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MK878901.1__QDF16749.1__SEA_HANNAHD_36__00036

Bact-Vir

MK878901.1__QDF16749.1__SEA_HANNAHD_36__00036

Identity

Accession:
MK878901 ↗
Kingdom:
phage

Quality

71.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Bowservirus› Gordonia_phage_HannahD

TaxID: 2583041

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 high residues 140-201
PDB
Domain cluster: rep: MK448393.1__QBX08513.1__JavanS276_0010__00009__D5-64
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF09954.15 best DUF2188 56.9 2.50e-15 98.4% 91.9%
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1z1bA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.77 53.0 5.48e-01 72.6% 77.2%
3cxbB00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.71 49.0 4.17e-01 72.6% 44.7%
1pzxA03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.67 59.0 4.76e-01 100.0% 91.0%
2dt8A02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.67 58.0 4.64e-01 100.0% 75.4%
7vbnL01 3.30.160.190 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › atu1810 like domain 0.67 51.0 4.50e-01 85.5% 78.9%
1mgpA02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.67 58.0 4.71e-01 100.0% 93.4%
1wv8A00 3.30.2390.10 Alpha Beta › 2-Layer Sandwich › TTHA1013/TTHA0281-like › TTHA1013-like 0.66 52.0 5.03e-01 87.1% 93.0%
8dkrB01 3.30.420.240 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.65 57.0 3.90e-01 100.0% 35.8%
3pc3A03 3.10.580.10 Alpha Beta › Roll › CBS-domain › CBS-domain 0.65 41.0 3.17e-01 100.0% 27.8%
1ewqB01 3.40.1170.10 Alpha Beta › 3-Layer(aba) Sandwich › MutS, DNA mismatch repair protein, domain I › DNA repair protein MutS, domain I 0.65 56.0 4.60e-01 100.0% 67.8%
2g7zA02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.64 54.0 4.49e-01 100.0% 74.2%
3r79A00 3.20.20.10 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Alanine racemase 0.63 44.0 3.04e-01 74.2% 48.0%
3k6qA02 3.30.160.620 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.62 49.0 4.38e-01 88.7% 95.5%
1aj6A00 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.60 51.0 3.71e-01 100.0% 75.8%
4bg8A01 3.30.420.430 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.60 51.0 4.13e-01 100.0% 69.8%
7v5yA01 3.40.1620.10 Alpha Beta › 3-Layer(aba) Sandwich › YefM-like fold › YefM-like domain 0.60 38.0 4.03e-01 98.4% 76.5%
3eyeA00 3.40.35.10 Alpha Beta › 3-Layer(aba) Sandwich › Fructose Permease › Phosphotransferase system, sorbose subfamily IIB component 0.60 38.0 2.93e-01 91.9% 26.1%
1vr6A02 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.59 48.0 3.16e-01 100.0% 20.9%
2hqyA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.58 47.0 3.73e-01 90.3% 86.2%
5is2A03 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.58 50.0 3.48e-01 100.0% 78.2%
3alfA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.58 48.0 3.13e-01 91.9% 39.6%
3fk5A02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.58 49.0 3.88e-01 100.0% 55.0%
2cfbA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.58 45.0 3.10e-01 85.5% 63.4%
1ctnA02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.57 48.0 3.03e-01 95.2% 32.7%
3nx3A02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.56 44.0 2.96e-01 85.5% 64.8%
1sb8A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 46.0 3.20e-01 98.4% 51.3%
1td2A00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.54 43.0 2.88e-01 100.0% 20.2%
2pmzB05 3.90.1070.20 Alpha Beta › Alpha-Beta Complex › Hypothetical Protein Ta0175; Chain: A, domain 2 › 0.54 37.0 3.55e-01 75.8% 61.3%
1ydmB00 3.40.50.10420 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NagB/RpiA/CoA transferase-like 0.53 37.0 2.71e-01 100.0% 25.3%
4wesB02 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.53 40.0 3.46e-01 83.9% 90.4%
3lzdA02 3.40.50.11850 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Diphthamide synthesis DPH1/DPH2 domain 2 0.53 45.0 3.79e-01 98.4% 82.6%
3ak5D02 2.160.20.20 Mainly Beta › 3 Solenoid › Pectate Lyase C-like › 0.52 44.0 2.56e-01 100.0% 13.2%
4s1hA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.52 43.0 2.88e-01 100.0% 29.3%
1ywyA00 3.40.1170.40 Alpha Beta › 3-Layer(aba) Sandwich › MutS, DNA mismatch repair protein, domain I › Protein of unknown function DUF3203 0.51 42.0 4.04e-01 95.2% 90.5%
3s6gA02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.51 41.0 3.24e-01 93.5% 71.9%
2xgtA02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.51 43.0 2.78e-01 100.0% 23.6%
7k98B04 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.51 41.0 2.87e-01 90.3% 70.4%
6mp7A01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.51 44.0 2.78e-01 100.0% 21.3%
ECOD (64)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3518950 214.1.1.10 ↗ a+b two layers › SH2 › SH2 › SH2 › DUF7145 0.73 50.0 4.36e-01 98.4% 47.4%
3250206 65.1.1.0 ↗ beta sandwiches › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases 0.70 56.0 5.29e-01 88.7% 94.7%
3180029 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.70 48.0 4.26e-01 72.6% 52.2%
3281041 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.70 62.0 4.89e-01 100.0% 68.5%
3962875 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.70 62.0 4.88e-01 100.0% 76.2%
3502261 214.1.1.10 ↗ a+b two layers › SH2 › SH2 › SH2 › DUF7145 0.69 48.0 3.79e-01 96.8% 34.1%
3508121 214.1.1.10 ↗ a+b two layers › SH2 › SH2 › SH2 › DUF7145 0.69 48.0 3.69e-01 96.8% 32.1%
4944466 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.69 61.0 4.85e-01 100.0% 97.6%
3967679 2484.6.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Periplasmic domain of ExbD/TolR › Periplasmic domain of ExbD/TolR › ExbD 0.68 59.0 5.08e-01 100.0% 76.0%
4944129 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.67 59.0 4.69e-01 100.0% 95.4%
1933261 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.67 59.0 4.77e-01 100.0% 91.7%
7730 4100.1.1.1 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › DUF1902 0.66 52.0 5.03e-01 87.1% 93.0%
4134161 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.66 58.0 4.57e-01 100.0% 97.8%
4538897 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.66 57.0 4.63e-01 100.0% 78.2%
4946414 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.66 58.0 4.65e-01 100.0% 74.0%
4376573 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.66 58.0 4.64e-01 100.0% 77.4%
4959480 4100.1.1.0 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like 0.66 48.0 4.88e-01 79.0% 91.7%
4349801 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.65 56.0 4.51e-01 100.0% 75.8%
4999937 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.65 56.0 4.55e-01 100.0% 60.8%
3518153 214.1.1.10 ↗ a+b two layers › SH2 › SH2 › SH2 › DUF7145 0.65 45.0 3.79e-01 96.8% 41.8%
4659593 2484.1.1.40 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvX 0.64 54.0 4.29e-01 100.0% 63.3%
4995200 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 0.63 56.0 4.57e-01 100.0% 64.3%
3224627 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.62 52.0 3.85e-01 100.0% 55.8%
4370398 288.1.1.2 ↗ a+b four layers › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases › CNF1/YfiH-like putative cysteine hydrolases › CheD 0.62 46.0 3.55e-01 82.3% 88.4%
5081740 2484.1.1.342 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF29288 0.62 53.0 3.97e-01 100.0% 44.2%
5007420 2484.1.1.333 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF1464 0.61 52.0 3.94e-01 100.0% 60.6%
4152182 2008.2.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like › tRNA_int_endo 0.61 43.0 3.81e-01 100.0% 49.5%
4981935 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.61 48.0 4.20e-01 95.2% 98.2%
4296492 2003.1.5.53 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › tRNA_U5-meth_tr 0.61 51.0 3.14e-01 91.9% 28.9%
4988335 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.61 51.0 4.19e-01 98.4% 59.2%
5022411 5104.1.1.1 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.61 43.0 3.57e-01 100.0% 40.9%
3213706 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.61 50.0 3.57e-01 100.0% 35.0%
3409623 2008.2.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like › tRNA_int_endo 0.60 44.0 3.77e-01 100.0% 48.0%
4997258 2492.1.1.0 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.60 47.0 3.65e-01 91.9% 78.1%
5046301 7601.1.1.1 ↗ a/b three-layered sandwiches › Lactate racemase N-terminal domain › Lactate racemase N-terminal domain › Lactate racemase N-terminal domain › Lar_N 0.60 41.0 2.75e-01 72.6% 42.8%
5035935 219.1.1.26 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Phytochelatin 0.59 41.0 3.00e-01 74.2% 93.0%
4481690 4263.2.1.1 ↗ a+b two layers › TTHA1528-like › FtsH Periplasmic Domain › FtsH Periplasmic Domain › FtsH_ext 0.59 42.0 4.13e-01 82.3% 70.0%
None — 0.58 47.0 2.96e-01 91.9% 30.9%
5044308 2500.1.1.5 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › NRDD 0.58 49.0 2.84e-01 96.8% 31.8%
3512572 220.1.1.125 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_PLEKHM2 0.57 45.0 3.54e-01 88.7% 44.1%
5000299 4961.1.1.0 ↗ a+b complex topology › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit › inserted a+b domain in yeast RNA polymerase beta subunit 0.57 41.0 3.73e-01 79.0% 55.6%
4561209 7510.1.1.0 ↗ a/b three-layered sandwiches › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like 0.57 42.0 3.32e-01 79.0% 75.6%
4949809 2003.1.5.33 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › UPF0146 0.57 49.0 3.95e-01 98.4% 86.4%
3518947 214.1.1.10 ↗ a+b two layers › SH2 › SH2 › SH2 › DUF7145 0.56 46.0 3.78e-01 93.5% 66.7%
2439599 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.56 34.0 3.92e-01 95.2% 100.0%
4295333 2003.1.5.33 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › UPF0146 0.56 49.0 3.83e-01 98.4% 86.2%
5000875 2008.2.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like › tRNA_int_endo 0.56 45.0 4.07e-01 91.9% 100.0%
3685699 2003.1.1.84 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › PRISE 0.55 48.0 2.91e-01 100.0% 43.1%
5028863 2003.1.1.20 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Epimerase 0.55 45.0 3.02e-01 98.4% 54.6%
5062828 2007.1.16.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Iron-sulphur enzyme Dph2 › Diphthamide_syn 0.54 46.0 3.88e-01 100.0% 80.0%
5072012 2008.1.1.3 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Hjc 0.54 44.0 3.94e-01 91.9% 95.6%
3251763 4161.1.1.0 ↗ beta complex topology › MOSC N-terminal domain-like › MOSC N-terminal domain-like › MOSC N-terminal domain-like 0.53 41.0 2.69e-01 90.3% 90.6%
4520708 2003.1.5.53 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › tRNA_U5-meth_tr 0.53 43.0 2.73e-01 91.9% 30.0%
4986405 7582.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like domain in CbiD › Rossmann-like domain in CbiD › Rossmann-like domain in CbiD 0.53 45.0 3.56e-01 100.0% 55.0%
5029896 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.52 41.0 3.07e-01 88.7% 73.7%
3257390 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.52 41.0 2.64e-01 98.4% 17.4%
3367535 2002.1.1.282 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › PF26146 0.52 44.0 2.83e-01 98.4% 42.1%
119490 57.1.1.2 ↗ beta complex topology › Cloacin translocation domain › Cloacin translocation domain › Cloacin translocation domain › Pyocin_S 0.52 43.0 3.39e-01 100.0% 63.3%
4301489 4126.1.1.6 ↗ a/b three-layered sandwiches › beta-carbonic anhydrase-like › beta-carbonic anhydrase › beta-carbonic anhydrase › DabA 0.52 37.0 2.51e-01 74.2% 56.0%
3338602 2008.1.1.107 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NERD 0.52 44.0 3.19e-01 98.4% 43.8%
3913068 2008.2.1.1 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like › tRNA_int_endo 0.52 42.0 3.58e-01 91.9% 86.7%
5059322 1.1.9.0 ↗ beta barrels › cradle loop barrel › RIFT-related › PUA domain 0.51 42.0 3.18e-01 91.9% 74.8%
3516319 7575.1.1.0 ↗ a/b three-layered sandwiches › Caspase-like › Caspase-like › Caspase-like 0.51 42.0 3.20e-01 100.0% 71.4%
3595091 109.1.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C 0.50 41.0 2.93e-01 90.3% 69.5%