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pre3_saliva_scaffold_7_prodigal-single.1__X__X__00282

Bact-Vir

pre3_saliva_scaffold_7_prodigal-single.1__X__X__00282

Identity

Kingdom:
phage

Quality

76.5 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 253-380
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vkeB00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.62 41.0 4.50e-01 75.0% 84.2%
2bnxB01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.57 39.0 3.22e-01 70.3% 54.2%
2qtqB00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.55 39.0 3.47e-01 75.0% 91.9%
4c9bB00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.51 44.0 3.49e-01 96.9% 54.5%
1zu2A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.51 35.0 3.33e-01 71.9% 59.5%
8e9gJ01 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.50 35.0 3.22e-01 93.8% 54.5%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4171353 3291.1.1.212 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › VTT_dom 0.66 48.0 4.12e-01 75.0% 83.0%
4960856 5050.1.1.9 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.63 43.0 3.81e-01 70.3% 95.3%
3763555 109.4.1.1505 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › ARM_FBXO47 0.62 45.0 3.81e-01 73.4% 69.5%
3544351 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.62 44.0 3.14e-01 73.4% 36.8%
3268430 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.60 41.0 3.43e-01 73.4% 40.0%
5070669 5050.1.1.0 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.57 40.0 3.45e-01 72.7% 93.5%
3999880 109.3.1.2 alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank,Ank_2 0.55 39.0 3.33e-01 72.7% 44.7%
3586830 182.1.3.2 alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX › PriCT_1 0.55 43.0 4.55e-01 100.0% 94.8%
4984330 3651.1.1.0 alpha bundles › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain 0.55 37.0 4.27e-01 74.2% 98.9%
3492550 188.1.1.0 alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain 0.53 43.0 3.28e-01 85.2% 99.7%
3942447 628.1.1.1 alpha bundles › Fatty acid responsive transcription factor FadR, C-terminal domain › Fatty acid responsive transcription factor FadR, C-terminal domain › Fatty acid responsive transcription factor FadR, C-terminal domain › FCD 0.53 35.0 3.44e-01 78.1% 59.3%
3964037 628.1.1.1 alpha bundles › Fatty acid responsive transcription factor FadR, C-terminal domain › Fatty acid responsive transcription factor FadR, C-terminal domain › Fatty acid responsive transcription factor FadR, C-terminal domain › FCD 0.52 34.0 3.32e-01 76.6% 57.2%
3732518 5050.1.1.9 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.52 38.0 3.16e-01 76.6% 88.9%
D2 medium residues 1-89
PDB
Domain cluster: representative
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4031372 862.1.1.12 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › PF29905 0.60 54.0 4.16e-01 100.0% 60.0%
D3 medium residues 90-242
PDB
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2kl8A00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.74 38.0 5.00e-01 72.5% 89.4%
2iruA02 3.30.70.3300 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 53.0 5.61e-01 85.0% 90.6%
5t0oA02 3.30.70.1430 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.68 43.0 5.13e-01 85.6% 95.1%
4zosB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 40.0 4.84e-01 72.5% 90.7%
6u26A01 3.30.70.80 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Peptidase S8 propeptide/proteinase inhibitor I9 0.68 34.0 4.35e-01 74.5% 83.0%
2gffA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 39.0 4.81e-01 74.5% 90.6%
4hl9A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 39.0 4.85e-01 72.5% 93.6%
2faoA01 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.66 60.0 4.82e-01 96.7% 61.0%
3pm9A04 3.30.70.2740 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.66 37.0 4.76e-01 73.2% 96.6%
3fgvA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 38.0 4.67e-01 72.5% 93.5%
3gz7B00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 38.0 4.64e-01 73.9% 90.8%
1mwqA00 3.30.70.1060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel 0.64 39.0 4.62e-01 72.5% 90.0%
3bm7A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 38.0 4.44e-01 72.5% 84.0%
2mq8A00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.62 39.0 4.45e-01 73.2% 85.7%
1j27A00 3.30.70.1120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › TT1725-like 0.62 37.0 4.39e-01 72.5% 90.8%
3bn7A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 38.0 4.59e-01 72.5% 93.1%
1m1hA01 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.61 38.0 4.51e-01 79.7% 94.0%
2od6C00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 38.0 4.44e-01 72.5% 89.7%
6c6uN00 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.60 38.0 4.52e-01 81.7% 96.9%
1vqyB01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 37.0 4.48e-01 72.5% 96.8%
1r9wA00 3.40.1310.10 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.60 40.0 4.19e-01 87.6% 73.2%
4oi3A00 3.30.70.3090 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ORF SCO4226, nickel-binding ferredoxin-like monomer 0.60 32.0 4.16e-01 76.5% 96.3%
3bb5A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 38.0 4.51e-01 72.5% 94.2%
1m55A00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.59 49.0 4.54e-01 87.6% 86.5%
4bbyA05 3.30.300.330 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › 0.59 36.0 4.20e-01 73.2% 85.2%
2xhcA01 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.59 36.0 4.31e-01 83.7% 94.7%
1lq9A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 36.0 4.09e-01 72.5% 82.1%
1iujA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 37.0 4.41e-01 86.9% 97.1%
1tuwA00 3.30.70.1090 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel. 0.58 37.0 4.27e-01 75.8% 91.5%
2op5B01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 37.0 4.31e-01 72.5% 96.0%
2abyA00 3.30.70.1980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Uncharacterised protein PF09406, DUF2004 0.56 37.0 4.12e-01 84.3% 82.8%
5k9fA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 37.0 4.32e-01 86.9% 97.1%
1nz8A00 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.56 40.0 4.50e-01 83.7% 96.6%
5ixuA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 36.0 4.25e-01 86.9% 97.1%
1wvfA03 3.40.462.10 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › FAD-linked oxidases, C-terminal domain 0.55 45.0 3.93e-01 87.6% 81.8%
3popA02 3.40.462.20 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › 0.54 45.0 3.87e-01 90.2% 69.4%
5d79A03 3.40.462.20 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › 0.54 43.0 4.05e-01 90.2% 69.5%
1pbuA00 3.30.70.1010 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Translation elongation factor EF1B, gamma chain, conserved domain 0.54 39.0 3.89e-01 86.3% 71.6%
3vteA03 3.40.462.20 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › 0.54 44.0 4.10e-01 90.2% 70.8%
2bvfA03 3.40.462.20 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › 0.53 44.0 3.99e-01 89.5% 74.8%
4ud8A03 3.40.462.20 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › 0.52 41.0 3.91e-01 90.2% 70.1%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3587269 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.73 57.0 5.18e-01 96.7% 63.6%
3961062 304.4.1.4 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › ABM 0.69 40.0 5.02e-01 72.5% 96.7%
None 0.68 62.0 4.87e-01 98.7% 55.8%
134566 304.4.1.4 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › ABM 0.65 39.0 4.71e-01 73.9% 92.7%
3952812 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.64 39.0 4.78e-01 89.5% 100.0%
3289745 304.4.1.4 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › ABM 0.64 38.0 4.71e-01 72.5% 94.7%
166596 304.4.1.4 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › ABM 0.64 38.0 4.61e-01 72.5% 92.7%
4963170 304.5.1.0 a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like 0.64 37.0 4.65e-01 95.4% 96.7%
3280788 304.4.1.4 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › ABM 0.63 37.0 4.56e-01 73.2% 92.6%
5052115 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.62 37.0 4.59e-01 71.9% 97.8%
3721344 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.62 36.0 4.40e-01 72.5% 91.6%
4928084 304.4.1.4 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › ABM 0.61 36.0 4.36e-01 74.5% 91.6%
4512382 304.4.1.4 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › ABM 0.60 39.0 4.41e-01 90.8% 86.1%
4051078 304.4.1.71 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › DUF4937 0.60 43.0 4.82e-01 85.6% 97.4%
4133039 304.8.1.81 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › REP_ORF2-G2P 0.58 47.0 4.63e-01 85.6% 84.8%
4151784 304.6.1.3 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.58 49.0 4.01e-01 89.5% 57.5%
3659633 304.7.1.2 a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › Inhibitor_I9 0.58 36.0 4.33e-01 74.5% 97.9%
4928095 304.4.1.4 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › ABM 0.57 40.0 4.46e-01 73.9% 91.6%
5010925 304.45.1.1 a+b two layers › Alpha-beta plaits › 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK › 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK › HPPK 0.57 46.0 4.53e-01 85.6% 97.6%
3181053 304.6.1.3 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.56 47.0 3.81e-01 90.2% 55.1%
4219489 304.6.1.3 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.56 48.0 3.89e-01 90.2% 55.3%
4016349 304.6.1.3 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.56 47.0 3.76e-01 89.5% 55.1%
4017351 304.6.1.3 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.56 47.0 3.80e-01 90.2% 62.4%
1807387 304.4.1.15 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › NIPSNAP 0.55 36.0 4.25e-01 86.9% 97.1%
4022887 304.6.1.0 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain 0.54 45.0 3.76e-01 90.2% 64.8%
3727919 304.6.1.0 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain 0.54 45.0 3.79e-01 89.5% 55.8%
3421609 304.7.1.0 a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.54 35.0 4.06e-01 74.5% 94.3%
3795859 390.1.1.0 few secondary structure elements › Hairpin loop containing domain-like › Hairpin loop containing domain-like › Hairpin loop containing domain-like 0.54 26.0 3.31e-01 89.5% 77.8%
4540010 304.6.1.3 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.53 44.0 3.57e-01 89.5% 54.6%
1698645 304.6.1.3 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.53 44.0 3.74e-01 89.5% 62.3%
4018928 304.6.1.0 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain 0.53 44.0 3.67e-01 89.5% 58.1%
4013989 304.6.1.0 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain 0.52 44.0 3.71e-01 89.5% 58.6%
3735269 304.6.1.0 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain 0.52 43.0 3.64e-01 89.5% 59.2%
4622719 304.6.1.0 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain 0.52 43.0 3.74e-01 89.5% 68.9%
4378266 304.6.1.3 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.51 43.0 3.65e-01 90.8% 63.5%
4015784 304.6.1.0 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain 0.51 42.0 3.57e-01 90.2% 57.3%