Back to structures

NC_055060.1__YP_010084067.1__KMD61_gp36__00007

Bact-Vir

NC_055060.1__YP_010084067.1__KMD61_gp36__00007

Identity

Accession:
NC_055060 ↗
Kingdom:
phage

Quality

78.7 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 30-108
PDB
CATH (44)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7qh2C03 3.30.70.2740 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.83 52.0 5.25e-01 88.6% 64.1%
1zkdA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.74 52.0 4.06e-01 98.7% 34.3%
3c6kB03 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.72 57.0 4.22e-01 100.0% 35.3%
4atnA03 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.71 58.0 4.38e-01 100.0% 37.9%
2lrrA00 3.30.1370.50 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain 0.70 47.0 5.01e-01 100.0% 78.6%
2c42A03 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.70 48.0 3.50e-01 87.3% 26.4%
1wyzA02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.68 61.0 5.41e-01 100.0% 70.9%
2ek0A00 3.30.110.20 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain 0.66 55.0 5.27e-01 100.0% 80.0%
2a2lC00 3.30.450.150 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Haem-degrading domain 0.65 47.0 3.80e-01 75.9% 80.4%
1m6yA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.64 52.0 3.94e-01 100.0% 38.5%
1u0sA00 3.30.70.1110 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Histidine kinase CheA-like, P2 response regulator-binding domain 0.63 46.0 4.51e-01 89.9% 72.1%
4g6vB00 3.30.70.2920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 43.0 3.91e-01 70.9% 82.5%
2ahmH02 3.30.70.3540 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nsp8 replicase, head domain 0.61 54.0 5.15e-01 100.0% 93.5%
5t17A00 3.30.1340.10 Alpha Beta › 2-Layer Sandwich › Histidine-containing Protein; Chain: A; › HPr-like 0.61 47.0 4.61e-01 84.8% 82.4%
4nmlA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.59 47.0 4.56e-01 87.3% 78.9%
3jwhA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.59 53.0 3.99e-01 100.0% 41.4%
3tiiA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.59 44.0 4.80e-01 81.0% 100.0%
2vdrB02 2.60.40.1510 Mainly Beta › Sandwich › Immunoglobulin-like › ntegrin, alpha v. Chain A, domain 3 0.58 52.0 4.21e-01 100.0% 56.9%
3ub0A02 3.30.70.3540 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nsp8 replicase, head domain 0.58 52.0 4.95e-01 100.0% 97.8%
3e10A00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.58 52.0 4.07e-01 98.7% 74.1%
1fu0A00 3.30.1340.10 Alpha Beta › 2-Layer Sandwich › Histidine-containing Protein; Chain: A; › HPr-like 0.58 44.0 4.34e-01 83.5% 78.2%
1jelP00 3.30.1340.10 Alpha Beta › 2-Layer Sandwich › Histidine-containing Protein; Chain: A; › HPr-like 0.58 45.0 4.38e-01 82.3% 80.0%
4ft4A02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.58 46.0 3.05e-01 100.0% 19.2%
1b24A01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.58 51.0 4.78e-01 100.0% 80.0%
3pt9A02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.58 46.0 3.16e-01 100.0% 23.7%
4h63Q04 3.90.1150.120 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › 0.57 39.0 3.45e-01 74.7% 48.3%
1e6vA02 3.30.70.470 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 44.0 3.46e-01 86.1% 62.9%
4bluB00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.56 48.0 3.41e-01 100.0% 37.7%
7b0xI01 2.60.40.1090 Mainly Beta › Sandwich › Immunoglobulin-like › Fimbrial-type adhesion domain 0.56 50.0 4.24e-01 100.0% 80.9%
2cfmA02 3.30.470.30 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme 0.56 38.0 2.86e-01 70.9% 86.6%
1rlhA02 3.40.1520.10 Alpha Beta › 3-Layer(aba) Sandwich › hypothetical protein tt1634 › Ta1353-like 0.56 45.0 4.19e-01 88.6% 74.3%
5zg8A02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.54 48.0 3.19e-01 98.7% 81.2%
3bb7A01 3.90.70.50 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Streptopain (SpeB) 0.53 41.0 3.27e-01 86.1% 49.4%
2kj6A01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.53 44.0 4.35e-01 94.9% 94.0%
6aqgD02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.52 46.0 3.03e-01 98.7% 85.1%
3a5yA00 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.52 46.0 3.12e-01 98.7% 86.5%
2q7eA02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.52 45.0 3.32e-01 97.5% 79.7%
3of6E00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 45.0 4.10e-01 96.2% 86.5%
4melA02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.52 42.0 4.04e-01 93.7% 80.9%
2im9A02 2.30.260.10 Mainly Beta › Roll › putative xylanase like fold › putative xylanase like domain 0.51 41.0 3.42e-01 89.9% 93.2%
4chkB00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.51 42.0 4.05e-01 94.9% 85.7%
2oo3A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.50 42.0 3.05e-01 100.0% 38.2%
4lesA00 2.60.40.1240 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 43.0 3.59e-01 97.5% 87.3%
4ew7A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.50 39.0 3.47e-01 83.5% 84.1%
ECOD (66)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4980833 2004.1.3.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.72 49.0 3.38e-01 84.8% 22.0%
4969811 2003.1.5.24 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Met_10 0.72 58.0 3.89e-01 100.0% 24.2%
3552466 320.1.1.1 a+b two layers › R3H domain-like › R3H domain › R3H domain › R3H 0.71 50.0 5.30e-01 100.0% 82.9%
3518340 2004.1.3.2 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III › POR,EKR 0.71 49.0 3.42e-01 92.4% 22.4%
1890392 2003.1.5.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.71 55.0 3.77e-01 100.0% 23.8%
4107956 1137.1.1.0 a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain 0.71 64.0 5.56e-01 100.0% 67.5%
5014341 2003.1.5.24 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Met_10 0.71 55.0 3.76e-01 100.0% 24.0%
4932802 2003.1.5.24 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Met_10 0.70 56.0 4.23e-01 100.0% 36.3%
3698585 320.1.1.1 a+b two layers › R3H domain-like › R3H domain › R3H domain › R3H 0.70 50.0 4.99e-01 100.0% 73.8%
3385565 320.1.1.16 a+b two layers › R3H domain-like › R3H domain › R3H domain › HP0268 0.69 51.0 5.19e-01 100.0% 80.8%
4030028 2003.1.5.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.67 59.0 3.78e-01 100.0% 21.4%
4975722 2003.1.5.24 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Met_10 0.66 55.0 3.80e-01 100.0% 26.5%
4486768 1137.1.1.0 a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain 0.65 58.0 5.17e-01 100.0% 70.9%
3108982 4315.1.1.1 beta barrels › Coronavirus NSP8-like › Coronavirus NSP8-like › Coronavirus NSP8-like › CoV_NSP8 0.65 52.0 4.02e-01 92.4% 38.0%
4994628 328.9.1.0 a+b two layers › IF3-like › SepF C-terminal domain › SepF C-terminal domain 0.65 53.0 5.11e-01 100.0% 78.9%
2818339 4315.1.1.1 beta barrels › Coronavirus NSP8-like › Coronavirus NSP8-like › Coronavirus NSP8-like › CoV_NSP8 0.65 52.0 5.24e-01 92.4% 87.7%
3031755 4315.1.1.1 beta barrels › Coronavirus NSP8-like › Coronavirus NSP8-like › Coronavirus NSP8-like › CoV_NSP8 0.65 54.0 4.79e-01 96.2% 64.0%
2605331 4315.1.1.1 beta barrels › Coronavirus NSP8-like › Coronavirus NSP8-like › Coronavirus NSP8-like › CoV_NSP8 0.64 52.0 4.53e-01 92.4% 56.3%
3512301 207.1.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.64 54.0 3.57e-01 100.0% 22.5%
4876705 4315.1.1.1 beta barrels › Coronavirus NSP8-like › Coronavirus NSP8-like › Coronavirus NSP8-like › CoV_NSP8 0.64 54.0 4.73e-01 96.2% 62.4%
3697697 390.1.1.0 few secondary structure elements › Hairpin loop containing domain-like › Hairpin loop containing domain-like › Hairpin loop containing domain-like 0.64 41.0 3.74e-01 84.8% 47.7%
5022617 1137.1.1.0 a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain 0.64 52.0 4.87e-01 100.0% 72.0%
3908804 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.64 49.0 4.46e-01 88.6% 61.9%
3395407 320.1.1.1 a+b two layers › R3H domain-like › R3H domain › R3H domain › R3H 0.63 44.0 4.33e-01 100.0% 68.2%
4953513 886.1.1.2 a+b duplicates or obligate multimers › Probable bacterial effector-binding domain › Probable bacterial effector-binding domain › Probable bacterial effector-binding domain › GyrI-like 0.63 47.0 3.76e-01 86.1% 40.5%
3924676 390.1.1.1 few secondary structure elements › Hairpin loop containing domain-like › Hairpin loop containing domain-like › Hairpin loop containing domain-like › PAN_1 0.62 38.0 3.63e-01 86.1% 51.6%
5056082 322.1.1.1 a+b two layers › HPr-like › HPr-like › HPr-like › PTS-HPr 0.62 47.0 4.22e-01 82.3% 65.5%
3948410 322.1.1.1 a+b two layers › HPr-like › HPr-like › HPr-like › PTS-HPr 0.62 48.0 4.62e-01 83.5% 77.8%
3893192 327.11.2.26 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_N4BP1_1st 0.62 44.0 4.52e-01 87.3% 80.0%
4219982 2003.1.5.23 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_4 0.61 52.0 3.71e-01 100.0% 33.0%
3491800 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.61 43.0 3.64e-01 74.7% 45.4%
3938782 10.32.1.207 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › GBD_ELAPOR1-like_3rd 0.60 54.0 4.16e-01 100.0% 82.9%
4009784 322.1.1.1 a+b two layers › HPr-like › HPr-like › HPr-like › PTS-HPr 0.59 47.0 4.53e-01 86.1% 76.7%
3214341 10.32.1.207 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › GBD_ELAPOR1-like_3rd 0.59 53.0 4.19e-01 100.0% 83.6%
3972112 322.1.1.1 a+b two layers › HPr-like › HPr-like › HPr-like › PTS-HPr 0.59 45.0 4.42e-01 82.3% 81.2%
3436141 2003.1.5.30 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_7 0.59 53.0 3.92e-01 100.0% 64.5%
3613740 304.44.1.0 a+b two layers › Alpha-beta plaits › Ribosomal protein S10 › Ribosomal protein S10 0.59 48.0 3.84e-01 88.6% 56.2%
3241250 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.58 48.0 4.47e-01 94.9% 83.8%
4514209 304.60.1.2 a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.58 41.0 3.38e-01 75.9% 68.4%
3657112 244.1.1.0 a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.57 41.0 3.18e-01 86.1% 33.7%
3471395 304.6.1.0 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain 0.57 46.0 3.04e-01 86.1% 27.1%
3944361 131.1.1.3 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.57 46.0 2.78e-01 86.1% 19.4%
3172253 2004.1.1.212 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Microtub_bd 0.57 48.0 3.17e-01 100.0% 22.1%
3824515 327.11.2.11 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1_3 0.57 44.0 4.17e-01 88.6% 76.0%
3248329 2003.1.5.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.56 45.0 3.11e-01 88.6% 60.0%
4977576 219.1.1.153 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › BtrH_N 0.56 45.0 3.37e-01 88.6% 86.8%
4058358 327.11.2.26 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_N4BP1_1st 0.56 42.0 4.22e-01 86.1% 80.0%
3502539 304.60.1.0 a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like 0.55 43.0 3.45e-01 86.1% 56.0%
4056966 304.60.1.2 a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10 0.55 43.0 3.59e-01 84.8% 70.0%
3173892 10.35.1.1 beta sandwiches › jelly-roll › ER-derived vesicles protein Erv41p lumenal domain › ER-derived vesicles protein Erv41p lumenal domain › COPIIcoated_ERV,ERGIC_N 0.55 44.0 3.06e-01 88.6% 34.2%
4301721 304.60.1.8 a+b two layers › Alpha-beta plaits › Ribosomal protein L10-like › Ribosomal protein L10-like › Ribosomal_L10, PF27436 0.55 40.0 3.17e-01 75.9% 64.0%
3474713 327.11.2.0 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.55 43.0 4.11e-01 87.3% 71.6%
4064225 2492.1.1.7 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.54 38.0 3.06e-01 72.2% 49.7%
4934117 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.54 43.0 4.21e-01 100.0% 82.4%
1255866 7.1.1.1 beta barrels › PDZ domain › PDZ domain › PDZ domain › PDZ 0.54 42.0 4.00e-01 86.1% 90.4%
3276558 12.3.1.0 beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich 0.54 48.0 3.24e-01 100.0% 37.5%
987926 304.15.1.5 a+b two layers › Alpha-beta plaits › Viral DNA-binding domain › Viral DNA-binding domain › CDI_Immunity_Comp 0.54 41.0 3.83e-01 84.8% 66.0%
4207073 10.9.1.1 beta sandwiches › jelly-roll › C-terminal domain of mullusc hemocyanin › C-terminal domain of mullusc hemocyanin › PPO1_KFDV 0.53 47.0 3.80e-01 100.0% 76.8%
3163824 4091.1.1.1 beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.53 46.0 3.18e-01 96.2% 31.6%
3172342 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.53 43.0 3.83e-01 87.3% 64.5%
3250505 11.2.1.8 beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › PTEN_C2 0.52 37.0 3.06e-01 74.7% 53.1%
3671182 225.1.1.7 a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c_3 0.52 43.0 3.04e-01 98.7% 66.0%
5034660 205.1.1.21 a+b two layers › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › Fer4_16 0.51 46.0 3.09e-01 100.0% 53.1%
3705250 708.1.1.0 beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain 0.51 45.0 3.52e-01 100.0% 64.4%
3642967 246.3.1.0 a+b four layers › Carbon-nitrogen hydrolase-like › DNase I-like › DNase I-like 0.51 44.0 3.03e-01 100.0% 49.5%
3567057 304.127.1.2 a+b two layers › Alpha-beta plaits › Notch heterodimerization domain › Notch heterodimerization domain › NOD,NODP 0.50 39.0 3.39e-01 84.8% 56.0%