Back to structures

SRR1747018_scaffold_396_prodigal-single.1__X__X__00046

Bact-Vir

SRR1747018_scaffold_396_prodigal-single.1__X__X__00046

Identity

Kingdom:
phage

Quality

89.8 mean pLDDT

3D Structure

Domains

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

D1 medium residues 1-40_103-166
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF05135.20 best Phage_connect_1 23.6 7.90e-05 78.8% 83.2%
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3jvoA00 1.10.3230.30 Mainly Alpha › Orthogonal Bundle › Hypothetical protein yqbg › Phage gp6-like head-tail connector protein 0.72 61.0 6.31e-01 97.1% 96.9%
3mvpA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.60 46.0 4.06e-01 80.8% 59.1%
2oerA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.60 42.0 3.55e-01 80.8% 43.0%
2bs2A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.58 40.0 2.84e-01 70.2% 84.8%
4a17H02 3.30.60.300 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.56 23.0 3.53e-01 79.8% 100.0%
4etsA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.53 32.0 3.43e-01 80.8% 71.3%
4ol9A02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.52 36.0 3.43e-01 72.1% 91.3%
1u8vB03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.50 35.0 2.88e-01 74.0% 58.2%
2xcqA02 3.90.199.10 Alpha Beta › Alpha-Beta Complex › Topoisomerase II; domain 5 › Topoisomerase II, domain 5 0.50 43.0 3.30e-01 100.0% 81.2%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3963507 4275.1.1.1 alpha arrays › Hypothetical protein YqbG-like › Hypothetical protein YqbG-like › Hypothetical protein YqbG-like › Phage_connect_1 0.79 73.0 7.14e-01 99.0% 98.2%
3250499 103.1.1.22 alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › ARI1_UBAl 0.64 33.0 4.20e-01 80.8% 86.7%
3274360 524.1.1.1 alpha arrays › Ypt/Rab-GAP domain of gyp1p-like › Ypt/Rab-GAP domain of gyp1p › Ypt/Rab-GAP domain of gyp1p › RabGAP-TBC 0.60 53.0 3.71e-01 98.1% 31.8%
3976621 162.1.1.1 alpha bundles › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PRD 0.59 50.0 4.98e-01 90.4% 97.3%
4879388 162.1.1.0 alpha bundles › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD 0.58 40.0 4.33e-01 77.9% 83.9%
3587501 162.1.1.1 alpha bundles › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PTS-regulatory domain, PRD › PRD 0.58 48.0 4.71e-01 92.3% 100.0%
3585138 4275.1.1.9 alpha arrays › Hypothetical protein YqbG-like › Hypothetical protein YqbG-like › Hypothetical protein YqbG-like › PF26809 0.57 49.0 4.18e-01 96.2% 85.1%
4979800 2003.1.2.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.52 39.0 2.86e-01 79.8% 63.7%
4873589 3694.1.1.2 alpha bundles › Tail specific protease helical domain › Tail specific protease helical domain › Tail specific protease helical domain › Tricorn_C1 0.51 31.0 3.29e-01 76.0% 67.4%
3715999 3817.1.1.1 alpha bundles › Peroxisomal biogenesis factor 19 › Peroxisomal biogenesis factor 19 › Peroxisomal biogenesis factor 19 › Pex19 0.51 33.0 3.43e-01 76.9% 68.0%
D2 medium residues 41-102
PDB
Domain cluster: representative
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1v0fB03 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.71 60.0 5.49e-01 98.4% 100.0%
4kktA02 2.40.30.170 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Efflux pump adaptor protein, beta barrel domain 0.70 62.0 5.22e-01 100.0% 94.3%
4wqmA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.68 59.0 5.12e-01 100.0% 94.9%
1qfjA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.67 56.0 4.96e-01 93.5% 96.7%
1qcsA01 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.67 57.0 5.22e-01 93.5% 100.0%
3wdhA04 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.65 51.0 4.63e-01 96.8% 64.3%
4dguA01 2.60.40.2680 Mainly Beta › Sandwich › Immunoglobulin-like › 0.64 49.0 4.04e-01 82.3% 80.4%
6melB02 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.63 50.0 4.67e-01 93.5% 98.8%
7nkdA01 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.61 51.0 4.77e-01 98.4% 76.6%
2omkA00 3.40.50.10240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Thiamin pyrophosphokinase, catalytic domain 0.60 50.0 3.46e-01 95.2% 34.7%
3wcyA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 48.0 4.37e-01 95.2% 84.9%
3h8uA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.58 47.0 3.86e-01 100.0% 46.7%
5x7qA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.57 49.0 3.97e-01 100.0% 66.1%
3skvA01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.57 49.0 3.74e-01 100.0% 50.6%
6tqdC01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 47.0 4.15e-01 96.8% 86.5%
2f4pA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.56 48.0 3.80e-01 96.8% 64.2%
4yokA01 2.60.40.1120 Mainly Beta › Sandwich › Immunoglobulin-like › Carboxypeptidase-like, regulatory domain 0.56 42.0 3.74e-01 82.3% 70.2%
6m9sD01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.56 46.0 4.08e-01 100.0% 84.2%
2q1mA00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.56 44.0 3.74e-01 93.5% 100.0%
4devD01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.56 47.0 3.87e-01 100.0% 57.6%
5hp5A01 2.60.40.1860 Mainly Beta › Sandwich › Immunoglobulin-like › Protein-arginine deiminase, N-terminal domain 0.55 44.0 3.61e-01 91.9% 71.4%
3clwC01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.55 46.0 4.00e-01 95.2% 66.0%
4xvhA01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.55 46.0 3.99e-01 100.0% 63.6%
1owwA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 44.0 3.99e-01 95.2% 84.9%
3r8qA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 45.0 4.11e-01 98.4% 85.4%
4jd0A00 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.54 40.0 2.76e-01 82.3% 61.2%
2yrbA01 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.54 41.0 3.28e-01 83.9% 58.5%
5f29B00 3.30.70.1450 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Regulator of K+ conductance, C-terminal domain 0.54 43.0 4.19e-01 98.4% 78.9%
2w9xB01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.54 45.0 3.96e-01 100.0% 97.0%
3ghmA03 2.60.120.830 Mainly Beta › Sandwich › Jelly Rolls › 0.54 46.0 3.60e-01 100.0% 64.1%
2kd7A00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.53 44.0 3.42e-01 98.4% 49.7%
2edzA01 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.53 45.0 3.80e-01 100.0% 78.4%
4nn5C01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 41.0 3.80e-01 87.1% 73.8%
4g65A04 3.30.70.1450 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Regulator of K+ conductance, C-terminal domain 0.53 43.0 3.92e-01 96.8% 78.0%
4nehA03 2.60.40.1460 Mainly Beta › Sandwich › Immunoglobulin-like › Integrin domains. Chain A, domain 2 0.52 42.0 3.25e-01 93.5% 76.8%
3bvxA05 2.60.40.1360 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 44.0 3.86e-01 98.4% 84.4%
6udkD00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 43.0 3.48e-01 98.4% 79.2%
3q2wA04 2.60.40.60 Mainly Beta › Sandwich › Immunoglobulin-like › Cadherins 0.51 40.0 3.51e-01 93.5% 81.0%
8d40A02 2.60.40.60 Mainly Beta › Sandwich › Immunoglobulin-like › Cadherins 0.51 40.0 3.57e-01 93.5% 82.8%
1aozA02 2.60.40.420 Mainly Beta › Sandwich › Immunoglobulin-like › Cupredoxins - blue copper proteins 0.50 41.0 2.98e-01 96.8% 66.5%
2wyhA07 2.60.40.2220 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 42.0 4.00e-01 98.4% 81.8%
ECOD (41)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5056460 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.71 63.0 5.91e-01 98.4% 94.7%
4223333 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.70 60.0 5.12e-01 98.4% 97.1%
4940909 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.69 56.0 5.12e-01 90.3% 100.0%
3617423 1.1.2.19 beta barrels › cradle loop barrel › RIFT-related › double psi › IML1_N 0.69 57.0 4.99e-01 91.9% 98.9%
5035362 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.68 55.0 4.96e-01 91.9% 95.6%
4946423 1.1.7.138 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › NAD_binding_1 0.68 58.0 5.05e-01 98.4% 95.0%
4932996 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.68 54.0 4.83e-01 88.7% 98.9%
5069408 1.1.7.7 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.67 55.0 4.90e-01 91.9% 98.9%
4944696 1.1.7.138 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › NAD_binding_1 0.67 58.0 5.00e-01 98.4% 99.0%
4946101 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.67 59.0 4.96e-01 100.0% 95.2%
4061526 1.1.7.7 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.66 58.0 4.95e-01 98.4% 100.0%
4930890 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.66 52.0 4.94e-01 87.1% 100.0%
4510320 1.1.7.7 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.66 53.0 4.75e-01 90.3% 96.7%
3602028 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.66 56.0 4.18e-01 98.4% 94.5%
3935683 206.1.3.57 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › FAM91_C 0.65 57.0 3.78e-01 98.4% 45.1%
4366786 1.1.7.7 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.64 54.0 4.57e-01 98.4% 90.0%
3704230 10.32.1.0 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.62 54.0 4.50e-01 100.0% 60.9%
5078441 10.12.1.0 beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.60 50.0 4.59e-01 100.0% 71.2%
3804991 1.1.7.94 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › PF28794 0.60 49.0 4.56e-01 96.8% 98.8%
2512620 10.12.1.39 beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_2 0.60 52.0 4.43e-01 100.0% 80.6%
3879285 10.4.1.23 beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain › CDCP1_CUB_6 0.58 50.0 4.09e-01 98.4% 81.7%
3473671 1.1.8.5 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › tRNA_Me_trans_C 0.58 42.0 3.60e-01 80.6% 68.2%
5042982 7516.1.1.24 a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › NTP_transf_3 0.56 42.0 2.91e-01 82.3% 63.8%
3263574 12.1.1.0 beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.56 47.0 4.20e-01 95.2% 73.3%
3848806 10.32.1.0 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.55 47.0 3.85e-01 100.0% 92.7%
4279440 11.1.1.148 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › FixG_C 0.55 47.0 3.87e-01 100.0% 56.7%
3795516 11.1.1.97 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › I-set 0.55 45.0 3.34e-01 98.4% 42.6%
3891879 11.1.1.117 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › EpoR_lig-bind 0.54 43.0 3.75e-01 91.9% 74.3%
3936887 10.4.1.0 beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain 0.54 46.0 3.82e-01 100.0% 84.7%
1243721 10.21.1.1 beta sandwiches › jelly-roll › Jelly-roll domain in ADAMTS13 › Jelly-roll domain in ADAMTS13 › ADAMTS_spacer1 0.54 46.0 3.62e-01 100.0% 65.0%
3398159 10.4.1.0 beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain 0.53 46.0 3.65e-01 100.0% 60.0%
3874549 10.21.1.1 beta sandwiches › jelly-roll › Jelly-roll domain in ADAMTS13 › Jelly-roll domain in ADAMTS13 › ADAMTS_spacer1 0.53 46.0 3.72e-01 100.0% 72.8%
3937659 11.2.1.50 beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2_GDE1 0.53 46.0 3.40e-01 100.0% 47.1%
3485793 10.4.1.0 beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain 0.53 45.0 3.47e-01 100.0% 76.7%
4975274 4261.1.1.1 a+b two layers › TrkA C-terminal domain-like › TrkA C-terminal domain-like › TrkA C-terminal domain-like › TrkA_C 0.53 44.0 4.29e-01 98.4% 95.7%
3997295 12.1.1.0 beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.53 43.0 3.71e-01 96.8% 86.4%
3424497 11.2.1.1 beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2 0.52 38.0 3.45e-01 82.3% 81.1%
3223711 10.32.1.0 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.52 42.0 3.19e-01 96.8% 81.8%
1566734 11.2.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.51 39.0 3.69e-01 83.9% 85.5%
3507371 10.4.1.1 beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain › CUB 0.51 41.0 3.50e-01 98.4% 87.5%
3740995 11.1.1.884 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Metallopep 0.50 41.0 3.75e-01 96.8% 85.6%