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NC_028945.1__YP_009212561.1__AVT40_gp212__00321

Bact-Vir

NC_028945.1__YP_009212561.1__AVT40_gp212__00321

Identity

Accession:
NC_028945 ↗
Kingdom:
phage

Quality

97.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Emdodecavirus› Sinorhizobium_phage_phiN3

TaxID: 1647405

Cluster

View cluster (4 members)

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 high residues 1-92
PDB
Domain cluster: rep: NC_027399.1__YP_010843536.1__ACQ27_gp652__00652__D183-285
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ck6C02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.75 52.0 4.76e-01 71.7% 68.9%
3craA02 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.74 68.0 6.05e-01 100.0% 83.6%
2q5zB00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.73 65.0 6.48e-01 94.6% 93.6%
2gtaA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.73 65.0 6.45e-01 97.8% 95.9%
2a3qA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.73 66.0 6.16e-01 100.0% 89.4%
2mtqA00 1.20.58.130 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.69 42.0 4.61e-01 72.8% 75.3%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.68 48.0 5.42e-01 73.9% 97.2%
3whjA00 6.10.140.1710 Special › Helix non-globular › Helix Hairpins › 0.67 49.0 4.57e-01 75.0% 76.6%
8hk0B03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.66 46.0 4.04e-01 72.8% 58.7%
4mhlA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.63 45.0 3.79e-01 75.0% 68.3%
3pe0A01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 44.0 4.32e-01 72.8% 82.2%
1vw4T01 6.10.330.20 Special › Helix non-globular › Monooxygenase › 0.63 45.0 4.24e-01 75.0% 61.6%
3edvB01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 44.0 3.88e-01 72.8% 62.5%
3uo2B02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.62 43.0 4.52e-01 72.8% 82.1%
1s35A01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 43.0 4.23e-01 73.9% 84.2%
8hixR01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.61 47.0 3.41e-01 84.8% 73.3%
3k3oA02 1.20.58.1360 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 43.0 4.48e-01 73.9% 82.1%
4fp4A00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.61 47.0 3.44e-01 81.5% 46.9%
2b5dX01 3.20.110.10 Alpha Beta › Alpha-Beta Barrel › 7-stranded beta/alpha barrel › Glycoside hydrolase 38, N terminal domain 0.60 45.0 2.97e-01 79.3% 22.8%
8sbeA02 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.60 52.0 4.23e-01 100.0% 58.3%
2jqqA00 1.20.58.1240 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 44.0 3.69e-01 78.3% 73.4%
4lixA03 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.57 49.0 3.58e-01 93.5% 85.2%
2oauA01 1.10.287.1260 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.56 45.0 4.42e-01 87.0% 83.3%
3o60A00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.56 48.0 3.89e-01 96.7% 50.5%
3f2bA08 1.10.150.870 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.55 38.0 3.33e-01 71.7% 61.3%
7dluA01 1.10.287.1260 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.54 41.0 3.95e-01 79.3% 72.4%
2hfiA00 1.20.120.440 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › YppE-like 0.53 40.0 3.66e-01 80.4% 65.9%
3kkbA00 1.20.120.880 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Histidine kinase (KinB), sensor domain 0.53 42.0 3.76e-01 85.9% 61.1%
ECOD (44)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4179648 192.4.1.1 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › Ribosomal_L29 0.81 54.0 6.38e-01 70.7% 96.9%
4033289 159.1.4.1 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › Type II deoxyuridine triphosphatase-related › dUTPase_2 0.80 74.0 5.92e-01 100.0% 56.5%
4494085 192.4.1.1 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › Ribosomal_L29 0.80 53.0 5.72e-01 71.7% 78.8%
3927159 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.79 56.0 4.78e-01 72.8% 85.7%
5054446 192.4.1.1 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › Ribosomal_L29 0.79 53.0 4.53e-01 70.7% 45.0%
3281235 192.4.1.1 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › Ribosomal_L29 0.79 53.0 5.86e-01 70.7% 85.3%
4365764 192.4.1.1 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › Ribosomal_L29 0.78 54.0 5.50e-01 72.8% 72.2%
3618651 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.78 55.0 5.76e-01 72.8% 88.2%
4393566 192.4.1.1 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › Ribosomal_L29 0.78 52.0 5.90e-01 70.7% 90.0%
4182984 6155.1.1.0 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter 0.77 55.0 5.17e-01 76.1% 61.8%
5052914 159.1.3.3 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › putative NTP pyrophosphohydrolase Exig_1061 › MazG 0.76 70.0 6.80e-01 100.0% 99.0%
3204414 1.1.17.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 0.76 54.0 3.48e-01 72.8% 39.7%
3914846 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.75 51.0 4.42e-01 70.7% 62.1%
4084570 192.4.1.1 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › Ribosomal_L29 0.75 53.0 5.98e-01 73.9% 95.7%
3472906 601.1.2.2 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › I_LWEQ 0.74 55.0 4.23e-01 77.2% 41.6%
3864955 633.22.1.6 ↗ alpha bundles › Bromodomain-like › Vitamin K epoxide reductase (VKOR) › Vitamin K epoxide reductase (VKOR) › TMD0_ABC 0.73 54.0 4.32e-01 77.2% 51.2%
3972536 150.1.1.4 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › COQ7 0.73 53.0 3.96e-01 75.0% 38.6%
5054079 192.4.1.0 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.72 56.0 5.97e-01 83.7% 93.8%
3305347 192.4.1.1 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › Ribosomal_L29 0.71 51.0 4.85e-01 78.3% 62.7%
3584465 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.71 62.0 5.53e-01 95.7% 74.6%
3060781 4163.1.1.1 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like › Sld5 0.69 47.0 4.08e-01 70.7% 53.8%
3744528 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.69 49.0 5.14e-01 75.0% 90.6%
3625559 633.21.1.0 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.67 49.0 4.22e-01 76.1% 97.9%
3214666 109.3.1.358 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Otopetrin 0.66 49.0 3.70e-01 77.2% 41.4%
3185917 375.1.9.12 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Zinc-nucleated domain of serine integrase › Wbp11 0.66 45.0 4.69e-01 70.7% 75.3%
3957445 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.66 55.0 5.16e-01 92.4% 81.7%
3603396 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.66 57.0 3.59e-01 93.5% 31.8%
3729610 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.65 47.0 4.16e-01 77.2% 93.6%
3304829 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.65 47.0 3.86e-01 76.1% 75.6%
3236642 109.4.1.1950 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF30196 0.64 57.0 3.78e-01 96.7% 58.4%
4228184 192.4.1.1 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › Ribosomal_L29 0.64 52.0 4.99e-01 92.4% 75.2%
4311291 109.4.1.2202 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF27584, PF27595 0.64 57.0 3.25e-01 98.9% 25.3%
3685822 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.63 55.0 3.63e-01 100.0% 65.1%
3712669 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.63 49.0 4.29e-01 83.7% 63.6%
3993403 616.1.1.26 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › NPP-6_helical 0.61 42.0 3.53e-01 70.7% 53.8%
4159893 604.13.1.0 ↗ alpha bundles › Spectrin repeat-like › USP8 N-terminal domain-like › USP8 N-terminal domain-like 0.61 52.0 4.54e-01 91.3% 74.8%
8997 2002.3.1.3 ↗ a/b barrels › TIM beta/alpha-barrel › Glycoside hydrolase/deacetylase › Glycoside hydrolase/deacetylase › Glyco_hydro_57 0.60 45.0 2.97e-01 79.3% 22.8%
3684033 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.60 51.0 3.70e-01 93.5% 59.6%
3579058 109.4.1.313 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › UTP20_N 0.60 50.0 3.77e-01 93.5% 60.0%
3715327 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.60 46.0 4.43e-01 82.6% 82.9%
5012649 150.1.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.59 47.0 3.70e-01 83.7% 84.2%
3735273 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 45.0 3.95e-01 88.0% 89.2%
3929776 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.55 46.0 2.88e-01 93.5% 29.8%
3535346 2004.1.1.184 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11 0.51 45.0 2.95e-01 100.0% 88.1%