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HM596271.1__ADP69208.1__X__00024

Bact-Vir

HM596271.1__ADP69208.1__X__00024

Identity

Accession:
HM596271 ↗
Kingdom:
phage

Quality

83.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Seongbukvirus› Leuconostoc_phage_phiMH1

TaxID: 912321

Cluster

View cluster (12 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 8-54
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4gxbA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.71 56.0 4.49e-01 100.0% 43.3%
1es6A02 2.60.510.10 Mainly Beta › Sandwich › EV matrix protein fold › EV matrix protein 0.71 61.0 4.86e-01 100.0% 98.0%
2qz8A02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.70 58.0 5.02e-01 100.0% 88.9%
4ewtA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 58.0 4.39e-01 97.9% 100.0%
2irmA00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.65 50.0 3.06e-01 87.2% 42.5%
7nitA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.65 55.0 4.20e-01 100.0% 58.3%
4llgM00 3.10.20.510 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNA polymerase inhibitor 0.64 50.0 5.00e-01 100.0% 92.0%
3p96A02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.64 51.0 4.43e-01 100.0% 92.9%
3znuA00 3.30.70.1060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel 0.64 54.0 4.39e-01 100.0% 89.4%
3w7bA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.63 51.0 4.35e-01 100.0% 95.5%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.62 51.0 3.63e-01 100.0% 29.3%
5y4mA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.62 53.0 3.79e-01 100.0% 35.3%
3egrA00 3.10.20.520 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phenylacetic acid degradation B 0.62 49.0 4.67e-01 100.0% 79.4%
3bn6A00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.61 51.0 3.64e-01 100.0% 34.8%
3o1lB01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.61 49.0 4.22e-01 100.0% 92.0%
2wadA02 3.90.1310.10 Alpha Beta › Alpha-Beta Complex › Penicillin-binding protein 2a (Domain 2) › Penicillin-binding protein 2a (Domain 2) 0.61 45.0 3.39e-01 100.0% 28.4%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.61 48.0 4.49e-01 100.0% 69.7%
5t89Y06 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 51.0 4.21e-01 100.0% 58.7%
6ztgA01 3.30.70.1070 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Sporulation related repeat 0.60 49.0 4.36e-01 100.0% 100.0%
1bquA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 51.0 3.98e-01 100.0% 50.9%
1yuzA02 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.60 39.0 4.17e-01 100.0% 84.2%
1yk9A00 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.59 48.0 3.37e-01 100.0% 56.0%
1sq2N00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 50.0 3.88e-01 100.0% 48.2%
6lnhB01 2.60.120.620 Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain 0.59 44.0 2.91e-01 100.0% 17.6%
1y6kR01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 47.0 3.87e-01 100.0% 46.1%
3pvlA02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.59 49.0 4.01e-01 100.0% 50.0%
3n0vA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.59 48.0 4.12e-01 100.0% 96.4%
2yuxA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 44.0 3.59e-01 100.0% 39.8%
2z5bB01 3.30.230.90 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.58 43.0 3.36e-01 85.1% 46.2%
3nngA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.58 47.0 3.47e-01 100.0% 56.2%
3weeA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.58 47.0 3.30e-01 97.9% 49.7%
3nrbB01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.58 47.0 4.08e-01 100.0% 95.2%
1d0nA06 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.58 43.0 3.24e-01 83.0% 71.7%
4ezeB00 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.57 44.0 2.89e-01 100.0% 26.0%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.57 46.0 3.89e-01 100.0% 57.6%
3lqmA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 41.0 3.40e-01 100.0% 39.2%
4msvA01 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.55 46.0 3.43e-01 100.0% 40.1%
5ce8A01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.55 41.0 3.10e-01 83.0% 44.7%
2qcsB02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.54 44.0 3.30e-01 100.0% 35.2%
4pofA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.54 42.0 4.17e-01 100.0% 88.0%
6dgiA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.53 42.0 3.04e-01 89.4% 75.0%
4ccjA01 2.60.120.650 Mainly Beta › Sandwich › Jelly Rolls › Cupin 0.53 41.0 2.72e-01 97.9% 18.3%
5eliA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 40.0 3.30e-01 100.0% 62.5%
4ccdA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.51 36.0 2.39e-01 83.0% 30.3%
4d8mA03 2.100.10.40 Mainly Beta › Aligned Prism › Vitelline Membrane Outer Layer Protein I, subunit A › 0.51 44.0 2.93e-01 100.0% 25.1%
4me3A03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.51 40.0 3.92e-01 100.0% 89.1%
1ltlA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.51 40.0 3.96e-01 100.0% 87.8%
2vtfA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.51 40.0 2.88e-01 100.0% 28.2%
ECOD (63)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3760983 3335.1.1.3 ↗ beta barrels › Handle domain in transferrin-binding protein B › Handle domain in transferrin-binding protein B › Handle domain in transferrin-binding protein B › KCTD18_C 0.75 67.0 5.20e-01 100.0% 99.0%
4985395 304.4.1.75 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › GYD 0.73 61.0 5.37e-01 100.0% 98.7%
4147528 4.1.1.307 ↗ beta barrels › SH3 › SH3 › SH3 › PF26132 0.73 62.0 5.49e-01 97.9% 100.0%
3646564 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.73 49.0 2.75e-01 70.2% 50.7%
3285401 3986.2.1.0 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.72 64.0 5.48e-01 100.0% 66.7%
4448678 4.1.1.307 ↗ beta barrels › SH3 › SH3 › SH3 › PF26132 0.72 62.0 5.36e-01 100.0% 97.3%
4338821 221.1.1.69 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › SNX17-27-31_F1_FERM 0.70 55.0 4.33e-01 100.0% 40.0%
3681440 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.70 47.0 2.65e-01 70.2% 53.2%
3194942 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.69 56.0 4.07e-01 100.0% 33.1%
4964337 3115.5.1.1 ↗ a+b two layers › GP2-like › phenylacetate-CoA oxygenase subunit PaaB › phenylacetate-CoA oxygenase subunit PaaB › PaaB 0.68 55.0 5.32e-01 100.0% 87.3%
4961379 4176.1.1.2 ↗ a/b three-layered sandwiches › a/b domain in CV3147-like proteins › a/b domain in CV3147-like proteins › a/b domain in CV3147-like proteins › S-Me-THD_N 0.66 54.0 3.54e-01 100.0% 20.5%
4456383 304.48.1.0 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.66 47.0 2.94e-01 80.9% 48.2%
4962335 3115.5.1.1 ↗ a+b two layers › GP2-like › phenylacetate-CoA oxygenase subunit PaaB › phenylacetate-CoA oxygenase subunit PaaB › PaaB 0.65 53.0 4.92e-01 100.0% 80.0%
5014007 3115.2.1.0 ↗ a+b two layers › GP2-like › GP2 › GP2 0.65 53.0 5.12e-01 100.0% 85.5%
4987385 304.4.1.2 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › MIase 0.64 52.0 4.42e-01 100.0% 94.4%
5025566 304.7.1.0 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.63 55.0 5.23e-01 100.0% 100.0%
4977919 329.1.1.2 ↗ a+b two layers › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › DUF4443 0.62 47.0 3.68e-01 83.0% 91.4%
3620456 221.1.1.64 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Formin_GBD_N 0.62 52.0 4.05e-01 100.0% 41.8%
4356447 329.1.1.1 ↗ a+b two layers › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › GAD 0.62 47.0 3.52e-01 85.1% 80.0%
3958896 4187.2.1.0 ↗ a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 0.62 48.0 4.57e-01 100.0% 73.3%
3278358 284.3.1.2 ↗ a+b two layers › FKBP-like › Colicin E3 immunity protein › Colicin E3 immunity protein › DUF7683 0.61 51.0 4.49e-01 100.0% 98.7%
3647077 2487.1.1.7 ↗ a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" › PA 0.61 51.0 3.34e-01 100.0% 99.1%
3535929 386.1.1.248 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2_ZNF592 0.60 48.0 3.34e-01 100.0% 24.0%
3326623 221.1.1.166 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PF26130 0.60 47.0 4.24e-01 100.0% 61.4%
3897763 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.60 52.0 4.01e-01 100.0% 56.4%
3684103 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.60 45.0 2.52e-01 85.1% 8.5%
5070107 304.56.1.0 ↗ a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like 0.60 48.0 4.40e-01 100.0% 100.0%
3701633 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.59 44.0 3.80e-01 100.0% 48.2%
5080205 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.59 47.0 4.66e-01 100.0% 92.0%
3583600 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.59 49.0 4.23e-01 100.0% 66.3%
3721040 4176.1.1.2 ↗ a/b three-layered sandwiches › a/b domain in CV3147-like proteins › a/b domain in CV3147-like proteins › a/b domain in CV3147-like proteins › S-Me-THD_N 0.59 50.0 3.24e-01 100.0% 19.2%
3320990 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.59 47.0 2.59e-01 89.4% 42.5%
3446121 109.4.1.3478 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, DYW_deaminase, Eplus_motif, E_motif, TPR_24 0.59 50.0 2.81e-01 100.0% 13.8%
3579556 10.32.1.2 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › F5_F8_type_C 0.59 49.0 3.41e-01 100.0% 28.6%
3922242 11.1.1.179 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.58 50.0 3.92e-01 100.0% 45.7%
3899215 11.1.1.850 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF28354 0.58 49.0 3.84e-01 100.0% 43.6%
3910912 11.1.1.3 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ig 0.58 50.0 3.87e-01 100.0% 43.6%
3830169 109.4.1.1383 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, Eplus_motif, E_motif 0.58 46.0 2.53e-01 87.2% 5.8%
4943853 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.58 43.0 3.19e-01 85.1% 35.2%
3429551 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.58 47.0 2.75e-01 89.4% 72.3%
5046689 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.58 42.0 3.28e-01 85.1% 82.3%
4289852 4007.1.1.1 ↗ a+b two layers › a+b domain in YebC-like proteins › a+b domain in YebC-like proteins › a+b domain in YebC-like proteins › Transcrip_reg 0.58 44.0 3.87e-01 97.9% 52.9%
4954188 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.58 45.0 3.40e-01 100.0% 45.0%
4004704 3115.6.1.2 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › PF28597 0.57 43.0 4.39e-01 100.0% 93.3%
3969006 3115.6.1.2 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › PF28597 0.56 44.0 4.51e-01 100.0% 97.8%
4463006 3115.2.1.0 ↗ a+b two layers › GP2-like › GP2 › GP2 0.56 42.0 4.27e-01 97.9% 93.3%
3968122 3115.6.1.2 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › PF28597 0.56 42.0 4.31e-01 100.0% 95.6%
3958011 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.56 46.0 3.12e-01 100.0% 26.2%
5039010 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.55 44.0 3.38e-01 100.0% 35.4%
3899253 3957.1.1.0 ↗ a+b two layers › EKC/KEOPS complex subunit GON7 › EKC/KEOPS complex subunit GON7 › EKC/KEOPS complex subunit GON7 0.55 39.0 3.96e-01 78.7% 91.1%
3244287 223.2.1.34 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › NPR2 0.55 39.0 2.87e-01 85.1% 69.4%
3646939 10.32.1.212 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › GUB_WAK_bind 0.54 44.0 3.06e-01 100.0% 30.3%
4013514 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.54 41.0 3.47e-01 100.0% 49.5%
3434515 109.4.1.2925 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, PPR_long, E_motif 0.54 46.0 2.56e-01 97.9% 40.9%
3892842 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.54 43.0 4.04e-01 100.0% 83.1%
3216210 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.53 41.0 4.07e-01 100.0% 98.0%
4015853 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.53 44.0 3.06e-01 100.0% 59.5%
None — 0.52 44.0 4.05e-01 100.0% 100.0%
3816579 109.4.1.1599 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase 0.52 45.0 2.61e-01 100.0% 65.8%
143003 205.1.1.19 ↗ a+b two layers › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › Fer4_13 0.52 43.0 3.96e-01 100.0% 100.0%
3787619 206.1.3.21 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › RimK 0.52 44.0 3.38e-01 100.0% 59.1%
3915794 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.52 39.0 3.30e-01 100.0% 42.7%
3422239 2487.1.1.7 ↗ a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" › PA 0.51 41.0 2.71e-01 93.6% 70.4%