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NC_041911.1__YP_009598903.1__FDH28_gp211__00210

Bact-Vir

NC_041911.1__YP_009598903.1__FDH28_gp211__00210

Identity

Accession:
NC_041911 ↗
Kingdom:
phage

Quality

44.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Chimalliviridae› Ripduovirus› Ralstonia_phage_RP12

TaxID: 1923889

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

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

D1 high residues 11-85
PDB
D2 medium residues 213-282
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1xeaA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.64 46.0 3.39e-01 77.1% 68.8%
4m0hA01 2.60.120.1440 Mainly Beta › Sandwich › Jelly Rolls › 0.63 50.0 4.09e-01 90.0% 76.3%
2jrbA00 3.30.250.20 Alpha Beta › 2-Layer Sandwich › Rec A Protein; domain 2 › L1 transposable element, C-terminal domain 0.62 46.0 4.76e-01 90.0% 86.2%
3uuwB02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.58 41.0 3.12e-01 75.7% 71.2%
1rwzA00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.57 41.0 2.90e-01 78.6% 38.1%
4aghA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.57 38.0 3.69e-01 70.0% 92.5%
3p8aA02 2.60.40.4320 Mainly Beta › Sandwich › Immunoglobulin-like › 0.57 40.0 3.69e-01 100.0% 57.8%
4ml0B00 3.30.2310.20 Alpha Beta › 2-Layer Sandwich › YaeB-like fold › RelE-like 0.56 35.0 3.25e-01 97.1% 48.9%
3uv0B00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.56 45.0 4.12e-01 92.9% 94.9%
2x8fA02 2.40.128.10 Mainly Beta › Beta Barrel › Lipocalin › 0.54 39.0 3.63e-01 80.0% 73.7%
6iikB00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.54 42.0 2.73e-01 84.3% 30.5%
3ottA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.54 45.0 3.06e-01 98.6% 96.0%
1nr0A01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 42.0 2.94e-01 94.3% 78.9%
4iimA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.53 31.0 3.34e-01 98.6% 68.4%
5kmpB00 3.50.50.100 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › 0.53 38.0 2.36e-01 75.7% 25.1%
2x4jA01 2.30.30.600 Mainly Beta › Roll › SH3 type barrels. › 0.53 40.0 3.59e-01 82.9% 86.3%
7apkF01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.52 41.0 2.72e-01 90.0% 64.9%
7pluA01 1.20.58.530 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.52 41.0 3.55e-01 100.0% 54.9%
3kd9A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.52 37.0 2.81e-01 75.7% 46.1%
3zqsA02 3.10.110.20 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › RWD domain-like 0.51 40.0 3.69e-01 91.4% 90.8%
1qtoA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.51 41.0 3.49e-01 91.4% 89.3%
2qpvA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.50 41.0 3.41e-01 92.9% 81.8%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3387014 3454.1.1.0 ↗ beta barrels › GspC HR domain/PilP-like › GspC HR domain/PilP-like › GspC HR domain/PilP-like 0.64 45.0 4.96e-01 78.6% 94.5%
3276253 388.1.1.0 ↗ few secondary structure elements › Huristasin-like › Huristasin-like › Huristasin-like 0.61 34.0 4.06e-01 70.0% 84.4%
4000199 3794.1.1.3 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit › ACCA_BT 0.61 44.0 4.28e-01 77.1% 95.0%
3926177 4357.1.1.0 ↗ beta barrels › WWE domain › WWE domain › WWE domain 0.60 45.0 4.70e-01 80.0% 95.2%
4302938 292.2.1.0 ↗ a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain 0.60 40.0 3.80e-01 70.0% 60.0%
3978720 3454.1.1.0 ↗ beta barrels › GspC HR domain/PilP-like › GspC HR domain/PilP-like › GspC HR domain/PilP-like 0.59 42.0 4.60e-01 75.7% 100.0%
3518934 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.58 44.0 2.86e-01 80.0% 25.0%
3614740 3794.1.1.0 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit 0.58 47.0 3.91e-01 91.4% 81.5%
4003998 3794.1.1.0 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit 0.58 47.0 3.92e-01 91.4% 83.1%
3443166 4099.1.1.11 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Med14 0.56 43.0 3.69e-01 87.1% 76.8%
None — 0.56 43.0 2.77e-01 81.4% 58.2%
5041549 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.56 43.0 2.90e-01 84.3% 37.5%
4127133 3794.1.1.3 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit › ACCA_BT 0.56 48.0 3.92e-01 100.0% 92.9%
3262013 3794.1.1.3 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit › ACCA_BT 0.56 49.0 4.03e-01 100.0% 71.5%
3169399 4099.1.1.11 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Med14 0.55 44.0 3.79e-01 88.6% 71.3%
4167925 5.1.4.309 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40, PF29630 0.55 46.0 3.08e-01 100.0% 95.5%
3240647 3794.1.1.3 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit › ACCA_BT 0.55 48.0 4.02e-01 100.0% 72.8%
3850091 4099.1.1.17 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Med14_RM2 0.55 43.0 3.15e-01 88.6% 44.2%
3267764 4099.1.1.11 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Med14 0.55 43.0 3.56e-01 88.6% 74.8%
4956695 4.15.1.0 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like 0.55 40.0 3.91e-01 80.0% 91.3%
None — 0.54 42.0 3.12e-01 88.6% 44.2%
3942150 252.2.1.5 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › Arm-DNA-bind_3 0.54 41.0 3.89e-01 87.1% 98.9%
3222051 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 41.0 4.25e-01 85.7% 90.8%
3499649 220.4.1.0 ↗ beta barrels › PH domain-like › second barrel domain in viral glycoproteins › second barrel domain in viral glycoproteins 0.53 39.0 3.59e-01 77.1% 75.6%
3523046 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.53 31.0 2.96e-01 100.0% 47.1%
3933788 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.53 38.0 4.09e-01 77.1% 91.7%
4079109 2007.1.1.6 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like › Peptidase_S51 0.52 44.0 3.19e-01 100.0% 88.0%
5009884 2003.1.5.24 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Met_10 0.52 43.0 2.95e-01 92.9% 55.2%
3628862 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.52 39.0 2.82e-01 82.9% 39.6%
3519861 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 37.0 4.00e-01 77.1% 95.0%
3737178 4099.1.1.11 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Med14 0.52 38.0 3.42e-01 81.4% 84.8%
3199325 241.1.1.11 ↗ a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone › Med14 0.52 42.0 3.13e-01 90.0% 52.2%
3402686 5.1.4.19 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Coatomer_WDAD 0.51 38.0 2.58e-01 82.9% 35.9%
4989861 247.1.1.12 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B_3 0.51 44.0 3.27e-01 100.0% 75.3%
4269668 7000.1.1.0 ↗ alpha arrays › inserted region in the C-terminal domain of the archeal LeuRS › inserted region in the C-terminal domain of the archeal LeuRS › inserted region in the C-terminal domain of the archeal LeuRS 0.50 35.0 3.93e-01 81.4% 92.7%
3606526 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.50 42.0 2.70e-01 98.6% 83.4%
D3 medium residues 293-335
PDB