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NC_070883.1__YP_010661294.1__PP934_gp165__00165

Bact-Vir

NC_070883.1__YP_010661294.1__PP934_gp165__00165

Identity

Accession:
NC_070883 ↗
Kingdom:
phage

Quality

81.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Trinifflemingvirus› Rhizobium_phage_RHph_Y68

TaxID: 2509787

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 17-87
PDB
Domain cluster: representative
CATH (56)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4qxaB00 2.30.29.230 Mainly Beta › Roll › PH-domain like › 0.71 55.0 4.33e-01 83.1% 65.3%
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.71 56.0 5.60e-01 84.5% 98.6%
3u12A00 2.30.29.180 Mainly Beta › Roll › PH-domain like › Ubiquitin carboxyl-terminal hydrolase 26/29/37, pleckstrin homology-like domain 0.71 52.0 4.57e-01 77.5% 78.8%
2l2nA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.68 54.0 5.40e-01 87.3% 100.0%
3zl8A02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.68 52.0 3.66e-01 83.1% 51.8%
2xzhA00 2.130.10.110 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Clathrin heavy-chain terminal domain 0.67 51.0 3.25e-01 83.1% 26.5%
7b9cA02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.67 52.0 3.21e-01 83.1% 36.4%
7ue1B01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.67 47.0 3.74e-01 74.6% 97.9%
3wyfE00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.67 50.0 4.05e-01 81.7% 56.3%
1srqA01 3.30.1120.160 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.67 53.0 4.33e-01 88.7% 50.0%
7ne4A01 2.130.10.120 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Prolyl oligopeptidase, N-terminal domain 0.66 54.0 3.44e-01 87.3% 24.3%
2ltrA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.65 51.0 4.55e-01 87.3% 61.0%
3hi2B00 3.30.2310.40 Alpha Beta › 2-Layer Sandwich › YaeB-like fold › 0.65 43.0 3.91e-01 81.7% 50.5%
1di2A00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.65 50.0 5.05e-01 84.5% 97.1%
2nugB02 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.64 51.0 5.14e-01 85.9% 97.2%
2dixA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.63 50.0 4.87e-01 85.9% 89.7%
1txdA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.63 49.0 4.15e-01 84.5% 66.1%
5z5dA02 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.63 45.0 3.28e-01 74.6% 58.8%
1v58A01 3.10.450.70 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Disulphide bond isomerase, DsbC/G, N-terminal 0.63 44.0 4.41e-01 73.2% 71.8%
5fgoA00 3.10.450.700 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.63 45.0 4.80e-01 78.9% 85.5%
7obmA01 2.130.10.120 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Prolyl oligopeptidase, N-terminal domain 0.62 47.0 3.02e-01 80.3% 23.1%
1mwsA04 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.62 53.0 3.52e-01 100.0% 77.6%
1e8cA02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.62 47.0 3.32e-01 83.1% 84.9%
3k44B00 3.30.2450.30 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.62 51.0 4.10e-01 90.1% 84.3%
1ei5A01 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.62 52.0 3.35e-01 91.5% 84.1%
2fblB00 2.40.320.10 Mainly Beta › Beta Barrel › Hypothetical Protein Pfu-838710-001 › Hypothetical Protein Pfu-838710-001 0.62 53.0 4.19e-01 95.8% 89.9%
1y5oA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.62 45.0 3.89e-01 78.9% 77.4%
1yw5A01 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.61 33.0 3.50e-01 77.5% 55.6%
2ojhA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.61 48.0 3.22e-01 85.9% 27.8%
1k32A02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.61 53.0 3.42e-01 100.0% 34.6%
3ottB02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.61 48.0 3.05e-01 83.1% 21.8%
1imuA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.60 50.0 4.48e-01 100.0% 81.3%
4f80A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 40.0 3.67e-01 70.4% 81.7%
1d1jB00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.58 49.0 4.08e-01 97.2% 51.5%
3cm1A00 2.30.31.20 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Sporulation-specific cell division protein SsgB 0.58 48.0 4.04e-01 97.2% 66.9%
2rqlA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.58 50.0 4.58e-01 100.0% 90.5%
2gfgA00 2.40.320.10 Mainly Beta › Beta Barrel › Hypothetical Protein Pfu-838710-001 › Hypothetical Protein Pfu-838710-001 0.58 46.0 3.36e-01 85.9% 37.7%
3kksB00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.57 51.0 4.00e-01 100.0% 75.0%
4bf3A00 2.30.31.50 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Borrelia outer surface protein E/F 0.57 47.0 3.97e-01 95.8% 82.0%
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 0.57 49.0 3.96e-01 98.6% 67.1%
1oxxK02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 35.0 4.13e-01 70.4% 100.0%
4qd4A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.56 48.0 3.12e-01 98.6% 82.6%
4aghA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.56 42.0 4.10e-01 80.3% 72.5%
2bklA02 2.130.10.120 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Prolyl oligopeptidase, N-terminal domain 0.55 44.0 2.89e-01 88.7% 30.5%
2it1A03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.55 38.0 4.00e-01 80.3% 85.2%
1epaA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.55 43.0 3.44e-01 90.1% 61.3%
4lqzA00 2.40.128.570 Mainly Beta › Beta Barrel › Lipocalin › Protein of unknown function DUF4909 0.55 44.0 3.63e-01 90.1% 48.1%
4nwyA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.55 46.0 3.92e-01 100.0% 77.3%
3hrgA01 3.30.420.250 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Protein of unknown function DUF3822, N-terminal domain 0.54 37.0 2.98e-01 70.4% 35.7%
3lxqA01 3.30.1120.80 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.54 33.0 2.99e-01 77.5% 41.4%
1khiA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.54 39.0 3.85e-01 77.5% 81.3%
1q67A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 43.0 3.50e-01 88.7% 79.3%
1sjiA03 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.54 41.0 3.50e-01 84.5% 97.6%
2acaA00 2.40.320.10 Mainly Beta › Beta Barrel › Hypothetical Protein Pfu-838710-001 › Hypothetical Protein Pfu-838710-001 0.54 45.0 3.53e-01 100.0% 87.9%
3tdgA01 3.10.450.520 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 38.0 3.97e-01 80.3% 86.4%
1e2tA03 2.40.128.150 Mainly Beta › Beta Barrel › Lipocalin › Cysteine proteinases 0.53 42.0 3.68e-01 93.0% 69.2%
ECOD (54)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3471615 220.1.1.158 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_LRR1 0.75 55.0 4.66e-01 77.5% 72.2%
3397645 5.1.4.85 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › NOL11_N 0.74 60.0 3.83e-01 87.3% 26.6%
5065441 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.72 48.0 5.45e-01 70.4% 92.5%
3750640 220.1.1.38 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › UCH_N 0.72 50.0 4.33e-01 73.2% 71.8%
3931272 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.70 52.0 3.89e-01 78.9% 85.7%
3938605 3131.1.1.1 ↗ a+b two layers › FYR domain › FYR domain › FYR domain › FYRN,FYRC 0.70 58.0 4.57e-01 90.1% 55.2%
3813657 220.1.1.172 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_PRMT_N 0.69 53.0 4.60e-01 83.1% 77.3%
3457141 5.1.3.118 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.68 50.0 3.27e-01 78.9% 29.7%
3592221 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.68 52.0 4.35e-01 80.3% 66.9%
3672898 295.1.1.3 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › PurA 0.68 47.0 3.85e-01 74.6% 40.8%
3438374 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.68 52.0 3.29e-01 83.1% 27.0%
1945733 2484.1.1.9 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › rve 0.67 50.0 3.75e-01 77.5% 91.3%
3394711 4026.1.1.1 ↗ a+b three layers › a+b domain in Rap/Ran-GAP (Pfam 02145) › a+b domain in Rap/Ran-GAP (Pfam 02145) › a+b domain in Rap/Ran-GAP (Pfam 02145) › Rap-GAP_dimer 0.67 53.0 4.10e-01 85.9% 46.3%
3737835 241.15.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain 0.67 55.0 4.84e-01 87.3% 73.0%
3978756 3197.1.1.1 ↗ a+b two layers › N-terminal domain of effector protein PipB2 › N-terminal domain of effector protein PipB2 › N-terminal domain of effector protein PipB2 › PipB2_N 0.67 48.0 4.03e-01 76.1% 46.7%
4933213 375.1.1.31 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Elf1 0.67 51.0 5.18e-01 84.5% 84.3%
3644145 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.66 51.0 3.27e-01 83.1% 26.9%
4030625 219.1.1.97 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › CEPT76_peptidase 0.66 52.0 3.62e-01 85.9% 33.9%
2575628 2484.1.1.9 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › rve 0.66 48.0 3.73e-01 77.5% 91.5%
5013176 4100.1.1.0 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like 0.65 52.0 5.16e-01 91.5% 82.7%
4028738 5.1.4.11 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Clathrin_propel 0.65 53.0 3.37e-01 87.3% 23.9%
3364229 5.1.3.118 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.65 51.0 3.29e-01 83.1% 26.9%
3673032 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.65 46.0 4.72e-01 74.6% 90.0%
3743289 241.15.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain 0.65 55.0 4.82e-01 95.8% 62.9%
3536447 4026.1.1.1 ↗ a+b three layers › a+b domain in Rap/Ran-GAP (Pfam 02145) › a+b domain in Rap/Ran-GAP (Pfam 02145) › a+b domain in Rap/Ran-GAP (Pfam 02145) › Rap-GAP_dimer 0.65 54.0 4.29e-01 93.0% 49.0%
5053966 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.64 43.0 4.09e-01 70.4% 67.1%
3510695 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.63 49.0 4.80e-01 87.3% 80.0%
3894031 330.1.1.6 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Staufen_C 0.63 50.0 4.80e-01 88.7% 74.1%
3591636 719.1.1.0 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain 0.62 53.0 4.13e-01 93.0% 76.0%
3184125 223.3.1.0 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins 0.62 50.0 4.26e-01 88.7% 96.7%
3241305 295.1.1.3 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › PurA 0.62 51.0 4.06e-01 90.1% 85.0%
2462934 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.62 47.0 3.12e-01 81.7% 20.4%
3550970 719.1.1.5 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain › PF27933 0.61 51.0 4.42e-01 91.5% 79.1%
2754825 5.1.4.14 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Peptidase_S9_N 0.61 49.0 3.04e-01 88.7% 19.9%
3671668 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.61 51.0 3.77e-01 93.0% 85.4%
3510850 3459.1.1.0 ↗ beta sandwiches › Fas apoptotic inhibitory molecule › Fas apoptotic inhibitory molecule › Fas apoptotic inhibitory molecule 0.61 47.0 4.32e-01 91.5% 65.6%
3610987 719.1.1.0 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain 0.60 51.0 4.21e-01 93.0% 72.8%
3589823 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.60 43.0 4.54e-01 76.1% 84.6%
None — 0.60 47.0 3.09e-01 85.9% 23.7%
4031638 7089.1.1.1 ↗ a+b two layers › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › DUF1108 0.60 51.0 4.81e-01 100.0% 80.0%
4028178 316.1.1.36 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › MTPAP-like_central 0.60 36.0 3.05e-01 98.6% 34.4%
3466098 5.1.4.101 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › DUF1618 0.60 47.0 3.10e-01 87.3% 33.1%
3485288 10.1.1.17 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_2 0.59 53.0 3.82e-01 100.0% 42.5%
3273324 5.1.4.36 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › MMS1_N 0.58 50.0 3.08e-01 98.6% 28.9%
3248039 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.58 48.0 4.38e-01 95.8% 92.0%
3959341 223.3.1.1 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins › Beta-lactamase 0.58 49.0 4.05e-01 100.0% 100.0%
4229035 2484.1.1.12 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Acetate_kinase 0.57 44.0 3.22e-01 84.5% 33.5%
3529982 5.1.4.156 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Ge1_WD40 0.56 47.0 2.88e-01 94.4% 19.4%
3570700 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.55 39.0 3.37e-01 77.5% 46.1%
4388251 5.1.4.35 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Lactonase 0.55 45.0 2.95e-01 94.4% 24.9%
3188402 4099.1.1.31 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › PF26204 0.54 45.0 3.37e-01 95.8% 56.0%
1153941 243.4.1.2 ↗ a+b two layers › Cystatin-like › DsbC/DsbG N-terminal domain-like › DsbC/DsbG N-terminal domain-like › DsbG_N 0.53 38.0 3.57e-01 80.3% 59.4%
3941356 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.51 42.0 3.62e-01 94.4% 68.3%
4950038 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.50 41.0 4.03e-01 94.4% 88.7%