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PH2015_22_scaffold_1_prodigal-single.1__X__X__00188

Bact-Vir

PH2015_22_scaffold_1_prodigal-single.1__X__X__00188

Identity

Kingdom:
phage

Quality

75.5 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 medium residues 1-44_125-225
PDB
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2avxA00 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.56 33.0 3.19e-01 77.2% 49.1%
4ysxC00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.54 42.0 4.21e-01 82.1% 79.7%
3a8tA02 1.10.287.890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain 0.53 38.0 4.31e-01 93.1% 97.3%
3wvoC02 1.10.132.100 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.52 37.0 3.95e-01 82.1% 83.1%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3705680 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.59 25.0 3.06e-01 82.1% 58.9%
5048512 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.55 36.0 4.32e-01 87.6% 100.0%
4101307 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.55 49.0 2.91e-01 100.0% 25.6%
D2 medium residues 45-124
PDB
Domain cluster: representative
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3215316 386.1.1.0 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.56 43.0 4.06e-01 86.3% 85.4%
5013205 7523.1.1.26 a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_6 0.56 42.0 3.07e-01 83.7% 89.0%
3838562 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.54 35.0 4.01e-01 70.0% 94.5%
3644493 219.1.1.0 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.51 36.0 2.34e-01 75.0% 18.8%
D3 medium residues 226-271_294-306_355-402_601-621
PDB
Domain cluster: representative
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3806349 109.4.1.1254 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, E_motif 0.57 42.0 2.83e-01 78.1% 65.7%
3442448 109.4.1.1272 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, E_motif 0.56 42.0 2.80e-01 79.7% 50.9%
3818641 109.4.1.2070 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_2, E_motif 0.53 39.0 2.91e-01 78.1% 82.4%
3817779 109.4.1.1254 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, E_motif 0.52 38.0 2.96e-01 77.3% 85.4%
3827142 109.4.1.1254 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, E_motif 0.52 38.0 2.62e-01 76.6% 60.2%
5023509 263.1.1.0 a+b three layers › SRF-like › SRF-like › SRF-like 0.52 21.0 3.13e-01 91.4% 100.0%
3442732 109.4.1.1269 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, E_motif 0.52 29.0 2.90e-01 96.9% 51.5%
3641031 109.4.1.1272 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, E_motif 0.51 38.0 2.86e-01 75.8% 83.1%
3382036 109.4.1.2177 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, E_motif, TPR_24 0.51 37.0 2.97e-01 76.6% 95.1%
3327782 109.4.1.1254 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, E_motif 0.51 38.0 2.39e-01 79.7% 40.2%
3451138 109.4.1.1272 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, E_motif 0.51 39.0 2.91e-01 81.2% 90.8%
3457807 109.4.1.1272 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, E_motif 0.50 37.0 2.98e-01 78.9% 95.9%
3828334 109.4.1.1254 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, E_motif 0.50 37.0 2.95e-01 79.7% 95.6%
D4 medium residues 272-293_307-354
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1m2vB01 1.20.120.730 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Sec23/Sec24 helical domain 0.55 42.0 3.25e-01 84.3% 72.8%
4l0mA00 3.40.50.1580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleoside phosphorylase domain 0.54 40.0 2.80e-01 80.0% 100.0%
3rlbA00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.52 40.0 3.08e-01 85.7% 48.3%
1ub1A00 3.30.890.10 Alpha Beta › 2-Layer Sandwich › Methyl-cpg-binding Protein 2; Chain A › Methyl-cpg-binding Protein 2; Chain A 0.52 40.0 3.41e-01 85.7% 50.4%
3hhmA03 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.52 39.0 3.19e-01 82.9% 78.7%
2xzmG00 1.10.455.10 Mainly Alpha › Orthogonal Bundle › Ribosomal Protein S7 › Ribosomal protein S7/S5 0.52 42.0 3.16e-01 94.3% 66.7%
6iikB00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.51 37.0 2.38e-01 75.7% 27.5%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4796845 284.1.3.1 a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.64 40.0 3.98e-01 85.7% 60.0%
3560901 601.19.1.20 alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › Fy-3 0.62 40.0 3.96e-01 88.6% 61.3%
3167354 284.1.3.1 a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.62 42.0 4.17e-01 88.6% 67.1%
3267836 284.1.3.1 a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.62 41.0 4.03e-01 88.6% 64.0%
3857887 5094.1.1.11 a+b duplicates or obligate multimers › OmpH-like › OmpH-like › OmpH-like › Fy-3 0.61 40.0 3.92e-01 88.6% 61.3%
4001707 284.1.3.0 a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.61 40.0 3.82e-01 88.6% 56.5%
3866247 252.1.1.1 a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD › MBD 0.55 37.0 3.70e-01 100.0% 68.6%
4200734 167.1.1.1 alpha arrays › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal_S7 0.55 43.0 3.28e-01 90.0% 94.0%
3827046 284.1.3.1 a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.54 36.0 3.38e-01 87.1% 54.4%
4568123 219.1.1.79 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Transglut_core2 0.53 39.0 3.03e-01 81.4% 45.1%
4661064 252.1.1.1 a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD › MBD 0.53 37.0 3.99e-01 85.7% 89.8%
3941023 207.1.1.156 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › PF27094 0.53 42.0 2.94e-01 87.1% 45.8%
3680555 284.1.3.0 a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.52 41.0 3.72e-01 85.7% 67.4%
4608174 284.1.3.1 a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › SNF5 0.51 41.0 3.83e-01 95.7% 68.9%
3979087 4100.1.1.7 a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › PF27115 0.50 32.0 3.25e-01 100.0% 62.9%
D5 medium residues 403-437_530-600_637-684
PDB
D6 medium residues 438-529
PDB
Domain cluster: representative
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3kkbA00 1.20.120.880 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Histidine kinase (KinB), sensor domain 0.69 49.0 4.40e-01 73.9% 57.1%
4etrB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.69 49.0 4.43e-01 73.9% 89.3%
2o36A01 1.20.1050.40 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › Endopeptidase. Chain P; domain 1 0.68 50.0 4.48e-01 76.1% 94.5%
1wkbA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.67 52.0 4.79e-01 84.8% 76.0%
1s35A01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 45.0 4.43e-01 71.7% 89.1%
1wrdA00 1.20.58.160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 45.0 4.47e-01 72.8% 82.7%
3fseB02 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.64 44.0 3.84e-01 71.7% 86.8%
4fxdA04 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.62 45.0 3.84e-01 76.1% 66.0%
3bjdA01 1.10.1240.20 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Lytic transglycosylase, superhelical linker domain 0.61 43.0 4.43e-01 100.0% 77.3%
1u89A00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.61 51.0 4.50e-01 93.5% 68.3%
3vkgB03 1.20.58.1120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dynein motor heavy chain, linker domain, subdomain 4 0.61 44.0 3.76e-01 77.2% 62.8%
1s0pA01 1.25.40.330 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Adenylate cyclase-associated CAP, N-terminal domain 0.58 50.0 4.17e-01 100.0% 93.6%
2ib0A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.57 42.0 3.79e-01 79.3% 89.6%
2w31A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.57 47.0 4.04e-01 92.4% 92.1%
4xt1A00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.55 47.0 3.34e-01 94.6% 80.8%
2lqgA00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.54 45.0 4.00e-01 94.6% 84.1%
1cpyA02 1.10.287.410 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 38.0 4.17e-01 75.0% 98.6%
3pe5A00 3.40.630.190 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › LCP protein 0.53 46.0 3.32e-01 96.7% 65.3%
3mzoB00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.53 46.0 3.55e-01 96.7% 68.6%
4ipeB02 3.30.230.80 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.51 42.0 3.51e-01 90.2% 77.0%
4yxtA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.51 37.0 3.14e-01 76.1% 70.4%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3626462 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.84 58.0 5.31e-01 70.7% 87.0%
3615985 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.81 56.0 5.23e-01 70.7% 74.5%
3621004 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.79 57.0 5.42e-01 73.9% 100.0%
3257684 109.4.1.1341 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › COG3_N, COG3_C 0.72 50.0 3.65e-01 70.7% 33.3%
5005588 5082.1.1.1 alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.71 49.0 3.83e-01 71.7% 89.7%
3762319 109.4.1.1341 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › COG3_N, COG3_C 0.69 48.0 3.36e-01 71.7% 26.7%
3767103 109.4.1.1355 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › COG6_N, COG6_C 0.69 50.0 3.06e-01 76.1% 15.2%
3447097 603.1.1.99 alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF27021 0.69 49.0 4.66e-01 75.0% 96.4%
4029382 4984.1.1.3 alpha bundles › Duffy-binding-like domain, C-terminal subdomain › Duffy-binding-like domain, C-terminal subdomain › Duffy-binding-like domain, C-terminal subdomain › PFEMP, DBL_C 0.68 48.0 3.20e-01 72.8% 44.7%
3684136 604.1.1.154 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF27021 0.68 49.0 4.62e-01 75.0% 94.5%
4545 109.4.1.1 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › 14-3-3 0.68 47.0 3.61e-01 72.8% 42.7%
3580283 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.68 47.0 4.85e-01 71.7% 90.6%
2157267 109.4.1.204 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_EZ 0.67 47.0 4.35e-01 71.7% 61.2%
4902866 101.1.2.552 alpha arrays › HTH › HTH › winged helix domain › eIF-3c_N 0.67 47.0 4.97e-01 71.7% 88.6%
3595067 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.66 46.0 4.95e-01 72.8% 100.0%
3512636 3930.1.1.6 alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase › Dicer_PBD 0.66 53.0 4.89e-01 94.6% 68.7%
3495501 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.66 50.0 3.49e-01 82.6% 49.8%
3704321 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.65 46.0 4.74e-01 73.9% 87.1%
3928678 109.4.1.669 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8,TTC7_N 0.64 45.0 2.70e-01 71.7% 14.8%
4931503 604.3.1.0 alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.64 46.0 4.94e-01 73.9% 94.7%
4396629 103.4.1.16 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 › AgrB 0.64 56.0 4.65e-01 96.7% 91.9%
3287071 601.1.1.0 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.63 55.0 4.66e-01 100.0% 96.9%
4034237 5055.1.1.0 extended segments › Small-conductance potassium channel › Small-conductance potassium channel › Small-conductance potassium channel 0.63 44.0 4.11e-01 94.6% 58.3%
4992256 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.62 44.0 4.32e-01 73.9% 96.0%
3912101 604.6.1.1 alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.62 44.0 4.27e-01 72.8% 80.0%
3874415 109.4.1.1341 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › COG3_N, COG3_C 0.61 47.0 3.36e-01 84.8% 45.5%
3755252 604.6.1.1 alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.60 42.0 4.10e-01 73.9% 81.9%
3586442 604.6.1.1 alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.60 42.0 4.04e-01 73.9% 77.3%
5045530 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.58 42.0 4.25e-01 75.0% 94.4%
3566877 601.33.1.0 alpha bundles › Four-helical up-and-down bundle › CHAD domain › CHAD domain 0.58 40.0 4.19e-01 71.7% 91.3%
3740645 604.6.1.1 alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.57 41.0 4.15e-01 73.9% 94.4%
3641813 604.6.1.1 alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.57 40.0 4.01e-01 73.9% 88.4%
3175565 633.24.1.0 alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain 0.56 42.0 4.04e-01 80.4% 86.7%
3251839 601.1.2.4 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Talin_R4 0.56 47.0 4.17e-01 94.6% 77.8%
3397095 515.1.1.1 alpha arrays › Transcription factor STAT-4 N-domain › Transcription factor STAT-4 N-domain › Transcription factor STAT-4 N-domain › STAT_int 0.53 41.0 3.75e-01 91.3% 61.6%
4021170 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.52 43.0 3.40e-01 93.5% 83.4%
3899554 3736.1.1.1 alpha superhelices › NLRC4 helical domain HD2 › NLRC4 helical domain HD2 › NLRC4 helical domain HD2 › NLRC4_HD2 0.50 40.0 3.64e-01 88.0% 100.0%