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NC_015284.1__YP_004323405.1__PHM2_036__00036

Bact-Vir

NC_015284.1__YP_004323405.1__PHM2_036__00036

Identity

Accession:
NC_015284 ↗
Kingdom:
phage

Quality

71.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Eurybiavirus› Prochlorococcus_phage_P-HM2

TaxID: 445696

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 49-117
PDB
Domain cluster: representative
CATH (39)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3p8bB02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.67 38.0 4.02e-01 72.5% 61.3%
2x45A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.62 48.0 3.77e-01 82.6% 46.5%
1g29102 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.62 39.0 4.50e-01 85.5% 97.8%
1c9rA04 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.62 48.0 4.24e-01 94.2% 56.1%
2lmcB00 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.61 42.0 4.38e-01 87.0% 80.3%
3dcxA00 2.30.29.50 Mainly Beta › Roll › PH-domain like › Bacterial Pleckstrin homology domain 0.61 43.0 3.66e-01 85.5% 44.4%
4iqfB01 3.40.50.170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Formyl transferase, N-terminal domain 0.60 52.0 3.75e-01 100.0% 87.0%
1mu5A01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.59 43.0 3.16e-01 79.7% 65.2%
2o1qA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.59 43.0 3.57e-01 78.3% 87.4%
3da8B00 3.40.50.170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Formyl transferase, N-terminal domain 0.59 50.0 3.68e-01 100.0% 84.9%
2fb7A00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.59 40.0 3.88e-01 71.0% 68.8%
3f6gA02 3.30.160.340 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.58 47.0 4.84e-01 98.6% 98.4%
3p9xA00 3.40.50.170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Formyl transferase, N-terminal domain 0.58 50.0 3.72e-01 100.0% 87.7%
3oyyA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.58 38.0 3.89e-01 73.9% 69.7%
3u4zA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.58 43.0 3.79e-01 91.3% 51.4%
6n9aB02 3.30.420.200 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.58 39.0 3.95e-01 87.0% 69.6%
5bv3D01 3.30.200.40 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Scavenger mRNA decapping enzyme, N-terminal domain 0.56 39.0 3.40e-01 73.9% 82.1%
4a4kA02 2.30.30.1160 Mainly Beta › Roll › SH3 type barrels. › 0.56 39.0 3.14e-01 72.5% 51.9%
2fgeA01 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.56 48.0 3.27e-01 95.7% 97.2%
1e3hA03 3.30.230.70 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › GHMP Kinase, N-terminal domain 0.56 46.0 3.31e-01 92.8% 81.7%
1e3hA01 3.30.230.70 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › GHMP Kinase, N-terminal domain 0.56 45.0 3.20e-01 94.2% 34.3%
7bspA01 2.70.150.10 Mainly Beta › Distorted Sandwich › Calcium-transporting ATPase, cytoplasmic transduction domain A › Calcium-transporting ATPase, cytoplasmic transduction domain A 0.55 41.0 3.22e-01 79.7% 38.8%
2o8bB04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.55 38.0 3.09e-01 72.5% 93.9%
3fdwA00 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.55 47.0 3.91e-01 100.0% 73.8%
2aehA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 38.0 3.30e-01 85.5% 45.9%
1oxxK02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.54 35.0 3.85e-01 87.0% 100.0%
2zwaA02 2.120.10.80 Mainly Beta › 6 Propeller › Neuraminidase › Kelch-type beta propeller 0.54 39.0 2.58e-01 88.4% 16.7%
4z9cB00 2.40.50.110 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.54 43.0 3.70e-01 89.9% 61.7%
3wxmB02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.54 41.0 3.46e-01 97.1% 47.5%
1iv0A00 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.53 37.0 3.38e-01 87.0% 52.0%
1vjhA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.53 41.0 3.45e-01 84.1% 95.0%
4hd5A01 2.60.40.3760 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 46.0 4.16e-01 100.0% 86.6%
2grvA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.53 42.0 3.24e-01 91.3% 80.5%
3pmiA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.53 38.0 3.90e-01 88.4% 81.5%
1yr2A02 2.130.10.120 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Prolyl oligopeptidase, N-terminal domain 0.52 44.0 2.90e-01 98.6% 22.7%
3iuzA00 3.10.180.50 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 0.51 41.0 2.80e-01 95.7% 90.6%
3ulbA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 36.0 3.45e-01 81.2% 63.9%
1i99I02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.51 43.0 3.63e-01 95.7% 89.7%
3stoA02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.50 43.0 3.47e-01 100.0% 69.2%
ECOD (65)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3389662 4.1.1.219 ↗ beta barrels › SH3 › SH3 › SH3 › LSM12_LSM 0.69 46.0 4.37e-01 72.5% 58.7%
5030187 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.66 49.0 4.76e-01 97.1% 70.5%
5077089 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.66 43.0 4.31e-01 81.2% 65.7%
3715664 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.64 54.0 4.53e-01 100.0% 96.9%
3260045 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.64 42.0 4.13e-01 88.4% 62.7%
3193761 10.13.1.1 ↗ beta sandwiches › jelly-roll › Calcium ATPase, transduction domain A › Calcium ATPase, transduction domain A › E1-E2_ATPase 0.63 45.0 3.18e-01 75.4% 29.5%
4147969 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.63 47.0 4.44e-01 97.1% 65.9%
3204007 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.63 55.0 4.44e-01 97.1% 81.5%
3864913 218.1.1.2 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › Enolase_N 0.62 53.0 4.21e-01 100.0% 87.7%
3928228 2484.1.1.43 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Endonuclease_5 0.62 53.0 3.70e-01 98.6% 29.2%
3257390 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.62 43.0 2.77e-01 92.8% 16.1%
5028870 708.1.1.0 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain 0.61 44.0 4.41e-01 98.6% 75.7%
3812766 4.1.1.42 ↗ beta barrels › SH3 › SH3 › SH3 › Agenet 0.61 39.0 3.97e-01 73.9% 65.7%
3873956 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.61 41.0 3.51e-01 85.5% 40.8%
3591158 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.60 47.0 3.91e-01 85.5% 52.8%
3433122 241.15.1.3 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain › SPC25 0.60 51.0 4.44e-01 100.0% 76.5%
4260969 2.4.1.2 ↗ beta barrels › OB-fold › MOP-like › MOP-like › TOBE_2 0.60 41.0 3.36e-01 94.2% 37.0%
4478350 218.1.1.2 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › Enolase_N 0.60 50.0 4.30e-01 100.0% 97.5%
4441682 2003.1.2.15 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3 0.59 48.0 3.11e-01 91.3% 72.1%
4940142 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.59 43.0 4.09e-01 81.2% 63.5%
3187356 2484.1.1.223 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27036 0.59 49.0 3.64e-01 97.1% 33.7%
3439646 284.1.3.2 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › OSR1_C 0.59 46.0 4.04e-01 89.9% 56.2%
3698724 245.2.1.0 ↗ a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB 0.59 41.0 3.28e-01 76.8% 35.7%
3177460 3270.1.1.0 ↗ a+b two layers › a+b domain in heme oxygenase › a+b domain in heme oxygenase › a+b domain in heme oxygenase 0.59 44.0 3.96e-01 81.2% 67.0%
4644171 7571.1.1.1 ↗ a/b three-layered sandwiches › Formyltransferase › Formyltransferase › Formyltransferase › Formyl_trans_N 0.59 51.0 3.72e-01 100.0% 88.5%
3408695 245.1.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.58 40.0 3.60e-01 78.3% 51.6%
4655719 4.1.1.92 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_9 0.58 35.0 3.23e-01 72.5% 44.4%
3753004 7571.1.1.1 ↗ a/b three-layered sandwiches › Formyltransferase › Formyltransferase › Formyltransferase › Formyl_trans_N 0.58 50.0 3.61e-01 100.0% 82.3%
3612383 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.58 45.0 2.84e-01 85.5% 57.7%
3929385 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.58 45.0 3.02e-01 82.6% 30.0%
3658323 284.1.2.1 ↗ a+b two layers › FKBP-like › FKBP-like › Conserved carboxy-terminal domain of oxidative-stress-responsive kinase 1-like kinases › OSR1_C 0.58 46.0 4.02e-01 87.0% 57.1%
5081683 2002.3.1.3 ↗ a/b barrels › TIM beta/alpha-barrel › Glycoside hydrolase/deacetylase › Glycoside hydrolase/deacetylase › Glyco_hydro_57 0.58 39.0 2.42e-01 71.0% 20.9%
3782292 4.1.1.170 ↗ beta barrels › SH3 › SH3 › SH3 › Rad9_Rad53_bind 0.58 40.0 3.83e-01 72.5% 70.0%
3216768 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.57 47.0 4.09e-01 100.0% 59.0%
1954221 2.26.1.1 ↗ beta barrels › OB-fold › Arcadin-1 › Arcadin-1 › Arcadin_1 0.57 45.0 4.47e-01 98.6% 81.3%
3283795 220.1.1.17 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_1 0.57 40.0 3.49e-01 85.5% 45.2%
3718301 330.2.1.0 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.57 50.0 4.54e-01 100.0% 77.9%
3783591 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.57 48.0 4.25e-01 97.1% 90.5%
5034195 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.57 37.0 4.01e-01 72.5% 85.5%
3274757 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.56 44.0 4.33e-01 87.0% 82.7%
3484787 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.56 48.0 3.68e-01 100.0% 66.3%
3832022 5.1.3.118 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.56 48.0 3.14e-01 98.6% 98.8%
3740252 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.56 46.0 4.05e-01 98.6% 70.4%
3476018 220.1.1.155 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PF26658 0.56 38.0 3.24e-01 79.7% 40.7%
3740052 220.1.1.57 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_20 0.55 39.0 3.33e-01 75.4% 62.5%
3264731 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.55 46.0 3.87e-01 100.0% 53.8%
4028630 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.55 37.0 3.78e-01 72.5% 73.8%
3782631 2484.8.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Separase pseudo-protease domain (PPD) › Separase pseudo-protease domain (PPD) › Peptidase_C50 0.55 45.0 3.08e-01 97.1% 54.8%
3710326 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 45.0 4.23e-01 97.1% 76.5%
3802590 5.1.3.118 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.54 41.0 2.72e-01 84.1% 34.4%
3988639 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 44.0 3.57e-01 92.8% 68.1%
3174883 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.53 44.0 3.85e-01 98.6% 70.4%
3826655 5.1.3.67 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_1 0.53 43.0 2.94e-01 95.7% 45.5%
4941253 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.53 39.0 3.52e-01 89.9% 56.0%
3197066 5.1.4.116 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › IKI3 0.52 42.0 2.71e-01 94.2% 26.0%
4543638 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.52 46.0 3.50e-01 100.0% 94.5%
3361873 4292.2.1.0 ↗ a+b two layers › FlaG-like › MAGUK binding stalk (MBS) domain › MAGUK binding stalk (MBS) domain 0.52 41.0 3.61e-01 88.4% 74.3%
3177726 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.52 43.0 3.30e-01 100.0% 56.2%
3493400 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.51 36.0 3.25e-01 76.8% 50.5%
5049182 3435.1.1.0 ↗ a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC 0.51 41.0 2.83e-01 88.4% 25.0%
4028464 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.51 41.0 2.73e-01 89.9% 77.9%
3709513 267.1.1.3 ↗ a+b complex topology › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain › Cation_ATPase 0.50 42.0 2.97e-01 94.2% 40.0%
4016853 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.50 39.0 2.97e-01 85.5% 50.6%
3739683 220.1.1.20 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_TFIIH 0.50 37.0 3.26e-01 81.2% 52.7%
3499456 5.1.7.2 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 10-bladed › Sortilin-Vps10 0.50 41.0 2.53e-01 95.7% 15.4%