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RifSed_csp1_19ft_3_scaffold_4_curated_prodigal-single.1__X__X__00571

Bact-Vir

RifSed_csp1_19ft_3_scaffold_4_curated_prodigal-single.1__X__X__00571

Identity

Kingdom:
phage

Quality

85.6 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

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

D1 high residues 7-58
PDB
Domain cluster: representative
CATH (42)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3fedA02 3.50.30.30 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › 0.74 59.0 3.91e-01 90.4% 97.7%
4tweA02 3.50.30.30 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › 0.72 57.0 3.78e-01 90.4% 97.8%
2x5pA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.69 49.0 3.91e-01 92.3% 37.5%
6fwvA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.69 49.0 4.12e-01 92.3% 44.4%
7sqxA02 3.30.70.2150 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 54.0 4.50e-01 92.3% 82.7%
2j1vA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.65 50.0 3.73e-01 96.2% 31.9%
1zczA02 3.40.140.20 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › AICAR transformylase, duplication domain 0.64 49.0 3.80e-01 90.4% 37.6%
3nqhA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.63 53.0 3.91e-01 94.2% 36.0%
3gzkA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 49.0 4.29e-01 90.4% 57.0%
2df7A02 2.60.120.660 Mainly Beta › Sandwich › Jelly Rolls › icosahedral virus 0.62 52.0 3.80e-01 92.3% 39.3%
2pw9C03 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.62 49.0 3.64e-01 90.4% 33.3%
4g5aA00 2.60.40.3080 Mainly Beta › Sandwich › Immunoglobulin-like › 0.61 47.0 3.84e-01 90.4% 44.4%
4cj0A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 48.0 4.02e-01 90.4% 52.6%
1p7hL02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 51.0 4.06e-01 96.2% 55.1%
4f7kA03 2.60.40.420 Mainly Beta › Sandwich › Immunoglobulin-like › Cupredoxins - blue copper proteins 0.60 38.0 3.03e-01 92.3% 29.8%
7pjjA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.60 51.0 3.83e-01 96.2% 79.8%
4zzfA02 2.60.40.4070 Mainly Beta › Sandwich › Immunoglobulin-like › 0.59 51.0 4.16e-01 96.2% 63.5%
1pjuA01 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.59 41.0 3.99e-01 88.5% 63.5%
2abjD02 3.20.10.10 Alpha Beta › Alpha-Beta Barrel › D-amino Acid Aminotransferase; Chain A, domain 2 › D-amino Acid Aminotransferase, subunit A, domain 2 0.59 50.0 3.54e-01 100.0% 34.9%
7uzsX03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 48.0 3.82e-01 96.2% 59.1%
2dk6A01 3.30.720.50 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.58 48.0 4.03e-01 96.2% 83.0%
4y2fA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.58 39.0 2.92e-01 71.2% 87.4%
3afgA03 2.60.120.380 Mainly Beta › Sandwich › Jelly Rolls › 0.58 44.0 3.60e-01 94.2% 43.1%
5a2fA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 47.0 3.87e-01 96.2% 64.2%
3ifrA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.57 47.0 3.15e-01 100.0% 34.0%
2o62A01 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.57 48.0 3.62e-01 96.2% 88.5%
3bgaA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 45.0 3.68e-01 96.2% 56.8%
2pn5A02 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.56 46.0 3.77e-01 96.2% 48.5%
3jqwC00 2.60.120.380 Mainly Beta › Sandwich › Jelly Rolls › 0.56 41.0 3.24e-01 92.3% 34.7%
2p9rA00 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.55 44.0 3.60e-01 90.4% 46.1%
6pwkA02 3.20.20.450 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › EAL domain 0.55 42.0 2.81e-01 86.5% 46.3%
3bgaA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 44.0 3.61e-01 96.2% 60.0%
3f1sB02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.53 40.0 3.56e-01 98.1% 52.7%
1wh2A01 3.30.1490.40 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › GYF domain 0.53 37.0 3.62e-01 98.1% 67.2%
1xr0B01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 40.0 3.49e-01 92.3% 80.2%
3pm9A02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.51 39.0 3.13e-01 88.5% 83.6%
2gnxA02 3.30.450.240 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.51 35.0 2.92e-01 78.8% 35.8%
6ixwB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 41.0 2.98e-01 92.3% 94.4%
4dz1A02 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.51 39.0 3.29e-01 90.4% 55.6%
2wb7A02 2.60.40.2050 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 41.0 3.03e-01 96.2% 56.8%
3g8qA01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.50 39.0 3.08e-01 86.5% 71.7%
2fh5A01 3.30.450.60 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.50 36.0 2.83e-01 78.8% 67.2%
ECOD (41)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4946541 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.67 46.0 4.04e-01 88.5% 47.5%
4594988 11.1.1.608 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Por_Secre_tail 0.65 49.0 4.45e-01 90.4% 60.0%
3994661 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.64 51.0 3.53e-01 96.2% 24.7%
3964245 3438.1.1.2 ↗ alpha arrays › Unknown function protein VPA0580 › Unknown function protein VPA0580 › Unknown function protein VPA0580 › DUF2322 0.64 51.0 4.15e-01 92.3% 84.8%
4250283 2492.1.1.0 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.63 54.0 4.39e-01 100.0% 99.0%
3252995 12.3.1.46 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › ComC_SSD 0.63 52.0 3.48e-01 96.2% 76.0%
3789849 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.61 50.0 4.81e-01 96.2% 80.0%
4950843 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.61 46.0 4.36e-01 84.6% 98.5%
4029586 10.32.1.203 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin 0.61 49.0 3.57e-01 92.3% 48.7%
4952123 3986.2.1.0 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.61 53.0 5.09e-01 98.1% 86.7%
3915206 10.32.1.203 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin 0.61 49.0 3.44e-01 92.3% 43.4%
3250018 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.61 50.0 3.49e-01 94.2% 71.7%
3333290 10.32.1.203 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin 0.60 49.0 3.44e-01 94.2% 41.7%
4999722 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.60 40.0 3.34e-01 71.2% 83.2%
4245789 304.150.1.1 ↗ a+b two layers › Alpha-beta plaits › Adapter protein mecA 2 C-terminal domain › Adapter protein mecA 2 C-terminal domain › MecA 0.60 49.0 4.22e-01 98.1% 80.0%
3184485 76.1.1.0 ↗ beta duplicates or obligate multimers › beta-Prism I › beta-Prism I › beta-Prism I 0.59 49.0 4.03e-01 100.0% 93.5%
3740347 10.32.1.203 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin 0.59 47.0 3.42e-01 92.3% 54.5%
3392690 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 50.0 3.68e-01 98.1% 46.9%
3409626 4114.1.1.2 ↗ a+b two layers › PHP14-like › PHP14-like › PHP14-like › Ocnus 0.58 49.0 3.96e-01 100.0% 69.1%
164160 4357.1.1.1 ↗ beta barrels › WWE domain › WWE domain › WWE domain › WWE 0.58 48.0 3.93e-01 96.2% 76.5%
3925830 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 49.0 3.61e-01 96.2% 44.3%
5081702 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.58 45.0 3.50e-01 96.2% 37.5%
4954628 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 48.0 3.91e-01 98.1% 53.3%
3248483 2492.1.1.1 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › dCMP_cyt_deam_1 0.57 48.0 3.35e-01 94.2% 70.1%
4944923 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.57 42.0 3.16e-01 78.8% 93.1%
3274214 859.1.1.1 ↗ a+b two layers › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 › HORMA 0.57 50.0 3.42e-01 100.0% 56.7%
3923897 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.57 43.0 3.08e-01 96.2% 25.6%
3167876 223.2.1.9 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Sedlin_N 0.56 41.0 2.86e-01 78.8% 94.3%
4977806 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.55 40.0 3.09e-01 80.8% 86.9%
3600531 4012.3.1.0 ↗ a+b two layers › SSHS domain › SSHS domain in CRISPR-associated endonuclease Cas9 › SSHS domain in CRISPR-associated endonuclease Cas9 0.54 45.0 4.53e-01 94.2% 98.1%
3619998 12.1.1.34 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Glyco_hydro38C2 0.54 44.0 3.65e-01 96.2% 50.0%
3272511 223.2.1.8 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Sybindin 0.54 39.0 2.97e-01 80.8% 93.6%
2640865 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.53 43.0 4.25e-01 92.3% 94.5%
4042767 223.1.1.103 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › CHASE7, PF30448 0.53 41.0 3.04e-01 82.7% 80.0%
4954709 2492.1.1.0 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.53 44.0 3.37e-01 98.1% 57.7%
5051010 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.53 39.0 3.15e-01 80.8% 80.9%
5006740 7.1.1.0 ↗ beta barrels › PDZ domain › PDZ domain › PDZ domain 0.52 44.0 3.54e-01 100.0% 90.4%
3945567 10.32.1.8 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › CBM_4_9 0.52 43.0 3.20e-01 96.2% 33.3%
5040622 2005.1.1.1 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1 0.52 38.0 2.38e-01 90.4% 73.2%
5071935 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 36.0 2.84e-01 78.8% 88.5%
3493644 10.32.1.203 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin 0.50 41.0 2.95e-01 94.2% 69.7%