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S2_005_003_R2_scaffold_7_prodigal-single.1__X__X__00480

Bact-Vir

S2_005_003_R2_scaffold_7_prodigal-single.1__X__X__00480

Identity

Kingdom:
phage

Quality

74.8 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 73-115
PDB
Domain cluster: representative
CATH (50)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1r9wA00 3.40.1310.10 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.76 64.0 4.55e-01 100.0% 56.5%
1f08B00 3.40.1310.10 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.74 62.0 4.39e-01 100.0% 53.8%
2v94B00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.74 57.0 4.47e-01 86.0% 47.3%
2qsdA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.73 60.0 5.31e-01 97.7% 79.1%
1ywxA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.70 53.0 4.25e-01 86.0% 45.7%
1wgyA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.67 55.0 4.67e-01 97.7% 90.8%
4f4oC03 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.67 56.0 4.56e-01 100.0% 96.6%
1o22A00 3.90.1000.10 Alpha Beta › Alpha-Beta Complex › Orphan Protein Tm0875; Chain: A; › Hypothetical protein TM0875 0.66 53.0 3.84e-01 100.0% 98.7%
2q14A02 1.20.1250.30 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.65 54.0 3.64e-01 93.0% 84.3%
3vzbB02 2.60.200.40 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.65 56.0 3.65e-01 100.0% 95.9%
1i9gA01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.64 55.0 4.83e-01 97.7% 87.5%
2kk8A01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.64 55.0 4.71e-01 100.0% 86.3%
3bcwA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.64 46.0 3.53e-01 100.0% 32.7%
1mg7A01 3.30.70.1000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Switch protein XOL-1, GHMP-like 0.63 53.0 3.60e-01 100.0% 76.6%
1o54A01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.63 54.0 4.60e-01 100.0% 79.2%
1u1sA00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.63 54.0 4.74e-01 100.0% 69.7%
6djwA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.62 50.0 4.42e-01 100.0% 88.9%
1we6A00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.61 48.0 3.83e-01 100.0% 59.5%
2xi8A00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.61 45.0 4.00e-01 81.4% 86.4%
2d93A00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.61 50.0 3.48e-01 100.0% 29.1%
6fwvA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 47.0 3.79e-01 100.0% 42.2%
4gi3C00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.61 44.0 4.16e-01 97.7% 63.2%
3m62B00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.60 51.0 4.42e-01 100.0% 87.5%
2lvhA00 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.60 46.0 4.61e-01 100.0% 91.1%
1a21A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 48.0 3.89e-01 100.0% 43.9%
1et9A01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.60 45.0 3.62e-01 95.3% 90.0%
5e4bA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.59 46.0 3.21e-01 95.3% 92.6%
1wmhA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.59 48.0 4.06e-01 100.0% 90.4%
4umgA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 46.0 3.62e-01 100.0% 41.2%
4eswA02 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.57 45.0 3.53e-01 100.0% 90.1%
2xqyA03 2.60.40.3190 Mainly Beta › Sandwich › Immunoglobulin-like › Herpesvirus glycoprotein H, C-terminal domain 0.56 48.0 3.46e-01 100.0% 35.3%
4lesA00 2.60.40.1240 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 47.0 3.36e-01 100.0% 55.6%
3nyiB01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.56 46.0 3.12e-01 90.7% 31.8%
3d3kA00 3.40.50.10260 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › YjeF N-terminal domain 0.56 42.0 2.75e-01 90.7% 97.0%
2qqrA02 3.10.330.70 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.56 44.0 4.27e-01 97.7% 100.0%
2je8A04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 46.0 3.60e-01 100.0% 60.8%
2r6fA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.55 44.0 3.93e-01 100.0% 63.9%
3l4rA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.55 43.0 3.16e-01 100.0% 91.4%
2dl9A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 45.0 3.69e-01 100.0% 53.9%
4c2dA02 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.55 42.0 3.46e-01 86.0% 48.2%
3ewiB00 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.54 43.0 3.05e-01 97.7% 82.9%
1wh2A01 3.30.1490.40 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › GYF domain 0.53 40.0 3.73e-01 100.0% 63.9%
3of6E00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 43.0 3.44e-01 100.0% 50.0%
2krxA01 3.90.940.40 Alpha Beta › Alpha-Beta Complex › Eukaryotic RPB6 RNA polymerase subunit › Protein CHLORORESPIRATORY REDUCTION 7 0.53 45.0 3.89e-01 100.0% 97.2%
3nrfA00 2.60.40.4110 Mainly Beta › Sandwich › Immunoglobulin-like › Protein of unknown function DUF4354 0.53 42.0 3.41e-01 100.0% 53.9%
3vynA01 2.60.40.3780 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 41.0 3.43e-01 100.0% 47.1%
5ck3C00 3.30.450.60 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.52 36.0 2.84e-01 74.4% 75.2%
6efyA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 41.0 3.33e-01 100.0% 54.1%
3rkgA01 2.40.128.330 Mainly Beta › Beta Barrel › Lipocalin › 0.51 43.0 3.40e-01 100.0% 80.9%
2kt4B01 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.50 37.0 2.82e-01 93.0% 93.7%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3513859 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.90 80.0 7.56e-01 97.7% 98.0%
3625417 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.89 70.0 6.90e-01 83.7% 100.0%
4133804 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.88 69.0 7.13e-01 83.7% 100.0%
3852431 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.88 69.0 6.81e-01 83.7% 100.0%
3477651 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.88 77.0 7.12e-01 97.7% 98.2%
3392685 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.88 74.0 6.83e-01 93.0% 100.0%
3779996 140.1.1.0 ↗ 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 0.88 68.0 6.75e-01 83.7% 100.0%
5065436 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.85 76.0 6.61e-01 100.0% 89.1%
4951473 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.83 74.0 6.53e-01 100.0% 90.5%
3867498 2005.1.1.40 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1+tRNA-synt_1g 0.83 75.0 4.22e-01 100.0% 10.9%
4996552 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.83 74.0 5.86e-01 100.0% 67.1%
5029082 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.82 72.0 4.79e-01 100.0% 55.3%
4583560 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.81 71.0 7.04e-01 97.7% 100.0%
4514749 3115.2.1.0 ↗ a+b two layers › GP2-like › GP2 › GP2 0.81 69.0 6.85e-01 95.3% 100.0%
2831852 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.79 68.0 5.21e-01 100.0% 56.4%
5112 304.55.1.10 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › PPV_E1_DBD 0.76 64.0 4.55e-01 100.0% 56.5%
5014684 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.75 64.0 5.88e-01 100.0% 84.5%
3717869 221.4.1.9 ↗ a+b two layers › beta-Grasp › Nudix › Nudix › NUDIX_4 0.70 56.0 3.78e-01 90.7% 69.0%
1733393 244.1.1.8 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C › Trp_halogenase 0.70 58.0 4.68e-01 100.0% 87.1%
5067363 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.69 59.0 4.80e-01 95.3% 98.8%
4158495 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.67 55.0 4.50e-01 100.0% 90.0%
3213903 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.65 52.0 4.10e-01 93.0% 97.9%
3924113 221.7.1.1 ↗ a+b two layers › beta-Grasp › E2-binding domain of E1 › E2-binding domain of E1 › E2_bind 0.65 45.0 3.67e-01 76.7% 74.2%
5009755 4176.1.1.2 ↗ a/b three-layered sandwiches › a/b domain in CV3147-like proteins › a/b domain in CV3147-like proteins › a/b domain in CV3147-like proteins › S-Me-THD_N 0.64 54.0 3.51e-01 100.0% 20.0%
3217707 5001.1.1.106 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Str 0.64 56.0 3.28e-01 100.0% 33.0%
3289027 7581.1.1.0 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like 0.64 48.0 3.50e-01 81.4% 93.1%
4637265 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.63 51.0 3.70e-01 100.0% 30.7%
5025086 101.1.11.0 ↗ alpha arrays › HTH › HTH › Ribbon-helix-helix 0.62 54.0 5.06e-01 100.0% 96.4%
5003527 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.62 50.0 3.62e-01 100.0% 30.7%
3475431 133.1.1.0 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) 0.62 54.0 3.33e-01 100.0% 40.4%
3617484 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.61 48.0 4.55e-01 100.0% 74.5%
3728216 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.60 45.0 2.59e-01 81.4% 29.8%
4945733 2006.1.3.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain 0.60 50.0 3.19e-01 100.0% 20.4%
4182437 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.60 51.0 3.96e-01 100.0% 59.0%
5050775 2492.1.1.0 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.59 47.0 3.64e-01 100.0% 37.3%
3991455 822.2.1.1 ↗ a+b two layers › GYF/BRK domain-like › BRK domain-like › BRK domain-like › BRK 0.59 46.0 4.29e-01 97.7% 69.1%
4540341 2003.1.1.48 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › YjeF_N 0.59 47.0 3.03e-01 97.7% 99.6%
3958896 4187.2.1.0 ↗ a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 0.57 48.0 4.40e-01 97.7% 73.3%
4681335 304.28.1.0 ↗ a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.57 46.0 3.48e-01 95.3% 92.2%
3352699 375.1.1.2 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Rubredoxin 0.57 44.0 4.34e-01 97.7% 88.0%
1088882 11.4.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Antigen MPT63/MPB63 (immunoprotective extracellular protein) › Antigen MPT63/MPB63 (immunoprotective extracellular protein) 0.56 47.0 3.36e-01 100.0% 55.6%
1937230 2010.1.1.1 ↗ a/b three-layered sandwiches › EDD domain › EDD domain › EDD domain › DegV 0.56 46.0 3.10e-01 90.7% 31.2%
3281173 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.56 39.0 4.04e-01 97.7% 91.4%
3964745 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.56 49.0 4.02e-01 100.0% 76.2%
168756 2003.1.1.48 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › YjeF_N 0.56 43.0 2.81e-01 93.0% 97.0%
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 0.55 44.0 2.72e-01 100.0% 15.8%
3618240 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.54 45.0 3.52e-01 100.0% 75.0%
4331897 235.1.1.41 ↗ a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › TraH_2 0.53 42.0 3.01e-01 95.3% 42.7%
3442611 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.52 44.0 2.59e-01 100.0% 87.4%
1546392 10.2.1.66 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › STIV-like_capsid 0.50 42.0 2.86e-01 97.7% 46.9%