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NC_051726.1__YP_009964157.1__I5J36_gp47__00047

Bact-Vir

NC_051726.1__YP_009964157.1__I5J36_gp47__00047

Identity

Accession:
NC_051726 ↗
Kingdom:
phage

Quality

80.6 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 10-90
PDB
Domain cluster: representative
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1no1A00 1.10.8.200 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Replisome organizer (g39p helicase loader/inhibitor protein) 0.87 68.0 7.54e-01 85.2% 100.0%
3ed5A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.73 40.0 3.98e-01 100.0% 51.2%
4wv4B00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.67 39.0 3.72e-01 100.0% 49.5%
1e7lA02 1.10.720.10 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.64 32.0 3.81e-01 96.3% 70.9%
4wz9A02 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.62 49.0 3.48e-01 86.4% 77.2%
3vwbA00 1.10.10.2830 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.60 45.0 4.03e-01 80.2% 64.7%
3keyA01 1.10.10.1080 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Stn1, N-terminal wHTH domain 0.60 35.0 3.43e-01 93.8% 52.9%
4bemJ00 1.20.120.610 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › lithium bound rotor ring of v- atpase 0.58 48.0 3.81e-01 93.8% 89.0%
1zp2A02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.58 44.0 3.97e-01 81.5% 58.9%
1b5lA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.58 45.0 3.64e-01 84.0% 60.5%
3h87B00 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.57 39.0 3.29e-01 85.2% 41.3%
4zqeA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.57 48.0 4.56e-01 93.8% 96.9%
1tjoB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.57 38.0 3.06e-01 70.4% 60.0%
3natA01 3.40.50.11250 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Protein of unknown function DUF3013 0.56 45.0 3.76e-01 88.9% 76.9%
3iieB03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.55 46.0 4.57e-01 93.8% 97.6%
2auaA02 1.10.3800.10 Mainly Alpha › Orthogonal Bundle › ADP-ribosylation fold › ADP-ribosylation domain 0.55 32.0 3.08e-01 72.8% 50.5%
5jazA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.55 46.0 4.51e-01 96.3% 98.9%
1k07A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.53 40.0 2.82e-01 80.2% 94.3%
3bvxA02 1.20.1270.50 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Glycoside hydrolase family 38, central domain 0.53 36.0 3.29e-01 70.4% 81.1%
4o6kA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.53 40.0 3.45e-01 82.7% 57.4%
4ywoA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 43.0 3.25e-01 91.4% 94.8%
3a06B03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.53 44.0 4.37e-01 95.1% 95.5%
1u61A00 1.10.1520.10 Mainly Alpha › Orthogonal Bundle › Ribonuclease iii, N-terminal Endonuclease Domain; Chain A › Ribonuclease III domain 0.53 40.0 3.46e-01 81.5% 87.4%
1gakA00 1.20.150.10 Mainly Alpha › Up-down Bundle › Lysin › Fertilization protein 0.53 39.0 3.31e-01 79.0% 81.8%
1jqkA03 1.20.1270.30 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.52 36.0 2.81e-01 70.4% 89.7%
1f45B00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.52 37.0 3.16e-01 93.8% 45.1%
2hwjA02 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.52 36.0 3.95e-01 79.0% 96.7%
3lynB00 1.20.150.10 Mainly Alpha › Up-down Bundle › Lysin › Fertilization protein 0.52 37.0 3.36e-01 79.0% 79.0%
1pduA00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.52 42.0 3.07e-01 90.1% 70.0%
3kflA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.51 38.0 3.03e-01 80.2% 55.4%
2xubA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.51 33.0 3.25e-01 92.6% 59.8%
ECOD (26)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4033485 571.1.1.1 alpha arrays › Replisome organizer (g39p helicase loader/inhibitor protein) › Replisome organizer (g39p helicase loader/inhibitor protein) › Replisome organizer (g39p helicase loader/inhibitor protein) › G39P_N 0.81 61.0 6.72e-01 88.9% 100.0%
3386111 6130.1.1.0 alpha complex topology › Selenocysteine synthase N-terminal domain › Selenocysteine synthase N-terminal domain › Selenocysteine synthase N-terminal domain 0.65 48.0 5.12e-01 79.0% 94.3%
3868 4204.1.1.1 alpha bundles › AF0941-like › AF0941-like › AF0941-like › AF0941-like 0.63 34.0 3.08e-01 93.8% 38.7%
3988210 4230.1.1.3 alpha arrays › DnaD domain › DnaD domain › DnaD domain › DnaB_2 0.62 52.0 4.97e-01 95.1% 84.2%
4408647 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.62 29.0 2.67e-01 92.6% 32.4%
4854386 6004.1.1.2 extended segments › FATC domain › FATC domain › FATC domain › ETC_C1_NDUFA5 0.58 41.0 3.81e-01 72.8% 78.4%
3787527 142.3.1.1 alpha complex topology › Sigma2 domain-like › Mitochondrial morphogenesis protein Sld7 C-terminal domain › Mitochondrial morphogenesis protein Sld7 C-terminal domain › Sld7_C 0.58 40.0 4.01e-01 72.8% 100.0%
3249199 375.8.1.0 few secondary structure elements › Rubredoxin-like › Zinc-binding domain of translation initiation factor 2 beta › Zinc-binding domain of translation initiation factor 2 beta 0.58 45.0 3.55e-01 86.4% 49.7%
3781416 5069.1.1.25 alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › Yip1 0.57 49.0 3.72e-01 97.5% 57.6%
3456418 632.7.1.17 alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › DUF1719 0.57 39.0 3.76e-01 70.4% 90.0%
4175392 4044.1.1.1 alpha bundles › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Prismane 0.56 38.0 3.41e-01 70.4% 60.0%
3533133 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.56 45.0 4.55e-01 96.3% 90.0%
3502904 611.8.1.0 alpha bundles › N-cbl like › C-terminal domain of E3 ubiquitin-protein ligase ARIH1 › C-terminal domain of E3 ubiquitin-protein ligase ARIH1 0.55 41.0 3.48e-01 82.7% 72.4%
3617266 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 37.0 3.30e-01 70.4% 79.2%
3686642 3755.4.1.0 alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.54 40.0 3.31e-01 80.2% 69.7%
3613157 632.19.1.6 alpha bundles › immunoglobulin/albumin-binding domain-like › Choline binding protein A › Choline binding protein A › PF27508 0.53 36.0 3.59e-01 70.4% 96.5%
3231541 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.52 40.0 2.73e-01 87.7% 22.3%
3315624 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.52 36.0 3.27e-01 71.6% 86.4%
4976974 159.1.2.1 alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › PRA-PH 0.52 35.0 3.29e-01 70.4% 91.0%
3559333 102.1.1.34 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › SAM_4 0.51 45.0 4.44e-01 100.0% 92.9%
280629 188.1.1.1 alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Hormone_recep 0.51 42.0 3.10e-01 93.8% 70.9%
4200880 188.1.1.1 alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Hormone_recep 0.51 42.0 2.89e-01 93.8% 53.7%
3180119 604.5.1.0 alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.50 34.0 3.41e-01 70.4% 100.0%
3672770 3567.1.1.0 a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer 0.50 35.0 3.32e-01 71.6% 92.6%
3609099 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 0.50 34.0 3.33e-01 70.4% 96.7%
5052864 171.1.1.1 alpha arrays › RNase III catalytic domain-like › RNase III catalytic domain-like › RNase III catalytic domain-like › Ribonuclease_3 0.50 36.0 3.09e-01 79.0% 70.3%
D2 high residues 105-162
PDB
Domain cluster: representative
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2etdA00 1.20.1440.20 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › LemA-like domain 0.82 58.0 4.25e-01 74.1% 40.4%
4kjmB01 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.81 57.0 5.58e-01 74.1% 88.9%
1dkxA02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.78 55.0 4.93e-01 74.1% 70.0%
6he1B01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.70 53.0 5.14e-01 81.0% 100.0%
4oevA03 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.70 59.0 3.99e-01 94.8% 84.5%
4m70I00 1.20.5.4130 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.68 51.0 4.17e-01 81.0% 63.0%
2p0tA01 1.10.60.30 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › PSPTO4464-like domains 0.68 54.0 4.94e-01 86.2% 77.6%
3geeA02 1.20.120.430 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › tRNA modification GTPase MnmE domain 2 0.68 52.0 3.76e-01 82.8% 68.5%
1y6xA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.68 55.0 4.72e-01 86.2% 79.3%
7vevA01 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.66 56.0 3.73e-01 98.3% 82.7%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.63 43.0 3.67e-01 75.9% 76.4%
2gf4A00 1.20.1270.110 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Uncharacterised protein family UPF0058 0.62 44.0 3.84e-01 75.9% 58.0%
4heoA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.60 42.0 4.28e-01 74.1% 78.2%
2dplA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.58 51.0 3.70e-01 100.0% 66.5%
4u2vA02 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.55 36.0 3.23e-01 82.8% 48.8%
1fcqA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.53 44.0 2.75e-01 89.7% 32.5%
3smtA02 3.90.1420.10 Alpha Beta › Alpha-Beta Complex › set domain protein methyltransferase, domain 2 › Rubisco LSMT, substrate-binding domain 0.52 43.0 3.14e-01 93.1% 87.8%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3586382 601.1.2.4 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Talin_R4 0.89 63.0 5.11e-01 74.1% 80.0%
3506336 3291.1.1.0 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.82 56.0 4.36e-01 70.7% 38.3%
3795608 601.1.1.0 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.80 66.0 5.24e-01 87.9% 78.2%
3629834 2004.1.1.629 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SNF2-rel_dom, Helicase_C, ResIII 0.80 60.0 3.45e-01 79.3% 9.6%
3516714 3291.1.1.0 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.79 53.0 3.76e-01 70.7% 25.9%
3791831 4177.1.1.2 alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.79 58.0 3.80e-01 77.6% 80.5%
5001312 632.15.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.74 52.0 4.68e-01 74.1% 57.5%
3581694 611.1.1.1 alpha bundles › N-cbl like › Transferrin receptor ectodomain, C-terminal domain › Transferrin receptor ectodomain, C-terminal domain › TFR_dimer 0.72 55.0 3.82e-01 82.8% 63.2%
3989298 601.19.1.0 alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein 0.66 53.0 3.87e-01 89.7% 76.4%
3879684 223.2.1.46 a+b three layers › Profilin-like › profilin-like › profilin-like › FNIP_N, FNIP_M 0.65 52.0 3.84e-01 91.4% 89.1%
3795974 2004.1.1.24 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SNF2-rel_dom,Helicase_C 0.64 59.0 3.38e-01 100.0% 49.9%
5078343 632.3.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Phosphoprotein XD domain › Phosphoprotein XD domain 0.63 43.0 4.19e-01 72.4% 64.1%
4424300 2004.1.1.5 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.63 51.0 2.97e-01 91.4% 33.1%
3668467 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.61 58.0 3.72e-01 100.0% 84.3%
3401755 632.13.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like 0.60 41.0 3.50e-01 72.4% 56.0%
2095513 142.1.1.3 alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.55 39.0 3.84e-01 74.1% 72.1%