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NC_001331.1__NP_039610.1__Pf1p11__00011

Bact-Vir

NC_001331.1__NP_039610.1__Pf1p11__00011

Identity

Accession:
NC_001331 ↗
Kingdom:
phage

Quality

93.6 mean pLDDT

Taxonomy

Loebvirae› Hofneiviricota› Faserviricetes› Tubulavirales› Inoviridae› Primolicivirus› Primolicivirus_Pf1

TaxID: 2011081

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 2-70
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2hgsA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.68 46.0 3.94e-01 100.0% 44.1%
3egrA00 3.10.20.520 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phenylacetic acid degradation B 0.63 45.0 4.65e-01 100.0% 82.5%
5ja1B00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.61 44.0 4.54e-01 76.8% 86.4%
3zoqC00 6.20.250.30 Special › Other non-globular › Double Stranded RNA Binding Domain › 0.61 41.0 4.60e-01 100.0% 92.5%
1m0wA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.57 39.0 3.40e-01 100.0% 45.4%
2w5fB01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.55 42.0 3.22e-01 100.0% 36.8%
1lkxA01 3.40.850.10 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain 0.55 38.0 2.63e-01 72.5% 47.6%
3nziA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.54 39.0 3.49e-01 100.0% 50.9%
1xe0C00 2.60.120.340 Mainly Beta › Sandwich › Jelly Rolls › Nucleoplasmin core domain 0.54 37.0 3.30e-01 98.6% 49.5%
2avxA00 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.53 41.0 3.17e-01 85.5% 97.1%
1nezH00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 46.0 3.87e-01 100.0% 60.8%
4gucA00 2.60.40.3720 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 39.0 3.36e-01 100.0% 49.6%
3vteA03 3.40.462.20 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › 0.52 45.0 3.31e-01 98.6% 45.9%
2lxxA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.51 44.0 3.47e-01 100.0% 45.4%
6uqjA02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.51 40.0 2.59e-01 87.0% 51.3%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.51 39.0 3.66e-01 88.4% 97.8%
2petA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 44.0 3.75e-01 100.0% 59.1%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.50 38.0 3.71e-01 98.6% 75.0%
2vpaA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.50 39.0 2.89e-01 100.0% 29.9%
ECOD (38)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3475092 10.12.1.1 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.71 49.0 3.42e-01 100.0% 23.3%
3734833 304.14.1.0 ↗ a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) 0.68 61.0 5.58e-01 98.6% 98.9%
4144303 11.1.1.3 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ig 0.67 46.0 3.64e-01 100.0% 33.8%
4284041 10.12.1.1 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.67 46.0 3.35e-01 100.0% 25.6%
3721982 304.14.1.0 ↗ a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) 0.66 58.0 5.24e-01 98.6% 97.9%
3969006 3115.6.1.2 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › PF28597 0.60 38.0 4.49e-01 98.6% 100.0%
4032409 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 49.0 4.80e-01 100.0% 85.3%
3884004 11.1.1.1016 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF30511 0.59 44.0 3.83e-01 100.0% 52.4%
3909420 11.1.1.129 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Interfer-bind 0.59 42.0 3.76e-01 100.0% 54.7%
2324048 1185.1.1.1 ↗ a+b two layers › A hypothetical protein from Neisseria gonorrhoeae › A hypothetical protein from Neisseria gonorrhoeae › A hypothetical protein from Neisseria gonorrhoeae › DUF6911 0.57 40.0 3.30e-01 100.0% 37.7%
4210460 264.2.1.0 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.57 51.0 4.27e-01 100.0% 97.5%
3922674 10.2.1.0 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) 0.57 47.0 2.99e-01 100.0% 18.8%
3216210 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.57 39.0 4.41e-01 95.7% 100.0%
3753133 10.2.1.0 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) 0.56 47.0 2.99e-01 100.0% 18.5%
3895559 10.2.1.5 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › TGFb_propeptide 0.56 46.0 3.16e-01 100.0% 25.8%
5061537 871.1.1.1 ↗ a+b two layers › SSo0622-like (Pfam 02676) › SSo0622-like (Pfam 02676) › SSo0622-like (Pfam 02676) › TYW3 0.55 39.0 2.93e-01 100.0% 27.2%
4270868 10.2.1.5 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › TGFb_propeptide 0.55 43.0 3.17e-01 100.0% 29.5%
3510263 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.55 45.0 3.57e-01 100.0% 43.3%
3926171 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 42.0 3.55e-01 100.0% 49.2%
2890419 304.139.1.1 ↗ a+b two layers › Alpha-beta plaits › Cas7-related › CRISPR-associated protein Cas7/Csa2-related › DevR 0.53 42.0 3.45e-01 88.4% 100.0%
4544238 304.128.1.0 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB 0.53 45.0 4.12e-01 97.1% 94.7%
5011928 206.1.3.7 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › ATP-grasp 0.52 35.0 2.41e-01 100.0% 17.0%
2106285 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.52 39.0 3.48e-01 100.0% 53.7%
4294583 10.2.1.31 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin 0.52 36.0 2.99e-01 98.6% 40.8%
5074648 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.52 39.0 3.82e-01 100.0% 76.0%
3579183 206.1.3.14 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › GSH_synth_ATP 0.52 43.0 2.78e-01 100.0% 53.4%
4927303 525.1.1.1 ↗ a+b two layers › Urease, gamma-subunit › Urease, gamma-subunit › Urease, gamma-subunit › Urease_gamma 0.52 42.0 3.68e-01 97.1% 90.0%
3193127 210.2.1.1 ↗ a+b four layers › Ntn/PP2C › Protein serine/threonine phosphatase 2C, catalytic domain › Protein serine/threonine phosphatase 2C, catalytic domain › PP2C 0.52 40.0 2.52e-01 84.1% 70.9%
4937773 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.52 38.0 4.06e-01 100.0% 98.3%
3703145 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 35.0 3.28e-01 100.0% 53.7%
4965895 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.51 36.0 3.31e-01 100.0% 54.0%
2887044 54.1.1.6 ↗ beta barrels › EV matrix protein › EV matrix protein › EV matrix protein › Matrix_Paramyxo_C 0.51 45.0 3.48e-01 100.0% 65.2%
3498945 109.4.1.291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PUF_NOP9 0.51 39.0 2.37e-01 89.9% 11.4%
4260704 224.1.1.2 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin 0.51 46.0 4.15e-01 100.0% 75.8%
3932049 10.2.1.0 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) 0.50 45.0 3.36e-01 100.0% 39.4%
3943285 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.50 45.0 3.87e-01 100.0% 72.5%
3935205 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.50 44.0 3.71e-01 100.0% 68.3%
4298891 4121.1.1.2 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like 0.50 38.0 2.67e-01 87.0% 55.9%