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NC_049919.1__YP_009907949.1__H3H24_gp04__00004

Bact-Vir

NC_049919.1__YP_009907949.1__H3H24_gp04__00004

Identity

Accession:
NC_049919 ↗
Kingdom:
phage

Quality

80.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Traversvirus› Escherichia_phage_SH2026Stx1

TaxID: 2108115

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 198-309
PDB
Domain cluster: rep: S2_012_000_R2_scaffold_0_prodigal-single.1__X__X__00432__D36-134
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6jzaA00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.67 25.0 2.91e-01 86.6% 44.4%
2cuwA00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.52 37.0 4.13e-01 92.9% 98.8%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3573640 11.2.1.16 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › PKC_C2 0.58 30.0 2.96e-01 88.4% 43.2%
5063945 304.100.1.0 ↗ a+b two layers › Alpha-beta plaits › PurS-like › PurS-like 0.54 37.0 4.33e-01 86.6% 100.0%
5072282 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.51 24.0 2.68e-01 70.5% 50.0%
3956448 304.100.1.1 ↗ a+b two layers › Alpha-beta plaits › PurS-like › PurS-like › PurS 0.51 35.0 3.98e-01 87.5% 100.0%
D2 medium residues 1-19_77-197
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF13935.12 best Ead_Ea22 77.1 2.70e-21 50.7% 54.0%
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2efkA01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.83 58.0 4.61e-01 79.3% 38.2%
1qu7A00 1.10.287.950 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Methyl-accepting chemotaxis protein 0.81 67.0 5.62e-01 87.1% 66.1%
D3 medium residues 20-76
PDB
Domain cluster: representative
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ei5A03 2.40.128.50 Mainly Beta › Beta Barrel › Lipocalin › 0.73 45.0 3.68e-01 75.4% 35.3%
4r03A00 2.40.128.720 Mainly Beta › Beta Barrel › Lipocalin › 0.64 49.0 4.04e-01 86.0% 73.4%
4r8oA00 2.40.128.720 Mainly Beta › Beta Barrel › Lipocalin › 0.64 44.0 3.77e-01 73.7% 67.3%
3mswA00 2.40.128.720 Mainly Beta › Beta Barrel › Lipocalin › 0.62 44.0 3.34e-01 73.7% 49.6%
2g8kA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.62 49.0 3.83e-01 100.0% 38.2%
1b7eA01 3.90.350.10 Alpha Beta › Alpha-Beta Complex › Transposase Inhibitor Protein From Tn5; Chain A, domain 1 › Transposase Inhibitor Protein From Tn5; Chain A, domain 1 0.62 53.0 3.54e-01 100.0% 26.0%
3my2A00 2.60.450.10 Mainly Beta › Sandwich › lipopolysaccharide transport protein A fold › Lipopolysaccharide (LPS) transport protein A like domain 0.62 52.0 4.02e-01 94.7% 88.1%
1ukxA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.62 52.0 4.06e-01 100.0% 48.9%
1eqnB01 3.90.980.10 Alpha Beta › Alpha-Beta Complex › DNA primase DNAg catalytic core, N-terminal domain › DNA primase, catalytic core, N-terminal domain 0.60 39.0 3.03e-01 70.2% 30.2%
3qz4A00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.59 48.0 3.15e-01 100.0% 30.1%
6fhoA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.59 45.0 3.19e-01 87.7% 83.7%
1p32B00 3.10.280.10 Alpha Beta › Roll › Mitochondrial Matrix Protein; Chain A › Mitochondrial glycoprotein 0.59 42.0 3.09e-01 78.9% 28.1%
3votB02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.58 45.0 2.93e-01 87.7% 69.6%
4e4tA03 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.58 50.0 3.44e-01 96.5% 82.2%
4hslA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.57 45.0 3.43e-01 96.5% 66.3%
2kw4A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.57 47.0 3.64e-01 100.0% 41.5%
2iv2X01 2.20.25.90 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › ADC-like domains 0.56 37.0 3.76e-01 80.7% 70.9%
4g3wA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.56 44.0 3.51e-01 94.7% 50.4%
2au3A02 3.90.980.10 Alpha Beta › Alpha-Beta Complex › DNA primase DNAg catalytic core, N-terminal domain › DNA primase, catalytic core, N-terminal domain 0.56 38.0 2.96e-01 71.9% 31.5%
4y2fA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.55 44.0 3.43e-01 93.0% 42.0%
3bt3A01 3.30.1900.10 Alpha Beta › 2-Layer Sandwich › glyoxalase-related enzyme like fold › glyoxalase-related enzyme like domain 0.55 37.0 3.50e-01 70.2% 59.7%
2aqjA00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.55 44.0 2.60e-01 91.2% 50.7%
4bg8A01 3.30.420.430 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.55 45.0 3.59e-01 98.2% 51.2%
2jxpA01 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.54 43.0 3.44e-01 100.0% 67.4%
2konA00 3.30.160.350 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.53 45.0 4.11e-01 100.0% 76.8%
5nz7A01 2.70.98.40 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Glycoside hydrolase, family 65, N-terminal domain 0.53 43.0 2.79e-01 98.2% 25.5%
3payB02 2.60.40.2090 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 45.0 3.55e-01 100.0% 69.7%
2p1jA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.53 43.0 3.40e-01 98.2% 57.2%
2avwD01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.53 43.0 3.26e-01 89.5% 44.0%
3hjhA02 3.30.2060.10 Alpha Beta › 2-Layer Sandwich › Penicillin-binding protein 1b fold › Penicillin-binding protein 1b domain 0.53 33.0 3.03e-01 98.2% 41.9%
1xvwA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 43.0 3.29e-01 100.0% 79.7%
1k0rA01 3.30.1480.10 Alpha Beta › 2-Layer Sandwich › N Utilization Substance Protein A; Chain:P; domain 4 › NusA, N-terminal domain 0.52 37.0 3.21e-01 77.2% 46.5%
4pqdA00 3.90.570.10 Alpha Beta › Alpha-Beta Complex › Sugar Binding Protein, Amyloid A4 Protein; Chain A › Amyloidogenic glycoprotein, heparin-binding domain 0.52 39.0 3.38e-01 100.0% 47.6%
1pjxA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.52 42.0 2.74e-01 98.2% 88.2%
4iglB00 2.180.10.10 Mainly Beta › Shell › RHS repeat-associated core › RHS repeat-associated core 0.52 46.0 2.59e-01 98.2% 98.2%
3kf8B00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.52 40.0 3.19e-01 86.0% 74.2%
3wodG00 2.30.30.1250 Mainly Beta › Roll › SH3 type barrels. › 0.52 43.0 3.47e-01 100.0% 63.8%
3nwsA01 2.40.50.800 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.52 44.0 3.35e-01 98.2% 73.8%
3d8pB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.52 40.0 2.95e-01 86.0% 56.2%
1j54A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.51 43.0 3.19e-01 98.2% 48.3%
3df7A02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.50 38.0 3.05e-01 89.5% 51.1%
ECOD (51)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
863 9.4.1.1 ↗ beta barrels › Lipocalins/Streptavidin › D-aminopeptidase, middle and C-terminal domains › D-aminopeptidase, middle and C-terminal domains › DAP_B 0.73 45.0 3.67e-01 75.4% 35.0%
4965302 7089.1.1.8 ↗ a+b two layers › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › PF25912 0.71 55.0 4.77e-01 98.2% 54.4%
1644186 2003.1.2.2 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › GMC_oxred_N 0.66 44.0 2.80e-01 86.0% 13.1%
3621211 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.66 39.0 4.50e-01 86.0% 85.0%
3978060 4023.1.1.3 ↗ a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DUF7146 0.65 44.0 3.62e-01 70.2% 44.0%
3363212 708.1.1.8 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › FAR1 0.65 52.0 4.30e-01 87.7% 66.0%
3612090 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.64 42.0 4.14e-01 91.2% 63.3%
9277 2003.1.2.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox 0.63 40.0 3.19e-01 91.2% 30.6%
2722572 3894.1.1.3 ↗ beta meanders › O-GlcNAc transferase GtfA beta-meander domain › O-GlcNAc transferase GtfA beta-meander domain › O-GlcNAc transferase GtfA beta-meander domain › GtfB_M 0.63 44.0 3.36e-01 89.5% 31.1%
3183104 9.4.1.2 ↗ beta barrels › Lipocalins/Streptavidin › D-aminopeptidase, middle and C-terminal domains › D-aminopeptidase, middle and C-terminal domains › DUF3471 0.63 41.0 3.16e-01 73.7% 30.0%
3708791 77.3.1.3 ↗ beta meanders › open-sided beta-meander › CPAP G-box domain › CPAP G-box domain › MORN 0.61 40.0 2.78e-01 89.5% 18.6%
3930408 2484.5.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase › RT_RNaseH 0.60 48.0 4.48e-01 100.0% 70.0%
3307408 708.1.1.0 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain 0.60 46.0 4.03e-01 87.7% 54.4%
4666811 243.3.1.51 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › HalC8_like_N 0.59 42.0 3.13e-01 75.4% 80.0%
4052313 2484.1.1.10 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TsaD 0.59 48.0 4.04e-01 100.0% 51.4%
4434598 4023.1.1.1 ↗ a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N 0.59 39.0 3.02e-01 71.9% 30.8%
3362014 708.1.1.8 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › FAR1 0.58 46.0 3.86e-01 87.7% 59.0%
3358346 708.1.1.8 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › FAR1 0.58 46.0 3.93e-01 87.7% 62.1%
3838066 7520.1.1.1 ↗ a/b three-layered sandwiches › CinA-like › CinA-like › CinA-like › CinA 0.58 48.0 3.64e-01 100.0% 39.9%
3348338 708.1.1.0 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain 0.58 46.0 4.51e-01 89.5% 92.1%
4401930 2.1.1.31 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DNA_ligase_A_C 0.58 50.0 3.89e-01 100.0% 89.9%
4930963 2003.1.10.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › PreATP-grasp domain 0.57 43.0 4.00e-01 98.2% 64.0%
3425526 897.1.1.1 ↗ a+b two layers › Acidic mitochondrial matrix protein p32-like › Acidic mitochondrial matrix protein p32 › Acidic mitochondrial matrix protein p32 › MAM33 0.57 42.0 3.02e-01 80.7% 29.0%
4043621 4023.1.1.1 ↗ a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N 0.56 38.0 2.85e-01 71.9% 27.6%
3679402 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.56 47.0 3.56e-01 100.0% 40.0%
4979773 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.56 44.0 3.03e-01 86.0% 45.5%
4130139 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.56 45.0 3.50e-01 96.5% 38.6%
3429972 708.1.1.8 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › FAR1 0.56 43.0 3.73e-01 87.7% 65.3%
4188272 71.1.1.3 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › LolB 0.55 43.0 3.31e-01 93.0% 38.4%
4200618 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.55 43.0 3.60e-01 96.5% 46.1%
3572103 220.1.1.74 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PIG-H 0.55 45.0 3.58e-01 100.0% 48.1%
3880540 389.1.2.1 ↗ few secondary structure elements › EGF-like › EGF-related › Complement control module/SCR domain › Sushi 0.55 42.0 4.15e-01 98.2% 81.7%
3293559 708.1.1.8 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › FAR1 0.54 43.0 3.70e-01 87.7% 68.9%
3514245 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.54 41.0 3.48e-01 91.2% 56.5%
5054600 2484.1.1.10 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TsaD 0.54 42.0 3.39e-01 100.0% 43.5%
3719596 77.1.1.3 ↗ beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein › MORN_DRC7 0.53 43.0 3.14e-01 91.2% 50.0%
4235559 304.8.1.61 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › GDH_ACT1 0.53 43.0 3.20e-01 100.0% 58.4%
3176064 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.53 44.0 3.38e-01 100.0% 64.5%
3275009 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.53 43.0 3.34e-01 98.2% 38.5%
3445327 708.1.1.8 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › FAR1 0.53 45.0 3.58e-01 98.2% 68.3%
3439556 708.1.1.8 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › FAR1 0.53 44.0 3.70e-01 98.2% 77.1%
3309117 708.1.1.8 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › FAR1 0.52 45.0 3.44e-01 98.2% 65.9%
3256042 2004.1.1.21 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › RecA 0.51 42.0 2.69e-01 91.2% 92.2%
1837665 206.1.3.25 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › ATP-grasp_4 0.51 37.0 2.68e-01 82.5% 55.4%
3738483 213.1.1.47 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Pho86 0.51 41.0 2.97e-01 87.7% 61.8%
4053143 1.1.5.6 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Peptidase_S7 0.51 37.0 3.01e-01 80.7% 72.5%
4874611 101.1.15.1 ↗ alpha arrays › HTH › HTH › HAT1, C-terminal domain › MOZ_SAS 0.51 40.0 3.24e-01 93.0% 72.3%
4505972 323.1.1.3 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.51 38.0 2.50e-01 87.7% 15.9%
4924545 206.1.3.10 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › CPSase_L_D2 0.50 36.0 2.85e-01 82.5% 36.1%
3479701 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.50 39.0 3.28e-01 100.0% 46.1%
3589604 213.1.1.31 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_10 0.50 39.0 2.96e-01 86.0% 57.6%