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JBCH_GD18_scaffold_652796_prodigal-single.1__X__X__00035

Bact-Vir

JBCH_GD18_scaffold_652796_prodigal-single.1__X__X__00035

Identity

Kingdom:
phage

Quality

85.4 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 19-93
PDB
Domain cluster: representative
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2yfaB01 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.74 51.0 4.35e-01 72.0% 82.4%
3kkbA00 1.20.120.880 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Histidine kinase (KinB), sensor domain 0.69 52.0 4.38e-01 80.0% 54.8%
1s2xA00 1.20.190.30 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › CAG pathogenicity island protein, CagZ 0.69 55.0 4.18e-01 88.0% 92.8%
3qhbA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.69 58.0 4.40e-01 93.3% 86.0%
1b5lA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.69 56.0 4.39e-01 88.0% 80.9%
1xeqB00 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.68 48.0 4.64e-01 73.3% 81.2%
1aj3A00 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 53.0 4.81e-01 82.7% 91.8%
3axjB01 1.20.58.190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 1 0.65 50.0 4.02e-01 85.3% 58.7%
2qtlA03 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.64 48.0 3.82e-01 94.7% 39.4%
1s9qA00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.63 50.0 3.63e-01 88.0% 33.9%
2pvqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.62 50.0 4.50e-01 89.3% 73.6%
2zcxA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.62 49.0 3.68e-01 89.3% 44.9%
1hciA04 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 48.0 4.22e-01 85.3% 78.1%
1m62A00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.61 44.0 4.29e-01 80.0% 80.5%
3w6vA00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.60 46.0 4.07e-01 82.7% 67.6%
1x42A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.60 42.0 4.06e-01 72.0% 73.5%
5nl6A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 46.0 4.12e-01 84.0% 81.5%
4wzxA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.59 46.0 4.69e-01 85.3% 85.3%
3gs3A00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.57 44.0 3.10e-01 84.0% 39.4%
3k1rA01 1.20.1160.20 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › 0.57 48.0 4.78e-01 97.3% 91.4%
2uvaG01 1.20.1050.120 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.55 47.0 3.97e-01 100.0% 89.7%
1u6zA03 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.55 43.0 3.64e-01 97.3% 47.3%
2rkkA01 1.25.40.270 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Vacuolar protein sorting-associated protein vta1 0.54 45.0 3.70e-01 100.0% 91.0%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3980912 601.4.1.0 alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.77 56.0 4.81e-01 76.0% 59.1%
3168018 109.4.1.1376 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › U3_assoc_6, HAT_PRP39_N 0.76 64.0 3.90e-01 89.3% 19.1%
3714093 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.74 59.0 5.35e-01 85.3% 77.0%
3612350 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.72 56.0 5.09e-01 84.0% 74.0%
4959629 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.70 55.0 3.91e-01 85.3% 32.2%
3595593 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.68 57.0 3.50e-01 90.7% 38.1%
3715444 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.68 55.0 3.79e-01 89.3% 28.1%
4288336 6132.1.1.1 alpha bundles › Nudix hydrolase N-terminal dimerization domain › Nudix hydrolase N-terminal dimerization domain › Nudix hydrolase N-terminal dimerization domain › Nudix_N 0.68 46.0 4.96e-01 70.7% 84.6%
3323966 185.1.1.0 alpha superhelices › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin-like › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin/Protein HNS-dependent expression A HdeA › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin 0.67 54.0 5.03e-01 89.3% 77.9%
4031794 601.19.1.0 alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein 0.67 48.0 3.76e-01 76.0% 95.0%
3710317 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.67 53.0 2.99e-01 88.0% 8.4%
3584294 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.64 50.0 3.38e-01 88.0% 24.5%
3391259 604.6.1.0 alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.64 48.0 4.59e-01 82.7% 77.8%
3820045 603.1.1.118 alpha bundles › STAT-like › t-snare proteins › t-snare proteins › DUF7610 0.64 50.0 4.85e-01 85.3% 89.4%
4991402 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.63 46.0 4.50e-01 76.0% 73.8%
5071229 4163.1.1.0 alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like 0.63 45.0 4.03e-01 74.7% 63.8%
4939412 4163.1.1.4 alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like › PF27418 0.62 45.0 3.79e-01 76.0% 53.6%
5073163 109.4.1.207 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_2 0.62 50.0 3.10e-01 89.3% 15.4%
143026 109.10.1.1 alpha superhelices › Repetitive alpha hairpins › Translin › Translin › Translin 0.61 48.0 3.45e-01 88.0% 46.3%
3757776 109.4.1.418 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Condensin2nSMC 0.60 51.0 3.41e-01 94.7% 35.8%
3788517 376.1.1.0 few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.60 46.0 3.96e-01 85.3% 65.4%
4590066 101.1.1.58 alpha arrays › HTH › HTH › Three-helical HTH › HTH_18 0.60 46.0 3.99e-01 81.3% 65.5%
4985649 629.1.1.1 alpha bundles › TorD-like (Pfam 06192) › TorD-like (Pfam 06192) › TorD-like (Pfam 06192) › Nitrate_red_del 0.60 47.0 3.46e-01 88.0% 43.6%
3290284 601.18.1.0 alpha bundles › Four-helical up-and-down bundle › Oxygen-evolving enhancer protein 3 › Oxygen-evolving enhancer protein 3 0.59 47.0 4.38e-01 85.3% 87.4%
None 0.59 45.0 4.15e-01 82.7% 75.0%
3854356 109.4.1.139 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Hyccin 0.58 44.0 3.02e-01 98.7% 21.7%
4162588 109.4.1.1276 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › FAT, HEAT_ATR 0.58 47.0 3.52e-01 92.0% 34.1%
3608268 633.10.1.0 alpha bundles › Bromodomain-like › IVS-encoded protein-like › IVS-encoded protein-like 0.57 40.0 3.51e-01 72.0% 70.4%
4079732 601.19.1.0 alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein 0.54 39.0 3.08e-01 76.0% 60.6%
4967993 4953.1.1.0 beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.53 40.0 3.92e-01 84.0% 88.0%
3183837 246.3.1.4 a+b four layers › Carbon-nitrogen hydrolase-like › DNase I-like › DNase I-like › Exo_endo_phos2 0.52 47.0 2.68e-01 100.0% 68.4%
D2 medium residues 107-134_181-250
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00589.28 best Phage_integrase 29.6 7.60e-07 94.9% 32.6%
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3nkhA00 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.79 73.0 5.49e-01 100.0% 81.9%
3cqcB01 1.20.58.1380 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 32.0 3.32e-01 94.9% 56.7%
4iv6B01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.51 32.0 3.03e-01 83.7% 50.9%
5m9dA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.51 35.0 3.15e-01 70.4% 80.4%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3581915 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.58 38.0 3.66e-01 94.9% 58.2%
3592368 159.1.4.0 alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › Type II deoxyuridine triphosphatase-related 0.55 45.0 3.43e-01 92.9% 92.3%
3413389 108.1.1.0 alpha arrays › EF-hand › EF-hand-related › EF-hand 0.52 35.0 3.93e-01 86.7% 97.1%
3497136 3930.1.1.0 alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase 0.51 38.0 3.53e-01 80.6% 96.2%
4100298 5051.1.1.10 alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › AA_permease_2 0.50 44.0 2.86e-01 100.0% 65.4%
D3 medium residues 135-180_251-277
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00589.28 best Phage_integrase 32.8 8.00e-08 68.5% 25.6%
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5jk0B01 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.87 75.0 5.51e-01 91.8% 84.4%
3uxuA00 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.80 57.0 4.41e-01 75.3% 66.0%
2h7fX02 3.90.15.10 Alpha Beta › Alpha-Beta Complex › Topoisomerase I; Chain A, domain 3 › Topoisomerase I; Chain A, domain 3 0.72 61.0 4.25e-01 94.5% 71.8%
3oajA02 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.57 39.0 3.10e-01 80.8% 36.1%
4rs6A01 3.30.1120.30 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › POLO box domain 0.56 39.0 3.31e-01 71.2% 78.0%
7wffb01 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.55 46.0 3.11e-01 95.9% 86.1%
1h8mA00 3.30.450.50 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Longin domain 0.53 37.0 3.10e-01 74.0% 84.3%
6hoxA01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.53 38.0 2.69e-01 75.3% 75.9%
7vjvA01 2.60.120.590 Mainly Beta › Sandwich › Jelly Rolls › Alpha-ketoglutarate-dependent dioxygenase AlkB-like 0.53 38.0 2.79e-01 76.7% 65.2%
1xksA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 36.0 2.33e-01 71.2% 27.0%
6wqbA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.52 39.0 3.25e-01 84.9% 81.8%
2hf6A00 3.30.450.60 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.51 37.0 2.96e-01 78.1% 77.2%
2xa7M01 3.30.450.60 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.51 38.0 3.21e-01 79.5% 95.8%
2j3tD01 3.30.450.70 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.50 37.0 3.08e-01 79.5% 91.0%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4928148 101.1.8.0 alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.74 66.0 4.98e-01 98.6% 88.7%
3891447 101.1.8.0 alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes 0.71 55.0 4.00e-01 83.6% 79.5%
4453818 101.1.8.1 alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Phage_integrase 0.60 47.0 3.69e-01 84.9% 76.0%
4049072 2.4.1.6 beta barrels › OB-fold › MOP-like › MOP-like › CysA_C_terminal 0.56 40.0 3.47e-01 74.0% 60.0%
3741860 223.2.1.7 a+b three layers › Profilin-like › profilin-like › profilin-like › SRP-alpha_N 0.53 39.0 3.26e-01 79.5% 91.5%
4307191 4.6.1.6 beta barrels › SH3 › PRC-barrel domain › PRC-barrel domain › PRC_RimM 0.53 39.0 3.80e-01 78.1% 86.3%
3511321 5.1.4.298 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_ELP1_1st, Beta-prop_ELP1_2nd 0.52 42.0 2.51e-01 91.8% 48.8%
3508716 223.2.1.7 a+b three layers › Profilin-like › profilin-like › profilin-like › SRP-alpha_N 0.52 38.0 3.16e-01 79.5% 90.4%
3432113 223.2.1.7 a+b three layers › Profilin-like › profilin-like › profilin-like › SRP-alpha_N 0.52 38.0 3.18e-01 78.1% 91.2%
3931143 223.2.1.7 a+b three layers › Profilin-like › profilin-like › profilin-like › SRP-alpha_N 0.52 38.0 3.18e-01 78.1% 83.2%
5052919 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 38.0 3.02e-01 79.5% 83.3%
3460642 223.2.1.8 a+b three layers › Profilin-like › profilin-like › profilin-like › Sybindin 0.51 38.0 3.10e-01 80.8% 88.1%
3715033 223.2.1.7 a+b three layers › Profilin-like › profilin-like › profilin-like › SRP-alpha_N 0.51 37.0 3.16e-01 78.1% 94.2%
5076775 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.50 37.0 3.14e-01 79.5% 93.1%
4999507 330.7.1.2 a+b two layers › dsRBD-like › PI-Pfui intein middle domain › PI-Pfui intein middle domain › HicA_toxin 0.50 38.0 3.88e-01 80.8% 84.3%
4946665 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.50 43.0 3.56e-01 98.6% 99.3%
4947665 223.2.1.58 a+b three layers › Profilin-like › profilin-like › profilin-like › Arf 0.50 37.0 3.19e-01 79.5% 95.8%
3267300 223.2.1.7 a+b three layers › Profilin-like › profilin-like › profilin-like › SRP-alpha_N 0.50 37.0 3.10e-01 79.5% 91.5%