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NC_021803.1__YP_008242131.1__Phi13-2_gp106__00106

Bact-Vir

NC_021803.1__YP_008242131.1__Phi13-2_gp106__00106

Identity

Accession:
NC_021803 ↗
Kingdom:
phage

Quality

84.6 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 6-99
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2eqjA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.52 31.0 3.51e-01 74.5% 81.8%
2digA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.52 34.0 3.80e-01 81.9% 92.6%
4qqgG00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.51 34.0 3.78e-01 86.2% 87.5%
5kcoA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.51 30.0 3.53e-01 72.3% 89.8%
2jz6A01 2.30.170.40 Mainly Beta › Roll › Ribosomal Protein L24e; Chain: T; › Ribosomal protein L28/L24 0.51 27.0 3.59e-01 91.5% 98.0%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3829139 231.1.3.1 a+b two layers › MocoBD/DmpA-related › MocoBD/DmpA-related › Neutral ceramidase large domain › Ceramidase_alk 0.53 42.0 2.65e-01 88.3% 83.6%
3718707 323.1.1.3 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.52 42.0 2.67e-01 91.5% 76.0%
3617355 4.1.1.348 beta barrels › SH3 › SH3 › SH3 › SMN_Tudor, SMN_YG-box 0.51 31.0 3.17e-01 88.3% 60.0%
3226400 4184.1.1.2 beta barrels › MFPT repeat › MFPT repeat › MFPT repeat › MFP2b 0.50 35.0 3.61e-01 95.7% 76.7%
D2 high residues 161-267
PDB
Domain cluster: representative
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.60 38.0 4.37e-01 76.6% 90.7%
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 0.56 39.0 3.47e-01 72.0% 62.8%
2dkwA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.56 43.0 4.04e-01 90.7% 67.2%
2ds2D01 1.10.110.10 Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › Plant lipid-transfer and hydrophobic proteins 0.55 30.0 3.77e-01 80.4% 94.7%
4etrB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.55 37.0 3.62e-01 90.7% 61.5%
4r42A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.53 47.0 3.93e-01 98.1% 91.4%
2lqgA00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.53 45.0 4.21e-01 95.3% 99.3%
5ja4D00 1.25.40.20 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Ankyrin repeat-containing domain 0.53 37.0 3.35e-01 72.0% 89.3%
2vl7A02 1.10.275.30 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › 0.53 42.0 4.26e-01 86.9% 88.2%
7dl9B02 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.53 47.0 3.77e-01 97.2% 99.5%
1d9cA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.52 39.0 3.77e-01 92.5% 69.4%
3s6jE02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.51 31.0 3.62e-01 81.3% 92.8%
3ejjB00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.50 36.0 3.35e-01 91.6% 56.6%
ECOD (26)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3739669 604.13.1.0 alpha bundles › Spectrin repeat-like › USP8 N-terminal domain-like › USP8 N-terminal domain-like 0.62 34.0 3.43e-01 87.9% 52.4%
3244637 5001.1.1.33 alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srh 0.59 53.0 3.76e-01 99.1% 68.6%
3338002 174.1.1.39 few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › HR_lesion 0.59 49.0 4.95e-01 91.6% 94.5%
4029952 4106.1.1.1 few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.59 50.0 4.13e-01 91.6% 81.1%
3803092 3615.1.1.22 alpha bundles › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › HR_lesion 0.59 49.0 4.79e-01 91.6% 90.8%
3993155 4106.1.1.1 few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.58 52.0 3.96e-01 98.1% 78.8%
3483278 4106.1.1.0 few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack 0.58 50.0 4.06e-01 94.4% 91.2%
3926402 639.2.1.0 alpha arrays › HHA-like › Regulator of acid resistance influenced by indole (AriR) › Regulator of acid resistance influenced by indole (AriR) 0.58 41.0 4.62e-01 91.6% 98.8%
4810647 109.47.1.1 alpha superhelices › Repetitive alpha hairpins › Helical C-terminal domain in magnesium chelatase catalytic subunit › Helical C-terminal domain in magnesium chelatase catalytic subunit › CobN-Mg_chel 0.57 36.0 3.99e-01 77.6% 82.5%
3543076 4106.1.1.1 few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.57 49.0 4.02e-01 94.4% 88.5%
4960003 150.1.1.1 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.57 46.0 4.33e-01 90.7% 71.5%
3316066 192.4.1.42 alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › WAV3_C 0.56 33.0 3.41e-01 78.5% 59.0%
3839206 101.11.1.1 alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase 0.56 30.0 3.43e-01 76.6% 68.8%
3243410 174.1.1.0 few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.55 46.0 3.99e-01 88.8% 100.0%
4528819 4106.1.1.1 few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.54 48.0 4.19e-01 99.1% 86.7%
3236271 3636.1.1.3 a+b two layers › XPD arch domain › XPD arch domain › XPD arch domain › ARCH_RTEL1 0.54 44.0 3.76e-01 90.7% 83.9%
1413973 150.1.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.53 38.0 3.54e-01 90.7% 57.4%
3991144 101.11.1.1 alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase 0.53 29.0 3.14e-01 75.7% 61.1%
3479515 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.53 40.0 3.82e-01 78.5% 80.0%
4180109 101.11.1.1 alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase 0.53 30.0 3.21e-01 74.8% 64.4%
4049101 603.2.1.1 alpha bundles › STAT-like › STAT › STAT › STAT_alpha 0.52 39.0 3.50e-01 79.4% 70.0%
4030167 4967.1.1.0 alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases 0.52 38.0 3.28e-01 77.6% 76.9%
3602354 1030.1.1.1 alpha duplicates or obligate multimers › Crispr-associated protein Csm2 › Crispr-associated protein Csm2 › Crispr-associated protein Csm2 › Csm2_III-A 0.52 38.0 3.67e-01 98.1% 69.2%
3733651 7015.1.1.0 alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.52 45.0 4.11e-01 100.0% 88.7%
4928305 7566.1.1.2 a/b three-layered sandwiches › HflX family GTPase N-terminal domain › HflX family GTPase N-terminal domain › HflX family GTPase N-terminal domain › GTP-bdg_N 0.51 35.0 2.97e-01 71.0% 54.6%
4025157 3810.1.1.0 alpha duplicates or obligate multimers › Uncharacterized protein YP_510488.1 › Uncharacterized protein YP_510488.1 › Uncharacterized protein YP_510488.1 0.51 36.0 3.93e-01 90.7% 94.1%
D3 medium residues 108-160
PDB
Domain cluster: representative
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1a62A01 1.10.720.10 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.71 52.0 5.52e-01 79.2% 93.5%
3icxA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.69 47.0 4.16e-01 98.1% 50.7%
3l0oA01 1.10.720.10 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.67 52.0 5.42e-01 84.9% 91.8%
2hszA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.65 39.0 3.48e-01 84.9% 42.7%
3nctA00 3.40.50.11880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Plasmid SOS inhibition protein 0.65 48.0 3.64e-01 83.0% 54.7%
4i8oA03 1.10.8.1130 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Bacterial toxin RNase RnlA/LsoA, C-terminal Dmd-binding domain 0.64 49.0 4.56e-01 98.1% 65.7%
4nqwA01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.63 42.0 3.73e-01 100.0% 45.2%
2g5cB02 1.10.3660.10 Mainly Alpha › Orthogonal Bundle › 6-phosphogluconate dehydrogenase C-terminal fold › 6-phosphogluconate dehydrogenase C-terminal like domain 0.61 42.0 3.32e-01 94.3% 34.5%
2y1eA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.60 41.0 3.60e-01 100.0% 43.7%
1qv9A02 6.10.140.120 Special › Helix non-globular › Helix Hairpins › 0.59 43.0 3.54e-01 100.0% 40.8%
5oklA01 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.59 42.0 3.46e-01 100.0% 39.6%
2dodA00 1.10.10.440 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain 0.59 39.0 3.37e-01 86.8% 43.9%
2jaeA03 1.20.1440.240 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.59 43.0 3.63e-01 100.0% 43.6%
2gwlA00 3.90.176.10 Alpha Beta › Alpha-Beta Complex › Toxin ADP-ribosyltransferase; Chain A, domain 1 › Toxin ADP-ribosyltransferase; Chain A, domain 1 0.58 45.0 3.12e-01 88.7% 28.0%
2ougA00 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.58 40.0 2.94e-01 73.6% 44.0%
2vlaA01 1.10.10.2080 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.57 41.0 3.71e-01 79.2% 65.4%
1pu6A01 1.10.1670.10 Mainly Alpha › Orthogonal Bundle › Endonuclease Iii, domain 2 › Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) 0.57 46.0 3.88e-01 92.5% 62.8%
3tl4X02 1.10.10.2420 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.57 39.0 3.61e-01 86.8% 54.2%
1jr8A00 1.20.120.310 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ERV/ALR sulfhydryl oxidase domain 0.57 47.0 3.94e-01 100.0% 81.9%
2ffjA02 1.10.285.20 Mainly Alpha › Orthogonal Bundle › Glutamate Dehydrogenase; Chain A, domain 3 › Uncharacterised protein PF01937, DUF89, domain 2 0.55 40.0 3.84e-01 96.2% 66.2%
2pe4A00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.55 46.0 2.73e-01 96.2% 12.0%
4ikhA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.54 44.0 3.39e-01 100.0% 37.8%
2oauA01 1.10.287.1260 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 44.0 3.68e-01 100.0% 52.0%
3l9tA01 1.10.1240.70 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.52 36.0 3.21e-01 75.5% 69.9%
3t46A00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.52 45.0 4.06e-01 100.0% 81.3%
1sj8A02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.52 46.0 3.50e-01 100.0% 100.0%
3lszA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.52 40.0 3.13e-01 88.7% 52.0%
3b9wA00 1.10.3430.10 Mainly Alpha › Orthogonal Bundle › Ammonium transporter fold › Ammonium transporter AmtB like domains 0.51 44.0 2.71e-01 100.0% 43.4%
1axdA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.51 39.0 3.09e-01 86.8% 52.8%
1nrwA02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.50 41.0 3.25e-01 100.0% 96.9%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4540906 101.1.4.82 alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › DUF3603 0.75 63.0 5.33e-01 100.0% 64.9%
3493457 3949.1.1.0 alpha arrays › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain 0.74 60.0 5.72e-01 94.3% 81.5%
4292699 130.1.1.3 alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Rho_N 0.74 54.0 5.82e-01 79.2% 95.6%
3168331 3949.1.1.1 alpha arrays › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › IPPT 0.74 62.0 5.52e-01 94.3% 72.0%
4433184 130.1.1.3 alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Rho_N 0.73 59.0 5.84e-01 88.7% 87.3%
4428371 130.1.1.3 alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Rho_N 0.72 55.0 5.83e-01 83.0% 100.0%
4336243 3949.1.1.1 alpha arrays › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › IPPT 0.70 54.0 5.06e-01 84.9% 76.9%
4356636 198.1.1.0 alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.68 49.0 4.48e-01 100.0% 58.6%
1233457 130.1.1.3 alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Rho_N 0.67 52.0 5.38e-01 84.9% 90.0%
4359663 3949.1.1.0 alpha arrays › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain 0.65 52.0 4.96e-01 92.5% 80.0%
4097923 7579.1.1.44 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_6 0.65 55.0 3.52e-01 98.1% 25.6%
4226665 7579.1.1.6 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_1 0.64 55.0 3.56e-01 100.0% 37.2%
4458386 7579.1.1.6 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_1 0.63 54.0 3.54e-01 100.0% 38.8%
3252664 130.1.1.31 alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › RNF34L-like_3rd 0.63 45.0 4.50e-01 81.1% 92.7%
3353067 101.1.2.37 alpha arrays › HTH › HTH › winged helix domain › E2F_TDP 0.60 39.0 3.40e-01 75.5% 43.8%
4979297 7064.1.1.1 alpha bundles › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › VIT1 0.60 54.0 3.65e-01 100.0% 29.0%
3846608 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.60 50.0 3.12e-01 96.2% 16.0%
3328213 101.21.1.2 alpha arrays › HTH › HTH domain in DNA topoisomerase IV alpha subunit › HTH domain in DNA topoisomerase IV alpha subunit › Nucleolin_bd 0.59 41.0 4.24e-01 81.1% 78.0%
5007734 7064.1.1.1 alpha bundles › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › VIT1 0.59 52.0 3.59e-01 100.0% 30.3%
3915655 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.58 41.0 3.79e-01 83.0% 57.1%
4958814 3457.1.1.3 alpha bundles › GxGD membrane protease › GxGD membrane protease › GxGD membrane protease › Arc_PepC_II 0.55 42.0 2.79e-01 100.0% 18.1%
3421046 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.52 45.0 3.87e-01 100.0% 60.0%
4033036 632.19.1.3 alpha bundles › immunoglobulin/albumin-binding domain-like › Choline binding protein A › Choline binding protein A › DUF1542 0.52 43.0 3.84e-01 100.0% 65.3%
5019807 101.1.2.894 alpha arrays › HTH › HTH › winged helix domain › DUF2240 0.52 38.0 2.85e-01 81.1% 42.1%
3934799 170.1.1.0 alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C 0.51 39.0 3.63e-01 94.3% 86.7%