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NC_062753.1__YP_010357459.1__M1M31_gp17__00017

Bact-Vir

NC_062753.1__YP_010357459.1__M1M31_gp17__00017

Identity

Accession:
NC_062753 ↗
Kingdom:
phage

Quality

88.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Assiduviridae› Nekkelsvirus› Cellulophaga_phage_Nekkels_1

TaxID: 2745692

Cluster

Singleton — not in a non-trivial cluster

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 1-52
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2da3A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.53 33.0 3.45e-01 82.7% 68.1%
1af7A01 1.10.155.10 Mainly Alpha › Orthogonal Bundle › Chemotaxis Receptor Methyltransferase Cher; domain 1 › Chemotaxis receptor methyltransferase CheR, N-terminal domain 0.52 43.0 3.84e-01 98.1% 67.5%
3idfA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.52 40.0 3.00e-01 86.5% 55.8%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3877278 2007.1.2.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.61 48.0 3.06e-01 100.0% 15.7%
3397226 377.1.1.18 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › zf-AD 0.61 53.0 4.27e-01 100.0% 50.5%
2554274 132.1.1.1 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.55 40.0 3.53e-01 82.7% 54.1%
D2 medium residues 53-105
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vkwA01 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.80 46.0 3.46e-01 98.1% 25.6%
2ltrA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.68 55.0 4.48e-01 92.5% 55.2%
1zc3B00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.67 55.0 4.36e-01 90.6% 45.9%
1pc6A00 1.10.3790.10 Mainly Alpha › Orthogonal Bundle › NinB fold › NinB 0.64 46.0 3.40e-01 75.5% 63.8%
1ts9A00 2.30.30.210 Mainly Beta › Roll › SH3 type barrels. › Ribonuclease P/MRP, subunit p29 0.63 50.0 4.07e-01 86.8% 98.0%
6htnA01 2.120.10.70 Mainly Beta › 6 Propeller › Neuraminidase › Fucose-specific lectin 0.62 43.0 3.22e-01 73.6% 52.6%
4iapA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.62 44.0 3.63e-01 79.2% 43.5%
1dpgA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.61 47.0 2.98e-01 88.7% 72.8%
3rv0B03 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.61 48.0 4.29e-01 90.6% 74.7%
4cswA02 3.40.366.30 Alpha Beta › 3-Layer(aba) Sandwich › Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 › 50S ribosomal protein L16 arginine hydroxylase; Chain A, Domain 2 0.61 46.0 3.27e-01 84.9% 40.3%
3mixA01 3.40.30.60 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › FHIPEP family, domain 1 0.60 48.0 3.78e-01 90.6% 78.3%
2ljwA00 3.30.428.40 Alpha Beta › 2-Layer Sandwich › HIT family, subunit A › Protein of unknown function DUF3067 0.58 52.0 4.17e-01 100.0% 98.1%
2da0A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 50.0 3.94e-01 100.0% 97.4%
2db5A00 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.57 43.0 3.42e-01 88.7% 51.6%
2vszB02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 43.0 3.39e-01 81.1% 51.3%
1dmrA03 3.90.55.10 Alpha Beta › Alpha-Beta Complex › Dimethylsulfoxide Reductase; domain 3 › Dimethylsulfoxide Reductase, domain 3 0.57 43.0 3.58e-01 86.8% 48.3%
1b8pA02 3.90.110.10 Alpha Beta › Alpha-Beta Complex › L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 › Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal 0.57 49.0 3.40e-01 96.2% 81.4%
3bs1A00 2.40.50.1020 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › LytTr DNA-binding domain 0.56 39.0 3.20e-01 75.5% 50.5%
5n1tA03 3.90.760.10 Alpha Beta › Alpha-Beta Complex › Flavocytochrome C Sulfide Dehydrogenase; Chain A Domain 3 › Flavocytochrome c sulphide dehydrogenase, flavin-binding domain 0.55 46.0 4.24e-01 96.2% 83.1%
7eqiA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.54 46.0 3.30e-01 94.3% 41.2%
3p54A02 3.30.67.10 Alpha Beta › 2-Layer Sandwich › Viral Envelope Glycoprotein; domain 2 › Viral Envelope Glycoprotein, domain 2 0.54 40.0 3.69e-01 81.1% 73.2%
1tmoA03 3.90.55.10 Alpha Beta › Alpha-Beta Complex › Dimethylsulfoxide Reductase; domain 3 › Dimethylsulfoxide Reductase, domain 3 0.54 39.0 3.30e-01 75.5% 75.6%
4cbvA02 2.40.50.1020 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › LytTr DNA-binding domain 0.54 38.0 2.97e-01 75.5% 46.6%
1yw5A01 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.54 35.0 3.32e-01 90.6% 57.1%
4qakA00 3.90.1140.10 Alpha Beta › Alpha-Beta Complex › Cyclic Phosphodiesterase; Chain: A, › Cyclic phosphodiesterase 0.53 42.0 3.01e-01 90.6% 39.2%
6grrB01 3.30.457.10 Alpha Beta › 2-Layer Sandwich › Copper Amine Oxidase; Chain A, domain 1 › Copper amine oxidase-like, N-terminal domain 0.53 38.0 3.45e-01 81.1% 60.8%
3hz4A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.52 39.0 3.28e-01 94.3% 80.0%
4l3rA00 2.40.128.270 Mainly Beta › Beta Barrel › Lipocalin › 0.52 40.0 2.96e-01 84.9% 57.3%
3fm2A00 3.40.1570.10 Alpha Beta › 3-Layer(aba) Sandwich › Heme iron utilization protein-like fold › HemS/ChuS/ChuX like domains 0.51 44.0 3.37e-01 100.0% 50.4%
3upsA00 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.51 43.0 3.35e-01 92.5% 50.9%
5w7zA01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.50 34.0 2.77e-01 71.7% 39.8%
1e2tA02 3.30.1120.150 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.50 35.0 3.08e-01 77.4% 73.3%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4338739 1046.1.1.1 ↗ alpha bundles › Lipoprotein signal peptidase › Lipoprotein signal peptidase › Lipoprotein signal peptidase › Peptidase_A8 0.83 55.0 3.78e-01 96.2% 22.5%
2722070 301.13.1.3 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › FakA-like_C 0.78 60.0 4.81e-01 84.9% 52.4%
4961481 4325.1.1.0 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.76 64.0 5.82e-01 92.5% 75.7%
3927790 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.76 53.0 5.71e-01 79.2% 86.7%
3930224 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.76 62.0 6.44e-01 94.3% 94.0%
3680934 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.76 52.0 5.71e-01 71.7% 100.0%
3584264 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.72 64.0 4.79e-01 98.1% 43.2%
3789602 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.72 64.0 4.79e-01 98.1% 43.2%
3924908 386.1.1.251 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › DUF7381 0.72 46.0 3.70e-01 71.7% 35.0%
3967950 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.72 55.0 5.93e-01 83.0% 100.0%
4929483 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.70 63.0 4.81e-01 100.0% 67.5%
4954522 878.1.1.1 ↗ a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 › DUF3194 0.70 51.0 4.18e-01 100.0% 43.6%
3510148 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.69 59.0 4.33e-01 96.2% 37.7%
3923930 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.69 60.0 4.69e-01 100.0% 46.4%
3275677 220.1.1.66 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SOS1_NGEF_PH 0.68 59.0 4.12e-01 98.1% 31.2%
3382157 4351.1.1.1 ↗ alpha arrays › ATP12-like › ATP12-like › ATP12-like › ATP12 0.66 49.0 3.15e-01 79.2% 53.1%
3224950 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.66 58.0 4.62e-01 100.0% 49.5%
3792816 220.1.1.33 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_8 0.66 59.0 4.48e-01 100.0% 44.2%
3936608 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.65 53.0 4.16e-01 96.2% 42.7%
5017154 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.65 53.0 3.85e-01 88.7% 38.5%
7698 829.1.1.1 ↗ a+b duplicates or obligate multimers › NinB › NinB › NinB › NinB 0.64 46.0 3.40e-01 75.5% 63.8%
3856901 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.64 50.0 3.05e-01 84.9% 94.9%
5001324 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 55.0 4.45e-01 98.1% 50.5%
3627795 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 53.0 4.51e-01 92.5% 56.5%
3566967 220.1.1.170 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_alsin 0.63 50.0 3.99e-01 90.6% 43.8%
4982093 213.1.1.29 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_9 0.63 44.0 3.24e-01 73.6% 64.3%
3999570 220.1.1.5 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PID 0.63 56.0 4.46e-01 98.1% 56.2%
3167802 220.1.1.33 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_8 0.63 52.0 4.05e-01 96.2% 43.5%
2077327 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.63 45.0 3.83e-01 79.2% 83.0%
4001872 220.1.1.123 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_SSH1-like_1st 0.62 55.0 3.76e-01 98.1% 27.6%
5008380 296.1.1.0 ↗ a+b three layers › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 0.62 45.0 3.72e-01 79.2% 60.0%
3912099 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.62 53.0 4.22e-01 98.1% 47.6%
4026701 180.1.1.1 ↗ alpha bundles › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase › PAP2 0.60 54.0 3.61e-01 100.0% 58.0%
3389782 3470.1.1.53 ↗ extended segments › Glycophorin-A transmembrane domain › Glycophorin-A transmembrane domain › Glycophorin-A transmembrane domain › CytochromB561_N 0.59 48.0 3.22e-01 92.5% 21.9%
4040812 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.59 43.0 3.70e-01 79.2% 84.3%
4996362 220.1.1.87 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_3 0.59 46.0 3.67e-01 84.9% 42.6%
3970772 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.59 47.0 3.73e-01 90.6% 62.3%
4406214 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.58 49.0 4.01e-01 90.6% 86.0%
3945055 2484.2.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Methylated DNA-protein cysteine methyltransferase domain › Methylated DNA-protein cysteine methyltransferase domain › Methyltransf_1N 0.58 44.0 3.87e-01 90.6% 52.9%
4449615 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.58 49.0 4.03e-01 90.6% 88.9%
4379527 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.57 48.0 4.02e-01 90.6% 94.1%
3963958 2484.2.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Methylated DNA-protein cysteine methyltransferase domain › Methylated DNA-protein cysteine methyltransferase domain 0.54 39.0 3.62e-01 88.7% 58.7%
4991717 2488.1.1.0 ↗ a/b three-layered sandwiches › alpha/beta knot › alpha/beta knot › alpha/beta knot 0.53 40.0 3.04e-01 86.8% 55.9%
5007103 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.52 36.0 3.32e-01 84.9% 51.2%
3480592 252.1.1.0 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD 0.50 35.0 3.42e-01 90.6% 66.7%