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NC_048767.1__YP_009845953.1__HWC23_gp19__00019

Bact-Vir

NC_048767.1__YP_009845953.1__HWC23_gp19__00019

Identity

Accession:
NC_048767 ↗
Kingdom:
phage

Quality

56.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Dibbivirus› Pantoea_phage_vB_PagM_PSKM

TaxID: 2588094

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

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

D1 high residues 251-451
PDB
D2 medium residues 44-154_225-250
PDB
Domain cluster: rep: OR354825.1__WNM51604.1__CoNPh2_CDS0050__00048__D273-380_559-584
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF20155.5 best TMP_3 67.0 2.70e-18 75.2% 52.6%
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7uzqK01 1.10.3430.10 Mainly Alpha › Orthogonal Bundle › Ammonium transporter fold › Ammonium transporter AmtB like domains 0.68 54.0 3.98e-01 84.7% 48.6%
1oj6A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.64 36.0 3.54e-01 97.8% 49.7%
4xaxB02 1.20.58.1290 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › CarD-like, C-terminal domain 0.63 27.0 3.18e-01 99.3% 54.5%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.62 29.0 3.85e-01 74.5% 81.1%
4ezcB00 1.10.3430.10 Mainly Alpha › Orthogonal Bundle › Ammonium transporter fold › Ammonium transporter AmtB like domains 0.62 46.0 3.47e-01 78.1% 85.5%
4j8sA00 1.25.40.840 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › CCR4-NOT transcription complex subunit 1 TTP binding domain 0.57 29.0 2.66e-01 98.5% 36.1%
3k3fA00 1.10.3430.10 Mainly Alpha › Orthogonal Bundle › Ammonium transporter fold › Ammonium transporter AmtB like domains 0.57 45.0 3.39e-01 83.2% 95.8%
4v1gA00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.52 24.0 2.93e-01 89.8% 64.7%
2vkjA00 1.20.58.2030 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 23.0 2.63e-01 99.3% 51.9%
8b70A01 1.20.1740.10 Mainly Alpha › Up-down Bundle › Amino acid/polyamine transporter I › Amino acid/polyamine transporter I 0.51 38.0 2.80e-01 80.3% 94.5%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3963765 159.1.2.5 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › TMP_3 0.91 78.0 6.85e-01 89.1% 100.0%
4032310 159.1.2.6 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › PhageMin_Tail 0.73 62.0 6.06e-01 91.2% 100.0%
3931463 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 0.70 41.0 5.16e-01 73.0% 94.1%
3248344 1076.1.1.6 ↗ alpha bundles › Intramembrane protease Rce1-related › Intramembrane protease Rce1-related › Intramembrane protease Rce1-related › DUF2053 0.57 41.0 3.66e-01 73.7% 98.5%
3251869 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 25.0 2.14e-01 97.1% 26.0%
3273235 148.1.3.40 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › ORC5_lid 0.52 37.0 3.71e-01 73.7% 90.3%
5082506 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 3.52e-01 81.0% 79.0%
D3 medium residues 155-224
PDB
Domain cluster: representative
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3op9A01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.61 43.0 4.41e-01 78.6% 77.9%
4jcyA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.60 42.0 3.92e-01 74.3% 59.8%
1el4A00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.60 52.0 3.85e-01 100.0% 70.6%
4ybaA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.60 46.0 4.50e-01 87.1% 76.6%
2bnmA01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.60 43.0 4.23e-01 77.1% 75.7%
7xi5A01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.59 40.0 4.42e-01 80.0% 100.0%
3hjeA03 1.10.150.200 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Maltooligosyl trehalose synthase; domain 3 0.58 39.0 3.63e-01 70.0% 82.4%
1y7yA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.58 41.0 4.19e-01 78.6% 78.3%
6rnzA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.58 41.0 4.24e-01 78.6% 81.8%
7n1nB01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.56 40.0 4.13e-01 81.4% 85.7%
2auwB02 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.56 43.0 4.33e-01 92.9% 87.1%
1v1gA00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.56 45.0 3.34e-01 90.0% 75.5%
1r69A00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.55 38.0 3.95e-01 72.9% 81.0%
2ef8A00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.54 41.0 3.91e-01 87.1% 70.2%
2mf4A01 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.54 40.0 3.88e-01 81.4% 92.7%
4c0kA01 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.54 45.0 3.99e-01 92.9% 67.3%
7oq4Z01 1.20.120.950 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Uncharacterised protein DUF5062 0.53 45.0 4.07e-01 95.7% 78.6%
7qv0F01 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.53 39.0 3.73e-01 78.6% 67.9%
3b4uA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.53 40.0 2.70e-01 81.4% 96.5%
4gxzD00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 36.0 2.76e-01 85.7% 28.8%
3h4sE00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.53 46.0 4.20e-01 100.0% 78.1%
2ofyA01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.52 38.0 3.86e-01 82.9% 80.0%
4pu7A00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.52 37.0 3.74e-01 77.1% 78.9%
4uyeA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.52 43.0 3.81e-01 97.1% 76.1%
4pcwC00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.52 42.0 3.97e-01 95.7% 72.5%
3a1iA02 3.90.1300.10 Alpha Beta › Alpha-Beta Complex › Amidase signature (AS) enzymes › Amidase signature (AS) domain 0.52 42.0 2.67e-01 98.6% 65.9%
3fmyA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.51 41.0 4.20e-01 91.4% 100.0%
1iv8A03 1.10.150.200 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Maltooligosyl trehalose synthase; domain 3 0.51 37.0 3.52e-01 78.6% 84.7%
2ki4B00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.51 39.0 3.60e-01 91.4% 63.5%
1ic8A01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.51 43.0 3.97e-01 100.0% 78.7%
1fafA00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.50 34.0 3.35e-01 74.3% 64.6%
ECOD (32)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3277653 101.1.4.18 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › HTH_31 0.64 44.0 4.22e-01 74.3% 62.4%
3924866 170.1.1.0 ↗ alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C 0.60 42.0 3.87e-01 98.6% 54.7%
4084920 101.1.4.0 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like 0.60 43.0 4.33e-01 77.1% 78.6%
2647253 101.1.4.3 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › HTH_3 0.59 40.0 3.92e-01 71.4% 67.9%
3288109 101.1.4.0 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like 0.58 42.0 4.28e-01 80.0% 80.0%
3711037 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.58 41.0 4.19e-01 91.4% 75.7%
3345464 108.1.1.73 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_5+EF-hand_7 0.58 48.0 4.49e-01 92.9% 74.4%
3965190 101.1.4.0 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like 0.57 42.0 4.37e-01 82.9% 93.8%
3613571 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.57 41.0 4.11e-01 91.4% 77.1%
2057229 101.1.4.23 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › MqsA_antitoxin 0.56 44.0 4.42e-01 88.6% 98.6%
3972740 101.1.4.17 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › HTH_26 0.56 39.0 4.02e-01 75.7% 80.0%
3715903 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.55 46.0 3.87e-01 94.3% 55.2%
4979008 601.28.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.55 44.0 4.14e-01 91.4% 79.5%
3838379 601.53.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Flagellin glycosyltransferase Maf helical bundle domain › Flagellin glycosyltransferase Maf helical bundle domain 0.55 44.0 3.93e-01 94.3% 76.4%
5013258 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.55 44.0 3.78e-01 92.9% 80.0%
5082802 101.1.4.3 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › HTH_3 0.55 45.0 4.14e-01 100.0% 68.0%
4970859 601.28.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.55 45.0 4.17e-01 100.0% 76.0%
3498092 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.55 47.0 3.52e-01 100.0% 42.1%
4984278 101.1.4.17 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › HTH_26 0.55 42.0 4.17e-01 87.1% 80.0%
3526520 101.1.4.5 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › HNF-1_N 0.54 43.0 3.73e-01 92.9% 60.0%
3983992 101.1.4.20 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › HTH_37 0.54 41.0 3.98e-01 87.1% 73.8%
3864569 108.1.1.8 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › S_100 0.54 45.0 4.08e-01 95.7% 69.4%
3407269 192.6.1.0 ↗ alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.54 45.0 3.82e-01 98.6% 92.3%
3260230 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.53 45.0 3.77e-01 95.7% 53.6%
2775 101.1.4.3 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › HTH_3 0.53 37.0 3.62e-01 77.1% 65.9%
3166016 101.1.4.17 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › HTH_26 0.53 39.0 4.13e-01 82.9% 95.0%
4961755 5069.1.1.26 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › NrfD 0.52 43.0 3.25e-01 100.0% 49.8%
148583 109.1.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › GST_C 0.52 35.0 3.01e-01 70.0% 70.8%
4570266 108.1.1.95 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › CCD48 0.52 37.0 3.04e-01 87.1% 37.9%
3720642 108.1.1.1 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_1 0.51 43.0 4.06e-01 94.3% 77.6%
3188112 108.1.1.25 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_4 0.51 41.0 3.49e-01 97.1% 54.8%
5068767 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.51 38.0 3.54e-01 81.4% 73.3%