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NC_025436.1__YP_009100355.1__S14_48__00048

Bact-Vir

NC_025436.1__YP_009100355.1__S14_48__00048

Identity

Accession:
NC_025436 ↗
Kingdom:
phage

Quality

77.8 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 49-105
PDB
Domain cluster: representative
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4fzbA02 1.20.5.3070 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.92 62.0 7.29e-01 73.7% 100.0%
1m5iA00 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.85 77.0 6.20e-01 100.0% 57.1%
2y44A00 1.20.1260.80 Mainly Alpha › Up-down Bundle › Ferritin › 0.84 77.0 5.28e-01 100.0% 83.7%
1h7cA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.82 73.0 5.93e-01 98.2% 56.3%
2w9mB01 1.10.150.110 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DNA polymerase beta, N-terminal domain-like 0.80 55.0 4.76e-01 71.9% 47.7%
1vpdA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.78 62.0 4.63e-01 84.2% 42.0%
6xxvC00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.78 68.0 5.52e-01 100.0% 55.9%
3pwfA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.77 67.0 5.08e-01 96.5% 44.3%
2cwyA00 1.10.3450.10 Mainly Alpha › Orthogonal Bundle › Hyaluronidase domain-like › TTHA0068-like 0.76 53.0 4.48e-01 77.2% 44.1%
5lb3B02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.76 62.0 4.08e-01 89.5% 75.9%
1cxzB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.76 67.0 5.87e-01 100.0% 67.4%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.76 62.0 4.77e-01 93.0% 42.5%
1urfA00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.76 65.0 5.82e-01 96.5% 76.5%
1ma1A01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.76 65.0 6.29e-01 94.7% 87.5%
4k0dA00 1.20.120.1730 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.75 62.0 4.72e-01 94.7% 40.6%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.75 63.0 6.06e-01 100.0% 82.1%
4d3dB02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.74 61.0 4.59e-01 89.5% 38.8%
3q18A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.74 60.0 4.89e-01 94.7% 48.3%
2ewfA02 1.20.1270.310 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.72 53.0 4.79e-01 80.7% 61.7%
2aplA01 1.10.8.330 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › PG0816-like 0.72 51.0 4.76e-01 75.4% 60.3%
3dkqA02 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.71 52.0 5.54e-01 80.7% 95.7%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 55.0 5.41e-01 87.7% 87.1%
2p0tA02 1.10.60.30 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › PSPTO4464-like domains 0.71 48.0 4.51e-01 73.7% 55.6%
2p0vA01 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.71 54.0 3.23e-01 84.2% 11.2%
6j7xA01 1.25.40.120 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Protein prenylyltransferase 0.70 52.0 3.33e-01 80.7% 16.7%
4k7cA01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.70 57.0 3.45e-01 94.7% 40.1%
1j1jA02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.69 53.0 4.68e-01 86.0% 56.5%
3juiA00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.68 51.0 3.68e-01 84.2% 28.7%
1ufvA02 3.30.1300.10 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › Pantoate-beta-alanine ligase, C-terminal domain 0.68 50.0 4.28e-01 82.5% 79.8%
5aj3N01 1.10.287.1480 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.62 51.0 4.43e-01 98.2% 59.3%
2rfqB01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.61 44.0 3.59e-01 77.2% 41.3%
3jamD02 3.30.1140.32 Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › Ribosomal protein S3, C-terminal domain 0.61 41.0 3.24e-01 71.9% 75.2%
3c57B00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.59 40.0 4.26e-01 70.2% 91.8%
4ye6A01 1.10.8.1290 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1, domain 1 0.59 40.0 3.21e-01 70.2% 38.5%
2jbrA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.56 43.0 3.50e-01 87.7% 45.4%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3742534 622.4.1.52 alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › TMEM254 0.91 83.0 6.65e-01 96.5% 56.0%
3705783 192.5.1.0 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat 0.85 78.0 6.61e-01 100.0% 67.8%
4485588 547.1.1.1 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.85 80.0 6.43e-01 100.0% 81.0%
5082622 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.85 69.0 6.00e-01 87.7% 60.0%
3718408 3922.1.1.0 alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.85 77.0 6.13e-01 100.0% 55.5%
3605626 192.12.1.0 alpha bundles › Long alpha-hairpin › Transcriptional repressor TraM › Transcriptional repressor TraM 0.84 77.0 6.19e-01 100.0% 58.1%
3560229 3291.1.1.230 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › TBCA_PH 0.84 77.0 5.67e-01 100.0% 51.4%
3423402 604.7.1.1 alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › TBCA 0.83 77.0 6.64e-01 100.0% 69.4%
3923888 4177.1.1.5 alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › Vps5 0.83 75.0 4.95e-01 100.0% 26.8%
3073109 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.83 75.0 6.85e-01 100.0% 82.4%
4059072 2003.1.1.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.83 78.0 4.86e-01 100.0% 30.9%
None 0.83 78.0 4.85e-01 100.0% 30.9%
4320306 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.83 75.0 5.90e-01 100.0% 50.9%
3252433 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.83 75.0 4.61e-01 100.0% 18.7%
5001019 4177.1.1.0 alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.83 73.0 5.19e-01 100.0% 36.5%
3518412 4177.1.1.2 alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.82 74.0 4.83e-01 98.2% 64.4%
3741234 605.2.1.3 alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Seryl_tRNA_N 0.82 74.0 5.77e-01 100.0% 48.7%
4429833 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.81 72.0 5.76e-01 100.0% 50.9%
4429194 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.81 72.0 5.75e-01 100.0% 50.9%
4470267 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.81 73.0 5.78e-01 100.0% 50.9%
4067677 3826.1.1.25 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › GlutR_dimer 0.81 69.0 6.12e-01 91.2% 97.4%
5063778 2004.1.1.87 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.81 72.0 4.21e-01 100.0% 28.2%
4200406 547.1.1.1 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.80 74.0 5.78e-01 100.0% 72.6%
4335871 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.80 72.0 5.70e-01 100.0% 50.9%
3492576 4177.1.1.5 alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › Vps5 0.80 70.0 4.81e-01 100.0% 29.5%
4937169 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.80 71.0 5.65e-01 100.0% 50.9%
4028650 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.80 56.0 5.57e-01 77.2% 70.0%
4305639 3826.1.1.25 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › GlutR_dimer 0.80 64.0 5.80e-01 86.0% 98.7%
3497897 3939.1.1.0 alpha duplicates or obligate multimers › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain 0.79 71.0 6.59e-01 98.2% 81.4%
3839273 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.79 70.0 5.60e-01 100.0% 50.9%
3784055 192.24.1.0 alpha bundles › Long alpha-hairpin › RPC62 helical hairpin domain › RPC62 helical hairpin domain 0.79 70.0 5.31e-01 98.2% 46.9%
4518916 4144.1.1.8 alpha duplicates or obligate multimers › YejL-like › YejL-like › YejL-like › GlutR_dimer 0.79 66.0 5.95e-01 89.5% 100.0%
5025813 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.79 71.0 5.66e-01 100.0% 52.7%
4057547 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.79 71.0 5.66e-01 100.0% 52.7%
4267174 614.1.1.24 alpha duplicates or obligate multimers › L27 domain › L27 domain › L27 domain › GlutR_dimer 0.79 66.0 5.93e-01 89.5% 100.0%
4110549 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.78 69.0 5.54e-01 100.0% 50.9%
4564711 547.1.1.1 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.78 66.0 5.92e-01 89.5% 100.0%
4242072 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.78 70.0 5.54e-01 100.0% 50.4%
4304756 605.2.1.3 alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Seryl_tRNA_N 0.78 70.0 5.57e-01 100.0% 52.7%
4266661 547.1.1.1 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.78 71.0 5.48e-01 100.0% 67.2%
3932692 604.6.1.0 alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.77 68.0 5.78e-01 96.5% 63.3%
4231284 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.77 68.0 5.48e-01 100.0% 50.9%
None 0.77 70.0 4.47e-01 100.0% 30.8%
4024219 3871.1.1.1 alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.77 67.0 4.87e-01 98.2% 38.1%
4987684 3755.1.1.0 alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related 0.76 68.0 5.20e-01 100.0% 45.4%
4213502 4336.1.1.1 alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF 0.76 58.0 4.63e-01 82.5% 42.7%
4175087 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.75 67.0 5.41e-01 100.0% 52.7%
3678035 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 0.75 66.0 6.24e-01 100.0% 82.9%
3603648 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.75 65.0 5.61e-01 96.5% 63.6%
3783023 6155.1.1.2 alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › PQ-loop 0.75 65.0 5.26e-01 94.7% 52.4%
3416186 3855.1.1.2 alpha arrays › Serum amyloid A-1 protein › Serum amyloid A-1 protein › Serum amyloid A-1 protein › DM4_12 0.74 64.0 4.83e-01 96.5% 73.1%
4995681 3788.1.1.0 alpha bundles › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) 0.73 52.0 4.93e-01 73.7% 83.1%
3680789 2004.1.1.505 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11, AAA_30 0.73 63.0 3.78e-01 96.5% 18.5%
4273807 314.1.1.0 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases 0.73 64.0 3.78e-01 100.0% 13.2%
3953703 601.33.1.1 alpha bundles › Four-helical up-and-down bundle › CHAD domain › CHAD domain › CHAD 0.73 64.0 4.89e-01 100.0% 43.6%
4965656 4336.1.1.1 alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF 0.73 58.0 4.62e-01 87.7% 43.5%
5078048 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 0.70 62.0 5.66e-01 100.0% 85.3%
3936693 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.67 55.0 4.72e-01 96.5% 55.0%