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NC_070884.1__YP_010661422.1__PP935_gp037__00037

Bact-Vir

NC_070884.1__YP_010661422.1__PP935_gp037__00037

Identity

Accession:
NC_070884 ↗
Kingdom:
phage

Quality

75.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Trinifflemingvirus› Rhizobium_phage_RHph_N34

TaxID: 2509586

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 2-65
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1b7tA02 2.30.30.360 Mainly Beta › Roll › SH3 type barrels. › Myosin S1 fragment, N-terminal 0.67 43.0 4.65e-01 89.1% 80.8%
4m4zA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.65 41.0 4.54e-01 79.7% 85.1%
2kigA00 2.30.29.110 Mainly Beta › Roll › PH-domain like › 0.64 54.0 4.12e-01 96.9% 67.1%
2rajA02 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.61 42.0 3.49e-01 75.0% 77.8%
3pg7A02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 51.0 4.37e-01 100.0% 80.9%
2dfkC02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 50.0 4.01e-01 100.0% 70.9%
6bogA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.59 39.0 4.27e-01 82.8% 84.6%
4cbvA02 2.40.50.1020 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › LytTr DNA-binding domain 0.59 51.0 4.20e-01 98.4% 78.0%
2cudA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.59 45.0 4.22e-01 96.9% 68.4%
7u32F02 2.30.30.10 Mainly Beta › Roll › SH3 type barrels. › Integrase, C-terminal domain superfamily, retroviral 0.58 39.0 4.28e-01 81.2% 88.2%
2evrA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.58 45.0 4.33e-01 96.9% 74.3%
5xbfA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 49.0 4.49e-01 100.0% 88.6%
2eczA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.57 39.0 3.81e-01 90.6% 64.3%
1q67A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 47.0 3.79e-01 96.9% 82.9%
1nrkA01 3.30.70.1630 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 38.0 3.41e-01 70.3% 82.5%
1uebA02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 43.0 4.39e-01 82.8% 98.4%
1ybyA02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 44.0 4.46e-01 85.9% 96.9%
4omfB02 3.10.450.750 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.56 34.0 3.69e-01 70.3% 78.7%
5j3tA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 46.0 3.85e-01 100.0% 73.0%
1ou8A00 2.30.30.220 Mainly Beta › Roll › SH3 type barrels. › SspB-like 0.55 45.0 3.94e-01 98.4% 57.5%
3netB02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.55 39.0 3.43e-01 75.0% 94.9%
4c5eC02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.55 46.0 4.03e-01 93.8% 68.8%
2kxcA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.55 37.0 3.70e-01 92.2% 68.7%
2lydA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 44.0 3.67e-01 100.0% 70.1%
1igqB00 2.30.30.150 Mainly Beta › Roll › SH3 type barrels. › KorB, C-terminal domain 0.54 36.0 3.73e-01 92.2% 78.9%
4e1pA00 3.30.60.230 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › Lsr2, dimerisation domain 0.53 36.0 3.80e-01 96.9% 81.8%
4chjA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 43.0 3.62e-01 98.4% 71.8%
1y0nA00 1.10.10.610 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › YehU-like 0.53 37.0 3.62e-01 73.4% 98.6%
1vq0A02 3.90.1280.10 Alpha Beta › Alpha-Beta Complex › CBS domain Like › HSP33 redox switch-like 0.52 39.0 4.12e-01 85.9% 94.7%
3ed4A02 3.30.1120.10 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.52 41.0 3.78e-01 85.9% 88.0%
6ptrB01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.52 39.0 3.36e-01 85.9% 61.9%
3a54A01 2.40.50.340 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.51 42.0 3.81e-01 93.8% 85.6%
3wt0A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 38.0 2.96e-01 82.8% 39.4%
2rsmA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.51 36.0 3.01e-01 75.0% 47.8%
1x9mA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.51 42.0 2.91e-01 93.8% 99.1%
4amcA01 2.30.30.20 Mainly Beta › Roll › SH3 type barrels. › Aspartate carbamoyltransferase regulatory subunit, C-terminal domain 0.51 34.0 3.87e-01 100.0% 97.8%
1ibaA00 3.30.1360.60 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Glucose permease domain IIB 0.50 38.0 3.65e-01 85.9% 96.2%
3picA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.50 43.0 2.74e-01 100.0% 32.3%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4424609 4.8.1.5 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.73 50.0 5.41e-01 89.1% 86.8%
3989262 4.8.1.5 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.67 47.0 5.08e-01 85.9% 94.0%
3893533 4292.2.1.0 ↗ a+b two layers › FlaG-like › MAGUK binding stalk (MBS) domain › MAGUK binding stalk (MBS) domain 0.64 48.0 4.19e-01 81.2% 81.0%
4974477 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.63 42.0 3.84e-01 78.1% 48.9%
4478971 4.1.1.174 ↗ beta barrels › SH3 › SH3 › SH3 › DUF951 0.63 44.0 4.43e-01 84.4% 72.3%
4935681 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.63 40.0 4.23e-01 82.8% 74.5%
3077774 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.63 43.0 3.52e-01 75.0% 86.6%
5014250 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.62 49.0 4.53e-01 84.4% 87.5%
3991186 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.61 52.0 4.42e-01 100.0% 75.7%
4957409 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.61 37.0 4.08e-01 90.6% 78.0%
4056117 4.8.1.5 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › LytTR 0.60 44.0 4.38e-01 90.6% 78.5%
4930179 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.60 38.0 4.01e-01 82.8% 74.5%
3174481 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.59 50.0 3.86e-01 100.0% 65.6%
3870514 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.59 50.0 4.27e-01 100.0% 72.2%
3744042 216.1.1.27 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › HGTP_anticodon2 0.59 40.0 3.18e-01 71.9% 79.3%
4998620 3740.1.1.4 ↗ alpha arrays › F420-reducing hydrogenase subunit beta › F420-reducing hydrogenase subunit beta › F420-reducing hydrogenase subunit beta › FrhB_FdhB_C 0.59 38.0 2.54e-01 75.0% 14.7%
4956219 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.59 40.0 3.26e-01 70.3% 52.5%
4823230 220.1.1.66 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SOS1_NGEF_PH 0.59 48.0 4.50e-01 93.8% 88.9%
3480535 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.58 49.0 4.30e-01 100.0% 80.0%
3314214 7502.1.1.7 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon2 0.58 41.0 3.42e-01 73.4% 91.8%
4492844 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.58 39.0 3.42e-01 70.3% 63.3%
5047657 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.57 37.0 3.97e-01 70.3% 78.2%
4498193 376.1.1.37 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › SLX1_C 0.57 45.0 3.42e-01 89.1% 88.5%
3263503 331.4.1.9 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 › CPSF73-100_C 0.57 35.0 3.39e-01 96.9% 53.3%
4962256 101.1.2.937 ↗ alpha arrays › HTH › HTH › winged helix domain › PF25943 0.57 42.0 3.64e-01 82.8% 70.9%
3966925 304.107.1.2 ↗ a+b two layers › Alpha-beta plaits › Aminomethyltransferase folate-binding domain › Aminomethyltransferase folate-binding domain › SoxG 0.56 38.0 2.79e-01 70.3% 86.2%
4579534 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.56 45.0 4.49e-01 87.5% 98.5%
3405538 219.1.1.111 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Transglut_core, Rad4 0.56 46.0 3.05e-01 95.3% 85.8%
3992641 331.4.1.9 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 › CPSF73-100_C 0.56 39.0 3.79e-01 73.4% 81.4%
4051852 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.55 44.0 4.38e-01 87.5% 98.5%
4112874 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.55 38.0 3.17e-01 75.0% 88.8%
3673445 376.1.1.16 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › FANCL_C 0.54 37.0 3.41e-01 70.3% 60.0%
4947834 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.54 46.0 4.02e-01 98.4% 81.0%
4043601 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.54 43.0 4.28e-01 87.5% 96.9%
3948516 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.54 42.0 4.24e-01 85.9% 98.5%
3739664 247.1.1.38 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › CPSF73-100_C 0.54 38.0 3.70e-01 92.2% 67.1%
3942961 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.54 42.0 3.95e-01 87.5% 75.0%
4944397 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.53 36.0 3.88e-01 70.3% 90.0%
4184764 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.53 42.0 4.20e-01 85.9% 96.9%
5058926 4.6.1.0 ↗ beta barrels › SH3 › PRC-barrel domain › PRC-barrel domain 0.53 40.0 3.81e-01 81.2% 72.0%
3407758 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.53 43.0 3.74e-01 100.0% 69.6%
4167626 2.1.1.10 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › EFP 0.53 43.0 4.29e-01 89.1% 98.5%
4973804 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.53 43.0 4.14e-01 96.9% 96.0%
4058764 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.52 36.0 3.49e-01 71.9% 87.7%
3706884 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.52 42.0 3.73e-01 100.0% 80.9%
3260335 5.1.4.14 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Peptidase_S9_N 0.52 38.0 2.45e-01 81.2% 42.7%
3781848 247.1.1.38 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › CPSF73-100_C 0.52 37.0 3.63e-01 92.2% 68.6%
3700863 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.52 32.0 2.85e-01 70.3% 39.4%
3212707 5.1.3.9 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › OLF 0.52 40.0 2.83e-01 89.1% 97.0%
5050610 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.52 38.0 3.74e-01 79.7% 100.0%
3806421 247.1.1.38 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › CPSF73-100_C 0.52 37.0 3.68e-01 92.2% 73.8%
3255560 376.1.1.16 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › FANCL_C 0.51 35.0 3.46e-01 71.9% 67.1%
3786078 109.4.1.1764 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF28917 0.51 41.0 2.52e-01 93.8% 41.4%
4564673 2002.1.1.73 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › TGT 0.51 44.0 2.77e-01 100.0% 22.5%
4191047 2484.1.1.245 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › SHS2_FTSA, PilM_2, FtsA 0.51 40.0 2.47e-01 85.9% 15.6%
5074455 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 43.0 3.63e-01 95.3% 85.5%