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NC_048736.1__YP_009841994.1__HWB92_gp126__00126

Bact-Vir

NC_048736.1__YP_009841994.1__HWB92_gp126__00126

Identity

Accession:
NC_048736 ↗
Kingdom:
phage

Quality

79.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Ackermannviridae› Miltonvirus› Serratia_phage_vB_SmaA_3M

TaxID: 2419930

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 medium residues 41-91
PDB
Domain cluster: representative
CATH (47)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2katA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.90 74.0 5.51e-01 88.2% 40.9%
1yuzB01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.89 69.0 4.95e-01 84.3% 41.3%
2yxyA01 1.10.287.880 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Hypothetical protein YfhH domain 0.87 67.0 6.78e-01 80.4% 82.0%
2rklF00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.86 60.0 6.06e-01 74.5% 76.9%
1j5wA02 1.20.58.180 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Class II aaRS and biotin synthetases; domain 2 0.85 66.0 5.73e-01 84.3% 57.1%
4u1cA01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.85 68.0 6.75e-01 84.3% 82.7%
4fymF00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.84 74.0 4.78e-01 96.1% 27.8%
1yzmA00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.83 69.0 7.24e-01 92.2% 100.0%
5jajA03 1.20.1320.30 Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › 0.83 67.0 5.07e-01 88.2% 40.5%
4hb1A00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.82 62.0 6.65e-01 86.3% 93.2%
6he1B01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.82 68.0 6.29e-01 90.2% 92.2%
1sr2A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.82 66.0 5.01e-01 88.2% 67.2%
3craB01 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.82 72.0 5.94e-01 96.1% 60.5%
1z0jB00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.82 70.0 7.07e-01 94.1% 94.1%
3r2qA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.82 67.0 5.07e-01 88.2% 76.1%
3nymA00 6.10.290.10 Special › Helix non-globular › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.81 67.0 4.98e-01 90.2% 39.5%
1vmgA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.81 66.0 5.64e-01 90.2% 61.0%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.81 69.0 6.17e-01 92.2% 68.1%
1q0gA00 1.20.120.400 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nickel-containing superoxide dismutase 0.81 65.0 4.92e-01 88.2% 50.4%
1cpqA00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.80 70.0 5.20e-01 100.0% 93.0%
1bbhA00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.79 69.0 5.07e-01 98.0% 91.6%
1yvwA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.79 69.0 5.60e-01 96.1% 55.4%
5jc3A02 1.20.1320.30 Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › 0.79 65.0 4.85e-01 90.2% 37.3%
1kfdA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.79 59.0 5.28e-01 80.4% 73.2%
1cgnA00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.78 66.0 5.00e-01 96.1% 57.3%
1luwA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.77 63.0 5.84e-01 90.2% 73.4%
2yxhA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.76 65.0 5.03e-01 96.1% 48.7%
3k59A06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.76 58.0 5.99e-01 78.4% 85.1%
1y6xA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.76 65.0 5.45e-01 96.1% 58.6%
2psmA00 1.20.1250.70 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › Interleukin-15/Interleukin-21 0.75 63.0 4.79e-01 94.1% 71.8%
8amzP01 1.25.40.570 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.74 65.0 3.82e-01 96.1% 22.7%
1zpyA00 6.10.140.1960 Special › Helix non-globular › Helix Hairpins › 0.74 57.0 4.71e-01 86.3% 47.3%
1rqgA04 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.73 64.0 4.57e-01 100.0% 85.4%
3kflA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.72 63.0 4.36e-01 100.0% 65.1%
2v0cA04 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.72 60.0 4.29e-01 96.1% 35.2%
1z5zA02 1.20.120.850 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SWI2/SNF2 ATPases, N-terminal domain 0.70 51.0 4.53e-01 92.2% 53.9%
1hr5A00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.68 53.0 5.39e-01 88.2% 93.8%
3ltoA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.67 59.0 4.34e-01 98.0% 44.0%
2zueA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.67 57.0 4.40e-01 98.0% 46.2%
1wkbA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.66 56.0 4.23e-01 94.1% 56.2%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.64 49.0 4.31e-01 88.2% 55.1%
1qguB04 1.20.89.10 Mainly Alpha › Up-down Bundle › Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 › Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 0.63 45.0 3.95e-01 82.4% 48.2%
2gv9A05 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.63 50.0 4.81e-01 94.1% 76.3%
1m4rB00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.63 45.0 3.42e-01 82.4% 29.1%
1f7uA02 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.62 53.0 4.06e-01 98.0% 48.8%
3vprA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.61 51.0 3.75e-01 96.1% 37.2%
6f1eA01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.56 48.0 3.54e-01 98.0% 38.8%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4996451 7516.1.1.2 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.95 79.0 4.75e-01 88.2% 16.3%
3806239 616.1.1.0 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.93 74.0 6.37e-01 84.3% 61.3%
4472442 192.11.1.1 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.93 68.0 7.58e-01 78.4% 97.5%
3809308 3826.1.1.66 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › DUF641 0.91 70.0 6.61e-01 82.4% 93.3%
4966900 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.89 71.0 6.46e-01 84.3% 70.8%
3643501 192.1.1.47 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain › DUF641 0.88 70.0 6.35e-01 84.3% 90.8%
3976258 616.1.1.0 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.87 69.0 6.76e-01 84.3% 78.2%
4928617 159.1.2.0 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related 0.87 72.0 6.26e-01 90.2% 66.7%
4088690 604.9.1.1 ↗ alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › Ribosomal_S20p 0.85 68.0 5.79e-01 86.3% 60.0%
3965757 159.1.2.1 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › PRA-PH 0.84 67.0 5.27e-01 88.2% 44.8%
4930198 605.1.1.2 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › H-kinase_dim 0.84 66.0 6.28e-01 86.3% 75.0%
3596737 604.8.1.0 ↗ alpha bundles › Spectrin repeat-like › Smac/diablo › Smac/diablo 0.83 70.0 5.12e-01 92.2% 58.5%
4181278 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 0.83 70.0 6.11e-01 92.2% 68.0%
4672360 604.1.1.4 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › SbsC_C 0.83 66.0 5.43e-01 84.3% 54.1%
3584539 192.17.1.6 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › CC2D1A-B_DM14 0.82 70.0 6.08e-01 92.2% 62.7%
5060747 601.14.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Hemerythrin › Hemerythrin › Hemerythrin 0.82 72.0 4.92e-01 96.1% 40.6%
3281203 604.17.1.0 ↗ alpha bundles › Spectrin repeat-like › MTH_863 C-terminal domain-like › MTH_863 C-terminal domain-like 0.82 62.0 6.26e-01 80.4% 82.0%
3240245 192.17.1.1 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › Rbsn 0.82 71.0 7.21e-01 94.1% 96.0%
5025189 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.81 70.0 6.87e-01 96.1% 87.3%
5082167 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.81 72.0 5.85e-01 96.1% 73.3%
140767 632.8.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › DUF6853 0.81 67.0 4.98e-01 90.2% 39.5%
3230775 192.1.1.25 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain › VPS18_RING_C 0.81 74.0 5.64e-01 100.0% 60.9%
4127 159.1.2.2 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › MazG 0.81 66.0 5.61e-01 90.2% 60.2%
3738041 192.5.1.1 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1 0.81 69.0 5.71e-01 92.2% 55.3%
3409005 192.17.1.6 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › CC2D1A-B_DM14 0.81 69.0 6.49e-01 92.2% 78.3%
3245655 101.1.2.552 ↗ alpha arrays › HTH › HTH › winged helix domain › eIF-3c_N 0.81 65.0 4.90e-01 88.2% 39.2%
3504819 192.17.1.6 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › CC2D1A-B_DM14 0.80 68.0 6.24e-01 92.2% 72.3%
3216492 601.18.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Oxygen-evolving enhancer protein 3 › Oxygen-evolving enhancer protein 3 0.80 68.0 5.35e-01 94.1% 45.7%
3186698 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.80 67.0 5.76e-01 92.2% 58.7%
3680600 604.12.1.67 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › eIF-3c_N 0.80 67.0 5.15e-01 92.2% 43.6%
3684312 192.17.1.10 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › eIF-3c_N 0.80 67.0 5.10e-01 92.2% 42.6%
3436931 192.6.1.11 ↗ alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain › eIF-3c_N 0.79 66.0 5.13e-01 92.2% 43.6%
3965106 605.1.1.4 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA_3 0.78 64.0 5.62e-01 90.2% 61.3%
2539030 601.2.1.4 ↗ alpha bundles › Four-helical up-and-down bundle › Cytochromes › Cytochromes › Cytochrom_C_2 0.77 68.0 5.30e-01 100.0% 94.6%
4618805 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.77 64.0 6.30e-01 92.2% 85.5%
4541925 5000.4.1.0 ↗ alpha arrays › Toxins' membrane translocation domains › delta-Endotoxin (insectocide), N-terminal domain › delta-Endotoxin (insectocide), N-terminal domain 0.77 67.0 4.33e-01 98.0% 76.4%
3360144 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.75 64.0 5.72e-01 98.0% 68.6%
3952558 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.75 61.0 4.71e-01 92.2% 40.9%
4063100 604.9.1.1 ↗ alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › Ribosomal_S20p 0.75 57.0 5.02e-01 86.3% 60.0%
4377147 4002.1.1.4 ↗ alpha bundles › alpha-helical domain in dehydroquinate synthase-like enzymes › alpha-helical domain in dehydroquinate synthase-like enzymes › alpha-helical domain in dehydroquinate synthase-like enzymes › DHQS_C 0.63 52.0 3.61e-01 98.0% 26.8%