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MN695334.1__QGT54567.1__b3_0326__00309

Bact-Vir

MN695334.1__QGT54567.1__b3_0326__00309

Identity

Accession:
MN695334 ↗
Kingdom:
phage

Quality

87.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Kyanoviridae› Synechococcus_phage_B3

TaxID: 2674978

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 8-167
PDB
Domain cluster: rep: NC_048757.1__YP_009844891.1__HWC13_gp082__00082__D259-407
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03734.20 best YkuD 39.1 1.60e-09 92.5% 76.2%
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6xj6A01 2.40.440.10 Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like 0.80 69.0 6.98e-01 100.0% 91.0%
4z7aA03 2.40.440.10 Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like 0.78 56.0 6.23e-01 95.0% 90.1%
4lpqA02 2.40.440.10 Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like 0.75 58.0 6.44e-01 100.0% 98.4%
3hrgA02 3.30.420.260 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Protein of unknown function DUF3822, C-terminal domain 0.68 29.0 3.42e-01 96.9% 55.3%
3bexA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.68 29.0 3.17e-01 95.6% 46.3%
3t69A01 3.30.420.300 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 2-keto-3-deoxy-galactonokinase, substrate binding domain 0.68 28.0 4.12e-01 93.8% 84.0%
3lm2A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.67 28.0 3.56e-01 97.5% 62.9%
2f9wA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.66 26.0 2.89e-01 95.0% 42.0%
1wiiA01 2.20.25.190 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.65 21.0 3.44e-01 87.5% 75.8%
4ijaB02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.64 30.0 3.04e-01 96.2% 43.9%
1xc3A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.64 26.0 3.23e-01 95.0% 56.3%
2m3xC02 2.40.10.360 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.64 24.0 3.68e-01 93.1% 81.2%
3psfA04 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.62 29.0 2.92e-01 98.1% 43.3%
3bzcA03 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.61 28.0 3.10e-01 95.6% 50.8%
3h6eB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.60 29.0 3.63e-01 95.6% 72.7%
2ychA03 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.55 34.0 3.92e-01 97.5% 82.6%
5aj3K00 3.30.420.80 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribosomal protein S11/S14 0.54 31.0 3.34e-01 98.8% 65.4%
4v19S00 3.30.420.80 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribosomal protein S11/S14 0.53 29.0 3.12e-01 99.4% 58.7%
1jceA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 32.0 3.31e-01 95.0% 64.7%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1558018 4091.1.1.1 ↗ beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.81 58.0 6.44e-01 100.0% 90.0%
4975998 4091.1.1.1 ↗ beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.77 64.0 6.88e-01 94.4% 98.6%
1120883 4091.1.1.1 ↗ beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.75 58.0 6.44e-01 100.0% 98.4%
3263338 4091.1.1.1 ↗ beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.74 70.0 6.64e-01 100.0% 94.6%
4679621 4091.1.1.1 ↗ beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.74 60.0 6.55e-01 96.9% 100.0%
3701860 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.70 32.0 4.12e-01 96.9% 73.7%
4840137 4091.1.1.1 ↗ beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.69 50.0 5.64e-01 93.8% 95.9%
4346158 4091.1.1.0 ↗ beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like 0.66 60.0 6.05e-01 96.9% 98.1%
3647663 5.1.10.8 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 12-bladed › ANAPC4_WD40 0.64 23.0 3.75e-01 84.4% 86.7%
11186 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.63 31.0 3.68e-01 96.2% 65.8%
4946976 3407.1.1.5 ↗ mixed a+b and a/b › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain › Nop 0.60 29.0 3.06e-01 94.4% 49.7%
3741985 2484.1.1.7 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Ribosomal_S11 0.59 30.0 3.36e-01 97.5% 61.6%
5072189 2484.1.1.6 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FGGY_N 0.59 32.0 3.25e-01 95.6% 51.0%
5083421 2484.1.1.6 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FGGY_N 0.58 30.0 3.92e-01 95.6% 87.8%
3370226 4263.2.1.0 ↗ a+b two layers › TTHA1528-like › FtsH Periplasmic Domain › FtsH Periplasmic Domain 0.55 22.0 3.22e-01 89.4% 83.1%
3528508 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.55 28.0 3.34e-01 95.6% 68.7%
4009809 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.55 28.0 3.15e-01 95.0% 60.0%
3960750 6.1.1.0 ↗ beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil 0.54 26.0 3.02e-01 88.7% 60.2%
4927504 3407.1.1.0 ↗ mixed a+b and a/b › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain 0.52 30.0 3.36e-01 95.6% 72.0%
3295513 2484.1.1.6 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FGGY_N 0.52 31.0 2.73e-01 96.9% 38.4%
4980315 2484.1.1.21 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › BcrAD_BadFG 0.51 39.0 3.30e-01 100.0% 48.5%
4953660 3407.1.1.2 ↗ mixed a+b and a/b › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain › Nop5_56-rel_N_Arc 0.51 29.0 3.39e-01 95.0% 75.8%
4980477 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.51 28.0 3.07e-01 95.0% 63.0%
4964668 2484.1.1.341 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Salactin 0.50 32.0 3.44e-01 96.2% 72.9%
4969491 2484.1.1.21 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › BcrAD_BadFG 0.50 38.0 3.77e-01 99.4% 75.8%
D2 high residues 254-419
PDB
Domain cluster: rep: BML_08012017_9_75m_scaffold_2_prodigal-single.1__X__X__00075__D114-200_257-347