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NC_003324.1__YP_010115368.1__PBC5_gp51__00051

Bact-Vir

NC_003324.1__YP_010115368.1__PBC5_gp51__00051

Identity

Accession:
NC_003324 ↗
Kingdom:
phage

Quality

75.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Sinorhizobium_phage_PBC5

TaxID: 179237

Cluster

View cluster (12 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 3-84
PDB
Domain cluster: rep: OR820515.1__WRQ05482.1__X__00033__D1-81
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4b6dB00 3.30.60.20 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.81 48.0 5.76e-01 81.7% 86.0%
1uw0A01 3.30.1740.10 Alpha Beta › 2-Layer Sandwich › first zn-finger domain of poly(adp-ribose) polymerase-1 › Zinc finger, PARP-type 0.79 56.0 5.35e-01 74.4% 67.7%
1v9xA00 3.30.1740.10 Alpha Beta › 2-Layer Sandwich › first zn-finger domain of poly(adp-ribose) polymerase-1 › Zinc finger, PARP-type 0.75 59.0 5.21e-01 82.9% 88.6%
3g1jA00 2.30.30.350 Mainly Beta › Roll › SH3 type barrels. › mobile metagenome of vibrio cholerae. Integron cassette protein vch_cass4. 0.71 42.0 4.13e-01 78.0% 54.4%
4m7xA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.71 39.0 3.79e-01 78.0% 47.3%
5fgoA00 3.10.450.700 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.69 42.0 4.70e-01 75.6% 80.6%
4p2iA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.60 47.0 4.17e-01 84.1% 97.4%
2ettA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.60 50.0 4.29e-01 91.5% 82.0%
2cqaA01 2.40.50.360 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RuvBL1 DNA/RNA binding domain 0.59 42.0 4.37e-01 90.2% 82.4%
1xteA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.59 46.0 4.10e-01 84.1% 93.1%
4oxwA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.58 47.0 4.32e-01 87.8% 100.0%
3f6gA01 3.30.160.740 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 37.0 4.28e-01 85.4% 93.1%
2kigA00 2.30.29.110 Mainly Beta › Roll › PH-domain like › 0.57 40.0 3.21e-01 78.0% 37.9%
2v14A00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.56 47.0 3.99e-01 91.5% 93.3%
4ntqB00 3.30.2450.20 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.56 49.0 4.12e-01 98.8% 69.0%
2it9A00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.55 40.0 3.48e-01 75.6% 68.3%
3jtzA00 3.30.160.390 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Integrase, DNA-binding domain 0.55 35.0 3.57e-01 78.0% 67.5%
3pieC05 2.170.260.40 Mainly Beta › Beta Complex › paz domain › 0.54 39.0 3.16e-01 78.0% 62.3%
3p0cA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.54 45.0 4.06e-01 91.5% 94.6%
2dixA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.52 32.0 3.32e-01 84.1% 64.1%
3ulbA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 33.0 3.31e-01 78.0% 61.4%
1vpbA01 3.30.2290.10 Alpha Beta › 2-Layer Sandwich › PmbA/TldD fold › PmbA/TldD superfamily 0.52 39.0 2.84e-01 84.1% 28.9%
2l33A00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.52 33.0 3.21e-01 85.4% 57.1%
4pmwA04 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.52 36.0 3.47e-01 79.3% 64.8%
2nvnA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.51 45.0 3.93e-01 95.1% 75.0%
4hasA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.51 42.0 3.92e-01 91.5% 100.0%
4p78C00 3.30.920.30 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Hypothetical protein. 0.51 31.0 3.37e-01 81.7% 74.2%
8aa9A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 42.0 3.82e-01 91.5% 69.3%
2dmyA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.51 37.0 3.53e-01 96.3% 64.9%
1d5aA01 3.30.342.10 Alpha Beta › 2-Layer Sandwich › DNA Polymerase; Chain A, domain 1 › DNA Polymerase, chain B, domain 1 0.51 37.0 3.05e-01 78.0% 86.1%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3923898 377.1.2.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › PARP-type zinc finger 0.83 51.0 5.17e-01 76.8% 63.7%
3889754 376.1.2.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_1 0.79 49.0 5.71e-01 80.5% 86.7%
8200 377.1.2.1 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › PARP-type zinc finger › zf-PARP 0.78 57.0 5.05e-01 76.8% 57.3%
3513068 376.1.2.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_1 0.76 48.0 5.38e-01 80.5% 81.5%
4654276 377.1.2.1 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › PARP-type zinc finger › zf-PARP 0.74 51.0 4.66e-01 70.7% 81.9%
4963795 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.74 53.0 5.50e-01 74.4% 86.7%
5034811 376.1.2.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain 0.74 52.0 6.04e-01 75.6% 100.0%
3394414 376.1.2.17 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › LIM+PET 0.70 53.0 4.30e-01 79.3% 52.0%
3985617 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.70 41.0 4.35e-01 73.2% 67.1%
3990002 802.1.1.0 ↗ a+b two layers › Hypothetical protein TM0160 › Hypothetical protein TM0160 › Hypothetical protein TM0160 0.69 48.0 4.77e-01 72.0% 69.4%
3164102 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.64 34.0 4.35e-01 81.7% 93.3%
3217638 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.63 37.0 3.84e-01 78.0% 61.3%
3990333 376.1.2.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_1 0.63 47.0 4.92e-01 86.6% 85.3%
5075212 802.1.1.1 ↗ a+b two layers › Hypothetical protein TM0160 › Hypothetical protein TM0160 › Hypothetical protein TM0160 › BFN_dom 0.61 36.0 3.52e-01 76.8% 51.1%
4973193 802.1.1.1 ↗ a+b two layers › Hypothetical protein TM0160 › Hypothetical protein TM0160 › Hypothetical protein TM0160 › BFN_dom 0.61 36.0 3.59e-01 76.8% 54.1%
4492006 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.61 37.0 2.57e-01 78.0% 18.5%
3518991 284.1.3.4 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › CCTL2_WNK 0.60 36.0 3.82e-01 84.1% 65.3%
4546371 220.1.1.219 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › CheF-arch 0.60 40.0 3.61e-01 78.0% 46.7%
158729 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.60 50.0 4.37e-01 91.5% 86.8%
3408101 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.59 46.0 3.96e-01 85.4% 85.2%
4390303 5.1.3.238 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › PF29568 0.59 39.0 2.31e-01 87.8% 9.2%
5039400 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.58 37.0 2.56e-01 82.9% 17.7%
3789520 223.2.1.32 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Fuz_longin_2 0.58 38.0 3.32e-01 82.9% 40.7%
3797447 896.1.1.0 ↗ a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related 0.58 43.0 4.10e-01 79.3% 67.4%
2665702 3146.1.1.3 ↗ a+b complex topology › gH main domain › gH main domain › gH main domain › Phage_glycop_gL 0.58 34.0 3.10e-01 72.0% 40.9%
1489902 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.58 47.0 4.32e-01 87.8% 100.0%
147620 4232.1.1.1 ↗ few secondary structure elements › Ribosomal protein bL28-related › Ribosomal protein bL28-related › Ribosomal protein L28 › Ribosomal_L28 0.58 40.0 3.81e-01 72.0% 100.0%
4486857 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.58 49.0 4.17e-01 93.9% 83.7%
4023312 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.57 45.0 3.94e-01 85.4% 100.0%
3738197 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.57 47.0 3.70e-01 87.8% 83.0%
3364063 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 0.57 49.0 4.06e-01 92.7% 63.6%
3864474 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.57 45.0 3.61e-01 86.6% 69.7%
3783181 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.56 44.0 4.05e-01 85.4% 98.2%
3709649 277.1.1.0 ↗ a+b two layers › PX domain › PX domain › PX domain 0.56 47.0 4.10e-01 93.9% 90.8%
3619859 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.56 44.0 3.87e-01 84.1% 91.7%
3927894 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.56 44.0 3.79e-01 86.6% 89.6%
402817 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.56 45.0 4.18e-01 89.0% 100.0%
1233328 4.1.1.116 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_14 0.56 38.0 3.26e-01 70.7% 71.5%
3893274 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.56 44.0 3.60e-01 85.4% 96.0%
4468497 7.1.1.0 ↗ beta barrels › PDZ domain › PDZ domain › PDZ domain 0.55 41.0 3.76e-01 78.0% 77.1%
5072273 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.55 39.0 3.47e-01 78.0% 50.8%
4069753 295.1.1.2 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › SsgA 0.55 39.0 3.26e-01 73.2% 47.4%
3262159 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.55 47.0 4.05e-01 95.1% 91.5%
3591633 1021.1.1.0 ↗ a+b two layers › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases 0.55 47.0 4.27e-01 93.9% 99.1%
3838288 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.55 44.0 3.98e-01 89.0% 90.4%
3251342 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.54 45.0 3.96e-01 90.2% 88.3%
3863194 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.54 46.0 3.96e-01 95.1% 92.3%
4017879 3385.1.1.0 ↗ beta barrels › Allergen Alt a 1 › Allergen Alt a 1 › Allergen Alt a 1 0.53 40.0 3.61e-01 82.9% 82.1%
4275948 220.1.1.52 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SNX17_FERM_C 0.53 37.0 3.32e-01 75.6% 50.8%
4951650 4121.1.1.1 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.52 44.0 3.20e-01 98.8% 80.8%
5058143 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.52 43.0 3.96e-01 92.7% 71.8%
3680043 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.52 38.0 3.41e-01 79.3% 76.7%
4946616 512.1.1.2 ↗ 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_2nd 0.51 38.0 3.75e-01 84.1% 73.3%
5072529 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 0.51 37.0 3.67e-01 82.9% 72.2%
4853066 2.1.1.22 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › HIN 0.51 40.0 3.63e-01 91.5% 62.8%
4975879 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.50 42.0 3.87e-01 92.7% 70.9%
4939419 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 0.50 39.0 3.85e-01 82.9% 81.2%
5074491 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.50 40.0 3.59e-01 91.5% 63.2%