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S16_GE16_scaffold_5545_prodigal-single.1__X__X__00255

Bact-Vir

S16_GE16_scaffold_5545_prodigal-single.1__X__X__00255

Identity

Kingdom:
phage

Quality

82.1 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 5-79
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01541.31 best GIY-YIG 35.1 1.80e-08 100.0% 88.5%
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ln0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.85 78.0 7.29e-01 100.0% 87.0%
4dohE02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.77 47.0 4.14e-01 84.0% 43.4%
2ww8A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.76 45.0 3.95e-01 78.7% 42.5%
1ltlA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.65 41.0 4.78e-01 77.3% 98.0%
1i8nA00 3.50.4.10 Alpha Beta › 3-Layer(bba) Sandwich › Hepatocyte Growth Factor › Hepatocyte Growth Factor 0.65 36.0 3.41e-01 76.0% 46.1%
1zc1A01 2.40.40.50 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › Ubiquitin fusion degradation protein UFD1, N-terminal domain 0.64 45.0 4.07e-01 93.3% 53.4%
2yuxA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 41.0 3.67e-01 90.7% 45.4%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.63 43.0 4.02e-01 77.3% 57.6%
1bw3A00 2.40.40.10 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › RlpA-like domain 0.62 48.0 4.08e-01 92.0% 50.4%
4avrA00 2.40.40.10 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › RlpA-like domain 0.62 43.0 4.03e-01 73.3% 59.6%
2jvuA00 2.60.40.2290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.62 41.0 3.77e-01 80.0% 52.0%
2b5eA03 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.60 36.0 3.06e-01 93.3% 33.9%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.60 41.0 3.84e-01 77.3% 57.4%
7ejoB01 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.58 42.0 4.13e-01 77.3% 75.9%
2aehA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.56 44.0 4.09e-01 89.3% 66.7%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.56 37.0 2.95e-01 78.7% 31.1%
6s2wA01 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.55 44.0 4.26e-01 88.0% 78.0%
4ekuA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.55 45.0 3.86e-01 89.3% 58.1%
2xy1A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 40.0 3.66e-01 77.3% 59.8%
5kycB02 2.20.210.10 Mainly Beta › Single Sheet › ubp-family deubiquitinating enzyme fold › ubp-family deubiquitinating enzyme superfamily 0.53 36.0 4.12e-01 80.0% 98.1%
2ftrA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 38.0 3.55e-01 78.7% 97.1%
1ca1A02 2.60.60.20 Mainly Beta › Sandwich › Lipoxygenase-1 › PLAT/LH2 domain 0.53 39.0 3.36e-01 78.7% 77.5%
3ir9A02 3.30.1330.30 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Ribosomal protein L30/S12 0.53 42.0 3.58e-01 85.3% 67.5%
2biiA02 2.60.40.650 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 37.0 2.85e-01 76.0% 42.5%
3tcaA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.52 41.0 3.92e-01 96.0% 71.1%
2j4xA01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.50 40.0 3.47e-01 90.7% 76.6%
ECOD (38)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4677975 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.88 81.0 6.86e-01 100.0% 69.5%
4669741 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.85 73.0 6.72e-01 100.0% 72.6%
4997210 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.84 76.0 7.13e-01 100.0% 80.0%
3505268 821.1.1.0 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.84 79.0 6.32e-01 100.0% 80.0%
4158495 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.83 75.0 7.00e-01 100.0% 80.0%
5046850 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.81 74.0 6.91e-01 100.0% 81.1%
4623707 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.81 74.0 6.75e-01 100.0% 76.8%
3467170 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.81 61.0 6.66e-01 84.0% 95.2%
3620613 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.71 42.0 5.27e-01 74.7% 100.0%
4929321 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.70 44.0 4.82e-01 100.0% 78.3%
3602534 375.1.1.199 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › MJ0401 0.70 39.0 4.92e-01 70.7% 100.0%
5045774 2492.1.1.7 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.70 46.0 3.69e-01 77.3% 35.7%
4970537 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.65 36.0 4.49e-01 73.3% 97.5%
4507405 375.1.1.128 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Zn_ribbon_SprT 0.64 37.0 4.52e-01 89.3% 95.6%
4648475 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.62 45.0 4.88e-01 76.0% 100.0%
5065792 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.62 48.0 3.82e-01 84.0% 54.8%
3590261 822.3.1.1 a+b two layers › GYF/BRK domain-like › conserved domain protein SP_1775 › conserved domain protein SP_1775 › DUF4649 0.61 39.0 4.06e-01 78.7% 72.1%
5027350 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.60 46.0 3.81e-01 84.0% 61.6%
3874464 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.59 51.0 3.28e-01 97.3% 28.2%
3406258 221.1.1.76 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.58 39.0 3.75e-01 70.7% 88.9%
4990489 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.58 38.0 4.35e-01 76.0% 100.0%
4332626 3532.1.1.0 alpha arrays › RNA-binding domain of telomerase › RNA-binding domain of telomerase › RNA-binding domain of telomerase 0.57 48.0 2.85e-01 93.3% 17.0%
3295672 1.1.2.3 beta barrels › cradle loop barrel › RIFT-related › double psi › Barwin 0.57 43.0 4.43e-01 88.0% 87.1%
3954522 3108.1.1.0 a+b two layers › Uncharacterized protein Atu1219 › Uncharacterized protein Atu1219 › Uncharacterized protein Atu1219 0.57 39.0 4.09e-01 72.0% 95.7%
3586126 221.1.1.76 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.56 38.0 3.29e-01 70.7% 64.8%
3551231 221.1.1.87 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › FERM_N_2 0.56 45.0 4.02e-01 93.3% 61.9%
4013619 887.1.1.0 a+b two layers › Ribosomal protein L30p/L7e › Ribosomal protein L30p/L7e › Ribosomal protein L30p/L7e 0.55 46.0 4.52e-01 100.0% 85.0%
5022263 322.1.1.2 a+b two layers › HPr-like › HPr-like › HPr-like › 3H 0.54 38.0 3.45e-01 74.7% 53.6%
3972526 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.54 39.0 4.06e-01 77.3% 94.3%
3962683 7579.1.1.10 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Thioesterase 0.53 42.0 3.68e-01 97.3% 54.4%
3816922 4081.1.1.0 beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related 0.53 39.0 2.61e-01 78.7% 23.6%
4019073 4154.1.1.0 beta duplicates or obligate multimers › E2F-DP heterodimerization region › E2F-DP heterodimerization region › E2F-DP heterodimerization region 0.52 42.0 3.87e-01 89.3% 68.0%
3404684 10.12.1.84 beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › VKGC_lumenal_dom 0.52 46.0 3.32e-01 98.7% 88.1%
3849943 221.1.1.76 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.52 41.0 3.32e-01 93.3% 44.8%
4794127 221.1.1.76 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.51 41.0 3.69e-01 93.3% 61.9%
5020794 206.1.3.19 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Dala_Dala_lig_C 0.51 43.0 3.10e-01 100.0% 54.1%
4947584 206.1.3.19 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Dala_Dala_lig_C 0.50 42.0 3.09e-01 98.7% 60.0%
3469991 11.1.1.55 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Mo-co_dimer 0.50 36.0 2.91e-01 76.0% 52.4%
D2 high residues 127-200
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1gccA00 3.30.730.10 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › AP2/ERF domain 0.89 63.0 6.84e-01 73.0% 90.5%
7wq5A01 3.30.730.10 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › AP2/ERF domain 0.87 65.0 7.27e-01 77.0% 100.0%
2af5A01 2.40.128.160 Mainly Beta › Beta Barrel › Lipocalin › C1 set domains (antibody constant domain-like) 0.67 37.0 4.17e-01 100.0% 72.2%
3d4eA01 3.30.1450.10 Alpha Beta › 2-Layer Sandwich › Beta-lactamase Inhibitory Protein; Chain:B, domain 1 › 0.67 36.0 3.51e-01 100.0% 46.4%
3k6qA02 3.30.160.620 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.66 46.0 4.36e-01 73.0% 86.5%
1vkzA02 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.62 37.0 3.81e-01 91.9% 62.9%
2l33A00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.55 36.0 3.42e-01 79.7% 54.9%
4e6xB00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.55 40.0 2.69e-01 78.4% 82.7%
2dmyA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.55 43.0 3.96e-01 97.3% 64.9%
4hvmD02 3.30.559.30 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Nonribosomal peptide synthetase, condensation domain 0.55 38.0 2.78e-01 71.6% 100.0%
3ke6B01 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.54 48.0 3.44e-01 100.0% 70.6%
6w0pA02 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.53 41.0 2.63e-01 86.5% 48.7%
4p6zM01 3.30.450.60 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.52 43.0 3.66e-01 90.5% 58.7%
1ospO01 2.40.128.160 Mainly Beta › Beta Barrel › Lipocalin › C1 set domains (antibody constant domain-like) 0.52 40.0 3.55e-01 91.9% 58.1%
1qo7A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 42.0 2.78e-01 95.9% 95.1%
5ksoA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 37.0 2.88e-01 77.0% 97.6%
1jw3A00 3.55.10.10 Alpha Beta › 3-Layer(bab) Sandwich › Archease, Possible Chaperone; Chain: A; domain 1 › Archease domain 0.51 36.0 2.94e-01 75.7% 85.0%
2xa7M01 3.30.450.60 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.50 42.0 3.63e-01 93.2% 59.2%
7nn3B01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.50 37.0 2.49e-01 81.1% 23.8%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3380188 252.2.1.1 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.89 62.0 7.14e-01 71.6% 100.0%
3335785 252.2.1.1 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.88 68.0 7.23e-01 79.7% 90.8%
3468885 252.2.1.1 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.87 66.0 6.41e-01 78.4% 73.8%
3333577 252.2.1.0 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.86 76.0 6.95e-01 94.6% 88.4%
3429505 252.2.1.1 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.86 75.0 6.50e-01 94.6% 91.8%
3370971 252.2.1.0 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.84 75.0 7.00e-01 95.9% 95.6%
3293480 252.2.1.1 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.84 65.0 6.97e-01 93.2% 92.3%
3331331 252.2.1.1 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.82 73.0 6.52e-01 95.9% 80.0%
3299337 252.2.1.1 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.82 72.0 6.50e-01 94.6% 87.8%
3467141 252.2.1.1 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.81 72.0 6.19e-01 94.6% 72.7%
3334492 252.2.1.0 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.78 69.0 6.70e-01 94.6% 87.5%
3440839 252.2.1.1 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.75 67.0 5.94e-01 94.6% 83.0%
3651077 252.2.1.0 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.75 60.0 6.18e-01 85.1% 97.1%
3991383 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.58 42.0 3.94e-01 82.4% 61.1%
3546736 389.1.2.1 few secondary structure elements › EGF-like › EGF-related › Complement control module/SCR domain › Sushi 0.58 30.0 3.35e-01 94.6% 61.7%
5082053 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.55 44.0 3.00e-01 85.1% 30.8%
4992459 4312.1.1.0 a+b two layers › RelE-like › RelE-like › RelE-like 0.55 32.0 3.28e-01 98.6% 61.4%
3585833 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.53 41.0 3.61e-01 83.8% 62.7%
4938243 295.1.1.0 a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.52 28.0 3.13e-01 81.1% 65.0%
3586911 101.1.9.0 alpha arrays › HTH › HTH › Putative DNA-binding domain 0.51 35.0 3.27e-01 71.6% 91.6%
3593588 7579.1.1.14 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Lipase_3 0.51 39.0 2.64e-01 81.1% 47.1%
3641797 5.3.1.0 beta duplicates or obligate multimers › beta-propeller-like › beta-Prism II › beta-Prism II 0.51 30.0 2.99e-01 100.0% 53.8%
5069282 244.2.1.0 a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain 0.50 35.0 3.21e-01 74.3% 54.0%