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PH2015_20_scaffold_1_prodigal-single.1__X__X__00315

Bact-Vir

PH2015_20_scaffold_1_prodigal-single.1__X__X__00315

Identity

Kingdom:
phage

Quality

88.9 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 medium residues 1-70
PDB
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4uzgA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 51.0 4.29e-01 87.1% 54.5%
5faaA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 51.0 4.26e-01 87.1% 69.9%
1sr4A00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.63 52.0 4.11e-01 98.6% 88.0%
2x7iA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.61 51.0 4.19e-01 92.9% 99.2%
1hibA00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.61 46.0 3.72e-01 85.7% 96.7%
1nunA00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.60 47.0 3.80e-01 85.7% 92.8%
5uc6A00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.60 47.0 3.71e-01 85.7% 91.4%
1hwmB02 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.59 45.0 3.83e-01 85.7% 99.2%
1xezA02 2.70.240.20 Mainly Beta › Distorted Sandwich › Leukocidin-like › Leukocidin/Hemolysin toxin, cytolysin domain 0.59 48.0 3.10e-01 97.1% 99.2%
1ggpB02 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.58 44.0 3.78e-01 85.7% 99.2%
2dy1A03 3.30.70.870 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Elongation Factor G (Translational Gtpase), domain 3 0.58 45.0 4.40e-01 85.7% 94.7%
2vxtI00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.57 43.0 3.47e-01 85.7% 95.5%
1md6A00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.57 43.0 3.47e-01 85.7% 96.8%
1wkiA01 3.90.1170.10 Alpha Beta › Alpha-Beta Complex › Aldehyde Oxidoreductase; domain 3 › Ribosomal protein L16/L10 0.56 45.0 3.96e-01 90.0% 99.1%
3glkA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.55 35.0 3.68e-01 87.1% 74.6%
2wryA00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.55 41.0 3.33e-01 84.3% 95.5%
3egrA00 3.10.20.520 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phenylacetic acid degradation B 0.55 39.0 4.07e-01 87.1% 85.7%
6ztgA01 3.30.70.1070 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Sporulation related repeat 0.54 40.0 4.00e-01 82.9% 100.0%
5t0oA03 3.30.70.1320 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain like 0.54 44.0 3.97e-01 94.3% 100.0%
2jveA00 2.10.60.10 Mainly Beta › Ribbon › CD59 › CD59 0.53 45.0 4.51e-01 92.9% 93.0%
1s7hA01 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 43.0 4.16e-01 90.0% 92.5%
3ramA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 43.0 3.68e-01 92.9% 96.6%
1s7iA00 3.30.70.1060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel 0.52 45.0 3.76e-01 97.1% 95.2%
5bk9A00 3.60.130.10 Alpha Beta › 4-Layer Sandwich › Double-stranded beta-helix › Clavaminate synthase-like 0.51 35.0 2.41e-01 72.9% 89.6%
3pfsB00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.50 41.0 3.44e-01 94.3% 100.0%
4cclA02 3.40.366.30 Alpha Beta › 3-Layer(aba) Sandwich › Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 › 50S ribosomal protein L16 arginine hydroxylase; Chain A, Domain 2 0.50 34.0 2.69e-01 72.9% 47.0%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3589722 11.1.4.36 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › SpaA 0.67 54.0 4.37e-01 87.1% 56.9%
3590224 11.1.4.36 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › SpaA 0.66 52.0 4.26e-01 87.1% 66.7%
1554318 11.1.4.36 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › SpaA 0.64 51.0 4.30e-01 87.1% 55.0%
142423 6.1.1.3 beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil › IL1 0.62 47.0 3.66e-01 85.7% 97.0%
4010783 223.8.1.2 a+b three layers › Profilin-like › LapD periplasmic domain › LapD periplasmic domain › CHASE8 0.61 40.0 3.42e-01 78.6% 42.7%
3764853 6.1.1.3 beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil › IL1 0.61 47.0 3.70e-01 85.7% 93.1%
5076536 5.1.2.19 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed › DUF4185 0.60 45.0 2.91e-01 80.0% 43.9%
2120 6.1.1.4 beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil › Ricin_B_lectin 0.59 45.0 3.80e-01 85.7% 95.4%
3641381 6.1.1.25 beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil › DUF569 0.59 46.0 3.65e-01 87.1% 91.0%
3244749 6.1.1.0 beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil 0.59 45.0 3.45e-01 85.7% 68.2%
169919 6.1.1.3 beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil › IL1 0.57 43.0 3.55e-01 85.7% 94.5%
3288314 358.3.1.0 a+b complex topology › SRCR-like › Putative uncharacterized protein TTHA0547 › Putative uncharacterized protein TTHA0547 0.56 45.0 3.85e-01 95.7% 53.3%
4260224 223.1.1.51 a+b three layers › Profilin-like › sensor domains › sensor domains › MCP-like_PDC_1 0.56 36.0 2.83e-01 72.9% 31.0%
3654117 6.1.1.4 beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil › Ricin_B_lectin 0.55 41.0 3.53e-01 84.3% 95.4%
3328202 6.1.1.25 beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil › DUF569 0.55 42.0 3.32e-01 87.1% 85.3%
140811 6.1.1.3 beta duplicates or obligate multimers › beta-Trefoil › beta-Trefoil › beta-Trefoil › IL1 0.55 41.0 3.33e-01 84.3% 95.5%
3997731 304.24.1.0 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.54 41.0 4.02e-01 85.7% 92.5%
4507657 10.9.1.3 beta sandwiches › jelly-roll › C-terminal domain of mullusc hemocyanin › C-terminal domain of mullusc hemocyanin › Tyrosinase_C 0.54 43.0 3.34e-01 91.4% 96.5%
169110 382.1.1.0 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.52 44.0 4.44e-01 92.9% 92.9%
None 0.52 45.0 2.88e-01 100.0% 87.6%
3405488 2002.1.1.42 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › A_deaminase,A_deaminase_N 0.51 43.0 2.68e-01 100.0% 32.8%
D2 medium residues 72-136
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5kfzA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.63 40.0 3.24e-01 76.9% 34.1%
3qwmA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.63 51.0 4.07e-01 100.0% 44.9%
6lpfA01 1.10.730.20 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › 0.60 43.0 3.21e-01 92.3% 30.1%
1dpgA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.59 46.0 2.99e-01 86.2% 81.6%
2avxA00 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.59 47.0 3.46e-01 87.7% 74.3%
2kvtA00 3.30.730.30 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › YaiA protein 0.57 42.0 4.07e-01 93.8% 70.4%
1ek9A00 1.20.1600.10 Mainly Alpha › Up-down Bundle › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) 0.57 46.0 2.74e-01 86.2% 13.1%
4oh1A01 3.90.180.10 Alpha Beta › Alpha-Beta Complex › Quinone Oxidoreductase; Chain A, domain 1 › Medium-chain alcohol dehydrogenases, catalytic domain 0.56 42.0 3.06e-01 86.2% 95.3%
3p0tA00 3.30.428.10 Alpha Beta › 2-Layer Sandwich › HIT family, subunit A › HIT-like 0.55 42.0 3.35e-01 89.2% 39.7%
3t4nA01 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.54 38.0 3.37e-01 90.8% 50.0%
3gg6A00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.54 45.0 3.53e-01 93.8% 92.4%
3m4rA01 3.40.225.10 Alpha Beta › 3-Layer(aba) Sandwich › L-fuculose-1-phosphate Aldolase › Class II aldolase/adducin N-terminal domain 0.54 44.0 3.08e-01 89.2% 46.8%
1b69A00 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.52 39.0 3.82e-01 86.2% 73.9%
3hv8A00 3.20.20.450 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › EAL domain 0.52 40.0 2.75e-01 84.6% 26.9%
2l6mA00 3.30.160.400 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.52 41.0 3.62e-01 100.0% 57.4%
2vpaA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 36.0 2.60e-01 73.8% 51.5%
1pu1A00 3.30.300.100 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › MTH677-like 0.51 41.0 3.65e-01 95.4% 61.5%
2v3sA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.51 38.0 3.44e-01 83.1% 91.7%
3cjlA00 3.10.20.850 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Protein of unknown function DUF3861 0.50 39.0 3.57e-01 84.6% 73.9%
6jptA00 3.30.230.90 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.50 37.0 3.05e-01 89.2% 42.1%
4zg5A00 3.40.1210.10 Alpha Beta › 3-Layer(aba) Sandwich › Stationary-phase Survival Protein Sure Homolog; Chain: A, › Survival protein SurE-like phosphatase/nucleotidase 0.50 39.0 2.76e-01 89.2% 59.1%
6p3xB01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.50 40.0 3.03e-01 90.8% 100.0%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4160831 109.4.1.1255 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Adaptin_N, Cnd1 0.64 42.0 2.36e-01 90.8% 6.2%
4343264 3747.1.1.1 a+b two layers › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flg_bb_rod 0.64 53.0 4.12e-01 87.7% 86.9%
3974732 3747.1.1.3 a+b two layers › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flg_bbr_C 0.63 53.0 4.32e-01 89.2% 77.9%
3798608 2492.1.1.4 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.62 48.0 3.03e-01 84.6% 92.6%
3971859 3747.1.1.2 a+b two layers › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flg_bb_rod,Flg_bbr_C 0.61 51.0 4.22e-01 89.2% 79.1%
4945650 878.1.1.0 a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 0.61 50.0 4.26e-01 95.4% 57.0%
4582665 140.1.1.6 alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon_1,tRNA-synt_1g 0.61 48.0 3.12e-01 84.6% 40.4%
4578107 67.1.1.1 beta sandwiches › HSP40/DnaJ peptide-binding domain › HSP40/DnaJ peptide-binding domain › HSP40/DnaJ peptide-binding domain › DnaJ_C 0.60 28.0 2.81e-01 83.1% 38.6%
4018546 2004.1.1.73 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MMR_HSR1 0.56 47.0 3.12e-01 92.3% 85.1%
3409888 1.1.17.1 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.56 41.0 2.82e-01 81.5% 80.4%
5024844 312.1.1.2 a+b three layers › HIT-like › HIT-related › HIT-related › HIT 0.56 43.0 3.34e-01 86.2% 38.6%
3521217 1.1.5.34 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Pyrid_oxidase_2 0.55 39.0 2.89e-01 73.8% 74.3%
3725624 327.11.2.19 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_11 0.55 49.0 3.56e-01 96.9% 92.4%
3577911 220.1.1.15 beta barrels › PH domain-like › PH domain-like › PH domain-like › BBL5 0.55 47.0 3.63e-01 95.4% 71.7%
4984088 7527.1.1.2 a/b three-layered sandwiches › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › SurE-like/CoA-transferase family III (CaiB/BaiF) › CoA_transf_3 0.55 45.0 2.78e-01 89.2% 44.4%
3632622 320.1.1.0 a+b two layers › R3H domain-like › R3H domain › R3H domain 0.54 43.0 3.62e-01 87.7% 51.8%
3339155 10.32.1.0 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.54 43.0 3.15e-01 87.7% 68.0%
3227441 375.10.1.0 few secondary structure elements › Rubredoxin-like › Zinc finger domain of DNA polymerase-alpha › Zinc finger domain of DNA polymerase-alpha 0.53 42.0 4.42e-01 84.6% 96.7%
3598683 109.20.1.0 alpha superhelices › Repetitive alpha hairpins › Coatomer subunit alpha C-terminal domain › Coatomer subunit alpha C-terminal domain 0.53 47.0 3.12e-01 96.9% 29.8%
3479948 2008.1.1.91 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NARG2_C 0.52 41.0 2.76e-01 89.2% 86.7%
3247288 2006.1.4.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.52 41.0 2.85e-01 84.6% 62.9%
3213645 267.1.1.0 a+b complex topology › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain 0.52 40.0 2.71e-01 83.1% 71.6%
3387236 2004.1.1.220 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SWI2_SNF2 0.51 37.0 2.55e-01 84.6% 21.8%
4605147 377.4.1.2 few secondary structure elements › Glucocorticoid receptor-like › YlxR-like › YlxR-like › RRG8 0.51 45.0 3.20e-01 100.0% 33.7%
4087729 221.1.1.97 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › DUF508 0.51 36.0 3.24e-01 75.4% 71.6%
3614175 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.50 41.0 3.33e-01 84.6% 68.2%
3578346 2492.1.1.4 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.50 40.0 2.65e-01 89.2% 78.9%