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NC_031074.1__YP_009287538.1__BIZ77_gp109__00068

Bact-Vir

NC_031074.1__YP_009287538.1__BIZ77_gp109__00068

Identity

Accession:
NC_031074 ↗
Kingdom:
phage

Quality

80.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Bantamvirus› Gordonia_phage_Bantam

TaxID: 1887641

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 3-70
PDB
Domain cluster: representative
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2p84A02 2.30.30.290 Mainly Beta › Roll › SH3 type barrels. › YopX-like domains 0.67 50.0 4.89e-01 79.4% 76.7%
3ca8A01 1.10.3620.10 Mainly Alpha › Orthogonal Bundle › YdcF fold › YdcF like domain 0.62 39.0 3.36e-01 85.3% 41.5%
1tltA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.58 50.0 3.69e-01 98.5% 99.5%
3ottA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.56 43.0 2.84e-01 82.4% 93.0%
4qarA00 3.40.50.1580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleoside phosphorylase domain 0.56 48.0 3.51e-01 98.5% 63.6%
4gniB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.55 42.0 3.38e-01 88.2% 86.3%
4a2lB01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.54 41.0 2.71e-01 82.4% 92.9%
2dy1A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 40.0 2.65e-01 98.5% 19.3%
2qxlB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.54 39.0 3.23e-01 79.4% 82.1%
4ckbD03 2.40.50.830 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.54 38.0 3.18e-01 77.9% 82.8%
2k2jA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 41.0 3.50e-01 88.2% 93.2%
2jsnA00 2.30.42.40 Mainly Beta › Roll › Pdz3 Domain › 0.51 33.0 3.06e-01 79.4% 46.9%
1md6A00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.51 41.0 3.31e-01 94.1% 89.0%
1nt2B01 3.30.2150.10 Alpha Beta › 2-Layer Sandwich › S-adenosyl-L-methionine-dependent methyltransferases › Fibrillarin homologue 0.50 42.0 4.20e-01 98.5% 90.1%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
676 4999.1.1.1 ↗ beta barrels › YopX, C-terminal domain-like › YopX, C-terminal domain-like › YopX, C-terminal domain-like › YopX 0.67 50.0 5.24e-01 79.4% 93.3%
3922742 2.6.1.0 ↗ beta barrels › OB-fold › Staphylococcal nuclease › Staphylococcal nuclease 0.58 47.0 3.90e-01 89.7% 88.0%
5075805 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.56 39.0 4.11e-01 73.5% 90.9%
4985499 206.1.3.21 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RimK 0.55 44.0 3.14e-01 86.8% 35.0%
3884605 219.1.1.80 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › DUF4796_C 0.54 40.0 3.35e-01 80.9% 84.7%
3970872 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.54 42.0 3.04e-01 86.8% 34.1%
3997517 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.52 42.0 4.15e-01 85.3% 94.3%
3778012 708.1.1.4 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › FLYWCH 0.51 40.0 3.76e-01 85.3% 81.2%
4943047 267.1.1.3 ↗ a+b complex topology › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain › Cation_ATPase 0.51 39.0 2.76e-01 83.8% 80.0%
4957115 206.1.3.21 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RimK 0.50 41.0 2.93e-01 92.6% 38.6%
D2 high residues 80-121
PDB
Domain cluster: representative
CATH (51)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2qz8A02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.74 62.0 5.09e-01 97.6% 90.1%
1ti2B03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.71 58.0 4.66e-01 100.0% 46.4%
2jveA00 2.10.60.10 Mainly Beta › Ribbon › CD59 › CD59 0.71 60.0 5.17e-01 100.0% 87.3%
2yweA03 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.71 57.0 4.75e-01 95.2% 90.2%
7uvpA02 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.70 54.0 4.71e-01 90.5% 100.0%
5fmvA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.70 56.0 4.53e-01 100.0% 46.4%
4qbuA03 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.69 55.0 4.92e-01 95.2% 100.0%
3dh1B00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.69 56.0 3.93e-01 100.0% 37.5%
5cw3C01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.68 58.0 4.08e-01 100.0% 51.0%
3p96A02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.68 54.0 4.55e-01 100.0% 95.2%
3o2sB01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.67 57.0 4.05e-01 100.0% 45.5%
3c6mC01 3.30.160.110 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Sirohaem synthase, central domain 0.67 53.0 5.33e-01 97.6% 97.7%
2xbzA00 2.60.40.2380 Mainly Beta › Sandwich › Immunoglobulin-like › 0.67 57.0 4.02e-01 100.0% 33.3%
1ej6A05 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 56.0 4.37e-01 100.0% 57.9%
5lf5A03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 54.0 4.46e-01 100.0% 49.4%
2vsdA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 57.0 4.46e-01 100.0% 48.4%
2vecA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.66 56.0 4.24e-01 100.0% 52.4%
2pw9C03 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.65 53.0 3.84e-01 100.0% 33.3%
6ztgA01 3.30.70.1070 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Sporulation related repeat 0.65 50.0 4.37e-01 95.2% 100.0%
2uvfA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.65 56.0 4.07e-01 100.0% 58.6%
2a74A05 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.64 54.0 4.16e-01 100.0% 43.8%
3pdgA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 54.0 4.26e-01 100.0% 45.1%
3tp4B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 54.0 4.28e-01 100.0% 46.2%
6grqA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 54.0 4.35e-01 100.0% 52.3%
1yq2A04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 53.0 3.99e-01 100.0% 46.1%
3ocpB00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.64 53.0 3.80e-01 100.0% 31.2%
2q3xA00 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.64 56.0 3.86e-01 100.0% 33.1%
1vq2A00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.63 53.0 3.59e-01 100.0% 49.7%
1ollA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 52.0 4.13e-01 100.0% 49.5%
5tipA01 2.70.9.10 Mainly Beta › Distorted Sandwich › Adenovirus Type 2 Hexon; domain 4 › Adenovirus Type 2 Hexon, domain 4 0.62 51.0 3.43e-01 100.0% 45.7%
3dadA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.62 50.0 2.97e-01 90.5% 23.8%
1zczA02 3.40.140.20 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › AICAR transformylase, duplication domain 0.62 51.0 3.84e-01 100.0% 37.6%
2pn5A05 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.62 51.0 4.05e-01 100.0% 46.9%
3n0aA02 2.60.40.1110 Mainly Beta › Sandwich › Immunoglobulin-like › 0.62 53.0 3.74e-01 100.0% 37.0%
1xgsA02 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 0.62 45.0 3.74e-01 76.2% 80.5%
3rbsA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 51.0 4.15e-01 100.0% 52.3%
2gy5A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 51.0 4.11e-01 100.0% 50.0%
1z3aA00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.61 50.0 3.52e-01 100.0% 71.8%
2vvfA01 2.60.120.730 Mainly Beta › Sandwich › Jelly Rolls › 0.61 51.0 3.63e-01 100.0% 53.9%
2q0oA01 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.61 46.0 3.13e-01 85.7% 93.5%
3nyiB01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.59 47.0 3.36e-01 100.0% 26.8%
2bv4A00 2.60.120.400 Mainly Beta › Sandwich › Jelly Rolls › Calcium-mediated lectin 0.59 51.0 3.80e-01 100.0% 38.1%
2qsdB02 3.50.100.10 Alpha Beta › 3-Layer(bba) Sandwich › protein il1583 fold › protein il1583 domain 0.58 48.0 3.99e-01 100.0% 51.3%
2wq4A01 2.60.120.760 Mainly Beta › Sandwich › Jelly Rolls › 0.58 49.0 3.53e-01 100.0% 72.9%
2oxgC00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 46.0 3.64e-01 100.0% 45.5%
3fdjA02 2.20.28.50 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › DegV, N-terminal domain, peripheral subdomain 0.57 46.0 4.72e-01 95.2% 100.0%
7wguB01 2.60.40.420 Mainly Beta › Sandwich › Immunoglobulin-like › Cupredoxins - blue copper proteins 0.57 45.0 3.68e-01 100.0% 45.1%
1pzxA02 2.20.28.50 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › DegV, N-terminal domain, peripheral subdomain 0.56 40.0 4.11e-01 92.9% 100.0%
2a90A02 3.30.720.50 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.56 43.0 3.90e-01 90.5% 100.0%
3n6xA03 3.30.1490.270 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.52 41.0 3.84e-01 92.9% 69.6%
2hjeA02 2.20.20.100 Mainly Beta › Single Sheet › Anthopleurin-A › LuxQ periplasmic domain, C-terminal subdomain 0.51 43.0 4.05e-01 100.0% 96.3%
ECOD (30)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4186857 4012.1.1.0 ↗ a+b two layers › SSHS domain › SSHS domain in type II DNA topoisomerase › SSHS domain in type II DNA topoisomerase 0.87 73.0 7.49e-01 100.0% 97.5%
3972855 304.14.1.1 ↗ a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) › SPOR 0.86 77.0 6.30e-01 100.0% 97.3%
3976762 304.14.1.1 ↗ a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) › SPOR 0.85 74.0 6.08e-01 97.6% 97.3%
4531584 4012.1.1.0 ↗ a+b two layers › SSHS domain › SSHS domain in type II DNA topoisomerase › SSHS domain in type II DNA topoisomerase 0.83 67.0 6.84e-01 100.0% 97.5%
4952123 3986.2.1.0 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.80 70.0 6.23e-01 100.0% 75.0%
4985395 304.4.1.75 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › GYD 0.78 65.0 5.44e-01 97.6% 100.0%
5025566 304.7.1.0 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.74 61.0 5.68e-01 95.2% 100.0%
3935475 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.71 61.0 3.72e-01 100.0% 23.8%
4105204 304.24.1.3 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_III 0.70 56.0 4.75e-01 100.0% 92.5%
4586345 304.28.1.2 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › Sec_GG 0.69 56.0 4.61e-01 97.6% 87.1%
4455319 304.24.1.3 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_III 0.68 56.0 4.69e-01 100.0% 92.5%
3590544 2492.1.1.18 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › Prok-JAB 0.68 56.0 3.94e-01 97.6% 53.4%
3958992 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.66 54.0 4.52e-01 97.6% 90.0%
3281154 304.24.1.3 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_III 0.65 53.0 4.46e-01 97.6% 90.0%
3213885 11.1.1.97 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › I-set 0.64 54.0 4.12e-01 100.0% 57.1%
3244813 11.1.1.179 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.63 54.0 3.81e-01 100.0% 44.4%
2995198 10.2.1.54 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Capsid_N 0.63 52.0 3.48e-01 100.0% 46.3%
5077049 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.63 48.0 4.19e-01 92.9% 89.3%
1753 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.63 52.0 4.13e-01 100.0% 49.5%
3392216 223.2.1.31 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Intu_longin_2 0.63 46.0 2.99e-01 78.6% 91.1%
3890425 11.2.1.8 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › PTEN_C2 0.62 53.0 3.68e-01 100.0% 34.5%
184942 10.2.1.56 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › P2_N 0.61 51.0 3.63e-01 100.0% 53.9%
5067811 219.1.1.13 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Transglut_core 0.61 53.0 3.45e-01 100.0% 45.8%
4963 4012.1.1.1 ↗ a+b two layers › SSHS domain › SSHS domain in type II DNA topoisomerase › SSHS domain in type II DNA topoisomerase › TOPRIM_C 0.60 46.0 4.64e-01 100.0% 97.7%
3775421 223.2.1.31 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Intu_longin_2 0.60 43.0 2.86e-01 78.6% 17.9%
3258276 4081.1.1.2 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › VIT 0.60 48.0 3.08e-01 92.9% 30.7%
3481499 223.1.1.119 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › Intu_longin_2 0.60 41.0 2.86e-01 73.8% 21.3%
4000363 223.1.1.119 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › Intu_longin_2 0.56 45.0 2.95e-01 95.2% 21.2%
3595378 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.54 45.0 3.14e-01 97.6% 94.0%
4662939 1077.1.1.1 ↗ few secondary structure elements › RelA zinc-finger domain › RelA zinc-finger domain › RelA zinc-finger domain › RelA_RIS 0.51 40.0 3.54e-01 97.6% 97.1%