.1.28 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp, TAXi_C, TAXi_N 0.52 43.0 2.76e-01 100.0% 50.3%
3266195 1.1.1.1 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp 0.52 44.0 2.74e-01 100.0% 51.5%
3945811 70.4.1.7 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › XM1_gp53_minor_capsid 0.52 37.0 3.80e-01 78.7% 86.7%
3407209 4.1.1.41 ↗ beta barrels › SH3 › SH3 › SH3 › NOT2_3_5_C 0.52 35.0 2.53e-01 70.5% 34.3%
3373122 1.1.1.20 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › TAXi_C+TAXi_N 0.52 44.0 2.73e-01 100.0% 46.3%
3593793 3529.1.1.0 ↗ beta sandwiches › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain 0.51 36.0 3.92e-01 85.2% 92.0%
1108449 4.1.1.41 ↗ beta barrels › SH3 › SH3 › SH3 › NOT2_3_5_C 0.50 35.0 2.44e-01 72.1% 35.1%