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NC_055783.1__YP_010100454.1__KNU35_gp014__00014

Bact-Vir

NC_055783.1__YP_010100454.1__KNU35_gp014__00014

Identity

Accession:
NC_055783 ↗
Kingdom:
phage

Quality

77.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Straboviridae› Dhakavirus› Escherichia_phage_vB_EcoM_005

TaxID: 2500761

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 high residues 6-53
PDB
Domain cluster: representative
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5u89A01 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.75 52.0 4.16e-01 97.9% 38.0%
1uzxA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.65 52.0 3.93e-01 100.0% 86.4%
2j3vA02 3.90.176.10 Alpha Beta › Alpha-Beta Complex › Toxin ADP-ribosyltransferase; Chain A, domain 1 › Toxin ADP-ribosyltransferase; Chain A, domain 1 0.60 48.0 3.17e-01 89.6% 46.7%
3i24B00 3.30.428.10 Alpha Beta › 2-Layer Sandwich › HIT family, subunit A › HIT-like 0.58 43.0 3.19e-01 87.5% 28.8%
4rudA00 2.10.60.10 Mainly Beta › Ribbon › CD59 › CD59 0.58 42.0 4.08e-01 100.0% 69.0%
1dw9A02 3.30.1160.10 Alpha Beta › 2-Layer Sandwich › Cyanate Lyase; Chain: A, domain 2 › Cyanate lyase, C-terminal domain 0.58 43.0 3.95e-01 85.4% 82.4%
1pu1A00 3.30.300.100 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › MTH677-like 0.56 41.0 3.49e-01 83.3% 46.2%
8g0cG01 3.40.1380.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate Kinase; Chain: A, domain 1 › ATP synthase, F1 complex, gamma subunit 0.56 46.0 3.14e-01 100.0% 55.5%
4k17B01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 42.0 3.34e-01 97.9% 38.7%
8dbsG01 3.40.1380.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate Kinase; Chain: A, domain 1 › ATP synthase, F1 complex, gamma subunit 0.53 42.0 2.87e-01 95.8% 52.3%
3g2fA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.53 37.0 3.20e-01 79.2% 54.0%
4do8A00 2.10.60.10 Mainly Beta › Ribbon › CD59 › CD59 0.52 39.0 3.71e-01 100.0% 66.7%
5fl7G02 3.40.1380.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate Kinase; Chain: A, domain 1 › ATP synthase, F1 complex, gamma subunit 0.52 42.0 2.91e-01 100.0% 57.4%
5mz2I00 3.30.190.10 Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribulose bisphosphate carboxylase, small subunit 0.51 39.0 3.00e-01 91.7% 57.6%
3n77A00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.51 37.0 2.66e-01 79.2% 66.7%
1e5tA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.50 41.0 2.54e-01 100.0% 80.7%
6jpaA01 1.20.120.350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C 0.50 41.0 3.05e-01 97.9% 75.9%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4671394 109.4.1.939 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_PRP39_C 0.69 47.0 3.04e-01 72.9% 22.9%
3632323 109.4.1.1580 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT, HAT_Syf1_CNRKL1_C, HAT_Syf1_CNRKL1_N, HAT_PRP39_N, HAT_PRP39_C 0.68 47.0 2.79e-01 72.9% 14.5%
5032433 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 0.64 42.0 3.02e-01 72.9% 21.3%
3450430 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.64 43.0 2.97e-01 72.9% 19.4%
1503829 3512.1.1.2 ↗ beta duplicates or obligate multimers › Trimeric autotransporter adhesin GIN domain › Trimeric autotransporter adhesin GIN domain › Trimeric autotransporter adhesin GIN domain › YadA_stalk 0.64 39.0 2.34e-01 77.1% 8.4%
4430197 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.63 47.0 4.60e-01 100.0% 72.7%
3303587 207.1.1.55 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_1,LRR_8 0.61 48.0 3.09e-01 91.7% 60.0%
4266807 812.1.1.1 ↗ a+b duplicates or obligate multimers › MinE-like › Cell division protein MinE topological specificity domain › Cell division protein MinE topological specificity domain › MinE 0.61 42.0 4.36e-01 87.5% 80.0%
3246937 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.61 46.0 4.12e-01 91.7% 58.6%
4029705 256.1.1.0 ↗ a+b two layers › MTH1598-like › MTH1598-like › MTH1598-like 0.60 44.0 4.17e-01 83.3% 76.7%
4012111 812.2.1.0 ↗ a+b duplicates or obligate multimers › MinE-like › Cyanase C-terminal domain › Cyanase C-terminal domain 0.59 45.0 4.16e-01 85.4% 88.9%
4976198 878.1.1.1 ↗ a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 › DUF3194 0.58 44.0 3.74e-01 85.4% 49.4%
3830346 207.1.1.137 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_1, LRR_4, LRR_8 0.57 43.0 2.61e-01 89.6% 41.0%
4948264 878.1.1.1 ↗ a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 › DUF3194 0.56 42.0 3.66e-01 85.4% 52.5%
3810414 812.2.1.1 ↗ a+b duplicates or obligate multimers › MinE-like › Cyanase C-terminal domain › Cyanase C-terminal domain › Cyanate_lyase 0.56 45.0 3.88e-01 91.7% 76.2%
4262649 812.2.1.1 ↗ a+b duplicates or obligate multimers › MinE-like › Cyanase C-terminal domain › Cyanase C-terminal domain › Cyanate_lyase 0.56 46.0 3.89e-01 91.7% 76.2%
4946 878.1.1.1 ↗ a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 › DUF3194 0.56 41.0 3.49e-01 83.3% 46.2%
3664523 304.55.1.15 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Helitron_like_N 0.56 41.0 3.29e-01 83.3% 38.9%
2041765 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 0.56 39.0 2.66e-01 97.9% 19.9%
3591474 4106.1.1.1 ↗ few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.55 45.0 3.07e-01 100.0% 88.2%
3739414 330.1.1.3 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Dicer_dimer 0.55 38.0 3.14e-01 77.1% 45.7%
2559786 3256.1.1.0 ↗ a+b two layers › DUF2233 N-terminal domain › DUF2233 N-terminal domain › DUF2233 N-terminal domain 0.54 35.0 3.60e-01 89.6% 71.1%
3684561 304.160.1.2 ↗ a+b two layers › Alpha-beta plaits › Gas vesicle protein GvpF › Gas vesicle protein GvpF › Helitron_like_N 0.54 39.0 2.99e-01 83.3% 30.4%
3305599 304.55.1.20 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Helitron_like_N, REP_ORF2-G2P 0.54 40.0 3.36e-01 83.3% 46.7%
3494818 207.1.1.102 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_1+LRR_8+LRR_14 0.54 41.0 2.71e-01 89.6% 28.3%
5078624 878.1.1.1 ↗ a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 › DUF3194 0.53 41.0 3.29e-01 91.7% 40.0%
3517917 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.53 40.0 3.81e-01 91.7% 81.5%
3336749 304.28.1.25 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › Helitron_like_N, REP_ORF2-G2P 0.53 39.0 3.10e-01 83.3% 36.5%
3495780 304.107.1.5 ↗ a+b two layers › Alpha-beta plaits › Aminomethyltransferase folate-binding domain › Aminomethyltransferase folate-binding domain › BCS1_N 0.53 36.0 2.67e-01 75.0% 59.4%
5011151 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.53 36.0 2.63e-01 75.0% 39.4%
3743393 59.1.4.2 ↗ beta complex topology › triple barrel › triple barrel › TFIID subunits TAF1-TAF7 › DUF3591 0.53 45.0 2.67e-01 100.0% 32.8%
3188358 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.52 37.0 2.27e-01 85.4% 10.0%
3735018 2487.1.1.9 ↗ a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" › Cyclase 0.51 36.0 2.29e-01 93.8% 13.7%
3553058 605.3.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Nonstructural protein ns2, Nep, M1-binding domain › Nonstructural protein ns2, Nep, M1-binding domain 0.51 37.0 2.67e-01 100.0% 27.1%
3194847 3343.1.1.2 ↗ alpha complex topology › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › GCP_C_terminal,GCP_N_terminal 0.51 34.0 1.95e-01 70.8% 7.9%
3964735 2.9.1.1 ↗ beta barrels › OB-fold › RNB domain-like › RNB domain-like › RNB 0.50 35.0 2.17e-01 79.2% 22.0%
D2 high residues 59-195
PDB
Domain cluster: rep: pig_ID_3053_F12_scaffold_0_curated_closed_complete_prodigal-single.1__X__X__00079__D84-124_161-231
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF14437.13 best MafB19-deam 68.6 7.00e-19 95.6% 73.5%
PF00383.30 dCMP_cyt_deam_1 84.1 7.70e-24 77.4% 96.1%