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BML_coassembly_scaffold_172_curated_closed_complete_prodigal-single.1__X__X__00389

Bact-Vir

BML_coassembly_scaffold_172_curated_closed_complete_prodigal-single.1__X__X__00389

Identity

Kingdom:
phage

Quality

88.1 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 2-198
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3k3fA00 1.10.3430.10 Mainly Alpha › Orthogonal Bundle › Ammonium transporter fold › Ammonium transporter AmtB like domains 0.52 37.0 3.11e-01 98.5% 42.5%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5002883 101.1.2.491 alpha arrays › HTH › HTH › winged helix domain › WHD_BREX_BrxC 0.53 24.0 2.65e-01 98.5% 46.9%
D2 high residues 339-434
PDB
Domain cluster: representative
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2lseA00 1.20.120.1360 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.74 53.0 5.29e-01 76.0% 83.2%
3i9yA00 1.20.58.920 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 51.0 3.84e-01 79.2% 42.8%
1y4cA03 1.20.120.660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain 0.67 51.0 4.82e-01 80.2% 85.0%
4xpwA00 1.20.120.50 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hemerythrin-like 0.66 50.0 4.57e-01 82.3% 84.0%
3sp1A02 1.20.120.1910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cysteine-tRNA ligase, C-terminal anti-codon recognition domain 0.65 42.0 3.62e-01 71.9% 41.7%
1w36F02 1.10.10.160 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.65 37.0 3.69e-01 71.9% 53.0%
1xwmA00 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.65 49.0 3.83e-01 81.2% 64.6%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.64 49.0 4.39e-01 81.2% 81.3%
7z0sE02 1.10.645.10 Mainly Alpha › Orthogonal Bundle › Cytochrome-c3 Hydrogenase; chain B › Cytochrome-c3 Hydrogenase, chain B 0.64 45.0 3.10e-01 71.9% 34.1%
5z7qA00 1.20.1330.10 Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain 0.64 51.0 4.18e-01 86.5% 81.8%
1wn0A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.63 52.0 4.67e-01 88.5% 80.2%
4iggB02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.63 48.0 4.48e-01 82.3% 86.0%
1jogA00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.62 41.0 3.67e-01 79.2% 47.4%
3jsbA01 1.20.1440.300 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › RNA-directed RNA polymerase L, helical domain 0.62 45.0 4.78e-01 76.0% 100.0%
2l10A00 1.20.1420.10 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › Talin, central domain 0.62 47.0 4.04e-01 82.3% 71.5%
1hxiA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.62 43.0 4.09e-01 71.9% 71.4%
3agtA00 1.20.120.50 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hemerythrin-like 0.61 47.0 4.24e-01 83.3% 81.2%
3hiuD00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.60 45.0 3.90e-01 79.2% 72.4%
2gs4A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.60 44.0 3.76e-01 77.1% 67.1%
3p5nA00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.60 45.0 3.78e-01 80.2% 81.0%
2qqyA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.60 43.0 3.86e-01 76.0% 69.6%
5kbwB00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.59 44.0 3.71e-01 80.2% 81.3%
1tjoB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.59 43.0 3.63e-01 79.2% 62.3%
2q00B00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.58 41.0 3.85e-01 80.2% 59.0%
6axfA01 1.20.870.10 Mainly Alpha › Up-down Bundle › Son of sevenless (SoS) protein; Chain S, domain 1 › Son of sevenless (SoS) protein Chain: S domain 1 0.57 40.0 3.70e-01 71.9% 59.0%
1xioA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.56 44.0 3.49e-01 87.5% 88.9%
6srbA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.56 36.0 3.50e-01 91.7% 57.8%
3purA03 1.20.58.1360 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 40.0 3.87e-01 92.7% 66.4%
2vxxA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.54 42.0 3.50e-01 84.4% 72.1%
2ex2A01 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.54 45.0 3.43e-01 94.8% 78.8%
2fjcB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.53 41.0 3.50e-01 83.3% 78.8%
3ihvA03 1.25.40.900 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.52 39.0 3.54e-01 80.2% 82.0%
2gfhA02 1.20.120.710 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Haloacid dehalogenase hydrolase-like domain 0.52 35.0 3.69e-01 70.8% 96.5%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3602094 3572.1.1.0 a+b complex topology › Cascade subunit Csa5 › Cascade subunit Csa5 › Cascade subunit Csa5 0.72 63.0 6.14e-01 97.9% 98.1%
3931307 601.1.2.4 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Talin_R4 0.69 52.0 4.50e-01 79.2% 86.2%
3782013 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 0.67 49.0 3.18e-01 78.1% 31.2%
4667477 633.21.1.6 alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › Aim19 0.67 49.0 4.65e-01 77.1% 93.0%
3799907 633.21.1.0 alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.67 49.0 4.48e-01 78.1% 86.2%
5001312 632.15.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.65 45.0 4.81e-01 70.8% 100.0%
3347110 3684.1.1.2 alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › BPS1 0.64 56.0 4.26e-01 100.0% 86.4%
5050181 3291.1.1.1 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Snf7 0.63 46.0 3.83e-01 77.1% 73.5%
3515944 109.4.1.443 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MOR2-PAG1_C 0.63 46.0 3.23e-01 79.2% 99.7%
3894393 601.1.2.0 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.62 45.0 3.92e-01 77.1% 80.0%
4947476 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 0.61 46.0 3.72e-01 81.2% 93.7%
3988184 138.1.1.0 alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain 0.60 48.0 4.93e-01 86.5% 88.9%
4976276 3352.1.1.15 alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › GT87 0.60 45.0 3.11e-01 79.2% 96.6%
3634581 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.60 41.0 3.32e-01 72.9% 35.8%
3798780 3198.1.1.1 alpha bundles › ABA-1 repeat unit › ABA-1 repeat unit › ABA-1 repeat unit › NPA 0.59 45.0 4.07e-01 82.3% 59.3%
5030197 601.7.1.0 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.59 46.0 3.78e-01 83.3% 86.2%
5074457 1030.1.1.0 alpha duplicates or obligate multimers › Crispr-associated protein Csm2 › Crispr-associated protein Csm2 › Crispr-associated protein Csm2 0.58 50.0 4.95e-01 100.0% 91.4%
3372974 3684.1.1.2 alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › BPS1 0.58 50.0 3.76e-01 100.0% 88.1%
5062416 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 0.57 51.0 4.03e-01 100.0% 69.8%
3965294 3558.1.1.0 alpha arrays › HSDR subunit helical domain › HSDR subunit helical domain › HSDR subunit helical domain 0.57 39.0 3.98e-01 100.0% 71.6%
5003109 1079.1.1.1 alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA › DsbD 0.57 50.0 3.87e-01 100.0% 78.7%
5033221 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 0.56 51.0 3.98e-01 100.0% 69.3%
3185980 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 0.56 47.0 3.02e-01 97.9% 41.3%
4030040 109.3.1.0 alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.56 38.0 2.40e-01 71.9% 29.0%
3208136 7022.1.1.1 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 › MBOAT 0.55 41.0 3.20e-01 76.0% 60.5%
3636496 7022.1.1.1 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 › MBOAT 0.55 38.0 2.61e-01 70.8% 74.1%
3398827 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 0.55 49.0 3.86e-01 100.0% 72.2%
4025637 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 0.54 45.0 3.95e-01 93.8% 80.7%
3729160 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 0.53 38.0 3.08e-01 75.0% 58.9%
3245993 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 0.53 45.0 3.57e-01 95.8% 87.8%
4947877 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 43.0 3.50e-01 92.7% 89.7%
3988230 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 0.52 44.0 3.61e-01 96.9% 91.3%
3622548 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 0.52 44.0 3.54e-01 95.8% 87.8%
3980445 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 47.0 3.78e-01 100.0% 77.3%
3784566 604.1.1.191 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF29057 0.51 39.0 3.85e-01 89.6% 77.0%
3387249 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 0.51 45.0 3.61e-01 100.0% 73.8%
D3 medium residues 199-283
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1cx8A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.54 44.0 3.07e-01 91.8% 89.9%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4030388 323.1.1.3 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.54 39.0 3.04e-01 80.0% 82.3%
3468223 101.1.2.90 alpha arrays › HTH › HTH › winged helix domain › HTH_9 0.51 37.0 2.54e-01 77.6% 47.0%
D4 medium residues 284-338
PDB
Domain cluster: representative
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1j1vA00 1.10.1750.10 Mainly Alpha › Orthogonal Bundle › Chromosomal Replication Initiator Protein Dnaa; Chain: A; › DnaA protein, C-terminal DNA-binding domain 0.74 61.0 5.14e-01 92.7% 95.7%
4hteA03 1.10.167.30 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › 0.70 54.0 4.75e-01 83.6% 83.7%
3ig5A04 1.10.8.960 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.66 46.0 4.32e-01 72.7% 74.2%
6tqpA01 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.60 44.0 3.38e-01 80.0% 65.4%
4h0oA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.60 41.0 2.93e-01 72.7% 24.2%
5x9vA01 1.10.560.10 Mainly Alpha › Orthogonal Bundle › GROEL; domain 1 › GroEL-like equatorial domain 0.53 45.0 2.97e-01 96.4% 69.0%
3hl6A02 1.20.58.700 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 38.0 3.15e-01 81.8% 69.6%
2v6eA01 1.10.287.3180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 40.0 3.61e-01 76.4% 77.3%
3cs1A02 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.52 35.0 3.10e-01 76.4% 45.8%
4fvmA07 1.20.1280.310 Mainly Alpha › Up-down Bundle › Monooxygenase › B family DNA polymerase, thumb domain, four helix bundle 0.50 40.0 3.84e-01 90.9% 93.8%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4998666 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.70 46.0 3.06e-01 72.7% 17.6%
3633320 4177.1.1.2 alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.69 47.0 2.97e-01 70.9% 64.4%
5004872 7512.1.1.0 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase 0.64 51.0 3.36e-01 85.5% 23.0%
3705683 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.59 50.0 4.06e-01 92.7% 65.0%
3251600 101.1.22.0 alpha arrays › HTH › HTH › double HTH 0.52 39.0 3.91e-01 90.9% 88.3%