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NC_016165.1__YP_004934686.1__RcapMu43__00043

Bact-Vir

NC_016165.1__YP_004934686.1__RcapMu43__00043

Identity

Accession:
NC_016165 ↗
Kingdom:
phage

Quality

68.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhodobacter_phage_RcapMu

TaxID: 1105286

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 5-43
PDB
Domain cluster: rep: JF974315.1__AGN38700.1__RHYG_00031__00031__D4-57
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3anwA02 3.40.5.50 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.80 68.0 6.04e-01 100.0% 79.3%
2hvfA00 3.40.5.10 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › Ribosomal protein L9, N-terminal domain 0.79 64.0 5.95e-01 100.0% 71.2%
2e9xB01 3.40.5.50 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.74 62.0 5.36e-01 100.0% 68.2%
2hjqA01 3.40.5.20 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › YqbF domain 0.72 59.0 5.73e-01 100.0% 89.1%
4fsdA02 3.40.5.100 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › 0.70 55.0 4.53e-01 100.0% 54.7%
2wiyA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.69 49.0 2.81e-01 76.9% 15.0%
2czrA02 3.90.79.30 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › TBP-interacting protein, C-terminal domain 0.67 49.0 3.51e-01 79.5% 65.0%
3pe0A03 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.65 54.0 4.71e-01 100.0% 75.0%
3l9aX01 3.30.720.180 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.64 44.0 3.66e-01 100.0% 38.7%
2hpuA02 3.30.70.2050 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 45.0 4.00e-01 100.0% 55.6%
3c19A02 3.10.20.300 Alpha Beta › Roll › Ubiquitin-like (UB roll) › mk0293 like domain 0.60 45.0 3.71e-01 84.6% 76.9%
7osfB01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.56 42.0 2.68e-01 84.6% 53.8%
4yerA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.56 45.0 2.85e-01 92.3% 27.9%
2yxdA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.56 39.0 2.65e-01 79.5% 21.2%
1vplA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.56 43.0 2.68e-01 84.6% 51.3%
7tchB01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 42.0 2.65e-01 87.2% 46.3%
2od0A00 3.30.1460.30 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › YgaC/TfoX-N like chaperone 0.53 41.0 3.23e-01 94.9% 93.2%
2xcqA01 3.40.50.670 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.53 37.0 2.48e-01 100.0% 16.0%
7vufD01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 38.0 2.57e-01 89.7% 65.1%
2yx1A01 3.30.70.2580 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 39.0 3.55e-01 100.0% 84.8%
4wiwA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.51 45.0 3.70e-01 100.0% 79.7%
2eyqA07 3.90.1150.50 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Transcription-repair-coupling factor, D7 domain 0.50 37.0 2.53e-01 82.1% 21.1%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5010674 4076.3.1.11 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › PF25865 0.88 77.0 6.91e-01 100.0% 70.9%
4994655 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.87 76.0 7.03e-01 100.0% 92.0%
5045837 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.86 77.0 6.62e-01 100.0% 75.0%
4935547 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.85 74.0 6.90e-01 100.0% 90.0%
4981952 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.85 74.0 6.88e-01 100.0% 86.0%
4967982 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.85 73.0 7.05e-01 97.4% 95.5%
4927873 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.84 73.0 6.34e-01 100.0% 71.7%
5028408 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.84 73.0 6.78e-01 100.0% 92.0%
5042275 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.84 72.0 6.46e-01 100.0% 83.6%
4956746 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.83 72.0 6.72e-01 100.0% 92.0%
4956745 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.83 73.0 6.73e-01 100.0% 90.0%
5035786 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.83 72.0 6.68e-01 100.0% 92.0%
5069341 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.83 71.0 6.64e-01 100.0% 90.0%
4978275 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.83 71.0 6.42e-01 100.0% 83.6%
4932593 4076.3.1.5 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Gins51_C 0.82 70.0 6.57e-01 100.0% 92.0%
4932084 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.82 70.0 6.55e-01 100.0% 90.0%
3977355 4076.3.1.1 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › Packaging_FI 0.82 69.0 6.34e-01 100.0% 88.9%
4939413 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.82 70.0 6.54e-01 100.0% 96.0%
5063665 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.82 72.0 6.88e-01 100.0% 93.3%
3716713 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.82 69.0 6.46e-01 100.0% 90.0%
4946969 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 70.0 6.48e-01 100.0% 92.0%
4991671 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.81 68.0 6.38e-01 100.0% 94.0%
4230268 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.80 69.0 6.65e-01 100.0% 97.8%
4944185 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.80 69.0 5.87e-01 100.0% 67.7%
5011186 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.80 67.0 5.95e-01 100.0% 73.3%
3601134 4076.1.1.0 ↗ a+b two layers › L9 N-domain-like › L9 N-domain-like › L9 N-domain-like 0.79 65.0 5.49e-01 100.0% 54.3%
5083883 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.75 65.0 6.23e-01 100.0% 88.9%
4932061 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.75 61.0 5.97e-01 100.0% 95.6%
4269273 4076.4.1.1 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain › PriS_C 0.73 58.0 5.72e-01 100.0% 97.8%
5009 4076.3.1.2 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain › YqbF 0.72 59.0 5.64e-01 100.0% 83.7%
4934987 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.72 61.0 5.94e-01 100.0% 93.3%
4654615 325.1.7.2 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › RNA_pol_Rpb2_6 0.71 58.0 3.66e-01 100.0% 20.4%
3355968 375.1.1.190 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Fra10Ac1 0.65 52.0 3.66e-01 87.2% 29.6%
3258638 4.8.1.28 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Fra10Ac1 0.64 51.0 3.69e-01 87.2% 33.3%
4244236 3681.1.1.0 ↗ a+b complex topology › Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit › Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit › Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit 0.61 48.0 3.69e-01 100.0% 42.7%
5012054 310.3.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.59 45.0 3.81e-01 87.2% 78.6%
4931277 101.1.2.14 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.58 43.0 2.87e-01 79.5% 31.6%
4951007 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.57 46.0 2.95e-01 94.9% 23.6%
2127864 325.1.1.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › CO dehydrogenase molybdoprotein N-domain-like 0.57 42.0 3.77e-01 82.1% 89.8%
3236725 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.57 42.0 2.77e-01 100.0% 53.5%
4033781 2004.1.1.417 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran, AAA_21 0.56 42.0 2.71e-01 84.6% 54.4%
5017355 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.55 46.0 2.79e-01 92.3% 25.4%
4875011 275.1.1.4 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › RNA_pol_Rpb1_5 0.54 47.0 3.56e-01 100.0% 44.2%
3941732 3115.6.1.0 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon 0.54 42.0 4.04e-01 100.0% 76.0%
4350668 275.1.1.0 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase 0.52 43.0 3.66e-01 100.0% 60.0%
4270226 275.1.1.0 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase 0.51 40.0 3.74e-01 100.0% 78.2%
4483444 7523.1.1.4 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_3 0.50 41.0 2.86e-01 94.9% 34.1%
D2 medium residues 48-89
PDB
Domain cluster: representative