Back to structures

NC_055914.1__YP_010114387.1__KNV72_gp18__00018

Bact-Vir

NC_055914.1__YP_010114387.1__KNV72_gp18__00018

Identity

Accession:
NC_055914 ↗
Kingdom:
phage

Quality

72.4 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 6-44
PDB
Domain cluster: representative
CATH (50)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3okqA00 1.20.58.1540 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Actin interacting protein 3, C-terminal domain 0.84 71.0 5.02e-01 100.0% 40.0%
6he1B01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.83 57.0 4.87e-01 100.0% 45.3%
4gpkB01 1.25.40.1000 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.82 68.0 5.04e-01 94.9% 40.4%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.82 69.0 5.94e-01 100.0% 96.9%
3sfvB02 6.10.140.2010 Special › Helix non-globular › Helix Hairpins › 0.80 67.0 4.27e-01 100.0% 24.0%
2gv9A05 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.79 64.0 5.79e-01 100.0% 66.1%
2qkdA02 2.60.120.1040 Mainly Beta › Sandwich › Jelly Rolls › ZPR1, A/B domain 0.79 63.0 4.31e-01 100.0% 25.0%
4djgB00 1.20.5.440 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › ATP synthase delta/epsilon subunit, C-terminal domain 0.78 63.0 6.07e-01 100.0% 85.1%
3fxdC00 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 0.77 66.0 6.13e-01 100.0% 80.0%
3txsC01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.77 65.0 5.36e-01 100.0% 56.0%
1z0jB00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.76 62.0 5.84e-01 100.0% 84.3%
2xkoC02 6.10.250.870 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.75 59.0 6.04e-01 97.4% 97.3%
6h9xA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.75 64.0 4.83e-01 100.0% 44.1%
1yzmA00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.75 60.0 5.82e-01 100.0% 93.5%
2a2cA03 1.20.1440.340 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.75 60.0 4.24e-01 97.4% 34.8%
1b3qA01 1.10.287.560 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Histidine kinase CheA-like, homodimeric domain 0.75 64.0 5.58e-01 100.0% 66.1%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 62.0 5.26e-01 100.0% 59.2%
1kfdA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.74 62.0 5.24e-01 100.0% 54.9%
1hr5A00 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 0.74 58.0 5.50e-01 100.0% 75.0%
3r6nA02 1.20.58.1060 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 60.0 4.11e-01 100.0% 26.5%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.73 62.0 5.02e-01 100.0% 85.9%
2yfaA02 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.73 60.0 4.43e-01 100.0% 100.0%
2xqyA01 3.30.500.50 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › 0.73 60.0 3.97e-01 100.0% 22.5%
7xrxB01 1.20.1420.20 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › M75 peptidase, HXXE motif 0.72 60.0 3.47e-01 100.0% 10.9%
1y71A00 2.30.30.430 Mainly Beta › Roll › SH3 type barrels. › Kinase associated protein B domain 0.72 57.0 4.29e-01 97.4% 35.8%
3k59A06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.72 58.0 5.55e-01 100.0% 80.9%
3if8B02 1.20.58.730 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 51.0 3.82e-01 79.5% 31.0%
1j1jA02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.70 53.0 4.44e-01 100.0% 44.7%
2kp8A00 1.20.5.170 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.70 54.0 4.72e-01 100.0% 73.6%
2nr4A02 1.20.58.290 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hypothetical membrane protein ta0354_69_121. 0.70 55.0 5.07e-01 97.4% 74.1%
3h6pC00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.70 56.0 4.99e-01 89.7% 98.2%
4gzrC00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.70 60.0 5.21e-01 100.0% 78.7%
4e4eA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.68 55.0 4.76e-01 100.0% 59.2%
4jvtA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.68 61.0 6.02e-01 100.0% 97.6%
3icxA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.68 53.0 4.56e-01 100.0% 58.7%
4ad9A02 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 0.67 54.0 4.21e-01 89.7% 63.1%
1y6xA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.66 52.0 4.30e-01 100.0% 47.1%
2py5A04 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.65 48.0 4.92e-01 92.3% 97.2%
2yi9A05 1.20.1270.270 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › VP1, C-terminal extension domain 0.65 53.0 4.46e-01 100.0% 50.6%
7b9cA02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.64 48.0 2.79e-01 82.1% 9.3%
1cpyA02 1.10.287.410 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.64 49.0 4.35e-01 100.0% 59.7%
1w53A00 1.10.1240.30 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › KaiA/RbsU domain 0.63 46.0 3.95e-01 97.4% 50.0%
3m1cB01 3.30.390.170 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.62 53.0 3.95e-01 100.0% 47.7%
2vx2G02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.62 51.0 4.72e-01 100.0% 76.4%
4qfeK02 1.10.287.2460 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 44.0 4.66e-01 82.1% 91.2%
4hbdA00 1.25.40.20 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Ankyrin repeat-containing domain 0.61 48.0 3.09e-01 100.0% 16.3%
2j5iA02 6.10.250.2850 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.61 50.0 5.11e-01 94.9% 100.0%
2qvaA02 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 0.61 45.0 4.38e-01 100.0% 75.5%
4jfcA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.57 48.0 4.32e-01 100.0% 83.9%
4jcsA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.53 43.0 3.87e-01 100.0% 71.0%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3556887 3758.1.1.66 alpha bundles › Bacterial hemolysins-like › Bacterial hemolysins › Bacterial hemolysins › TMEM120A-B 0.87 74.0 5.61e-01 100.0% 41.1%
3747935 192.29.1.181 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › TMEM120A-B 0.87 75.0 5.64e-01 100.0% 41.1%
5049840 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 0.85 72.0 5.90e-01 100.0% 57.3%
3809308 3826.1.1.66 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › DUF641 0.85 71.0 6.30e-01 100.0% 96.7%
4776699 3282.1.1.1 a+b complex topology › LidA › LidA › LidA › LidA_Long_CC 0.84 72.0 4.61e-01 100.0% 28.1%
3629808 3291.1.1.130 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › CHDCT2 0.84 72.0 5.51e-01 100.0% 47.8%
5050356 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 0.84 70.0 5.91e-01 100.0% 61.4%
4934784 632.22.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.83 71.0 5.54e-01 100.0% 47.1%
3919878 2006.1.1.8 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › 5_nucleotid 0.83 71.0 4.14e-01 100.0% 12.4%
4943532 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 0.82 70.0 5.85e-01 100.0% 55.7%
3691003 601.1.2.0 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.82 71.0 4.69e-01 100.0% 24.4%
4436455 7022.1.1.1 alpha bundles › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein › central core domain of D-alanyl transfer protein › MBOAT 0.82 68.0 3.90e-01 100.0% 10.5%
3643501 192.1.1.47 alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain › DUF641 0.82 67.0 5.86e-01 100.0% 87.7%
3663959 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.82 70.0 4.86e-01 100.0% 30.0%
3976258 616.1.1.0 alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.81 68.0 6.20e-01 100.0% 78.2%
3940891 3291.1.1.0 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.81 68.0 4.64e-01 100.0% 26.9%
3275886 109.4.1.1126 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_SYO1 0.81 68.0 4.21e-01 100.0% 21.7%
3888160 192.4.1.0 alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.80 66.0 6.42e-01 97.4% 100.0%
5040661 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 0.80 66.0 5.62e-01 100.0% 61.4%
3167298 3711.1.1.0 alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein 0.79 69.0 5.05e-01 100.0% 38.1%
3296414 192.29.1.168 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › DUF641 0.79 66.0 5.58e-01 100.0% 62.9%
4116112 192.8.1.353 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › Med10 0.79 65.0 5.30e-01 100.0% 57.5%
3623190 174.1.1.31 few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › DUF7027 0.78 68.0 4.46e-01 100.0% 27.5%
3704748 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.78 63.0 5.32e-01 100.0% 53.3%
5040606 5054.1.1.0 alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels 0.78 64.0 3.92e-01 100.0% 46.3%
5044800 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 0.77 63.0 5.14e-01 100.0% 52.5%
3499472 3758.1.1.42 alpha bundles › Bacterial hemolysins-like › Bacterial hemolysins › Bacterial hemolysins › Choline_transpo 0.76 62.0 3.77e-01 100.0% 14.6%
5044888 101.1.2.136 alpha arrays › HTH › HTH › winged helix domain › HTH_20 0.76 65.0 4.49e-01 100.0% 30.0%
2323907 212.1.1.24 a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Morc6_S5 0.75 65.0 4.03e-01 100.0% 18.5%
4303085 3755.3.1.467 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › DRC7_C 0.75 61.0 4.49e-01 100.0% 41.7%
3943184 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 0.75 59.0 5.13e-01 100.0% 61.4%
3752758 3755.3.1.467 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › DRC7_C 0.75 65.0 4.39e-01 100.0% 29.5%
3346189 109.4.1.759 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Dymeclin 0.75 61.0 3.67e-01 100.0% 13.1%
3375617 192.5.1.30 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › DUF641 0.74 60.0 4.98e-01 100.0% 55.0%
3915218 5076.2.1.9 alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › Choline_transpo 0.72 61.0 3.68e-01 100.0% 15.0%
4681339 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.72 57.0 3.84e-01 97.4% 42.9%
3207606 5076.2.1.9 alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › Choline_transpo 0.72 62.0 3.64e-01 100.0% 12.6%
4995391 604.6.1.0 alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.71 56.0 4.52e-01 100.0% 43.3%
3527434 6006.1.1.6 extended segments › Voltage gated calcium channel IQ domain › Voltage gated calcium channel IQ domain › Voltage gated calcium channel IQ domain › PF27661 0.70 59.0 3.99e-01 100.0% 94.8%
4322913 192.6.1.0 alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.68 53.0 5.35e-01 100.0% 97.5%
4960288 101.1.2.48 alpha arrays › HTH › HTH › winged helix domain › PadR 0.66 54.0 3.70e-01 100.0% 23.4%
3692454 192.1.1.29 alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain › Es2 0.64 52.0 4.81e-01 100.0% 72.7%