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NC_070967.1__YP_010671478.1__PQC17_gp312__00329

Bact-Vir

NC_070967.1__YP_010671478.1__PQC17_gp312__00329

Identity

Accession:
NC_070967 ↗
Kingdom:
phage

Quality

96.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Kleczkowskaviridae› Cuauhnahuacvirus› Rhizobium_phage_RHph_Y65

TaxID: 2509785

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 2-41
PDB
Domain cluster: representative
CATH (47)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4paaA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.70 52.0 3.19e-01 100.0% 13.5%
3fehA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.69 49.0 3.53e-01 77.5% 33.1%
2eayB02 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.68 49.0 4.70e-01 100.0% 65.3%
1c48A00 2.40.50.70 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.68 54.0 4.61e-01 100.0% 53.6%
4xtvB02 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.67 48.0 4.57e-01 100.0% 64.6%
3dsoA00 2.40.10.300 Mainly Beta › Beta Barrel › Thrombin, subunit H › Copper resistance protein K 0.67 46.0 3.98e-01 75.0% 43.9%
3f0zA01 3.30.310.260 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › 0.66 55.0 4.00e-01 95.0% 70.5%
4gp0B02 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.65 43.0 3.11e-01 70.0% 54.5%
2wfwA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.65 54.0 4.88e-01 100.0% 89.7%
2jrbA00 3.30.250.20 Alpha Beta › 2-Layer Sandwich › Rec A Protein; domain 2 › L1 transposable element, C-terminal domain 0.64 49.0 4.39e-01 92.5% 64.6%
4cswA02 3.40.366.30 Alpha Beta › 3-Layer(aba) Sandwich › Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 › 50S ribosomal protein L16 arginine hydroxylase; Chain A, Domain 2 0.64 51.0 3.40e-01 100.0% 21.0%
5nr1A01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.63 52.0 3.96e-01 100.0% 76.4%
4fk5A02 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.63 46.0 2.79e-01 100.0% 10.7%
1aq3A00 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.62 46.0 3.29e-01 82.5% 46.5%
4gv2A02 3.90.228.10 Alpha Beta › Alpha-Beta Complex › Phosphoenolpyruvate Carboxykinase; domain 3 › 0.61 36.0 2.31e-01 87.5% 10.5%
1xkpC00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.61 46.0 3.30e-01 85.0% 60.3%
2cs7A00 3.10.50.90 Alpha Beta › Roll › Chitinase A; domain 3 › 0.60 47.0 4.37e-01 100.0% 69.1%
3ca8A01 1.10.3620.10 Mainly Alpha › Orthogonal Bundle › YdcF fold › YdcF like domain 0.60 45.0 3.37e-01 85.0% 50.9%
4m7xA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.59 46.0 3.78e-01 100.0% 67.0%
2hzmA02 2.20.140.20 Mainly Beta › Single Sheet › q64v53_bacfr protein fold › 0.58 47.0 3.86e-01 100.0% 67.1%
6az1E02 2.40.50.740 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Ribosomal protein S4, central domain 0.58 39.0 3.75e-01 95.0% 56.9%
2egtA01 6.20.50.50 Special › Other non-globular › N-terminal domain of TfIIb › 0.58 39.0 4.03e-01 70.0% 100.0%
2e8eA00 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.58 41.0 3.04e-01 82.5% 27.3%
4ah6A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.57 46.0 3.48e-01 100.0% 70.2%
3ottA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.57 45.0 2.76e-01 97.5% 93.3%
1f44A01 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.56 44.0 3.01e-01 100.0% 21.1%
1z1bA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.56 42.0 3.93e-01 92.5% 63.2%
4npsA02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.55 43.0 3.95e-01 95.0% 70.7%
1hxdA03 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.55 36.0 3.58e-01 80.0% 60.5%
3cxgA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.55 43.0 3.29e-01 100.0% 73.8%
4bndA01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.55 45.0 3.10e-01 100.0% 28.2%
2wvxA01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.55 45.0 2.76e-01 100.0% 77.9%
2p39A00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.55 42.0 3.08e-01 100.0% 62.0%
1tk7A01 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.54 40.0 4.12e-01 82.5% 91.9%
1q5qH00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.54 38.0 2.47e-01 77.5% 90.2%
3va7A07 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.54 42.0 3.54e-01 92.5% 73.7%
4h0oA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 43.0 2.92e-01 100.0% 55.6%
1ncsA00 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.53 37.0 3.63e-01 92.5% 68.1%
2jozA01 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.53 43.0 3.35e-01 95.0% 100.0%
4msxA02 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.52 41.0 2.53e-01 97.5% 84.8%
5kmpB00 3.50.50.100 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › 0.52 40.0 2.43e-01 100.0% 9.9%
1mkfA02 2.60.40.1340 Mainly Beta › Sandwich › Immunoglobulin-like › Chemokine-binding protein M3-like 0.51 41.0 2.79e-01 95.0% 54.1%
4ijaA03 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 42.0 2.88e-01 97.5% 29.3%
1nrkA02 3.30.70.1400 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Aminomethyltransferase beta-barrel domains 0.51 37.0 3.19e-01 97.5% 66.7%
4b9gA00 2.60.40.3480 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 40.0 2.87e-01 97.5% 92.5%
2d5wA03 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.50 36.0 2.29e-01 72.5% 31.9%
2jxwA00 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.50 35.0 3.10e-01 100.0% 45.3%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3607606 3794.1.1.3 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit › ACCA_BT 0.78 55.0 3.81e-01 75.0% 28.0%
3964033 4.1.1.28 ↗ beta barrels › SH3 › SH3 › SH3 › BPL_C 0.74 53.0 5.05e-01 100.0% 64.0%
3997581 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.72 50.0 2.90e-01 75.0% 8.6%
4881660 4.1.1.28 ↗ beta barrels › SH3 › SH3 › SH3 › BPL_C 0.70 49.0 4.92e-01 100.0% 75.0%
3164374 4.1.1.28 ↗ beta barrels › SH3 › SH3 › SH3 › BPL_C 0.68 47.0 4.44e-01 90.0% 60.0%
429187 330.9.1.1 ↗ a+b two layers › dsRBD-like › C-terminal domain in LINE-1 ORF1p › C-terminal domain in LINE-1 ORF1p › Tnp_22_dsRBD 0.67 55.0 4.55e-01 97.5% 58.4%
134297 331.1.1.5 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like › OGG_N 0.66 55.0 3.99e-01 95.0% 69.9%
3212411 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.65 54.0 3.43e-01 100.0% 30.2%
3748837 330.9.1.1 ↗ a+b two layers › dsRBD-like › C-terminal domain in LINE-1 ORF1p › C-terminal domain in LINE-1 ORF1p › Tnp_22_dsRBD 0.65 54.0 4.44e-01 100.0% 55.0%
3706744 331.1.1.5 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like › OGG_N 0.65 52.0 3.72e-01 92.5% 78.4%
5041793 2003.1.10.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › PreATP-grasp domain 0.63 43.0 3.47e-01 100.0% 33.3%
4928056 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.63 48.0 4.50e-01 85.0% 74.0%
4065466 220.1.1.150 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › DUF986 0.63 52.0 4.27e-01 100.0% 50.0%
3903430 220.1.1.123 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_SSH1-like_1st 0.62 51.0 4.13e-01 100.0% 45.9%
847 9.1.1.20 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › DUF3255 0.62 43.0 3.07e-01 75.0% 27.8%
4944335 331.1.1.0 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.62 47.0 3.62e-01 85.0% 83.9%
5012791 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.61 49.0 3.44e-01 100.0% 27.3%
4278911 4.8.1.5 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.61 42.0 4.08e-01 95.0% 64.0%
3289895 247.1.1.11 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B_2 0.61 49.0 2.99e-01 100.0% 68.1%
4679015 220.1.1.150 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › DUF986 0.61 50.0 4.13e-01 100.0% 50.0%
3789517 2003.1.2.24 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox_2 0.60 50.0 2.89e-01 100.0% 9.5%
3988565 4.16.1.0 ↗ beta barrels › SH3 › PhtA domain-like › PhtA domain-like 0.60 45.0 4.41e-01 97.5% 75.6%
4960280 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 48.0 3.81e-01 97.5% 62.1%
3584930 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 45.0 3.98e-01 92.5% 55.0%
3628460 3308.1.1.0 ↗ beta duplicates or obligate multimers › periplasmic lysozyme inhibitor of I-type lysozyme-like › periplasmic lysozyme inhibitor of I-type lysozyme › periplasmic lysozyme inhibitor of I-type lysozyme 0.59 42.0 3.46e-01 75.0% 50.0%
4047703 71.1.1.2 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › LolA 0.59 40.0 2.75e-01 72.5% 69.7%
5038360 2006.1.1.11 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase_3 0.59 50.0 3.11e-01 100.0% 50.2%
5079725 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.59 44.0 3.96e-01 85.0% 60.0%
4935756 242.2.1.0 ↗ a+b two layers › Homing endonucleases-like › tRNA-intron endonuclease N-terminal domain-like › tRNA-intron endonuclease N-terminal domain-like 0.57 43.0 4.09e-01 97.5% 83.6%
3216450 2484.1.1.200 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FTH 0.56 48.0 3.31e-01 100.0% 44.0%
4959095 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.56 37.0 3.70e-01 72.5% 65.0%
3964608 220.1.1.104 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Cpta_toxin 0.56 43.0 3.86e-01 100.0% 75.7%
3696026 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.55 43.0 3.95e-01 97.5% 68.3%
4018231 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.55 46.0 2.99e-01 100.0% 79.5%
3929201 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.55 36.0 3.52e-01 70.0% 55.1%
3983052 300.1.1.8 ↗ a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease › PLDc_2 0.55 39.0 2.47e-01 82.5% 13.6%
3926653 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.54 46.0 2.71e-01 100.0% 12.7%
150402 392.1.1.1 ↗ beta meanders › N-terminal domains of the minor coat protein g3p › N-terminal domains of the minor coat protein g3p › N-terminal domains of the minor coat protein g3p › Phage_Coat_A 0.54 38.0 3.37e-01 77.5% 59.7%
3250378 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.53 39.0 3.55e-01 85.0% 55.0%
3616247 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 39.0 3.08e-01 82.5% 74.5%
134360 252.2.1.3 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › Arm-DNA-bind_1 0.53 40.0 3.58e-01 92.5% 54.7%
5004274 331.1.1.0 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.53 40.0 3.53e-01 97.5% 78.7%
5066058 7571.1.1.1 ↗ a/b three-layered sandwiches › Formyltransferase › Formyltransferase › Formyltransferase › Formyl_trans_N 0.53 33.0 2.12e-01 77.5% 9.8%
8321 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.53 37.0 3.63e-01 92.5% 68.1%
4444512 394.1.1.2 ↗ few secondary structure elements › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › CBM_19 0.53 40.0 3.94e-01 87.5% 88.9%
3236014 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.53 43.0 2.60e-01 97.5% 20.0%
3257763 2003.1.2.18 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.53 40.0 2.43e-01 100.0% 13.2%
3190584 2003.1.2.146 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › GMC_oxred_N, FAD_binding_2 0.52 40.0 2.29e-01 100.0% 40.5%
5010744 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.52 37.0 3.32e-01 80.0% 95.4%
3201543 5074.1.1.0 ↗ extended segments › Bacterial light-harvesting complex subunits › Bacterial light-harvesting complex subunits › Bacterial light-harvesting complex subunits 0.52 34.0 3.31e-01 75.0% 100.0%
3576239 110.3.1.1 ↗ alpha arrays › DEATH domain › SLED domain › SLED domain › SLED 0.51 38.0 2.77e-01 82.5% 66.1%
3403471 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 0.51 40.0 3.87e-01 97.5% 84.0%
3589184 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.51 37.0 3.07e-01 100.0% 42.7%
5077887 304.139.1.2 ↗ a+b two layers › Alpha-beta plaits › Cas7-related › CRISPR-associated protein Cas7/Csa2-related › RAMPs 0.51 37.0 2.45e-01 82.5% 30.7%
3362766 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 0.50 35.0 3.36e-01 92.5% 62.0%
5013701 3572.1.1.2 ↗ a+b complex topology › Cascade subunit Csa5 › Cascade subunit Csa5 › Cascade subunit Csa5 › Cas_Csa5 0.50 41.0 3.15e-01 100.0% 99.0%
D2 high residues 55-165
PDB
Domain cluster: rep: BML_08042016_6_5m_scaffold_3_prodigal-single.1__X__X__00175__D95-204
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF14301.13 best DUF4376 55.4 1.10e-14 99.1% 80.2%