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GDP-D-mannose_dehydratase
Euk-VirOnly_Syngen_Nebraska_virus_5
GDP-D-mannose_dehydratase__YP_009325563__Only_Syngen_Nebraska_virus_5__1917232
Identity
- Accession:
- YP_009325563 ↗
- Protein ID:
- GDP-D-mannose_dehydratase
- Kingdom:
- euk
Quality
94.3
mean pLDDT
Taxonomy
Bamfordvirae›
Nucleocytoviricota›
Megaviricetes›
Algavirales›
Phycodnaviridae›
Chlorovirus›
Only_Syngen_Nebraska_virus_5
TaxID: 1917232
Cluster
View cluster (115 members)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 6-180_220-244
Domain cluster:
rep: NC_043427__YP_009666084.1__FK997-gp39__00039__D5-203_243-266_355-370
Pfam (6)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF01370.28 best | Epimerase | 186.8 | 6.40e-55 | 88.5% | 72.5% |
| PF04321.24 | RmlD_sub_bind | 38.7 | 8.90e-10 | 88.0% | 44.6% |
| PF16363.12 | GDP_Man_Dehyd | 256.5 | 6.40e-76 | 86.5% | 55.1% |
| PF13460.13 | NAD_binding_10 | 32.0 | 1.60e-07 | 78.0% | 57.6% |
| PF05368.20 | NmrA | 44.5 | 2.20e-11 | 58.0% | 22.1% |
| PF16363.12 | GDP_Man_Dehyd | 27.5 | 3.00e-06 | 12.5% | 7.5% |
D2
high
residues 190-218_249-308_329-344
Domain cluster:
representative
CATH (14)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 6gpkA02 | 3.90.25.10 | Alpha Beta › Alpha-Beta Complex › UDP-galactose 4-epimerase; domain 1 › UDP-galactose 4-epimerase, domain 1 | 0.96 | 88.0 | 8.67e-01 | 100.0% | 89.9% |
| 1db3A02 | 3.90.25.10 | Alpha Beta › Alpha-Beta Complex › UDP-galactose 4-epimerase; domain 1 › UDP-galactose 4-epimerase, domain 1 | 0.93 | 90.0 | 8.69e-01 | 100.0% | 92.2% |
| 1n7hB01 | 3.90.25.10 | Alpha Beta › Alpha-Beta Complex › UDP-galactose 4-epimerase; domain 1 › UDP-galactose 4-epimerase, domain 1 | 0.92 | 71.0 | 7.32e-01 | 100.0% | 83.2% |
| 2shpB03 | 3.90.190.10 | Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily | 0.60 | 46.0 | 3.45e-01 | 83.8% | 34.2% |
| 6aonA02 | 3.50.50.60 | Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain | 0.59 | 33.0 | 3.19e-01 | 79.0% | 46.3% |
| 4fh3A02 | 3.30.460.10 | Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 | 0.56 | 42.0 | 3.98e-01 | 78.1% | 70.4% |
| 4nhxA01 | 2.60.120.620 | Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain | 0.56 | 39.0 | 3.08e-01 | 71.4% | 85.6% |
| 4xqkB01 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.56 | 43.0 | 3.39e-01 | 81.9% | 99.1% |
| 4pavB00 | 3.10.180.10 | Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 | 0.55 | 40.0 | 3.69e-01 | 74.3% | 79.4% |
| 1cl8A00 | 3.40.580.10 | Alpha Beta › 3-Layer(aba) Sandwich › ECO RI Endonuclease; Chain A › Eco RI Endonuclease, subunit A | 0.52 | 39.0 | 2.95e-01 | 79.0% | 50.6% |
| 4evsA02 | 3.40.50.2300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator | 0.52 | 44.0 | 3.71e-01 | 90.5% | 99.4% |
| 4exrA02 | 3.10.450.40 | Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › | 0.51 | 27.0 | 3.18e-01 | 77.1% | 71.8% |
| 3dxvA01 | 3.90.1150.10 | Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 | 0.51 | 39.0 | 3.48e-01 | 81.9% | 79.6% |
| 4p78C00 | 3.30.920.30 | Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Hypothetical protein. | 0.51 | 32.0 | 3.82e-01 | 96.2% | 100.0% |
ECOD (26)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| None | — | 0.98 | 96.0 | 6.19e-01 | 100.0% | 42.1% | |
| 3977765 | 2003.1.1.141 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Polysacc_synt_2, GDP_Man_Dehyd | 0.98 | 95.0 | 6.18e-01 | 100.0% | 42.1% |
| 3838118 | 2003.1.1.72 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › GDP_Man_Dehyd | 0.97 | 94.0 | 6.11e-01 | 100.0% | 43.7% |
| None | — | 0.91 | 89.0 | 5.80e-01 | 100.0% | 40.3% | |
| 3706593 | 2003.1.1.72 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › GDP_Man_Dehyd | 0.91 | 88.0 | 6.74e-01 | 100.0% | 72.7% |
| None | — | 0.74 | 72.0 | 4.86e-01 | 100.0% | 40.6% | |
| 5021241 | 243.6.1.0 ↗ | a+b two layers › Cystatin-like › Pre-PUA domain › Pre-PUA domain | 0.61 | 28.0 | 3.38e-01 | 79.0% | 62.9% |
| 5072222 | 243.6.1.0 ↗ | a+b two layers › Cystatin-like › Pre-PUA domain › Pre-PUA domain | 0.58 | 29.0 | 3.34e-01 | 80.0% | 64.0% |
| 3688914 | 283.1.1.4 ↗ | a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › Creatinase/aminopeptidase › Creatinase/aminopeptidase › ThrE | 0.57 | 47.0 | 4.27e-01 | 89.5% | 70.0% |
| 5026193 | 873.1.1.0 ↗ | a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain | 0.55 | 38.0 | 3.52e-01 | 70.5% | 80.7% |
| 3604572 | 243.6.1.1 ↗ | a+b two layers › Cystatin-like › Pre-PUA domain › Pre-PUA domain › DUF1947 | 0.55 | 28.0 | 3.35e-01 | 79.0% | 72.9% |
| 3285963 | 873.1.1.7 ↗ | a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › Arabinose_bd | 0.54 | 39.0 | 3.17e-01 | 73.3% | 70.8% |
| 3985024 | 207.6.1.1 ↗ | beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Serralysin-like metalloprotease-C › Serralysin-like metalloprotease-C › HemolysinCabind | 0.54 | 46.0 | 3.72e-01 | 91.4% | 74.4% |
| 3973641 | 873.1.1.0 ↗ | a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain | 0.54 | 37.0 | 3.08e-01 | 71.4% | 70.8% |
| 3415450 | 7.1.1.1 ↗ | beta barrels › PDZ domain › PDZ domain › PDZ domain › PDZ | 0.54 | 33.0 | 3.67e-01 | 88.6% | 76.5% |
| 3968730 | 873.1.1.7 ↗ | a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › Arabinose_bd | 0.54 | 38.0 | 3.12e-01 | 73.3% | 71.3% |
| 4971611 | 2004.1.1.19 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras | 0.53 | 42.0 | 3.54e-01 | 84.8% | 86.5% |
| 3282198 | 873.1.1.7 ↗ | a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › Arabinose_bd | 0.53 | 37.0 | 3.07e-01 | 73.3% | 71.0% |
| 5014813 | 2004.1.1.95 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF257 | 0.52 | 40.0 | 3.20e-01 | 83.8% | 85.3% |
| 150565 | 316.1.1.36 ↗ | a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › MTPAP-like_central | 0.51 | 38.0 | 3.51e-01 | 79.0% | 59.2% |
| 4963224 | 2002.1.1.172 ↗ | a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › PHP_C | 0.51 | 35.0 | 2.85e-01 | 70.5% | 83.8% |
| 5058786 | 5104.1.1.1 ↗ | a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 | 0.51 | 36.0 | 3.44e-01 | 71.4% | 88.3% |
| 3408186 | 2003.1.7.5 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NagB/RpiA/CoA transferase-like › 5-FTHF_cyc-lig | 0.51 | 39.0 | 3.23e-01 | 81.9% | 74.9% |
| 3729561 | 2003.4.1.1 ↗ | a/b three-layered sandwiches › Rossmann-like › Tryptophan synthase beta subunit-like PLP-dependent enzymes › Tryptophan synthase beta subunit-like PLP-dependent enzymes › PALP | 0.51 | 40.0 | 3.29e-01 | 82.9% | 88.4% |
| 3284448 | 873.1.1.7 ↗ | a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › Arabinose_bd | 0.51 | 39.0 | 3.25e-01 | 82.9% | 99.5% |
| 3263816 | 2004.1.1.120 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ResIII | 0.50 | 39.0 | 2.97e-01 | 83.8% | 47.9% |