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NC_070888.1__YP_010662552.1__PP939_gp144__00144

Bact-Vir

NC_070888.1__YP_010662552.1__PP939_gp144__00144

Identity

Accession:
NC_070888 ↗
Kingdom:
phage

Quality

78.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Innesvirus› Rhizobium_phage_RL38J1

TaxID: 2663232

Cluster

View cluster (2 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 2-81
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1dbzA01 3.30.540.10 Alpha Beta › 2-Layer Sandwich › Fructose-1,6-Bisphosphatase; Chain A, domain 1 › Fructose-1,6-Bisphosphatase, subunit A, domain 1 0.71 57.0 4.36e-01 87.5% 47.8%
3isxA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.69 47.0 3.30e-01 71.2% 41.5%
3upsA00 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.68 52.0 4.70e-01 81.2% 81.5%
4p4mA02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.64 52.0 4.68e-01 92.5% 99.1%
2fvgA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.62 43.0 3.11e-01 72.5% 45.1%
1vhoA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.62 45.0 3.17e-01 76.2% 45.6%
1xdxA01 3.30.1140.40 Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › Tctex-1 0.62 48.0 4.51e-01 85.0% 99.0%
2hzmG01 3.30.310.180 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › 0.61 38.0 3.40e-01 83.7% 43.5%
2rioA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.60 45.0 3.44e-01 80.0% 92.5%
3b0xA03 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.59 49.0 4.54e-01 92.5% 84.8%
3jyyA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.59 45.0 3.87e-01 83.7% 65.7%
1u02A02 3.30.70.1020 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Trehalose-6-phosphate phosphatase related protein; domain 2 0.58 43.0 4.45e-01 80.0% 100.0%
2greA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.58 40.0 2.96e-01 73.8% 48.3%
2k19A00 1.20.1440.140 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.57 43.0 4.05e-01 81.2% 75.5%
1a41A02 1.20.120.380 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Type 1-topoisomerase catalytic fragment, domain 2 0.56 42.0 3.99e-01 92.5% 67.0%
6fhpD00 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.56 40.0 4.47e-01 97.5% 98.4%
2bvlA01 1.20.58.1190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 42.0 4.12e-01 82.5% 95.3%
1t82A00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.55 42.0 3.53e-01 82.5% 72.5%
1u60A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.55 46.0 3.14e-01 92.5% 76.1%
3r4qA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.55 46.0 3.99e-01 96.2% 90.2%
1lfwA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.55 43.0 3.08e-01 88.7% 54.4%
4dmvA01 1.20.58.1190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 40.0 4.01e-01 82.5% 95.3%
3r7wC02 3.30.450.190 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.54 38.0 3.53e-01 91.3% 57.0%
4hb9A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 43.0 2.84e-01 91.3% 95.7%
2lahA00 1.25.40.430 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.53 36.0 2.98e-01 71.2% 55.0%
4l8kA01 3.30.750.44 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › 0.52 43.0 4.18e-01 93.8% 95.6%
3au4A04 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 38.0 3.64e-01 100.0% 65.6%
1na6B02 3.40.91.80 Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › 0.52 36.0 2.64e-01 72.5% 33.9%
3kcpA02 2.60.40.1120 Mainly Beta › Sandwich › Immunoglobulin-like › Carboxypeptidase-like, regulatory domain 0.51 40.0 3.82e-01 91.3% 90.9%
5m43A00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.51 43.0 3.43e-01 96.2% 74.4%
1twuA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.50 43.0 3.65e-01 96.2% 84.7%
2pb2B01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.50 46.0 3.74e-01 100.0% 61.3%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4995145 331.4.1.0 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 0.72 45.0 4.41e-01 77.5% 58.8%
4377282 310.1.1.2 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain › Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain › Arg_tRNA_synt_N 0.72 51.0 4.85e-01 75.0% 93.7%
3926066 316.1.1.36 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › MTPAP-like_central 0.71 60.0 4.93e-01 92.5% 82.1%
4675620 310.1.1.2 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain › Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain › Arg_tRNA_synt_N 0.69 49.0 4.44e-01 75.0% 87.3%
4152826 310.1.1.2 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain › Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain › Arg_tRNA_synt_N 0.68 50.0 4.58e-01 77.5% 89.5%
4075031 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.64 53.0 3.96e-01 92.5% 71.0%
3719128 310.3.1.16 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related › PF30974 0.64 47.0 4.37e-01 80.0% 87.6%
4006693 3012.1.1.0 ↗ a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.64 51.0 5.04e-01 86.3% 94.1%
5008407 873.1.1.12 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › PF27313 0.63 45.0 3.90e-01 75.0% 65.6%
4979013 2011.1.1.11 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M42 0.63 43.0 2.95e-01 71.2% 50.0%
4985569 873.1.1.12 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › PF27313 0.62 45.0 3.82e-01 76.2% 59.3%
4936975 2011.1.1.11 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M42 0.62 45.0 3.13e-01 76.2% 43.1%
3972808 2011.1.1.11 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M42 0.62 42.0 2.96e-01 71.2% 45.6%
4253738 2004.1.1.17 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Myosin_head 0.61 53.0 3.02e-01 100.0% 12.7%
3178861 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.61 52.0 2.98e-01 100.0% 11.6%
4077309 331.1.1.6 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like › DUF3378 0.61 39.0 3.97e-01 100.0% 66.3%
4964620 2011.1.1.11 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M42 0.60 43.0 3.01e-01 75.0% 43.1%
1837127 331.1.1.6 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like › DUF3378 0.60 39.0 3.80e-01 100.0% 60.7%
4933185 873.1.1.13 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › ATC_hydrolase 0.60 48.0 3.87e-01 90.0% 63.0%
5078655 873.1.1.15 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › PF27323 0.58 46.0 3.89e-01 88.7% 77.9%
3981104 1.1.7.22 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Peptidase_M42 0.58 41.0 2.90e-01 76.2% 43.6%
3239737 3890.1.1.0 ↗ alpha bundles › Transmembrane Bax inhibitor motif (TMBIM) proteins › Transmembrane Bax inhibitor motif (TMBIM) proteins › Transmembrane Bax inhibitor motif (TMBIM) proteins 0.58 48.0 3.59e-01 92.5% 94.8%
4983622 873.1.1.0 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain 0.57 46.0 3.63e-01 87.5% 98.8%
4979691 873.1.1.0 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain 0.57 45.0 3.58e-01 87.5% 93.5%
5017105 873.1.1.0 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain 0.57 45.0 3.64e-01 87.5% 77.5%
5079456 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 0.57 46.0 3.68e-01 93.8% 42.2%
4988401 873.1.1.1 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › V4R 0.57 45.0 3.81e-01 90.0% 87.5%
3954965 873.1.1.7 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › Arabinose_bd 0.56 45.0 3.45e-01 90.0% 51.0%
3512870 873.1.1.4 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › TRAPP 0.56 45.0 3.63e-01 90.0% 80.0%
4958980 331.2.1.14 ↗ a+b two layers › TBP-like › Phosphoglucomutase, C-terminal domain › Phosphoglucomutase, C-terminal domain › Fer4_7 0.56 39.0 3.20e-01 93.8% 38.7%
5071258 873.1.1.0 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain 0.54 43.0 3.28e-01 90.0% 67.9%
4174949 331.1.1.1 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like › TBP 0.54 36.0 3.47e-01 100.0% 61.1%
4239881 328.3.1.2 ↗ a+b two layers › IF3-like › Translation initiation factor IF3, C-terminal domain › Translation initiation factor IF3, C-terminal domain › mIF3 0.54 42.0 3.63e-01 83.7% 84.8%
1390065 3018.1.1.1 ↗ a+b two layers › MesJ substrate recognition domain-like › MesJ substrate recognition domain-like › MesJ substrate recognition domain-like › TilS 0.52 35.0 3.36e-01 71.2% 66.0%
3920767 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.51 38.0 3.51e-01 100.0% 62.0%
3699577 220.1.1.236 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_27 0.51 41.0 3.71e-01 100.0% 62.7%
5078530 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 37.0 3.47e-01 91.3% 61.0%
3890749 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.50 38.0 3.65e-01 100.0% 70.0%
4603347 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 0.50 46.0 3.94e-01 100.0% 81.6%
3264236 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.50 36.0 3.33e-01 100.0% 59.0%