←Back to structures

NC_062746.1__YP_010356727.1__M1M24_gp38__00038

Bact-Vir

NC_062746.1__YP_010356727.1__M1M24_gp38__00038

Identity

Accession:
NC_062746 ↗
Kingdom:
phage

Quality

90.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Forsetiviridae› Freyavirus› Polaribacter_phage_Freya_1

TaxID: 2745662

Cluster

Singleton — not in a non-trivial cluster

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 7-79
PDB
Domain cluster: representative
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2kt4B01 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.67 46.0 3.70e-01 71.2% 47.9%
1xkiA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.67 46.0 3.79e-01 71.2% 50.0%
6fopA01 2.70.98.30 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Golgi alpha-mannosidase II; domain 4 0.66 48.0 3.42e-01 78.1% 38.1%
3w9kA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.65 53.0 4.36e-01 89.0% 68.9%
1nkgA01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.64 48.0 3.33e-01 80.8% 25.9%
1dfvA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.64 47.0 3.61e-01 79.5% 83.8%
4i8oA02 3.30.160.690 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Bacterial toxin RNase RnlA/LsoA, N repeated domain 0.63 49.0 4.59e-01 83.6% 68.9%
2qm4A01 2.170.210.10 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › DNA double-strand break repair and VJ recombination XRCC4, N-terminal 0.61 53.0 4.29e-01 97.3% 98.6%
3auxA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.60 46.0 3.01e-01 83.6% 33.0%
1p32B00 3.10.280.10 Alpha Beta › Roll › Mitochondrial Matrix Protein; Chain A › Mitochondrial glycoprotein 0.60 51.0 3.93e-01 95.9% 72.5%
8bddA02 2.70.98.70 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.60 48.0 3.17e-01 93.2% 59.2%
2it9A00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.60 47.0 4.10e-01 89.0% 85.0%
3lm3A02 3.30.1120.110 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.59 42.0 3.74e-01 75.3% 99.1%
6v04A01 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.59 47.0 4.02e-01 90.4% 59.8%
2vt8A00 3.40.1000.30 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › 0.58 44.0 3.67e-01 84.9% 74.8%
1mpgA01 3.30.310.20 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › DNA-3-methyladenine glycosylase AlkA, N-terminal domain 0.58 45.0 3.94e-01 84.9% 80.4%
7r8iA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.58 49.0 3.64e-01 100.0% 97.2%
1yqfB00 3.10.280.10 Alpha Beta › Roll › Mitochondrial Matrix Protein; Chain A › Mitochondrial glycoprotein 0.58 47.0 3.71e-01 95.9% 76.8%
2iayA00 3.30.1820.10 Alpha Beta › 2-Layer Sandwich › Lp2179-like fold › Lp2179-like 0.57 42.0 3.68e-01 79.5% 71.1%
3qf7A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.57 50.0 3.30e-01 97.3% 99.0%
2nvnA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.57 45.0 3.91e-01 90.4% 85.0%
1z94B00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.56 45.0 3.76e-01 93.2% 76.2%
1u17A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.56 43.0 3.26e-01 83.6% 84.9%
2giaB00 2.30.31.40 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › 0.56 48.0 3.91e-01 100.0% 71.9%
3tqmA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.55 39.0 3.67e-01 75.3% 68.9%
2bs6A01 2.40.128.190 Mainly Beta › Beta Barrel › Lipocalin › 0.54 38.0 3.71e-01 75.3% 83.3%
1vyfA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.54 46.0 3.80e-01 95.9% 70.4%
4jocA00 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.53 42.0 2.76e-01 87.7% 27.5%
1o8vA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.53 44.0 3.69e-01 95.9% 71.4%
2l8oA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.53 39.0 3.27e-01 83.6% 67.4%
3cm1A00 2.30.31.20 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Sporulation-specific cell division protein SsgB 0.52 43.0 3.65e-01 100.0% 52.9%
1yemB00 2.40.320.10 Mainly Beta › Beta Barrel › Hypothetical Protein Pfu-838710-001 › Hypothetical Protein Pfu-838710-001 0.52 45.0 3.54e-01 100.0% 83.1%
1dhkB00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 42.0 3.17e-01 93.2% 69.2%
1lfoA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.51 44.0 3.78e-01 100.0% 73.2%
2ijrA01 3.30.70.1270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Api92-like domains 0.51 36.0 3.38e-01 76.7% 91.8%
5vxzA01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 43.0 3.22e-01 94.5% 67.9%
3gxwC00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.51 35.0 3.25e-01 72.6% 86.0%
2wjsA02 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 44.0 3.35e-01 98.6% 73.8%
1fx5B00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 41.0 2.96e-01 93.2% 74.1%
1e2rA02 2.140.10.20 Mainly Beta › 8 Propeller › Methanol Dehydrogenase; Chain A › C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase 0.50 39.0 2.53e-01 90.4% 90.5%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2581425 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.71 48.0 5.36e-01 71.2% 92.7%
2998372 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.67 45.0 5.13e-01 72.6% 96.2%
3663326 292.2.1.1 ↗ a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain › POLO_box 0.65 55.0 4.92e-01 93.2% 68.6%
4870764 7579.1.1.49 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › GCE_fung 0.65 58.0 3.74e-01 100.0% 37.9%
5009130 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.65 46.0 2.96e-01 74.0% 21.2%
4400687 2004.1.1.782 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_23, AAA_29, SbcC_Walker_B 0.65 46.0 2.83e-01 74.0% 16.6%
2027 12.3.1.17 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › RhgB_N 0.64 48.0 3.34e-01 80.8% 26.0%
3972580 331.1.1.3 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like › AlkA_N 0.63 47.0 4.62e-01 80.8% 75.0%
4480602 2004.1.1.199 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23,SbcC_Walker_B 0.62 47.0 2.88e-01 82.2% 24.4%
1390452 2004.1.1.748 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_15, AAA_23, SbcC_Walker_B 0.62 46.0 3.50e-01 80.8% 62.1%
5013018 274.1.1.0 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.62 47.0 3.92e-01 82.2% 73.1%
3620045 883.1.1.6 ↗ a+b complex topology › Aha1/BPI domain-like › Aha1/BPI domain-like › Aha1/BPI domain-like › Aha1_N 0.61 52.0 4.22e-01 100.0% 66.5%
3415592 241.15.1.2 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain › PI31_Prot_N 0.61 47.0 3.77e-01 84.9% 78.0%
1780951 2004.1.1.514 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23, AAA_29, SbcC_Walker_B 0.60 45.0 2.88e-01 79.5% 22.8%
3394516 241.15.1.2 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain › PI31_Prot_N 0.60 45.0 3.69e-01 83.6% 75.7%
4363805 292.2.1.9 ↗ a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain › Polo_box_4 0.60 49.0 4.68e-01 94.5% 93.3%
3208276 883.1.1.6 ↗ a+b complex topology › Aha1/BPI domain-like › Aha1/BPI domain-like › Aha1/BPI domain-like › Aha1_N 0.59 51.0 4.05e-01 100.0% 66.9%
4014368 883.1.1.0 ↗ a+b complex topology › Aha1/BPI domain-like › Aha1/BPI domain-like › Aha1/BPI domain-like 0.59 51.0 4.05e-01 100.0% 66.9%
1764974 2004.1.1.514 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23, AAA_29, SbcC_Walker_B 0.59 45.0 3.45e-01 83.6% 62.2%
3474457 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.59 49.0 4.52e-01 91.8% 85.3%
3604518 3111.1.1.0 ↗ beta barrels › STT3/PglB/AglB beta-barrel domain › STT3/PglB/AglB beta-barrel domain › STT3/PglB/AglB beta-barrel domain 0.59 52.0 4.70e-01 98.6% 86.0%
4544568 719.1.1.5 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain › PF27933 0.59 40.0 3.52e-01 71.2% 99.1%
3733356 298.1.1.25 ↗ a+b two layers › FwdE/GAPDH domain-like › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › ox_reductase_C 0.59 51.0 4.00e-01 100.0% 89.7%
3743289 241.15.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain 0.58 40.0 3.58e-01 71.2% 86.7%
3892482 883.1.1.10 ↗ a+b complex topology › Aha1/BPI domain-like › Aha1/BPI domain-like › Aha1/BPI domain-like › SMP_C2CD2L 0.58 44.0 3.21e-01 82.2% 55.7%
5072279 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.58 45.0 2.91e-01 87.7% 33.3%
4221174 243.19.1.0 ↗ a+b two layers › Cystatin-like › Phi ETA orf 56-like protein C-terminal domains › Phi ETA orf 56-like protein C-terminal domains 0.58 41.0 3.78e-01 74.0% 96.8%
3616213 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.58 44.0 3.05e-01 84.9% 89.1%
4262159 2004.1.1.308 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_21 0.57 49.0 3.15e-01 93.2% 84.1%
3220848 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.57 43.0 3.46e-01 79.5% 96.4%
3480143 241.15.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain 0.57 42.0 3.44e-01 82.2% 76.0%
5054272 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.56 41.0 2.45e-01 100.0% 9.8%
4982005 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.56 45.0 2.81e-01 87.7% 29.3%
4937307 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.56 42.0 3.15e-01 80.8% 68.9%
5014331 2004.1.1.293 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_15 0.56 47.0 2.73e-01 93.2% 92.0%
4568749 2004.1.1.585 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_15, AAA_21, AAA_23 0.56 47.0 3.05e-01 93.2% 83.1%
4954761 241.1.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone 0.56 41.0 3.52e-01 78.1% 79.2%
3461718 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.56 39.0 2.83e-01 74.0% 52.2%
4938533 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.55 44.0 2.55e-01 87.7% 17.0%
3263638 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.55 40.0 2.71e-01 82.2% 61.4%
5064158 4019.1.1.1 ↗ alpha complex topology › alpha-helical domain in beta-lactamase/transpeptidase-like proteins › alpha-helical domain in beta-lactamase/transpeptidase-like proteins › alpha-helical domain in beta-lactamase/transpeptidase-like proteins › Beta-lactamase 0.54 38.0 2.56e-01 75.3% 99.7%
3910955 10.1.1.17 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_2 0.54 45.0 3.21e-01 90.4% 51.4%
4945471 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.54 37.0 3.89e-01 90.4% 81.5%
5011693 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.54 45.0 3.32e-01 94.5% 87.3%
4936791 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 0.54 47.0 2.88e-01 97.3% 92.7%
5032886 2004.1.1.293 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_15 0.53 46.0 2.69e-01 97.3% 99.4%
4293129 10.1.1.2 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Lectin_legB 0.53 44.0 3.09e-01 93.2% 66.4%
3737835 241.15.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain 0.52 39.0 3.58e-01 82.2% 78.0%
5059555 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 0.52 44.0 2.86e-01 97.3% 98.9%
185116 295.1.1.2 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › SsgA 0.52 43.0 3.65e-01 100.0% 52.6%
5018282 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.52 46.0 3.02e-01 100.0% 97.2%
4985494 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.51 40.0 2.50e-01 87.7% 26.1%
3315619 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.51 39.0 2.66e-01 84.9% 92.1%
3702988 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.51 39.0 3.45e-01 82.2% 80.0%
3196041 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.51 35.0 2.30e-01 74.0% 30.3%
3788749 6109.1.1.0 ↗ a+b two layers › N-terminal domain of chitin biosynthesis protein CHS6 › N-terminal domain of chitin biosynthesis protein CHS6 › N-terminal domain of chitin biosynthesis protein CHS6 0.51 42.0 3.37e-01 93.2% 76.0%