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NC_022765.1__YP_008770572.1__Riggi_15__00015

Bact-Vir

NC_022765.1__YP_008770572.1__Riggi_15__00015

Identity

Accession:
NC_022765 ↗
Kingdom:
phage

Quality

69.6 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 79-187
PDB
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ey4D00 2.40.10.230 Mainly Beta › Beta Barrel › Thrombin, subunit H › Probable tRNA pseudouridine synthase domain 0.75 42.0 4.93e-01 98.2% 78.7%
1o6eA00 3.20.16.10 Alpha Beta › Alpha-Beta Barrel › Serine Protease, Human Cytomegalovirus Protease; Chain A › Herpesvirus/Caudovirus protease domain 0.75 70.0 5.43e-01 100.0% 60.0%
1at3A00 3.20.16.10 Alpha Beta › Alpha-Beta Barrel › Serine Protease, Human Cytomegalovirus Protease; Chain A › Herpesvirus/Caudovirus protease domain 0.75 71.0 5.49e-01 100.0% 53.5%
3ttgA00 3.30.1360.120 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Probable tRNA modification gtpase trme; domain 1 0.71 44.0 3.05e-01 100.0% 19.9%
3u28C00 2.40.10.230 Mainly Beta › Beta Barrel › Thrombin, subunit H › Probable tRNA pseudouridine synthase domain 0.69 43.0 4.68e-01 95.4% 75.0%
1cmvB00 3.20.16.10 Alpha Beta › Alpha-Beta Barrel › Serine Protease, Human Cytomegalovirus Protease; Chain A › Herpesvirus/Caudovirus protease domain 0.68 64.0 5.03e-01 100.0% 55.8%
2v3mA00 2.40.10.230 Mainly Beta › Beta Barrel › Thrombin, subunit H › Probable tRNA pseudouridine synthase domain 0.66 40.0 4.30e-01 98.2% 69.1%
1yelA00 2.40.330.10 Mainly Beta › Beta Barrel › At1g16640 B3 domain › DNA-binding pseudobarrel domain 0.64 44.0 4.58e-01 100.0% 75.5%
6f2mA02 2.40.30.290 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.64 39.0 4.28e-01 98.2% 75.9%
2eqnA01 2.40.10.230 Mainly Beta › Beta Barrel › Thrombin, subunit H › Probable tRNA pseudouridine synthase domain 0.63 39.0 4.26e-01 97.2% 75.9%
1nrkA03 2.40.30.160 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.62 40.0 3.86e-01 100.0% 56.6%
2zzeA03 2.40.30.130 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.62 37.0 3.88e-01 98.2% 65.3%
2gmlA02 3.30.70.1560 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Alpha-L RNA-binding motif 0.60 36.0 4.20e-01 92.7% 87.8%
2f1lA01 2.40.30.60 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › RimM 0.59 39.0 4.28e-01 94.5% 83.1%
2ynaA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.59 38.0 4.13e-01 73.4% 79.5%
2dyiA02 2.30.30.240 Mainly Beta › Roll › SH3 type barrels. › PRC-barrel domain 0.59 37.0 4.46e-01 86.2% 98.6%
2cxiA01 3.30.56.10 Alpha Beta › 2-Layer Sandwich › Phenylalanyl-tRNA Synthetase; Chain B, domain 1 › 0.58 36.0 4.16e-01 100.0% 86.1%
1xqbA01 2.40.30.70 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › YaeB-like 0.58 42.0 4.24e-01 97.2% 76.1%
1ywuA00 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.57 38.0 3.68e-01 76.1% 59.2%
1nrkA01 3.30.70.1630 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 32.0 3.44e-01 77.1% 63.9%
3mahA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.56 32.0 3.80e-01 79.8% 87.0%
4p02A03 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.56 37.0 3.64e-01 73.4% 61.5%
2sfaA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.55 33.0 3.58e-01 71.6% 70.3%
3cnrB00 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.55 35.0 3.70e-01 75.2% 73.1%
2r6vA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 37.0 3.29e-01 70.6% 89.6%
1rzmA01 3.30.70.1140 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Phospho-2-dehydro-3-deoxyheptonate aldolase; domain 1 0.54 31.0 3.45e-01 78.9% 72.5%
1vbkA01 3.30.70.1510 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › THUMP domain-like 0.54 37.0 4.10e-01 100.0% 91.6%
1uscA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 37.0 3.18e-01 70.6% 81.5%
3f56A01 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.54 30.0 3.11e-01 78.9% 55.7%
1dn0D02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 37.0 3.94e-01 100.0% 83.0%
2rdeA02 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.54 38.0 3.79e-01 75.2% 72.1%
2jheA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.53 31.0 3.53e-01 79.8% 76.5%
3nfwA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 36.0 3.11e-01 72.5% 74.3%
1yx2A02 3.30.70.1400 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Aminomethyltransferase beta-barrel domains 0.51 35.0 3.81e-01 78.9% 89.5%
ECOD (51)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5083161 50.1.1.3 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Peptidase_S78 0.85 80.0 7.15e-01 100.0% 84.8%
5004197 1.1.16.0 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain 0.85 66.0 6.95e-01 81.7% 98.0%
3166306 50.1.1.4 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › DUF2213 0.84 79.0 6.96e-01 100.0% 88.2%
5003309 50.1.1.0 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin 0.84 79.0 7.37e-01 100.0% 90.8%
3945977 50.1.1.4 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › DUF2213 0.83 78.0 6.69e-01 100.0% 87.9%
4995675 50.1.1.0 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin 0.83 77.0 6.61e-01 100.0% 80.6%
4960055 1.1.16.0 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain 0.82 76.0 6.97e-01 99.1% 89.1%
3585229 50.1.1.2 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Peptidase_S77 0.81 75.0 6.87e-01 100.0% 90.7%
3954964 50.1.1.3 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Peptidase_S78 0.80 74.0 6.70e-01 100.0% 85.5%
3964948 1.1.16.4 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › Peptidase_S78 0.80 74.0 7.05e-01 100.0% 87.2%
1933303 50.1.1.2 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Peptidase_S77 0.79 73.0 6.31e-01 100.0% 78.9%
5083920 50.1.1.0 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin 0.79 74.0 6.75e-01 100.0% 95.0%
3959024 1.1.16.0 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain 0.78 50.0 5.17e-01 100.0% 67.6%
3290618 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.78 50.0 4.58e-01 100.0% 50.7%
3957158 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.78 50.0 5.13e-01 100.0% 67.6%
3347366 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.76 49.0 4.88e-01 100.0% 62.6%
3602442 1.1.16.0 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain 0.76 69.0 6.94e-01 100.0% 96.4%
788 50.1.1.1 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Peptidase_S21 0.75 71.0 5.49e-01 100.0% 53.5%
5059785 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.75 44.0 5.01e-01 97.2% 78.8%
27577 50.1.1.1 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Peptidase_S21 0.75 69.0 5.31e-01 100.0% 58.4%
4969578 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.74 42.0 4.94e-01 98.2% 81.1%
1304358 50.1.1.1 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Peptidase_S21 0.74 70.0 5.38e-01 100.0% 55.9%
3602200 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.73 40.0 4.81e-01 97.2% 82.9%
4964309 1.1.7.20 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Gar1 0.72 41.0 4.87e-01 98.2% 82.4%
5041607 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.72 41.0 4.80e-01 98.2% 81.1%
1150480 50.1.1.1 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Peptidase_S21 0.71 55.0 5.71e-01 80.7% 96.1%
5051893 1.1.7.20 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Gar1 0.71 42.0 4.86e-01 97.2% 81.2%
5041953 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.71 39.0 5.13e-01 98.2% 100.0%
5017568 1.1.7.20 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Gar1 0.70 43.0 4.88e-01 97.2% 82.5%
5038467 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.70 42.0 4.83e-01 98.2% 82.3%
4945432 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.70 41.0 4.55e-01 97.2% 74.1%
3483841 1.1.7.20 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Gar1 0.64 43.0 4.45e-01 95.4% 72.8%
5024522 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.64 50.0 4.37e-01 97.2% 55.8%
3982061 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.64 51.0 4.83e-01 100.0% 72.8%
3943528 1.1.16.0 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain 0.63 50.0 4.88e-01 100.0% 75.8%
5036479 1.1.7.9 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › tRNA-synt_2c 0.63 38.0 3.87e-01 96.3% 60.0%
4634180 1.1.7.11 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.62 40.0 4.37e-01 97.2% 80.0%
4913412 1.1.16.0 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain 0.61 48.0 4.59e-01 100.0% 72.0%
3838338 1.1.5.0 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.61 42.0 4.71e-01 75.2% 91.8%
5000784 1.1.7.20 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Gar1 0.61 43.0 4.48e-01 97.2% 80.0%
3172185 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.59 38.0 3.82e-01 97.2% 63.6%
2771876 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.57 47.0 4.69e-01 89.0% 89.4%
4508428 1.1.7.11 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RimM 0.56 41.0 4.40e-01 94.5% 88.4%
3442148 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.56 32.0 3.69e-01 81.7% 80.0%
3661948 1.1.11.1 beta barrels › cradle loop barrel › RIFT-related › Type II restriction endonuclease effector domain › B3 0.54 35.0 4.00e-01 81.7% 93.3%
77 1.1.5.25 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZ 0.54 38.0 3.81e-01 75.2% 72.7%
4026390 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.53 46.0 4.25e-01 96.3% 74.8%
3853734 244.1.1.0 a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.52 42.0 4.34e-01 91.7% 94.0%
3777373 304.47.1.1 a+b two layers › Alpha-beta plaits › SEA domain › SEA domain › SEA 0.52 46.0 4.52e-01 100.0% 91.7%
3369437 1.1.9.5 beta barrels › cradle loop barrel › RIFT-related › PUA domain › LON_substr_bdg 0.52 37.0 2.92e-01 75.2% 64.8%
5078052 331.6.1.0 a+b two layers › TBP-like › MoaD-related protein, C-terminal domain › MoaD-related protein, C-terminal domain 0.50 32.0 3.73e-01 78.0% 93.2%
D2 high residues 220-287
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4k08A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.80 56.0 4.31e-01 75.0% 34.7%
6mh4A03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.69 47.0 4.47e-01 70.6% 81.0%
5jazA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.68 47.0 4.28e-01 72.1% 79.1%
3iieB03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.67 47.0 4.39e-01 73.5% 78.8%
2wwwA03 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.60 52.0 5.32e-01 100.0% 100.0%
1wa8A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.59 47.0 4.17e-01 85.3% 60.6%
2p67A03 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.51 42.0 4.34e-01 100.0% 98.5%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3971072 5058.1.1.0 alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.82 64.0 5.72e-01 83.8% 61.1%
3693339 3922.1.1.228 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 › LisH 0.82 65.0 4.60e-01 82.4% 47.8%
4405271 4207.1.1.0 alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › RNA polymerase II holoenzyme component SRB7 (MED21) 0.80 63.0 4.71e-01 82.4% 54.8%
3720672 109.4.1.1591 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › U-box 0.80 63.0 4.08e-01 83.8% 21.1%
4554624 5073.1.2.0 alpha bundles › Calcium ATPase transmembrane domain-related › Calcium ATPase transmembrane domain-related › Copper efflux ATPase transmembrane domain 0.75 49.0 3.19e-01 70.6% 16.1%
3993361 622.4.1.41 alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › DUF7753 0.73 50.0 5.15e-01 72.1% 80.0%
4080592 166.1.1.1 alpha superhelices › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › DXPR_C 0.66 47.0 4.34e-01 76.5% 75.6%
4478129 166.1.1.1 alpha superhelices › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › DXPR_C 0.65 46.0 4.20e-01 73.5% 76.7%
4002218 633.6.1.6 alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › ACAD9-ACADV_C 0.61 52.0 4.07e-01 92.6% 50.7%
3805810 109.4.1.1425 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Exo84_C, PF27696 0.60 50.0 2.93e-01 91.2% 36.8%
4943605 2006.1.1.18 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › HAD_2 0.59 51.0 3.51e-01 100.0% 36.9%
3663440 109.4.1.359 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Exo70_C 0.55 49.0 2.87e-01 97.1% 34.0%