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gwf2_scaffold_96_prodigal-single.1__X__X__00229

Bact-Vir

gwf2_scaffold_96_prodigal-single.1__X__X__00229

Identity

Kingdom:
phage

Quality

63.7 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 491-670
PDB
D2 medium residues 28-126_223-240
PDB
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1dikA01 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.60 45.0 4.11e-01 77.8% 68.0%
3f7pD01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 38.0 4.28e-01 97.4% 84.6%
6mfaA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 37.0 4.34e-01 97.4% 97.5%
2dm4A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 38.0 4.18e-01 97.4% 85.1%
6hyfA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 38.0 4.00e-01 92.3% 75.5%
2dn7A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 37.0 3.92e-01 98.3% 72.9%
7y8sB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 37.0 4.22e-01 97.4% 92.0%
1x5lA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 37.0 4.13e-01 97.4% 90.9%
2edyA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 37.0 3.92e-01 92.3% 77.7%
4p04A01 2.60.40.3100 Mainly Beta › Sandwich › Immunoglobulin-like › Arylsulphate sulphotransferase monomer, N-terminal domain 0.54 37.0 3.92e-01 91.5% 78.3%
5hccB02 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.54 37.0 4.03e-01 98.3% 86.3%
5jtwA02 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.54 37.0 3.93e-01 96.6% 82.0%
5e55B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 38.0 4.15e-01 97.4% 92.5%
5e53A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 38.0 4.14e-01 97.4% 91.4%
4n5uA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 37.0 3.85e-01 93.2% 78.7%
3c12A02 2.60.40.4070 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 35.0 3.92e-01 88.9% 92.0%
2xzlA02 2.40.30.230 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.52 32.0 3.80e-01 73.5% 92.4%
2a74A02 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.51 36.0 3.80e-01 97.4% 84.2%
2v5yA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 36.0 3.83e-01 92.3% 84.3%
7ox5A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 39.0 4.16e-01 97.4% 94.2%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
185296 862.1.1.4 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › RepB_primase 0.76 58.0 4.70e-01 78.6% 78.9%
5011497 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.65 61.0 5.02e-01 100.0% 94.0%
3215148 11.1.1.2 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.64 41.0 4.70e-01 98.3% 88.2%
3627192 11.1.4.71 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › NOMO1-like_7th 0.61 35.0 4.29e-01 87.2% 91.4%
3230798 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 40.0 4.38e-01 95.7% 85.3%
3854504 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 39.0 4.42e-01 97.4% 94.1%
5051647 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.57 52.0 4.10e-01 100.0% 84.2%
3550207 11.1.1.2 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.57 39.0 4.06e-01 97.4% 77.1%
4385229 206.1.1.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.56 39.0 2.48e-01 93.2% 13.1%
3539074 11.1.1.2 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.56 38.0 4.18e-01 97.4% 86.3%
4162915 11.1.1.31 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › MG2 0.54 38.0 3.85e-01 96.6% 73.9%
3878741 11.1.1.2 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.53 38.0 4.06e-01 96.6% 86.0%
4030677 1116.1.1.0 a+b two layers › Polycystin-mucolipin domain › Polycystin-mucolipin domain › Polycystin-mucolipin domain 0.52 39.0 3.66e-01 80.3% 82.0%
4263639 323.1.1.0 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.51 45.0 3.89e-01 99.1% 64.7%
3533876 10.32.1.0 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.50 34.0 3.50e-01 91.5% 70.4%
D3 medium residues 127-222_241-278
PDB
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2faoA01 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.72 61.0 4.72e-01 89.6% 82.3%
3h20A02 3.30.70.1790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RepB DNA-primase, N-terminal domain 0.67 50.0 5.72e-01 78.4% 100.0%
5axmB00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.62 45.0 3.68e-01 73.9% 96.2%
2d9oA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.60 40.0 4.49e-01 70.9% 89.0%
2r7rA04 3.30.70.2480 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 42.0 4.00e-01 71.6% 85.4%
4lowA00 3.30.1360.20 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Transcriptional coactivator/pterin dehydratase 0.60 34.0 4.11e-01 95.5% 86.9%
5wm1A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.59 44.0 4.81e-01 94.8% 94.5%
1r89A03 3.30.70.590 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Poly(A) polymerase predicted RNA binding domain 0.56 40.0 4.04e-01 73.9% 86.6%
4er8A00 3.30.70.1290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Transposase IS200-like 0.54 39.0 3.70e-01 76.1% 83.6%
3znuA00 3.30.70.1060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel 0.54 33.0 3.89e-01 76.1% 88.3%
1rniA02 3.30.2250.10 Alpha Beta › 2-Layer Sandwich › Prim-pol fold › Bifunctional DNA primase/polymerase domain 0.53 40.0 4.26e-01 94.8% 93.0%
4clfA02 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.51 44.0 4.01e-01 94.0% 97.8%
2lu1A00 3.30.70.2370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 33.0 3.87e-01 94.8% 96.6%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4441734 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.84 70.0 6.13e-01 85.8% 69.7%
5004227 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.81 70.0 5.59e-01 91.8% 61.2%
2721360 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.79 67.0 5.92e-01 89.6% 64.3%
3589190 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.77 71.0 5.78e-01 96.3% 59.6%
3602638 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.76 65.0 4.53e-01 90.3% 36.0%
5059790 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.74 68.0 4.77e-01 100.0% 89.6%
3959043 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.72 65.0 4.85e-01 97.8% 68.9%
1779551 862.1.1.5 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.72 61.0 4.63e-01 89.6% 78.6%
2711606 862.1.1.5 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.72 66.0 4.87e-01 99.3% 72.7%
5011497 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.71 56.0 4.84e-01 82.8% 58.0%
None 0.70 64.0 4.83e-01 99.3% 71.9%
4986859 862.1.1.5 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.70 59.0 4.51e-01 90.3% 73.2%
4987159 862.1.1.5 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.68 54.0 4.31e-01 83.6% 72.3%
4031372 862.1.1.12 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › PF29905 0.68 60.0 5.20e-01 94.8% 65.5%
3284431 862.1.1.5 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.67 62.0 4.65e-01 99.3% 72.6%
4962169 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.66 49.0 4.01e-01 76.1% 78.4%
4315665 304.8.1.91 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › DUF1424 0.65 47.0 4.03e-01 74.6% 82.4%
4048379 304.55.1.24 a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › DUF1424 0.64 47.0 4.06e-01 76.1% 86.3%
185296 862.1.1.4 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › RepB_primase 0.63 55.0 4.77e-01 92.5% 76.9%
4242475 304.28.1.4 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › SecD_1st 0.62 38.0 4.61e-01 74.6% 100.0%
4102871 304.28.1.13 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › MMPL 0.61 44.0 2.79e-01 74.6% 59.3%
4126752 304.20.1.5 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › tRNA_synt_2f 0.61 42.0 3.54e-01 70.1% 96.4%
5068786 304.28.1.0 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.60 39.0 4.50e-01 75.4% 92.6%
5058809 1075.1.2.1 alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.60 42.0 2.79e-01 71.6% 21.3%
4247266 304.20.1.5 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › tRNA_synt_2f 0.59 40.0 3.35e-01 70.1% 90.8%
3962574 5067.1.1.0 alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain 0.58 41.0 2.83e-01 72.4% 49.0%
3322835 304.20.1.5 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › tRNA_synt_2f 0.57 42.0 3.51e-01 75.4% 97.8%
5037866 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.57 41.0 3.66e-01 73.9% 95.3%
5026545 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.57 41.0 3.70e-01 73.9% 92.9%
3790536 3122.1.1.1 a+b complex topology › MESD › MESD › MESD › Mesd 0.57 38.0 4.26e-01 95.5% 90.0%
5033367 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.56 39.0 3.52e-01 70.9% 89.7%
4930192 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.56 40.0 3.70e-01 73.9% 96.6%
4092955 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.56 39.0 3.64e-01 70.9% 96.4%
4552979 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.55 39.0 3.67e-01 71.6% 95.0%
4942434 304.28.1.0 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.55 37.0 4.27e-01 76.1% 96.8%
3315278 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 0.54 40.0 4.10e-01 76.1% 92.0%
5078562 304.55.2.1 a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like › Y1_Tnp 0.52 39.0 3.54e-01 79.1% 83.8%
3419698 390.1.1.0 few secondary structure elements › Hairpin loop containing domain-like › Hairpin loop containing domain-like › Hairpin loop containing domain-like 0.52 26.0 3.28e-01 70.9% 80.0%
4945348 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.51 37.0 3.86e-01 74.6% 88.3%
4251107 321.1.1.6 a+b two layers › Glutamine synthetase-like › Glutamine synthetase/guanido kinase › Glutamine synthetase/guanido kinase › Pup_ligase 0.51 45.0 3.26e-01 100.0% 89.4%
D4 medium residues 393-489
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5cq2A02 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.61 28.0 3.97e-01 70.1% 97.7%
2i2lA01 2.10.70.50 Mainly Beta › Ribbon › Complement Module; domain 1 › 0.58 30.0 3.95e-01 77.3% 94.2%
1ospO02 3.90.930.1 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › 0.52 36.0 3.17e-01 71.1% 89.0%
8adlB01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.51 38.0 2.72e-01 80.4% 72.6%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3587270 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.87 79.0 7.37e-01 97.9% 80.9%
4964255 601.7.1.0 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.56 44.0 3.57e-01 99.0% 44.3%
2740640 64.1.1.1 beta meanders › WW domain-like › WW domain › WW domain › WW 0.55 30.0 3.59e-01 72.2% 83.1%
3172864 331.3.1.17 a+b two layers › TBP-like › Bet v1-like › Bet v1-like › VASt 0.54 44.0 3.51e-01 93.8% 87.0%
3877814 4357.1.1.5 beta barrels › WWE domain › WWE domain › WWE domain › WWE_4 0.52 27.0 3.20e-01 76.3% 72.3%
4467900 6129.1.1.1 beta barrels › Repulsive guidance molecule (RGM) family › Repulsive guidance molecule (RGM) family › Repulsive guidance molecule (RGM) family › VWD 0.50 42.0 3.35e-01 94.8% 80.0%