Family Search for PF07286 (D-Glu_cyclase)

April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.

Running HMMer for PF07286

PF07286 hits 20 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

A1S_1268 hypothetical protein from Acinetobacter baumannii ATCC 17978
Aligns to 86:228 / 236 (60.6%), covers 100.0% of PF07286, 235.3 bits

• Insights Into Mechanisms of Biofilm Formation in Acinetobacter baumannii and Implications for Uropathogenesis
  Colquhoun, Frontiers in cellular and infection microbiology 2020
  • “...NRAMP 1.09 ATCC 17978 Rumbo-Feal et al., 2013 5.49 ATCC 17978 Kentache et al., 2017 A1S_1268 hypothetical protein 2.9 AB5075_UW Penesyan et al., 2019 5.34 ATCC 17978 Kentache et al., 2017 A1S_1319 hypothetical protein 22.56 ATCC 17978 Rumbo-Feal et al., 2013 2.7 ATCC 17978 Kentache et...”
• The Manganese-Responsive Transcriptional Regulator MumR Protects Acinetobacter baumannii from Oxidative Stress
  Green, Infection and immunity 2020 (secret)
• Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing
  Camarena, PLoS pathogens 2010
  • “...0.33 Putative transporter protein (Mn2+/Fe2+), COG, 1914 A1S_1267 0.33 Putative lactam utilization protein, LamB/YscF superfamily A1S_1268 0.31 Hypothetical protein, DUF1445 A1S_1269 0.4 Putative allophanate hydrolase subunit 1 and 2, COG2049/1984 A1S_1270 0.27 Putative carboxylase, COG4770 A1S_1320 0.3 MerR family of transcriptional regulators; highly similar to SoxR...”

P42966 Putative hydro-lyase YcsI from Bacillus subtilis (strain 168)
Aligns to 106:248 / 257 (55.6%), covers 100.0% of PF07286, 234.1 bits

• Discovery of a widespread prokaryotic 5-oxoprolinase that was hiding in plain sight
  Niehaus, The Journal of biological chemistry 2017
  • “...ycsG (Uniprot ID: P42964), and ycsI (Uniprot ID: P42966) coding sequences were PCR-amplified, digested with SpeI and BamHI, and ligated into pHCMC04. To create...”
• Genetic snapshots of the Rhizobium species NGR234 genome
  Viprey, Genome biology 2000
  • “...08g04 overlaps clone 11b08 876 22f08 P33362 930 11f08 P96683 877 25f09 P76397 931 09c03 P42966 878 28e04 P76397 932 17f04 O34398 879 25f10 P77470 933 24b07 P35155 880 26e05 AAC74522 934 18c06 O05220 881 27a05 AAC75727 935 24d11 Q07835 882 27e02 P39829 936 13a01 O07618...”

Atu3911 hypothetical protein from Agrobacterium tumefaciens str. C58 (Cereon)
Aligns to 119:261 / 269 (53.2%), covers 100.0% of PF07286, 228.3 bits

• Identification of a Highly Conserved Hypothetical Protein TON_0340 as a Probable Manganese-Dependent Phosphatase
  Sohn, PloS one 2016
  • “...The other domain in these proteins belongs to the DUF1445 superfamily and is homologous to Atu3911 from Agrobacterium tumefaciens , a hypothetical protein whose structure is available (PDB ID: 3DB9). Homologues of Atu3911 are found in bacteria, fungi, zebrafish, frog, chicken, rat and human, but not...”

blr2921 blr2921 from Bradyrhizobium japonicum USDA 110
Aligns to 120:262 / 271 (52.8%), covers 100.0% of PF07286, 227.4 bits

• Identification of Genes Regulated by the Antitermination Factor NasT during Denitrification in Bradyrhizobium diazoefficiens
  Sánchez, Microbes and environments 2019
  • “...bll3385 ABC transporter ATP-binding protein; putative LIV transport +5.42 bll3386 AraC family transcriptional regulator +2.30 blr2921 Conserved hypothetical protein +31.63 blr2922 ABC transporter amino acid-binding protein; putative LIV transport +18.76 blr2923 Amino acid ABC transporter permease protein; putative LIV transport +25.39 blr2924 Amino acid ABC transporter...”

AZC_4080 hypothetical protein from Azorhizobium caulinodans ORS 571
Aligns to 121:263 / 272 (52.6%), covers 100.0% of PF07286, 221.6 bits

• Comparative genome-wide transcriptional profiling of Azorhizobium caulinodans ORS571 grown under free-living and symbiotic conditions
  Tsukada, Applied and environmental microbiology 2009
  • “...transporter genes for branched-chain amino acids (AZC_4072 to AZC_4080 and AZC_4583 to AZC_4589), were expressed to a lesser degree in bacteroids than in...”
  • “...containing branched-chain amino acid transporter genes (AZC_4072 to AZC_4080 and AZC_4583 to AZC_4589) were expressed to a lesser extent in minimal medium (Fig....”

SCA_2211 putative hydro-lyase from Staphylococcus carnosus subsp. carnosus TM300
Sca_2211 hypothetical protein from Staphylococcus carnosus subsp. carnosus TM300
Aligns to 112:254 / 262 (54.6%), covers 100.0% of PF07286, 220.6 bits

• Transcriptomic analysis of staphylococcal sRNAs: insights into species-specific adaption and the evolution of pathogenesis
  Broach, Microbial genomics 2016
  • “...2199217..2199338 SCA_2172 < SCA_2173 1628.55 SCAs057 jacL-57 2224729..2224907 SCA_2191 < SCA_2192 848.25 SCAs058 jacL-58 2266552..2266687 SCA_2211 > SCAs059 4277.68 SCAs059 jacL-59 2266688..2266868 SCAs058 < SCAs060 2180.71 SCAs060 jacL-60 2267000..2267107 SCAs059 > SCAs061 1239.77 SCAs061 jacL-61 2267108..2267271 SCAs060 < tatA 1847.62 SCAs062 jacL-62 2294415..2294594 SCA_2236 < SCA_2237...”
• Transcriptomic analysis of staphylococcal sRNAs: insights into species-specific adaption and the evolution of pathogenesis
  Broach, Microbial genomics 2016
  • “...2199217..2199338 SCA_2172 < SCA_2173 1628.55 SCAs057 jacL-57 2224729..2224907 SCA_2191 < SCA_2192 848.25 SCAs058 jacL-58 2266552..2266687 SCA_2211 > SCAs059 4277.68 SCAs059 jacL-59 2266688..2266868 SCAs058 < SCAs060 2180.71 SCAs060 jacL-60 2267000..2267107 SCAs059 > SCAs061 1239.77 SCAs061 jacL-61 2267108..2267271 SCAs060 < tatA 1847.62 SCAs062 jacL-62 2294415..2294594 SCA_2236 < SCA_2237...”

I35_RS18920 putative hydro-lyase from Burkholderia cenocepacia H111
Aligns to 106:248 / 257 (55.6%), covers 100.0% of PF07286, 214.5 bits

• Transcriptional Response of Burkholderia cenocepacia H111 to Severe Zinc Starvation
  Barnett, British journal of biomedical science 2023
  • “...0.039419489 I35_RS06170 TonB-dependent receptor 2.762808558 1.03E16 I35_RS29380 Glyoxalase 2.680789605 3.92E26 I35_RS23575 TonB-dependent receptor 2.48708683 0.000346391 I35_RS18920 Hypothetical protein 2.423450935 0.039764095 I35_RS10860 Imidazolonepropionase 2.326828435 0.022280782 I35_RS06165 Phenol degradation protein 2.320499563 2.27E28 I35_RS22340 Hypothetical protein 2.300982216 0.00000167 I35_RS20825 Alpha/beta hydrolase 2.246852811 0.035832439 I35_RS13380 ABC transporter permease 2.238628283 5.97E30...”

BCAM0576 hypothetical protein from Burkholderia cenocepacia J2315
Aligns to 106:248 / 257 (55.6%), covers 100.0% of PF07286, 214.5 bits

• NtrC-dependent control of exopolysaccharide synthesis and motility in Burkholderia cenocepacia H111
  Liu, PloS one 2017
  • “...5.9 I35_4195 BCAM0196 Hypothetical protein 4.7 I35_4401 BCAM0507 Uncharacterized protein conserved in bacteria -3.5 I35_4471 BCAM0576 Hypothetical protein -3.4 I35_4651 BCAM0752 Hydrolase-related protein -3.6 I35_4652 BCAM0753 Hypothetical protein -3.9 I35_4669 BCAM0770 Hypothetical protein -7.4 I35_4766 BCAM0853 Transposase and inactivated derivatives -4.1 I35_4943 BCAM1098 MutT/nudix family protein...”
• σ54-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111
  Lardi, Applied and environmental microbiology 2015
  • “...ND BCAL1247 BCAL2308 BCAL3509 BCAM0087 BCAM0148 BCAM0576 BCAM0716 BCAM0718 BCAM0720 BCAM0770 BCAM0852 Hypothetical protein Hypothetical protein Hypothetical...”

Dshi_3152 protein of unknown function DUF1445 from Dinoroseobacter shibae DFL 12
Aligns to 128:270 / 300 (47.7%), covers 100.0% of PF07286, 212.1 bits

• Transposon mutagenesis identified chromosomal and plasmid genes essential for adaptation of the marine bacterium Dinoroseobacter shibae to anaerobic conditions
  Ebert, Journal of bacteriology 2013
  • “...dmsA1 nirJ Dshi_2304 Dshi_0664 Dshi_3165 Dshi_0543 Dshi_3152 Dshi_1449 Dshi_3163 Dshi_2233 Dshi_3558 Dshi_1968 Dshi_3066 Dshi_2363 Dshi_0432 Dshi_3590 Dshi_0563...”

SAR11_0660 hypothetical protein from Candidatus Pelagibacter ubique HTCC1062
Aligns to 109:252 / 261 (55.2%), covers 99.3% of PF07286, 210.2 bits

• Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data
  Wilhelm, Biology direct 2007
  • “...(0.0838) 0.415 0.124 SAR11_0655 AA transport 6 0.8693 (0.437 0.0370 (0.0163) 0.0425 (0.0274) 0.497 0.042 SAR11_0660 AA transport 8 0.9990 (0.443 0.0776 (0.0394) 0.0777 (0.0365) 0.513 0.076 SAR11_0677 Unknown 5 1.5142 (0.742 0.1599 (0.0940) 0.1056 (0.0477) 0.531 0.531 SAR11_0764 Conserved hypothetical 5 1.5142 (0.742 0.1599 (0.0940)...”

ACG06_RS15915 putative hydro-lyase from Pseudomonas aeruginosa
Aligns to 117:259 / 265 (54.0%), covers 100.0% of PF07286, 204.6 bits

• Whole-transcriptome analysis reveals mechanisms underlying antibacterial activity and biofilm inhibition by a malic acid combination (MAC) in Pseudomonas aeruginosa
  Song, PeerJ 2023
  • “...genes, encompassing aldol/keto reductases ( ACG06_RS17845 , fold change (FC) = 9.25), putative hydro-lyases ( ACG06_RS15915 , FC = 7.96), ribose-phosphate pyrophosphokinase ( ACG06_RS12730 , FC = 7.35), betaine-aldehyde dehydrogenase ( ACG06_RS30685 , FC = 7.28), FMN-dependent NADH-azoreductase AzoR2 ( ACG06_RS16675 , FC = 7.27), uroporphyrinogen-III...”

PA2116 hypothetical protein from Pseudomonas aeruginosa PAO1
Aligns to 117:259 / 265 (54.0%), covers 100.0% of PF07286, 204.3 bits

• A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria
  Kaleta, NPJ biofilms and microbiomes 2022
  • “...PAO1 WT-like WT-like WT-like PA0452::IS WT-like WT-like WT-like PA0452 9.0974175 5.26 PA2116::IS WT-like WT-like WT-like PA2116 4.4021755 n.d. PA2134::IS WT-like WT-like WT-like PA2134 3.3907125 n.d. PA2377::IS WT-like WT-like WT-like PA2377 18.138506 n.d. PA2508::IS WT-like WT-like WT-like PA2508 6.0312799 n.d. PA2531::IS WT-like WT-like WT-like PA2531 10.285887 n.d....”
• The novel two-component regulatory system BfiSR regulates biofilm development by controlling the small RNA rsmZ through CafA
  Petrova, Journal of bacteriology 2010
  • “...h 144 h 144 h clpP PA2023 galU PA2116 PA2385 PA2386 PA2396 PA2413 pvdQ pvdA pvdF pvdH ATP-dependent Clp protease proteolytic subunit UTP-glucose-1-phosphate...”
• The Pseudomonas aeruginosa proteome during anaerobic growth
  Wu, Journal of bacteriology 2005
  • “...PA2008 PA2009 PA2012* PA2014* PA2044 PA2069 PA2081 PA2112* PA2116 PA2194 PA2195 PA2247 PA2248 PA2250 PA2366* PA2552* PA2553* PA2555* PA2850 PA2939 PA2981 PA3049...”
• Screening for quorum-sensing inhibitors (QSI) by use of a novel genetic system, the QSI selector
  Rasmussen, Journal of bacteriology 2005
  • “...University of California, Berkeley PA2111 PA2112 PA2113 PA2114 PA2116 PA2134 PA2137 PA2139 PA2142 PA2143 PA2144 PA2146 PA2149 PA2151 PA2153 PA2158 PA2159 PA2162...”

AFUA_5G01690 DUF1445 domain protein from Aspergillus fumigatus Af293
Aligns to 132:280 / 301 (49.5%), covers 100.0% of PF07286, 195.9 bits

• Characterization of gprK Encoding a Putative Hybrid G-Protein-Coupled Receptor in Aspergillus fumigatus
  Jung, PloS one 2016
  • “...5746300 AFUA_6G03140 oligopeptide transporter, putative -4.836 0.0079149 5733915 AFUA_2G02000 conserved hypothetical protein -4.321 6.404E-05 5743196 AFUA_5G01690 DUF1445 domain protein -4.293 0.0386637 5733419 AFUA_1G17470 high affinity nitrate transporter NrtB -4.035 0.0242195 5733093 AFUA_1G16070 conserved hypothetical protein -3.943 0.0178849 5730314 AFUA_1G01960 conserved hypothetical protein -3.737 0.0060923 5732457 AFUA_1G13210...”

CNE05290 hypothetical protein from Cryptococcus neoformans var. neoformans JEC21
Aligns to 122:268 / 276 (53.3%), covers 100.0% of PF07286, 195.1 bits

• Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans
  Hu, Genome biology 2008
  • “...Bt63. CGH confirmed these findings and further revealed that other genes within the region (CNE05250, CNE05290, CNE05320, CNE05330, CNE05300, and CNE00020) were present in 125.91 (VNI) but absent in Bt63 (VNB; Additional data file 4). Interestingly, several genes within the region (CNE05310, CNE05340, CNE05350, CNE05320, and...”

Q09674 Putative hydro-lyase C5H10.01 from Schizosaccharomyces pombe (strain 972 / ATCC 24843)
SPAC5H10.01 DUF1445 family protein from Schizosaccharomyces pombe
Aligns to 151:296 / 301 (48.5%), covers 100.0% of PF07286, 186.0 bits

• A novel histidine kinase inhibitor regulating development in Bacillus subtilis
  Wang, Genes & development 1997
  • “...Schizosaccharomyces pombe whose function is unknown (accession no. Q09674). Genes four and five, kipI and kipA, were designated as ycsJ in the original...”
• Klf1, a C2H2 zinc finger-transcription factor, is required for cell wall maintenance during long-term quiescence in differentiated G0 phase
  Shimanuki, PloS one 2013
  • “...between klf1 and WT cells in the VE phase was rather small. Only one transcript (spac5H10.01, encoding a protein containing a motif DUF1445 of unknown function) was reproducibly diminished below 1/6-fold in klf1 cells in VE. The physiologic relevance of this decrease is unknown. A small...”
• Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study
  Rustici, Genome biology 2007
  • “...genes that are specifically downregulated in response to high copper ( ptr2 , SPBC13A2.04c, SPAP7G5.06, SPAC5H10.01, SPCC132.04c, SPCC1223.09, SPAC11D3.18c, SPAC11D3.15, and SPAC1039.08). Most of these genes are involved in amino acid metabolism. S. cerevisiae cannot compensate for the loss of Ace1p with a general stress response...”

GLUCM_MOUSE / Q8BH86 D-glutamate cyclase, mitochondrial; EC 4.2.1.48 from Mus musculus (Mouse) (see paper)
Q8BH86 D-glutamate cyclase (EC 4.2.1.48) from Mus musculus (see 2 papers)
Aligns to 115:257 / 617 (23.2%), covers 99.3% of PF07286, 177.3 bits

• function: D-glutamate cyclase that converts D-glutamate to 5-oxo-D- proline.
  catalytic activity: D-glutamate = 5-oxo-D-proline + H2O (RHEA:22360)
  disruption phenotype: Accumulation of D-glutamate in heart. Mice develop normally and do not display any visible phenotype under normal conditions.
• Effects of long-term low dose saxitoxin exposure on nerve damage in mice
  Sun, Aging 2021
  • “...-0.394583 Q80TB8 Synaptic vesicle membrane protein VAT-1 homolog-like OS=Mus musculus OX=10090 GN=Vat1l -0.304523 -0.511452 -0.336342 Q8BH86 D-glutamate cyclase, mitochondrial OS=Mus musculus OX=10090 GN=Dglucy -0.280367 -0.266742 -0.269957 Q8BI08 Protein MAL2 OS=Mus musculus OX=10090 GN=Mal2 0.278012 0.268981 0.29278 Q8VCY8 Phospholipid phosphatase-related protein type 2 OS=Mus musculus OX=10090 GN=Plppr2...”
• Protein kinase A catalytic-α and catalytic-β proteins have nonredundant regulatory functions
  Raghuram, American journal of physiology. Renal physiology 2020 (secret)
• CypD(-/-) hearts have altered levels of proteins involved in Krebs cycle, branch chain amino acid degradation and pyruvate metabolism
  Menazza, Journal of molecular and cellular cardiology 2013
  • “...0.002 34 (Q8CIM3) D-2-hydroxyglutarate dehydrogenase, mitochondrial D2HDH_MOUSE 12.15 6 0.964 0.038 0.674 0.057 0.005 30 (Q8BH86) UPF0317 protein C14orf159 homolog, mitochondrial CN159_MOUSE 3.57 3 0.975 0.069 0.702 0.064 0.027 28 (Q9CZB0) Succinate dehydrogenase cytochrome b560 subunit, mitochondrial C560_MOUSE 28.99 22 1.015 0.061 0.764 0.034 0.011 25...”

NP_001347946 D-glutamate cyclase, mitochondrial isoform 1 from Mus musculus
E9QMK9 D-glutamate cyclase from Mus musculus
Aligns to 145:287 / 647 (22.1%), covers 99.3% of PF07286, 177.2 bits

• D-Glutamate is metabolized in the heart mitochondria.
  Ariyoshi, Scientific reports 2017
  • GeneRIF: Further analysis of D-glutamate metabolism indicated that 9030617O03Rik is a D-glutamate cyclase that converts D-glutamate to 5-oxo-D-proline.
• Proteomic Analysis of Protective Effects of Dl-3-n-Butylphthalide against mpp + -Induced Toxicity via downregulating P53 pathway in N2A Cells
  Zhao, Proteome science 2023
  • “...Speg Striated muscle-specific serine/threonine-protein kinase 0.005699 E9QP49 Ehbp1l1 EH domain-binding protein 1-like protein 1 0.034701 E9QMK9 Dglucy \D-glutamate cyclase, mitochondrial \"" 0.037768 E9QLZ9 Enah Protein enabled homolog 0.005109 E9QA16 Cald1 Caldesmon 1 0.00029 E9QA15 Cald1 Caldesmon 1 0.002066 E9Q7X7 Nrxn2 Neurexin-2 0.020083 E9Q634 Myo1e Unconventional myosin-Ie...”

NP_001273399 D-glutamate cyclase, mitochondrial isoform b precursor from Homo sapiens
Aligns to 118:260 / 621 (23.0%), covers 100.0% of PF07286, 170.2 bits

• Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  Hendrickson, PloS one 2010
  • GeneRIF: Observational study of gene-disease association. (HuGE Navigator)

D4A9W3 D-glutamate cyclase from Rattus norvegicus
Aligns to 130:272 / 632 (22.6%), covers 98.6% of PF07286, 169.4 bits

• Alterations in mitochondrial protein glycosylation in myocardial ischaemia reperfusion injury.
  Feng, Biochemistry and biophysics reports 2023
  • “...2 Q4FZT0 G3V7Y3 Q5RKI1 A0A0G2K7N1 Q7TP75 P61016 D4AB01 D3ZIL6 Q6AYS7 P57093 Q5BK81 Q3MIE0 Q9EPB1 Q3KRE0 D4A9W3 Q7TMB9 G3V879 Q499R7 P29418 M0R544 A0A140TAE0 A0A023ILN9 Q5XI97 P11951 Q4QRB4 O88637 D4ADD7 Q5RKI8 D3ZBS2 D4A8Y1 Q64560 A0A0G2K719 M0R5R0 Q7TQ70 D3ZFJ6 Q5M891 D3ZY96 Q6IFZ5 A0A096P6L8 A0A0H2UHP1 G3V928 C0JPT7 G3V640 A0A0G2K777 B0BMY7...”

Q7Z3D6 D-glutamate cyclase, mitochondrial from Homo sapiens
Aligns to 118:255 / 616 (22.4%), covers 100.0% of PF07286, 153.7 bits

• Insight into the Molecular Signature of Skeletal Muscle Characterizing Lifelong Football Players
  Orrù, International journal of environmental research and public health 2022
  • “...P15880 40S ribosomal protein S2 RPS2 2.58 Q5T3I0 G patch domain-containing protein 4 GPATCH4 2.58 Q7Z3D6 UPF0317 protein C14orf159, mitochondrial DGLUCY 2.58 P54868 Hydroxymethylglutaryl-CoA synthase, mitochondrial HMGCS2 2.58 Q13555 Calcium/calmodulin-dependent protein kinase type II subunit gamma CAMK2G 2.58 Q969N2 GPI transamidase component PIG-T PIGT 2.58 Q92523...”
• Bioenergetic and Proteomic Profiling of Immune Cells in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Patients: An Exploratory Study
  Fernandez-Guerra, Biomolecules 2021
  • “...0.023 O95497 Pantetheinase VNN1 0.75 0.028 P13645 Keratin, type I cytoskeletal 10 KRT10 0.66 0.036 Q7Z3D6 D-glutamate cyclase, mitochondrial DGLUCY 0.60 0.030...”
• Neuronal ceroid lipofuscinosis with DNAJC5/CSPα mutation has PPT1 pathology and exhibit aberrant protein palmitoylation.
  Henderson, Acta neuropathologica 2016
  • “...<0.05, FDR (p) > 0.05 DECREASED Q6PUV4 CPLX2 Complexin-2 CPLX2 7.47 2.71E-02 1.43E-01 Cytoplasm - Q7Z3D6 CN159 UPF0317 protein C14orf159, mitochondrial C14orf159 4.15 7.31E-03 7.44E-02 Mitochondria A Q13526 PIN1 Peptidyl-prolyl cis-trans isomerase Pin1 PIN1 4.07 7.39E-03 7.44E-02 Nucleus, Cytoplasm - P11137 MTAP2 Microtubule-associated protein 2 MAP2...”

Or search for genetic data about PF07286 in the Fitness Browser