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JGI24723J26617_10000007_prodigal-single.1__X__X__00351

Bact-Vir

JGI24723J26617_10000007_prodigal-single.1__X__X__00351

Identity

Kingdom:
phage

Quality

67.5 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 3-46
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ek0A00 3.30.110.20 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain 0.71 51.0 4.07e-01 77.3% 46.7%
2cpxA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.70 57.0 4.92e-01 100.0% 57.0%
2pn2A00 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.69 57.0 4.16e-01 100.0% 39.4%
2b4vA03 3.30.70.1970 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.69 52.0 4.20e-01 100.0% 40.4%
4k3cA01 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.65 47.0 3.97e-01 81.8% 51.2%
3evzA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.65 46.0 3.15e-01 79.5% 20.5%
1wvqA00 3.40.1520.10 Alpha Beta › 3-Layer(aba) Sandwich › hypothetical protein tt1634 › Ta1353-like 0.64 51.0 3.63e-01 100.0% 41.7%
4rx6D00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 52.0 4.10e-01 100.0% 52.3%
2nrqA00 3.30.1440.10 Alpha Beta › 2-Layer Sandwich › 50s Ribosomal Protein L5; Chain: A, › Ribosomal protein L5 0.63 54.0 3.86e-01 100.0% 61.3%
4ozjA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 51.0 4.09e-01 100.0% 45.2%
2azeB00 6.10.250.540 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.63 44.0 3.44e-01 88.6% 32.7%
1htwA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.62 48.0 3.52e-01 97.7% 89.2%
4ebjA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.61 47.0 3.58e-01 95.5% 36.7%
7o4xA01 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 49.0 4.00e-01 100.0% 51.5%
1p1lA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 48.0 3.91e-01 100.0% 53.9%
4noiA01 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.60 45.0 3.81e-01 100.0% 56.3%
3o27B00 2.10.260.10 Mainly Beta › Ribbon › Pemi-like Protein 1; Chain: D › 0.60 43.0 4.02e-01 77.3% 77.2%
1j2vA00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 47.0 3.86e-01 100.0% 54.5%
1whnA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.59 49.0 3.90e-01 100.0% 65.3%
2qzbA00 2.60.460.10 Mainly Beta › Sandwich › protein yfey like fold › protein yfey like domain 0.59 46.0 3.39e-01 97.7% 86.9%
4ivkA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.58 49.0 2.89e-01 100.0% 17.6%
1zkkB00 2.170.270.10 Mainly Beta › Beta Complex › Beta-clip-like › SET domain 0.58 41.0 2.91e-01 79.5% 21.7%
2n8lA00 3.30.310.210 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › 0.58 46.0 3.18e-01 100.0% 26.2%
3aonA00 1.10.287.3240 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.58 41.0 2.79e-01 79.5% 33.5%
2wnyA00 3.30.1440.10 Alpha Beta › 2-Layer Sandwich › 50s Ribosomal Protein L5; Chain: A, › Ribosomal protein L5 0.58 47.0 3.45e-01 100.0% 52.6%
6zzmA01 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.58 48.0 3.14e-01 100.0% 66.2%
3go9A02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.57 45.0 3.04e-01 100.0% 23.5%
5cm2Z00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.57 37.0 2.55e-01 84.1% 15.2%
7qssA01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.57 46.0 3.09e-01 95.5% 37.2%
1cx8A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.56 47.0 2.88e-01 100.0% 24.8%
1ti2B01 3.30.70.20 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 46.0 3.40e-01 100.0% 62.4%
4kt5C00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.56 41.0 3.38e-01 84.1% 39.8%
2v8qB00 6.20.250.60 Special › Other non-globular › Double Stranded RNA Binding Domain › 0.55 39.0 3.35e-01 77.3% 61.6%
1oi2A02 3.30.1180.20 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › Dihydroxyacetone kinase; domain 2 0.55 38.0 2.71e-01 77.3% 22.8%
2yxdA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.55 46.0 3.12e-01 100.0% 41.3%
5b55A01 3.40.50.1100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.54 38.0 2.62e-01 75.0% 34.2%
4dzdA01 3.30.70.1200 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Crispr-associated protein; domain 1 0.54 43.0 3.88e-01 97.7% 64.3%
3ks7A02 2.60.120.230 Mainly Beta › Sandwich › Jelly Rolls › 0.54 42.0 2.92e-01 95.5% 70.9%
5dymA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.54 38.0 3.14e-01 81.8% 41.7%
1l3iA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 43.0 2.98e-01 100.0% 40.5%
1itpA00 3.30.70.80 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Peptidase S8 propeptide/proteinase inhibitor I9 0.53 38.0 3.43e-01 100.0% 51.9%
1v1qA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 41.0 3.15e-01 88.6% 86.4%
6vq6H01 1.10.287.3240 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 36.0 2.49e-01 75.0% 29.9%
4ad8A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 35.0 2.22e-01 75.0% 77.0%
3wgtA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 35.0 2.45e-01 79.5% 65.2%
2e55A00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 39.0 2.71e-01 100.0% 48.6%
2mlgA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.50 35.0 3.03e-01 75.0% 44.2%
1y4uB01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.50 38.0 2.70e-01 100.0% 28.9%
ECOD (49)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2085058 2004.1.1.14 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › GTP_EFTU 0.73 53.0 3.73e-01 79.5% 46.2%
3254433 3012.1.1.0 a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain 0.73 61.0 4.92e-01 100.0% 47.8%
5032176 1.1.3.2 beta barrels › cradle loop barrel › RIFT-related › AbrB › MazE_antitoxin 0.72 52.0 4.70e-01 77.3% 65.0%
3419370 6063.1.1.0 alpha duplicates or obligate multimers › BNIP3 transmembrane domain › BNIP3 transmembrane domain › BNIP3 transmembrane domain 0.71 56.0 5.48e-01 100.0% 80.0%
4285299 3121.1.1.1 a+b duplicates or obligate multimers › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain › POTRA 0.71 52.0 4.35e-01 81.8% 50.0%
3687618 304.9.1.79 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › PF28976 0.69 58.0 4.01e-01 100.0% 29.1%
3826354 376.1.3.10 few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › PHD_2,zf-HC5HC2H_2 0.69 48.0 3.26e-01 75.0% 95.3%
5075421 267.1.1.3 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 › Cation_ATPase 0.68 48.0 3.04e-01 77.3% 39.2%
3484326 7579.1.1.0 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases 0.68 48.0 2.95e-01 77.3% 28.0%
3163632 3313.1.1.1 a+b two layers › Uncharacterized protein VC_A0919 › Uncharacterized protein VC_A0919 › Uncharacterized protein VC_A0919 › DUF406 0.68 54.0 4.69e-01 100.0% 60.0%
5027694 1.1.3.0 beta barrels › cradle loop barrel › RIFT-related › AbrB 0.65 48.0 4.52e-01 79.5% 70.4%
4538961 304.14.1.1 a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) › SPOR 0.64 50.0 4.43e-01 100.0% 69.3%
5056727 3926.1.1.1 alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D › ATP-synt_D 0.63 46.0 3.01e-01 79.5% 28.8%
4330210 327.6.1.6 a+b two layers › Alpha-lytic protease prodomain-like › Fe-S cluster assembly (FSCA) domain-like › Fe-S cluster assembly (FSCA) domain-like › Secretin 0.63 53.0 3.29e-01 100.0% 75.6%
5011019 3268.1.1.0 a+b two layers › N-terminal domain in xanthine dehydrogenase › N-terminal domain in xanthine dehydrogenase › N-terminal domain in xanthine dehydrogenase 0.62 47.0 4.15e-01 93.2% 54.3%
5030555 3433.1.1.0 a+b duplicates or obligate multimers › ParB dimerization domain › ParB dimerization domain › Plasmid-encoded ParB dimerization domain 0.62 48.0 4.95e-01 97.7% 95.0%
4933528 3926.1.1.1 alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D › ATP-synt_D 0.62 44.0 2.87e-01 77.3% 28.6%
4598415 3926.1.1.1 alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D › ATP-synt_D 0.62 44.0 2.91e-01 77.3% 29.0%
3663211 309.1.1.2 a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase › Peptidase_M16,Peptidase_M16_C 0.62 44.0 2.74e-01 77.3% 46.8%
4931923 304.5.1.7 a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › DUF2179 0.62 51.0 4.33e-01 100.0% 58.7%
5078891 1.1.3.2 beta barrels › cradle loop barrel › RIFT-related › AbrB › MazE_antitoxin 0.62 43.0 4.06e-01 75.0% 92.7%
5051923 304.8.1.12 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_8 0.61 47.0 4.42e-01 100.0% 70.0%
5078639 3926.1.1.1 alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D › ATP-synt_D 0.61 44.0 2.95e-01 79.5% 28.9%
4120506 243.11.1.4 a+b two layers › Cystatin-like › NP_346341.1 protein › NP_346341.1 protein › PF29632 0.61 44.0 3.70e-01 77.3% 60.0%
5000798 3926.1.1.1 alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D › ATP-synt_D 0.61 43.0 2.90e-01 77.3% 29.2%
3586391 3937.1.1.2 alpha bundles › Connexin 26 › Connexin 26 › Connexin 26 › Innexin 0.60 42.0 2.56e-01 75.0% 59.0%
4981316 3926.1.1.1 alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D › ATP-synt_D 0.60 43.0 2.88e-01 79.5% 29.5%
3187032 3926.1.1.1 alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D › ATP-synt_D 0.60 42.0 2.79e-01 75.0% 30.2%
4953653 304.114.1.0 a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.60 47.0 4.17e-01 100.0% 60.0%
3819021 2003.1.5.73 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.60 47.0 3.02e-01 93.2% 53.1%
5027304 3926.1.1.1 alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D › ATP-synt_D 0.59 40.0 2.81e-01 75.0% 36.0%
3659492 109.2.1.0 alpha superhelices › Repetitive alpha hairpins › alpha/alpha toroid › alpha/alpha toroid 0.58 49.0 2.69e-01 100.0% 14.7%
4943172 3926.1.1.1 alpha bundles › V-type proton ATPase subunit D › V-type proton ATPase subunit D › V-type proton ATPase subunit D › ATP-synt_D 0.58 42.0 2.81e-01 79.5% 32.0%
3038102 1.1.3.0 beta barrels › cradle loop barrel › RIFT-related › AbrB 0.58 43.0 4.04e-01 81.8% 69.6%
4949473 5086.1.1.230 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › ATP-synt_D 0.58 41.0 2.72e-01 79.5% 29.0%
3596282 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.57 43.0 3.64e-01 100.0% 44.2%
3508353 2484.1.1.1 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.57 38.0 2.45e-01 72.7% 12.0%
4961983 3755.1.1.32 alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related › ATP-synt_D 0.57 40.0 2.62e-01 77.3% 26.5%
3365774 109.4.1.1560 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_3, E_motif 0.57 43.0 2.56e-01 86.4% 68.2%
4402684 7573.1.1.4 a/b three-layered sandwiches › PRTase-like › PRTase-like › PRTase-like › UPRTase 0.56 41.0 2.71e-01 81.8% 39.0%
3271024 2003.1.5.73 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.55 39.0 2.68e-01 79.5% 46.3%
3701882 331.4.1.0 a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 0.55 39.0 3.16e-01 75.0% 37.9%
4931277 101.1.2.14 alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.54 39.0 2.81e-01 81.8% 57.4%
3941757 101.1.9.32 alpha arrays › HTH › HTH › Putative DNA-binding domain › ANT 0.53 41.0 3.05e-01 90.9% 34.6%
4981961 101.1.2.819 alpha arrays › HTH › HTH › winged helix domain › PF27231 0.53 41.0 2.87e-01 88.6% 75.0%
5023262 327.11.2.82 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › PF27275 0.53 39.0 3.73e-01 100.0% 75.4%
3317524 225.1.1.0 a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.52 39.0 2.69e-01 95.5% 70.2%
5047947 5050.1.1.0 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.52 40.0 2.65e-01 100.0% 66.8%
3896484 220.1.1.7 beta barrels › PH domain-like › PH domain-like › PH domain-like › IRS 0.50 39.0 3.01e-01 93.2% 74.2%