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NC_020845.1__YP_007673813.1__CPMG_00067__00067

Bact-Vir

NC_020845.1__YP_007673813.1__CPMG_00067__00067

Identity

Accession:
NC_020845 ↗
Kingdom:
phage

Quality

78.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Eurybiavirus› Prochlorococcus_phage_MED4-213

TaxID: 889956

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 4-65
PDB
Domain cluster: rep: NC_070839.1__YP_010656485.1__PP650_gp002__00002__D2-54
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ftxB01 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.77 62.0 4.89e-01 88.7% 48.4%
1imuA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.71 58.0 4.81e-01 88.7% 70.1%
3mazA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.71 54.0 4.69e-01 87.1% 52.5%
3mh9A00 2.50.20.20 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › 0.69 46.0 3.21e-01 71.0% 21.0%
4hdoA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.68 50.0 4.40e-01 77.4% 73.9%
1ntvA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.68 49.0 3.70e-01 77.4% 66.4%
5xbfA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.68 48.0 4.30e-01 75.8% 73.9%
2r31A01 3.30.2180.10 Alpha Beta › 2-Layer Sandwich › ATP12-like › ATP12-like 0.67 50.0 4.98e-01 80.6% 81.8%
3ihpA03 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.67 45.0 2.78e-01 72.6% 12.8%
1srqA01 3.30.1120.160 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.67 52.0 4.09e-01 87.1% 46.4%
4h5bA00 3.30.1460.70 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.67 52.0 4.01e-01 88.7% 67.1%
3i3tA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.66 46.0 2.92e-01 74.2% 14.5%
1wguA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.66 48.0 3.93e-01 77.4% 84.3%
2eo6A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.66 52.0 4.41e-01 88.7% 62.0%
2vifA01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.66 53.0 4.21e-01 88.7% 54.8%
4innA00 2.40.128.520 Mainly Beta › Beta Barrel › Lipocalin › 0.65 54.0 4.18e-01 95.2% 71.2%
2c9wA01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.65 50.0 4.21e-01 87.1% 52.2%
2dx0B01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.64 45.0 4.30e-01 80.6% 62.7%
3zx7A02 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.64 54.0 4.20e-01 95.2% 87.6%
5cvmA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.63 47.0 2.97e-01 79.0% 18.2%
1txdA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.63 45.0 3.73e-01 77.4% 62.8%
2ltrA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.63 52.0 4.39e-01 91.9% 73.3%
5vmzA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.63 39.0 4.49e-01 82.3% 97.4%
2wdtC02 3.30.1490.420 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Ubiquitin carboxyl-terminal hydrolase, domain 2 0.63 48.0 4.21e-01 87.1% 64.4%
6hgcA01 3.40.532.10 Alpha Beta › 3-Layer(aba) Sandwich › Ubiquitin C-terminal Hydrolase UCH-l3 › Peptidase C12, ubiquitin carboxyl-terminal hydrolase 0.62 46.0 3.30e-01 80.6% 76.4%
7oufB01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.62 51.0 3.92e-01 93.5% 83.2%
2dx0A00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.61 46.0 3.85e-01 88.7% 44.4%
1qw2A00 3.30.1980.10 Alpha Beta › 2-Layer Sandwich › Hypothetical protein Ta1206 fold › Hypothetical protein YunC 0.61 52.0 4.47e-01 96.8% 81.4%
2elbA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 44.0 3.79e-01 79.0% 65.7%
4tyzA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 44.0 3.69e-01 79.0% 65.1%
1o70A02 2.30.180.10 Mainly Beta › Roll › FAS1 domain › FAS1 domain 0.59 47.0 3.53e-01 88.7% 39.1%
2obdA02 3.15.10.10 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › Bactericidal permeability-increasing protein; domain 1 0.58 45.0 3.26e-01 87.1% 64.0%
2k2jA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 40.0 3.40e-01 75.8% 70.9%
2izvA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.57 45.0 3.45e-01 91.9% 35.0%
2bs6A01 2.40.128.190 Mainly Beta › Beta Barrel › Lipocalin › 0.56 45.0 4.22e-01 95.2% 96.4%
3a7sA00 3.40.532.10 Alpha Beta › 3-Layer(aba) Sandwich › Ubiquitin C-terminal Hydrolase UCH-l3 › Peptidase C12, ubiquitin carboxyl-terminal hydrolase 0.56 42.0 3.06e-01 85.5% 71.1%
1dwnA00 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.55 47.0 3.84e-01 100.0% 94.5%
2bbuA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.55 42.0 3.27e-01 88.7% 95.5%
1x9yA01 3.10.500.10 Alpha Beta › Roll › prostaphopain b, domain 1 › Staphopain proregion domain 0.54 45.0 3.46e-01 100.0% 60.0%
3a54A01 2.40.50.340 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.53 40.0 3.64e-01 83.9% 62.2%
6jptA00 3.30.230.90 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.53 43.0 3.53e-01 91.9% 83.5%
4azpA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.53 44.0 3.57e-01 100.0% 88.1%
4chjA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 42.0 3.53e-01 95.2% 54.0%
4qa8A00 2.50.20.20 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › 0.52 45.0 3.16e-01 100.0% 38.6%
1y9lA00 2.40.128.230 Mainly Beta › Beta Barrel › Lipocalin › Pilot protein MxiM 0.52 41.0 3.58e-01 95.2% 72.7%
ECOD (63)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4119222 375.1.1.135 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Lar_restr_allev 0.80 58.0 6.41e-01 75.8% 100.0%
3240084 5.1.4.661 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_WDR36-Utp21_1st 0.78 55.0 3.45e-01 74.2% 22.5%
3244743 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.69 46.0 3.49e-01 74.2% 28.7%
3217981 2484.1.1.200 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FTH 0.69 48.0 3.54e-01 74.2% 29.4%
3592335 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.69 54.0 3.33e-01 85.5% 22.0%
5047657 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.68 54.0 5.61e-01 87.1% 100.0%
3578128 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.68 53.0 5.57e-01 87.1% 100.0%
3620992 386.1.1.4 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-BED 0.68 46.0 4.96e-01 83.9% 88.0%
140426 71.1.1.6 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › LppX_LprAFG 0.68 45.0 3.18e-01 71.0% 21.2%
3238801 2484.1.1.200 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FTH 0.67 49.0 2.95e-01 79.0% 12.8%
3940760 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.67 44.0 2.80e-01 74.2% 13.6%
3213146 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.67 52.0 4.31e-01 85.5% 55.5%
None — 0.66 51.0 3.37e-01 88.7% 54.0%
3550970 719.1.1.5 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain › PF27933 0.65 54.0 4.53e-01 93.5% 95.5%
5001720 850.1.1.2 ↗ a+b three layers › Hypothetical protein Ta1206-like › Hypothetical protein Ta1206-like › Hypothetical protein Ta1206-like › DUF1805 0.65 53.0 4.63e-01 90.3% 95.8%
3932677 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.65 43.0 3.23e-01 74.2% 28.2%
3659251 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.65 46.0 2.99e-01 75.8% 26.2%
3239485 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.64 46.0 3.69e-01 79.0% 42.3%
3937459 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.63 46.0 3.95e-01 77.4% 79.0%
4989457 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.63 47.0 5.08e-01 87.1% 100.0%
5033737 71.1.1.0 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB 0.63 43.0 3.10e-01 71.0% 23.4%
3312716 220.1.1.172 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_PRMT_N 0.63 47.0 3.98e-01 80.6% 74.3%
4561925 6.1.1.0 ↗ beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil 0.62 53.0 4.39e-01 95.2% 87.3%
3232904 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.61 45.0 3.16e-01 80.6% 26.2%
3233353 3794.1.1.3 ↗ 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 › ACCA_BT 0.61 52.0 3.97e-01 91.9% 67.4%
4530314 375.13.1.0 ↗ few secondary structure elements › Rubredoxin-like › Mycobacterium tuberculosis Topoisomerase I C-terminal domain › Mycobacterium tuberculosis Topoisomerase I C-terminal domain 0.61 46.0 4.76e-01 91.9% 91.4%
3404595 219.1.1.14 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Josephin 0.60 44.0 3.22e-01 79.0% 75.6%
4024708 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.60 41.0 2.59e-01 74.2% 12.0%
3164898 4.11.1.1 ↗ beta barrels › SH3 › LexA/Signal peptidase › LexA/Signal peptidase › Peptidase_S24 0.60 42.0 3.70e-01 77.4% 48.4%
3215907 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.60 45.0 3.04e-01 85.5% 22.6%
5039400 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.60 41.0 2.63e-01 72.6% 57.0%
3219544 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.59 43.0 2.83e-01 80.6% 17.1%
3178227 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.59 41.0 2.62e-01 74.2% 25.0%
3467267 4.1.1.94 ↗ beta barrels › SH3 › SH3 › SH3 › SAWADEE 0.59 43.0 4.32e-01 79.0% 83.1%
3515688 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.59 43.0 3.52e-01 77.4% 79.2%
3326962 3794.1.1.3 ↗ 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 › ACCA_BT 0.58 47.0 3.71e-01 90.3% 65.9%
3607308 2498.1.1.14 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M8 0.58 44.0 2.69e-01 87.1% 13.6%
3702383 2498.1.1.14 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M8 0.57 44.0 2.98e-01 87.1% 22.6%
4028948 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.57 47.0 2.94e-01 100.0% 41.6%
3793075 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.57 45.0 3.60e-01 88.7% 51.9%
3878636 3794.1.1.0 ↗ 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 0.57 51.0 3.90e-01 100.0% 52.4%
4434185 3804.1.1.1 ↗ alpha bundles › CRISPR-Cas system RNase C2c2 N-terminal domain › CRISPR-Cas system RNase C2c2 N-terminal domain › CRISPR-Cas system RNase C2c2 N-terminal domain › Cas13a_endoribonuclease 0.57 38.0 2.88e-01 82.3% 26.1%
5047128 3662.1.1.0 ↗ a+b two layers › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related 0.57 47.0 3.98e-01 93.5% 88.1%
3223396 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 48.0 4.00e-01 98.4% 56.5%
4450355 3662.1.1.1 ↗ a+b two layers › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › PAC3 0.56 44.0 3.63e-01 88.7% 86.7%
3703370 2498.1.1.14 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M8 0.56 43.0 2.61e-01 87.1% 12.4%
5060431 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.56 43.0 2.75e-01 87.1% 14.7%
3483808 295.1.1.3 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › PurA 0.56 41.0 4.01e-01 79.0% 77.1%
3392305 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.56 48.0 3.95e-01 95.2% 71.8%
3928614 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.56 47.0 3.50e-01 96.8% 57.6%
3719115 220.4.1.6 ↗ beta barrels › PH domain-like › second barrel domain in viral glycoproteins › second barrel domain in viral glycoproteins › Peptidase_M8 0.55 42.0 3.25e-01 87.1% 41.2%
3990496 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.55 46.0 4.51e-01 95.2% 88.6%
3625965 4184.1.1.2 ↗ beta barrels › MFPT repeat › MFPT repeat › MFPT repeat › MFP2b 0.55 37.0 3.27e-01 79.0% 46.3%
3998663 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.55 36.0 3.49e-01 93.5% 60.0%
3994002 148.1.3.103 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › Spectrin 0.55 43.0 3.54e-01 88.7% 90.8%
3791839 4184.1.1.2 ↗ beta barrels › MFPT repeat › MFPT repeat › MFPT repeat › MFP2b 0.54 36.0 3.43e-01 79.0% 56.2%
3622643 4184.1.1.2 ↗ beta barrels › MFPT repeat › MFPT repeat › MFPT repeat › MFP2b 0.54 36.0 3.36e-01 79.0% 52.9%
3230771 4184.1.1.2 ↗ beta barrels › MFPT repeat › MFPT repeat › MFPT repeat › MFP2b 0.53 36.0 3.29e-01 79.0% 50.0%
262552 52.1.1.1 ↗ beta sandwiches › E2 regulatory, transactivation domain › E2 regulatory, transactivation domain › E2 regulatory, transactivation domain › PPV_E2_N 0.53 42.0 3.63e-01 88.7% 64.6%
3306595 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.52 43.0 3.13e-01 91.9% 62.3%
4940665 9.16.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Hypothetical protein Atu4866 › Hypothetical protein Atu4866 0.51 40.0 3.77e-01 95.2% 89.0%
3509892 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.50 43.0 3.22e-01 100.0% 72.6%
4935681 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.50 33.0 3.48e-01 75.8% 78.2%