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SRR1747065_scaffold_5_prodigal-single.1__X__X__00032

Bact-Vir

SRR1747065_scaffold_5_prodigal-single.1__X__X__00032

Identity

Kingdom:
phage

Quality

94.3 mean pLDDT

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 362-461
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF07733.19 best DNA_pol3_alpha 91.5 1.00e-25 98.0% 35.0%
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2mqaA00 1.10.274.60 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain 0.67 45.0 4.20e-01 95.0% 55.2%
1tj7A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.58 41.0 4.05e-01 96.0% 68.6%
3h4cA01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.54 47.0 4.84e-01 98.0% 97.9%
2i53A01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.53 48.0 4.28e-01 100.0% 75.5%
1c9bA01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.51 42.0 4.31e-01 96.0% 91.8%
2q0tB01 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.50 40.0 3.08e-01 88.0% 91.5%
ECOD (24)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4064450 316.1.1.17 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › DNA_pol3_alpha 0.97 91.0 6.32e-01 100.0% 35.9%
4156755 316.1.1.17 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › DNA_pol3_alpha 0.94 81.0 5.97e-01 100.0% 40.5%
1117589 316.1.1.17 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › DNA_pol3_alpha 0.92 89.0 5.94e-01 100.0% 41.9%
4142452 316.1.1.17 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › DNA_pol3_alpha 0.91 84.0 6.01e-01 100.0% 38.4%
4660116 316.1.1.17 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › DNA_pol3_alpha 0.86 79.0 5.52e-01 100.0% 34.6%
4074186 4953.1.1.32 beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › NA37 0.76 47.0 4.94e-01 96.0% 68.9%
4106111 4009.1.1.11 alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › NA37 0.75 46.0 4.90e-01 96.0% 68.9%
3247352 174.1.1.0 few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.63 42.0 3.90e-01 89.0% 53.6%
3824761 142.1.1.0 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.61 41.0 4.78e-01 93.0% 98.6%
4954713 186.1.1.0 alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.55 50.0 4.76e-01 100.0% 90.0%
3981019 3950.1.1.1 alpha complex topology › Bacterial vitamin C transporter UlaA/SgaT › Bacterial vitamin C transporter UlaA/SgaT › Bacterial vitamin C transporter UlaA/SgaT › EIIC-GAT 0.55 47.0 3.13e-01 98.0% 70.4%
4030134 101.1.10.3 alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.53 47.0 4.24e-01 100.0% 70.4%
5076381 101.1.10.3 alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.53 44.0 4.49e-01 98.0% 90.0%
4950795 131.1.1.3 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.52 43.0 3.47e-01 89.0% 75.6%
5078898 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.52 46.0 4.53e-01 98.0% 94.5%
5026540 101.1.10.3 alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.52 46.0 4.58e-01 100.0% 90.5%
3255346 101.1.10.1 alpha arrays › HTH › HTH › Cyclin-like › Cyclin_N 0.52 48.0 4.37e-01 100.0% 86.9%
5064398 101.1.10.3 alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.52 45.0 4.53e-01 98.0% 93.0%
4978149 101.1.10.3 alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.52 45.0 4.61e-01 99.0% 97.9%
4969272 101.1.10.3 alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.52 47.0 4.39e-01 100.0% 81.7%
3754716 101.1.17.0 alpha arrays › HTH › HTH › FF domain 0.52 41.0 3.74e-01 86.0% 76.3%
3721781 101.1.10.3 alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.51 44.0 3.74e-01 100.0% 57.0%
3227203 101.1.10.3 alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.50 44.0 3.88e-01 100.0% 64.7%
3940293 188.1.1.0 alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain 0.50 46.0 3.52e-01 100.0% 64.1%
D2 medium residues 79-126
PDB
Domain cluster: representative
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1yfmA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.78 69.0 5.01e-01 97.9% 65.9%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.78 53.0 3.94e-01 70.8% 30.8%
4kb2A01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.78 53.0 4.00e-01 70.8% 33.0%
3qnmA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.77 53.0 4.26e-01 70.8% 47.8%
2e9fB01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.77 68.0 5.40e-01 100.0% 81.2%
6ig5A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.76 67.0 4.82e-01 100.0% 56.5%
6vudA01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.76 53.0 3.99e-01 70.8% 33.0%
1tj7A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.76 65.0 5.07e-01 97.9% 73.3%
3c8tA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.73 64.0 5.08e-01 100.0% 79.4%
4k7rA01 1.20.1600.10 Mainly Alpha › Up-down Bundle › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) 0.70 53.0 3.15e-01 83.3% 54.4%
1c3cA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.69 59.0 4.85e-01 100.0% 81.3%
1vq8P03 1.10.1200.60 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › 0.67 55.0 5.27e-01 91.7% 90.9%
1bcrA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.65 56.0 3.59e-01 100.0% 23.6%
1bxiA00 1.10.1200.20 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Colicin E immunity protein 0.65 39.0 3.24e-01 81.2% 36.1%
2n7zA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.63 53.0 4.15e-01 95.8% 50.9%
2o38A01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.62 50.0 4.63e-01 93.8% 78.5%
2fnaA02 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.62 45.0 3.89e-01 79.2% 76.3%
5jazA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.61 50.0 4.10e-01 91.7% 74.7%
6mh4A03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.61 50.0 4.22e-01 89.6% 74.7%
2y1eA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.61 52.0 4.23e-01 93.8% 74.7%
3iieB03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.61 52.0 4.25e-01 93.8% 74.1%
1zp2A02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.59 46.0 3.72e-01 97.9% 73.2%
2v3sA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.57 46.0 3.74e-01 91.7% 71.9%
6dv2G02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.57 52.0 3.41e-01 100.0% 73.4%
2yfqB01 1.10.8.1210 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.57 42.0 4.17e-01 93.8% 75.0%
5dicA00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.57 46.0 3.69e-01 100.0% 42.6%
2pbiA02 1.10.1240.60 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.56 42.0 3.33e-01 81.2% 79.2%
1m6yA02 1.10.150.170 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative methyltransferase TM0872, insert domain 0.55 44.0 3.65e-01 100.0% 76.2%
1w36F02 1.10.10.160 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.53 42.0 3.49e-01 95.8% 85.0%
3llmA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 44.0 2.91e-01 93.8% 29.8%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3509327 2003.1.2.12 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › DAO 0.86 59.0 3.32e-01 70.8% 64.7%
4169323 4952.1.1.1 alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › Lyase_1 0.80 74.0 5.20e-01 100.0% 68.9%
5023598 4952.1.1.0 alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.80 67.0 5.21e-01 91.7% 72.0%
4251398 4952.1.1.0 alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.80 65.0 5.06e-01 91.7% 76.2%
3386456 3718.1.1.0 alpha bundles › Flagellar protein fliT › Flagellar protein fliT › Flagellar protein fliT 0.79 54.0 4.47e-01 70.8% 42.5%
4933446 4952.1.1.0 alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.76 69.0 5.34e-01 100.0% 73.0%
4168631 101.1.6.20 alpha arrays › HTH › HTH › TrpR › PF28388 0.75 45.0 4.42e-01 95.8% 58.0%
3392566 3929.1.1.2 alpha bundles › THO1 C-terminal domain › THO1 C-terminal domain › THO1 C-terminal domain › DUF7084 0.71 55.0 5.51e-01 95.8% 87.5%
3961272 632.3.1.9 alpha bundles › immunoglobulin/albumin-binding domain-like › Phosphoprotein XD domain › Phosphoprotein XD domain › DUF1707 0.71 57.0 5.91e-01 87.5% 100.0%
3955218 632.2.1.17 alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › DUF1707 0.71 57.0 5.90e-01 87.5% 100.0%
3960029 632.3.1.9 alpha bundles › immunoglobulin/albumin-binding domain-like › Phosphoprotein XD domain › Phosphoprotein XD domain › DUF1707 0.71 59.0 6.10e-01 89.6% 100.0%
3277930 632.2.1.17 alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › DUF1707 0.70 59.0 5.85e-01 91.7% 96.0%
3286824 632.2.1.17 alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › DUF1707 0.69 56.0 5.83e-01 87.5% 100.0%
3952457 632.2.1.17 alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › DUF1707 0.69 61.0 5.87e-01 97.9% 90.9%
3509762 311.1.1.2 a+b three layers › Phoshotransferase/anion transport protein › Phoshotransferase/anion transport protein › Phoshotransferase/anion transport protein › Band_3_cyto 0.69 47.0 3.37e-01 89.6% 25.2%
4026676 110.1.1.0 alpha arrays › DEATH domain › DEATH domain › DEATH domain 0.69 59.0 5.28e-01 93.8% 69.2%
3353641 3361.1.1.3 alpha bundles › C-terminal Pdr1-activating domain of J-protein Zuo1 › C-terminal Pdr1-activating domain of J-protein Zuo1 › C-terminal Pdr1-activating domain of J-protein Zuo1 › VIN3_C 0.68 57.0 5.00e-01 91.7% 92.9%
3282626 632.3.1.9 alpha bundles › immunoglobulin/albumin-binding domain-like › Phosphoprotein XD domain › Phosphoprotein XD domain › DUF1707 0.66 55.0 5.64e-01 89.6% 100.0%
3288394 632.2.1.17 alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › DUF1707 0.66 57.0 5.51e-01 97.9% 90.9%
3465537 7579.1.1.5 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Peptidase_S10 0.64 51.0 3.32e-01 100.0% 22.6%
3431353 1128.1.1.10 alpha bundles › LYR protein › LYR protein › LYR protein › VIN3_C 0.62 56.0 4.92e-01 100.0% 75.7%
4275352 166.1.1.1 alpha superhelices › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › DXPR_C 0.62 51.0 4.04e-01 91.7% 64.2%
3901819 193.1.1.18 alpha bundles › CH domain-like › Calponin-homology domain-like › Calponin-homology domain-like › DUF2465 0.61 48.0 3.79e-01 100.0% 38.4%
4257656 166.1.1.1 alpha superhelices › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › DXPR_C 0.60 53.0 4.27e-01 97.9% 71.1%
4013825 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.59 49.0 4.24e-01 91.7% 93.3%
2504456 7069.1.1.1 alpha complex topology › Head domain of SBV glycoprotein Gc › Head domain of SBV glycoprotein Gc › Head domain of SBV glycoprotein Gc › Bunya_G1 0.59 50.0 3.22e-01 100.0% 39.8%
4263712 166.1.1.1 alpha superhelices › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › DXPR_C 0.58 51.0 4.04e-01 97.9% 66.3%
3962789 608.1.1.1 alpha arrays › AhpD-like › AhpD-like › AhpD-like › CMD 0.56 46.0 3.07e-01 87.5% 68.8%
4342279 103.1.1.6 alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › RuvA_C 0.56 46.0 4.35e-01 100.0% 75.0%
3617454 101.1.1.76 alpha arrays › HTH › HTH › Three-helical HTH › Integrase_H2C2 0.55 37.0 3.67e-01 93.8% 66.0%
3403652 632.13.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like 0.54 39.0 4.14e-01 85.4% 100.0%
3793635 632.13.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like 0.54 42.0 4.22e-01 95.8% 90.0%
3988499 632.13.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like 0.54 39.0 3.90e-01 85.4% 80.0%
4148430 103.1.1.6 alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › RuvA_C 0.51 41.0 4.07e-01 93.8% 92.0%