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NC_015287.1__YP_004324088.1__SSSM7_035__00035

Bact-Vir

NC_015287.1__YP_004324088.1__SSSM7_035__00035

Identity

Accession:
NC_015287 ↗
Kingdom:
phage

Quality

85.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Kyanoviridae› Lipsvirus› Synechococcus_phage_S-SSM7

TaxID: 445686

Cluster

View cluster (8 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 439-501
PDB
Domain cluster: rep: SR-VP_0-2_scaffold_141_4556078_prodigal-single.1__X__X__00088__D33-109
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01844.30 best HNH 22.3 1.70e-04 71.4% 59.6%
D2 medium residues 16-137_194-205
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7zmgL01 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.55 31.0 3.83e-01 87.3% 92.5%
3t8iA00 3.90.245.10 Alpha Beta › Alpha-Beta Complex › Inosine-uridine Nucleoside N-ribohydrolase; Chain A › Ribonucleoside hydrolase-like 0.54 42.0 3.24e-01 81.3% 96.1%
3ozbA00 3.40.50.1580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleoside phosphorylase domain 0.52 39.0 3.22e-01 77.6% 68.5%
3rkoG00 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.51 30.0 3.32e-01 86.6% 75.0%
D3 medium residues 138-193
PDB
Domain cluster: representative
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3h95A02 4.10.80.100 Few Secondary Structures › Irregular › Rhinovirus 14, subunit 4 › 0.70 38.0 4.59e-01 73.2% 96.7%
4c0dB00 2.30.30.1020 Mainly Beta › Roll › SH3 type barrels. › CCR4-NOT complex subunit 2/3/5, C-terminal domain 0.65 38.0 2.57e-01 78.6% 16.8%
1oi2A02 3.30.1180.20 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › Dihydroxyacetone kinase; domain 2 0.64 44.0 3.13e-01 71.4% 88.9%
2d5lA02 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.64 44.0 2.85e-01 71.4% 45.3%
5cxxB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.63 46.0 2.92e-01 76.8% 43.1%
1aalB00 4.10.410.10 Few Secondary Structures › Irregular › Factor Xa Inhibitor › Pancreatic trypsin inhibitor Kunitz domain 0.61 38.0 3.87e-01 89.3% 63.2%
6q61A00 4.10.410.10 Few Secondary Structures › Irregular › Factor Xa Inhibitor › Pancreatic trypsin inhibitor Kunitz domain 0.60 38.0 3.79e-01 89.3% 61.0%
2b9dA01 3.30.160.330 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.59 37.0 4.13e-01 83.9% 89.7%
1bikA00 4.10.410.10 Few Secondary Structures › Irregular › Factor Xa Inhibitor › Pancreatic trypsin inhibitor Kunitz domain 0.58 38.0 3.03e-01 91.1% 33.6%
5jm6A02 2.30.250.10 Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 0.58 45.0 3.45e-01 89.3% 91.6%
5yv7A00 4.10.410.10 Few Secondary Structures › Irregular › Factor Xa Inhibitor › Pancreatic trypsin inhibitor Kunitz domain 0.57 36.0 3.61e-01 89.3% 60.0%
4bd9B01 4.10.410.10 Few Secondary Structures › Irregular › Factor Xa Inhibitor › Pancreatic trypsin inhibitor Kunitz domain 0.57 37.0 3.75e-01 89.3% 66.7%
4obmA00 3.40.630.190 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › LCP protein 0.57 45.0 3.04e-01 96.4% 69.0%
1neiA00 3.30.160.220 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › YoaG 0.55 38.0 3.76e-01 76.8% 68.3%
1q9jB02 3.30.559.30 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Nonribosomal peptide synthetase, condensation domain 0.55 47.0 3.36e-01 100.0% 56.5%
4ntwB00 4.10.410.10 Few Secondary Structures › Irregular › Factor Xa Inhibitor › Pancreatic trypsin inhibitor Kunitz domain 0.55 35.0 3.51e-01 89.3% 61.0%
3bvxA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.54 44.0 3.30e-01 91.1% 66.7%
3i3lA02 3.30.390.160 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.52 39.0 3.12e-01 83.9% 66.4%
3dohA02 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 43.0 2.94e-01 100.0% 67.9%
6vq6H01 1.10.287.3240 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 42.0 2.87e-01 91.1% 40.7%
3hhmA03 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.52 43.0 3.30e-01 96.4% 51.1%
1pvgA01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.51 41.0 2.81e-01 96.4% 81.6%
2xssA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.51 35.0 2.72e-01 76.8% 36.5%
3wbiA04 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.51 41.0 3.17e-01 96.4% 71.7%
6zwwC01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.50 34.0 2.49e-01 71.4% 98.3%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3574486 384.1.1.1 ↗ few secondary structure elements › BPTI-like › BPTI-like › BPTI-like › Kunitz_BPTI 0.70 41.0 4.31e-01 85.7% 64.0%
3922954 384.1.1.1 ↗ few secondary structure elements › BPTI-like › BPTI-like › BPTI-like › Kunitz_BPTI 0.65 41.0 4.09e-01 89.3% 62.1%
5053243 67.1.1.1 ↗ beta sandwiches › HSP40/DnaJ peptide-binding domain › HSP40/DnaJ peptide-binding domain › HSP40/DnaJ peptide-binding domain › DnaJ_C 0.64 50.0 4.54e-01 89.3% 80.0%
3472023 384.1.1.0 ↗ few secondary structure elements › BPTI-like › BPTI-like › BPTI-like 0.63 44.0 4.19e-01 89.3% 63.1%
3941746 301.13.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › Dak1 0.61 41.0 2.93e-01 71.4% 88.6%
4242930 4232.1.1.1 ↗ few secondary structure elements › Ribosomal protein bL28-related › Ribosomal protein bL28-related › Ribosomal protein L28 › Ribosomal_L28 0.58 34.0 2.94e-01 75.0% 34.4%
4408923 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 43.0 3.21e-01 83.9% 65.2%
3440533 2.1.1.27 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › RNA_pol_Rpb8 0.57 33.0 2.84e-01 78.6% 31.6%
3714786 2004.1.1.19 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.56 39.0 2.74e-01 75.0% 73.5%
3717261 7579.1.1.0 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases 0.56 49.0 3.18e-01 98.2% 29.6%
3600031 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.55 38.0 3.17e-01 75.0% 44.1%
3499445 110.3.1.1 ↗ alpha arrays › DEATH domain › SLED domain › SLED domain › SLED 0.54 37.0 3.05e-01 73.2% 62.7%
3175336 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.54 36.0 3.43e-01 75.0% 54.7%
3961948 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.54 36.0 2.56e-01 71.4% 86.3%
4943172 3926.1.1.1 ↗ alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D › ATP-synt_D 0.53 43.0 2.98e-01 91.1% 42.5%
3608009 2004.1.1.19 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.52 37.0 2.58e-01 75.0% 71.0%
3825952 221.1.1.4 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.52 41.0 3.59e-01 98.2% 59.0%
3499892 389.1.3.0 ↗ few secondary structure elements › EGF-like › EGF-related › TNF receptor-like 0.52 36.0 3.49e-01 85.7% 63.1%
3740226 5051.1.1.7 ↗ alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Nramp 0.52 38.0 2.33e-01 85.7% 52.2%
5018200 2004.1.1.220 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SWI2_SNF2 0.51 41.0 2.48e-01 100.0% 20.2%
3672794 207.1.1.67 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_1,LRRNT_2,LRR_4,LRR_6 0.51 36.0 2.15e-01 78.6% 30.1%
4943803 2007.1.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like 0.51 42.0 2.81e-01 100.0% 67.0%
3357805 3887.2.1.1 ↗ a+b two layers › Yeast killer toxin-like › Antifungal protein ginkbilobin-2 › Antifungal protein ginkbilobin-2 › Stress-antifung 0.51 35.0 3.29e-01 75.0% 61.3%
3356297 5.1.2.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed 0.51 41.0 3.28e-01 96.4% 47.7%
3328712 4964.1.1.0 ↗ alpha arrays › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I › helical bundle in Bacillus stearothermophilus-like DNA polymerase I 0.50 40.0 2.82e-01 98.2% 37.4%
3363678 7504.1.1.3 ↗ a/b three-layered sandwiches › ITPase-like › ITPase-like › ITPase-like › Maf 0.50 39.0 2.75e-01 87.5% 51.3%
3675509 192.3.1.0 ↗ alpha bundles › Long alpha-hairpin › Fe,Mn superoxide dismutase (SOD), N-terminal domain › Fe,Mn superoxide dismutase (SOD), N-terminal domain 0.50 38.0 3.03e-01 92.9% 66.2%
D4 medium residues 220-320
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1dc1A02 1.10.238.90 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Restriction endonuclease BsobI, helical domain 0.57 38.0 4.08e-01 92.1% 79.5%
1pwuA04 3.40.390.10 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › Collagenase (Catalytic Domain) 0.56 40.0 3.17e-01 75.2% 75.6%
3iieB03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.53 39.0 4.23e-01 99.0% 92.9%
2y1eA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.52 39.0 4.17e-01 96.0% 93.1%
3ljcA02 1.20.58.1480 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 40.0 3.76e-01 93.1% 69.8%
1rypK00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.50 35.0 2.86e-01 72.3% 65.7%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4025565 4250.1.1.1 ↗ alpha bundles › Duffy-binding-like domain, N-terminal subdomain › Duffy-binding-like domain, N-terminal subdomain › Duffy-binding-like domain, N-terminal subdomain › Duffy_binding 0.52 36.0 3.01e-01 71.3% 85.4%
D5 medium residues 321-433
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1gq2A02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.58 52.0 3.84e-01 100.0% 87.7%
2oo2A00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.54 29.0 3.49e-01 76.1% 78.9%
5llmA00 1.10.3860.10 Mainly Alpha › Orthogonal Bundle › Proton glutamate symport protein › Sodium:dicarboxylate symporter 0.54 45.0 3.18e-01 94.7% 82.0%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.53 33.0 3.97e-01 83.2% 94.7%
5uayA02 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.53 30.0 3.33e-01 85.8% 71.1%
4djbA00 3.30.70.2870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Mastadenovirus E4 ORF3 0.52 41.0 4.13e-01 85.8% 87.3%
2kiwA01 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.52 31.0 3.46e-01 87.6% 76.7%
8agyA01 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.51 42.0 3.31e-01 89.4% 79.5%
2wzvA01 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.50 35.0 2.89e-01 72.6% 90.8%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3797423 3226.1.1.0 ↗ alpha complex topology › Uracil Transporter UraA › Uracil Transporter UraA › Uracil Transporter UraA 0.56 45.0 3.00e-01 87.6% 87.2%
3412378 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 22.0 3.50e-01 76.1% 95.6%
3288303 5051.1.1.3 ↗ alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › SSF 0.55 49.0 3.19e-01 98.2% 74.8%
3630322 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.52 44.0 2.89e-01 94.7% 93.0%
5048933 3646.1.1.1 ↗ alpha complex topology › T-component of energy-coupling factor (ECF) transporters › T-component of energy-coupling factor (ECF) transporters › T-component of energy-coupling factor (ECF) transporters › CbiQ 0.52 39.0 3.08e-01 79.6% 80.8%
5075193 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.51 40.0 3.86e-01 83.2% 91.5%
3230531 633.1.1.0 ↗ alpha bundles › Bromodomain-like › Bromodomain › Bromodomain 0.51 36.0 3.79e-01 85.8% 82.0%
3630034 3226.1.1.1 ↗ alpha complex topology › Uracil Transporter UraA › Uracil Transporter UraA › Uracil Transporter UraA › Xan_ur_permease 0.51 44.0 2.95e-01 97.3% 85.1%
5074961 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.50 39.0 3.80e-01 83.2% 91.5%
3590722 162.1.1.0 ↗ alpha bundles › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD 0.50 44.0 4.47e-01 95.6% 99.1%