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NC_007623.1__YP_418072.1__PPEV_gp039__00039

Bact-Vir

NC_007623.1__YP_418072.1__PPEV_gp039__00039

Identity

Accession:
NC_007623 ↗
Kingdom:
phage

Quality

80.5 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

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

D1 high residues 3-132
PDB
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1owaA02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 40.0 4.33e-01 96.2% 85.8%
1vq0A02 3.90.1280.10 Alpha Beta › Alpha-Beta Complex › CBS domain Like › HSP33 redox switch-like 0.56 24.0 3.53e-01 88.5% 91.2%
3ry7A00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.53 39.0 2.99e-01 77.7% 42.2%
5lvxC02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.51 27.0 2.92e-01 90.0% 55.6%
5c40B00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.50 37.0 2.80e-01 76.2% 46.5%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2841988 4959.1.1.0 a+b complex topology › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit 0.81 77.0 7.46e-01 100.0% 96.5%
3842287 3922.1.1.0 alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.69 35.0 3.36e-01 85.4% 41.3%
4172986 4959.1.1.1 a+b complex topology › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_3 0.67 48.0 4.74e-01 100.0% 70.4%
5039049 601.7.1.2 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN 0.62 32.0 3.77e-01 87.7% 70.0%
5064069 2008.2.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like 0.59 25.0 3.03e-01 99.2% 57.5%
3702788 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.58 37.0 3.46e-01 96.2% 53.5%
5072033 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 34.0 2.88e-01 96.2% 35.9%
3797496 601.7.1.0 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.55 35.0 3.78e-01 97.7% 77.1%
4036498 601.7.1.1 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HepT-like 0.54 31.0 3.17e-01 100.0% 56.2%
3602540 601.7.1.2 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN 0.53 37.0 3.66e-01 98.5% 68.9%
5030702 601.7.1.3 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › PaREP1 0.53 35.0 3.61e-01 95.4% 69.6%
4955104 601.7.1.3 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › PaREP1 0.52 35.0 3.62e-01 94.6% 73.7%
D2 high residues 139-230
PDB
D3 high residues 248-362_577-611
PDB
D4 medium residues 377-495
PDB
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7qssA01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.82 70.0 5.93e-01 100.0% 57.4%
1m0sA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.60 33.0 4.13e-01 84.0% 90.3%
2ab5B01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.59 42.0 4.15e-01 74.8% 72.7%
5zwnQ01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.57 35.0 4.04e-01 84.0% 90.0%
1x4hA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.55 36.0 3.69e-01 84.0% 68.5%
7nadw01 3.40.50.12760 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.54 34.0 3.55e-01 90.8% 68.2%
4iufA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.53 32.0 3.69e-01 84.0% 88.3%
7o4xA01 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 33.0 3.54e-01 86.6% 72.7%
5w0hA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.53 31.0 3.65e-01 84.9% 85.0%
3kkiA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.53 39.0 3.57e-01 94.1% 58.4%
2j8aA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.53 34.0 3.84e-01 84.0% 88.5%
3hi9D00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.52 31.0 3.62e-01 84.0% 85.4%
5vnxA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.52 36.0 3.51e-01 93.3% 63.7%
2jdjA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 36.0 3.77e-01 86.6% 80.8%
2jgtA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.51 38.0 3.60e-01 94.1% 64.5%
3wy7D01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.51 35.0 3.49e-01 92.4% 68.3%
2w40A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 37.0 2.99e-01 76.5% 91.1%
5b08A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 36.0 3.85e-01 84.0% 86.0%
2jvzA01 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.51 32.0 3.71e-01 86.6% 92.5%
3ke3A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.51 37.0 3.87e-01 95.0% 82.1%
4v19R01 3.90.1030.10 Alpha Beta › Alpha-Beta Complex › 50s Ribosomal Protein L17; Chain: A, › Ribosomal protein L17 0.50 26.0 2.72e-01 79.0% 48.2%
ECOD (38)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4993129 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.75 67.0 6.64e-01 96.6% 90.4%
5028751 304.28.1.0 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain 0.65 37.0 4.16e-01 84.0% 72.2%
5036327 304.114.1.0 a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.58 31.0 4.00e-01 82.4% 93.8%
3595211 3501.1.1.0 a+b two layers › protein PCC1 › protein PCC1 › protein PCC1 0.57 37.0 4.25e-01 87.4% 91.8%
4512382 304.4.1.4 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › ABM 0.57 37.0 3.80e-01 85.7% 67.8%
3787745 304.9.1.38 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › SET_assoc 0.57 37.0 2.83e-01 84.0% 26.9%
4109532 304.9.1.178 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › SET_assoc, SET1_RBD 0.56 37.0 2.92e-01 84.9% 30.0%
3513861 304.162.1.0 a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain 0.56 33.0 3.87e-01 84.9% 85.0%
3547153 304.162.1.2 a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › FLAD1_M 0.56 33.0 3.90e-01 84.9% 86.3%
3498546 304.162.1.2 a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › FLAD1_M 0.56 33.0 3.95e-01 84.9% 90.7%
4981653 305.1.1.1 a+b two layers › DCoH-like › RBP11-like subunits of RNA polymerase › RBP11-like subunits of RNA polymerase › RNA_pol_L 0.56 39.0 4.38e-01 89.9% 95.6%
3737322 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.55 33.0 3.91e-01 84.9% 93.3%
4930471 304.4.1.79 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › MCR_D 0.55 34.0 3.65e-01 85.7% 72.0%
3858621 3016.1.1.0 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.54 36.0 4.14e-01 89.1% 100.0%
1837772 3016.1.1.0 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.54 39.0 4.13e-01 94.1% 86.4%
3615464 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.54 41.0 4.29e-01 84.9% 88.2%
3056284 304.51.1.0 a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related 0.53 35.0 3.85e-01 85.7% 84.0%
3596489 3016.1.1.1 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_1_2 0.53 37.0 3.68e-01 93.3% 68.0%
3384982 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.53 37.0 3.87e-01 84.0% 81.0%
3307901 304.7.1.20 a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › MBTP1_N 0.53 31.0 3.69e-01 84.0% 94.3%
5045726 304.162.1.0 a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain 0.53 33.0 3.89e-01 84.0% 92.5%
4592125 3016.1.1.1 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_1_2 0.53 38.0 4.05e-01 95.0% 85.7%
3187734 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.53 33.0 3.69e-01 83.2% 82.2%
3536760 304.7.1.20 a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › MBTP1_N 0.52 33.0 3.81e-01 86.6% 93.8%
3823835 304.4.1.78 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › DUF7036 0.52 39.0 4.09e-01 84.9% 89.5%
4014672 3016.1.1.1 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_1_2 0.52 38.0 3.61e-01 78.2% 86.0%
3675586 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.52 33.0 3.42e-01 85.7% 67.0%
3716287 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.51 39.0 4.08e-01 84.9% 88.2%
2397654 304.5.1.5 a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › HisG_C 0.51 30.0 3.25e-01 83.2% 67.0%
3671807 320.1.1.1 a+b two layers › R3H domain-like › R3H domain › R3H domain › R3H 0.51 34.0 3.91e-01 86.6% 100.0%
3715326 325.1.8.0 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Ribosomal L27 protein 0.51 31.0 3.40e-01 83.2% 75.6%
1152673 3016.1.1.0 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.51 38.0 3.97e-01 95.0% 86.8%
4475311 304.162.1.0 a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain 0.51 33.0 3.78e-01 84.9% 91.8%
3714142 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.51 40.0 4.07e-01 84.0% 87.0%
4221300 304.9.1.109 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › PF28459 0.51 35.0 3.39e-01 84.9% 62.2%
3406890 304.120.1.9 a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI › MBTP1_N 0.50 33.0 3.73e-01 86.6% 88.9%
4116735 304.4.1.14 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › Dabb 0.50 35.0 3.79e-01 85.7% 89.5%
3798478 327.19.1.0 a+b two layers › Alpha-lytic protease prodomain-like › DNA mismatch repair protein MutL regulatory subdomain › DNA mismatch repair protein MutL regulatory subdomain 0.50 30.0 3.31e-01 85.7% 74.4%
D5 medium residues 496-576
PDB
D6 medium residues 776-897
PDB
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ydzA00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 36.0 3.54e-01 100.0% 60.0%
4pkcC00 6.20.90.20 Special › Other non-globular › SH3 type barrels. › Benzylsuccinate synthase gamma subunit 0.54 21.0 3.32e-01 86.9% 100.0%
5aj3Q00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 33.0 3.46e-01 97.5% 71.6%
2fggA01 3.30.160.240 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Rv1738 0.50 23.0 2.77e-01 85.2% 62.7%
2a1rB01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.50 39.0 3.05e-01 84.4% 90.8%
7skhB01 2.60.40.60 Mainly Beta › Sandwich › Immunoglobulin-like › Cadherins 0.50 30.0 3.26e-01 97.5% 72.2%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3555586 4.1.1.19 beta barrels › SH3 › SH3 › SH3 › LSM 0.61 34.0 3.81e-01 72.1% 69.5%
1559028 319.1.1.1 beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.55 36.0 3.54e-01 100.0% 60.0%
3628210 319.1.1.1 beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.54 34.0 3.93e-01 100.0% 91.8%
3490957 319.1.1.1 beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.52 31.0 3.77e-01 95.9% 96.0%
5003966 295.1.1.0 a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.51 26.0 3.53e-01 74.6% 95.4%
3058947 221.1.1.8 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PI3K_rbd 0.50 24.0 2.51e-01 73.8% 43.7%