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NC_003324.1__YP_010115350.1__PBC5_gp33__00033

Bact-Vir

NC_003324.1__YP_010115350.1__PBC5_gp33__00033

Identity

Accession:
NC_003324 ↗
Kingdom:
phage

Quality

91.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Sinorhizobium_phage_PBC5

TaxID: 179237

Cluster

View cluster (11 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 2-74
PDB
Domain cluster: representative
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1mgtA01 3.30.160.70 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Methylated DNA-protein cysteine methyltransferase domain 0.72 49.0 4.60e-01 72.6% 58.0%
1d1jB00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.71 58.0 4.72e-01 89.0% 58.1%
2aehA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.67 46.0 4.00e-01 72.6% 46.8%
4gf3A00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.67 58.0 4.93e-01 100.0% 85.4%
6u5uG07 3.30.1120.100 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.66 46.0 3.87e-01 74.0% 47.7%
2uvaG07 3.30.1120.100 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.64 45.0 3.72e-01 74.0% 47.8%
2k4vA00 3.30.160.370 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Domain of unknown function DUF5064 0.64 56.0 4.71e-01 98.6% 64.0%
1ospO02 3.90.930.1 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › 0.64 50.0 4.05e-01 86.3% 43.2%
2lg1A02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.63 41.0 3.52e-01 71.2% 42.6%
7oufB01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.62 43.0 3.39e-01 71.2% 37.6%
6u5vB07 3.30.1120.100 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.62 43.0 3.67e-01 74.0% 46.5%
4paaA03 3.30.1360.120 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Probable tRNA modification gtpase trme; domain 1 0.62 50.0 3.88e-01 94.5% 75.7%
2dixA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.61 51.0 5.01e-01 100.0% 87.2%
2hjjA00 3.30.160.130 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › ykff protein like domains 0.61 39.0 4.14e-01 91.8% 72.7%
1imuA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.61 53.0 4.72e-01 98.6% 81.3%
4htgA03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.61 49.0 4.83e-01 90.4% 100.0%
3d2mA02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.60 45.0 3.59e-01 79.5% 62.0%
3dpuB03 3.30.310.200 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › 0.60 42.0 3.67e-01 72.6% 68.5%
3a32A02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.59 51.0 4.23e-01 100.0% 83.0%
3bp6B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 43.0 4.05e-01 76.7% 90.9%
4cy8A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.59 47.0 3.28e-01 89.0% 35.2%
2xrnA02 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.59 47.0 3.62e-01 90.4% 40.1%
1t6aA02 3.30.310.120 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Rbstp2229 like protein 0.58 42.0 4.15e-01 83.6% 70.5%
5aykA07 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.58 48.0 4.17e-01 91.8% 99.1%
2ky6A00 2.40.290.30 Mainly Beta › Beta Barrel › Ku70; Chain: A; Domain 2 › Mediator complex subunit 25, ACID domain 0.58 40.0 3.17e-01 74.0% 80.1%
2giaA00 2.30.31.40 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › 0.58 44.0 3.50e-01 82.2% 46.8%
3nroA00 3.40.630.190 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › LCP protein 0.57 41.0 2.89e-01 74.0% 99.1%
1txdA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 39.0 3.34e-01 100.0% 43.0%
4fb5A02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.57 41.0 2.90e-01 78.1% 63.6%
7t8tA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 39.0 3.27e-01 72.6% 50.4%
2q04F00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.56 42.0 3.10e-01 82.2% 70.9%
1z87A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 37.0 3.41e-01 72.6% 50.0%
2l33A00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.55 43.0 4.05e-01 100.0% 70.3%
4yg6B00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.55 44.0 3.50e-01 90.4% 73.6%
4chjA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 46.0 3.89e-01 93.2% 99.2%
5hy7B02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.54 46.0 3.06e-01 95.9% 56.1%
1y96D00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.54 39.0 3.74e-01 75.3% 71.1%
3zl8A02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.54 48.0 3.40e-01 100.0% 35.0%
2dmyA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.54 45.0 4.17e-01 95.9% 78.4%
3cm1A00 2.30.31.20 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Sporulation-specific cell division protein SsgB 0.54 41.0 3.42e-01 83.6% 69.1%
2l5pA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.53 37.0 2.85e-01 74.0% 89.7%
1m4iB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.52 41.0 3.17e-01 87.7% 68.2%
1gpqB00 3.40.1420.10 Alpha Beta › 3-Layer(aba) Sandwich › Inhibitor of vertebrate lysozyme, Ivy › Inhibitor of vertebrate lysozyme 0.52 41.0 3.42e-01 86.3% 74.2%
7mwzD01 3.40.50.12100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Stimulator of interferon genes protein 0.52 36.0 2.69e-01 74.0% 55.6%
4fpwB00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.51 44.0 3.49e-01 98.6% 86.3%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4952518 881.1.1.0 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.71 48.0 4.16e-01 72.6% 46.4%
2512615 330.10.1.0 ↗ a+b two layers › dsRBD-like › Heterocyclase TruD C-terminal domain › Heterocyclase TruD C-terminal domain 0.70 55.0 5.69e-01 84.9% 100.0%
3846404 220.1.1.61 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C_FAK1 0.68 47.0 3.67e-01 72.6% 34.7%
3262788 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.66 44.0 3.89e-01 72.6% 47.6%
3987799 4221.1.1.1 ↗ a+b two layers › YkuJ-like › YkuJ-like › YkuJ-like › DUF1797 0.66 54.0 5.54e-01 90.4% 98.6%
3390004 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.65 44.0 3.91e-01 71.2% 47.3%
3479408 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 42.0 3.21e-01 72.6% 27.2%
4311698 241.2.1.6 ↗ a+b two layers › Type III secretory system chaperone-like › Frataxin-like › Frataxin-like › PF26204 0.64 55.0 4.92e-01 100.0% 73.6%
3291683 4221.1.1.0 ↗ a+b two layers › YkuJ-like › YkuJ-like › YkuJ-like 0.63 54.0 5.02e-01 94.5% 84.4%
3699899 214.1.1.6 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2_2 0.63 54.0 4.68e-01 100.0% 62.5%
3516087 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.63 41.0 4.15e-01 71.2% 65.3%
5049481 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.63 50.0 4.23e-01 87.7% 54.5%
3699374 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.63 43.0 3.58e-01 72.6% 43.0%
4025256 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.63 48.0 4.69e-01 83.6% 95.0%
3582821 220.1.1.5 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PID 0.63 42.0 3.87e-01 71.2% 55.6%
3995314 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.62 43.0 3.47e-01 71.2% 43.7%
3560565 220.1.1.47 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_16 0.62 42.0 2.98e-01 72.6% 24.3%
3901160 220.1.1.47 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_16 0.62 41.0 3.03e-01 72.6% 27.0%
3851566 4099.1.1.20 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Med14_RM6 0.61 52.0 4.38e-01 100.0% 65.2%
222972 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 0.61 50.0 4.75e-01 91.8% 85.4%
3552038 4099.1.1.20 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Med14_RM6 0.61 52.0 3.91e-01 100.0% 44.0%
5078475 881.1.1.0 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.61 46.0 3.72e-01 82.2% 44.8%
3290300 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.60 41.0 3.93e-01 71.2% 62.4%
4040973 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 0.60 49.0 5.03e-01 97.3% 97.1%
4944561 512.1.1.0 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) 0.60 48.0 4.42e-01 91.8% 88.0%
4285345 4099.1.1.20 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Med14_RM6 0.60 50.0 4.38e-01 100.0% 70.8%
None — 0.59 45.0 2.85e-01 83.6% 78.0%
3911301 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.59 45.0 4.35e-01 98.6% 72.9%
4933830 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.59 47.0 3.56e-01 93.2% 42.9%
5050831 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.58 43.0 3.43e-01 79.5% 98.7%
5073695 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.58 47.0 4.36e-01 93.2% 89.0%
4941649 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.58 38.0 3.47e-01 71.2% 50.5%
3246050 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.58 47.0 4.41e-01 98.6% 72.2%
5794 295.1.1.7 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › MRP 0.58 44.0 3.50e-01 82.2% 46.8%
3742330 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.57 37.0 3.23e-01 72.6% 42.6%
3797649 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.57 50.0 4.36e-01 98.6% 71.8%
3940247 4099.1.1.1 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › MAD 0.56 48.0 4.18e-01 100.0% 61.7%
4138663 4099.1.1.3 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Spc24 0.56 43.0 4.54e-01 93.2% 93.8%
3787121 241.15.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain 0.56 46.0 3.93e-01 94.5% 83.2%
3565211 3223.1.1.1 ↗ beta sandwiches › Amiloride-sensitive cation channel 2 › Amiloride-sensitive cation channel 2 › Amiloride-sensitive cation channel 2 › ASC 0.55 48.0 2.94e-01 100.0% 18.0%
3280079 331.4.1.0 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 0.55 42.0 3.50e-01 82.2% 60.0%
5075588 512.1.1.0 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) 0.55 46.0 4.39e-01 98.6% 94.4%
3762104 331.18.1.11 ↗ a+b two layers › TBP-like › C-terminal TBP-like domain of Roc › C-terminal TBP-like domain of Roc › PF28312 0.55 38.0 3.47e-01 89.0% 53.0%
3743938 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.54 36.0 3.06e-01 72.6% 38.5%
5073634 300.1.1.0 ↗ a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease 0.54 37.0 3.16e-01 71.2% 76.0%
3177460 3270.1.1.0 ↗ a+b two layers › a+b domain in heme oxygenase › a+b domain in heme oxygenase › a+b domain in heme oxygenase 0.54 43.0 3.93e-01 87.7% 97.0%
3191989 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.54 36.0 2.93e-01 72.6% 34.5%
3342566 5.1.3.118 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.54 44.0 3.01e-01 95.9% 60.3%
3788003 220.1.1.112 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_10 0.53 37.0 2.99e-01 100.0% 36.6%
4001056 220.1.1.5 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PID 0.51 37.0 3.36e-01 76.7% 66.0%
3363566 5.1.10.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 12-bladed 0.51 36.0 3.44e-01 75.3% 98.9%
3233965 59.1.1.9 ↗ beta complex topology › triple barrel › triple barrel › Rap30/74 interaction domains-like › EAF 0.50 36.0 3.08e-01 75.3% 70.0%
4000395 2007.1.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like 0.50 42.0 3.15e-01 98.6% 50.5%
4195924 5.1.4.277 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40, Beta-prop_EIPR1 0.50 43.0 2.77e-01 100.0% 96.8%
3929330 220.1.1.11 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Rpn13_ADRM1_Pru 0.50 39.0 3.26e-01 84.9% 74.6%
D2 high residues 87-195
PDB
Domain cluster: rep: MT889387.1__QOP66146.1__SEA_DANIELLEIGNACE_5__00005__D28-163