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NC_041929.1__YP_009601295.1__FDH46_gp308__00170

Bact-Vir

NC_041929.1__YP_009601295.1__FDH46_gp308__00170

Identity

Accession:
NC_041929 ↗
Kingdom:
phage

Quality

73.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Emdodecavirus› Sinorhizobium_phage_phiM7

TaxID: 1647403

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 39-91
PDB
Domain cluster: rep: IMGVR_UViG_3300028840_006907-3300028840-Ga0309773_1000015171__D7-59
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3hrgA01 3.30.420.250 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Protein of unknown function DUF3822, N-terminal domain 0.72 47.0 3.43e-01 84.9% 25.2%
1sfeA01 3.30.160.70 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Methylated DNA-protein cysteine methyltransferase domain 0.70 35.0 3.00e-01 100.0% 30.9%
2qg7B01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.67 47.0 3.85e-01 94.3% 39.6%
2r41A00 3.10.450.150 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › enterococcus faecalis protein 0.66 47.0 3.87e-01 96.2% 39.8%
2db2A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.65 52.0 4.43e-01 92.5% 66.0%
4ivkA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.64 54.0 3.31e-01 100.0% 93.3%
3bs4A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.63 50.0 3.28e-01 88.7% 92.7%
2vqeE01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.63 43.0 4.04e-01 71.7% 67.2%
1xhsA00 3.10.490.10 Alpha Beta › Roll › Hypothetical upf0131 protein ytfp › Gamma-glutamyl cyclotransferase-like 0.61 49.0 3.83e-01 88.7% 65.5%
2n3gA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.61 49.0 4.54e-01 96.2% 87.5%
3r4rA02 2.60.40.2590 Mainly Beta › Sandwich › Immunoglobulin-like › 0.60 51.0 3.92e-01 98.1% 44.0%
3dohA02 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.59 40.0 2.69e-01 73.6% 56.2%
7b1xA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.59 46.0 2.88e-01 86.8% 60.3%
3omlA03 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.59 52.0 3.34e-01 100.0% 78.4%
2ltrA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.58 46.0 3.84e-01 94.3% 52.4%
1tkjA00 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.58 51.0 3.26e-01 100.0% 35.0%
4ejoA00 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 0.58 40.0 3.24e-01 88.7% 35.7%
3wewA00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.58 51.0 3.31e-01 100.0% 82.4%
1u2eA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.57 41.0 2.61e-01 77.4% 58.7%
3ga7A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.57 40.0 2.56e-01 75.5% 52.6%
1i5eA00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.57 48.0 3.30e-01 100.0% 62.5%
5bw0F00 3.30.1300.30 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › GSPII I/J protein-like 0.57 42.0 3.57e-01 81.1% 83.5%
3cngA01 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.56 35.0 4.01e-01 86.8% 97.1%
1zs7A01 3.10.450.120 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Pre-PUA domain; domain 1 0.56 43.0 3.48e-01 92.5% 42.3%
2dr3A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.56 44.0 3.03e-01 94.3% 89.7%
6toaF01 3.30.2000.30 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.56 45.0 3.51e-01 94.3% 96.9%
3u4yA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.56 40.0 2.54e-01 100.0% 13.2%
3hurA01 2.40.37.10 Mainly Beta › Beta Barrel › Lyase, Ornithine Decarboxylase; Chain A, domain 1 › Lyase, Ornithine Decarboxylase; Chain A, domain 1 0.56 40.0 2.93e-01 79.2% 83.9%
5c82A00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.55 41.0 2.94e-01 83.0% 38.8%
3aa0B02 3.90.1150.210 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › F-actin capping protein, beta subunit 0.55 43.0 3.14e-01 88.7% 32.9%
3nybA02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.55 45.0 3.65e-01 96.2% 90.9%
3dmgA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.55 46.0 3.24e-01 100.0% 68.6%
2xssA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.55 38.0 2.77e-01 81.1% 25.0%
4fkeA01 2.60.40.1730 Mainly Beta › Sandwich › Immunoglobulin-like › tricorn interacting facor f3 domain 0.55 42.0 2.90e-01 90.6% 88.6%
4kx7A01 2.60.40.1730 Mainly Beta › Sandwich › Immunoglobulin-like › tricorn interacting facor f3 domain 0.55 42.0 2.88e-01 88.7% 85.4%
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 0.55 47.0 3.48e-01 100.0% 81.8%
5jd5A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 43.0 2.66e-01 86.8% 56.8%
4q05A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 42.0 2.63e-01 86.8% 54.4%
3c5vA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 41.0 2.61e-01 84.9% 25.9%
2retA00 3.30.1300.30 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › GSPII I/J protein-like 0.54 41.0 3.50e-01 81.1% 81.0%
2k75A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 35.0 2.89e-01 77.4% 35.9%
1b24A01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.53 37.0 3.21e-01 96.2% 44.2%
1gkkA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.53 37.0 2.43e-01 79.2% 15.5%
4akrA02 3.90.1150.210 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › F-actin capping protein, beta subunit 0.52 42.0 3.14e-01 94.3% 45.6%
4mtnA01 3.30.1480.10 Alpha Beta › 2-Layer Sandwich › N Utilization Substance Protein A; Chain:P; domain 4 › NusA, N-terminal domain 0.51 43.0 3.53e-01 94.3% 51.6%
2hc5A01 3.30.160.170 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › FlaG-like 0.51 41.0 3.50e-01 98.1% 55.1%
6w0pA02 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.50 43.0 2.61e-01 100.0% 85.4%
6iw6A02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.50 44.0 3.52e-01 100.0% 89.8%
ECOD (52)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3673032 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.78 50.0 4.53e-01 83.0% 50.0%
5065441 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.72 45.0 4.59e-01 81.1% 64.2%
3248039 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.70 45.0 3.64e-01 81.1% 35.0%
3784907 896.1.1.3 ↗ a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › SRP9-21 0.66 50.0 4.31e-01 100.0% 51.8%
5039125 375.1.1.83 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › zf-TFIIB 0.66 44.0 4.12e-01 88.7% 55.4%
4966836 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.66 44.0 4.35e-01 88.7% 65.5%
4998404 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.66 52.0 5.06e-01 86.8% 88.3%
4988831 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.66 41.0 4.14e-01 81.1% 61.8%
143267 227.1.1.1 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_N 0.66 47.0 3.57e-01 100.0% 31.5%
4932673 375.1.1.26 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Rpr2 0.66 51.0 4.36e-01 100.0% 51.1%
3898522 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.64 42.0 4.32e-01 88.7% 72.0%
5038361 4294.1.1.13 ↗ few secondary structure elements › Trm112p-like › Trm112p-like › Trm112p-like › Zn_ribbon_TFIIB 0.63 41.0 4.35e-01 86.8% 77.8%
4202852 375.1.1.26 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Rpr2 0.63 50.0 4.07e-01 98.1% 45.7%
3680162 375.1.1.148 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › RPA_interact_C 0.62 40.0 4.50e-01 81.1% 100.0%
3607693 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.62 44.0 2.74e-01 94.3% 13.1%
3710891 330.1.1.22 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › PF26536 0.62 51.0 4.33e-01 100.0% 66.0%
3682832 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.62 43.0 3.04e-01 100.0% 25.2%
4590962 3604.1.1.1 ↗ a+b two layers › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Ni_insertion 0.60 35.0 3.44e-01 73.6% 51.7%
416386 11.1.4.46 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › Fim1F_C 0.60 51.0 3.90e-01 98.1% 43.0%
3433500 386.1.1.4 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-BED 0.60 35.0 3.62e-01 81.1% 60.0%
3683776 219.1.1.16 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C48 0.59 50.0 3.18e-01 98.1% 59.3%
4928584 109.4.1.5 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_1 0.57 39.0 2.69e-01 90.6% 17.8%
5047435 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.57 50.0 3.68e-01 100.0% 88.9%
3186255 223.1.1.21 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › HODM_asu-like 0.57 44.0 2.77e-01 100.0% 14.7%
3327282 5.1.3.67 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_1 0.57 46.0 2.96e-01 96.2% 18.2%
4028178 316.1.1.36 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › MTPAP-like_central 0.57 48.0 3.70e-01 98.1% 80.0%
3649955 6.1.1.12 ↗ beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil › Agglutinin 0.57 45.0 3.19e-01 86.8% 44.4%
3707891 243.3.1.73 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › DUF7920 0.56 45.0 3.92e-01 94.3% 70.0%
3553623 719.1.1.2 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain › XLF 0.56 49.0 3.75e-01 100.0% 93.6%
4436049 1190.1.1.1 ↗ a+b two layers › Curli production assembly/transport component CsgF › Curli production assembly/transport component CsgF › Curli production assembly/transport component CsgF › CsgF 0.56 43.0 3.50e-01 84.9% 60.0%
4094714 4292.2.1.1 ↗ a+b two layers › FlaG-like › MAGUK binding stalk (MBS) domain › MAGUK binding stalk (MBS) domain › FlaG 0.56 47.0 4.06e-01 96.2% 72.9%
3882464 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.55 46.0 4.19e-01 98.1% 68.0%
4992408 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.55 37.0 3.95e-01 88.7% 80.0%
3685094 708.1.2.6 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › Mss4-like › GFA 0.55 47.0 3.47e-01 100.0% 47.3%
3722095 223.1.1.21 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › HODM_asu-like 0.54 43.0 2.69e-01 100.0% 14.3%
4037650 161.1.1.0 ↗ alpha complex topology › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA 0.54 47.0 2.61e-01 100.0% 60.4%
3881671 719.1.1.2 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain › XLF 0.54 46.0 3.66e-01 100.0% 79.2%
4583081 2011.2.1.5 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Peptidyl-tRNA hydrolase-like › Peptidyl-tRNA hydrolase-like › Peptidase_A25 0.54 42.0 2.69e-01 100.0% 41.1%
3246854 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.54 40.0 3.84e-01 98.1% 69.2%
5000798 3926.1.1.1 ↗ alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D › ATP-synt_D 0.54 44.0 3.18e-01 100.0% 40.0%
3308072 375.1.1.53 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Nudix_N_2 0.54 35.0 3.90e-01 94.3% 90.0%
3508353 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.54 40.0 2.57e-01 79.2% 22.8%
3970048 4292.2.1.0 ↗ a+b two layers › FlaG-like › MAGUK binding stalk (MBS) domain › MAGUK binding stalk (MBS) domain 0.53 43.0 3.94e-01 100.0% 69.2%
3356481 386.1.1.117 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › DUF7028 0.52 39.0 3.51e-01 100.0% 54.2%
3388135 4292.2.1.1 ↗ a+b two layers › FlaG-like › MAGUK binding stalk (MBS) domain › MAGUK binding stalk (MBS) domain › FlaG 0.52 47.0 4.15e-01 100.0% 77.3%
3929357 708.1.1.0 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain 0.52 41.0 3.61e-01 92.5% 64.3%
2756575 2003.1.10.20 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › PreATP-grasp domain › ATPgraspMvdD 0.52 44.0 3.39e-01 98.1% 51.2%
3612312 4001.1.1.4 ↗ a+b duplicates or obligate multimers › a+b domain in cullin-like proteins › a+b domain in cullin-like proteins › a+b domain in cullin-like proteins › Cullin_AB 0.52 42.0 3.51e-01 94.3% 70.0%
4192565 5.1.4.29 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › PD40 0.52 42.0 2.58e-01 86.8% 78.3%
4370909 9.4.1.1 ↗ beta barrels › Lipocalins/Streptavidin › D-aminopeptidase, middle and C-terminal domains › D-aminopeptidase, middle and C-terminal domains › DAP_B 0.51 41.0 3.56e-01 94.3% 80.0%
3540949 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.51 42.0 2.68e-01 94.3% 22.1%
5056676 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.50 39.0 3.29e-01 98.1% 48.0%