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NC_023584.1__YP_009007897.1__S-MbCM100_040__00040

Bact-Vir

NC_023584.1__YP_009007897.1__S-MbCM100_040__00040

Identity

Accession:
NC_023584 ↗
Kingdom:
phage

Quality

90.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Kyanoviridae› Acionnavirus› Synechococcus_phage_S-MbCM100

TaxID: 1340812

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 164-368
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2wsuB02 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.54 34.0 3.95e-01 95.1% 87.5%
2huhA01 2.60.40.1600 Mainly Beta › Sandwich › Immunoglobulin-like › Smr-associated-like 0.54 27.0 3.28e-01 89.8% 71.3%
3nziA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.52 23.0 3.04e-01 97.6% 74.5%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2337056 269.1.1.1 ↗ a+b complex topology › Fibrinogen C-terminal domain-like › Fibrinogen C-terminal domain-like › Fibrinogen C-terminal domain-like › Fibrinogen_C 0.62 58.0 5.18e-01 100.0% 85.8%
1563854 269.1.1.0 ↗ a+b complex topology › Fibrinogen C-terminal domain-like › Fibrinogen C-terminal domain-like › Fibrinogen C-terminal domain-like 0.62 57.0 5.15e-01 100.0% 85.8%
397505 10.1.1.4 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Gal-bind_lectin 0.54 34.0 3.95e-01 95.1% 87.5%
3798404 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.53 33.0 3.81e-01 96.6% 86.2%
3187444 1.1.7.81 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › SEN1_barrel 0.51 29.0 3.68e-01 97.6% 96.5%
D2 medium residues 28-78
PDB
Domain cluster: representative
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vhkA01 2.40.240.20 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Hypothetical PUA domain-like; domain 1 0.74 56.0 4.94e-01 80.4% 95.9%
4j3cA01 2.40.240.20 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Hypothetical PUA domain-like; domain 1 0.73 53.0 4.97e-01 78.4% 95.3%
3vseA01 2.30.130.10 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › PUA domain 0.69 52.0 4.77e-01 82.4% 97.1%
2gksB01 3.10.400.10 Alpha Beta › Roll › Sulfate adenylyltransferase › Sulfate adenylyltransferase 0.67 51.0 3.76e-01 84.3% 93.6%
2kksA00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.67 49.0 3.59e-01 80.4% 37.7%
4evqA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.66 51.0 3.55e-01 82.4% 27.2%
6upsA01 3.40.395.10 Alpha Beta › 3-Layer(aba) Sandwich › Adenoviral Proteinase; Chain › Adenoviral Proteinase; Chain A 0.64 49.0 3.60e-01 88.2% 69.0%
3c0kA01 2.30.130.10 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › PUA domain 0.63 46.0 4.25e-01 82.4% 95.8%
2j5vA02 2.30.130.10 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › PUA domain 0.63 46.0 3.90e-01 82.4% 100.0%
2as0A01 2.30.130.10 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › PUA domain 0.62 45.0 4.15e-01 80.4% 95.7%
3ktzA01 3.40.420.10 Alpha Beta › 3-Layer(aba) Sandwich › Ricin (A subunit); domain 1 › Ricin (A subunit), domain 1 0.59 45.0 3.30e-01 92.2% 92.9%
4amcA01 2.30.30.20 Mainly Beta › Roll › SH3 type barrels. › Aspartate carbamoyltransferase regulatory subunit, C-terminal domain 0.59 39.0 4.11e-01 70.6% 82.6%
4kv7A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.58 41.0 3.08e-01 80.4% 28.7%
2qhpA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.58 42.0 2.69e-01 82.4% 20.8%
3ry7A00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.58 41.0 2.66e-01 82.4% 18.8%
1eqtA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.58 40.0 3.70e-01 74.5% 70.1%
4esnA00 2.60.320.10 Mainly Beta › Sandwich › mini-chromosome maintenance (MCM) complex, domain 2 › N-utilization substance G protein NusG, insert domain 0.57 43.0 3.82e-01 84.3% 64.1%
2dcnA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.57 41.0 2.62e-01 82.4% 17.2%
1tyyA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.56 41.0 2.63e-01 82.4% 18.2%
3riqA00 2.160.20.20 Mainly Beta › 3 Solenoid › Pectate Lyase C-like › 0.56 39.0 2.29e-01 78.4% 8.1%
4e84B00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.55 39.0 2.53e-01 82.4% 18.4%
3ljsA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.54 40.0 2.52e-01 82.4% 17.3%
1iftA01 3.40.420.10 Alpha Beta › 3-Layer(aba) Sandwich › Ricin (A subunit); domain 1 › Ricin (A subunit), domain 1 0.54 42.0 3.14e-01 100.0% 90.8%
1nr4C00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.54 38.0 3.56e-01 76.5% 72.7%
3uboB00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.53 39.0 2.45e-01 82.4% 16.2%
7afrX02 2.30.30.180 Mainly Beta › Roll › SH3 type barrels. › Ribosome maturation factor RimP, C-terminal domain 0.53 35.0 3.46e-01 70.6% 80.0%
3vasA01 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.53 38.0 2.49e-01 82.4% 23.8%
3otxB01 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.53 38.0 2.49e-01 82.4% 23.3%
2qe8A00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.52 37.0 2.35e-01 78.4% 36.5%
3vpbE00 2.20.28.160 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.51 34.0 3.38e-01 72.5% 66.1%
3kd6A00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.51 37.0 2.40e-01 86.3% 43.3%
1e4eA03 3.40.50.20 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 36.0 2.93e-01 80.4% 50.0%
3pl2A01 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.50 36.0 2.38e-01 82.4% 30.6%
4gdxB00 3.60.20.40 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Gamma-glutamyltranspeptidase, small (S) subunit 0.50 36.0 2.57e-01 82.4% 54.0%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5081065 3761.1.1.5 ↗ beta duplicates or obligate multimers › Major tropism determinant (Mtd) trimerization domain-related › Major tropism determinant (Mtd) trimerization domain-related › Major tropism determinant (Mtd) trimerization domain-related › PF26696 0.85 65.0 6.88e-01 82.4% 95.6%
3417171 394.1.1.1 ↗ few secondary structure elements › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › CBM_14 0.74 51.0 5.18e-01 72.5% 74.0%
4117456 2007.1.2.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.73 56.0 3.97e-01 82.4% 94.5%
3411165 394.1.1.1 ↗ few secondary structure elements › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › CBM_14 0.72 53.0 5.05e-01 78.4% 66.7%
3405831 394.1.1.1 ↗ few secondary structure elements › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › CBM_14 0.71 49.0 4.81e-01 72.5% 67.3%
3405830 394.1.1.1 ↗ few secondary structure elements › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › CBM_14 0.70 49.0 4.78e-01 72.5% 67.3%
4962756 2007.1.2.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.68 51.0 3.72e-01 82.4% 94.5%
3405832 394.1.1.0 ↗ few secondary structure elements › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins 0.68 47.0 4.60e-01 72.5% 67.3%
3399624 394.1.1.1 ↗ few secondary structure elements › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › CBM_14 0.68 46.0 4.54e-01 70.6% 66.7%
3908573 356.1.1.3 ↗ few secondary structure elements › PMP inhibitors › PMP inhibitors › PMP inhibitors › VWC2L_2nd 0.67 44.0 4.37e-01 72.5% 63.6%
5039505 3761.1.1.0 ↗ beta duplicates or obligate multimers › Major tropism determinant (Mtd) trimerization domain-related › Major tropism determinant (Mtd) trimerization domain-related › Major tropism determinant (Mtd) trimerization domain-related 0.62 46.0 4.52e-01 82.4% 81.8%
3375279 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.61 45.0 2.73e-01 82.4% 15.3%
4981068 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.61 44.0 2.84e-01 82.4% 18.6%
4988593 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.60 44.0 2.80e-01 82.4% 17.7%
4436247 7582.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like domain in CbiD › Rossmann-like domain in CbiD › Rossmann-like domain in CbiD 0.59 42.0 2.91e-01 76.5% 59.2%
1140436 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.56 41.0 2.56e-01 82.4% 18.3%
3592440 2011.1.1.0 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases 0.56 44.0 2.81e-01 94.1% 75.2%
5052437 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.56 40.0 2.57e-01 82.4% 28.5%
3889621 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.55 39.0 3.73e-01 74.5% 76.7%
3974358 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.55 40.0 2.55e-01 82.4% 17.4%
138411 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.54 40.0 2.53e-01 82.4% 17.3%
3977922 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.54 38.0 2.48e-01 82.4% 31.1%
3831660 5.3.1.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-Prism II › beta-Prism II 0.54 41.0 3.00e-01 84.3% 75.2%
4609520 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.53 38.0 2.49e-01 82.4% 15.9%
4969707 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.53 38.0 2.49e-01 82.4% 18.2%
4932153 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.53 38.0 2.51e-01 82.4% 33.0%
3880422 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.52 37.0 3.44e-01 74.5% 69.1%
3971129 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.52 37.0 2.39e-01 82.4% 29.8%
3944874 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.52 36.0 2.38e-01 82.4% 30.6%
4983295 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.52 36.0 2.37e-01 82.4% 28.8%
4024179 210.1.3.4 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases › GATase_6 0.51 40.0 2.82e-01 100.0% 44.3%
319225 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.51 35.0 3.21e-01 76.5% 63.5%
141437 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.50 36.0 2.31e-01 82.4% 26.1%
1282876 3829.1.1.1 ↗ beta meanders › Flavivirus non-structural protein 1 (NS1) beta-meander domain › Flavivirus non-structural protein 1 (NS1) beta-meander domain › Flavivirus non-structural protein 1 (NS1) beta-meander domain › Flavi_NS1 0.50 43.0 2.96e-01 100.0% 70.4%
4875075 3828.1.1.1 ↗ a/b three-layered sandwiches › Flavivirus non-structural protein 1 (NS1) a/b domain › Flavivirus non-structural protein 1 (NS1) a/b domain › Flavivirus non-structural protein 1 (NS1) a/b domain › Flavi_NS1 0.50 42.0 3.01e-01 100.0% 77.2%
4958823 2003.6.1.1 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.50 35.0 2.29e-01 82.4% 29.5%