Back to structures

LD_Run2_13_scaffold_0_prodigal-single.1__X__X__00237

Bact-Vir

LD_Run2_13_scaffold_0_prodigal-single.1__X__X__00237

Identity

Kingdom:
phage

Quality

88.3 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 high residues 16-72
PDB
Domain cluster: representative
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3hr0B01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.77 67.0 6.01e-01 98.2% 72.2%
2a3qA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.73 56.0 4.37e-01 80.7% 46.9%
3icxA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.73 61.0 5.60e-01 94.7% 74.7%
5f1cA01 1.10.287.940 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › atp-gated p2x4 ion channel 0.71 54.0 5.40e-01 84.2% 89.8%
2kiwA01 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.71 47.0 4.13e-01 73.7% 46.5%
5g5gB02 3.30.390.50 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › CO dehydrogenase flavoprotein, C-terminal domain 0.71 47.0 4.01e-01 75.4% 42.6%
2ynqB00 1.25.40.680 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Type VII secretion system EssB, C-terminal-like domain 0.70 56.0 4.09e-01 89.5% 33.1%
7a0hA01 3.30.1140.60 Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › F-actin capping protein, alpha subunit 0.68 45.0 3.72e-01 70.2% 38.6%
1ij5A01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 56.0 5.19e-01 98.2% 77.6%
1rypK00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.64 45.0 3.04e-01 73.7% 28.8%
2ouwB00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.64 50.0 3.77e-01 84.2% 35.3%
6muwN00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.52 38.0 2.58e-01 80.7% 19.6%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3713900 6087.1.1.0 extended segments › N-terminal region of NMB0537 › N-terminal region of NMB0537 › N-terminal region of NMB0537 0.94 85.0 6.97e-01 96.5% 57.9%
3595910 622.4.1.0 alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.80 64.0 5.73e-01 100.0% 62.5%
3313420 611.9.1.4 alpha bundles › N-cbl like › Resistance protein (Rx) N-terminal domain › Resistance protein (Rx) N-terminal domain › Rx_N 0.75 68.0 5.00e-01 98.2% 62.9%
3780651 3602.1.1.0 alpha bundles › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain 0.75 59.0 5.62e-01 84.2% 78.5%
4284004 4106.1.1.1 few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.74 62.0 4.24e-01 93.0% 71.8%
3597496 192.4.1.0 alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.71 64.0 4.43e-01 100.0% 47.0%
4320989 7015.1.1.0 alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.70 62.0 4.82e-01 98.2% 62.5%
3513468 210.1.1.1 a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.67 47.0 3.13e-01 86.0% 19.1%
3904086 101.1.1.112 alpha arrays › HTH › HTH › Three-helical HTH › MADF_DNA_bdg 0.61 55.0 4.67e-01 98.2% 65.6%
3601586 7516.1.1.40 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Stealth_CR2 0.58 49.0 2.97e-01 91.2% 61.5%
3391717 101.1.1.112 alpha arrays › HTH › HTH › Three-helical HTH › MADF_DNA_bdg 0.58 52.0 4.37e-01 96.5% 62.2%
3887051 101.1.1.112 alpha arrays › HTH › HTH › Three-helical HTH › MADF_DNA_bdg 0.57 49.0 4.14e-01 91.2% 61.1%
D2 medium residues 82-230
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3qexA03 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.83 73.0 5.99e-01 100.0% 55.6%
2f7vA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 36.0 4.07e-01 97.3% 88.0%
3tx8A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 37.0 4.17e-01 87.9% 88.6%
2xhsA00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.55 39.0 3.40e-01 74.5% 65.8%
2rb7A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 34.0 3.92e-01 98.7% 86.9%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3575094 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.87 51.0 6.28e-01 95.3% 88.0%
3602459 304.25.1.1 a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.64 41.0 4.60e-01 98.7% 83.5%
5071358 304.25.1.1 a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.63 47.0 5.00e-01 98.0% 88.5%
4964282 304.25.1.1 a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.62 41.0 4.47e-01 96.6% 80.8%
3290869 304.25.1.1 a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.57 40.0 4.31e-01 88.6% 85.6%
3602375 4953.1.1.0 beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.55 38.0 4.39e-01 74.5% 100.0%
4933479 304.25.1.1 a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.54 34.0 3.91e-01 98.7% 86.4%
4980045 304.25.1.1 a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.52 40.0 4.23e-01 96.6% 88.9%
3998117 148.1.3.208 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_NAV1 0.51 36.0 3.76e-01 83.9% 79.3%
D3 medium residues 246-297_396-422
PDB
Domain cluster: representative
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4qclA05 1.10.132.60 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › B family DNA polymerase, thumb domain 0.80 71.0 5.53e-01 98.7% 96.4%
4a64A02 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.72 55.0 4.83e-01 81.0% 60.7%
2d2sA02 1.20.58.1220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Exo84p, C-terminal helical domain 0.71 56.0 5.26e-01 88.6% 87.1%
4ffbC00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.64 52.0 3.78e-01 91.1% 47.2%
1n81A00 1.10.3030.10 Mainly Alpha › Orthogonal Bundle › Gametocyte protein Pfg27 › Gametocyte protein Pfg27 0.62 46.0 3.60e-01 82.3% 41.4%
4adnA01 1.20.1280.250 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.62 45.0 4.47e-01 79.7% 77.6%
5uh5D02 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.61 50.0 4.15e-01 88.6% 82.6%
4exjA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.61 52.0 4.52e-01 93.7% 94.2%
4dmvA01 1.20.58.1190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 47.0 4.68e-01 91.1% 89.4%
4wr4A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.59 47.0 4.41e-01 92.4% 87.6%
4hacB01 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.58 44.0 3.50e-01 86.1% 91.6%
3oxfA05 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.55 38.0 3.93e-01 78.5% 76.0%
4id0A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.55 46.0 4.23e-01 100.0% 94.6%
1xzpA02 1.20.120.430 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › tRNA modification GTPase MnmE domain 2 0.53 42.0 3.43e-01 89.9% 84.3%
3bz6A01 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 0.53 46.0 4.42e-01 96.2% 85.6%
3ihvA03 1.25.40.900 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.50 42.0 3.57e-01 96.2% 76.3%
3b4qA00 1.10.1200.100 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › conserved protein domain from corynebacterium diphtheriae 0.50 38.0 3.69e-01 84.8% 74.7%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4929241 4969.1.1.1 alpha bundles › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_B 0.74 65.0 5.28e-01 100.0% 94.8%
4931233 4969.1.1.1 alpha bundles › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_B 0.73 59.0 4.82e-01 87.3% 97.9%
4978606 4969.1.1.0 alpha bundles › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I 0.72 63.0 5.06e-01 97.5% 100.0%
3185102 6155.1.1.0 alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter 0.70 55.0 4.67e-01 87.3% 75.6%
4453642 223.1.1.0 a+b three layers › Profilin-like › sensor domains › sensor domains 0.70 53.0 4.11e-01 82.3% 93.7%
5025844 4969.1.1.0 alpha bundles › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I 0.69 57.0 4.61e-01 89.9% 90.7%
3302202 3745.1.1.1 alpha bundles › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Na_Ca_ex 0.64 54.0 3.61e-01 96.2% 72.9%
3570731 4973.1.1.6 alpha bundles › helical domain in DNA primase DnaG catalytic core › helical domain in DNA primase DnaG catalytic core › helical domain in DNA primase DnaG catalytic core › UBN_AB 0.64 56.0 5.42e-01 100.0% 86.7%
3970769 3921.1.1.0 alpha complex topology › Na(+)-translocating NADH-quinone reductase subunit D › Na(+)-translocating NADH-quinone reductase subunit D › Na(+)-translocating NADH-quinone reductase subunit D 0.61 47.0 3.57e-01 84.8% 54.1%
4941280 7000.1.1.0 alpha arrays › inserted region in the C-terminal domain of the archeal LeuRS › inserted region in the C-terminal domain of the archeal LeuRS › inserted region in the C-terminal domain of the archeal LeuRS 0.60 49.0 4.09e-01 89.9% 63.6%
4940179 2.21.1.3 beta barrels › OB-fold › Small protein B (SmpB) › Small protein B (SmpB) › HTH_OrfB_IS605 0.59 48.0 3.88e-01 89.9% 55.6%
3877909 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.58 43.0 4.42e-01 79.7% 89.3%
3503335 604.1.1.124 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin_6 0.58 43.0 3.90e-01 81.0% 90.4%
3592539 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.57 43.0 3.89e-01 82.3% 68.7%
3269341 101.1.10.22 alpha arrays › HTH › HTH › Cyclin-like › ORC6 0.56 43.0 4.15e-01 84.8% 73.3%
D4 medium residues 300-390
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3qexA06 3.40.1820.10 Alpha Beta › 3-Layer(aba) Sandwich › Ribonuclease H-like motif › DnaQ-like 3'-5' exonuclease 0.80 74.0 7.45e-01 100.0% 97.8%
1uw0A01 3.30.1740.10 Alpha Beta › 2-Layer Sandwich › first zn-finger domain of poly(adp-ribose) polymerase-1 › Zinc finger, PARP-type 0.63 40.0 4.00e-01 93.4% 61.5%
1tgoA05 1.10.132.60 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › B family DNA polymerase, thumb domain 0.60 44.0 3.67e-01 100.0% 42.5%
1wfqA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.57 41.0 4.49e-01 87.9% 94.5%
2i9wA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 42.0 3.49e-01 90.1% 89.2%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1256613 4969.1.1.0 alpha bundles › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I 0.79 74.0 5.82e-01 100.0% 51.7%
4939490 4969.1.1.0 alpha bundles › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I 0.74 58.0 4.70e-01 100.0% 46.0%
4138994 2.1.1.14 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › RuvA_N 0.58 42.0 4.69e-01 84.6% 100.0%
3211783 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.57 42.0 4.37e-01 90.1% 84.7%
4950307 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.56 41.0 4.37e-01 87.9% 88.7%
5071208 2.1.1.17 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › OB_aCoA_assoc 0.56 45.0 4.33e-01 87.9% 95.2%
4968816 2.1.1.17 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › OB_aCoA_assoc 0.56 45.0 4.48e-01 87.9% 87.4%
4965857 377.1.1.0 few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.56 38.0 4.27e-01 96.7% 94.2%
4985735 2.1.1.17 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › OB_aCoA_assoc 0.56 43.0 4.30e-01 87.9% 80.0%
3962565 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.54 43.0 4.19e-01 85.7% 84.0%
4029250 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.53 42.0 4.32e-01 86.8% 98.9%
3235864 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.53 39.0 4.17e-01 87.9% 96.0%
3959123 2.1.1.17 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › OB_aCoA_assoc 0.52 41.0 3.98e-01 86.8% 76.2%
4182979 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.51 35.0 3.94e-01 83.5% 100.0%
3408766 5001.1.1.41 alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srw 0.51 36.0 2.41e-01 72.5% 65.2%
3242799 2.1.1.249 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › OB_DEPS-1_2nd 0.51 36.0 3.72e-01 89.0% 81.2%