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NC_028676.1__YP_009189635.1__AU106_gp250__00250

Bact-Vir

NC_028676.1__YP_009189635.1__AU106_gp250__00250

Identity

Accession:
NC_028676 ↗
Kingdom:
phage

Quality

87.1 mean pLDDT

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 8-109
PDB
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6ldiF01 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 0.74 56.0 5.84e-01 95.1% 84.4%
1rp3A01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.74 56.0 6.10e-01 85.3% 95.3%
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 0.62 43.0 4.64e-01 71.6% 83.9%
2fu2A00 1.20.1440.50 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like 0.60 34.0 3.85e-01 71.6% 73.1%
1s7bA00 1.10.3730.20 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › 0.59 40.0 4.02e-01 85.3% 67.0%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.58 49.0 4.48e-01 92.2% 88.1%
1n5uA02 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.57 40.0 4.27e-01 95.1% 83.3%
2gbbB00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.57 46.0 4.07e-01 89.2% 85.2%
3fhnA02 1.20.58.1420 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dsl1p vesicle tethering complex, Tip20p subunit, domain B 0.57 37.0 3.60e-01 72.5% 58.1%
3vkgA09 1.20.920.30 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › 0.56 43.0 3.88e-01 90.2% 58.3%
1nzeA00 1.20.120.290 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle 0.56 46.0 4.52e-01 91.2% 92.9%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.56 39.0 3.87e-01 73.5% 70.0%
3sqnA02 1.10.1790.40 Mainly Alpha › Orthogonal Bundle › PTS-regulatory domain, PRD › 0.55 39.0 3.80e-01 74.5% 83.9%
2hz8A00 1.20.120.660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain 0.54 44.0 4.23e-01 87.3% 95.7%
3vvmA02 1.10.1740.110 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › 0.54 41.0 4.20e-01 83.3% 91.2%
1dkxA02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.54 32.0 3.61e-01 92.2% 76.2%
5xtck00 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 35.0 3.58e-01 73.5% 69.1%
2or0B01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.53 39.0 3.74e-01 100.0% 66.1%
8d3mA02 1.20.120.920 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain 0.53 40.0 3.15e-01 83.3% 82.5%
2b0hA01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.52 42.0 3.91e-01 88.2% 89.1%
4hwhE00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.52 36.0 3.81e-01 74.5% 84.1%
4f0uA00 1.10.490.20 Mainly Alpha › Orthogonal Bundle › Globin-like › Phycocyanins 0.51 41.0 3.58e-01 87.3% 78.1%
4iggB02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.51 42.0 4.04e-01 93.1% 93.4%
3kyiA00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.50 45.0 4.22e-01 99.0% 89.1%
1zzpA00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.50 41.0 4.06e-01 91.2% 95.4%
1dowA00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.50 42.0 3.41e-01 94.1% 55.6%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4349095 142.1.1.3 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.80 66.0 6.31e-01 100.0% 77.4%
4258677 142.1.1.0 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.78 66.0 4.99e-01 100.0% 40.4%
4570076 142.1.1.0 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.78 67.0 4.78e-01 100.0% 33.2%
None 0.76 70.0 5.92e-01 100.0% 79.4%
None 0.76 66.0 5.02e-01 100.0% 42.7%
4107589 142.1.1.3 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.73 56.0 5.37e-01 94.1% 71.3%
4995712 142.1.1.0 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.72 61.0 6.28e-01 98.0% 97.9%
3487928 3277.2.1.0 alpha arrays › Thymine dioxygenase JBP1 DNA-binding domain-like › a C-terminal domain in chromodomain helicase DNA-binding protein 1 › a C-terminal domain in chromodomain helicase DNA-binding protein 1 0.65 41.0 3.93e-01 75.5% 55.7%
4966460 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.60 43.0 4.42e-01 97.1% 77.0%
3331953 633.4.1.1 alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.59 39.0 3.45e-01 74.5% 46.0%
4027570 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.59 47.0 3.88e-01 100.0% 48.3%
3960309 191.1.1.0 alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.58 46.0 4.65e-01 94.1% 87.0%
3686452 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.58 48.0 4.62e-01 89.2% 95.7%
3513588 174.1.1.14 few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › NKAIN 0.57 41.0 4.03e-01 74.5% 69.1%
5009683 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.57 47.0 4.22e-01 89.2% 80.7%
3931312 601.1.2.6 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Talin_IBS2B 0.57 47.0 4.51e-01 91.2% 99.2%
3970468 191.1.1.4 alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_C_2 0.57 50.0 4.63e-01 100.0% 97.0%
3964052 7014.1.1.2 alpha bundles › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › TauE 0.56 43.0 4.20e-01 96.1% 74.5%
3529790 601.1.1.57 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Talin_VBS2 0.56 46.0 4.26e-01 90.2% 84.6%
4941161 1075.5.1.2 alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › MurJ 0.56 40.0 3.03e-01 73.5% 61.6%
3696969 174.1.1.0 few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.55 37.0 3.54e-01 75.5% 58.3%
None 0.55 40.0 2.84e-01 76.5% 61.3%
3740238 601.1.2.0 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.55 45.0 3.93e-01 91.2% 74.8%
3576223 604.33.1.1 alpha bundles › Spectrin repeat-like › Repulsive guidance molecule (RGM) N-terminal domain › Repulsive guidance molecule (RGM) N-terminal domain › RGM_N 0.55 30.0 3.42e-01 87.3% 71.6%
3356704 601.18.1.0 alpha bundles › Four-helical up-and-down bundle › Oxygen-evolving enhancer protein 3 › Oxygen-evolving enhancer protein 3 0.53 42.0 3.67e-01 85.3% 99.4%
3062952 108.1.1.0 alpha arrays › EF-hand › EF-hand-related › EF-hand 0.53 41.0 4.12e-01 98.0% 82.7%
3275768 601.1.1.7 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Talin_IBS2B 0.53 44.0 4.26e-01 93.1% 98.3%
3950589 601.18.1.5 alpha bundles › Four-helical up-and-down bundle › Oxygen-evolving enhancer protein 3 › Oxygen-evolving enhancer protein 3 › DUF4395 0.53 42.0 4.27e-01 86.3% 98.0%
3965343 601.1.1.0 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.53 44.0 3.53e-01 90.2% 50.3%
3356941 7023.1.1.3 alpha bundles › helical ridge domain of D-alanyl transfer protein › helical ridge domain of D-alanyl transfer protein › helical ridge domain of D-alanyl transfer protein › MBOAT_2 0.52 46.0 3.27e-01 100.0% 71.0%
4984703 5065.1.1.3 alpha bundles › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › BPD_transp_2 0.52 43.0 3.26e-01 94.1% 74.2%
3967978 191.1.1.49 alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_C_13_2 0.51 44.0 4.34e-01 98.0% 98.2%
3270731 5001.1.1.82 alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › WLS-like_TM 0.51 45.0 3.30e-01 98.0% 42.5%
3440212 601.18.1.13 alpha bundles › Four-helical up-and-down bundle › Oxygen-evolving enhancer protein 3 › Oxygen-evolving enhancer protein 3 › Vwaint 0.51 41.0 4.08e-01 87.3% 86.7%
3513505 191.1.1.0 alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.51 44.0 4.07e-01 100.0% 80.7%
5000147 3960.1.1.0 alpha arrays › Aminoglycoside adenyltransferase AadA C-terminal domain › Aminoglycoside adenyltransferase AadA C-terminal domain › Aminoglycoside adenyltransferase AadA C-terminal domain 0.50 42.0 4.25e-01 93.1% 96.2%
3242954 3939.1.1.161 alpha duplicates or obligate multimers › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain › Mitofilin 0.50 40.0 3.99e-01 87.3% 92.7%
3413881 601.19.1.0 alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein 0.50 41.0 3.34e-01 89.2% 64.1%
4943152 601.1.1.0 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.50 42.0 4.16e-01 93.1% 88.2%
D2 medium residues 110-165
PDB
Domain cluster: representative
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2e5yA02 1.20.5.440 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › ATP synthase delta/epsilon subunit, C-terminal domain 0.67 47.0 5.13e-01 100.0% 91.1%
1egdA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.66 58.0 4.33e-01 100.0% 51.1%
1mhyG01 1.20.1280.10 Mainly Alpha › Up-down Bundle › Monooxygenase › Methane monooxygenase, gamma chain, domain 1 0.64 51.0 4.84e-01 94.6% 72.1%
3bqkA02 1.20.1310.20 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Duffy-antigen binding domain 0.63 48.0 3.54e-01 83.9% 76.8%
3nyjA00 1.20.120.770 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Amyloid precursor protein, E2 domain 0.63 54.0 3.83e-01 100.0% 38.7%
2pg0A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.62 54.0 4.04e-01 100.0% 38.9%
3tufA00 1.10.287.4300 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Stage III sporulation protein AH-like 0.62 56.0 4.39e-01 100.0% 48.7%
1r2jA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.60 53.0 3.94e-01 100.0% 49.3%
2wbiB03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.59 51.0 3.75e-01 100.0% 38.0%
4dwlA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.59 52.0 4.20e-01 100.0% 54.6%
4am6A03 3.30.420.580 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.57 41.0 2.66e-01 78.6% 16.7%
2wzkA01 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.53 44.0 3.49e-01 98.2% 73.2%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4202640 192.6.1.1 alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain › ATP-synt_DE 0.71 54.0 5.49e-01 94.6% 83.6%
4944942 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 0.68 54.0 5.02e-01 100.0% 68.0%
3993978 192.7.1.0 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.63 55.0 5.15e-01 100.0% 88.6%
5029847 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.62 54.0 4.85e-01 100.0% 70.7%
3583169 5086.1.1.0 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.59 51.0 4.61e-01 100.0% 72.5%
4184330 4006.1.1.1 alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.58 46.0 3.94e-01 92.9% 52.0%
5031064 604.3.1.0 alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.58 50.0 4.20e-01 98.2% 58.0%
3731383 192.7.1.0 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.58 51.0 4.24e-01 100.0% 57.0%
3290328 159.1.1.1 alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › Hypothetical protein AF_0060 › MazG 0.55 46.0 3.82e-01 96.4% 59.0%
3276527 109.4.1.526 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Atx10homo_assoc 0.55 46.0 3.05e-01 100.0% 27.3%
3369452 310.2.1.38 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › Hobbit 0.54 45.0 3.92e-01 94.6% 58.9%
4978090 101.1.2.48 alpha arrays › HTH › HTH › winged helix domain › PadR 0.54 46.0 3.23e-01 100.0% 31.2%
5065894 4995.1.1.1 alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like › B12-binding_2 0.53 43.0 3.93e-01 100.0% 67.1%
5066592 1030.1.1.0 alpha duplicates or obligate multimers › Crispr-associated protein Csm2 › Crispr-associated protein Csm2 › Crispr-associated protein Csm2 0.51 43.0 3.53e-01 91.1% 51.0%