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KC821618.1__AGO48355.1__Phi10-1_gp014__00014

Bact-Vir

KC821618.1__AGO48355.1__Phi10-1_gp014__00014

Identity

Accession:
KC821618 ↗
Kingdom:
phage

Quality

95.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Assiduviridae› Cebadecemvirus› Cellulophaga_phage_phi10:1

TaxID: 1327981

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 11-64
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3f42A00 3.30.1310.10 Alpha Beta › 2-Layer Sandwich › Ybab; Chain: A; › Nucleoid-associated protein YbaB-like domain 0.71 48.0 4.06e-01 72.2% 81.7%
4gqcA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.69 59.0 4.25e-01 98.1% 80.6%
2kpiA01 2.20.25.10 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.68 41.0 4.68e-01 81.5% 82.1%
2drvA00 3.30.1960.10 Alpha Beta › 2-Layer Sandwich › SSo0622-like fold › tRNA wybutosine-synthesizing-like 0.65 54.0 3.83e-01 100.0% 64.4%
1eo1A00 3.30.420.130 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Dinitrogenase iron-molybdenum cofactor biosynthesis domain 0.65 49.0 3.85e-01 85.2% 53.2%
1ybxA00 3.30.1310.10 Alpha Beta › 2-Layer Sandwich › Ybab; Chain: A; › Nucleoid-associated protein YbaB-like domain 0.61 45.0 3.86e-01 79.6% 50.5%
4khbC00 2.30.29.210 Mainly Beta › Roll › PH-domain like › FACT complex subunit Spt16p/Cdc68p 0.61 53.0 4.27e-01 100.0% 53.8%
4chjA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.59 48.0 3.79e-01 100.0% 41.9%
3u37A02 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.59 50.0 3.32e-01 100.0% 56.0%
5jr6A02 3.40.350.10 Alpha Beta › 3-Layer(aba) Sandwich › Creatine Amidinohydrolase; Chain A, domain 1 › Creatinase/prolidase N-terminal domain 0.59 48.0 3.58e-01 98.1% 57.1%
7r8iA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.58 47.0 3.27e-01 100.0% 42.9%
2ywqA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.57 48.0 4.17e-01 98.1% 61.4%
2ph7A01 1.10.3400.10 Mainly Alpha › Orthogonal Bundle › af_2093 domain like fold › af_2093 domain like 0.57 41.0 3.16e-01 92.6% 33.1%
4wfsA01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.57 42.0 2.80e-01 79.6% 26.6%
2vszB02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 48.0 3.85e-01 100.0% 51.3%
2el8A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.56 46.0 4.02e-01 100.0% 73.6%
2e9hA02 2.20.25.350 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.55 35.0 3.77e-01 70.4% 79.5%
6rarI02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.55 43.0 3.70e-01 88.9% 61.8%
3fm2A00 3.40.1570.10 Alpha Beta › 3-Layer(aba) Sandwich › Heme iron utilization protein-like fold › HemS/ChuS/ChuX like domains 0.55 43.0 3.50e-01 98.1% 45.1%
1sg5A01 2.30.30.400 Mainly Beta › Roll › SH3 type barrels. › Rof-like 0.54 34.0 3.12e-01 79.6% 45.5%
7s00D01 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.54 44.0 3.41e-01 90.7% 74.6%
3k1lA02 3.30.457.30 Alpha Beta › 2-Layer Sandwich › Copper Amine Oxidase; Chain A, domain 1 › 0.54 44.0 3.85e-01 98.1% 77.8%
6grrB01 3.30.457.10 Alpha Beta › 2-Layer Sandwich › Copper Amine Oxidase; Chain A, domain 1 › Copper amine oxidase-like, N-terminal domain 0.52 40.0 3.64e-01 90.7% 60.8%
5uh5D02 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.52 46.0 3.42e-01 100.0% 39.1%
5ah1A01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 41.0 2.55e-01 100.0% 24.7%
2i6tA02 3.90.110.10 Alpha Beta › Alpha-Beta Complex › L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 › Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal 0.51 41.0 2.96e-01 87.0% 82.9%
3ajvC02 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.51 39.0 3.30e-01 83.3% 69.2%
2qmiA02 2.40.128.210 Mainly Beta › Beta Barrel › Lipocalin › Pab87 octamerisation domain 0.51 38.0 3.34e-01 90.7% 67.0%
3fgbA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.51 41.0 2.56e-01 96.3% 20.3%
3ol0B00 6.20.90.30 Special › Other non-globular › SH3 type barrels. › 0.50 32.0 3.53e-01 90.7% 85.4%
1csnA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.50 44.0 2.98e-01 100.0% 74.4%
6fndA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.50 41.0 2.83e-01 90.7% 33.3%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4027686 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.77 67.0 6.71e-01 96.3% 96.4%
5018525 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.74 39.0 4.40e-01 74.1% 67.5%
4026577 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.72 63.0 6.26e-01 96.3% 94.5%
3800251 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.71 48.0 4.28e-01 87.0% 50.7%
4027687 330.3.1.0 ↗ a+b two layers › dsRBD-like › Peptidyl-tRNA hydrolase domain-like › Peptidyl-tRNA hydrolase domain-like 0.70 59.0 5.96e-01 96.3% 94.5%
4026211 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.69 57.0 5.86e-01 92.6% 100.0%
4954852 101.1.2.136 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_20 0.69 48.0 3.27e-01 72.2% 25.4%
3958788 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.67 57.0 4.60e-01 98.1% 48.2%
3733008 2484.1.1.114 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Med13_C 0.66 56.0 3.52e-01 100.0% 18.1%
4022865 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.65 54.0 3.67e-01 100.0% 24.9%
5014656 148.1.1.0 ↗ alpha arrays › Histone-like › Histone-related › Histone 0.65 41.0 3.86e-01 72.2% 52.3%
3266831 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 51.0 4.20e-01 87.0% 56.8%
4498285 245.2.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.63 47.0 3.91e-01 79.6% 48.4%
3384455 4.1.1.12 ↗ beta barrels › SH3 › SH3 › SH3 › PWWP 0.62 54.0 3.77e-01 100.0% 47.6%
4637448 245.2.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.61 46.0 3.81e-01 79.6% 48.4%
4933213 375.1.1.31 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Elf1 0.61 43.0 4.01e-01 87.0% 58.6%
3190113 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.60 44.0 2.78e-01 81.5% 20.3%
3629558 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.59 47.0 3.72e-01 87.0% 76.4%
3854036 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.59 43.0 3.31e-01 77.8% 51.2%
3279395 213.1.1.35 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_CG 0.59 45.0 3.77e-01 85.2% 55.8%
3782631 2484.8.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Separase pseudo-protease domain (PPD) › Separase pseudo-protease domain (PPD) › Peptidase_C50 0.57 47.0 3.07e-01 100.0% 39.3%
4974213 2484.1.1.77 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Terminase_6C 0.57 45.0 3.31e-01 100.0% 34.4%
3658408 4325.1.1.13 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF4371 0.56 45.0 4.15e-01 92.6% 85.3%
4139864 245.2.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.56 51.0 4.11e-01 100.0% 90.8%
3496663 5.1.5.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed 0.55 45.0 2.95e-01 100.0% 29.5%
3975953 243.1.1.74 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › DUF2950 0.55 39.0 3.17e-01 77.8% 45.7%
3711635 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.54 42.0 3.39e-01 92.6% 42.5%
1758949 4216.1.1.1 ↗ a+b duplicates or obligate multimers › Heme iron utilization protein-like › Heme iron utilization protein-like › Heme iron utilization protein-like › HemS 0.53 37.0 2.88e-01 77.8% 36.0%
5060345 2002.1.1.54 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › DHO_dh 0.52 44.0 2.80e-01 100.0% 93.8%
4201477 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.52 42.0 3.37e-01 92.6% 73.0%
3959062 245.2.1.0 ↗ a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB 0.52 47.0 4.01e-01 100.0% 67.1%
4343474 245.2.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.52 47.0 3.88e-01 100.0% 61.1%
3956336 245.2.1.0 ↗ a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB 0.52 46.0 3.55e-01 100.0% 47.5%
4068261 245.2.1.1 ↗ a+b two layers › Ribonuclease PH domain 2-like › YbaB › YbaB › YbaB_DNA_bd 0.51 46.0 4.34e-01 100.0% 84.6%
3451633 330.1.1.3 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Dicer_dimer 0.51 40.0 4.06e-01 98.1% 96.4%
D2 medium residues 68-106
PDB
Domain cluster: representative
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4toiA02 1.10.287.610 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.84 73.0 6.88e-01 100.0% 85.4%
7dukB01 1.10.287.610 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.82 71.0 6.76e-01 100.0% 89.1%
1s5jA04 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.80 69.0 6.00e-01 100.0% 63.9%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.77 67.0 5.68e-01 100.0% 60.9%
1vp7A00 1.10.287.1040 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Exonuclease VII, small subunit 0.76 62.0 5.18e-01 94.9% 52.9%
1ya0A01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.75 62.0 3.94e-01 100.0% 18.4%
1xqrA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.73 59.0 3.63e-01 100.0% 15.4%
3n5lA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 55.0 5.00e-01 92.3% 75.4%
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 0.70 60.0 5.71e-01 100.0% 83.0%
2vdwG00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.70 52.0 3.15e-01 82.1% 29.3%
3cazB00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.70 56.0 3.65e-01 100.0% 21.0%
3ns4A00 1.10.357.110 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Vacuolar protein sorting-associated protein 53, C-terminus 0.70 57.0 3.67e-01 97.4% 38.5%
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 0.69 56.0 5.24e-01 97.4% 74.0%
2zfuA01 1.10.10.2150 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Ribosomal RNA-processing protein 8, N-terminal domain 0.66 52.0 4.88e-01 92.3% 78.4%
1u7lA02 1.20.1460.10 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › subunit c (vma5p) of the yeast v-atpase, domain 2 0.63 51.0 3.41e-01 100.0% 21.3%
2gsvA00 6.10.140.40 Special › Helix non-globular › Helix Hairpins › 0.59 49.0 4.22e-01 97.4% 61.2%
2db7A01 6.10.250.980 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.57 47.0 4.31e-01 100.0% 71.7%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3644495 7022.1.1.0 ↗ 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 0.86 77.0 5.27e-01 100.0% 31.2%
4195 4970.1.1.1 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_B 0.80 69.0 6.20e-01 100.0% 69.6%
3254275 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.78 66.0 4.34e-01 100.0% 22.9%
3258522 601.48.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › vWA2 C-terminal domain › vWA2 C-terminal domain 0.70 60.0 5.13e-01 100.0% 60.0%
3386552 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.68 55.0 4.73e-01 100.0% 58.6%
2772104 103.1.1.13 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › RNA_pol_Rpo13 0.66 55.0 5.32e-01 100.0% 84.1%
4383676 3922.1.1.67 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Val_tRNA-synt_C 0.64 49.0 4.34e-01 100.0% 91.4%
4387824 192.7.1.4 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Val_tRNA-synt_C 0.64 49.0 4.34e-01 100.0% 91.4%
4420750 192.7.1.4 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Val_tRNA-synt_C 0.64 50.0 4.41e-01 100.0% 57.1%
4563674 192.7.1.4 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Val_tRNA-synt_C 0.63 50.0 4.37e-01 100.0% 57.1%
4503822 3922.1.1.67 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Val_tRNA-synt_C 0.63 48.0 4.28e-01 100.0% 92.6%