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NC_041929.1__YP_009601132.1__FDH46_gp007__00007

Bact-Vir

NC_041929.1__YP_009601132.1__FDH46_gp007__00007

Identity

Accession:
NC_041929 ↗
Kingdom:
phage

Quality

91.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Emdodecavirus› Sinorhizobium_phage_phiM7

TaxID: 1647403

Cluster

View cluster (14 members)

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 medium residues 1-71
PDB
Domain cluster: rep: LacPavin_0818_WC50_scaffold_3810_prodigal-single.1__X__X__00283__D1-67
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2epkX01 3.30.160.230 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › N-acetyl-beta-d-glucosaminidase 0.79 57.0 5.52e-01 100.0% 67.5%
5zi7A02 3.30.2010.30 Alpha Beta › 2-Layer Sandwich › Zincin-like › 0.74 64.0 6.04e-01 100.0% 78.8%
7y7oA01 3.40.390.30 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › "Metalloproteases (""zincins""), catalytic domain" 0.71 62.0 5.00e-01 100.0% 58.7%
4l63A00 3.40.390.10 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › Collagenase (Catalytic Domain) 0.69 61.0 4.19e-01 100.0% 32.9%
1eb6A00 3.40.390.10 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › Collagenase (Catalytic Domain) 0.61 53.0 4.02e-01 100.0% 61.6%
2p90A01 3.40.50.10900 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › PAC-like subunit 0.57 50.0 3.58e-01 100.0% 83.5%
1xo1A02 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.56 48.0 3.74e-01 97.2% 78.0%
3gdwB00 3.40.50.510 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphotransferase system, mannose-type IIA component 0.55 43.0 3.51e-01 85.9% 80.4%
1q25A02 2.70.130.10 Mainly Beta › Distorted Sandwich › Cation-dependent Mannose-6-phosphate Receptor; Chain A › Mannose-6-phosphate receptor binding domain 0.54 43.0 3.48e-01 94.4% 96.2%
1gg1A00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.54 46.0 3.04e-01 100.0% 85.0%
3wz2B00 3.40.50.10900 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › PAC-like subunit 0.54 47.0 3.33e-01 100.0% 74.6%
1jhdA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.53 45.0 3.35e-01 100.0% 68.5%
3tsnA00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.53 44.0 2.88e-01 100.0% 91.2%
3ctzA02 3.40.350.10 Alpha Beta › 3-Layer(aba) Sandwich › Creatine Amidinohydrolase; Chain A, domain 1 › Creatinase/prolidase N-terminal domain 0.52 43.0 3.33e-01 91.5% 93.3%
1b0zA01 3.40.50.10490 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glucose-6-phosphate isomerase like protein; domain 1 0.51 40.0 2.91e-01 88.7% 94.3%
6lpwA02 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.51 39.0 2.85e-01 84.5% 95.3%
1ad1A00 3.20.20.20 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Dihydropteroate synthase-like 0.51 41.0 2.86e-01 91.5% 89.4%
2btoA01 3.40.50.1440 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Tubulin/FtsZ, GTPase domain 0.51 40.0 2.79e-01 90.1% 60.7%
4l22A02 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.50 40.0 2.62e-01 87.3% 83.8%
1k7cA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.50 45.0 3.14e-01 100.0% 73.0%
4ncbA05 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.50 44.0 3.50e-01 100.0% 65.3%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4966006 2498.1.1.163 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › DUF5781 0.78 61.0 4.19e-01 100.0% 25.0%
4413769 2498.1.1.22 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › YbeY 0.78 70.0 5.36e-01 100.0% 65.0%
3435061 2498.1.1.72 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › BSP 0.78 71.0 4.89e-01 100.0% 41.3%
5072067 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.76 60.0 3.70e-01 84.5% 16.6%
4299039 2498.1.1.22 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › YbeY 0.75 67.0 5.17e-01 100.0% 66.9%
3927830 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.75 61.0 4.07e-01 93.0% 23.3%
4024134 2498.1.1.65 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › MATCAP 0.74 53.0 3.36e-01 83.1% 15.0%
4094432 2498.1.1.22 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › YbeY 0.74 66.0 4.87e-01 100.0% 53.5%
3731317 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.74 67.0 4.58e-01 100.0% 36.3%
4118871 2498.1.1.22 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › YbeY 0.74 66.0 5.17e-01 100.0% 63.3%
4027214 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.74 59.0 5.54e-01 87.3% 71.8%
4105249 2498.1.1.22 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › YbeY 0.73 65.0 4.95e-01 98.6% 67.3%
4978358 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.73 58.0 3.61e-01 85.9% 16.4%
4075047 2498.1.1.22 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › YbeY 0.73 65.0 4.95e-01 100.0% 64.8%
3506802 2498.1.1.4 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Reprolysin 0.73 65.0 4.65e-01 100.0% 57.6%
3277622 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.73 58.0 3.55e-01 85.9% 15.6%
5058128 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.72 64.0 4.67e-01 98.6% 40.5%
4949375 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.72 56.0 3.48e-01 84.5% 15.6%
3502798 2498.1.1.4 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Reprolysin 0.72 63.0 4.24e-01 100.0% 43.6%
4929032 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.70 58.0 4.53e-01 98.6% 41.9%
3501889 2498.1.1.4 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Reprolysin 0.70 61.0 4.39e-01 100.0% 57.1%
3652295 2498.1.1.39 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › SprT-like 0.70 60.0 4.79e-01 97.2% 48.6%
3574082 2498.1.1.39 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › SprT-like 0.69 51.0 4.80e-01 81.7% 63.3%
3604193 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.69 54.0 4.29e-01 90.1% 42.1%
None — 0.68 61.0 4.20e-01 100.0% 39.2%
4421669 2498.1.1.45 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Reprolysin_5 0.68 60.0 4.16e-01 100.0% 38.4%
3505325 2498.1.1.4 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Reprolysin 0.68 59.0 4.11e-01 100.0% 49.0%
5046713 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.67 53.0 3.34e-01 87.3% 18.0%
4971428 2498.1.1.10 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M48 0.66 50.0 3.54e-01 94.4% 25.8%
3571521 2498.1.1.4 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Reprolysin 0.66 57.0 4.06e-01 100.0% 53.3%
3285500 2498.1.1.1 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M10 0.66 58.0 4.45e-01 100.0% 44.8%
3390011 2498.1.1.39 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › SprT-like 0.66 59.0 4.20e-01 100.0% 51.0%
2888860 2498.1.1.29 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M78 0.64 48.0 3.81e-01 78.9% 43.8%
3803299 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.64 55.0 4.31e-01 100.0% 86.3%
3782755 109.4.1.3316 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF29173, PF29177 0.64 42.0 2.69e-01 73.2% 14.0%
None — 0.63 54.0 4.65e-01 100.0% 59.2%
3714457 2498.1.1.36 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › WLM 0.63 54.0 4.19e-01 100.0% 47.1%
3714462 2498.1.1.36 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › WLM 0.63 53.0 4.35e-01 100.0% 51.7%
3256855 2004.1.1.150 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DRMBL 0.62 56.0 4.35e-01 100.0% 78.0%
3257543 220.1.1.12 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Myosin_TH1 0.61 47.0 3.43e-01 83.1% 65.6%
3407498 63.1.1.1 ↗ beta barrels › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › CIMR 0.60 50.0 4.06e-01 94.4% 96.6%
4991400 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.60 46.0 3.49e-01 87.3% 85.8%
3597997 63.1.1.0 ↗ beta barrels › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain 0.59 49.0 3.99e-01 91.5% 92.6%
5037366 2011.2.1.7 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Peptidyl-tRNA hydrolase-like › Peptidyl-tRNA hydrolase-like › PAC2 0.58 51.0 3.64e-01 100.0% 79.0%
4026205 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.56 47.0 3.56e-01 100.0% 63.5%
4680266 2498.5.1.0 ↗ mixed a+b and a/b › Zincin-like › GroEL-intermediate domain like › GroEL-intermediate domain like 0.55 40.0 4.04e-01 76.1% 78.6%
3332111 7590.1.1.2 ↗ a/b three-layered sandwiches › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs › Piwi 0.55 48.0 3.54e-01 100.0% 56.5%
3258301 63.1.1.0 ↗ beta barrels › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain 0.55 47.0 3.82e-01 95.8% 97.9%
5054545 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.54 42.0 3.62e-01 85.9% 91.6%
3062314 2003.1.5.30 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_7 0.54 40.0 2.63e-01 80.3% 96.7%
3387662 2003.1.9.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.54 41.0 3.16e-01 85.9% 83.8%
4475046 2007.1.14.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Chelatase-like › Oxidored_nitro 0.53 36.0 2.77e-01 70.4% 49.1%
3290935 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.53 44.0 3.37e-01 91.5% 79.4%
4972412 7512.1.1.30 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_4 0.53 49.0 3.47e-01 100.0% 42.6%
4996738 2484.1.1.291 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › MutS_V 0.51 43.0 2.55e-01 100.0% 77.0%
3387860 7510.1.1.5 ↗ a/b three-layered sandwiches › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › PdxA 0.51 44.0 3.25e-01 100.0% 87.5%
D2 medium residues 72-136
PDB
Domain cluster: rep: MG592671.1__AUS02684.1__NVP2275O_103__00103__D96-174