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NC_055716.1__YP_010089820.1__KNT60_gp240__00240

Bact-Vir

NC_055716.1__YP_010089820.1__KNT60_gp240__00240

Identity

Accession:
NC_055716 ↗
Kingdom:
phage

Quality

94.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Straboviridae› Tegunavirus› Yersinia_phage_fHe-Yen9-01

TaxID: 1965363

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 1-93
PDB
Domain cluster: representative
CATH (50)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4od4A01 1.10.357.140 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › UbiA prenyltransferase 0.77 70.0 5.85e-01 100.0% 67.9%
1e3pA02 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.72 49.0 5.19e-01 81.7% 79.5%
3h36A00 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.71 51.0 5.49e-01 74.2% 89.7%
2yfaB01 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.68 61.0 5.65e-01 100.0% 84.9%
3kmiA00 1.20.120.940 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Putative aromatic acid exporter, C-terminal domain 0.68 59.0 4.87e-01 97.8% 94.8%
2hxiB02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.65 58.0 5.19e-01 100.0% 92.5%
1y4cA03 1.20.120.660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain 0.65 60.0 5.60e-01 100.0% 89.4%
1sj7C00 1.20.1420.10 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › Talin, central domain 0.64 57.0 4.76e-01 100.0% 69.9%
4l8iB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.64 46.0 4.33e-01 74.2% 89.3%
2dnxA00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 44.0 3.94e-01 71.0% 73.1%
4i1mB01 1.20.120.1700 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.64 53.0 4.75e-01 90.3% 91.5%
3ls1A00 1.20.120.290 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle 0.63 57.0 5.07e-01 100.0% 78.9%
3g5uA01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.63 55.0 3.33e-01 100.0% 70.8%
6z3yB01 1.20.1530.20 Mainly Alpha › Up-down Bundle › Na+/H+ antiporter like fold › 0.63 55.0 3.71e-01 100.0% 48.4%
3b9qA01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.63 45.0 4.59e-01 98.9% 78.7%
4adnA01 1.20.1280.250 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.62 47.0 4.92e-01 100.0% 92.9%
4fjqA02 1.50.10.130 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › Terpene synthase, N-terminal domain 0.62 48.0 4.08e-01 95.7% 49.4%
2i5uA00 1.10.10.630 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › DnaD domain-like 0.62 42.0 4.53e-01 81.7% 84.4%
2l1lB00 1.20.1440.250 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.61 41.0 3.76e-01 73.1% 52.0%
4p9tA01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.60 52.0 4.87e-01 100.0% 85.8%
4g12A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.60 52.0 4.54e-01 98.9% 77.2%
3kyiA00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.60 54.0 4.88e-01 100.0% 74.2%
3q5dA02 1.20.58.420 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › AHSP 0.60 43.0 4.29e-01 75.3% 82.5%
1nlxA00 1.20.120.320 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Group V grass pollen allergen 0.59 51.0 4.95e-01 97.8% 86.5%
4ciuA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 50.0 3.86e-01 90.3% 79.7%
3fdqA01 1.20.120.1030 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Motility repressor MogR, DNA-binding domain 0.58 48.0 4.46e-01 100.0% 70.5%
2ib0A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.58 47.0 4.21e-01 89.2% 86.7%
3rvyA01 1.20.120.350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C 0.58 51.0 4.78e-01 97.8% 87.7%
5l3wA01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.58 40.0 4.22e-01 86.0% 79.8%
1aueB00 1.20.120.150 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › FKBP12-rapamycin binding domain 0.57 49.0 4.94e-01 100.0% 93.6%
3q18A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.57 50.0 4.64e-01 94.6% 84.5%
3s84A02 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.57 44.0 3.79e-01 84.9% 79.6%
7eqeB01 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.57 50.0 4.16e-01 100.0% 55.0%
1ls1A01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.57 46.0 4.67e-01 100.0% 92.1%
2dq0A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.56 51.0 4.85e-01 98.9% 100.0%
6cnzF00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.56 48.0 4.05e-01 94.6% 93.7%
3e70C01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.55 48.0 4.77e-01 100.0% 92.8%
1nktA04 1.10.3060.10 Mainly Alpha › Orthogonal Bundle › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA 0.55 44.0 3.62e-01 88.2% 81.9%
1ujnA02 1.20.1090.10 Mainly Alpha › Up-down Bundle › Dehydroquinate synthase-like, alpha domain › Dehydroquinate synthase-like - alpha domain 0.55 46.0 3.88e-01 95.7% 79.8%
2ewfA03 3.40.91.50 Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › 0.54 47.0 3.54e-01 94.6% 59.1%
5h5mA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.54 47.0 4.30e-01 100.0% 93.8%
4yosA02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.54 43.0 3.60e-01 86.0% 64.4%
1f5qB01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.53 40.0 3.82e-01 83.9% 67.9%
2fp1B00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.53 46.0 3.86e-01 97.8% 93.9%
4jzaA03 1.20.120.1720 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.53 39.0 3.34e-01 88.2% 47.7%
5ts9B00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.52 45.0 3.84e-01 97.8% 95.0%
1hn0A02 1.50.10.100 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › Chondroitin AC/alginate lyase 0.52 46.0 3.07e-01 97.8% 37.0%
4cxfA01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.51 40.0 4.18e-01 89.2% 93.1%
3vr4B04 1.10.1140.10 Mainly Alpha › Orthogonal Bundle › Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 › Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 0.51 45.0 3.88e-01 100.0% 67.5%
1u7lA02 1.20.1460.10 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › subunit c (vma5p) of the yeast v-atpase, domain 2 0.51 39.0 3.08e-01 80.6% 83.1%
ECOD (52)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5082911 141.1.1.0 ↗ alpha bundles › Terpenoid synthases › Terpenoid synthases › Terpenoid synthases 0.75 68.0 4.60e-01 100.0% 33.4%
4034504 601.4.1.47 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains › MspA_staph 0.74 67.0 6.44e-01 100.0% 95.2%
3563871 603.1.1.121 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF30821 0.73 51.0 4.79e-01 73.1% 77.4%
3601984 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.68 48.0 4.44e-01 74.2% 90.8%
3974221 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.68 60.0 5.41e-01 100.0% 76.2%
4475459 601.1.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Vinculin 0.67 59.0 5.18e-01 98.9% 85.0%
3278832 106.1.1.11 ↗ alpha arrays › Globin-like › Globin-like › Globin-like › RsbRD_N 0.67 47.0 4.18e-01 77.4% 51.1%
4609538 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.66 52.0 4.83e-01 100.0% 67.8%
3169705 601.4.1.36 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains › Aip3p_Bud6_N 0.65 57.0 5.15e-01 100.0% 77.7%
3691938 219.1.1.17 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C1_2 0.64 55.0 3.59e-01 100.0% 25.5%
3626133 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.64 57.0 5.15e-01 98.9% 84.8%
3420329 109.4.1.1184 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DUF747 0.64 46.0 3.28e-01 76.3% 45.6%
3586824 601.1.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Vinculin 0.63 56.0 3.65e-01 98.9% 25.2%
3936516 604.8.1.0 ↗ alpha bundles › Spectrin repeat-like › Smac/diablo › Smac/diablo 0.63 45.0 3.72e-01 75.3% 69.7%
4823728 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.62 53.0 5.14e-01 92.5% 89.4%
4780326 601.19.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein 0.62 44.0 3.53e-01 74.2% 90.1%
3300142 601.1.2.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.61 54.0 4.69e-01 100.0% 84.7%
4952530 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.61 55.0 4.86e-01 100.0% 83.7%
3605672 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.61 55.0 4.16e-01 100.0% 74.8%
3414050 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.60 53.0 5.14e-01 98.9% 85.7%
3969845 1075.5.1.16 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › PelG 0.59 47.0 3.63e-01 87.1% 45.5%
3509088 109.4.1.257 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PDS5 0.59 40.0 3.05e-01 73.1% 29.5%
3735237 601.19.1.18 ↗ alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › Mmc1_C 0.59 51.0 4.44e-01 100.0% 74.0%
2539030 601.2.1.4 ↗ alpha bundles › Four-helical up-and-down bundle › Cytochromes › Cytochromes › Cytochrom_C_2 0.58 51.0 4.87e-01 100.0% 88.3%
3360588 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.58 53.0 3.89e-01 100.0% 61.7%
4980072 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.58 45.0 3.83e-01 84.9% 90.5%
3590444 5081.1.1.1 ↗ alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › Rhomboid 0.58 49.0 3.81e-01 97.8% 67.6%
4938440 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.58 49.0 4.79e-01 91.4% 85.0%
3788546 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.56 46.0 3.31e-01 91.4% 62.8%
4975796 4953.1.1.0 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.55 40.0 3.98e-01 81.7% 73.7%
5076373 633.21.1.0 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.55 43.0 4.13e-01 90.3% 73.3%
3414564 2008.1.1.29 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Dna2 0.54 45.0 3.27e-01 92.5% 58.6%
4561607 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.54 45.0 4.15e-01 90.3% 87.5%
5055941 181.1.1.1 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N 0.54 48.0 4.67e-01 100.0% 94.3%
4060910 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.54 47.0 4.49e-01 93.5% 97.1%
4591574 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.54 46.0 4.27e-01 92.5% 90.4%
4057021 605.4.1.20 ↗ alpha duplicates or obligate multimers › ROP-like › ROP protein › ROP protein › DUF6092 0.54 40.0 4.04e-01 83.9% 82.2%
3370201 101.1.8.17 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › PF26576 0.54 39.0 3.69e-01 77.4% 96.5%
4060154 4974.1.1.0 ↗ alpha bundles › CRISPR-Cas system first helical domain › CRISPR-Cas system first helical domain › CRISPR-Cas system RNase C2c2 first helical domain 0.54 45.0 3.72e-01 98.9% 59.5%
4368654 103.4.1.2 ↗ 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 › TFIIS_M 0.53 42.0 3.83e-01 87.1% 64.2%
4944703 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.53 46.0 4.22e-01 100.0% 72.3%
3649076 3939.1.1.207 ↗ alpha duplicates or obligate multimers › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain › NET2A 0.53 46.0 3.66e-01 95.7% 93.2%
3693457 109.3.1.242 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Fungal_trans_2 0.53 48.0 3.94e-01 98.9% 56.4%
3979848 1075.1.1.22 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › ABCG5/ABCG8 transmembrane domain › MlaE 0.53 45.0 3.52e-01 100.0% 65.2%
3704554 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.53 39.0 4.04e-01 87.1% 84.1%
4090297 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.52 47.0 4.55e-01 96.8% 88.6%
4437810 3860.1.1.305 ↗ alpha bundles › Myosin VI lever arm › Myosin VI lever arm › Myosin VI lever arm › DUF697 0.52 43.0 3.39e-01 88.2% 59.5%
3722559 1075.5.1.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › MatE 0.52 44.0 3.45e-01 100.0% 65.8%
4579811 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.51 47.0 4.55e-01 100.0% 90.5%
3492576 4177.1.1.5 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › Vps5 0.51 46.0 3.53e-01 96.8% 75.5%
4223425 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.50 47.0 4.47e-01 100.0% 87.6%
4200274 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.50 46.0 4.47e-01 100.0% 91.4%