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SR-VP_0-2_scaffold_141_4939684_prodigal-single.1__X__X__00335

Bact-Vir

SR-VP_0-2_scaffold_141_4939684_prodigal-single.1__X__X__00335

Identity

Kingdom:
phage

Quality

87.4 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

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 2-58
PDB
Domain cluster: representative
CATH (53)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2od4B01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.69 53.0 4.62e-01 86.0% 98.9%
4lizA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.67 50.0 3.83e-01 93.0% 34.1%
1hqz800 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.66 49.0 3.75e-01 91.2% 34.1%
1iujA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 52.0 4.40e-01 91.2% 98.0%
1t3yA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.66 46.0 3.59e-01 93.0% 32.8%
1x67A01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.65 50.0 3.80e-01 93.0% 35.3%
1yk9A00 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.65 56.0 4.00e-01 100.0% 59.8%
2h6uA00 2.60.40.180 Mainly Beta › Sandwich › Immunoglobulin-like › Transthyretin/hydroxyisourate hydrolase domain 0.65 51.0 4.15e-01 89.5% 44.7%
3au4A02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.64 50.0 4.36e-01 100.0% 55.3%
4d7pA00 2.60.40.730 Mainly Beta › Sandwich › Immunoglobulin-like › SOR catalytic domain 0.63 51.0 4.32e-01 89.5% 53.1%
1zldA00 2.60.40.1920 Mainly Beta › Sandwich › Immunoglobulin-like › Proteinaceous host-selective toxin ToxA 0.63 52.0 4.31e-01 91.2% 52.0%
4kg8A00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.63 51.0 3.96e-01 91.2% 41.1%
2re9A01 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.62 53.0 3.89e-01 96.5% 38.2%
5ynrA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.62 48.0 3.71e-01 93.0% 36.2%
5eliA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 51.0 4.19e-01 94.7% 64.3%
4msvA01 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.62 51.0 3.89e-01 93.0% 43.1%
1gtdA00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.61 46.0 4.22e-01 87.7% 100.0%
1wfuA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 46.0 3.97e-01 94.7% 51.6%
2pttB00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 48.0 4.02e-01 91.2% 61.1%
3e1uA00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.60 50.0 3.56e-01 96.5% 81.5%
2zw2A00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.59 47.0 4.23e-01 93.0% 97.6%
3pv7A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 47.0 3.82e-01 91.2% 56.8%
1cfyA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.59 44.0 3.48e-01 93.0% 36.1%
2iboA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 47.0 4.16e-01 93.0% 94.4%
2e26A02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.59 48.0 3.58e-01 93.0% 36.1%
1gwmA00 2.60.120.430 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding lectin 0.58 46.0 3.45e-01 91.2% 32.7%
1y6kR01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 47.0 3.97e-01 94.7% 52.0%
1q67A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 46.0 3.47e-01 87.7% 74.3%
1o5lA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.58 43.0 3.36e-01 89.5% 35.7%
1sq2N00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 46.0 3.79e-01 91.2% 53.6%
3shrA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.58 43.0 3.33e-01 89.5% 33.6%
2fauA01 2.60.40.640 Mainly Beta › Sandwich › Immunoglobulin-like › 0.58 48.0 3.65e-01 98.2% 49.0%
3shsA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 47.0 3.75e-01 94.7% 54.5%
2kvkA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.56 42.0 3.27e-01 86.0% 42.4%
1m0wA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.56 42.0 3.47e-01 93.0% 43.5%
1r9fA01 3.30.390.180 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › RNA silencing suppressor P19 0.56 44.0 3.72e-01 94.7% 68.8%
4x83A03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 43.0 3.65e-01 89.5% 49.0%
1axiB02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 43.0 3.68e-01 94.7% 50.5%
3hvnA01 3.90.840.10 Alpha Beta › Alpha-Beta Complex › HIV-1 Reverse Transcriptase; Chain A, domain 3 › Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain 0.55 42.0 3.21e-01 93.0% 36.6%
4a4aA01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.55 41.0 3.29e-01 87.7% 59.3%
3egrA00 3.10.20.520 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phenylacetic acid degradation B 0.55 42.0 4.19e-01 93.0% 88.9%
1wkyA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.54 44.0 3.46e-01 98.2% 58.3%
3l50A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.54 42.0 3.39e-01 94.7% 45.6%
1ddvA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 42.0 3.49e-01 87.7% 79.8%
2q0zX03 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.53 43.0 3.55e-01 96.5% 48.7%
2c60A01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.53 36.0 3.35e-01 89.5% 53.2%
2e4tA01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.53 36.0 3.03e-01 87.7% 36.4%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.53 40.0 3.57e-01 89.5% 56.5%
4iufA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.52 38.0 3.55e-01 82.5% 98.7%
2qsdA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.51 39.0 3.80e-01 89.5% 80.6%
2pbzA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.51 37.0 2.74e-01 80.7% 74.0%
2eefA01 2.60.40.2440 Mainly Beta › Sandwich › Immunoglobulin-like › Carbohydrate binding type-21 domain 0.51 39.0 3.19e-01 91.2% 47.2%
2y38A01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.50 37.0 2.58e-01 84.2% 62.2%
ECOD (54)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5064795 264.2.1.1 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain › Topoisom_bac 0.69 58.0 4.60e-01 94.7% 100.0%
3226640 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.67 56.0 4.78e-01 96.5% 60.6%
3406956 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.66 50.0 3.79e-01 93.0% 34.8%
3237938 10.4.1.1 ↗ beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain › CUB 0.65 47.0 3.74e-01 91.2% 37.4%
3540023 382.1.1.1 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › UPAR_LY6 0.65 54.0 4.74e-01 96.5% 96.7%
3898135 10.2.1.5 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › TGFb_propeptide 0.65 54.0 3.80e-01 94.7% 31.6%
4955430 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.65 54.0 4.26e-01 100.0% 68.7%
4928621 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.63 53.0 4.07e-01 100.0% 48.6%
4997424 304.4.1.1 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.62 52.0 4.09e-01 100.0% 68.1%
3171963 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.62 50.0 3.89e-01 94.7% 40.0%
3369575 2492.1.1.36 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › ODR4-like 0.62 52.0 3.72e-01 100.0% 72.1%
3734885 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.62 50.0 3.24e-01 94.7% 50.3%
4890006 11.1.1.99 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › V-set 0.62 51.0 4.01e-01 94.7% 58.3%
3484685 224.1.1.1 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Cofilin_ADF 0.62 47.0 3.66e-01 93.0% 36.9%
3895813 11.1.1.99 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › V-set 0.62 49.0 3.83e-01 91.2% 46.7%
3748734 11.1.1.99 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › V-set 0.61 50.0 3.88e-01 91.2% 51.5%
3533957 10.1.1.10 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › MAM 0.61 50.0 3.86e-01 98.2% 37.9%
3496598 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.60 36.0 3.14e-01 93.0% 36.7%
3928287 12.5.1.1 ↗ beta sandwiches › Glycosyl hydrolase domain-like › ZU5/Nup98-C/GAIN-B autoproteolytic domain-related › ZU5/Nup98-C/GAIN-B autoproteolytic domain-related › ZU5 0.60 47.0 3.44e-01 87.7% 38.7%
3986774 821.1.1.9 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › PF30054 0.59 46.0 4.01e-01 93.0% 60.0%
4962335 3115.5.1.1 ↗ a+b two layers › GP2-like › phenylacetate-CoA oxygenase subunit PaaB › phenylacetate-CoA oxygenase subunit PaaB › PaaB 0.59 47.0 4.58e-01 93.0% 86.2%
4236834 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.59 47.0 4.22e-01 93.0% 75.3%
3691249 2492.1.1.0 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.59 49.0 3.89e-01 100.0% 80.0%
3239399 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.59 47.0 3.47e-01 93.0% 32.5%
4025708 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.59 47.0 3.43e-01 91.2% 40.2%
4654177 1119.1.1.1 ↗ a+b complex topology › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › BioW 0.58 48.0 3.20e-01 94.7% 95.9%
3598717 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 47.0 3.77e-01 91.2% 45.8%
5070409 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.58 45.0 4.05e-01 93.0% 64.8%
3407995 11.1.1.536 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF1091 0.58 46.0 3.52e-01 94.7% 61.9%
3411043 11.1.1.536 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF1091 0.57 46.0 3.50e-01 94.7% 63.0%
5030770 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.57 45.0 3.91e-01 93.0% 60.0%
5051674 11.1.1.471 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Kre9_KNH 0.57 44.0 3.87e-01 93.0% 54.7%
3460834 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.57 44.0 3.45e-01 91.2% 37.8%
4399557 4020.1.1.1 ↗ a+b two layers › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › a+b domain in D-aminoacid aminotransferase-like PLP-dependent enzymes › Aminotran_4 0.57 39.0 3.16e-01 75.4% 84.0%
5049794 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.56 45.0 3.55e-01 100.0% 40.7%
3569682 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.56 45.0 3.67e-01 96.5% 46.1%
4014216 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.56 42.0 2.66e-01 96.5% 13.9%
3682507 210.1.3.0 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases 0.55 44.0 2.96e-01 93.0% 23.6%
3488019 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.55 44.0 3.42e-01 93.0% 38.9%
4040586 2492.1.1.4 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.55 43.0 3.02e-01 98.2% 48.3%
3924467 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.55 44.0 3.92e-01 96.5% 73.3%
3396597 11.1.1.536 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF1091 0.55 43.0 3.15e-01 89.5% 51.8%
4000498 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 44.0 3.43e-01 96.5% 62.1%
3928432 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.55 44.0 3.75e-01 93.0% 90.0%
3437928 11.2.1.37 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › DUF6598 0.54 42.0 3.36e-01 89.5% 48.0%
4980668 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.53 36.0 2.36e-01 73.7% 56.0%
3403560 11.1.1.536 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF1091 0.53 41.0 3.21e-01 94.7% 64.1%
3955667 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.52 43.0 3.65e-01 100.0% 93.3%
3553704 382.1.1.1 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › UPAR_LY6 0.52 43.0 3.75e-01 94.7% 68.9%
5082586 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 41.0 3.40e-01 94.7% 57.5%
3390883 11.1.1.536 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF1091 0.51 42.0 3.19e-01 94.7% 63.6%
3795522 11.1.1.9 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_N 0.51 42.0 3.36e-01 100.0% 62.2%
4927303 525.1.1.1 ↗ a+b two layers › Urease, gamma-subunit › Urease, gamma-subunit › Urease, gamma-subunit › Urease_gamma 0.50 41.0 3.41e-01 100.0% 86.7%
3488745 11.1.1.805 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_PDGFR_d4 0.50 39.0 3.35e-01 94.7% 61.8%