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NC_048740.1__YP_009842188.1__HWB96_gp13__00013

Bact-Vir

NC_048740.1__YP_009842188.1__HWB96_gp13__00013

Identity

Accession:
NC_048740 ↗
Kingdom:
phage

Quality

80.4 mean pLDDT

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 309-427_623-641
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3u12A00 2.30.29.180 Mainly Beta › Roll › PH-domain like › Ubiquitin carboxyl-terminal hydrolase 26/29/37, pleckstrin homology-like domain 0.61 27.0 3.13e-01 81.2% 54.8%
6vtmB00 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.59 32.0 3.76e-01 98.6% 74.0%
3bpnC03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 31.0 3.53e-01 98.6% 67.3%
6gszA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 32.0 3.59e-01 99.3% 74.5%
3vmnA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.54 29.0 2.97e-01 97.8% 50.7%
4bf3A00 2.30.31.50 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Borrelia outer surface protein E/F 0.54 30.0 3.04e-01 92.8% 51.9%
1g0dA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 32.0 3.21e-01 98.6% 58.4%
4eq3A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 32.0 3.58e-01 98.6% 77.8%
2e8yA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 26.0 3.02e-01 100.0% 65.3%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1842912 3367.1.1.1 beta complex topology › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › phi29_gp9_C 0.84 61.0 4.51e-01 88.4% 31.6%
2989726 3367.1.1.1 beta complex topology › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › phi29_gp9_C 0.79 74.0 4.94e-01 100.0% 47.5%
3597350 73.1.1.0 beta sandwiches › SMAD/FHA domain › SMAD/FHA domain › SMAD/FHA domain 0.66 28.0 3.56e-01 94.2% 65.1%
3401428 11.2.1.1 beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2 0.64 33.0 3.29e-01 98.6% 47.1%
3273362 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.63 32.0 3.84e-01 100.0% 75.3%
5061361 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.61 32.0 4.04e-01 98.6% 86.3%
4561898 11.1.1.535 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Peptidase_M26_N 0.59 32.0 3.16e-01 100.0% 47.9%
3849839 4210.1.1.0 a+b two layers › WGR domain › WGR domain › WGR domain 0.58 36.0 4.15e-01 100.0% 86.0%
3273763 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 28.0 3.30e-01 97.8% 65.3%
3999575 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 0.57 30.0 3.09e-01 99.3% 51.1%
2441964 11.32.1.1 beta sandwiches › Immunoglobulin-like beta-sandwich › Calcium-dependent cell adhesion molecule-1 C-terminal domain › Calcium-dependent cell adhesion molecule-1 C-terminal domain › Membrane_bind 0.54 28.0 2.97e-01 100.0% 53.4%
D2 medium residues 23-146
PDB
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4gj4D00 3.30.450.260 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Haem NO binding associated domain 0.64 44.0 4.54e-01 100.0% 74.4%
2rdeA02 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.62 43.0 4.54e-01 97.6% 80.2%
8hbfB02 3.30.450.260 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Haem NO binding associated domain 0.58 39.0 3.80e-01 99.2% 63.2%
4hh3A01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 33.0 3.49e-01 92.7% 63.2%
4ci2B02 2.30.130.40 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › LON domain-like 0.56 46.0 4.61e-01 87.1% 93.6%
2qckA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.56 50.0 4.67e-01 95.2% 80.1%
3licA02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 31.0 3.57e-01 94.4% 74.7%
2cuiA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 36.0 3.76e-01 82.3% 70.5%
5choF00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 49.0 4.46e-01 95.2% 78.8%
2d37A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 49.0 4.57e-01 96.8% 79.4%
1i0rA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 49.0 4.49e-01 96.8% 80.1%
2p3hA00 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.54 33.0 3.71e-01 96.0% 77.6%
1rz1A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 48.0 4.50e-01 95.2% 78.9%
8ct0B01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 48.0 4.34e-01 95.2% 75.3%
1zboA01 2.30.130.40 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › LON domain-like 0.54 40.0 4.17e-01 76.6% 100.0%
3bnkA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 49.0 4.27e-01 98.4% 72.6%
4xhyA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 47.0 4.33e-01 95.2% 75.2%
2aneH00 2.30.130.40 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › LON domain-like 0.53 39.0 4.21e-01 76.6% 100.0%
2byoA00 2.50.20.20 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › 0.53 32.0 2.80e-01 100.0% 38.8%
4z85A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 49.0 4.18e-01 100.0% 68.5%
3fgeA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 47.0 4.24e-01 97.6% 77.9%
7cayA01 2.30.130.40 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › LON domain-like 0.53 38.0 4.25e-01 75.8% 100.0%
1uscA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 47.0 4.18e-01 97.6% 71.3%
3zhnA00 2.60.40.4150 Mainly Beta › Sandwich › Immunoglobulin-like › Type VI secretion system, lipoprotein SciN 0.52 44.0 4.33e-01 91.1% 87.8%
3w5mA04 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.52 34.0 3.48e-01 82.3% 67.5%
3rx9A00 2.60.40.4150 Mainly Beta › Sandwich › Immunoglobulin-like › Type VI secretion system, lipoprotein SciN 0.52 44.0 4.41e-01 96.0% 88.5%
2r6hA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.51 36.0 3.44e-01 71.8% 84.6%
6x3aA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 35.0 3.76e-01 79.8% 82.7%
3nfwA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.51 45.0 3.99e-01 97.6% 70.4%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3501754 1.1.13.19 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Caud_tail_N 0.90 74.0 8.11e-01 93.5% 100.0%
2989727 1.1.13.19 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Caud_tail_N 0.82 67.0 7.22e-01 89.5% 99.1%
3970015 1.1.5.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.70 46.0 5.24e-01 93.5% 89.4%
4796695 223.1.1.11 a+b three layers › Profilin-like › sensor domains › sensor domains › HNOBA 0.63 39.0 4.22e-01 100.0% 72.2%
4932825 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.63 42.0 4.97e-01 87.9% 100.0%
3517676 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.61 43.0 4.38e-01 71.8% 84.2%
3498265 223.1.1.11 a+b three layers › Profilin-like › sensor domains › sensor domains › HNOBA 0.60 44.0 4.21e-01 99.2% 66.4%
3267962 11.1.1.1308 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF28710 0.59 38.0 4.32e-01 79.0% 85.3%
3256764 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.57 41.0 4.08e-01 74.2% 78.5%
4458331 1.1.9.5 beta barrels › cradle loop barrel › RIFT-related › PUA domain › LON_substr_bdg 0.57 42.0 3.41e-01 77.4% 48.5%
3956124 1.1.9.5 beta barrels › cradle loop barrel › RIFT-related › PUA domain › LON_substr_bdg 0.57 42.0 3.53e-01 77.4% 89.0%
4995815 1.1.13.0 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.57 50.0 4.99e-01 98.4% 92.8%
4313132 1.1.9.5 beta barrels › cradle loop barrel › RIFT-related › PUA domain › LON_substr_bdg 0.57 47.0 3.70e-01 88.7% 50.2%
4358643 1.1.9.5 beta barrels › cradle loop barrel › RIFT-related › PUA domain › LON_substr_bdg 0.56 43.0 3.53e-01 80.6% 52.3%
3395164 11.1.1.447 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › NDNF_C 0.56 42.0 4.28e-01 80.6% 79.2%
4637249 1.1.9.5 beta barrels › cradle loop barrel › RIFT-related › PUA domain › LON_substr_bdg 0.55 44.0 3.62e-01 83.9% 53.6%
3688711 1.1.7.81 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › SEN1_barrel 0.55 39.0 4.17e-01 87.1% 83.6%
4026305 1.1.5.36 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Pyrid_ox_like 0.54 50.0 4.30e-01 100.0% 92.1%
4531216 1.1.9.5 beta barrels › cradle loop barrel › RIFT-related › PUA domain › LON_substr_bdg 0.54 43.0 3.45e-01 83.9% 77.1%
3971942 1.1.9.0 beta barrels › cradle loop barrel › RIFT-related › PUA domain 0.54 40.0 3.43e-01 77.4% 56.9%
4933308 1.1.5.17 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › DUF447_N 0.54 48.0 4.49e-01 96.8% 78.7%
3469965 223.1.1.0 a+b three layers › Profilin-like › sensor domains › sensor domains 0.54 39.0 3.81e-01 100.0% 67.1%
4655335 1.1.9.5 beta barrels › cradle loop barrel › RIFT-related › PUA domain › LON_substr_bdg 0.54 42.0 3.45e-01 83.1% 55.1%
5075917 1.1.5.17 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › DUF447_N 0.53 48.0 4.54e-01 98.4% 85.3%
5012011 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.53 42.0 4.19e-01 98.4% 83.2%
4983682 1.1.5.17 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › DUF447_N 0.53 48.0 4.64e-01 98.4% 91.4%
3980899 1.1.13.0 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.53 43.0 4.55e-01 87.9% 98.2%
3347068 1.1.9.5 beta barrels › cradle loop barrel › RIFT-related › PUA domain › LON_substr_bdg 0.53 43.0 3.56e-01 91.9% 51.0%
3509057 11.1.1.310 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PDE12-like_N 0.52 38.0 3.75e-01 83.9% 71.5%
1031099 11.1.4.18 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › T6SS-SciN 0.52 44.0 4.33e-01 91.1% 87.8%
3969279 11.1.4.18 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › T6SS-SciN 0.52 43.0 4.32e-01 96.0% 86.2%
5036926 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 35.0 3.36e-01 79.8% 61.4%
3948784 11.1.4.18 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › T6SS-SciN 0.51 45.0 4.31e-01 96.0% 85.7%
3510405 1.1.17.1 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.51 42.0 3.57e-01 89.5% 84.4%
3978682 11.1.4.18 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › T6SS-SciN 0.51 42.0 4.08e-01 90.3% 85.7%
4048581 1.1.9.5 beta barrels › cradle loop barrel › RIFT-related › PUA domain › LON_substr_bdg 0.50 38.0 3.09e-01 81.5% 75.1%
D3 medium residues 147-182_642-733
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF20934.4 best phi29_gp9_C 31.4 2.10e-07 78.1% 24.1%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2989726 3367.1.1.1 beta complex topology › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › phi29_gp9_C 0.79 72.0 4.76e-01 96.9% 97.7%
1117749 3367.1.1.1 beta complex topology › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › phi29_gp9_C 0.78 70.0 4.89e-01 96.1% 97.4%
D4 medium residues 183-307_428-463
PDB
Domain cluster: representative
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1118267 3367.1.1.1 beta complex topology › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › phi29_gp9_C 0.83 66.0 5.39e-01 82.6% 82.5%
1117749 3367.1.1.1 beta complex topology › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › phi29_gp9_C 0.82 67.0 4.85e-01 83.2% 59.4%
2989726 3367.1.1.1 beta complex topology › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › C-terminal domain in bacteriophage C1 tail knob protein, gp12 › phi29_gp9_C 0.78 62.0 4.28e-01 82.0% 49.8%
3642679 220.1.1.78 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_2 0.67 23.0 2.81e-01 83.2% 43.5%