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NC_009814.1__YP_001468836.1__LiPP35_gp52__00052

Bact-Vir

NC_009814.1__YP_001468836.1__LiPP35_gp52__00052

Identity

Accession:
NC_009814 ↗
Kingdom:
phage

Quality

75.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Listeria_phage_P35

TaxID: 330398

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 2-61
PDB
Domain cluster: representative
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1qnaA01 3.30.310.10 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › TATA-Binding Protein 0.73 46.0 3.94e-01 86.7% 41.9%
5zwlE01 2.60.15.10 Mainly Beta › Sandwich › ATP Synthase; domain 1 › F0F1 ATP synthase delta/epsilon subunit, N-terminal 0.67 42.0 3.72e-01 100.0% 43.2%
1jheA00 2.10.109.10 Mainly Beta › Ribbon › Umud Fragment, subunit A › Umud Fragment, subunit A 0.67 51.0 4.14e-01 100.0% 41.9%
5dn6I00 2.60.15.10 Mainly Beta › Sandwich › ATP Synthase; domain 1 › F0F1 ATP synthase delta/epsilon subunit, N-terminal 0.67 42.0 3.89e-01 100.0% 50.7%
1aqtA01 2.60.15.10 Mainly Beta › Sandwich › ATP Synthase; domain 1 › F0F1 ATP synthase delta/epsilon subunit, N-terminal 0.66 41.0 3.65e-01 100.0% 43.2%
2hh8A00 3.30.1810.10 Alpha Beta › 2-Layer Sandwich › YdfO-like fold › YdfO-like 0.63 50.0 3.98e-01 88.3% 74.8%
4pmwA04 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.63 45.0 4.05e-01 80.0% 65.9%
2k57A00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.61 45.0 4.69e-01 96.7% 90.9%
2gqtA02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.61 42.0 3.43e-01 100.0% 37.2%
1smpI00 2.40.128.10 Mainly Beta › Beta Barrel › Lipocalin › 0.59 47.0 4.17e-01 96.7% 96.0%
3s6gA02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.59 46.0 3.56e-01 88.3% 45.9%
2ra2B00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.58 46.0 4.69e-01 96.7% 93.1%
1uirA01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.57 42.0 4.45e-01 85.0% 94.2%
1h8eH00 2.60.15.10 Mainly Beta › Sandwich › ATP Synthase; domain 1 › F0F1 ATP synthase delta/epsilon subunit, N-terminal 0.57 46.0 4.18e-01 95.0% 78.7%
2l3rA02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.56 47.0 4.51e-01 100.0% 82.2%
6igbA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.56 45.0 2.78e-01 90.0% 38.3%
3oe3C00 2.40.128.200 Mainly Beta › Beta Barrel › Lipocalin › C-type lysozyme inhibitor 0.55 42.0 3.84e-01 90.0% 97.7%
2hldH01 2.60.15.10 Mainly Beta › Sandwich › ATP Synthase; domain 1 › F0F1 ATP synthase delta/epsilon subunit, N-terminal 0.55 43.0 4.00e-01 93.3% 84.5%
2e5yA01 2.60.15.10 Mainly Beta › Sandwich › ATP Synthase; domain 1 › F0F1 ATP synthase delta/epsilon subunit, N-terminal 0.55 42.0 3.92e-01 95.0% 79.5%
2hyxA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.54 40.0 3.19e-01 100.0% 37.4%
3o4fC01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.54 40.0 4.19e-01 85.0% 96.1%
3c6kA02 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.54 40.0 4.16e-01 85.0% 91.1%
6focH01 2.60.15.10 Mainly Beta › Sandwich › ATP Synthase; domain 1 › F0F1 ATP synthase delta/epsilon subunit, N-terminal 0.54 43.0 3.76e-01 95.0% 65.7%
2vz8A04 3.10.129.110 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Polyketide synthase dehydratase 0.53 44.0 2.96e-01 95.0% 80.7%
3kfvA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.53 45.0 3.91e-01 100.0% 83.0%
4fmrB01 2.70.50.70 Mainly Beta › Distorted Sandwich › Coagulation Factor XIII; Chain A, domain 1 › 0.53 39.0 2.97e-01 80.0% 70.5%
1gxrA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 44.0 2.78e-01 95.0% 76.4%
3n6rA03 3.30.700.30 Alpha Beta › 2-Layer Sandwich › Glycoprotein, Type 4 Pilin › 0.53 41.0 3.38e-01 95.0% 78.9%
4csqA00 2.30.29.190 Mainly Beta › Roll › PH-domain like › 0.52 39.0 3.38e-01 88.3% 88.5%
1dzkA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.52 44.0 3.38e-01 98.3% 56.8%
5hkeA01 3.60.60.10 Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A 0.52 42.0 2.71e-01 91.7% 95.1%
1iy9A02 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.52 38.0 3.98e-01 80.0% 96.2%
2cofA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 42.0 3.64e-01 98.3% 77.6%
4wfsA01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.51 37.0 2.66e-01 81.7% 35.6%
1wfwA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.51 43.0 4.13e-01 100.0% 81.1%
2e5wA01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.51 37.0 3.79e-01 83.3% 87.5%
2gumB03 2.30.29.100 Mainly Beta › Roll › PH-domain like › 0.51 42.0 3.50e-01 100.0% 89.3%
4k8wA00 2.10.109.10 Mainly Beta › Ribbon › Umud Fragment, subunit A › Umud Fragment, subunit A 0.51 42.0 3.52e-01 100.0% 83.1%
7oode01 3.90.930.12 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › Ribosomal protein L6 0.51 37.0 3.65e-01 85.0% 92.6%
3o46A00 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.50 37.0 3.39e-01 81.7% 79.8%
ECOD (41)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
151096 4050.1.1.2 ↗ few secondary structure elements › beta-barrel domain in Capz › beta-barrel domain in Capz › beta-barrel domain in Capz › F-actin_cap_A 0.71 37.0 4.06e-01 81.7% 61.2%
3442276 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.68 50.0 4.01e-01 80.0% 66.7%
3740511 2.1.1.89 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Dis3l2_C_term 0.67 51.0 4.52e-01 83.3% 57.8%
4063948 56.1.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › ATP-synt_DE_N 0.67 42.0 3.75e-01 100.0% 44.7%
4963803 832.1.1.0 ↗ a+b three layers › N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 › N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 › N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 0.66 48.0 4.09e-01 78.3% 92.0%
3591459 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.65 50.0 4.44e-01 83.3% 81.2%
3582712 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 51.0 4.30e-01 88.3% 82.9%
3738728 2.1.1.89 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Dis3l2_C_term 0.64 48.0 4.21e-01 83.3% 52.6%
3945544 4317.1.1.1 ↗ a+b duplicates or obligate multimers › YdfO-like › YdfO-like › YdfO-like › DUF1398 0.64 44.0 4.48e-01 73.3% 80.0%
4033267 4317.1.1.1 ↗ a+b duplicates or obligate multimers › YdfO-like › YdfO-like › YdfO-like › DUF1398 0.63 43.0 4.37e-01 71.7% 81.7%
4020997 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.63 47.0 3.97e-01 83.3% 54.1%
3266831 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.62 50.0 4.30e-01 88.3% 96.8%
4681343 2.10.1.0 ↗ beta barrels › OB-fold › CheW › CheW 0.62 46.0 4.06e-01 91.7% 52.6%
3473109 220.1.1.247 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_34 0.62 44.0 4.45e-01 75.0% 91.7%
4948490 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.61 49.0 4.56e-01 88.3% 88.0%
3534694 4050.1.1.2 ↗ few secondary structure elements › beta-barrel domain in Capz › beta-barrel domain in Capz › beta-barrel domain in Capz › F-actin_cap_A 0.61 34.0 3.80e-01 88.3% 68.9%
3688923 2.1.1.89 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Dis3l2_C_term 0.61 45.0 4.24e-01 83.3% 65.3%
3289944 4.1.1.323 ↗ beta barrels › SH3 › SH3 › SH3 › WYL 0.60 52.0 4.61e-01 100.0% 68.9%
3721951 220.1.1.96 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › DUF3292 0.60 49.0 3.71e-01 93.3% 84.0%
3281271 4.31.1.1 ↗ beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.58 51.0 4.50e-01 100.0% 70.0%
4118552 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.58 50.0 4.67e-01 100.0% 78.7%
4600226 5.1.4.307 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › PF29630 0.58 43.0 2.56e-01 80.0% 13.5%
4464245 56.1.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › ATP-synt_DE_N 0.57 46.0 4.18e-01 93.3% 82.4%
4441621 3943.1.1.3 ↗ beta sandwiches › Flagellar hook-associated protein 1 beta-sandwich domains › Flagellar hook-associated protein 1 beta-sandwich domains › Flagellar hook-associated protein 1 beta-sandwich domains › flgK_1st_1 0.57 41.0 3.61e-01 76.7% 76.7%
3192402 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.56 44.0 3.40e-01 91.7% 62.3%
3641981 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.56 42.0 4.30e-01 83.3% 85.0%
3586554 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.56 49.0 4.04e-01 100.0% 85.5%
4025305 56.1.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › ATP-synt_DE_N 0.56 43.0 3.90e-01 93.3% 85.3%
3978401 56.1.1.0 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N 0.56 46.0 4.11e-01 93.3% 74.4%
4155945 56.1.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › ATP-synt_DE_N 0.55 44.0 4.05e-01 95.0% 87.1%
3408648 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.55 48.0 4.09e-01 100.0% 83.0%
4119797 56.1.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › ATP-synt_DE_N 0.55 43.0 3.99e-01 95.0% 84.7%
4168086 56.1.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › ATP-synt_DE_N 0.54 43.0 3.97e-01 93.3% 82.4%
4101475 56.1.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › ATP-synt_DE_N 0.54 44.0 3.99e-01 93.3% 84.7%
4212368 56.1.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › ATP-synt_DE_N 0.53 41.0 3.80e-01 91.7% 81.2%
4681832 56.1.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › ATP-synt_DE_N 0.53 41.0 3.82e-01 95.0% 85.9%
4273393 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.53 44.0 3.79e-01 93.3% 97.9%
3479384 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.52 44.0 3.10e-01 100.0% 49.5%
4445927 56.1.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › ATP-synt_DE_N 0.52 40.0 3.74e-01 93.3% 85.9%
4191237 56.1.1.1 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › ATP-synt_DE_N 0.52 41.0 3.82e-01 93.3% 85.0%
3333061 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.50 41.0 2.39e-01 93.3% 15.2%