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HM596271.1__ADP69220.1__X__00036

Bact-Vir

HM596271.1__ADP69220.1__X__00036

Identity

Accession:
HM596271 ↗
Kingdom:
phage

Quality

81.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Seongbukvirus› Leuconostoc_phage_phiMH1

TaxID: 912321

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 1-69
PDB
Domain cluster: rep: NC_027368.1__YP_009948776.1__ACQ26_gp23__00023__D1-69
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3zgzD04 2.20.28.290 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.68 47.0 4.96e-01 92.8% 80.6%
1d0nA06 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.61 37.0 3.10e-01 94.2% 33.1%
4akmB00 2.40.160.110 Mainly Beta › Beta Barrel › Porin › 0.59 50.0 3.98e-01 100.0% 87.3%
3gasB02 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.58 39.0 3.07e-01 71.0% 89.3%
2f5tX02 2.30.30.690 Mainly Beta › Roll › SH3 type barrels. › 0.57 47.0 4.42e-01 95.7% 94.4%
2ckkA02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.56 43.0 4.57e-01 94.2% 100.0%
1vw4M01 2.30.30.790 Mainly Beta › Roll › SH3 type barrels. › 0.56 44.0 3.68e-01 89.9% 51.5%
1flmA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.56 45.0 3.84e-01 92.8% 92.6%
1vl7A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 41.0 3.36e-01 81.2% 88.9%
2wzpP01 2.40.30.210 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.55 45.0 3.95e-01 92.8% 66.1%
1aqbA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.55 43.0 3.36e-01 89.9% 68.0%
1t9hA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.55 40.0 3.94e-01 76.8% 95.9%
3q6kA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.55 43.0 2.78e-01 88.4% 93.9%
6eotD01 2.140.10.30 Mainly Beta › 8 Propeller › Methanol Dehydrogenase; Chain A › Dipeptidylpeptidase IV, N-terminal domain 0.55 45.0 2.72e-01 92.8% 35.4%
1xf1A05 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 39.0 3.49e-01 92.8% 53.5%
6mv2A02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.54 43.0 3.79e-01 89.9% 68.6%
2cy5A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 47.0 3.85e-01 98.6% 91.5%
1m0wA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.53 36.0 3.16e-01 92.8% 45.4%
3cz8A02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.53 36.0 3.84e-01 71.0% 98.2%
5c98B02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.52 39.0 3.18e-01 79.7% 69.0%
5jh8A02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.52 35.0 3.63e-01 71.0% 77.6%
6gbuD00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.52 41.0 4.28e-01 89.9% 98.4%
1wfwA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.52 42.0 4.12e-01 89.9% 87.8%
1xreA02 3.55.40.20 Alpha Beta › 3-Layer(bab) Sandwich › minor pseudopilin epsh fold › Iron/manganese superoxide dismutase, C-terminal domain 0.52 33.0 2.89e-01 100.0% 39.3%
2hbpA00 2.30.30.700 Mainly Beta › Roll › SH3 type barrels. › SLA1 homology domain 1 0.52 37.0 3.78e-01 89.9% 80.3%
2eixA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.51 42.0 3.74e-01 94.2% 61.3%
1txdA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 44.0 3.74e-01 100.0% 81.8%
4u3qB00 2.40.128.640 Mainly Beta › Beta Barrel › Lipocalin › 0.51 40.0 3.65e-01 89.9% 88.9%
4wsfA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 40.0 3.53e-01 91.3% 78.4%
1k5dB00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 43.0 3.47e-01 100.0% 74.0%
5inwA02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.51 36.0 3.18e-01 76.8% 77.8%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4034031 4056.1.1.0 ↗ beta barrels › Barrel domain in upper collar protein › Barrel domain in upper collar protein › Barrel domain in upper collar protein 0.77 64.0 6.66e-01 89.9% 93.8%
3026414 4056.1.1.4 ↗ beta barrels › Barrel domain in upper collar protein › Barrel domain in upper collar protein › Barrel domain in upper collar protein › Head-tail_con 0.76 62.0 5.00e-01 88.4% 91.3%
4031151 4056.1.1.0 ↗ beta barrels › Barrel domain in upper collar protein › Barrel domain in upper collar protein › Barrel domain in upper collar protein 0.73 61.0 5.96e-01 89.9% 85.3%
5081122 4056.1.1.0 ↗ beta barrels › Barrel domain in upper collar protein › Barrel domain in upper collar protein › Barrel domain in upper collar protein 0.71 56.0 5.01e-01 87.0% 89.0%
5004293 4056.1.1.0 ↗ beta barrels › Barrel domain in upper collar protein › Barrel domain in upper collar protein › Barrel domain in upper collar protein 0.70 57.0 5.21e-01 87.0% 77.8%
4044129 375.14.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) 0.69 48.0 5.07e-01 92.8% 83.3%
4249207 375.14.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) 0.67 46.0 5.21e-01 92.8% 100.0%
4205352 375.14.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) 0.66 45.0 5.01e-01 92.8% 98.0%
4607738 4.1.1.17 ↗ beta barrels › SH3 › SH3 › SH3 › Ribosomal_L19 0.66 52.0 4.55e-01 89.9% 58.2%
3760441 224.1.1.2 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin 0.66 41.0 3.39e-01 94.2% 35.8%
3861601 3369.1.1.1 ↗ beta meanders › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 › Lamp2-like_luminal 0.62 49.0 3.85e-01 89.9% 74.2%
3715264 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.61 48.0 4.08e-01 88.4% 75.0%
3258303 63.1.1.0 ↗ beta barrels › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain 0.60 46.0 3.72e-01 85.5% 93.2%
2701957 6023.1.1.1 ↗ beta barrels › Restriction endonuclease PabI › Restriction endonuclease PabI › Restriction endonuclease PabI › RE_R_Pab1 0.60 43.0 3.03e-01 75.4% 79.9%
3719860 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.58 46.0 3.96e-01 89.9% 58.3%
4964141 4.15.1.2 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.58 47.0 4.38e-01 92.8% 94.4%
4079710 3369.1.1.1 ↗ beta meanders › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 › Lamp2-like_luminal 0.58 49.0 3.89e-01 100.0% 86.5%
4400596 4.1.1.17 ↗ beta barrels › SH3 › SH3 › SH3 › Ribosomal_L19 0.57 47.0 3.68e-01 94.2% 42.5%
3636379 220.1.1.203 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_23 0.57 50.0 3.91e-01 100.0% 70.3%
5028555 4292.2.1.0 ↗ a+b two layers › FlaG-like › MAGUK binding stalk (MBS) domain › MAGUK binding stalk (MBS) domain 0.57 41.0 4.24e-01 87.0% 81.5%
3630687 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 51.0 3.95e-01 100.0% 74.7%
3266702 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.56 46.0 4.26e-01 100.0% 69.9%
5010832 4.15.1.2 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.56 44.0 4.17e-01 91.3% 93.3%
3504380 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.56 43.0 3.40e-01 89.9% 38.1%
3925367 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.55 48.0 3.81e-01 100.0% 73.3%
5026284 4.15.1.2 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.55 44.0 4.07e-01 92.8% 89.5%
3189285 220.1.1.213 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › DUF7614 0.55 44.0 3.90e-01 89.9% 95.2%
3645842 4.1.1.162 ↗ beta barrels › SH3 › SH3 › SH3 › DUF502 0.54 42.0 4.06e-01 88.4% 76.2%
3260945 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 38.0 4.02e-01 94.2% 88.3%
4970104 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.54 39.0 3.65e-01 79.7% 87.8%
3497957 220.1.1.4 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Ran_BP1 0.53 45.0 3.55e-01 100.0% 65.5%
4030715 220.1.1.4 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Ran_BP1 0.53 45.0 3.76e-01 100.0% 82.3%
3920853 3369.1.1.1 ↗ beta meanders › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 › Lamp2-like_luminal 0.53 43.0 3.47e-01 95.7% 87.0%
3237030 2.1.1.89 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Dis3l2_C_term 0.52 38.0 3.30e-01 79.7% 50.4%
3250597 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.52 44.0 3.89e-01 100.0% 84.5%
4024504 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.52 45.0 4.05e-01 100.0% 76.0%
3616263 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.52 40.0 3.60e-01 85.5% 65.0%
3923150 220.1.1.4 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Ran_BP1 0.52 43.0 3.67e-01 100.0% 88.8%
5012425 4.11.1.0 ↗ beta barrels › SH3 › LexA/Signal peptidase › LexA/Signal peptidase 0.51 43.0 3.55e-01 100.0% 63.6%
3242963 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.51 37.0 3.92e-01 95.7% 91.7%
3845542 220.1.1.38 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › UCH_N 0.51 39.0 3.59e-01 89.9% 90.0%
3953109 4.31.1.1 ↗ beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.51 41.0 3.81e-01 94.2% 68.4%
3418365 4081.1.1.7 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Ribophorin_I 0.51 40.0 2.45e-01 91.3% 14.1%
3389706 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.50 36.0 3.43e-01 81.2% 62.4%
3488211 387.1.1.0 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › omega toxin-related 0.50 40.0 3.71e-01 89.9% 81.1%
D2 medium residues 83-171
PDB
Domain cluster: rep: OP066531.2__UUW40189.1__phageB13_3__00003__D178-274
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF04860.18 best Phage_portal 45.8 6.80e-12 100.0% 26.5%
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4mt1A07 3.30.70.1440 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.63 46.0 4.42e-01 77.5% 97.1%
3zqmA00 6.10.140.2160 Special › Helix non-globular › Helix Hairpins › 0.57 34.0 4.02e-01 83.1% 89.8%
7ewsB02 3.30.590.10 Alpha Beta › 2-Layer Sandwich › Creatine Kinase; Chain A, domain 2 › Glutamine synthetase/guanido kinase, catalytic domain 0.54 39.0 2.93e-01 78.7% 87.8%
6oyfA01 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.51 39.0 3.19e-01 80.9% 85.0%
5awwY00 1.10.3370.10 Mainly Alpha › Orthogonal Bundle › Preprotein translocase SecY subunit › SecY subunit domain 0.50 44.0 2.87e-01 100.0% 45.8%
1vx4q01 3.30.70.1730 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein L10, N-terminal RNA-binding domain 0.50 36.0 3.21e-01 76.4% 84.2%
3bn7A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.50 36.0 3.48e-01 76.4% 100.0%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4032886 4038.1.1.1 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Phage_portal 0.81 74.0 5.18e-01 100.0% 36.2%
4031453 4038.1.1.1 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Phage_portal 0.75 63.0 4.57e-01 100.0% 32.5%
3943006 4038.1.1.1 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Phage_portal 0.73 65.0 4.55e-01 100.0% 32.1%
3980782 4038.1.1.7 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Phage_portal_2 0.71 62.0 4.15e-01 100.0% 25.4%
4410228 4038.1.1.1 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Phage_portal 0.70 62.0 4.42e-01 100.0% 33.5%
3590909 4038.1.1.1 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Phage_portal 0.68 59.0 4.19e-01 95.5% 34.4%
3589399 4038.1.1.1 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Phage_portal 0.68 59.0 4.23e-01 100.0% 35.4%
4360285 323.1.1.0 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.68 36.0 3.01e-01 86.5% 30.7%
5039294 4038.1.1.1 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Phage_portal 0.66 57.0 4.05e-01 100.0% 30.7%
4954546 4038.1.1.0 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein 0.61 55.0 3.83e-01 100.0% 52.8%
3878040 3937.1.1.2 ↗ alpha bundles › Connexin 26 › Connexin 26 › Connexin 26 › Innexin 0.54 50.0 3.31e-01 100.0% 28.2%
4100834 3223.1.1.1 ↗ beta sandwiches › Amiloride-sensitive cation channel 2 › Amiloride-sensitive cation channel 2 › Amiloride-sensitive cation channel 2 › ASC 0.52 45.0 3.15e-01 95.5% 90.7%
3771989 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.52 47.0 4.09e-01 100.0% 73.3%
4062717 2006.1.6.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › VWA 0.52 35.0 2.45e-01 70.8% 58.4%
3494392 3937.1.1.2 ↗ alpha bundles › Connexin 26 › Connexin 26 › Connexin 26 › Innexin 0.51 44.0 2.98e-01 100.0% 61.9%
3238753 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.50 46.0 3.64e-01 100.0% 55.4%
D3 medium residues 205-282
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4asvA00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.56 35.0 3.52e-01 88.5% 62.0%
1yozA00 1.10.3200.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af0941 › AF0941-like 0.54 42.0 3.75e-01 83.3% 85.0%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3587162 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.73 42.0 3.32e-01 89.7% 29.4%
3503611 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.59 43.0 4.06e-01 76.9% 78.9%
4955174 2006.1.4.2 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › PIN 0.56 43.0 3.47e-01 80.8% 51.4%
3509762 311.1.1.2 ↗ a+b three layers › Phoshotransferase/anion transport protein › Phoshotransferase/anion transport protein › Phoshotransferase/anion transport protein › Band_3_cyto 0.54 42.0 3.50e-01 83.3% 82.2%