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NC_015288.1__YP_004324411.1__Syn1_040__00039

Bact-Vir

NC_015288.1__YP_004324411.1__Syn1_040__00039

Identity

Accession:
NC_015288 ↗
Kingdom:
phage

Quality

79.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Kyanoviridae› Vellamovirus› Prochlorococcus_phage_Syn1

TaxID: 444861

Cluster

View cluster (2 members)

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 19-34_46-146_284-313
PDB
Domain cluster: rep: FM207411.1__CAR63406.1__SRSM4_209__00209__D6-110
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1d06A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.50 29.0 3.04e-01 86.4% 60.8%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3996931 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 25.0 3.44e-01 82.3% 92.3%
5072207 2484.1.1.59 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › NurA 0.51 37.0 2.91e-01 75.5% 82.6%
D2 high residues 152-277
PDB
Domain cluster: representative
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ni3A03 1.10.150.300 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Obg-related GTPase Ych/YyaF, coiled-coil domain 0.68 41.0 4.79e-01 85.7% 83.5%
1lq7A00 1.20.1270.70 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Designed single chain three-helix bundle 0.66 36.0 4.75e-01 87.3% 100.0%
2ip6A00 1.20.1440.140 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.66 39.0 4.59e-01 93.7% 83.9%
3m7gA02 1.10.8.1010 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.66 45.0 5.06e-01 91.3% 91.6%
3d2eA06 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.63 40.0 4.22e-01 91.3% 70.8%
1h6gA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.62 45.0 4.59e-01 88.1% 76.6%
1yo7A00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.60 46.0 4.75e-01 92.1% 84.2%
1jqkA03 1.20.1270.30 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.58 49.0 4.40e-01 91.3% 87.4%
3vadA01 1.20.140.20 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain 0.58 49.0 4.57e-01 92.9% 73.7%
1ivhA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.57 48.0 4.65e-01 95.2% 80.9%
3cxbA03 1.10.1740.30 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › Secreted effector protein SifA helical domain 0.56 31.0 3.79e-01 90.5% 85.2%
3op0A01 1.20.930.20 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Adaptor protein Cbl, N-terminal domain 0.56 44.0 4.31e-01 92.1% 78.7%
4fz4A00 1.20.140.130 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › 0.55 45.0 4.24e-01 88.1% 86.4%
3um7B01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 30.0 3.42e-01 93.7% 74.2%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3420431 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.74 41.0 4.92e-01 87.3% 81.2%
3651012 3755.4.1.17 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Rx_N 0.73 49.0 4.76e-01 91.3% 62.1%
4137264 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.69 41.0 4.90e-01 86.5% 88.2%
4101843 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.69 41.0 4.45e-01 88.9% 70.5%
4131078 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.68 41.0 4.94e-01 88.9% 92.5%
3584512 632.19.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Choline binding protein A › Choline binding protein A 0.68 43.0 5.11e-01 90.5% 94.1%
3662390 632.15.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) › GAUT_1 0.68 43.0 4.85e-01 95.2% 84.2%
3830809 633.4.1.0 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor 0.67 50.0 5.11e-01 90.5% 80.8%
3499218 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.67 45.0 4.80e-01 89.7% 79.1%
4367207 632.22.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › EzrA 0.65 42.0 4.60e-01 88.9% 78.1%
4528489 633.2.1.0 ↗ alpha bundles › Bromodomain-like › Carnobacteriocin B2 immunity protein › Carnobacteriocin B2 immunity protein 0.65 40.0 4.58e-01 90.5% 82.1%
4428399 632.11.1.10 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like › EzrA 0.65 42.0 4.50e-01 90.5% 75.5%
4439930 632.22.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › EzrA 0.64 42.0 3.95e-01 90.5% 53.9%
3287736 632.15.1.9 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) › DUF2516 0.64 41.0 4.66e-01 91.3% 85.3%
3510392 6157.1.1.1 ↗ alpha bundles › GKAP homology domain 1 › GKAP homology domain 1 › GKAP homology domain 1 › GKAP 0.64 50.0 5.32e-01 88.1% 92.7%
3589798 632.1.1.14 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › EzrA 0.64 41.0 4.66e-01 88.9% 86.3%
3454274 632.1.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › Alpha-mann_mid 0.64 42.0 4.52e-01 92.1% 79.0%
3953975 632.1.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › Alpha-mann_mid 0.63 43.0 4.87e-01 92.1% 91.6%
2507421 632.2.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › FIVAR 0.63 37.0 4.64e-01 88.1% 100.0%
3959665 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.63 43.0 4.83e-01 91.3% 91.6%
3802170 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.63 50.0 4.73e-01 92.9% 70.7%
3321494 632.2.1.27 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › GAUT_1 0.63 40.0 4.53e-01 94.4% 85.3%
3312398 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.62 51.0 4.64e-01 93.7% 66.1%
3377582 632.21.1.4 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › GAUT_1 0.62 41.0 4.63e-01 95.2% 88.4%
4955906 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.61 34.0 4.30e-01 86.5% 95.7%
3757924 7004.1.1.0 ↗ 0.59 29.0 3.42e-01 79.4% 65.9%
3918077 601.1.2.83 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Dynactin 0.58 45.0 4.33e-01 81.0% 93.1%
3625874 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.58 51.0 4.99e-01 93.7% 90.4%
3393821 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.56 48.0 4.48e-01 91.3% 78.7%
3215073 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.56 32.0 3.98e-01 88.9% 92.0%
3940769 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.56 47.0 4.21e-01 88.9% 94.1%
3676602 3755.4.1.17 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Rx_N 0.56 42.0 4.01e-01 81.0% 81.3%
4653531 632.1.1.14 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › EzrA 0.56 44.0 4.69e-01 97.6% 95.5%
4367113 632.22.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › EzrA 0.55 43.0 4.68e-01 94.4% 100.0%
3741788 633.21.1.10 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › MARVEL 0.54 46.0 4.30e-01 91.3% 80.6%
4555998 4025.1.1.0 ↗ alpha complex topology › alpha-helical domain in nickel-iron hydrogenase, large subunit › alpha-helical domain in nickel-iron hydrogenase, large subunit › alpha-helical domain in nickel-iron hydrogenase, large subunit 0.53 48.0 4.04e-01 99.2% 75.2%
4365580 4025.1.1.0 ↗ alpha complex topology › alpha-helical domain in nickel-iron hydrogenase, large subunit › alpha-helical domain in nickel-iron hydrogenase, large subunit › alpha-helical domain in nickel-iron hydrogenase, large subunit 0.52 45.0 3.91e-01 92.9% 89.5%
5061992 5054.1.1.6 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › TrkH 0.52 46.0 4.14e-01 99.2% 86.3%
3233752 1016.1.1.0 ↗ alpha arrays › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 0.51 42.0 4.43e-01 96.0% 100.0%
4386119 102.1.1.42 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › RNAseD_HRDC_C 0.51 27.0 3.52e-01 87.3% 92.9%