Back to structures

NC_052972.1__YP_009997444.1__JT314_gp63__00063

Bact-Vir

NC_052972.1__YP_009997444.1__JT314_gp63__00063

Identity

Accession:
NC_052972 ↗
Kingdom:
phage

Quality

69.1 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 medium residues 144-211
PDB
Domain cluster: representative
CATH (52)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1zoyD00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.85 70.0 6.05e-01 95.6% 58.8%
5uh5D02 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.82 63.0 4.93e-01 82.4% 40.6%
2vkzA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.80 71.0 4.73e-01 98.5% 29.8%
2uv8A07 6.10.140.1410 Special › Helix non-globular › Helix Hairpins › 0.80 71.0 6.61e-01 100.0% 85.9%
3nkuA00 1.10.357.170 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.79 66.0 4.80e-01 91.2% 39.2%
2rdcA00 1.10.287.800 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › protein ne1242 0.78 65.0 5.15e-01 89.7% 45.9%
3onjA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.75 64.0 5.66e-01 94.1% 70.1%
6lumG01 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.74 65.0 5.51e-01 98.5% 59.8%
3zdmB00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.73 46.0 5.17e-01 75.0% 86.0%
4okvE00 6.10.140.1890 Special › Helix non-globular › Helix Hairpins › 0.72 60.0 6.08e-01 97.1% 98.5%
6qumQ00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.71 57.0 5.56e-01 88.2% 100.0%
1avoB00 1.20.120.180 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Proteasome activator pa28, C-terminal domain 0.70 61.0 4.87e-01 98.5% 77.9%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.70 54.0 4.78e-01 82.4% 58.2%
5b1oA00 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.70 54.0 5.49e-01 83.8% 87.7%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.70 53.0 4.50e-01 82.4% 50.0%
1jogA00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.69 53.0 4.24e-01 82.4% 41.5%
1qsdA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.69 55.0 4.76e-01 88.2% 56.9%
1vf7A03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.69 47.0 4.97e-01 77.9% 80.0%
1wa8A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.69 56.0 5.00e-01 89.7% 71.7%
1sg2A00 3.30.910.20 Alpha Beta › 2-Layer Sandwich › Protein Binding, DinI Protein; Chain A › Skp domain 0.69 60.0 4.73e-01 97.1% 64.5%
4adzA00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.68 57.0 5.18e-01 91.2% 74.4%
2q0oC00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.68 54.0 5.00e-01 88.2% 68.6%
2c5iT00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 57.0 5.15e-01 94.1% 71.3%
3n5lA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 50.0 5.35e-01 88.2% 94.7%
2cazD00 6.10.140.820 Special › Helix non-globular › Helix Hairpins › 0.67 51.0 5.38e-01 88.2% 93.3%
3jcuZ00 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.67 50.0 5.23e-01 83.8% 88.5%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.67 58.0 4.97e-01 98.5% 66.4%
2fb5A01 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.66 55.0 5.44e-01 89.7% 97.2%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 54.0 5.30e-01 88.2% 91.8%
2mpnA00 6.10.140.1340 Special › Helix non-globular › Helix Hairpins › 0.66 51.0 5.13e-01 89.7% 86.8%
1m62A00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.65 50.0 4.67e-01 89.7% 65.5%
1kyoF00 1.10.287.20 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Ubiquinol-cytochrome C reductase hinge domain 0.65 48.0 4.70e-01 82.4% 71.6%
1f45B00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.65 55.0 4.44e-01 94.1% 69.2%
3txsC01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.64 53.0 5.15e-01 92.6% 100.0%
4nv0A02 1.10.150.340 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain 0.64 45.0 4.30e-01 77.9% 62.2%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.64 52.0 4.74e-01 88.2% 84.4%
4asvA00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.64 40.0 3.83e-01 85.3% 53.2%
1b48A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.64 51.0 4.38e-01 86.8% 56.0%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 49.0 4.40e-01 88.2% 60.9%
4cqiA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 55.0 4.76e-01 98.5% 68.2%
6t0bc01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.63 54.0 5.25e-01 98.5% 88.5%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.63 52.0 5.40e-01 91.2% 100.0%
4e6nA02 6.10.140.1010 Special › Helix non-globular › Helix Hairpins › 0.62 47.0 4.77e-01 82.4% 83.3%
2hh7A00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.61 50.0 4.74e-01 94.1% 76.5%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 54.0 5.13e-01 98.5% 93.8%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.60 51.0 4.96e-01 98.5% 96.1%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.60 51.0 5.09e-01 97.1% 90.1%
1wp7A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.60 51.0 5.29e-01 95.6% 100.0%
1nt2B02 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.60 54.0 5.45e-01 98.5% 100.0%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.59 46.0 4.92e-01 88.2% 100.0%
1hwyA01 1.10.287.140 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.58 40.0 4.36e-01 89.7% 96.1%
5tprA02 1.20.1090.10 Mainly Alpha › Up-down Bundle › Dehydroquinate synthase-like, alpha domain › Dehydroquinate synthase-like - alpha domain 0.54 45.0 3.14e-01 92.6% 28.7%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4346136 605.1.1.108 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › GrpE 0.88 72.0 7.37e-01 91.2% 90.8%
3988447 5043.1.1.0 extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like 0.84 63.0 6.91e-01 80.9% 100.0%
3992719 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.83 67.0 6.11e-01 88.2% 65.6%
3742303 310.2.1.1 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.83 75.0 5.35e-01 100.0% 35.1%
3720672 109.4.1.1591 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › U-box 0.81 74.0 4.80e-01 100.0% 50.4%
5039692 605.1.1.0 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.81 69.0 6.13e-01 94.1% 66.3%
5017842 5058.1.1.0 alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.81 67.0 6.20e-01 89.7% 78.8%
1498377 4958.1.1.1 a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5,RNA_pol_Rpb1_4 0.80 65.0 5.93e-01 91.2% 67.4%
3691750 376.1.1.8 few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › U-box 0.80 72.0 5.50e-01 100.0% 94.6%
4452302 605.1.1.162 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › COX4_pro 0.77 63.0 5.67e-01 91.2% 66.3%
4428645 3826.1.1.80 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › GrpE 0.76 60.0 6.27e-01 85.3% 100.0%
4996069 604.10.1.0 alpha bundles › Spectrin repeat-like › Enzyme IIa from lactose specific PTS, IIa-lac › Enzyme IIa from lactose specific PTS, IIa-lac 0.74 56.0 5.09e-01 83.8% 61.1%
3282651 2004.1.1.5 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.74 66.0 3.88e-01 100.0% 13.7%
4189586 192.29.1.264 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › COX4_pro 0.73 60.0 5.39e-01 91.2% 67.4%
4493879 4992.1.1.23 extended segments › RelB-like › RelB-like › RelB-like › Seryl_tRNA_N 0.73 53.0 4.49e-01 83.8% 47.3%
4937236 5058.1.1.0 alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.72 60.0 5.37e-01 94.1% 65.0%
3582379 3826.1.1.0 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.71 55.0 5.48e-01 83.8% 81.2%
4008053 4168.1.1.7 alpha duplicates or obligate multimers › HAMP domain › HAMP domain › HAMP domain › PF26769 0.70 59.0 4.51e-01 98.5% 39.4%
4587250 547.1.1.1 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.70 56.0 4.90e-01 89.7% 57.1%
4276514 3826.1.1.88 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › CC_BshC 0.70 56.0 5.58e-01 94.1% 87.1%
4637522 547.1.1.1 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.70 60.0 5.08e-01 100.0% 57.4%
3735607 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.70 58.0 5.49e-01 89.7% 77.5%
5083776 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.70 53.0 4.73e-01 86.8% 57.9%
3831 604.7.1.1 alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › TBCA 0.69 55.0 4.76e-01 88.2% 56.9%
4086475 3755.3.1.466 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › CC_BshC 0.69 57.0 4.49e-01 98.5% 41.9%
3410594 4177.1.1.6 alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR_3_WASP_bdg 0.69 56.0 3.99e-01 89.7% 31.7%
4333013 547.1.1.1 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.68 56.0 5.34e-01 97.1% 78.8%
4660205 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.68 56.0 4.47e-01 89.7% 45.9%
4995305 604.5.1.2 alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.68 56.0 5.05e-01 91.2% 65.3%
4946898 375.1.9.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Zinc-nucleated domain of serine integrase 0.67 55.0 5.30e-01 88.2% 80.0%
4463205 2004.1.1.5 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.66 59.0 3.54e-01 100.0% 15.0%
3988454 605.1.1.1 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.66 53.0 5.29e-01 88.2% 94.3%
4501744 632.22.1.1 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › EzrA 0.66 57.0 5.05e-01 97.1% 72.0%
4541657 547.1.1.1 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.65 54.0 5.22e-01 97.1% 81.2%
4311810 605.1.1.1 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.65 53.0 5.17e-01 89.7% 92.0%
3169326 192.15.1.77 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › OST3_OST6 0.65 56.0 4.40e-01 95.6% 63.4%
3933048 4992.1.1.12 extended segments › RelB-like › RelB-like › RelB-like › LIN9_C 0.64 52.0 4.58e-01 88.2% 67.0%
3387484 375.1.9.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Zinc-nucleated domain of serine integrase 0.64 58.0 5.39e-01 100.0% 92.9%
4619538 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.64 57.0 4.79e-01 100.0% 90.4%
4165971 632.22.1.1 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › EzrA 0.64 56.0 4.91e-01 97.1% 73.0%
3936188 109.4.1.32 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MIF4G 0.63 53.0 3.12e-01 89.7% 12.1%
3543713 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.61 52.0 4.82e-01 98.5% 78.9%
3595968 605.2.1.0 alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 0.61 54.0 5.13e-01 98.5% 85.0%
1879027 244.1.1.6 a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C › Amino_oxidase 0.60 53.0 3.30e-01 100.0% 19.4%
3229891 5057.1.1.0 alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.60 52.0 4.21e-01 100.0% 85.9%
3705837 192.12.1.5 alpha bundles › Long alpha-hairpin › Transcriptional repressor TraM › Transcriptional repressor TraM › Cmc1 0.58 51.0 4.72e-01 95.6% 78.8%
3380124 109.4.1.1266 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Arm, ARM_PUB 0.58 47.0 2.91e-01 86.8% 16.2%
3780286 244.1.1.6 a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C › Amino_oxidase 0.57 50.0 2.96e-01 98.5% 13.5%
3794577 3331.1.1.14 a+b two layers › Uncharacterized protein yibL › Uncharacterized protein yibL › Uncharacterized protein yibL › CHDCT2 0.56 46.0 4.34e-01 94.1% 76.5%
4595635 148.1.3.26 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_9 0.56 48.0 3.77e-01 100.0% 46.3%