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NC_070889.1__YP_010662826.1__PP940_gp148__00148

Bact-Vir

NC_070889.1__YP_010662826.1__PP940_gp148__00148

Identity

Accession:
NC_070889 ↗
Kingdom:
phage

Quality

89.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Innesvirus› Rhizobium_phage_RL2RES

TaxID: 103371

Cluster

View cluster (26 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 medium residues 1-63
PDB
Domain cluster: rep: ON615601.1__UTS52108.1__X__00160__D1-53
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3dl1A01 1.10.472.150 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Glucose-regulated metallo-peptidase M90, N-terminal domain 0.62 43.0 3.66e-01 92.1% 46.5%
1j4xA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.59 44.0 3.21e-01 81.0% 96.6%
2im9A01 1.10.3670.10 Mainly Alpha › Orthogonal Bundle › Putative xylanase fold › Putative xylanase like domain 0.59 48.0 4.01e-01 93.7% 74.1%
3kd4A02 3.10.620.30 Alpha Beta › Roll › C8orf32 fold › 0.58 48.0 3.68e-01 95.2% 39.4%
3gt2A00 3.90.1720.10 Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › endopeptidase domain like (from Nostoc punctiforme) 0.58 48.0 3.84e-01 95.2% 44.4%
8d88A01 3.20.20.10 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Alanine racemase 0.53 40.0 2.76e-01 85.7% 100.0%
3vkgA11 1.20.920.20 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › 0.52 45.0 3.77e-01 98.4% 60.0%
3bqkA02 1.20.1310.20 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Duffy-antigen binding domain 0.51 44.0 3.37e-01 98.4% 42.6%
4byfC01 1.20.120.720 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Myosin VI head, motor domain, U50 subdomain 0.50 35.0 3.24e-01 93.7% 53.9%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4234616 5054.1.1.7 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › KdpA 0.58 47.0 3.10e-01 90.5% 53.5%
3513887 219.1.1.97 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › CEPT76_peptidase 0.58 48.0 3.47e-01 96.8% 31.5%
3720140 219.1.1.97 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › CEPT76_peptidase 0.56 45.0 3.08e-01 93.7% 24.0%
3173380 148.1.3.19 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_3 0.55 34.0 2.84e-01 92.1% 35.5%
3635814 5069.1.3.60 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › OST3_OST6 0.54 47.0 4.01e-01 100.0% 63.8%
3388735 5050.1.1.11 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › UNC-93 0.54 38.0 2.63e-01 100.0% 20.4%
4664283 5054.1.1.7 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › KdpA 0.54 46.0 3.71e-01 95.2% 49.2%
3598706 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.53 43.0 3.73e-01 93.7% 70.5%
4278078 131.1.1.0 ↗ alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like 0.52 43.0 2.93e-01 98.4% 98.5%
4350626 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 0.52 44.0 3.60e-01 95.2% 71.7%
2546511 2002.1.1.101 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Orn_Arg_deC_N 0.52 41.0 2.85e-01 93.7% 99.6%
5078404 3646.1.1.1 ↗ alpha complex topology › T-component of energy-coupling factor (ECF) transporters › T-component of energy-coupling factor (ECF) transporters › T-component of energy-coupling factor (ECF) transporters › CbiQ 0.50 43.0 2.88e-01 100.0% 75.1%
D2 medium residues 64-119
PDB
Domain cluster: representative
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6e1kA01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.71 52.0 4.12e-01 78.6% 61.6%
2fdrA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.69 52.0 4.94e-01 82.1% 100.0%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.69 43.0 4.16e-01 82.1% 57.4%
7x0fB01 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.68 51.0 4.77e-01 83.9% 65.8%
2hszA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.67 57.0 5.19e-01 94.6% 100.0%
3ljcA02 1.20.58.1480 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 50.0 3.88e-01 82.1% 63.5%
2ap1A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.66 53.0 3.79e-01 89.3% 65.1%
2hoqA02 1.10.150.520 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.66 55.0 4.96e-01 96.4% 96.2%
5hayA02 1.25.40.440 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Nucleoporin, helical domain, central subdomain 0.65 43.0 3.85e-01 87.5% 48.1%
3r72A00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.65 54.0 4.19e-01 92.9% 42.6%
2erbA01 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.65 55.0 4.43e-01 94.6% 49.5%
3v2lA00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.64 54.0 4.22e-01 92.9% 43.3%
4okvE00 6.10.140.1890 Special › Helix non-globular › Helix Hairpins › 0.62 44.0 4.19e-01 92.9% 64.6%
4eekA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.61 49.0 4.70e-01 91.1% 97.0%
3tacB02 1.10.150.50 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Transcription Factor, Ets-1 0.60 46.0 4.15e-01 83.9% 86.3%
1nv8B01 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.60 48.0 4.52e-01 94.6% 74.6%
5jrtA00 1.10.150.50 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Transcription Factor, Ets-1 0.59 40.0 3.92e-01 73.2% 95.3%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.59 45.0 3.64e-01 83.9% 99.1%
3pvlA01 1.25.40.530 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › MyTH4 domain 0.58 43.0 2.94e-01 80.4% 77.4%
4evfA02 1.10.220.10 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Annexin 0.58 40.0 3.68e-01 73.2% 56.8%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.58 42.0 3.08e-01 76.8% 30.3%
7zxkC01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.58 43.0 3.20e-01 80.4% 64.7%
2guzA00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.57 40.0 3.76e-01 75.0% 78.9%
4nsmA00 6.10.250.2770 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.57 42.0 3.88e-01 78.6% 84.5%
4ielA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.57 41.0 3.28e-01 78.6% 50.9%
2guzB00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.57 39.0 3.78e-01 87.5% 63.1%
2a3vB01 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.56 43.0 3.80e-01 92.9% 53.2%
1lvfB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 42.0 3.46e-01 82.1% 71.2%
1j1jA02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.54 42.0 3.65e-01 83.9% 62.4%
2ycdA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.54 42.0 3.30e-01 83.9% 50.4%
6lo8F01 1.10.287.810 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Mitochondrial import inner membrane translocase subunit tim13 like domains 0.53 43.0 4.08e-01 96.4% 78.3%
7ep1B01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.52 36.0 2.50e-01 76.8% 29.8%
4jbeB01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.52 41.0 2.71e-01 92.9% 59.6%
4hteA03 1.10.167.30 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › 0.50 37.0 3.37e-01 82.1% 61.3%
1uajA02 1.10.1270.20 Mainly Alpha › Orthogonal Bundle › Trp Operon Repressor; Chain A › tRNA(m1g37)methyltransferase, domain 2 0.50 38.0 3.53e-01 91.1% 64.4%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3960812 132.1.1.1 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.73 57.0 5.01e-01 85.7% 56.5%
4033983 132.1.1.1 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.70 54.0 4.78e-01 85.7% 56.5%
3967858 132.1.1.1 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.69 49.0 4.74e-01 76.8% 67.7%
4378877 3711.1.1.20 ↗ alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein › DUF444 0.68 44.0 4.00e-01 80.4% 49.3%
3287939 132.1.1.1 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.68 51.0 4.61e-01 83.9% 58.7%
3782437 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.67 44.0 3.62e-01 83.9% 38.0%
3950197 132.1.1.1 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.66 51.0 4.59e-01 91.1% 58.8%
4501825 6056.1.1.2 ↗ alpha arrays › SP1917-like › SP1917-like › SP1917-like › PrmC_N 0.66 54.0 4.98e-01 94.6% 73.3%
3408508 3712.1.1.1 ↗ a+b complex topology › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 › Med11 0.65 43.0 3.85e-01 82.1% 47.5%
4468389 5086.1.1.101 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › SH3BP5 0.65 41.0 3.21e-01 78.6% 30.0%
4187242 132.1.1.1 ↗ alpha bundles › ACP-like › Acyl-carrier protein (ACP) › Acyl-carrier protein (ACP) › PP-binding 0.65 52.0 4.44e-01 89.3% 53.7%
3963955 6056.1.1.2 ↗ alpha arrays › SP1917-like › SP1917-like › SP1917-like › PrmC_N 0.62 50.0 4.83e-01 92.9% 80.0%
3283519 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.62 52.0 4.18e-01 100.0% 51.7%
3447438 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.62 48.0 3.81e-01 83.9% 82.7%
3246206 3919.1.1.2 ↗ alpha duplicates or obligate multimers › N-terminal domain of COMMD9 › N-terminal domain of COMMD9 › N-terminal domain of COMMD9 › COMM_HN 0.61 42.0 3.35e-01 71.4% 79.6%
5013940 101.1.4.0 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like 0.61 45.0 4.70e-01 91.1% 90.0%
3545485 110.1.1.0 ↗ alpha arrays › DEATH domain › DEATH domain › DEATH domain 0.61 49.0 4.00e-01 91.1% 66.4%
4999590 4070.1.1.0 ↗ alpha arrays › FtsH protease domain-like › FtsH protease domain-like › FtsH protease domain-like 0.60 52.0 3.52e-01 100.0% 43.6%
3244744 4967.1.1.0 ↗ alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases 0.60 38.0 3.68e-01 71.4% 55.4%
3888162 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.60 41.0 3.27e-01 82.1% 34.2%
4025377 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.59 42.0 3.69e-01 75.0% 90.6%
3588414 2004.1.1.430 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran, ABC_tran_Xtn 0.59 49.0 2.86e-01 94.6% 15.5%
4345341 102.1.1.9 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › RNA_pol_A_CTD 0.59 42.0 3.77e-01 76.8% 78.8%
4000262 192.5.1.1 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1 0.58 44.0 3.77e-01 82.1% 74.4%
4156067 192.5.1.1 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1 0.58 44.0 3.51e-01 82.1% 60.9%
3790121 603.1.1.114 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › HR1 0.58 43.0 3.61e-01 82.1% 67.0%
2507424 6091.1.1.1 ↗ alpha bundles › Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase › Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase › Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase › FIVAR 0.57 47.0 4.06e-01 89.3% 82.4%
3288702 2004.1.1.712 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF87, HerA_C, TrwB_AAD_bind 0.57 45.0 2.68e-01 92.9% 9.9%
3387205 3922.1.1.0 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.56 42.0 3.58e-01 80.4% 71.1%
3619662 192.12.1.3 ↗ alpha bundles › Long alpha-hairpin › Transcriptional repressor TraM › Transcriptional repressor TraM › DUF747 0.56 42.0 3.74e-01 82.1% 65.0%
4976893 633.21.1.0 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.55 43.0 3.49e-01 85.7% 69.1%
3836565 193.1.1.1 ↗ alpha bundles › CH domain-like › Calponin-homology domain-like › Calponin-homology domain-like › CH 0.53 43.0 3.24e-01 94.6% 77.4%
3469077 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.52 46.0 3.46e-01 100.0% 87.1%
4270580 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.51 42.0 2.74e-01 100.0% 41.4%
3690804 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.50 41.0 2.59e-01 96.4% 29.4%