Family Search for PF02130 (UPF0054)

PF02130.17 hits 58 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

BSU25320 putative metalloprotease (RefSeq) from Bacillus subtilis subsp. subtilis str. 168
Aligns to 12:152 / 157 (89.8%), covers 96.9% of PF02130, 164.1 bits

• Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC
  Engelen, BMC genomics 2012
  • “...homolog) 2 BSU24790 yqgX yqgX ycbL putative metal-binding hydrolase BSU24890 folN yqgN ygfA 5-formyltetrahydrofolate cyclo-ligase BSU25320 yqfG yqfG ybeY putative metal-dependent hydrolase BSU25620 yqeL yqeL ybeB putative ribosomal maturation protein 2 BSU27370 yrrL yrrL yceG conserved hypothetical protein BSU27390 yrrK yrrK yqgF putative Holliday junction resolvase...”

SAOUHSC_01672 hypothetical protein (NCBI) from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_1530 hypothetical protein (NCBI) from Staphylococcus aureus subsp. aureus USA300_FPR3757
Aligns to 12:150 / 155 (89.7%), covers 95.3% of PF02130, 160.7 bits

• Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH)
  Chaudhuri, BMC genomics 2009
  • “...b) Agarose gel showing sample results. M size markers, lane 1 SAOUHSC_00862 (non-essential), lane 2 SAOUHSC_01672 (essential). Each band represents a PCR product of a different size, corresponding to a transposon insertion in a different position. The white boxes represent the product size range expected for...”
• Novel Regulation of Alpha-Toxin and the Phenol-Soluble Modulins by Peptidyl-Prolyl cis/trans Isomerase Enzymes in Staphylococcus aureus
  Keogh, Toxins 2019
  • “...protein SAUSA300_2197 RplP 0.45 Protein synthesis SAUSA300_1443 RluB 0.45 Protein synthesis SAUSA300_1159 NusA 0.45 Transcription SAUSA300_1530 YbeY 0.44 Conserved hypothetical protein SAUSA300_0820 SufS 0.44 Biosynthesis of cofactors, prosthetic groups, and carriers SAUSA300_1937 0.44 Mobile and extrachromosomal element functions SAUSA300_1049 MurI 0.43 Cell envelope SAUSA300_1679 AcsA 0.43...”

lmo1465 similar to unknown proteins (NCBI ptt file) from Listeria monocytogenes EGD-e
Aligns to 13:157 / 161 (90.1%), covers 95.3% of PF02130, 154.0 bits

• An HD-domain phosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect bacterial growth and virulence
  Huynh, Proceedings of the National Academy of Sciences of the United States of America 2015
  • “...response (lmo1467) (20), ribosome maturation and assembly (lmo1465 and era) (21, 22), lipid biogenesis (lmo1464) (23), and nucleotide metabolism (lmo1463) (24)....”

HMPREF0389_00692 rRNA maturation RNase YbeY from Filifactor alocis ATCC 35896
Aligns to 9:156 / 162 (91.4%), covers 94.5% of PF02130, 144.3 bits

• Filifactor alocis--a new emerging periodontal pathogen
  Aruni, Microbes and infection 2015
  • “...protease family protein (BFO_0185) Pseudo (BFO_1506) [CAAX amino terminal protease family protein] 8. Metalloprotease Metalloprotease (HMPREF0389_00692) Membrane-associated zinc metalloprotease (PGTDC60_1498) Transmembrane AAA- metalloprotease FtsH (PGTDC60_0044) Zinc metalloprotease (PGN_1582) Membrane-associated zinc metalloprotease (PG0383) Transmembrane AAA- metalloprotease FtsH (PGN_0043) Metalloprotease (TDE1242) Membrane-associated zinc metalloprotease (TDE2341) (TDE2337) aminopeptidase [Peptidase_M29;...”
• Proteome variation among Filifactor alocis strains
  Aruni, Proteomics 2012
  • “...zinc metalloprotease FtsH HMPREF0389_01001 Caax amino protease family protein HMPREF0389_00677 Caax amino protease HMPREF0389_00590 Metalloprotease HMPREF0389_00692 Glycoprotease family protein HMPREF0389_01443 Xaa pro dipeptidase HMPREF0389_01538 O-sialoglycoprotein endopeptidase HMPREF0389_01445 Serine protease HtrA HMPREF0389_01460 ATP-dependent Clp protease HMPREF0389_01648 Carboxy-processing protease HMPREF0389_00522 Oligoendopeptidase F HMPREF0389_00926 HMPREF0389_00527 Table 6 Proteome profiling...”

Csac_1839 protein of unknown function UPF0054 (RefSeq) from Caldicellulosiruptor saccharolyticus DSM 8903
Aligns to 8:154 / 158 (93.0%), covers 96.9% of PF02130, 140.8 bits

• Genome Wide Re-Annotation of Caldicellulosiruptor saccharolyticus with New Insights into Genes Involved in Biomass Degradation and Hydrogen Production
  Chowdhary, PloS one 2015
  • “...). Among the list of essential genes, 7 of them Csac_2571, Csac_1262, Csac_0970, Csac_1701, Csac_2220, Csac_1839 and Csac_2091, were found to be hypothetical and the re-annotation study predicted their function as O-antigen polymerase, histone family DNA-binding protein, uracil-DNA glycosylase, glycyl-tRNA synthase subunit, dCTP deaminase, metalloprotease ybeY...”

SSA_1613 hypothetical protein (NCBI) from Streptococcus sanguinis SK36
Aligns to 10:160 / 165 (91.5%), covers 96.9% of PF02130, 139.8 bits

• Availability of Zinc Impacts Interactions between Streptococcus sanguinis and Pseudomonas aeruginosa in Coculture
  Li, Journal of bacteriology 2020 (secret)

SGO_RS03500 rRNA maturation RNase YbeY from Streptococcus gordonii str. Challis substr. CH1
Aligns to 11:160 / 165 (90.9%), covers 96.1% of PF02130, 139.0 bits

• Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq
  Mutha, Scientific reports 2019
  • “...of textmining. The dgkA gene was linked to the gene immediately upstream, a putative metalloprotease SGO_RS03500 ( ybeY ). Similarly, thrB was linked to the adjacent (downstream) gene, SGO_RS03940 (SGO_0803), an uncharacterised protein. Finally, the closely localised genes SGO_RS02580 (SGO_0522) and SGO_RS02590 (SGO_0524), encoding putative acylphosphatase...”

SP_0967 putative metalloprotease (RefSeq) from Streptococcus pneumoniae TIGR4
Aligns to 10:160 / 165 (91.5%), covers 96.9% of PF02130, 138.3 bits

• A transcription factor contributes to pathogenesis and virulence in Streptococcus pneumoniae
  Mahdi, PloS one 2013
  • “...for genes that might be important to the disease process revealed 4 genes, SP_2089, SP_0569, SP_0967 and SP_0800, which showed high level of expression in both blood and brain. Two of these 4 genes are part of a highly connected network ( Figure 5 ) suggesting...”
  • “...further analysis. 10.1371/journal.pone.0070862.g005 Figure 5 Interaction network data for connectivity of SP_0746 to SP_0800 and SP_0967 (highlighted in yellow). We then evaluated the contribution of selected genes preferentially up-regulated in various tissues to pathogenesis and virulence by targeted mutagenesis. Deletion replacement mutation of these genes (SP_0746,...”

SPD_0855 conserved hypothetical protein TIGR00043 (NCBI) from Streptococcus pneumoniae D39
spr0869 Conserved hypothetical protein (NCBI ptt file) from Streptococcus pneumoniae R6
Aligns to 10:160 / 165 (91.5%), covers 96.9% of PF02130, 138.0 bits

• The Small Molecule DAM Inhibitor, Pyrimidinedione, Disrupts Streptococcus pneumoniae Biofilm Growth In Vitro
  Yadav, PloS one 2015
  • “...protein -1.8 (0.005) SPD_1729 conserved hypothetical protein -1.6 (0.002) SPD_1858 conserved hypothetical protein -1.5 (0.007) SPD_0855 conserved hypothetical protein -1.4 (0.05) SPD_1836 conserved hypothetical protein -1.4 (0.05) The functional annotation of the differentially regulated genes revealed that genes involved in galactose metabolism were exclusively up-regulated in...”
• The highly conserved bacterial RNase YbeY is essential in Vibrio cholerae, playing a critical role in virulence, stress regulation, and RNA processing
  Vercruysse, PLoS pathogens 2014
  • “...b0659 of E. coli MG1655, VC0960 of V. cholerae C6706, PA3982 of P. aeruginosa PAO1, SPR0869 of S. pneumoniae R6, and Rv2367c of M. tuberculosis H37v), and subsequently cloned into pBR322 under control of the constitutive tetracycline promoter. DNA manipulations were performed according to the methods...”

BAB1_2156 Protein of unknown function UPF0054 (NCBI) from Brucella melitensis biovar Abortus 2308
Aligns to 8:142 / 158 (85.4%), covers 95.3% of PF02130, 137.5 bits

• Endoribonuclease YbeY Is Linked to Proper Cellular Morphology and Virulence in Brucella abortus
  Budnick, Journal of bacteriology 2018
  • “...cellular morphology of Brucella abortus. Brucella abortus 1_2156 (bab1_2156; also known as bab_rs26200) is located on chromosome I of Brucella melitensis biovar...”
  • “...the results outlined in this report, here we refer to bab1_2156 as ybeY. An isogenic deletion of ybeY in B. abortus 2308 resulted in impaired growth in vitro...”

BruAb1_2129 conserved hypothetical protein TIGR00043 (NCBI) from Brucella abortus biovar 1 str. 9-941
Aligns to 21:155 / 171 (78.9%), covers 95.3% of PF02130, 137.2 bits

• A highly conserved protein of unknown function is required by Sinorhizobium meliloti for symbiosis and environmental stress protection
  Davies, Journal of bacteriology 2008
  • “...S. meliloti, SMc01113; Brucella abortus, BruAb1_2129; Rhizobium etli, RHE_CH00374; Rhizobium leguminosarum, RL0393; Bradyrhizobium japonicum, b110793;...”

T303_04255 rRNA maturation RNase YbeY from Streptococcus thermophilus ASCC 1275
Aligns to 10:160 / 165 (91.5%), covers 96.9% of PF02130, 136.6 bits

• Functional Genomic Analyses of Exopolysaccharide-Producing Streptococcus thermophilus ASCC 1275 in Response to Milk Fermentation Conditions
  Wu, Frontiers in microbiology 2019
  • “...listed in Supplementary Table S2 . Only three differentially up-regulated proteins (T303_02515, 2.59-fold; T303_2740, 2.66-fold; T303_04255, 1.87-fold) were detected. T303_02515 encodes a pseudouridine synthetase, one of the assembly factors, is critical for ribosome assembly in addition to two rRNAs and 33 ribosomal proteins ( Jiang et...”

SaSA53_1276 rRNA maturation RNase YbeY from Streptococcus agalactiae
Aligns to 10:160 / 165 (91.5%), covers 96.9% of PF02130, 135.7 bits

• Transcriptome and Proteome of Fish-Pathogenic Streptococcus agalactiae Are Modulated by Temperature
  Tavares, Frontiers in microbiology 2018
  • “...23 151.58 Hypothetical protein 2.77 S CYT SaSA53_1182 5 26.28 SAM-dependent methyltransferase 74.54 J CYT SaSA53_1276 14 92.26 ybeY Endoribonuclease 4.19 J CYT SaSA53_1291 8 39.72 Nickel ABC transporter substrate-binding protein 3.22 E PSE SaSA53_1348 10 66.78 tRNA [cytidine(34)-2-O]-methyltransferase 2.31 J CYT SaSA53_1381 30 208.69 Primosomal...”

WP_010970840 rRNA maturation RNase YbeY from Agrobacterium tumefaciens
Atu0358 hypothetical protein (RefSeq) from Agrobacterium tumefaciens str. C58 (Cereon)
Aligns to 16:156 / 168 (83.9%), covers 95.3% of PF02130, 134.7 bits

• The RNase YbeY Is Vital for Ribosome Maturation, Stress Resistance, and Virulence of the Natural Genetic Engineer Agrobacterium tumefaciens.
  Möller, Journal of bacteriology 2019
  • GeneRIF: The RNase YbeY is vital for ribosome maturation, stress resistance, and virulence in Agrobacterium tumefaciens.
• The RNase YbeY Is Vital for Ribosome Maturation, Stress Resistance, and Virulence of the Natural Genetic Engineer Agrobacterium tumefaciens
  Möller, Journal of bacteriology 2019
  • “...Here, we classify the A. tumefaciens YbeY ortholog Atu0358 as another chromosomally encoded virulence factor with a major impact on Agrobacterium physiology and...”
  • “...is a RNase involved in rRNA processing. RESULTS Atu0358 is the A. tumefaciens YbeY homologue. The fundamental influence of riboregulation on the fitness and...”
• A highly conserved protein of unknown function is required by Sinorhizobium meliloti for symbiosis and environmental stress protection
  Davies, Journal of bacteriology 2008
  • “...names are as follows: Agrobacterium tumefaciens, Atu0358; S. meliloti, SMc01113; Brucella abortus, BruAb1_2129; Rhizobium etli, RHE_CH00374; Rhizobium...”

YbeY / b0659 endoribonuclease YbeY from Escherichia coli K-12 substr. MG1655 (see 17 papers)
YBEY_ECOLI / P0A898 Endoribonuclease YbeY; EC 3.1.-.- from Escherichia coli (strain K12) (see 6 papers)
ybeY / MB|P0A898 putative metalloprotease ybeY from Escherichia coli K12 (see paper)
NP_415192 endoribonuclease YbeY from Escherichia coli str. K-12 substr. MG1655
b0659 hypothetical protein (NCBI) from Escherichia coli str. K-12 substr. MG1655
Aligns to 15:144 / 155 (83.9%), covers 93.8% of PF02130, 133.8 bits

• function: Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. Acts together with the RNase R to eliminate defective 70S ribosomes, but not properly matured 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. Involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both the 5'- and 3'- ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs.
  cofactor: Zn(2+) (Binds 1 zinc ion.)
  disruption phenotype: Mutants show defects in 16S rRNA maturation, ribosome activity, translational fidelity, and ribosome assembly. They have severe growth defect at high temperatures, essentially no thermotolerance at lethal temperatures. They also show a decrease in polysomes and a large increase in both free 50S and free 30S ribosomal subunits relative to 70S ribosomes.
• Elevated Levels of Era GTPase Improve Growth, 16S rRNA Processing, and 70S Ribosome Assembly of Escherichia coli Lacking Highly Conserved Multifunctional YbeY Endoribonuclease.
  Ghosal, Journal of bacteriology 2018
  • GeneRIF: YbeY binds to Era and is involved in the 3'-end processing of 16S rRNA
• C21orf57 is a human homologue of bacterial YbeY proteins.
  Ghosal, Biochemical and biophysical research communications 2017
  • GeneRIF: This observation suggests that the function of HuYbeY in human cells is likely regulated through specific interactions with partner proteins similarly to the way YbeY is regulated in bacteria.
• Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in Escherichia coli.
  Vercruysse, mBio 2016
  • GeneRIF: This work provides the first evidence that YbeY is recruited to the ribosome through interaction with proteins involved in ribosome biogenesis (i.e., ribosomal protein S11, Era).
• The Escherichia coli translation-associated heat shock protein YbeY is involved in rRNA transcription antitermination.
  Grinwald, PloS one 2013
  • GeneRIF: evidence which tie YbeY to the transcription antitermination process
• The heat shock protein YbeY is required for optimal activity of the 30S ribosomal subunit.
  Rasouly, Journal of bacteriology 2010
  • GeneRIF: Data show that the in vitro activity of the translation machinery of ybeY deletion mutants is significantly lower than that of the wild type.
• Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing.
  Davies, Molecular microbiology 2010
  • GeneRIF: Deletion of ybeY strongly affects the maturation of rRNA, and causes striking defects in ribosome function including decreased ribosome activity, reduced translational fidelity and altered translation initiation factor binding.
• YbeY, a heat shock protein involved in translation in Escherichia coli.
  Rasouly, Journal of bacteriology 2009
  • GeneRIF: The authors provide evidence that YbeY, a conserved heat shock protein with unknown function, is involved in the translation process.
• The ybeY protein from Escherichia coli is a metalloprotein.
  Zhan, Acta crystallographica. Section F, Structural biology and crystallization communications 2005
  • GeneRIF: ybeY protein from Escherichia coli is a metalloprotein
• The highly conserved bacterial RNase YbeY is essential in Vibrio cholerae, playing a critical role in virulence, stress regulation, and RNA processing
  Vercruysse, PLoS pathogens 2014
  • “...various organisms were constructed by PCR amplification of each ybeY homolog from chromosomal DNA (i.e. b0659 of E. coli MG1655, VC0960 of V. cholerae C6706, PA3982 of P. aeruginosa PAO1, SPR0869 of S. pneumoniae R6, and Rv2367c of M. tuberculosis H37v), and subsequently cloned into pBR322...”
  • “...purification of YbeY and RNase R To construct the overexpression plasmid, ybeY of E. coli (b0659) and V. cholerae (VC0960) was cloned into pET28a under control of a T7 promoter with an N-terminal His-MBP-TEV(site)-tag. Purification of YbeY without RNase I contamination was accomplished by expression in...”
• Genome-wide expression profiling in Escherichia coli K-12
  Richmond, Nucleic acids research 1999
  • “...NarQ) b1593 b1593 5.7 -1.4 ORF, hypothetical protein b0659 ybeY 5.6 5.8 ORF, hypothetical protein b0281 intF 5.5 2.8 Putative phage integrase b1274 *topA...”

VC0960 conserved hypothetical protein (NCBI ptt file) from Vibrio cholerae O1 biovar eltor str. N16961
Aligns to 13:143 / 154 (85.1%), covers 93.8% of PF02130, 133.3 bits

• The highly conserved bacterial RNase YbeY is essential in Vibrio cholerae, playing a critical role in virulence, stress regulation, and RNA processing
  Vercruysse, PLoS pathogens 2014
  • “...large-scale, saturating transposon library of V. cholerae showed no hits for the ybeY homolog, designated VC0960 [36] . To experimentally verify the essentiality of ybeY in V. cholerae , we attempted to create a non-polar deletion of ybeY , which is part of the ybeZY operon...”
  • “...ybeY strain in V. cholerae . A ) Genomic organization of the ybeZ (VC0961)- ybeY (VC0960) locus in the V. cholerae strain C6706. An in-frame deletion of ybeY was carried out in C6706; the position of the chromosomal ybeY deletion is indicated (). B ) Growth...”

RPA0446 Protein of unknown function UPF0054 (NCBI) from Rhodopseudomonas palustris CGA009
Aligns to 42:177 / 190 (71.6%), covers 94.5% of PF02130, 132.8 bits

• Molecular Basis of Bacterial Longevity
  Pechter, mBio 2017 (no snippet)

YP_003431738 putative metalloprotease (RefSeq) from Hydrogenobacter thermophilus TK-6
Aligns to 16:147 / 147 (89.8%), covers 93.8% of PF02130, 131.5 bits

• Phylogenetic position of aquificales based on the whole genome sequences of six aquificales species
  Oshima, International journal of evolutionary biology 2012
  • “...S9 YP_003432379 ribosomal protein L18 YP_003432892 4-hydroxy-3-methylbut-2-enyl diphosphate reductase YP_003432936 ATP-dependent protease YP_003433556 UDP-N-acetylglucosamine pyrophosphorylase YP_003431738 putative metalloprotease YP_003431749 diaminopimelate decarboxylase YP_003431809 dihydrodipicolinate reductase YP_003431998 UDP-N-acetylglucosamine 1-carboxyvinyltransferase YP_003432481 ribosomal protein S20 YP_003432953 queuine tRNA-ribosyltransferase YP_003431834 ATP-dependent protease La YP_003431839 tRNA delta(2)-isopentenylpyrophosphate transferase YP_003431873 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase...”

YBEY_HAEIN / P71335 Endoribonuclease YbeY; EC 3.1.-.- from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (see paper)
HI0004 conserved hypothetical protein (NCBI ptt file) from Haemophilus influenzae Rd KW20
Aligns to 14:144 / 154 (85.1%), covers 93.0% of PF02130, 131.2 bits

• function: Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA.
  cofactor: Zn(2+) (Binds 1 zinc ion.)
• The non-canonical hydroxylase structure of YfcM reveals a metal ion-coordination motif required for EF-P hydroxylation
  Kobayashi, Nucleic acids research 2014
  • “...Yeh D.C. Parsons L.M. Parsons J.F. Liu F. Eisenstein E. Orban J. NMR structure of HI0004, a putative essential gene product from Haemophilus influenzae, and comparison with the X-ray structure of an Aquifex aeolicus homolog Protein Sci. 2005 14 424 430 15632286 39. Penhoat C.H. Li...”
• Architecture and function of metallopeptidase catalytic domains
  Cerdà-Costa, Protein science : a publication of the Protein Society 2014
  • “...Eisenstein E, Orban J (2005) NMR structure of HI0004, a putative essential gene product from Haemophilus influenzae, and comparison with the X-ray structure of...”
• The Escherichia coli translation-associated heat shock protein YbeY is involved in rRNA transcription antitermination
  Grinwald, PloS one 2013
  • “..., Liu F , Eisenstein E , et al ( 2005 ) NMR structure of HI0004, a putative essential gene product from Haemophilus influenzae , and comparison with the X-ray structure of an Aquifex aeolicus homolog . Protein Sci 14 : 424 430 . 15632286 24...”
• Prokaryotic diacylglycerol kinase and undecaprenol kinase
  Van, Annual review of biophysics 2012
  • “...DC Parsons LM Parsons JF Fang L Eisenstein E Orban J 2005 NMR structure of HI0004, a putative essential gene product from Haemophilus influenzae, and comparison with the X-ray structure of an Aquifex aeolicus homolog Protein Sci 14 424 30 15632286 108 Yoon HS Hackett JD...”
• Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing
  Davies, Molecular microbiology 2010
  • “...DC Parsons LM Parsons JF Liu F Eisenstein E Orban J 2005 NMR structure of HI0004, a putative essential gene product from Haemophilus influenzae, and comparison with the X-ray structure of an Aquifex aeolicus homolog Protein Sci 14 424 430 15632286 Zhan C Fedorov EV Shi...”
• NMR structure of HI0004, a putative essential gene product from Haemophilus influenzae, and comparison with the X-ray structure of an Aquifex aeolicus homolog
  Yeh, Protein science : a publication of the Protein Society 2005
  • “...HI0004, a putative essential gene product from Haemophilus influenzae, and comparison with the X-ray structure of an Aquifex aeolicus homolog DEOK CHEON YEH, LISA M. PARSONS, JAMES F. PARSONS, FANG...”
  • “...of the 154-residue conserved hypothetical protein HI0004 has been determined using multidimensional heteronuclear NMR spectroscopy. HI0004 has sequence...”
• NMR assignment of the hypothetical protein HI0004 from Haemophilus influenzae--a putative essential gene product
  Cheon, Journal of biomolecular NMR 2004
• A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae
  Akerley, Proceedings of the National Academy of Sciences of the United States of America 2002
  • “...Vch Bbu Tpa N E N N N N E N HI0004 HI0175 HI0303 HI0338 HI0466 HI0570 HI0767 HI1086 HI1282 HI1608 HI1654 HI1731 N N E N E UPF0054 Predicted transmembrane...”
  • “...in viability for several conserved genes (homologs of HI0004, HI0767, HI1282, HI1608, and HI1654) that have been examined in B. subtilis (ref. 4;...”
• More

D7S_01459 rRNA maturation RNase YbeY from Aggregatibacter actinomycetemcomitans D7S-1
Aligns to 15:144 / 154 (84.4%), covers 91.4% of PF02130, 129.5 bits

• Transcriptomic Analysis of Aggregatibacter actinomycetemcomitans Core and Accessory Genes in Different Growth Conditions
  Tjokro, Pathogens (Basel, Switzerland) 2019
  • “...stress response. In both keratinocyte and RPMI media, the transcription of metal-binding heat shock protein (D7S_01459) was found to be significantly upregulated. Although the importance of HSPs are evident, neither the mechanisms of protection by HSPs nor the cellular responses to the stress of nutrient limitation...”

NGR_c00430 hypothetical protein (RefSeq) from Rhizobium sp. NGR234
Aligns to 17:156 / 173 (80.9%), covers 85.2% of PF02130, 129.1 bits

• Involvement of multiple loci in quorum quenching of autoinducer I molecules in the nitrogen-fixing symbiont Rhizobium (Sinorhizobium) sp. strain NGR234
  Krysciak, Applied and environmental microbiology 2011
  • “...NGR_c27960 NGR_c05660 NGR_c03760 NGR_c05950 NGR_c16020 NGR_c00430 NGR_c08460 NGR_c06480 NGR_c32270 NGR_c17430 NGR_c10940 NGR_b22150 NGR_c03800 NGR_c23150c...”

ZMO0074 hypothetical protein (RefSeq) from Zymomonas mobilis subsp. mobilis ZM4
Aligns to 13:158 / 176 (83.0%), covers 96.9% of PF02130, 129.0 bits

• Mechanism of Tolerance to the Lignin-Derived Inhibitor p-Benzoquinone and Metabolic Modification of Biorefinery Fermentation Strains
  Yan, Applied and environmental microbiology 2019
  • “...gene, ZMO1399; and two hypothetical 174 protein genes, ZMO0074 and ZMO1821. The two downregulated genes were oxidoreductase 175 encoding gene ZMO1116 and...”
  • “...374 ZMO0833, ZMO1303, ZMO1984, ZMO1949, ZMO1696, ZMO1576, ZMO1399, ZMO0074, 375 ZMO1821, ZMO1116 and ZMO1335) for overexpression. The pHW20a plasmid we used was...”
• Transcriptome analysis of Zymomonas mobilis ZM4 reveals mechanisms of tolerance and detoxification of phenolic aldehyde inhibitors from lignocellulose pretreatment
  Yi, Biotechnology for biofuels 2015
  • “...2.84 2.01 Metabolism of other amino acids ZMO1309 Leucyl aminopeptidase 2.33 2.03 Genetic/environmental/cellular process/organismal systems ZMO0074 Hypothetical protein 5.02 3.61 Genetic/environmental/cellular process/organismal systems ZMO0143 c ATP - binding cassette superfamily 2.11 2.00 Genetic/environmental/cellular process/organismal systems ZMO0282 RND family efflux transporter subunit MFP 6.05 7.14 2.55 Genetic/environmental/cellular...”
  • “...up-regulated over twofold change under at least two phenolic aldehyde inhibitors. ZMO0020 , ZMO0021 , ZMO0074 , ZMO0268 , ZMO0270 , ZMO0384 , ZMO0388 , ZMO0391 , ZMO0440 , ZMO0486 , ZMO1334 , ZMO1346 , ZMO1386 , ZMO1602 , ZMO1821 , ZMO1880 , ZZM4_0133 , and...”

RL0393 hypothetical protein (NCBI) from Rhizobium leguminosarum bv. viciae 3841
Aligns to 18:156 / 171 (81.3%), covers 81.2% of PF02130, 128.9 bits

• The Use of Transposon Insertion Sequencing to Interrogate the Core Functional Genome of the Legume Symbiont Rhizobium leguminosarum
  Perry, Frontiers in microbiology 2016
  • “...protein RL0128 GI 8 0.13 1 ES 8 0 0 ES 0.0.1 Conserved hypothetical protein RL0393 GI 8 0.38 9.33 GD 8 0.5 4.25 GD 0.0.1 Conserved hypothetical protein RL0412 GI 10 0 0 ES 10 0 0 ES 0.0.1 Conserved hypothetical protein RL0548 GI 7...”
• A highly conserved protein of unknown function is required by Sinorhizobium meliloti for symbiosis and environmental stress protection
  Davies, Journal of bacteriology 2008
  • “...Rhizobium etli, RHE_CH00374; Rhizobium leguminosarum, RL0393; Bradyrhizobium japonicum, b110793; Mesorhizobium loti, mlr5536; and "Aquifex aeolicus," Aq1354....”

YPO2618 conserved hypothetical protein (NCBI ptt file) from Yersinia pestis CO92
Aligns to 15:144 / 157 (82.8%), covers 93.8% of PF02130, 127.1 bits

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPO3151 conserved hypothetical protein 1.553 (0.047) YPTB1061 (yapC) YPO2796 putaive autotransporter protein 1.82 (0.003) YPTB1111 YPO2618 conserved hypothetical protein 0.577 (0.001) YPTB1155 YPO1120 conserved hypothetical protein 1.404 (0.003) YPTB1159 (tolB) YPO1124 TolB colicin import protein 1.46 (0.025) YPTB1194 YPO1163 putative membrane protein 0.678 (< 0.001) YPTB1210...”

YPTB1111 hypothetical protein (NCBI) from Yersinia pseudotuberculosis IP 32953
Aligns to 15:144 / 157 (82.8%), covers 93.8% of PF02130, 126.3 bits

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPTB0965 YPO3151 conserved hypothetical protein 1.553 (0.047) YPTB1061 (yapC) YPO2796 putaive autotransporter protein 1.82 (0.003) YPTB1111 YPO2618 conserved hypothetical protein 0.577 (0.001) YPTB1155 YPO1120 conserved hypothetical protein 1.404 (0.003) YPTB1159 (tolB) YPO1124 TolB colicin import protein 1.46 (0.025) YPTB1194 YPO1163 putative membrane protein 0.678 (< 0.001)...”

Rv2367c hypothetical protein (NCBI) from Mycobacterium tuberculosis H37Rv
Aligns to 14:153 / 182 (76.9%), covers 89.1% of PF02130, 126.2 bits

• Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions
  Perrone, Scientific reports 2017
  • “...GGG TCGCCACCATCA GGG Rv0896 gltA2 23 GGG ATGACCCGCCTGCCC GGGG T GGGG TCTCT GG CACCAT GGG Rv2367c 34 GGG TC GGGG CTGAATC GGG C GG CTC GG C GGG Rv0166 fadD5 36 GGG TC GGG CC GGG ATTGCC GGGG ACTTGCC GGGG GCTT GG C GGGGG Rv1704c cycA...”
• A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis
  Bhagavat, Scientific reports 2017
  • “...14 FAH Rv3536c Probable hydratase 15 Thioesterase/thiol ester dehydrase-isomerase Rv1532c Conserved hypothetical protein 16 Zincin-like Rv2367c Conserved hypothetical protein 17 MFS general substrate transporter Rv3331 Probable sugar-transport integral membrane protein SugI 18 Rhomboid-like Rv1337 Probable integral membrane protein 19 MetI-like Rv0929 Phosphate-transport integral membrane ABC transporter...”
• The highly conserved bacterial RNase YbeY is essential in Vibrio cholerae, playing a critical role in virulence, stress regulation, and RNA processing
  Vercruysse, PLoS pathogens 2014
  • “...of V. cholerae C6706, PA3982 of P. aeruginosa PAO1, SPR0869 of S. pneumoniae R6, and Rv2367c of M. tuberculosis H37v), and subsequently cloned into pBR322 under control of the constitutive tetracycline promoter. DNA manipulations were performed according to the methods of Sambrook [90] and cloning products...”
• Identifying co-targets to fight drug resistance based on a random walk model
  Chen, BMC systems biology 2012
  • “...] atpB 0.46 In Vitro essential ATP synthase A chain [ 55 , 67 ] Rv2367c 0.28 Not Essential hypothetical protein Rv3355c 0.01 Not Essential conserved hypothetical protein Rv2199c 0.55 Not Essential conserved membrane protein Rv3310 1.38 Not Essential acid phosphatase [ 68 ] nadC 0.59...”
• The gene expression data of Mycobacterium tuberculosis based on Affymetrix gene chips provide insight into regulatory and hypothetical genes
  Fu, BMC microbiology 2007
  • “...Rv3885C MMPL7 Rv2475C LTP1 Rv0236C NUOJ NUOB NUON MMPL9 Rv2752C Rv0177 Rv0176 HEMB PRCA Rv2553C Rv2367C RPLT GID CMK Rv3122 EMBB Rv1303 Rv1907C Rv2792C) Energy production and respiration 3 (FTSZ WAG31 Rv0902C HEMK NARL Rv2147C Rv3267 Rv1477 LPPW SIGC Rv2864C RECA Rv2826C Rv1697 LEUC LEUD Rv3909...”
  • “...Rv1711 Rv3672c Rv2554c Rv3856c Rv3212 Rv1043c Rv0525 Rv1339 Rv2956 Rv2759c Rv2879c Rv1780 Rv2475c Rv2752c Rv0177 Rv2367c) (Rv1632c Rv2808 Rv3122 Rv1907c) Zone-3 (Information Pathways) (Rv2147c Rv3267 Rv1697 Rv3909 Rv2574 Rv3376 Rv2125 Rv1546 Rv1099c Rv2908c Rv1073 Rv0636 Rv0637 Rv0277c) (Rv2826c Rv2360c Rv2827c Rv3647c Rv0299 Rv2822c Rv0057) Zone-4 (Cell...”

SMc01113 CONSERVED HYPOTHETICAL PROTEIN (NCBI ptt file) from Sinorhizobium meliloti 1021
Aligns to 17:156 / 168 (83.3%), covers 95.3% of PF02130, 125.5 bits

• Riboregulation in Nitrogen-Fixing Endosymbiotic Bacteria
  Robledo, Microorganisms 2020
  • “...growth and overall symbiotic performance on alfalfa roots [ 134 ]. The gene annotated as SMc01113 in the chromosome of the S. meliloti reference strain Rm1021 is almost ubiquitous in bacteria and has been included in the proposed minimal prokaryotic genome [ 135 ]. It encodes...”
• Sinorhizobium meliloti YbeY is a zinc-dependent single-strand specific endoribonuclease that plays an important role in 16S ribosomal RNA processing
  Babu, Nucleic acids research 2020
  • “...any ybeY mutant was described in an earlier study, which showed that the ybeY gene (SMc01113) is critically required for Sinorhizobium meliloti symbiosis with alfalfa ( Medicago sativa ) plants ( 2 ). In addition to being symbiotically defective, loss of YbeY also rendered the S....”
• OxyR-Dependent Transcription Response of Sinorhizobium meliloti to Oxidative Stress
  Lehman, Journal of bacteriology 2018
  • “...Antioxidants and regulators katA cpo oxyR glgA1 SMc03924 SMc01113 ABC ABC ABC ABC transporter transporter transporter transporter 0.5 mM oxyR mutant 0.65 1.09...”
  • “...secreted peroxidase (SMc01944) and a gene of unknown function (SMc01113) whose expression has been previously shown to be induced by H2O2 (48, 49). Role of...”
• Sinorhizobium meliloti YbeY is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation
  Saramago, Nucleic acids research 2017
  • “...S. meliloti mutants and derivative strains Sm YbeY is encoded by the gene annotated as SMc01113 in the genome of the reference Rm1021 strain ( 31 ). S. meliloti Sm ybeY and Sm ybeY FLAG derivatives were both generated in the ExpR + Sm2011 derivative strain...”
  • “...To create an in-frame deletion of ybeY , 938-bp and 921-bp DNA fragments flanking the SMc01113 ORF were PCR amplified from genomic DNA with primer pairs YbeY_F1/YbeY_iR and YbeY_iF/YbeY_R1. Primers YbeY_iR and YbeY_iF carry Hind III sites at their 5-ends. The resulting PCR products were thus...”
• RNA-binding proteins involved in post-transcriptional regulation in bacteria
  Van, Frontiers in microbiology 2015
  • “...models assigned a probable RNA-binding site for YbeY. Phenotypically, there are striking similarities between an smc01113 mutant, the ybeY ortholog in S. meliloti , and an hfq mutant ( Pandey et al., 2011 ). Mutated YbeY indeed causes an increased sensitivity to various stresses, similarly to...”
• Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria
  Pandey, BMC genomics 2014
  • “...in this process. We have recently reported evidence that the highly conserved bacterial protein YbeY (SMc01113 in Sinorhizobium meliloti ) may play a major, previously unrecognized role in bacterial sRNA regulation [ 16 ]. ybeY , which is one of the 206 genes that comprise the...”
  • “...YbeY cavity. Second, we noted striking parallels between the phenotypes of S. meliloti hfq and smc01113 ( ybeY ) mutants, an observation that suggested there might be an underlying mechanistic connection. To test this hypothesis, we carried out a limited study in S. meliloti in which...”
• Riboregulation in plant-associated α-proteobacteria
  Becker, RNA biology 2014
  • “...may be related to riboregulation is the S. meliloti SMc01113 protein, a homolog to E. coli YbeY. This protein is broadly conserved in bacteria and comprises an...”
  • “...proteins involved in RNA silencing.68 Phenotypes of a SMc01113 mutant are pleiotropic and resemble those of hfq mutants.68 In E. coli, YbeY modulates...”
• Genome-wide profiling of Hfq-binding RNAs uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons in Sinorhizobium meliloti
  Torres-Quesada, RNA biology 2014
  • “...is the widely conserved Argonaute-like protein YbeY (SMc01113), whose loss-of-function has been shown to produce phenotypes and to compromise trans-sRNA...”
• More

PA3982 hypothetical protein (NCBI) from Pseudomonas aeruginosa PAO1
PA14_12310 hypothetical protein (NCBI) from Pseudomonas aeruginosa UCBPP-PA14
Aligns to 14:142 / 160 (80.6%), covers 94.5% of PF02130, 122.5 bits

• Endoribonuclease YbeY Is Essential for RNA Processing and Virulence in Pseudomonas aeruginosa
  Xia, mBio 2020
  • “...is essential for the 16S rRNA maturation and ribosome assembly. In P. aeruginosa , gene PA3982 (PA14_12310 in the PA14 genome) encodes an YbeY homolog. To examine the function of YbeY in P. aeruginosa , we constructed a ybeY mutant in wild-type PA14. Deletion of the...”
  • “...the Creative Commons Attribution 4.0 International license . To confirm that the P. aeruginosa ybeY (PA3982) gene is a true ortholog of the ybeY gene in E. coli , we complemented the PA14 ybeY mutant with an E. coli ybeY gene, which restored the bacterial growth...”
• The highly conserved bacterial RNase YbeY is essential in Vibrio cholerae, playing a critical role in virulence, stress regulation, and RNA processing
  Vercruysse, PLoS pathogens 2014
  • “...homolog from chromosomal DNA (i.e. b0659 of E. coli MG1655, VC0960 of V. cholerae C6706, PA3982 of P. aeruginosa PAO1, SPR0869 of S. pneumoniae R6, and Rv2367c of M. tuberculosis H37v), and subsequently cloned into pBR322 under control of the constitutive tetracycline promoter. DNA manipulations were...”
• Endoribonuclease YbeY Is Essential for RNA Processing and Virulence in Pseudomonas aeruginosa
  Xia, mBio 2020
  • “...essential for the 16S rRNA maturation and ribosome assembly. In P. aeruginosa , gene PA3982 (PA14_12310 in the PA14 genome) encodes an YbeY homolog. To examine the function of YbeY in P. aeruginosa , we constructed a ybeY mutant in wild-type PA14. Deletion of the ybeY...”

BL0861 hypothetical protein (NCBI) from Bifidobacterium longum NCC2705
Aligns to 8:145 / 182 (75.8%), covers 84.4% of PF02130, 120.7 bits

• Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum
  Ventura, Microbiology and molecular biology reviews : MMBR 2007
  • “...through apparent C-terminal domain BL0861 ......................................COG family, predicted metal-dependent hydrolase; PFAM_ID, UPF0054 BL0870...”

mlr5536 hypothetical protein (NCBI) from Mesorhizobium loti MAFF303099
Q98BK1 Endoribonuclease YbeY from Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
Aligns to 26:159 / 166 (80.7%), covers 94.5% of PF02130, 119.4 bits

• A highly conserved protein of unknown function is required by Sinorhizobium meliloti for symbiosis and environmental stress protection
  Davies, Journal of bacteriology 2008
  • “...RL0393; Bradyrhizobium japonicum, b110793; Mesorhizobium loti, mlr5536; and "Aquifex aeolicus," Aq1354. Downloaded from http://jb.asm.org/ on February 12, 2017...”
• Differential protein profiling of soil diazotroph Rhodococcus qingshengii S10107 towards low-temperature and nitrogen deficiency.
  Suyal, Scientific reports 2019
  • “...B7K5E6), MurC (UDP-N-acetylmuramateL-alanine ligase, B2JHF9), MloA (Protein MloA, Q8RN11), LipB (Octanoyltransferase, Q89JM6), YbeY (Endoribonuclease YbeY, Q98BK1), ProB, atpA, AtpH, ThrB, TufA, GpmA (2,3-bisphosphoglycerate-dependent phosphoglycerate mutase, B2JC95), AskA (Acetate kinase, B8HVB6), ThyA (Thymidylate synthase, Q0SEI1), RpsF (30S ribosomal protein S6), Tkt, AccC (Biotin carboxylase, Q06862), PanD (Aspartate...”

Q9K0P7 Endoribonuclease YbeY from Neisseria meningitidis serogroup B (strain MC58)
Aligns to 28:160 / 169 (78.7%), covers 87.5% of PF02130, 119.4 bits

• Towards New Drug Targets? Function Prediction of Putative Proteins of Neisseria meningitidis MC58 and Their Virulence Characterization
  Shahbaaz, Omics : a journal of integrative biology 2015
  • “...Q9JXB2 Q9JXE8 Q9JXK0 Q9JY57 Q9JY92 Q9JYB3 Q9JYE4 Q9JZG7 Q9JZW7 Q9K0P7 Q9K0V2 Q9K137 Q9K191 Q9K1D2 Q7DDI9 Q9JXJ9 88. Q9JZ63 89. 90. Q9JZF6 Q9JXZ5 91. 92. 93. 94....”

DIP1717 Conserved hypothetical protein (NCBI) from Corynebacterium diphtheriae NCTC 13129
Aligns to 11:150 / 196 (71.4%), covers 89.8% of PF02130, 119.2 bits

• Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation
  Wittchen, BMC genomics 2018
  • “...Cell wall, membrane, envelop biogenesis DIP1720 - DIP1713 8 not detected dnaJ2 , DIP1719, DIP1718, DIP1717, DIP1716, DIP1715, era , recO . Replication, recombination and repair; Cell wall, membrane, envelop biogenesis; Coenzyme metabolism; Inorganic ion transport and metabolism; Function unknown; Signal transduction mechanisms; Post-translational modification, protein...”

PD1781 conserved hypothetical protein (NCBI ptt file) from Xylella fastidiosa Temecula1
Aligns to 19:151 / 161 (82.6%), covers 92.2% of PF02130, 118.5 bits

• The Secreted Protease PrtA Controls Cell Growth, Biofilm Formation and Pathogenicity in Xylella fastidiosa
  Gouran, Scientific reports 2016
  • “...RNAs (43 out of 49), tRNA maturation queA (PD0562), elongation factor efp (PD1253), endoribunuclease ybeY (PD1781), and chaperone dnaJ (PD1279) to assist in protein folding, are all indicative of the increased cell division rate in X. fastidiosa prtA . Despite increased cell proliferation, DSF production and...”

CJM1cam_0120 rRNA maturation RNase YbeY from Campylobacter jejuni
Aligns to 4:122 / 134 (88.8%), covers 82.8% of PF02130, 117.8 bits

• Motility defects in Campylobacter jejuni defined gene deletion mutants caused by second-site mutations
  de, Microbiology (Reading, England) 2015
  • “...S3). Unique variants to the fliW mutant clone A were an intergenic A insertion between CJM1cam_0120 (putative metalloprotease) and CJM1cam_0121 (hypothetical protein) and a synonymous SNP (A to G) in CJM1cam_0791 (hypothetical protein), indicating that the non-motile phenotype is not caused by second-site mutations. Electron micrographs...”

CJSA_0112 rRNA maturation RNase YbeY from Campylobacter jejuni subsp. jejuni IA3902
Cj0121 hypothetical protein Cj0121 (NCBI ptt file) from Campylobacter jejuni subsp. jejuni NCTC 11168
Aligns to 4:122 / 135 (88.1%), covers 82.8% of PF02130, 117.8 bits

• RNAseq Reveals Complex Response of Campylobacter jejuni to Ovine Bile and In vivo Gallbladder Environment
  Kreuder, Frontiers in microbiology 2017
  • “...lipoprotein 1.8 2.3 obgE GTPase ObgE 1.5 3.4 CJSA_0111 Putative recombination protein RecO 5.4 5.6 CJSA_0112 Putative metalloprotease 3.1 1.9 thrB Homoserine kinase 2.2 2.0 CJSA_0149 Cytochrome c family protein 1.5 1.6 CJSA_0150 Putative 6-pyruvoyl tetrahydropterin synthase 1.8 1.9 CJSA_0228 Hypothetical protein 1.6 1.7 CJSA_0233 Sulfatase...”
• Structure and genotypic plasticity of the Campylobacter fetus sap locus
  Tu, Molecular microbiology 2003
  • “...26% respectively. The Cf0020 product shares 59% identity with Cj0121, the function of which is unknown, and the Cf0013 and Cf0019 predicted products have no...”

YBEY_THEMA / Q9X1J7 Endoribonuclease YbeY; EC 3.1.-.- from Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (see paper)
TM1509 conserved hypothetical protein (NCBI ptt file) from Thermotoga maritima MSB8
Aligns to 9:133 / 150 (83.3%), covers 94.5% of PF02130, 117.0 bits

• function: Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA.
  cofactor: Zn(2+) (Binds 1 zinc ion.)
• C21orf57 is a human homologue of bacterial YbeY proteins
  Ghosal, Biochemical and biophysical research communications 2017
  • “...12832766 12 Penhoat CH Li Z Atreya HS NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure J Struct Funct Genomics 6 2005 51 62 15965736 13 Davies BW Walker GC A highly conserved protein of unknown function is required by Sinorhizobium...”
• Polypeptide backbone, C(β) and methyl group resonance assignments of the 24 kDa plectin repeat domain 6 from human protein plectin
  Pulavarti, Biomolecular NMR assignments 2015
  • “...Xiao R Murray D Arrowsmith CH Szyperski T NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure J Struc Func Genomics 2005 6 51 62 Huang YJ Hang D Lu LJ Tong L Gerstein MB Montelione GT Targeting the human cancer pathway...”
• High-quality NMR structure of human anti-apoptotic protein domain Mcl-1(171-327) for cancer drug design
  Liu, PloS one 2014
  • “...Yee A , et al ( 2005 ) NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure . J Struct Funct Genomics 6 : 51 62 . 15965736 27 Delaglio F , Grzesiek S , Vuister GW , Zhu G , Pfeifer...”
• The non-canonical hydroxylase structure of YfcM reveals a metal ion-coordination motif required for EF-P hydroxylation
  Kobayashi, Nucleic acids research 2014
  • “...Xiao R. Murray D. Arrowsmith C.H. Szyperski T. NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure J. Struct. Funct. Genomics 2005 6 51 62 15965736 40. Pandey S.P. Minesinger B.K. Kumar J. Walker G.C. A highly conserved protein of unknown function...”
• Architecture and function of metallopeptidase catalytic domains
  Cerdà-Costa, Protein science : a publication of the Protein Society 2014
  • “...NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure. J Struct Funct Genom 6:51-62. 108. Oganesyan...”
• Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation
  Jacob, Molecular cell 2013
  • “...Xiao R Murray D Arrowsmith CH Szyperski T NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure J Struct Funct Genomics 2005 6 51 62 15965736 Powers T Noller HF Dominant lethal mutations in a conserved loop in 16S rRNA Proc Natl...”
• Increasing sequence diversity with flexible backbone protein design: the complete redesign of a protein hydrophobic core
  Murphy, Structure (London, England : 1993) 2012
  • “...Xiao R Murray D Arrowsmith CH Szyperski T NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure J Struct Funct Genomics 2005 6 51 62 15965736 Pokala N Handel TM Review: protein design--where we were, where we are, where were going J...”
• NMR structure of lipoprotein YxeF from Bacillus subtilis reveals a calycin fold and distant homology with the lipocalin Blc from Escherichia coli
  Wu, PloS one 2012
  • “...Z Atreya HS Kim S Yee A 2005 NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure. J Struct Funct Genomics 6 51 62 15965736 42 Delaglio F Grzesiek S Vuister GW Zhu G Pfeifer J 1995 NMRPipe: a multidimensional spectral processing...”
• More

SPOA0008 rRNA maturation RNase YbeY from Ruegeria pomeroyi DSS-3
SPOA0008 conserved hypothetical protein TIGR00043 (NCBI) from Silicibacter pomeroyi DSS-3
Aligns to 15:156 / 165 (86.1%), covers 91.4% of PF02130, 113.9 bits

• Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3
  Rivers, Frontiers in microbiology 2016
  • “...Yes cis90 230 SPO3787 sugar ABC transporter, periplasmic Transport Antisense 1.30 0.493 Yes cis92 148 SPOA0008 Hypothetical protein Antisense 1.86 NA cis93 221 SPOA0011 S-adenosylmethionine synthase Coenzyme metabolism Antisense 1.07 NA cis94 297 SPOA0026 3,4-dihydroxyphenylacetate 2,3-dioxygenase Antisense 2.75 0.000 cis95 180 SPOA0082 Hypothetical protein Antisense 1.21...”

H375_7840 rRNA maturation RNase YbeY from Rickettsia prowazekii str. Breinl
Aligns to 14:161 / 167 (88.6%), covers 95.3% of PF02130, 113.0 bits

• Transcriptional profiling of Rickettsia prowazekii coding and non-coding transcripts during in vitro host-pathogen and vector-pathogen interactions
  Schroeder, Ticks and tick-borne diseases 2017
  • “...synthase F0 sector subunit b H375_2300 18.23 3-deoxy-manno-octulosonate cytidylyltransferase H375_7500 15.25 LSU ribosomal protein L32p H375_7840 14.91 Metal-dependent hydrolase YbeY H375_1210 12.76 rickettsial conserved H375_4640 12.37 hypothetical protein H375_9060 12.35 guanosine-3,5-bis(diphosphate) 3-pyrophosphohydrolase SpoTc H375_2110 12.26 Signal peptide peptidase SppA, 36K type H375_0670 11.93 Citrate synthase H375_8910...”

RP741 unknown (NCBI ptt file) from Rickettsia prowazekii str. Madrid E
Aligns to 27:174 / 180 (82.2%), covers 95.3% of PF02130, 112.7 bits

• Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect
  Kondo, Proceedings of the National Academy of Sciences of the United States of America 2002
  • “...detected: ftsZ, sdhB, pgpA, g3pdh, czcR, an ORF homologous to RP741 in the genome of R. prowazekii, and an ORF homologous to BMEI0172 in the genome of Brucella...”
  • “...was an unidentified ORF located between BMEI0172 and RP741. In the upstream region of ftsZ, where Kondo et al. non-LTR retrotransposon-like sequence was...”

TDE1242 conserved hypothetical protein TIGR00043 (NCBI) from Treponema denticola ATCC 35405
Aligns to 18:147 / 155 (83.9%), covers 90.6% of PF02130, 109.8 bits

• Filifactor alocis--a new emerging periodontal pathogen
  Aruni, Microbes and infection 2015
  • “...FtsH (PGTDC60_0044) Zinc metalloprotease (PGN_1582) Membrane-associated zinc metalloprotease (PG0383) Transmembrane AAA- metalloprotease FtsH (PGN_0043) Metalloprotease (TDE1242) Membrane-associated zinc metalloprotease (TDE2341) (TDE2337) aminopeptidase [Peptidase_M29; Thermophilic metalloprotease (M29)] Hypothetical protein (BFO_1297) [Zinc-dependent metalloprotease] Hypothetical protein (BFO_2661) [Zinc-dependent metalloprotease] 9. Glycoprotease family protein Glycoprotease family protein (HMPREF0389_01443) Putative glycoprotease...”

RSP_3598 Protein of unknown function UPF0054 (NCBI) from Rhodobacter sphaeroides 2.4.1
Aligns to 14:161 / 167 (88.6%), covers 93.8% of PF02130, 109.6 bits

• Convergence of the transcriptional responses to heat shock and singlet oxygen stresses
  Dufour, PLoS genetics 2012
  • “...RSP_2638, RSP_2640, RSP_2641, RSP_2739, RSP_2763, RSP_2764, RSP_2816, RSP_2952, RSP_2953, RSP_3067, RSP_3068, RSP_3378, RSP_3426, RSP_3552, RSP_3597, RSP_3598, RSP_3634, RSP_3809, RSP_3810, RSP_4244, RSP_4245, RSP_4248, RSP_4305 RpoHII regulon (99 genes) Energy metabolism Biosynthesis and degradation of polysaccharides RSP_0482 Electron transport RSP_0108, RSP_0109, RSP_0110, RSP_0112, RSP_0474, RSP_2785, RSP_3212, RSP_3305, RSP_3537...”

YBEY_ARATH / Q8L5Z4 Endoribonuclease YBEY, chloroplastic; EC 3.1.-.- from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
NP_850072 haloacid dehalogenase-like hydrolase family protein from Arabidopsis thaliana
AT2G25870 haloacid dehalogenase-like hydrolase family protein (RefSeq) from Arabidopsis thaliana
Aligns to 140:271 / 584 (22.6%), covers 81.2% of PF02130, 107.8 bits

• function: Endoribonuclease required for chloroplast ribosomal RNA (rRNA) processing and essential for normal growth and development. May be involved in maturation of both the 5' and 3' ends of 16S, 23S, and 4.5S rRNAs. Cleaves chloroplast rRNAs, mRNAs and tRNAs in vitro.
  cofactor: Zn(2+) (Binds 1 zinc ion.)
  disruption phenotype: Seedling lethality.
• The conserved endoribonuclease YbeY is required for chloroplast ribosomal RNA processing in Arabidopsis.
  Liu, Plant physiology 2015
  • GeneRIF: AtYbeY is a chloroplast-localized endoribonuclease that is required for chloroplast rRNA processing and thus for normal growth and development.[YbeY]
• A sugar phosphatase regulates the methylerythritol phosphate (MEP) pathway in malaria parasites
  Guggisberg, Nature communications 2014
  • “...sequences: E. coli YidA, EOU46719; M. tuberculosis Rv3813c, NP_218330; C. reinhardtii FER_156463, ADF43173; A. thaliana At2g25870, ABO38782. Figure 4 PfHAD1 fosmidomycin-resistance alleles result in loss of phosphatase activity Displayed are the means standard error of the mean (SEM) of enzyme activity from at least three independent...”
• Mining the soluble chloroplast proteome by affinity chromatography
  Bayer, Proteomics 2011
  • “...AT2G17340 Pantothenate kinase-related O + AT2G21350 RNA binding C + AT2G23390 Acyl-CoA N-acyltransferase M + AT2G25870 Haloacid dehalogenase-like family protein M + AT2G31890 b) ATRAP; putative RNA binding domain C + AT2G44760 Unknown protein C + AT3G02900 a) Unknown protein C + AT3G04650 FAD-dependent oxidoreductase C...”
  • “...C O O + AT2G17240 CUP2 Chloroplast unknown protein 1 C C C C + AT2G25870 HAC Haloacid dehalogenase-like family protein M C O M + AT2G35800 SUC Substrate carrier family protein O O O O + AT3G04650 ORE FAD-dependent oxidoreductase C C C C +...”
• Co-option of EDM2 to distinct regulatory modules in Arabidopsis thaliana development
  Tsuchiya, BMC plant biology 2010
  • “...EDM2 -induced" catalytic activity (MF) 2.60e-06 AT5G39080, AT3G63510, AAE14, PSD2, AT1G22430, SAL1, ATALN, AT5G09300, AT4G31390, AT2G25870, SRS, FC2, AT2G47880, AtCXE17, CSLA11, PKp3, UGT80B1, MCM4, ADC1, AT5G61480, AT2G26870 AT4G33920, CYP78A8, B120, XCP1, ATPREP2, CYP79B2, AT2G04845, AT5G24670, PAL4, CINV2, AT5G38710 set 10 "only EDM2 -suppressed" response to biotic...”
• Identification, cloning and characterization of sis7 and sis10 sugar-insensitive mutants of Arabidopsis
  Huang, BMC plant biology 2008
  • “...AT1G71870 1830 4621 0.40 0.016 glutathione S-transferase AT2G30860 36776 92522 0.40 0.002 hydrolase family protein AT2G25870 981 2438 0.40 0.000 endo-beta-1,4-glucanase AT1G64390 2208 5381 0.41 0.011 heat shock protein 100, putative AT5G15450 1817 4398 0.41 0.026 eIF-2 family protein AT1G76810 748 1809 0.41 0.035 auxin transport...”
  • “...brassinosteroids 0.66 0.99 AT2G17033 pentatricopeptide repeat-containing protein 0.61 0.71 AT2G19640 SET domain-containing protein 0.51 0.93 AT2G25870 hydrolase family protein 0.63 1.14 AT2G30860 glutathione S-transferase 0.70 0.91 AT2G30870 early dehydration-induced gene ERD13 0.91 1.08 AT2G31400 pentatricopeptide repeat-containing protein 0.53 0.73 AT2G31660 importin beta-2 subunit family protein 0.76...”

TTHA1045 hypothetical protein (NCBI) from Thermus thermophilus HB8
Aligns to 12:139 / 139 (92.1%), covers 88.3% of PF02130, 105.9 bits

• The role of ribonucleases in regulating global mRNA levels in the model organism Thermus thermophilus HB8
  Ohyama, BMC genomics 2014
  • “...[ 21 ] (21%) -CASP family protein TTHA0252 YP_143518.1 mRNA? Exo [ 6 ] YbeY TTHA1045 YP_144311.1 rRNA precursor? Endo [ 16 ] (29%) (21%) PhoH-like protein TTHA1046 YP_144312.1 ? ?? [ 22 ]** (50%) (47%) L-PSP TTHA0137 YP_143403.1 ? Endo [ 23 ] (50%) (37%)...”
  • “...motif. Therefore, we predicted that TTHA1046 is a putative RNase. The E. coli ortholog of TTHA1045, YbeY, may be involved with rRNA maturation based on mutagenic studies and its strong genetic interactions with PNPase and RNase R [ 28 ]. Furthermore, there is tertiary structural similarity...”

YBEY_HUMAN / P58557 Endoribonuclease YbeY; EC 3.1.-.- from Homo sapiens (Human) (see paper)
Aligns to 11:148 / 167 (82.6%), covers 88.3% of PF02130, 104.9 bits

• function: Single strand-specific metallo-endoribonuclease involved in rRNA maturation.
  cofactor: Zn(2+) (Binds 1 zinc ion.)

HP1160 conserved hypothetical protein (NCBI ptt file) from Helicobacter pylori 26695
Aligns to 6:128 / 140 (87.9%), covers 79.7% of PF02130, 103.6 bits

• High-Salt Conditions Alter Transcription of Helicobacter pylori Genes Encoding Outer Membrane Proteins
  Loh, Infection and immunity 2018
  • “...HP1484 HP1459 HP1426 HP1288 HP1240 HP1193 HP1162 HP1160 HP1546 HP1116 HP0385 HP1412 jhp0955 jhp0954 HP0441 jhp0936 HP0996 jhp1408 HP0008 HP0903 HP0681...”
• Helicobacter Pylori's plasticity zones are novel transposable elements
  Kersulyte, PloS one 2009
  • “...Shi32, in jhp0244 (methyltransferase of type II restriction modification system); strain Shi417, between hp1159 and hp1160 ; strain G27, between HPP12_1009 and the tRNA gene HPP12_t21 . Type 1b TnPZ insertion site: strain P12 in gene HPAG1_0439 (encodes type I restriction-modification R protein (hsdR)). Type 2...”
  • “...group (one strain) the TnPZs were located at other sites (type 1, between hp1159 and hp1160 ; type 2, in hp1402 ); this strain lacked the above-mentioned 0.5 kb deletion in or near orfQ and the orfG ::IS Hp608 insertion. The genome sequence of German strain...”

TWT283 unknown (NCBI ptt file) from Tropheryma whipplei str. Twist
Aligns to 14:145 / 171 (77.2%), covers 82.0% of PF02130, 98.8 bits

• Global transcriptome analysis of Tropheryma whipplei in response to temperature stresses
  Crapoulet, Journal of bacteriology 2006
  • “...integral membrane protein TWT671 TWT569 Cellular processes TWT775 TWT200 TWT283 --b ftsW ftsXb --b 1.7 2 2.6 1.6 1.5 3.3 Cell division protein FtsW Cell...”
  • “...(EC 1.2.4.1) ATP synthase beta chain (EC 3.6.3.14) TWT283 --b 1.5 Predicted metal-dependent hydrolase TWT248 qcrA 1.6 TWT757 TWT213 TWT630 TWT755 TWT783 TWT655...”

TP0650 conserved hypothetical protein (NCBI ptt file) from Treponema pallidum subsp. pallidum str. Nichols
Aligns to 19:148 / 160 (81.2%), covers 86.7% of PF02130, 98.6 bits

• Complete genome sequence of Treponema paraluiscuniculi, strain Cuniculi A: the loss of infectivity to humans is associated with genome decay
  Šmajs, PloS one 2011
  • “...for important cellular functions. Indeed, the functions of three of these proteins were predicted recently: TP0650 as a protein involved in translation, TP0772 as a transcriptional regulator and TP0941 as a regulator of motility [29] . Comparison of number of genes containing frameshifts and/or major sequence...”
• The binary protein interactome of Treponema pallidum--the syphilis spirochete
  Titz, PloS one 2008
  • “...synthesis (dTMP sugar) PI (uridylate kinase) (enzyme complex); DOM (GtrA): generation of sugar building block TP0650 Translation GBAA (translation); GT (tRNA-synthetases); PI (peptide deformylase; ribosomal protein L32) TP0658 (f) Flagellar assembly factor fliW PI (flagellin); GT (motility) TP0772 Transcription Regulator PI (RNA-polymerase, TP0701); HOM (LysR family...”

BPSL0672 unkown domain/putative metalloprotease fusion protein (RefSeq) from Burkholderia pseudomallei K96243
Aligns to 137:263 / 270 (47.0%), covers 95.3% of PF02130, 97.2 bits

• Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei
  Mohd-Padil, Scientific reports 2017
  • “...and BPNC10048R that was predicted to interact with two genes at its 3 site - bpsl0672 , a metalloprotease fusion protein (FC=0.76) and bpsl0671 , a hypothetical protein (FC=0.72) (Fig. 2C ). Three sRNA candidates, BPNC10196F_1129_SIPHT, BPNC10209R and BPNC10146R, are located between genes encoding ribosomal proteins....”
  • “...BPNC10113R bpsl1725 up up up up Candidate_369_SIPHT bpss1184 up up nd na BPNC10048R bpsl0671 , bpsl0672 down down, down up nd, up BPNC10196F_1129_SIPHT bpsl3221 down down up down BPNC10209R bpsl3223 down down down down BPNC10146R bpsl2159 down down down down BPNC10037R bpsl0493 , bpsl0494 up up,...”

PG0510 conserved hypothetical protein (NCBI) from Porphyromonas gingivalis W83
Aligns to 13:138 / 151 (83.4%), covers 90.6% of PF02130, 83.3 bits

• VimA-dependent modulation of the secretome in Porphyromonas gingivalis
  Osbourne, Molecular oral microbiology 2012
  • “...kDa 0 49 Pyruvate ferredoxin/flavodoxin oxidoreductase PG0498 Energy metabolism 132 kDa 0 2 Hypothetical protein PG0510 Hypothetical 34 kDa 0 5 Beta-galactosidase PG0598 Energy metabolism 127 kDa 0 11 DNA topoisomerase I PG0680 DNA metabolism 90 kDa 0 17 Acyl-CoA dehydrogenase (coenzyme A dehydrogenase) PG0696 Metabolic...”
• FimR and FimS: biofilm formation and gene expression in Porphyromonas gingivalis
  Lo, Journal of bacteriology 2010
  • “...2017 by University of California, Berkeley PG0508 PG0509 PG0510 PG0511 PG0512 PG0513 PG2130 PG2131 PG2132 PG2133 PG2134 PG2135 PG2136 PG0214 PG0928 PG0985...”

CT422 possible metalloenzyme (NCBI ptt file) from Chlamydia trachomatis D/UW-3/CX
Aligns to 17:150 / 161 (83.2%), covers 93.0% of PF02130, 82.3 bits

• Autoprocessing and self-activation of the secreted protease CPAF in Chlamydia-infected cells
  Chen, Microbial pathogenesis 2010
  • “...GCGGCCGC .TTA.AAC.CCC.AGG.GAA.AGC.AAT-3(reverse); For cloning CT408, 5-CGC GGATCC .ATG.CCG.ACC.CGT.TCT.CTC-3(forward) and 5-TTTCCTTTT GCGGCCGC .TTA.AAA.GTA.TTT.TTT.ACT.TTC.TTT-3 (reverse); For cloning CT422, 5-CGC GGATCC .ATG.CTT.ATT.TTG.GAT.CGA.TCT.TCT-3 (forward) and 5-TTTCCTTTT GCGGCCGC .TTA.TAC.TGC.AGG.ACG.TAA.TAA-3 (reverse); For cloning CT431, 5-CGC GGATCC .ATG.CCT.GAA.GGG.GAA.ATG.ATG-3 (forward) and 5-TTTCCTTTT GCGGCCGC .CTA.CAA.GTC.GTT.AAA.AGA.GAA-3 (reverse); For cloning CT441, 5-CCG GAATTC .ATG.ATG.AGA.TTC.GCT.CGC.TTT-3(forward) and 5-TTTCCTTTT GCGGCCGC...”
• Profiling of human antibody responses to Chlamydia trachomatis urogenital tract infection using microplates arrayed with 156 chlamydial fusion proteins
  Sharma, Infection and immunity 2006
  • “...dnaK CT406, hypothetical CT407, dksA CT421, hypothetical CT422, metalloproteas CT425, hypothetical CT427, hypothetical CT431, clpP CT442, crpA CT446, euo CT449,...”

CTL0681 hypothetical protein (RefSeq) from Chlamydia trachomatis 434/Bu
Aligns to 17:150 / 161 (83.2%), covers 93.0% of PF02130, 79.3 bits

• Interrogating Genes That Mediate Chlamydia trachomatis Survival in Cell Culture Using Conditional Mutants and Recombination
  Brothwell, Journal of bacteriology 2016
  • “...alleles mapped to cORFs (ctl0322, ctl0456, ctl0597, and ctl0681). DISCUSSION TS mutants can provide insights into poorly explored areas of chlamydial biology...”
  • “...Mid-late Mid-late HS11b ctl0322 M51I Unknown Mid-late HS13a ctl0681 P159L rRNA processing Mid-early HS17 rpsH A119V Ribosomal protein Mid-early HS19b atpB G339D...”

TC0705 conserved hypothetical protein (NCBI ptt file) from Chlamydia muridarum Nigg
Aligns to 18:150 / 161 (82.6%), covers 96.1% of PF02130, 76.1 bits

• Identification of immunodominant antigens by probing a whole Chlamydia trachomatis open reading frame proteome microarray using sera from immunized mice
  Cruz-Fisher, Infection and immunity 2011
  • “...TC0661 TC0664 TC0675 TC0677 TC0680 TC0688 TC0691 TC0701 TC0705 Antibody response to the indicated immunization regimen 252 CRUZ-FISHER ET AL. INFECT. IMMUN....”

CPn0509 predicted Metalloenzyme (NCBI ptt file) from Chlamydophila pneumoniae CWL029
Aligns to 17:149 / 158 (84.2%), covers 89.1% of PF02130, 73.2 bits

• Novel Chlamydia pneumoniae vaccine candidates confirmed by Th1-enhanced genetic immunization
  Li, Vaccine 2010
  • “...in Round 3: cutE , Cpn0420, ide , oppA_2 , ssb , glgX , Cpn0020, Cpn0509, fabD , rl1 , atoC , and Cpn0095 [ 14 ]. These 12 highest ranking ORFs were now cloned as full-length genes into genetic immunization plasmid CMVi-UB. Candidates ide and...”
  • “..._a, ide _b, Cpn0095_a, oppA _2_a, glgX _b, Cpn0020_b) or full-length genes (Cpn0420, ssb , Cpn0509, fabD , atoC , rl1 ) with the plasmid-based vaccination with gene fragments ( ide _ab, Cpn0095_a) or full-length genes ( cutE , Cpn0420, oppA _2, ssb , Cpn0509, fabD...”

TGME49_003420 4'-phosphopantetheinyl transferase domain-containing protein from Toxoplasma gondii ME49
Aligns to 618:819 / 1145 (17.6%), covers 87.5% of PF02130, 72.6 bits

• Lipid synthesis in protozoan parasites: a comparison between kinetoplastids and apicomplexans
  Ramakrishnan, Progress in lipid research 2013
  • “...TGME49_121570 EAR Enoyl ACP reductase Tb927.10.11930 LmjF.04.0290 PF3D7_0420200 TGME49_051930 PPTase Phosphopantetheinyl transferase Tb927.3.1840 LmjF.25.1770 PF3D7_0420200 TGME49_003420 FASI pathway FASI Fatty acid synthase type I - - - TGME49_094820 PPTase Phosphopantetheinyl transferase - - - TGME49_014440 Table 2 Comparison of fatty acid synthesis and modification pathways in...”

YBEY_MYCGE / P47628 Endoribonuclease YbeY; EC 3.1.-.- from Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195) (see paper)
Aligns to 15:148 / 154 (87.0%), covers 80.5% of PF02130, 70.5 bits

• function: Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA.
  cofactor: Zn(2+) (Binds 1 zinc ion.)
  disruption phenotype: Probably essential, it was not disrupted in a global transposon mutagenesis study.

PF3D7_0420200 holo-[acyl-carrier-protein] synthase, putative from Plasmodium falciparum 3D7
Aligns to 193:302 / 594 (18.5%), covers 55.5% of PF02130, 62.6 bits

• Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes: molecular insight into sex-specific processes and translational repression
  Lasonder, Nucleic acids research 2016
  • “...GO terms in the apicoplast including type II fatty acid synthesis with 4 repressed transcripts (PF3D7_0420200 (Holo-ACP synthase); PF3D7_0615100 (Fabl); PF3D7_1020800 (Dihydrolipoamide S-acetyltraferase) and PF3D7_1124500 (Pyruvate dehyrdogenase E1 subunit) in the pathway (Supplementary Figure S7). We previously found an important distinction for this pathway between rodent...”
• Imputation-based population genetics analysis of Plasmodium falciparum malaria parasites
  Samad, PLoS genetics 2015
  • “...4 PF3D7_0412300 1.77 1.77 1.20 1.46 12 4 PF3D7_0418000 1.23 - 1.43 - 32 4 PF3D7_0420200 - - 2.72 1.84 14 4 PF3D7_0424900 1.88 - - - 11 4 PF3D7_0425000 1.61 1.06 - - 27 5 PF3D7_0503200 - - 1.11 - 11 5 PF3D7_0511300 - -...”
• Genome-wide analysis of selection on the malaria parasite Plasmodium falciparum in West African populations of differing infection endemicity
  Mobegi, Molecular biology and evolution 2014
  • “...2.03 20 1.80 Plasmodium-exported protein PF3D7_0321200 PFC0935c 17 1.65 15 1.68 N -acetylglucosamine-1-phosphate transferase, putative PF3D7_0420200 PFD0980w 16 1.30 13 2.02 Holo-(acyl-carrier protein) synthase PF3D7_0508800 PFE0435c 5 1.10 4 1.07 Single-stranded DNA-binding protein (SSB) PF3D7_0601500 PFF0075c 6 1.05 5 1.64 Plasmodium-exported protein (PHISTb) PF3D7_0710200 PF07_0042 131...”
• Lipid synthesis in protozoan parasites: a comparison between kinetoplastids and apicomplexans
  Ramakrishnan, Progress in lipid research 2013
  • “...HAD Hydroxyacyl ACP dehydratase Tb927.8.1440 LmjF07.0430 LmjF07.0440 PF3D7_1323000 TGME49_121570 EAR Enoyl ACP reductase Tb927.10.11930 LmjF.04.0290 PF3D7_0420200 TGME49_051930 PPTase Phosphopantetheinyl transferase Tb927.3.1840 LmjF.25.1770 PF3D7_0420200 TGME49_003420 FASI pathway FASI Fatty acid synthase type I - - - TGME49_094820 PPTase Phosphopantetheinyl transferase - - - TGME49_014440 Table 2 Comparison...”

PVX_090105 holo-(acyl-carrier protein) synthase, putative from Plasmodium vivax
Aligns to 49:247 / 511 (38.9%), covers 89.8% of PF02130, 56.9 bits

• Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure
  Diez, PloS one 2017
  • “...PVX_003795 serine-repeat antigen (SERA) 4 629831630120 5.205 PVX_003770 merozoite surface protein 5 5 1132736 10.20 PVX_090105 holo-[acyl-carrier-protein] synthase, putative (ACPS) 5 964771 3.624 PVX_089950 bifunctional dihydrofolate reductase-thymidylate synthase, DHFR-TS 6 199049199165 4.703 PVX_001850 hypothetical protein 6 605656608119 3.788 PVX_111260 hypothetical protein, conserved 6 635433635539 4.406 PVX_111220...”

XP_016883883 endoribonuclease YbeY isoform X5 from Homo sapiens
Aligns to 141:203 / 254 (24.8%), covers 35.2% of PF02130, 56.2 bits

• YBEY is an essential biogenesis factor for mitochondrial ribosomes.
  Summer, Nucleic acids research 2020
  • GeneRIF: YBEY is an essential biogenesis factor for mitochondrial ribosomes.
• C21orf57 is a human homologue of bacterial YbeY proteins.
  Ghosal, Biochemical and biophysical research communications 2017
  • GeneRIF: This observation suggests that the function of HuYbeY in human cells is likely regulated through specific interactions with partner proteins similarly to the way YbeY is regulated in bacteria.
• Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  Hendrickson, PloS one 2010
  • GeneRIF: Observational study of gene-disease association. (HuGE Navigator)

Or search for genetic data about PF02130 in the Fitness Browser