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KR063281.1__AKJ72644.1__GMA2_106__00106

Bact-Vir

KR063281.1__AKJ72644.1__GMA2_106__00106

Identity

Accession:
KR063281 ↗
Kingdom:
phage

Quality

76.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Gimaduovirus› Gordonia_phage_GMA2

TaxID: 1647283

Cluster

View cluster (4 members)

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 27-79
PDB
Domain cluster: representative
CATH (46)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3td9A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.70 48.0 3.42e-01 71.7% 43.7%
4bt2A01 3.30.1330.80 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Hypothetical protein, similar to alpha- acetolactate decarboxylase; domain 2 0.69 58.0 4.64e-01 100.0% 60.5%
1xv2C01 3.30.1330.80 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Hypothetical protein, similar to alpha- acetolactate decarboxylase; domain 2 0.68 57.0 4.65e-01 100.0% 62.2%
5ycqA00 2.30.30.390 Mainly Beta › Roll › SH3 type barrels. › Hemimethylated DNA-binding domain 0.66 52.0 4.64e-01 88.7% 74.0%
3gg8C03 2.40.33.10 Mainly Beta › Beta Barrel › M1 Pyruvate Kinase; Domain 3 › PK beta-barrel domain-like 0.65 56.0 4.58e-01 96.2% 94.8%
4b6mB00 2.30.30.190 Mainly Beta › Roll › SH3 type barrels. › CAP Gly-rich-like domain 0.65 50.0 4.45e-01 86.8% 93.7%
3t05A02 2.40.33.10 Mainly Beta › Beta Barrel › M1 Pyruvate Kinase; Domain 3 › PK beta-barrel domain-like 0.65 56.0 4.56e-01 96.2% 94.8%
3p26B02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.65 56.0 4.59e-01 100.0% 91.1%
1yzbA01 3.90.70.40 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.65 53.0 4.23e-01 100.0% 60.5%
6su1D01 2.40.33.10 Mainly Beta › Beta Barrel › M1 Pyruvate Kinase; Domain 3 › PK beta-barrel domain-like 0.64 52.0 4.35e-01 88.7% 100.0%
2rlpA01 2.10.70.10 Mainly Beta › Ribbon › Complement Module; domain 1 › Complement Module, domain 1 0.64 45.0 4.16e-01 73.6% 64.2%
1wzoA01 2.30.30.370 Mainly Beta › Roll › SH3 type barrels. › FAH 0.64 44.0 4.74e-01 73.6% 100.0%
1vziA01 2.20.28.100 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › Desulphoferrodoxin, N-terminal domain 0.64 42.0 4.76e-01 79.2% 97.4%
3qtgA02 2.40.33.10 Mainly Beta › Beta Barrel › M1 Pyruvate Kinase; Domain 3 › PK beta-barrel domain-like 0.63 54.0 4.55e-01 98.1% 93.6%
4r3dA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.63 52.0 4.01e-01 100.0% 45.3%
1l1dA00 2.170.150.20 Mainly Beta › Beta Complex › Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A › Peptide methionine sulfoxide reductase. 0.62 49.0 3.79e-01 94.3% 77.8%
7oo1A01 2.40.33.10 Mainly Beta › Beta Barrel › M1 Pyruvate Kinase; Domain 3 › PK beta-barrel domain-like 0.62 50.0 4.41e-01 88.7% 67.5%
3gqbA01 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.62 53.0 4.86e-01 100.0% 97.2%
3x3mA01 3.30.2390.20 Alpha Beta › 2-Layer Sandwich › TTHA1013/TTHA0281-like › Type VII secretion system EccB, repeat 1 domain 0.61 42.0 3.58e-01 71.7% 61.0%
2aaaA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.60 53.0 4.29e-01 100.0% 91.2%
3vm7A02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.60 52.0 4.28e-01 100.0% 90.8%
7razA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 46.0 4.09e-01 92.5% 68.2%
5h7jA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.59 48.0 3.88e-01 94.3% 72.2%
2ewvA01 3.30.450.90 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.59 42.0 3.35e-01 75.5% 82.4%
1txqA00 2.30.30.190 Mainly Beta › Roll › SH3 type barrels. › CAP Gly-rich-like domain 0.58 49.0 4.48e-01 100.0% 100.0%
4e2oA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.57 48.0 4.19e-01 100.0% 69.3%
1yuzA02 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.56 36.0 4.01e-01 73.6% 92.1%
4xtvB02 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.56 39.0 4.04e-01 77.4% 95.8%
1kzlA02 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.55 45.0 3.80e-01 98.1% 85.1%
2ki8A01 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.54 45.0 3.53e-01 98.1% 88.0%
5ajiB02 2.30.30.60 Mainly Beta › Roll › SH3 type barrels. › 0.54 43.0 4.37e-01 100.0% 100.0%
4nzjA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.54 46.0 3.99e-01 100.0% 72.4%
7nz1G01 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.53 42.0 3.50e-01 86.8% 65.6%
3hslX00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.53 38.0 2.41e-01 77.4% 31.0%
1ktbA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.53 43.0 3.77e-01 100.0% 74.7%
5i0fB04 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.53 45.0 3.95e-01 100.0% 65.5%
1i8dA01 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.52 40.0 3.60e-01 98.1% 97.8%
3kcpA02 2.60.40.1120 Mainly Beta › Sandwich › Immunoglobulin-like › Carboxypeptidase-like, regulatory domain 0.51 39.0 3.25e-01 84.9% 57.6%
2j6aA00 2.20.25.10 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.51 37.0 2.85e-01 81.1% 77.2%
1hxnA00 2.110.10.10 Mainly Beta › 4 Propeller › Hemopexin › Hemopexin-like domain 0.51 40.0 2.79e-01 92.5% 74.8%
1tyyA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.51 43.0 2.71e-01 98.1% 32.7%
4cswA02 3.40.366.30 Alpha Beta › 3-Layer(aba) Sandwich › Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 › 50S ribosomal protein L16 arginine hydroxylase; Chain A, Domain 2 0.51 41.0 3.01e-01 98.1% 55.1%
2d93A00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.51 42.0 3.27e-01 100.0% 53.7%
2ej9A01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.51 39.0 2.79e-01 88.7% 69.7%
3cc1A02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.50 40.0 3.57e-01 100.0% 73.9%
1dfxA00 2.60.40.730 Mainly Beta › Sandwich › Immunoglobulin-like › SOR catalytic domain 0.50 40.0 3.24e-01 100.0% 61.6%
ECOD (65)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4963446 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.77 59.0 5.47e-01 81.1% 95.4%
4512216 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.75 52.0 5.40e-01 73.6% 96.0%
3733260 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.72 52.0 3.20e-01 77.4% 84.5%
4025294 4.1.1.60 ↗ beta barrels › SH3 › SH3 › SH3 › YccV-like 0.70 52.0 4.46e-01 83.0% 83.3%
5048696 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.70 57.0 4.07e-01 94.3% 35.9%
6452 4111.1.1.1 ↗ a+b two layers › AF0104/ALDC/Ptd012-like › AF0104/ALDC/Ptd012-like › AF0104/ALDC/Ptd012-like › AAL_decarboxy 0.68 58.0 5.20e-01 100.0% 89.6%
3988738 4111.1.1.1 ↗ a+b two layers › AF0104/ALDC/Ptd012-like › AF0104/ALDC/Ptd012-like › AF0104/ALDC/Ptd012-like › AAL_decarboxy 0.68 57.0 3.80e-01 100.0% 64.3%
5004050 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.68 54.0 4.96e-01 88.7% 77.1%
3982999 4.1.1.60 ↗ beta barrels › SH3 › SH3 › SH3 › YccV-like 0.66 52.0 4.31e-01 88.7% 76.0%
3684527 221.1.5.3 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Chemotaxis inhibitory protein CHIPS › DUF7734 0.66 53.0 4.53e-01 92.5% 69.9%
3630385 9.1.1.49 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › DUF7043 0.66 50.0 4.01e-01 84.9% 96.5%
3603239 2.1.1.42 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Rep_fac-A_C 0.66 43.0 3.13e-01 94.3% 24.0%
3975132 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.66 57.0 4.84e-01 100.0% 76.7%
2697704 4.1.1.13 ↗ beta barrels › SH3 › SH3 › SH3 › MS_channel_2nd 0.65 52.0 4.96e-01 92.5% 89.2%
5008884 1.1.15.1 ↗ beta barrels › cradle loop barrel › RIFT-related › PK beta-barrel domain-like › PK 0.65 56.0 4.80e-01 96.2% 94.1%
3626593 633.23.1.5 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › Clc-like 0.65 46.0 3.04e-01 75.5% 66.8%
3382832 4.1.1.302 ↗ beta barrels › SH3 › SH3 › SH3 › tSH3-B_UBE2O 0.64 55.0 3.89e-01 100.0% 98.3%
3504860 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.64 50.0 4.57e-01 84.9% 100.0%
4972564 1.1.15.1 ↗ beta barrels › cradle loop barrel › RIFT-related › PK beta-barrel domain-like › PK 0.64 55.0 4.55e-01 96.2% 93.7%
4932588 4.1.1.13 ↗ beta barrels › SH3 › SH3 › SH3 › MS_channel_2nd 0.64 50.0 4.80e-01 90.6% 92.3%
3192436 220.1.1.129 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Swc3 0.64 45.0 3.24e-01 77.4% 49.7%
4880433 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.64 51.0 4.72e-01 90.6% 75.7%
1969 12.1.1.16 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Cyc-maltodext_C 0.64 51.0 4.41e-01 88.7% 81.9%
3932908 633.23.1.5 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › Clc-like 0.63 44.0 2.97e-01 75.5% 69.5%
3739033 12.1.1.14 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › A_amylase_dom_C 0.63 52.0 4.48e-01 92.5% 92.9%
3188921 12.1.1.14 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › A_amylase_dom_C 0.63 52.0 4.48e-01 92.5% 94.1%
4619721 12.1.1.14 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › A_amylase_dom_C 0.63 52.0 4.34e-01 92.5% 87.4%
3204011 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.63 54.0 4.58e-01 98.1% 78.9%
3739851 12.1.1.14 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › A_amylase_dom_C 0.63 51.0 4.43e-01 92.5% 81.2%
4665407 4.1.1.175 ↗ beta barrels › SH3 › SH3 › SH3 › MSSS 0.63 50.0 5.18e-01 100.0% 98.0%
4631118 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.62 50.0 2.80e-01 88.7% 11.3%
4025536 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.62 55.0 4.47e-01 100.0% 85.0%
3620101 391.1.2.1 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related › VWC 0.60 50.0 4.56e-01 90.6% 78.6%
4386251 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.60 49.0 4.11e-01 94.3% 91.6%
4122447 12.1.1.24 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Malt_amylase_C 0.60 49.0 4.13e-01 94.3% 88.4%
4020418 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.59 44.0 4.51e-01 90.6% 86.0%
4034156 1.1.7.5 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Lum_binding 0.59 49.0 4.23e-01 100.0% 96.7%
3229069 633.23.1.5 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › Clc-like 0.58 40.0 2.80e-01 75.5% 68.1%
4505111 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.58 40.0 4.01e-01 73.6% 90.9%
4090116 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.57 47.0 4.41e-01 96.2% 97.1%
3518485 633.23.1.5 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › Clc-like 0.57 40.0 2.79e-01 75.5% 69.2%
4221307 880.1.1.1 ↗ a+b duplicates or obligate multimers › ADC synthase › ADC synthase › ADC synthase › Chorismate_bind 0.57 42.0 2.41e-01 77.4% 18.3%
3241473 12.1.1.50 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Glyco_hydro_31_3rd 0.57 50.0 4.29e-01 100.0% 67.1%
3978012 11.1.4.25 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › PapC_C 0.57 45.0 3.82e-01 90.6% 52.2%
3524786 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.56 39.0 2.79e-01 77.4% 72.3%
3285086 3268.1.1.0 ↗ a+b two layers › N-terminal domain in xanthine dehydrogenase › N-terminal domain in xanthine dehydrogenase › N-terminal domain in xanthine dehydrogenase 0.56 39.0 3.59e-01 75.5% 81.3%
1345445 11.1.4.25 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › PapC_C 0.56 45.0 3.87e-01 90.6% 54.5%
4247667 11.1.1.1053 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › A2M, A2M_BRD, MG4, MG1 0.56 49.0 2.83e-01 100.0% 15.4%
4203469 375.1.1.47 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › BshC 0.55 38.0 3.80e-01 75.5% 96.4%
4120366 375.1.1.47 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › BshC 0.55 38.0 3.77e-01 73.6% 94.5%
4968836 11.1.4.23 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › CarboxypepD_reg 0.55 44.0 3.98e-01 90.6% 68.0%
3166575 12.1.1.50 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Glyco_hydro_31_3rd 0.55 47.0 4.09e-01 98.1% 68.2%
5058895 11.1.4.23 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › CarboxypepD_reg 0.55 43.0 3.99e-01 88.7% 72.9%
3669435 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.55 38.0 3.37e-01 98.1% 47.5%
3799048 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.54 37.0 2.65e-01 75.5% 70.5%
3680238 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.53 36.0 2.60e-01 98.1% 21.7%
5058340 1.1.8.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain 0.53 42.0 3.92e-01 90.6% 74.3%
4887633 11.1.4.24 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › CarbopepD_reg_2 0.53 42.0 3.76e-01 90.6% 62.8%
4344687 220.1.1.19 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Rttp106-like_middle 0.53 36.0 3.08e-01 77.4% 88.6%
4539117 220.1.1.19 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Rttp106-like_middle 0.52 36.0 2.79e-01 77.4% 61.3%
1806777 12.1.1.53 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Alpha-amylase_C_2 0.52 43.0 3.85e-01 100.0% 70.6%
3649749 2.1.1.76 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › REPA_OB_2 0.52 36.0 2.44e-01 96.2% 17.4%
5059960 11.1.4.24 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › CarbopepD_reg_2 0.51 41.0 3.57e-01 90.6% 58.8%
5008249 304.131.1.0 ↗ a+b two layers › Alpha-beta plaits › Phosphonoacetate hydrolase insertion domain › Phosphonoacetate hydrolase insertion domain 0.51 40.0 3.22e-01 100.0% 54.8%
4946049 79.1.1.0 ↗ beta duplicates or obligate multimers › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain 0.50 37.0 3.34e-01 83.0% 62.5%