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SR-VP_0-2_scaffold_141_4953755_prodigal-single.1__X__X__00081

Bact-Vir

SR-VP_0-2_scaffold_141_4953755_prodigal-single.1__X__X__00081

Identity

Kingdom:
phage

Quality

75.3 mean pLDDT

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 high residues 1110-1252
PDB
Domain cluster: rep: LC554890.1__BCG50042.1__X__00024__D127-241
D2 medium residues 34-170_248-267_343-363
PDB
D3 medium residues 171-224
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3dd9D02 6.10.140.2060 Special › Helix non-globular › Helix Hairpins › 0.68 41.0 4.59e-01 77.8% 80.5%
2vxdA00 1.10.10.2100 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Nucleophosmin, C-terminal domain 0.66 46.0 4.70e-01 83.3% 75.9%
5xe7A01 1.20.140.160 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › PhyR, sigma-like (SL) domain 0.63 50.0 3.80e-01 92.6% 65.5%
4mtdD01 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 0.62 48.0 4.17e-01 87.0% 93.2%
4heoA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.61 36.0 3.65e-01 88.9% 58.2%
3bbzA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.61 37.0 3.87e-01 87.0% 66.7%
1pu6A02 1.10.340.30 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2 0.60 46.0 3.76e-01 100.0% 41.5%
3l8nA01 1.10.220.20 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › 0.59 43.0 3.93e-01 90.7% 57.9%
2vixA02 1.10.150.630 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.58 43.0 3.87e-01 87.0% 61.8%
1t33A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.58 46.0 3.48e-01 98.1% 79.7%
2nn4A00 1.10.287.760 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YqgQ-like 0.57 44.0 4.23e-01 90.7% 72.6%
1oksA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.57 38.0 3.91e-01 70.4% 73.6%
1go3F02 6.10.140.10 Special › Helix non-globular › Helix Hairpins › 0.57 40.0 4.23e-01 94.4% 85.1%
1p4wA00 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 0.57 43.0 3.73e-01 87.0% 51.7%
2o4cA03 3.30.1370.170 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › Erythronate-4-phosphate dehydrogenase, dimerisation domain 0.57 40.0 3.40e-01 74.1% 96.6%
3gwiA00 3.40.1110.10 Alpha Beta › 3-Layer(aba) Sandwich › Calcium-transporting ATPase, cytoplasmic domain N › Calcium-transporting ATPase, cytoplasmic domain N 0.56 41.0 3.02e-01 83.3% 72.6%
1b5lA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.56 42.0 3.03e-01 81.5% 98.7%
2w02B01 1.10.150.640 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › AcsD, thumb domain, helical bundle 0.54 41.0 3.81e-01 87.0% 75.7%
6n2nA01 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.54 46.0 3.26e-01 100.0% 86.5%
2janA02 1.10.240.10 Mainly Alpha › Orthogonal Bundle › Tyrosyl-Transfer RNA Synthetase › Tyrosyl-Transfer RNA Synthetase 0.53 45.0 3.73e-01 96.3% 67.3%
5jjxA01 1.25.40.1040 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.52 42.0 2.74e-01 98.1% 31.3%
2yi9A05 1.20.1270.270 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › VP1, C-terminal extension domain 0.52 38.0 3.43e-01 92.6% 55.8%
2rldA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.52 46.0 3.59e-01 100.0% 62.3%
3g3oA00 3.20.100.30 Alpha Beta › Alpha-Beta Barrel › mRNA Triphosphatase Cet1; Chain A › VTC, catalytic tunnel domain 0.50 39.0 2.60e-01 94.4% 25.6%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3786647 592.6.1.1 ↗ alpha arrays › PWI domain-like › Pre-mRNA-splicing helicase BRR2 plug domain › Pre-mRNA-splicing helicase BRR2 plug domain › BRR2_plug 0.79 64.0 5.60e-01 88.9% 61.3%
3815745 592.6.1.1 ↗ alpha arrays › PWI domain-like › Pre-mRNA-splicing helicase BRR2 plug domain › Pre-mRNA-splicing helicase BRR2 plug domain › BRR2_plug 0.74 58.0 5.14e-01 87.0% 60.0%
4456963 563.1.1.1 ↗ alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP 0.74 53.0 3.61e-01 75.9% 26.5%
3458695 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 0.68 43.0 3.92e-01 75.9% 48.6%
3661867 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.68 42.0 3.46e-01 75.9% 34.0%
3688281 3922.1.1.0 ↗ 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 0.66 42.0 3.52e-01 77.8% 36.8%
4609007 101.1.17.0 ↗ alpha arrays › HTH › HTH › FF domain 0.66 48.0 4.94e-01 85.2% 86.0%
4935262 101.8.1.2 ↗ alpha arrays › HTH › An anticodon-binding domain of class I aminoacyl-tRNA synthetases › An anticodon-binding domain of class I aminoacyl-tRNA synthetases › Anticodon_2 0.65 50.0 3.66e-01 87.0% 29.4%
4938693 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.64 47.0 4.20e-01 85.2% 80.0%
4558680 101.1.2.807 ↗ alpha arrays › HTH › HTH › winged helix domain › MC6 0.63 48.0 4.26e-01 85.2% 75.0%
3606915 1189.1.1.2 ↗ alpha bundles › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG_B 0.61 48.0 2.95e-01 87.0% 17.4%
4181400 184.1.1.1 ↗ alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N 0.60 55.0 5.09e-01 98.1% 93.8%
4031004 184.1.1.0 ↗ alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N 0.60 54.0 5.06e-01 98.1% 93.8%
3672635 101.1.1.295 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_70 0.59 44.0 4.10e-01 87.0% 64.0%
3280929 101.1.1.125 ↗ alpha arrays › HTH › HTH › Three-helical HTH › DUF3263 0.57 43.0 3.90e-01 85.2% 63.7%
4575479 3281.1.1.1 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M 0.57 43.0 2.59e-01 88.9% 45.6%
3262288 4030.1.1.0 ↗ alpha bundles › alpha-helical domain in subunits of heterodimeric actin filament capping protein Capz › alpha-helical domain in subunits of heterodimeric actin filament capping protein Capz › alpha-helical domain in subunits of heterodimeric actin filament capping protein Capz 0.56 39.0 3.80e-01 85.2% 66.7%
4643518 101.1.1.63 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_28 0.56 41.0 4.15e-01 85.2% 85.5%
4165729 101.1.1.31 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r4 0.55 42.0 3.08e-01 87.0% 29.1%
3979831 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.55 37.0 3.57e-01 72.2% 63.1%
4964860 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.54 39.0 3.68e-01 85.2% 60.0%
4929103 101.1.2.150 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_45 0.54 41.0 3.63e-01 96.3% 80.0%
3297570 109.4.1.1308 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, PPR_3, TPR_24 0.54 44.0 2.89e-01 92.6% 37.6%
3839906 3201.1.1.1 ↗ alpha arrays › HP0721 › HP0721 › HP0721 › DUF1104 0.53 44.0 4.16e-01 100.0% 82.6%
3596650 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.52 38.0 3.58e-01 85.2% 62.9%
3620214 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.52 40.0 3.46e-01 88.9% 66.3%
4020971 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.52 44.0 2.91e-01 100.0% 76.7%
3738195 190.1.1.0 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box 0.51 37.0 3.14e-01 77.8% 54.4%
3646493 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.51 35.0 3.28e-01 72.2% 62.9%
D4 medium residues 376-507
PDB
Domain cluster: rep: gwf2_scaffold_96_prodigal-single.1__X__X__00453__D4-126
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01467.33 best CTP_transf_like 29.5 1.00e-06 82.6% 54.1%
D5 medium residues 508-560
PDB
Domain cluster: rep: IMGVR_UViG_3300000172_000157-3300000172-SI34jun09_200mDRAFT_100346313__D153-196
D6 medium residues 581-634
PDB
D7 medium residues 673-826
PDB
Domain cluster: rep: IMGVR_UViG_3300013099_000017-3300013099-Ga0164315_10000001230__D94-207
D8 medium residues 955-1029
PDB
Domain cluster: rep: GWB1_scaffold_combined_curated_closed_complete_prodigal-single.1__X__X__00361__D339-417
D9 medium residues 1262-1375
PDB
Domain cluster: rep: BML_coassembly_scaffold_234_prodigal-single.1__X__X__00197__D135-231
D10 medium residues 1389-1449
PDB