←Back to structures

rifcsphigho2-12_scaffold_combined_curated_prodigal-single.1__X__X__00257

Bact-Vir

rifcsphigho2-12_scaffold_combined_curated_prodigal-single.1__X__X__00257

Identity

Kingdom:
phage

Quality

84.3 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 16-61
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4wiwA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.69 56.0 5.02e-01 95.7% 98.6%
3pp2A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.65 46.0 3.50e-01 89.1% 31.2%
2cuwA00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.64 52.0 4.49e-01 100.0% 92.8%
3o2iA00 3.30.70.2710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 42.0 3.39e-01 89.1% 35.5%
1x9tA02 3.90.1620.10 Alpha Beta › Alpha-Beta Complex › adenovirus 2 penton base, domain 2 › adenovirus 2 penton base, domain 2 0.61 48.0 3.10e-01 100.0% 37.9%
2kx2A00 3.30.780.30 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor Eif1 › 0.61 44.0 3.55e-01 82.6% 38.5%
2nyiA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.60 50.0 4.27e-01 100.0% 87.7%
1q5yC00 3.30.70.1150 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT-like. Chain A, domain 2 0.59 50.0 4.21e-01 100.0% 89.0%
1bdyA00 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.57 45.0 3.53e-01 100.0% 37.4%
3al5B01 2.60.120.650 Mainly Beta › Sandwich › Jelly Rolls › Cupin 0.57 48.0 3.03e-01 100.0% 19.4%
6spbZ00 3.30.1390.20 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L30; Chain: A, › Ribosomal protein L30/L7 0.56 47.0 4.48e-01 100.0% 100.0%
5kfzA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.56 47.0 3.55e-01 100.0% 51.2%
5zneA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 46.0 4.07e-01 100.0% 93.2%
2bw2A01 3.10.20.420 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Bypass-of-forespore C, N-terminal domain 0.56 46.0 4.42e-01 100.0% 83.6%
4lejA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.56 40.0 2.89e-01 100.0% 23.1%
5d79A03 3.40.462.20 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › 0.56 42.0 3.05e-01 100.0% 42.8%
3e0jB00 3.90.1030.20 Alpha Beta › Alpha-Beta Complex › 50s Ribosomal Protein L17; Chain: A, › DNA polymerase delta, p66 (Cdc27) subunit, wHTH domain 0.55 42.0 3.05e-01 100.0% 28.0%
2hjqA01 3.40.5.20 Alpha Beta › 3-Layer(aba) Sandwich › Ribosomal Protein L9; domain 1 › YqbF domain 0.55 47.0 4.78e-01 97.8% 97.8%
2y8yA02 3.30.70.1210 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Crispr-associated protein; domain 2 0.55 45.0 3.50e-01 100.0% 95.7%
5cadA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.55 42.0 2.88e-01 100.0% 21.5%
5e1qA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.54 44.0 3.60e-01 100.0% 46.9%
2eenA00 2.40.320.10 Mainly Beta › Beta Barrel › Hypothetical Protein Pfu-838710-001 › Hypothetical Protein Pfu-838710-001 0.54 42.0 2.97e-01 93.5% 24.9%
2zewB00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.54 41.0 2.95e-01 87.0% 44.9%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.54 45.0 3.92e-01 100.0% 61.8%
6toaE01 2.40.10.270 Mainly Beta › Beta Barrel › Thrombin, subunit H › Bacteriophage SPP1 head-tail adaptor protein 0.54 41.0 3.50e-01 100.0% 74.5%
2mraA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.54 42.0 3.36e-01 100.0% 47.0%
2qsdA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.53 43.0 3.94e-01 100.0% 74.6%
2qgyB01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.53 43.0 3.21e-01 100.0% 73.7%
2nytD00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.53 46.0 3.10e-01 97.8% 44.7%
4njcA00 3.10.20.730 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNAP, epsilon subunit-like 0.53 45.0 4.23e-01 100.0% 81.7%
7kx7A03 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.53 40.0 2.76e-01 93.5% 74.0%
1mkfA02 2.60.40.1340 Mainly Beta › Sandwich › Immunoglobulin-like › Chemokine-binding protein M3-like 0.52 42.0 3.01e-01 100.0% 43.0%
6cc0A01 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.52 40.0 2.86e-01 91.3% 39.6%
3wa7A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 41.0 2.42e-01 97.8% 42.4%
5l10B00 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.52 39.0 2.81e-01 91.3% 34.7%
5jtwA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 40.0 3.19e-01 89.1% 78.4%
4dyoA02 2.30.250.10 Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 0.52 42.0 3.10e-01 97.8% 97.8%
6inxA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.52 40.0 3.78e-01 100.0% 100.0%
4kg8A00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.51 45.0 3.29e-01 100.0% 62.8%
4htgA03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.51 38.0 3.34e-01 91.3% 50.6%
1kf6B01 3.10.20.30 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Beta-grasp domain 0.51 44.0 3.43e-01 100.0% 79.8%
4a18X01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.51 42.0 3.65e-01 100.0% 74.7%
3rb5A02 2.60.40.2030 Mainly Beta › Sandwich › Immunoglobulin-like › CalX-beta domain 0.51 35.0 2.68e-01 76.1% 38.4%
6brbD00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 38.0 3.32e-01 100.0% 49.4%
1vwxS01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.50 43.0 3.79e-01 100.0% 83.1%
1oi2A02 3.30.1180.20 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › Dihydroxyacetone kinase; domain 2 0.50 40.0 2.88e-01 93.5% 74.7%
1hq6B00 3.50.20.10 Alpha Beta › 3-Layer(bba) Sandwich › Pyruvoyl-Dependent Histidine Decarboxylase; Chain B › Pyruvoyl-Dependent Histidine Decarboxylase, subunit B 0.50 39.0 2.67e-01 100.0% 31.1%
5jm6A02 2.30.250.10 Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 0.50 42.0 3.03e-01 97.8% 97.9%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3399490 379.1.1.0 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors 0.78 62.0 5.58e-01 100.0% 63.1%
3686997 304.9.1.6 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › Smg4_UPF3 0.74 65.0 5.69e-01 100.0% 92.9%
4680886 69.1.1.14 ↗ beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Hint_2 0.70 59.0 4.13e-01 100.0% 30.9%
3940556 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.67 49.0 3.78e-01 100.0% 33.6%
3257433 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.66 45.0 3.25e-01 71.7% 23.7%
3582833 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.65 55.0 4.26e-01 100.0% 60.9%
4978692 1075.1.2.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain 0.65 55.0 3.39e-01 100.0% 45.2%
4647263 304.8.1.2 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT 0.64 55.0 4.67e-01 100.0% 88.5%
3276865 2492.1.1.0 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.64 54.0 4.26e-01 100.0% 45.0%
3508212 3115.1.1.6 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › DUF4494 0.62 49.0 4.52e-01 100.0% 75.7%
3406669 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.62 46.0 3.72e-01 100.0% 39.0%
3858396 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.62 49.0 3.72e-01 100.0% 35.2%
4963357 304.8.1.124 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › HVO_2525_N 0.62 48.0 3.59e-01 91.3% 97.8%
3614316 1116.1.1.0 ↗ a+b two layers › Polycystin-mucolipin domain › Polycystin-mucolipin domain › Polycystin-mucolipin domain 0.61 51.0 3.50e-01 100.0% 28.6%
3702557 3945.1.1.0 ↗ alpha superhelices › N-terminal fragment of dynein heavy chain › N-terminal fragment of dynein heavy chain › N-terminal fragment of dynein heavy chain 0.61 50.0 3.68e-01 100.0% 33.8%
143130 306.3.1.3 ↗ a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like › DUF5750 0.61 44.0 3.55e-01 82.6% 38.5%
5025432 304.165.1.0 ↗ a+b two layers › Alpha-beta plaits › Uncharacterized protein Ta1207 › Uncharacterized protein Ta1207 0.60 52.0 3.63e-01 100.0% 86.7%
3268123 192.15.1.184 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › RA 0.59 48.0 3.92e-01 100.0% 48.6%
3655111 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.59 48.0 3.81e-01 100.0% 55.5%
3448591 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.59 41.0 4.01e-01 87.0% 68.0%
3787050 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.59 49.0 3.99e-01 100.0% 62.1%
3686913 101.1.2.115 ↗ alpha arrays › HTH › HTH › winged helix domain › CDC27 0.58 45.0 3.19e-01 100.0% 27.3%
2794885 807.1.1.1 ↗ a+b two layers › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › CpcD 0.58 49.0 4.49e-01 100.0% 73.4%
2095485 1.1.5.38 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Peptidase_C107 0.58 49.0 3.23e-01 100.0% 22.1%
3896560 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.58 48.0 3.37e-01 100.0% 34.1%
4951473 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.57 48.0 4.44e-01 100.0% 74.6%
3926687 302.1.1.1 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.57 49.0 3.65e-01 100.0% 44.2%
4939739 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.57 49.0 4.59e-01 100.0% 79.7%
5048008 2008.1.1.7 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › ERCC4 0.57 43.0 3.04e-01 91.3% 29.1%
4967222 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.56 48.0 4.48e-01 100.0% 78.3%
4031645 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.56 47.0 4.64e-01 100.0% 94.0%
4937773 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.56 47.0 4.46e-01 100.0% 81.0%
3205532 4004.1.1.0 ↗ beta sandwiches › NAD kinase beta sandwich domain-like › NAD kinase beta sandwich domain-like › NAD kinase beta sandwich domain-like 0.56 43.0 2.79e-01 91.3% 34.4%
3965010 3115.4.1.1 ↗ a+b two layers › GP2-like › Uncharacterized conserved protein Il1583 › Uncharacterized conserved protein Il1583 › DUF1543 0.56 46.0 3.83e-01 100.0% 55.6%
3991293 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.56 44.0 3.31e-01 100.0% 34.4%
3409700 4114.1.1.2 ↗ a+b two layers › PHP14-like › PHP14-like › PHP14-like › Ocnus 0.55 48.0 3.64e-01 100.0% 40.0%
5047498 3662.1.1.4 ↗ a+b two layers › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › PAC_bac 0.55 40.0 3.17e-01 84.8% 85.2%
4981234 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 0.55 44.0 4.08e-01 100.0% 73.8%
4886584 3115.6.1.1 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › RpoY 0.55 47.0 4.15e-01 100.0% 70.0%
2106284 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.54 44.0 4.06e-01 100.0% 82.1%
4931277 101.1.2.14 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.54 36.0 2.59e-01 71.7% 47.7%
3217805 386.1.1.366 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › BPTI_nem 0.54 40.0 3.49e-01 100.0% 50.0%
223776 3115.4.1.1 ↗ a+b two layers › GP2-like › Uncharacterized conserved protein Il1583 › Uncharacterized conserved protein Il1583 › DUF1543 0.53 43.0 3.88e-01 100.0% 70.4%
3621694 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.53 43.0 3.48e-01 100.0% 83.8%
4003316 10.7.1.0 ↗ beta sandwiches › jelly-roll › Hypothetical protein TM1070 › Hypothetical protein TM1070 0.53 44.0 3.33e-01 100.0% 70.4%
3396683 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.53 44.0 3.81e-01 100.0% 58.2%
3405278 382.1.1.3 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › Activin_recp 0.53 42.0 3.47e-01 100.0% 52.0%
4654177 1119.1.1.1 ↗ a+b complex topology › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › 6-carboxyhexanoate-CoA ligase › BioW 0.53 42.0 2.79e-01 100.0% 20.0%
3698084 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.53 42.0 2.53e-01 100.0% 21.0%
5079276 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.52 43.0 3.41e-01 100.0% 67.3%
3891753 3369.1.1.1 ↗ beta meanders › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 › Lamp2-like_luminal 0.51 40.0 2.84e-01 100.0% 71.0%
3885857 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.51 38.0 3.40e-01 87.0% 90.7%
4002369 304.47.1.0 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain 0.51 39.0 3.24e-01 87.0% 91.1%
3514713 11.1.1.41 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_C 0.51 37.0 2.74e-01 84.8% 55.5%
3933692 11.1.1.41 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_C 0.51 37.0 2.66e-01 84.8% 62.2%