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NC_021347.1__YP_008061118.1__M176_gp081__00080

Bact-Vir

NC_021347.1__YP_008061118.1__M176_gp081__00080

Identity

Accession:
NC_021347 ↗
Kingdom:
phage

Quality

52.6 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 5-141_179-223_746-759
PDB
D2 high residues 523-587
PDB
Domain cluster: representative
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2id3A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.73 50.0 5.61e-01 100.0% 95.9%
2zb9A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.69 46.0 5.15e-01 100.0% 90.0%
2gfhA02 1.20.120.710 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Haloacid dehalogenase hydrolase-like domain 0.67 49.0 4.44e-01 76.9% 95.3%
4jneA03 3.90.640.10 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › ATPase, substrate binding domain, subdomain 4 0.67 48.0 4.27e-01 73.8% 87.5%
3e3vA03 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 0.66 51.0 5.35e-01 100.0% 98.2%
3hlzA02 1.20.120.1090 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.66 58.0 4.64e-01 98.5% 50.4%
2qytA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.66 58.0 5.01e-01 100.0% 67.3%
3we9A00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.61 54.0 3.63e-01 98.5% 80.2%
3tedA02 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.60 48.0 4.14e-01 100.0% 55.2%
8ctsB01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.60 47.0 4.27e-01 84.6% 78.2%
1af7A01 1.10.155.10 Mainly Alpha › Orthogonal Bundle › Chemotaxis Receptor Methyltransferase Cher; domain 1 › Chemotaxis receptor methyltransferase CheR, N-terminal domain 0.60 42.0 3.94e-01 76.9% 60.0%
2icwG02 1.10.10.530 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › mam-mhc complex, Chain D, Domain 2 0.59 51.0 4.68e-01 100.0% 87.6%
4m0mA03 1.20.1270.430 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.59 42.0 3.95e-01 75.4% 84.8%
4dmvA01 1.20.58.1190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 45.0 4.15e-01 86.2% 83.5%
2c5zA00 1.10.1740.100 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › Set2, Rpb1 interacting domain 0.58 40.0 3.62e-01 73.8% 57.0%
2ccyA00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.58 43.0 3.46e-01 80.0% 76.4%
4o6kA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.57 48.0 3.94e-01 100.0% 95.6%
2w0gA00 1.20.58.610 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Cdc37, Hsp90 binding domain 0.56 39.0 3.26e-01 75.4% 39.5%
4dxwA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.55 42.0 3.62e-01 86.2% 55.4%
2aplA02 1.10.8.340 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › PG0816-like 0.55 37.0 3.58e-01 73.8% 66.7%
3k8pC01 1.20.58.1440 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 44.0 3.84e-01 92.3% 74.3%
1kyqA03 1.10.3280.10 Mainly Alpha › Orthogonal Bundle › Siro heme synthase C-terminal domain-like › Siroheme synthase; domain 3 0.54 40.0 3.71e-01 78.5% 97.6%
6e1kA01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.54 41.0 3.56e-01 86.2% 57.1%
2go7A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.54 42.0 4.19e-01 92.3% 83.6%
1bgcA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.54 45.0 3.52e-01 98.5% 82.3%
1x4oA00 1.10.10.790 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Surp module 0.54 43.0 4.12e-01 100.0% 76.9%
1c20A00 1.10.150.60 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › ARID DNA-binding domain 0.53 44.0 3.66e-01 100.0% 78.1%
1yfmA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.53 46.0 3.73e-01 98.5% 50.8%
7odyC01 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.52 41.0 3.76e-01 90.8% 68.5%
3mogC02 1.10.1040.50 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › 0.52 44.0 3.27e-01 100.0% 42.1%
4g6dB02 6.10.140.1800 Special › Helix non-globular › Helix Hairpins › 0.52 39.0 3.72e-01 84.6% 77.8%
4dwlA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.52 40.0 3.51e-01 89.2% 91.7%
2w02B06 1.10.340.60 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › AcsD, palm domain, helix bundle 0.51 46.0 4.08e-01 100.0% 79.3%
1f45B00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.51 42.0 3.34e-01 89.2% 54.9%
3ragB00 3.40.50.410 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › von Willebrand factor, type A domain 0.51 44.0 3.08e-01 98.5% 41.6%
2uubT00 1.20.58.110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Ribosomal protein S20 0.51 36.0 3.28e-01 78.5% 62.6%
3pubA01 1.10.10.2400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Lepidopteran low molecular weight (30 kD) lipoprotein, N-terminal domain 0.51 36.0 3.50e-01 84.6% 66.2%
4j4hA01 3.40.50.12150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.50 45.0 3.51e-01 98.5% 94.1%
2xvtC00 1.10.150.510 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Receptor activity modifying family 0.50 43.0 4.08e-01 100.0% 83.5%
4hg2A02 1.10.10.2560 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.50 38.0 3.82e-01 83.1% 91.2%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4032570 101.1.2.231 alpha arrays › HTH › HTH › winged helix domain › Staph_reg_Sar_Rot 0.74 53.0 4.19e-01 75.4% 87.2%
4978391 186.1.1.1 alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N › Phage_int_SAM_1 0.73 63.0 5.43e-01 98.5% 62.0%
5034821 632.11.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.71 38.0 3.73e-01 100.0% 50.0%
4410163 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 0.58 48.0 3.52e-01 98.5% 77.5%
3394577 7039.1.1.1 a+b complex topology › Helical domain of PCIF1/CAPAM › Helical domain of PCIF1/CAPAM › Helical domain of PCIF1/CAPAM › PCIF1_WW 0.55 50.0 3.41e-01 100.0% 86.5%
4032823 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.55 41.0 3.86e-01 80.0% 86.3%
3686422 621.1.1.0 alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain 0.54 45.0 3.96e-01 100.0% 94.3%
5069994 632.11.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.52 40.0 3.90e-01 90.8% 74.3%
3197209 7579.1.1.5 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Peptidase_S10 0.51 44.0 2.59e-01 100.0% 11.1%
4983021 3877.1.1.0 alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.51 43.0 3.40e-01 100.0% 81.3%
D3 medium residues 793-847
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2nsfA01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.79 70.0 5.02e-01 100.0% 49.7%
1on2A02 1.10.60.10 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › Iron dependent repressor, metal binding and dimerisation domain 0.77 62.0 5.95e-01 90.9% 79.4%
6ofuA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.72 39.0 2.51e-01 81.8% 11.6%
6mh4A03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.71 53.0 4.71e-01 80.0% 74.7%
2pbiA02 1.10.1240.60 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.71 50.0 4.05e-01 74.5% 69.3%
5t3wA00 1.20.120.1160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.69 58.0 4.38e-01 94.5% 62.8%
2ntxA01 1.20.58.2010 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › PRONE domain, subdomain 1 0.66 41.0 2.71e-01 90.9% 16.7%
2a6cA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.65 55.0 4.91e-01 92.7% 85.5%
1zv1A00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.61 42.0 4.12e-01 72.7% 64.4%
1tj7A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.61 46.0 3.73e-01 81.8% 81.0%
3hhcC00 1.20.1250.60 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › Interferon lambda 0.58 44.0 3.24e-01 83.6% 49.0%
6vmsR00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.57 49.0 3.14e-01 98.2% 36.0%
3r2kA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.55 46.0 3.47e-01 100.0% 83.1%
3bemB00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.55 44.0 3.01e-01 89.1% 27.8%
1ztdA00 1.10.1520.20 Mainly Alpha › Orthogonal Bundle › Ribonuclease iii, N-terminal Endonuclease Domain; Chain A › Ribonuclease III 0.55 44.0 3.54e-01 96.4% 66.4%
4didB01 1.20.58.450 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Cell division control protein 42 homolog 0.55 44.0 3.66e-01 98.2% 75.4%
2mpkA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.55 38.0 3.45e-01 72.7% 82.4%
3eslA02 1.25.40.930 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.54 41.0 3.23e-01 83.6% 87.4%
2khmA01 1.10.10.1350 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Spidroin domain, C-terminal domain 0.54 37.0 3.11e-01 72.7% 44.4%
1q0gA00 1.20.120.400 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nickel-containing superoxide dismutase 0.53 45.0 3.63e-01 100.0% 82.1%
5u1aL00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.52 43.0 3.08e-01 92.7% 51.2%
3ziuA01 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.51 42.0 2.89e-01 100.0% 48.1%
8bauA01 1.10.357.40 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › YbiA-like 0.51 42.0 3.04e-01 98.2% 42.0%
1zq3P00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.50 37.0 3.47e-01 85.5% 63.2%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4864636 7008.1.1.1 alpha arrays › N-terminal domain of hexon-associated protein (IIIa) › N-terminal domain of hexon-associated protein (IIIa) › N-terminal domain of hexon-associated protein (IIIa) › Hex_IIIa 0.85 73.0 6.00e-01 94.5% 61.9%
4941346 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 0.79 66.0 5.99e-01 92.7% 93.3%
5073149 2488.1.1.1 a/b three-layered sandwiches › alpha/beta knot › alpha/beta knot › alpha/beta knot › SpoU_methylase 0.78 71.0 4.57e-01 100.0% 27.2%
3943344 183.1.1.0 alpha duplicates or obligate multimers › Iron-dependent repressor protein, dimerization domain › Iron-dependent repressor protein, dimerization domain › Iron-dependent repressor protein, dimerization domain 0.76 62.0 4.66e-01 92.7% 37.1%
4956886 101.1.2.652 alpha arrays › HTH › HTH › winged helix domain › Fe_dep_repr_C 0.75 65.0 4.90e-01 100.0% 89.3%
3233806 5001.1.1.0 alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.66 53.0 3.41e-01 96.4% 33.0%
3373591 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.65 49.0 5.33e-01 89.1% 100.0%
1716751 103.4.1.5 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 › KIX_2 0.64 51.0 4.58e-01 96.4% 87.2%
3239014 198.1.1.0 alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.61 42.0 3.47e-01 74.5% 58.7%
3551992 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 0.61 43.0 2.97e-01 78.2% 57.7%
3517600 632.2.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains 0.59 48.0 4.46e-01 96.4% 72.0%
185681 3413.1.1.1 alpha bundles › Inositol phosphate phosphatase sopB N-terminal domain › Inositol phosphate phosphatase sopB N-terminal domain › Inositol phosphate phosphatase sopB N-terminal domain › IpgD 0.57 45.0 3.68e-01 98.2% 66.9%
3331372 5086.1.1.0 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.56 38.0 3.25e-01 70.9% 62.4%
4218247 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 42.0 3.01e-01 90.9% 68.8%
3546057 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 45.0 3.04e-01 98.2% 64.8%
4280108 3415.1.1.2 alpha complex topology › Concentrative nucleoside transporter › Concentrative nucleoside transporter › Concentrative nucleoside transporter › FeoB_C,Gate 0.54 44.0 2.70e-01 96.4% 48.7%
4929121 140.1.1.5 alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon_1 0.54 44.0 3.18e-01 92.7% 47.6%
3247448 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 0.54 44.0 3.03e-01 98.2% 67.8%
3854672 5050.1.1.1 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr 0.54 45.0 3.10e-01 100.0% 69.3%
3860666 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 0.53 42.0 2.88e-01 94.5% 63.2%
4561057 5041.1.1.41 extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › prePAAR_I 0.52 35.0 3.32e-01 70.9% 70.0%
4933632 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 40.0 2.81e-01 87.3% 39.0%
3983978 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 42.0 2.96e-01 94.5% 83.9%
4953831 140.1.1.5 alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon_1 0.50 39.0 2.89e-01 92.7% 48.3%
4077250 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 0.50 39.0 2.69e-01 92.7% 60.1%