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NC_042013.1__YP_009612364.1__FDI40_gp699__00699

Bact-Vir

NC_042013.1__YP_009612364.1__FDI40_gp699__00699

Identity

Accession:
NC_042013 ↗
Kingdom:
phage

Quality

77.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Polybotosvirus› Agrobacterium_phage_Atu_ph07

TaxID: 2024264

Cluster

Singleton — not in a non-trivial cluster

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 medium residues 32-141
PDB
Domain cluster: rep: ALT_07252016_14_scaffold_0_prodigal-single.1__X__X__00132__D29-77_93-127
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF04717.19 best Phage_base_V 25.7 1.60e-05 32.7% 41.3%
D2 medium residues 147-287
PDB
Domain cluster: rep: IMGVR_UViG_3300026212_000090-3300026212-Ga0208409_10005035__D137-224_260-330
D3 medium residues 503-657
PDB
Domain cluster: rep: OR032571.1__WJZ48267.1__X__00077__D150-291
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1am7A00 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.78 67.0 6.76e-01 100.0% 90.3%
1qsaA03 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.59 52.0 5.04e-01 100.0% 83.2%
3ddhA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.58 29.0 3.87e-01 100.0% 90.1%
3bkhA02 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.56 52.0 4.95e-01 100.0% 86.3%
4gc5A02 1.10.8.100 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › rRNA adenine dimethylase, C-terminal domain 0.55 32.0 3.90e-01 92.3% 94.4%
2xqoA00 1.10.530.60 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.53 49.0 4.40e-01 100.0% 75.2%
3h4cA01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.52 28.0 3.42e-01 96.8% 82.3%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3965879 235.1.1.32 ↗ a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › SLT, PF27553 0.65 54.0 5.28e-01 100.0% 80.6%
D4 medium residues 677-763
PDB
Domain cluster: rep: hypothetical_protein_1__YP_009336648__Shahe_heteroptera_virus_4__1923420__D768-848
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2w5eA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.89 63.0 7.32e-01 83.9% 98.5%
4ic6C01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.82 77.0 7.03e-01 100.0% 90.0%
3otpA01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.80 74.0 5.46e-01 100.0% 41.9%
2z9iC01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.79 74.0 7.28e-01 100.0% 96.7%
4yo1A01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.78 73.0 7.26e-01 100.0% 95.5%
3k6yA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.78 72.0 7.11e-01 100.0% 92.4%
1l1jA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.77 73.0 6.48e-01 100.0% 99.2%
6oqrA01 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.77 51.0 5.07e-01 79.3% 65.6%
4rqyA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.76 72.0 6.28e-01 100.0% 74.0%
4ri0A01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.76 71.0 5.31e-01 100.0% 46.5%
2zu2A01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.76 65.0 6.22e-01 92.0% 89.8%
4rt0A00 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.75 62.0 5.74e-01 88.5% 84.4%
5y2dA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.75 69.0 6.07e-01 100.0% 70.8%
5hmaA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.73 68.0 6.88e-01 100.0% 98.9%
4p02A03 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.72 58.0 5.21e-01 87.4% 88.5%
2dpyA00 3.40.50.12240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.72 52.0 3.30e-01 78.2% 15.6%
4i86A00 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.72 58.0 5.56e-01 88.5% 89.2%
1z85A01 2.40.240.20 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Hypothetical PUA domain-like; domain 1 0.71 50.0 5.58e-01 74.7% 94.0%
1vhkA01 2.40.240.20 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Hypothetical PUA domain-like; domain 1 0.70 51.0 5.53e-01 75.9% 94.5%
6k2lA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.69 52.0 4.79e-01 79.3% 88.3%
4q63A00 2.40.10.430 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.69 56.0 5.47e-01 88.5% 89.2%
2xzlA02 2.40.30.230 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.68 51.0 5.34e-01 78.2% 86.1%
1ywuA00 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.68 55.0 4.91e-01 88.5% 77.6%
3zugB02 2.40.30.30 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like 0.67 49.0 4.21e-01 78.2% 61.3%
2w1kA00 2.40.260.10 Mainly Beta › Beta Barrel › Sortase; Chain: A; › Sortase 0.66 55.0 4.21e-01 92.0% 84.6%
1wxrA01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.66 55.0 3.97e-01 92.0% 79.4%
2w1jA00 2.40.260.10 Mainly Beta › Beta Barrel › Sortase; Chain: A; › Sortase 0.65 53.0 4.14e-01 89.7% 95.9%
5k9aA00 2.40.260.10 Mainly Beta › Beta Barrel › Sortase; Chain: A; › Sortase 0.65 54.0 4.12e-01 93.1% 90.2%
4d70A00 2.40.260.10 Mainly Beta › Beta Barrel › Sortase; Chain: A; › Sortase 0.65 52.0 4.37e-01 90.8% 93.8%
1t2pA00 2.40.260.10 Mainly Beta › Beta Barrel › Sortase; Chain: A; › Sortase 0.63 50.0 4.27e-01 86.2% 100.0%
5go5A00 2.40.260.10 Mainly Beta › Beta Barrel › Sortase; Chain: A; › Sortase 0.62 50.0 4.25e-01 89.7% 89.5%
3fn5B00 2.40.260.10 Mainly Beta › Beta Barrel › Sortase; Chain: A; › Sortase 0.62 50.0 4.14e-01 89.7% 82.2%
2kw8A00 2.40.260.10 Mainly Beta › Beta Barrel › Sortase; Chain: A; › Sortase 0.62 51.0 4.21e-01 90.8% 82.3%
4ew7A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.55 40.0 3.72e-01 94.3% 60.2%
3ijtB00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.53 41.0 3.43e-01 80.5% 67.1%
2jheA02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.52 38.0 3.62e-01 86.2% 63.0%
4esqA00 3.40.1000.70 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › PknH-like extracellular domain 0.52 41.0 3.21e-01 85.1% 68.6%
4gw9A02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.52 37.0 3.66e-01 83.9% 70.7%
1xn5A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.52 39.0 3.37e-01 80.5% 67.4%
5cwaA00 3.60.120.10 Alpha Beta › 4-Layer Sandwich › Anthranilate synthase › Anthranilate synthase 0.52 39.0 2.55e-01 85.1% 90.5%
2hx0A01 3.30.1330.80 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Hypothetical protein, similar to alpha- acetolactate decarboxylase; domain 2 0.51 38.0 3.37e-01 80.5% 62.9%
4hh2B03 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.51 39.0 3.78e-01 83.9% 74.0%
2bf1A00 2.170.40.20 Mainly Beta › Beta Complex › HIV Envelope Protein Gp120; Chain G › Human immunodeficiency virus 1, Gp160, envelope glycoprotein 0.50 42.0 2.99e-01 96.6% 54.9%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3281996 1.1.17.3 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin_2 0.84 74.0 5.36e-01 92.0% 41.0%
3284172 1.1.17.3 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin_2 0.84 74.0 5.39e-01 100.0% 39.0%
4028981 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.83 72.0 5.20e-01 92.0% 42.3%
3816110 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.82 72.0 5.13e-01 92.0% 44.0%
3375203 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.82 71.0 4.86e-01 92.0% 31.6%
3276425 1.1.17.3 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin_2 0.80 75.0 5.06e-01 100.0% 49.3%
3284072 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.79 73.0 5.17e-01 98.9% 40.6%
140973 1.1.17.3 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin_2 0.78 72.0 5.15e-01 100.0% 37.4%
3428387 1.1.17.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 0.77 72.0 5.56e-01 100.0% 56.7%
3464866 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.77 72.0 5.90e-01 100.0% 70.7%
3443107 1.1.17.3 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin_2 0.77 72.0 5.20e-01 100.0% 43.1%
3957702 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.77 73.0 6.14e-01 100.0% 65.2%
3464880 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.76 72.0 5.23e-01 100.0% 41.4%
4683578 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.76 72.0 5.17e-01 100.0% 50.7%
3421481 1.1.17.3 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin_2 0.76 72.0 4.92e-01 100.0% 36.7%
3843527 1.1.17.3 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin_2 0.76 72.0 5.15e-01 100.0% 43.6%
3930882 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.76 57.0 5.58e-01 79.3% 83.2%
3280955 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.76 72.0 5.14e-01 100.0% 39.1%
3393350 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.76 65.0 4.86e-01 92.0% 39.0%
4319764 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.75 54.0 4.98e-01 78.2% 59.1%
3967745 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.75 53.0 5.72e-01 78.2% 85.3%
3976283 1.1.13.32 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › DUF1480 0.74 56.0 5.82e-01 79.3% 98.7%
4973665 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.74 51.0 5.18e-01 71.3% 80.0%
3409584 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.74 66.0 4.64e-01 100.0% 42.9%
3288253 1.1.13.55 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › DUF4873 0.74 59.0 5.92e-01 87.4% 100.0%
4338510 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.73 69.0 5.00e-01 100.0% 40.9%
3963092 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.73 59.0 5.76e-01 87.4% 90.5%
3710311 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.72 54.0 4.74e-01 79.3% 77.7%
4072878 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.72 53.0 5.54e-01 80.5% 83.7%
3710460 1.1.7.45 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › eEFSec_4th 0.72 54.0 5.02e-01 79.3% 73.4%
4883586 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.71 51.0 5.17e-01 78.2% 75.6%
3956293 1.1.5.75 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › DUF4873 0.71 58.0 5.52e-01 87.4% 89.0%
3388311 1.1.7.100 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › PGBA_N 0.71 51.0 5.17e-01 74.7% 88.2%
4246480 1.1.5.25 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZ 0.70 56.0 5.49e-01 87.4% 91.6%
3698630 1.1.8.4 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › eIF2_C 0.69 49.0 4.61e-01 73.6% 69.5%
3810482 1.1.7.46 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › SMUBP-2_HCS1_1B 0.69 51.0 4.45e-01 79.3% 64.4%
1291989 1.1.5.42 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZ-like 0.69 56.0 5.47e-01 88.5% 89.2%
3322961 1.1.15.1 ↗ beta barrels › cradle loop barrel › RIFT-related › PK beta-barrel domain-like › PK 0.68 49.0 4.93e-01 74.7% 93.3%
3970225 1.1.13.68 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › PF27125 0.68 56.0 5.60e-01 88.5% 96.7%
2832652 290.1.1.1 ↗ beta barrels › Sortase › Sortase › Sortase › Sortase 0.68 56.0 4.36e-01 90.8% 95.8%
3943844 1.1.5.25 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZ 0.68 55.0 5.26e-01 88.5% 88.0%
3205875 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.67 59.0 5.01e-01 95.4% 85.2%
3587062 290.1.1.1 ↗ beta barrels › Sortase › Sortase › Sortase › Sortase 0.66 53.0 4.02e-01 89.7% 83.6%
3599398 1.1.8.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain 0.65 47.0 4.52e-01 75.9% 76.0%
1842342 290.1.1.1 ↗ beta barrels › Sortase › Sortase › Sortase › Sortase 0.65 54.0 4.12e-01 93.1% 90.2%
154269 290.1.1.1 ↗ beta barrels › Sortase › Sortase › Sortase › Sortase 0.65 52.0 4.06e-01 89.7% 88.7%
1566317 290.1.1.1 ↗ beta barrels › Sortase › Sortase › Sortase › Sortase 0.65 52.0 4.37e-01 90.8% 93.8%
3589952 290.1.1.1 ↗ beta barrels › Sortase › Sortase › Sortase › Sortase 0.63 52.0 4.08e-01 89.7% 84.3%
3321067 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.62 44.0 4.37e-01 73.6% 100.0%
5024134 290.1.1.1 ↗ beta barrels › Sortase › Sortase › Sortase › Sortase 0.62 50.0 4.29e-01 88.5% 87.1%
4995824 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.62 43.0 4.61e-01 73.6% 87.7%
428579 290.1.1.1 ↗ beta barrels › Sortase › Sortase › Sortase › Sortase 0.60 49.0 4.27e-01 89.7% 91.2%
4172447 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.60 43.0 4.55e-01 75.9% 93.3%
3276714 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.57 41.0 3.44e-01 83.9% 43.3%
3200887 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.56 40.0 3.73e-01 82.8% 59.1%
4965138 331.3.1.11 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Polyketide_cyc2 0.51 39.0 3.41e-01 81.6% 62.2%
D5 medium residues 764-865
PDB
Domain cluster: rep: IMGVR_UViG_3300005520_000196-3300005520-Ga0066864_100047611__D25-128
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF13365.13 best Trypsin_2 30.0 1.10e-06 84.3% 46.9%