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LacPavin_0818_WC40_scaffold_86355_prodigal-single.1__X__X__00161

Bact-Vir

LacPavin_0818_WC40_scaffold_86355_prodigal-single.1__X__X__00161

Identity

Kingdom:
phage

Quality

82.6 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 5-145
PDB
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.60 39.0 4.67e-01 81.6% 100.0%
3nqzA02 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.58 33.0 4.14e-01 85.1% 92.9%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.58 46.0 4.35e-01 83.0% 97.6%
4mp8A01 3.30.1780.10 Alpha Beta › 2-Layer Sandwich › ornithine cyclodeaminase, domain 1 › ornithine cyclodeaminase, domain 1 0.58 39.0 3.72e-01 75.9% 59.6%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.57 37.0 4.48e-01 83.0% 100.0%
3ktaA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 41.0 3.88e-01 75.9% 80.5%
7vd7A01 3.10.450.530 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Ribonuclease toxin, BrnT, of type II toxin-antitoxin system 0.55 30.0 3.60e-01 95.0% 79.3%
2lxxA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.54 47.0 4.58e-01 92.9% 93.4%
2qpvA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.54 37.0 3.84e-01 83.0% 74.2%
4i99A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 40.0 3.05e-01 75.9% 42.2%
1hjrA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.53 35.0 3.37e-01 95.7% 58.2%
1qhlA00 3.40.1140.10 Alpha Beta › 3-Layer(aba) Sandwich › N-terminal domain of mukB › 0.53 40.0 3.61e-01 80.1% 88.2%
2h36X00 3.30.160.300 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.53 32.0 3.60e-01 86.5% 77.8%
2mv2A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.53 45.0 4.47e-01 92.9% 90.5%
3q9oA01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.53 39.0 3.43e-01 78.0% 69.0%
1r4sA00 3.10.270.10 Alpha Beta › Roll › Urate Oxidase › Urate Oxidase; 0.51 43.0 3.39e-01 90.1% 66.3%
2r5rA00 3.10.270.10 Alpha Beta › Roll › Urate Oxidase › Urate Oxidase; 0.51 41.0 3.46e-01 85.8% 62.6%
4jhyA00 3.30.530.80 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › 0.50 39.0 3.79e-01 83.7% 73.7%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3289401 274.1.1.0 a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.83 68.0 7.05e-01 93.6% 92.3%
4629131 9.29.1.1 beta barrels › Lipocalins/Streptavidin › VirK › VirK › VirK 0.72 38.0 4.11e-01 77.3% 60.2%
3228525 241.15.1.0 a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain 0.63 34.0 3.89e-01 75.9% 69.1%
3400513 77.1.1.4 beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein › Chitin_bind_4 0.61 31.0 4.04e-01 84.4% 88.5%
4119667 243.3.1.3 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › PepSY 0.59 34.0 4.30e-01 85.1% 94.1%
3783000 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.58 36.0 4.29e-01 94.3% 92.6%
3408388 4.1.1.326 beta barrels › SH3 › SH3 › SH3 › Chitin_bind_4 0.57 31.0 3.97e-01 90.1% 91.3%
4972214 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.57 41.0 2.85e-01 75.2% 27.9%
4262043 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.57 33.0 4.10e-01 83.7% 98.8%
4013508 5.1.3.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.56 46.0 3.49e-01 87.9% 95.9%
4993562 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.55 37.0 4.26e-01 80.1% 92.4%
3599539 11.8.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Osmotin-like › Osmotin-like 0.55 41.0 3.92e-01 78.7% 74.5%
3594978 11.8.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Osmotin-like › Osmotin-like 0.54 43.0 3.61e-01 83.0% 67.9%
4940923 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.54 30.0 3.96e-01 76.6% 98.8%
3813180 210.1.4.1 a+b four layers › Ntn/PP2C › Ntn › (Glycosyl)asparaginase › Asparaginase_2 0.53 46.0 3.46e-01 96.5% 95.4%
5040084 283.2.1.0 a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like 0.53 39.0 4.22e-01 94.3% 91.7%
3398162 11.2.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.53 36.0 3.46e-01 86.5% 60.0%
3488069 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.52 39.0 2.84e-01 78.0% 86.3%
3520918 881.1.1.0 a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.52 38.0 3.58e-01 75.9% 90.9%
4995161 7504.1.1.2 a/b three-layered sandwiches › ITPase-like › ITPase-like › ITPase-like › NTPase_I-T 0.52 41.0 3.92e-01 85.1% 97.6%
5077479 7504.1.1.2 a/b three-layered sandwiches › ITPase-like › ITPase-like › ITPase-like › NTPase_I-T 0.52 41.0 3.79e-01 84.4% 90.8%
3948040 5084.5.1.2 beta barrels › Outer membrane meander beta-barrels › Porins › Porin › Omp85 0.52 38.0 2.88e-01 76.6% 48.3%
5040360 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.51 33.0 3.90e-01 88.7% 96.8%
3185727 5.1.4.298 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_ELP1_1st, Beta-prop_ELP1_2nd 0.51 39.0 2.95e-01 79.4% 48.4%
3604446 2004.1.1.480 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_21, AAA_29 0.50 39.0 2.59e-01 82.3% 89.8%
D2 high residues 195-281
PDB
Domain cluster: representative
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3fnbA01 1.20.1440.110 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › acylaminoacyl peptidase 0.65 49.0 4.54e-01 81.6% 74.6%
5n17A01 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.63 48.0 4.63e-01 85.1% 100.0%
1eqfA02 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.62 51.0 4.59e-01 92.0% 87.2%
2r0yA01 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.62 49.0 4.55e-01 88.5% 92.1%
2felA00 1.20.200.10 Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain) 0.60 53.0 3.58e-01 100.0% 52.2%
4hr1A00 1.20.1270.410 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.59 48.0 4.40e-01 90.8% 97.5%
2rldA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.59 47.0 4.38e-01 88.5% 81.6%
1td6A03 1.10.472.40 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Hypothetical protein mg237 homolog; domain 3 0.59 42.0 4.21e-01 98.9% 71.7%
3hmfA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.59 47.0 4.37e-01 92.0% 98.3%
2fu2A00 1.20.1440.50 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like 0.58 44.0 4.62e-01 81.6% 97.4%
1tj7A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.58 49.0 4.61e-01 98.9% 76.2%
4usaA02 1.10.150.120 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › [2Fe-2S]-binding domain 0.58 48.0 4.36e-01 93.1% 79.8%
1v85A00 1.10.150.50 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Transcription Factor, Ets-1 0.57 44.0 4.39e-01 92.0% 81.3%
1ldjA01 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.57 39.0 3.51e-01 71.3% 97.6%
6vw7B03 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.57 43.0 4.42e-01 83.9% 98.8%
2e9fB01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.56 47.0 4.58e-01 100.0% 82.3%
2lm4A01 1.10.150.250 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Flavinator of succinate dehydrogenase 0.56 44.0 4.33e-01 96.6% 81.5%
1u5kA02 1.20.1440.120 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Recombination protein O, C-terminal domain 0.56 46.0 4.14e-01 92.0% 95.2%
1e7lA02 1.10.720.10 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.55 33.0 4.04e-01 93.1% 96.4%
1l9lA00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.55 40.0 4.26e-01 78.2% 94.6%
4v2kA01 1.10.760.10 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain 0.54 43.0 3.86e-01 89.7% 85.0%
4bpxD00 1.20.930.80 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.54 41.0 3.18e-01 82.8% 85.9%
2kp7A01 1.10.150.110 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DNA polymerase beta, N-terminal domain-like 0.54 42.0 4.42e-01 90.8% 100.0%
3c8tA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.54 43.0 4.24e-01 100.0% 80.4%
3kavA00 1.20.1270.360 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.54 43.0 4.14e-01 88.5% 99.0%
5xnyA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.54 45.0 4.27e-01 100.0% 76.6%
4xfkA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.53 46.0 3.51e-01 98.9% 70.7%
2cg5B00 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.53 36.0 3.99e-01 71.3% 88.7%
5figA00 1.20.1270.360 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.52 42.0 4.04e-01 89.7% 91.0%
1yfmA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.52 46.0 4.06e-01 100.0% 68.3%
3e4bA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.52 46.0 2.99e-01 98.9% 29.9%
6vxcA01 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.51 39.0 2.32e-01 82.8% 32.4%
5yjlB01 3.30.460.30 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Glutamyl-tRNA reductase, N-terminal domain 0.50 44.0 3.62e-01 97.7% 68.9%
1x9fA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.50 44.0 3.75e-01 100.0% 78.2%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3431353 1128.1.1.10 alpha bundles › LYR protein › LYR protein › LYR protein › VIN3_C 0.75 47.0 5.25e-01 98.9% 80.0%
3798302 103.4.1.0 alpha arrays › RuvA-C › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein 0.73 48.0 5.29e-01 100.0% 82.9%
3485484 633.2.1.0 alpha bundles › Bromodomain-like › Carnobacteriocin B2 immunity protein › Carnobacteriocin B2 immunity protein 0.71 55.0 5.88e-01 88.5% 97.3%
3651135 3788.1.1.20 alpha bundles › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › VIN3_C 0.70 45.0 4.84e-01 98.9% 76.0%
3813741 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.65 55.0 4.71e-01 93.1% 75.7%
4930122 2007.1.3.61 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › TfuA 0.61 50.0 3.88e-01 93.1% 71.9%
3986322 4270.1.1.0 alpha bundles › N-terminal domain of Hypothetical protein MPN330 › N-terminal domain of Hypothetical protein MPN330 › N-terminal domain of Hypothetical protein MPN330 0.60 45.0 4.69e-01 89.7% 88.7%
4946511 2003.1.2.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.59 50.0 3.45e-01 98.9% 33.9%
3230536 632.3.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Phosphoprotein XD domain › Phosphoprotein XD domain 0.58 51.0 4.75e-01 100.0% 96.4%
3257435 193.1.1.1 alpha bundles › CH domain-like › Calponin-homology domain-like › Calponin-homology domain-like › CH 0.58 46.0 3.73e-01 97.7% 44.1%
4959244 102.3.1.1 alpha arrays › HhH/H2TH › eIF2alpha middle domain › eIF2alpha middle domain › EIF_2_alpha 0.58 47.0 4.82e-01 89.7% 92.9%
4035675 103.7.1.2 alpha arrays › RuvA-C › Hypothetical protein MTH1615 › Hypothetical protein MTH1615 › DUF494 0.58 45.0 4.63e-01 96.6% 91.3%
5062170 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.58 45.0 4.16e-01 88.5% 67.5%
4059140 632.3.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Phosphoprotein XD domain › Phosphoprotein XD domain 0.57 50.0 4.36e-01 100.0% 90.7%
4011611 10.12.1.0 beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.57 49.0 3.45e-01 97.7% 86.7%
3847320 632.2.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains 0.57 51.0 4.44e-01 100.0% 94.1%
3469337 633.4.1.0 alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor 0.57 47.0 3.76e-01 89.7% 76.5%
3016249 532.2.1.0 alpha arrays › Type III secretion system domain-like › Type III secretion system domains › Type III secretion system domains 0.56 43.0 4.18e-01 92.0% 75.8%
3356672 5069.1.1.0 alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes 0.56 39.0 3.47e-01 72.4% 99.2%
3994395 5038.2.1.0 alpha superhelices › Cytochrome c oxidase subunit I-like › MAPEG domain-like › MAPEG domain-like 0.54 38.0 3.48e-01 72.4% 76.5%
1041203 3239.1.1.1 alpha complex topology › Cas1 › Cas1 › Cas1 › Cas_Cas1 0.54 46.0 3.28e-01 100.0% 44.1%
3921048 601.1.2.14 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › DLEU7 0.54 44.0 3.83e-01 88.5% 75.9%
3428029 632.1.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.54 36.0 3.51e-01 70.1% 100.0%
4014053 148.1.3.216 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › DUF7069 0.54 43.0 4.51e-01 85.1% 95.0%
3221752 3684.1.1.0 alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like 0.54 36.0 2.98e-01 70.1% 51.2%
4020945 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.53 41.0 4.40e-01 80.5% 96.0%
5004502 159.1.2.0 alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related 0.53 38.0 2.92e-01 97.7% 32.0%
5065203 316.1.1.18 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › AbiEii 0.53 44.0 3.20e-01 93.1% 42.1%
3177591 633.23.1.9 alpha bundles › Bromodomain-like › Claudin › Claudin › SUR7 0.52 44.0 3.39e-01 100.0% 63.9%
3742353 633.23.1.9 alpha bundles › Bromodomain-like › Claudin › Claudin › SUR7 0.52 44.0 3.32e-01 95.4% 66.7%
5009805 2006.1.4.2 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › PIN 0.50 40.0 3.58e-01 89.7% 60.0%