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KX879600.1__APC45983.1__PSGCA5_02__00002

Bact-Vir

KX879600.1__APC45983.1__PSGCA5_02__00002

Identity

Accession:
KX879600 ↗
Kingdom:
phage

Quality

80.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Liberibacter_phage_SGCA5-1

TaxID: 1903184

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 73-152
PDB
Domain cluster: rep: MT899444.1__QOI69845.1__PPA191_gp04__00004__D205-282
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4r8oA00 2.40.128.720 Mainly Beta › Beta Barrel › Lipocalin › 0.63 48.0 4.49e-01 81.2% 79.6%
2af5A02 3.90.930.1 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › 0.63 56.0 4.67e-01 100.0% 87.7%
4mjdA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.62 36.0 3.26e-01 73.8% 40.7%
3w9kA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.59 42.0 3.52e-01 75.0% 47.4%
3wasA00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.58 44.0 2.87e-01 83.7% 33.9%
4c89C00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.57 48.0 3.23e-01 95.0% 68.4%
3vsfC01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.57 44.0 2.99e-01 88.7% 36.3%
3vsmA02 2.70.98.100 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Baculovirus E66 occlusion-derived virus envelope protein, domain 2 0.56 40.0 3.15e-01 76.2% 67.7%
2wuqB00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.56 40.0 2.82e-01 77.5% 64.0%
5h8iI00 3.60.110.10 Alpha Beta › 4-Layer Sandwich › Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase › Carbon-nitrogen hydrolase 0.55 44.0 3.02e-01 87.5% 93.9%
4ewfA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.54 38.0 2.68e-01 73.8% 60.8%
3dxoB00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 38.0 3.40e-01 76.2% 100.0%
2ex2A01 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.53 38.0 2.72e-01 75.0% 71.4%
3gmvX00 3.10.450.730 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › BLIP domain 0.53 44.0 3.60e-01 93.8% 75.0%
2db2A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.52 34.0 3.33e-01 88.7% 57.4%
6mlyB01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.52 38.0 2.79e-01 81.2% 42.0%
1jovA00 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.52 44.0 3.10e-01 96.2% 93.3%
3lygA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 34.0 3.00e-01 72.5% 44.2%
3eliA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.51 41.0 3.40e-01 87.5% 53.5%
7pk0A01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.51 40.0 3.40e-01 83.7% 80.8%
3dtdD00 2.60.40.1880 Mainly Beta › Sandwich › Immunoglobulin-like › Invasion associated locus B (IalB) protein 0.51 38.0 3.17e-01 80.0% 64.8%
3bgaA05 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.50 38.0 2.73e-01 83.7% 70.0%
1uuzB00 3.40.1420.10 Alpha Beta › 3-Layer(aba) Sandwich › Inhibitor of vertebrate lysozyme, Ivy › Inhibitor of vertebrate lysozyme 0.50 39.0 3.42e-01 87.5% 78.1%
1olzA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.50 40.0 2.52e-01 88.7% 47.6%
2qubA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.50 39.0 2.71e-01 90.0% 48.3%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4027722 77.2.1.1 ↗ beta meanders › open-sided beta-meander › Histone H3 K4-specific methyltransferase SET7/9-N › Histone H3 K4-specific methyltransferase SET7/9-N › MORN 0.64 53.0 4.62e-01 91.3% 72.0%
3965061 5084.3.1.1 ↗ beta barrels › Outer membrane meander beta-barrels › Autotransporter › Autotransporter › Autotransporter 0.64 48.0 3.37e-01 80.0% 64.6%
4959370 71.1.1.0 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB 0.62 47.0 3.70e-01 81.2% 48.2%
5074996 844.1.1.2 ↗ beta barrels › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › LOR 0.61 46.0 3.66e-01 82.5% 48.8%
3253682 77.2.1.1 ↗ beta meanders › open-sided beta-meander › Histone H3 K4-specific methyltransferase SET7/9-N › Histone H3 K4-specific methyltransferase SET7/9-N › MORN 0.60 52.0 4.25e-01 96.2% 75.3%
3483806 295.1.1.3 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › PurA 0.59 40.0 3.29e-01 70.0% 81.3%
4956163 71.1.1.0 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB 0.58 43.0 3.30e-01 77.5% 35.0%
4016769 844.1.1.0 ↗ beta barrels › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain 0.58 45.0 3.38e-01 93.8% 33.0%
3261183 71.1.1.0 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB 0.57 47.0 3.60e-01 87.5% 98.9%
1227254 5.1.2.8 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed › Glyco_hydro_43 0.57 45.0 3.08e-01 88.7% 38.9%
4945614 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.57 42.0 3.41e-01 78.8% 82.6%
5080820 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.55 40.0 3.25e-01 78.8% 83.6%
4975626 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.55 48.0 4.02e-01 98.8% 68.5%
3818015 844.1.1.2 ↗ beta barrels › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › LOR 0.55 43.0 3.35e-01 86.3% 49.5%
2448551 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.54 40.0 3.54e-01 78.8% 92.4%
3762123 213.1.1.16 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.54 39.0 3.13e-01 76.2% 63.7%
3924310 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.53 42.0 2.75e-01 87.5% 52.7%
3191953 844.1.1.2 ↗ beta barrels › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › LOR 0.53 41.0 3.21e-01 86.3% 45.4%
3710328 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.52 36.0 3.29e-01 95.0% 50.0%
3939687 220.1.1.2 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › WH1 0.52 35.0 3.34e-01 71.2% 79.0%
2012 12.3.1.3 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › Aldose_epim 0.52 44.0 3.10e-01 96.2% 93.3%
3830571 844.1.1.5 ↗ beta barrels › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › DUF3527 0.52 43.0 3.33e-01 98.8% 58.4%
5046458 844.1.1.2 ↗ beta barrels › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › LOR 0.52 41.0 3.29e-01 90.0% 49.1%
3833804 5.1.2.35 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed › GINT1_N 0.51 42.0 2.86e-01 93.8% 42.1%
4967383 844.1.1.2 ↗ beta barrels › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › LOR 0.51 39.0 3.07e-01 85.0% 53.2%
3403399 220.1.1.2 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › WH1 0.51 35.0 3.17e-01 71.2% 74.8%
3459823 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.50 40.0 2.87e-01 91.3% 45.5%
4017740 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.50 35.0 3.15e-01 75.0% 80.8%
D2 high residues 158-231
PDB
Domain cluster: representative
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2pp6A02 2.40.10.210 Mainly Beta › Beta Barrel › Thrombin, subunit H › Phage tail proteins (gpFII-like) 0.78 46.0 4.93e-01 100.0% 69.8%
6my0A02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.76 38.0 4.09e-01 86.5% 55.4%
4epcA01 2.30.30.170 Mainly Beta › Roll › SH3 type barrels. › 0.73 50.0 4.88e-01 86.5% 64.2%
2nwaA01 2.40.240.20 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Hypothetical PUA domain-like; domain 1 0.69 45.0 4.49e-01 100.0% 65.3%
2dyiA01 2.40.30.60 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › RimM 0.68 41.0 3.93e-01 100.0% 52.4%
6f2mA02 2.40.30.290 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.66 43.0 4.04e-01 100.0% 56.3%
2qggA01 2.40.30.60 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › RimM 0.65 43.0 4.01e-01 100.0% 54.8%
2zzeA03 2.40.30.130 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.62 41.0 3.72e-01 100.0% 51.0%
3gs9A01 6.20.110.10 Special › Other non-globular › Thrombin, subunit H › 0.57 35.0 3.51e-01 100.0% 57.0%
1v29B02 2.30.30.50 Mainly Beta › Roll › SH3 type barrels. › 0.57 45.0 4.09e-01 90.5% 63.9%
4p02A03 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.56 42.0 3.56e-01 100.0% 49.2%
2f1lA01 2.40.30.60 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › RimM 0.54 34.0 3.26e-01 100.0% 52.8%
2cqoA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.52 43.0 4.03e-01 90.5% 83.7%
1pcfA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.51 34.0 3.56e-01 74.3% 75.8%
2zu2A01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.51 39.0 3.54e-01 100.0% 61.2%
5xd6B01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.51 34.0 3.13e-01 100.0% 53.2%
2ynaA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.50 40.0 3.83e-01 100.0% 72.7%
ECOD (30)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5001586 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.81 50.0 4.66e-01 100.0% 52.2%
3975275 1.1.13.15 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Gifsy-2 0.78 46.0 4.18e-01 100.0% 46.3%
3965594 1.1.13.53 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Phage-tail_3 0.74 50.0 4.57e-01 100.0% 54.7%
4995824 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.70 46.0 4.70e-01 100.0% 68.5%
5010878 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.69 48.0 4.08e-01 100.0% 46.1%
4521547 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.69 42.0 3.98e-01 100.0% 51.1%
4048207 6012.1.1.0 ↗ few secondary structure elements › Antimicrobial peptide LCI › Antimicrobial peptide LCI › Antimicrobial peptide LCI 0.67 39.0 4.81e-01 100.0% 100.0%
1213522 1.1.13.25 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › DTP-pb9_B-dom 0.65 42.0 4.02e-01 100.0% 56.3%
4596341 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.64 40.0 3.71e-01 100.0% 49.5%
4060133 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.63 44.0 4.12e-01 100.0% 60.0%
4161414 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.63 45.0 4.06e-01 100.0% 56.0%
4051652 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.62 42.0 3.83e-01 100.0% 53.7%
4214180 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.61 40.0 3.72e-01 100.0% 52.6%
4255584 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.61 44.0 3.99e-01 100.0% 57.0%
3951894 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.60 45.0 4.10e-01 100.0% 61.1%
4138546 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.60 39.0 3.72e-01 100.0% 55.6%
4188663 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.60 38.0 3.52e-01 100.0% 50.5%
4087903 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.60 41.0 3.85e-01 100.0% 58.9%
4267752 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.60 41.0 3.84e-01 100.0% 56.8%
4634180 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.59 41.0 3.88e-01 100.0% 60.0%
3983246 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.59 39.0 3.62e-01 100.0% 53.7%
4353877 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.58 39.0 3.62e-01 100.0% 53.7%
4399542 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.58 38.0 3.58e-01 100.0% 55.6%
4055193 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.57 37.0 3.42e-01 100.0% 50.5%
5012991 1.1.9.23 ↗ beta barrels › cradle loop barrel › RIFT-related › PUA domain › DUF473 0.53 48.0 4.05e-01 98.6% 98.3%
4929979 2.1.1.17 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › OB_aCoA_assoc 0.53 41.0 3.70e-01 86.5% 78.7%
3695570 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.52 38.0 2.46e-01 81.1% 65.7%
4286344 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.52 37.0 3.43e-01 100.0% 57.9%
4666540 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.52 35.0 3.36e-01 100.0% 61.2%
4508428 1.1.7.11 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.51 40.0 3.71e-01 100.0% 66.3%