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NC_021559.1__YP_008130124.1__PRAG_00198__00191

Bact-Vir

NC_021559.1__YP_008130124.1__PRAG_00198__00191

Identity

Accession:
NC_021559 ↗
Kingdom:
phage

Quality

92.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Kyanoviridae› Ronodorvirus› Prochlorococcus_phage_P-SSM3

TaxID: 536453

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 8-71
PDB
Domain cluster: rep: MK268344.1__AZU97954.1__CPT_Munch_010__00010__D44-96
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3lqyA00 3.40.50.850 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Isochorismatase-like 0.67 40.0 2.80e-01 90.6% 20.3%
6bfnB02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.66 39.0 2.77e-01 95.3% 18.8%
3fxqB01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.65 50.0 4.48e-01 82.8% 65.6%
1lnwF01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.61 46.0 3.74e-01 82.8% 57.3%
4anjA06 1.20.5.4820 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.60 43.0 3.60e-01 76.6% 59.3%
4dxwA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.59 48.0 4.04e-01 100.0% 51.8%
1bjaA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.59 46.0 4.07e-01 85.9% 65.3%
1xdsB01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.59 47.0 4.21e-01 89.1% 69.6%
7b00A01 1.20.1740.10 Mainly Alpha › Up-down Bundle › Amino acid/polyamine transporter I › Amino acid/polyamine transporter I 0.59 45.0 2.73e-01 84.4% 62.5%
4mndA02 1.20.120.1760 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CDP-alcohol phosphotransferase transmembrane (TM) domain 0.58 50.0 3.64e-01 100.0% 40.3%
5zyrA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.58 47.0 3.59e-01 89.1% 78.1%
1fxkB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.58 44.0 3.61e-01 79.7% 50.5%
4l80D00 3.20.20.60 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Phosphoenolpyruvate-binding domains 0.58 37.0 2.40e-01 71.9% 12.2%
2fa5A00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.58 47.0 3.66e-01 89.1% 54.0%
2esnA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.57 43.0 3.93e-01 84.4% 74.2%
3r4iA02 6.10.140.960 Special › Helix non-globular › Helix Hairpins › 0.57 42.0 4.35e-01 81.2% 90.0%
1gkuB06 1.10.460.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; domain 2 › Topoisomerase I, domain 2 0.56 48.0 3.71e-01 100.0% 76.9%
1yf2A02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.56 43.0 3.63e-01 82.8% 49.5%
5y2vC01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.56 45.0 4.17e-01 90.6% 92.9%
2p1aB01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.56 42.0 3.18e-01 79.7% 64.4%
3szpA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.55 42.0 3.82e-01 84.4% 74.2%
6pwkA02 3.20.20.450 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › EAL domain 0.54 44.0 3.17e-01 98.4% 32.5%
3k1hA00 3.30.1120.180 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › Flagellar FLiS export co-chaperone, HP1076 0.54 39.0 3.30e-01 79.7% 87.0%
1i7dA02 1.10.460.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; domain 2 › Topoisomerase I, domain 2 0.53 42.0 3.08e-01 87.5% 95.6%
2cgqA00 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.52 32.0 3.14e-01 90.6% 54.1%
1dq3A03 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.52 38.0 3.52e-01 81.2% 100.0%
2ganA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.52 45.0 3.46e-01 96.9% 47.2%
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.51 40.0 3.38e-01 84.4% 89.6%
1kgqA01 1.10.166.10 Mainly Alpha › Orthogonal Bundle › Tetrahydrodipicolinate-N-succinyltransferase; Chain A, domain 1 › Tetrahydrodipicolinate-N-succinyltransferase, N-terminal domain 0.51 36.0 3.58e-01 76.6% 87.1%
4iggB06 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.51 38.0 2.67e-01 79.7% 26.0%
4bgpA01 1.20.142.20 Mainly Alpha › Up-down Bundle › Poly(ADP-ribose) Polymerase; domain 1 › 0.51 38.0 3.20e-01 87.5% 77.2%
7po9A01 3.40.1800.20 Alpha Beta › 3-Layer(aba) Sandwich › His-Me finger endonuclease fold › 0.50 45.0 4.05e-01 98.4% 80.2%
1m2vB01 1.20.120.730 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Sec23/Sec24 helical domain 0.50 43.0 3.29e-01 100.0% 50.9%
2oexA01 1.20.120.560 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › alix/aip1 in complex with the ypdl late domain 0.50 38.0 2.99e-01 82.8% 60.8%
ECOD (57)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3226591 5054.1.1.0 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels 0.69 49.0 3.84e-01 100.0% 35.0%
4858145 2002.1.1.111 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › HpcH_HpaI 0.68 42.0 2.77e-01 71.9% 14.7%
3274079 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.66 47.0 3.00e-01 100.0% 15.0%
3477557 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.66 44.0 3.40e-01 70.3% 79.3%
5040463 2002.1.1.111 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › HpcH_HpaI 0.65 42.0 2.71e-01 70.3% 13.9%
4014117 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.63 41.0 2.68e-01 70.3% 13.9%
3187789 2002.1.1.111 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › HpcH_HpaI 0.63 41.0 2.64e-01 70.3% 12.8%
3509323 101.1.1.10 ↗ alpha arrays › HTH › HTH › Three-helical HTH › ARID 0.61 48.0 4.36e-01 87.5% 66.7%
4017347 5001.1.1.133 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Git3, GPR_Gpa2_C 0.61 40.0 2.50e-01 78.1% 12.8%
4928111 2005.1.1.4 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Asn_synthase 0.61 46.0 3.16e-01 84.4% 72.8%
3596100 4957.1.1.0 ↗ a+b complex topology › helical domain in yeast RNA-polymerases › third helical domain in yeast RNA-polymerase II beta-prime subunit › third helical domain in yeast RNA-polymerase II beta-prime subunit 0.61 46.0 3.20e-01 81.2% 26.8%
3737536 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.60 51.0 3.41e-01 100.0% 51.7%
3733292 5069.1.1.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes 0.58 45.0 3.16e-01 84.4% 28.3%
2583940 601.7.1.8 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › Cas_Csm6_HEPN 0.58 48.0 3.60e-01 96.9% 92.5%
4939346 242.2.1.2 ↗ a+b two layers › Homing endonucleases-like › tRNA-intron endonuclease N-terminal domain-like › tRNA-intron endonuclease N-terminal domain-like › tRNA_int_endo_N 0.58 48.0 4.19e-01 95.3% 89.0%
4981980 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.58 43.0 3.53e-01 79.7% 48.7%
4978597 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.57 43.0 3.09e-01 84.4% 27.6%
3704925 192.20.1.0 ↗ alpha bundles › Long alpha-hairpin › helical hairpin domain in transcriptional anti-activator ExsD › helical hairpin domain in transcriptional anti-activator ExsD 0.57 42.0 3.81e-01 92.2% 58.8%
4257661 3001.1.1.1 ↗ alpha arrays › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › THDPS_N_2 0.57 40.0 3.61e-01 75.0% 68.9%
3703086 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.57 41.0 2.29e-01 76.6% 6.2%
3734050 5050.1.1.1 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr 0.57 46.0 3.05e-01 96.9% 49.7%
4142789 2002.1.1.111 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › HpcH_HpaI 0.56 41.0 2.64e-01 79.7% 20.3%
3814043 101.1.10.21 ↗ alpha arrays › HTH › HTH › Cyclin-like › Cyclin_N,Cyclin_C 0.56 46.0 3.19e-01 100.0% 26.8%
3284225 101.1.2.1 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_1 0.56 42.0 4.00e-01 84.4% 83.7%
3973617 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.56 38.0 2.57e-01 75.0% 17.0%
3644530 502.1.1.1 ↗ a+b two layers › Anti-LPS factor/recA domain › Anti-LPS factor/recA domain › Anti-LPS factor/recA domain › RecA_C 0.56 41.0 4.19e-01 79.7% 90.0%
4181293 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.56 43.0 3.58e-01 84.4% 48.2%
3633523 5001.1.1.80 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Dicty_CAR 0.55 39.0 2.77e-01 81.2% 22.9%
4946863 3896.1.1.2 ↗ alpha duplicates or obligate multimers › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase › DUF92 0.55 48.0 3.31e-01 100.0% 39.1%
3998932 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.55 48.0 3.56e-01 100.0% 55.3%
3866268 109.4.1.235 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SRP68 0.55 48.0 3.20e-01 100.0% 43.7%
3205061 5001.1.1.179 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Dicty_CAR, GPR_Gpa2_C 0.54 41.0 2.65e-01 84.4% 17.0%
3555108 109.4.1.235 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SRP68 0.54 46.0 2.79e-01 100.0% 16.1%
3775175 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.54 41.0 3.48e-01 79.7% 74.0%
4520394 5063.1.1.1 ↗ alpha bundles › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › PSI_PSAK 0.53 39.0 3.86e-01 78.1% 82.6%
3972450 4033.1.1.1 ↗ alpha arrays › Acyl-CoA dehydrogenase N-terminal domain-like › Acyl-CoA dehydrogenase N-terminal domain-like › Acyl-CoA dehydrogenase N-terminal domain-like › Acyl-CoA_dh_N 0.53 44.0 3.50e-01 100.0% 64.0%
3223572 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.53 33.0 3.32e-01 75.0% 61.5%
4995127 3843.1.1.1 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › Oxidored_q2 0.53 39.0 3.16e-01 89.1% 41.7%
3639531 5001.1.1.30 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › GPR_Gpa2_C 0.53 40.0 2.59e-01 84.4% 17.1%
3808801 192.2.1.31 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › PRA1 0.52 46.0 3.52e-01 100.0% 46.7%
4599024 3001.1.1.1 ↗ alpha arrays › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › THDPS_N_2 0.52 37.0 3.48e-01 78.1% 71.8%
4214015 101.11.1.0 ↗ alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 0.52 45.0 3.79e-01 96.9% 77.3%
4025655 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.52 40.0 3.57e-01 84.4% 87.4%
5062752 2498.1.1.6 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M3 0.52 45.0 2.71e-01 100.0% 31.8%
3775826 4016.1.1.0 ↗ alpha bundles › alpha-helical domain in type II DNA topoisomerase › alpha-helical domain in type II DNA topoisomerase › alpha-helical domain in type II DNA topoisomerase 0.52 43.0 3.39e-01 96.9% 80.0%
3938199 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.52 45.0 3.30e-01 98.4% 46.3%
4337722 3001.1.1.1 ↗ alpha arrays › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › THDPS_N_2 0.52 36.0 3.37e-01 75.0% 69.4%
3601242 616.1.1.35 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › PRA1 0.51 39.0 3.17e-01 84.4% 46.2%
4082175 3001.1.1.1 ↗ alpha arrays › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › THDPS_N_2 0.51 37.0 3.41e-01 78.1% 74.1%
3498627 7015.1.1.1 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › DHHC 0.51 42.0 2.90e-01 96.9% 72.5%
5029796 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.51 39.0 3.18e-01 82.8% 43.3%
4659871 3001.1.1.1 ↗ alpha arrays › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › THDPS_N_2 0.51 39.0 3.55e-01 87.5% 72.6%
3235218 5001.1.1.106 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Str 0.51 39.0 2.49e-01 84.4% 17.6%
3249793 5001.1.1.80 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Dicty_CAR 0.51 41.0 2.65e-01 87.5% 28.6%
4457710 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.51 40.0 3.27e-01 85.9% 50.0%
5013911 1075.5.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › MatE 0.50 42.0 3.00e-01 100.0% 80.0%
4585740 101.11.1.0 ↗ alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 0.50 41.0 3.70e-01 90.6% 86.7%