Family Search for PF03729 (DUF308)

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

PF03729 hits 32 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

Q7VYU1 Membrane protein from Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)
3 alignments in 19:185 / 186 (89.8%), covering up to 100.0% of PF03729, 116.2 bits

• Experimental determination and data-driven prediction of homotypic transmembrane domain interfaces.
  Xiao, Computational and structural biotechnology journal 2020
  • “...N M L IAL M 46 CRCB TM1 (Q7VYU0, 5nkqA1) f FIAIGIGATLGAWLRWVLG 47 CRCB TM3 (Q7VYU1, 5nkqA3) AAVTGF LG GL TTFS TFSAETV 48 PC2 (Q13563, 5t4dA6) e RVLGPIYFTTFVFFMF F IL LN MF LA II N 49 BCNG-1 (O60741, 5u6oA6) e ITMLSMIVG A TC YAMF VG H...”

LMRG_00278 hypothetical protein from Listeria monocytogenes 10403S
3 alignments in 11:175 / 175 (94.3%), covering up to 100.0% of PF03729, 112.7 bits

• Effectiveness of Phage-Based Inhibition of Listeria monocytogenes in Food Products and Food Processing Environments
  Kawacka, Microorganisms 2020
  • “...selected 10 distinct L. monocytogenes 10403S LP-018-insensitive mutants. The mutants had a single mutation in LMRG_00278 or LMRG_01613 or in both genes. The phage was still able to bind to a representative phage-insensitive mutant with mutations in both genes, what clearly suggest that these mutations confer...”
• Homburgvirus LP-018 Has a Unique Ability to Infect Phage-Resistant Listeria monocytogenes
  Song, Viruses 2019
  • “...by whole genome sequencing. In each mutant, a single mutation was identified in either the LMRG_00278 or LMRG_01613 encoding genes. Interesting, LP-018 was able to bind to a representative phage-resistant mutant with a mutation in each gene, suggesting these mutations confer resistance through a mechanism independent...”
  • “...were found to contain only a single mutation. Three of these mutations were found in LMRG_00278, which was annotated as an HdeD family acid-resistance protein, and six of these mutations were found in LMRG_01613, which was annotated as a precursor to the foldase protein PrsA2 (...”
• PrfA-like transcription factor gene lmo0753 contributes to L-rhamnose utilization in Listeria monocytogenes strains associated with human food-borne infections
  Salazar, Applied and environmental microbiology 2013
  • “...LMRG_02602 LMRG_01030 LMRG_01444 LMRG_01763 LMRG_01236 LMRG_00278 LMRG_01602 LMRG_00472 LMRG_01574 LMRG_02611 LMRG_01103 LMRG_01849 Fold change 23.5 20.3...”
• Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
  Oliver, BMC genomics 2009
  • “...protein 3.93 32.87 8.47 LMRG_00482 lmo0794 similar to B. subtilis YwnB protein 67.02 32.5 0.72 LMRG_00278 lmo0596 similar to unknown proteins 170.5 32.33 0.09 LMRG_02218 lmo2673 conserved hypothetical protein 150.5 31.92 0.11 LMRG_02013 lmo0913 similar to succinate semialdehyde dehydrogenase 330.38 30.05 0.11 LMRG_00469 lmo0781 similar to...”

lmo0596 similar to unknown proteins from Listeria monocytogenes EGD-e
LMOf6854_0637 membrane protein, putative from Listeria monocytogenes str. 1/2a F6854
3 alignments in 11:175 / 175 (94.3%), covering up to 100.0% of PF03729, 111.4 bits

• The influence of stress factors on selected phenotypic and genotypic features of Listeria monocytogenes - a pilot study
  Wiktorczyk-Kapischke, BMC microbiology 2023
  • “...of sigB (stress induced regulator of genes), agrA, agrB (associated with biofilm formation) and lmo2230, lmo0596 (acid and alkali stress) (qPCR)for three strains of L. monocytogenes . Results Applied stress conditions contributed to changes in phenotypic features and expression levels of sigB , agrA , agrB...”
  • “...stress (55C), lmo2230 transcript level after exposure to acid and alkali stress (ATCC 19111), and lmo0596 transcript level after exposure to acid stress (ATCC 19111). Conclusions Environmental stress changes the ability to form a biofilm and the MIC values of antibiotics and affect the level of...”
• Acid stress signals are integrated into the σB-dependent general stress response pathway via the stressosome in the food-borne pathogen Listeria monocytogenes
  Guerreiro, PLoS pathogens 2022
  • “...this pathogen in food, food-processing environments and in the gastrointestinal tract. Results The transcription of lmo0596 is induced by acid in B -dependent manner The B regulon in L . monocytogenes is composed of a large number of genes that are heterogeneously expressed in response to...”
  • “...however we sought to use an additional B -reporter gene in this study. The gene lmo0596 was a potential target, as it possesses a B promoter and had been shown in other studies to belong to the B regulon [ 9 , 60 , 61 ]....”
• Listeria monocytogenes Requires the RsbX Protein To Prevent SigB Activation under Nonstressed Conditions
  Oliveira, Journal of bacteriology 2022
  • “...the transcription of two strongly SigB-dependent genes, lmo2230 , encoding a putative arsenate reductase, and lmo0596 , encoding a putative trans -membrane protein with an unknown function ( 33 , 34 ). Also, we examined expression of lmo1699 , encoding a chemotaxis protein which is only...”
  • “...at 600nm [OD 600 ], 0.8) before being subject to Northern blot analysis. lmo2230 and lmo0596 transcription was induced under nonstressed (dark) conditions in the rsbX mutant compared to the wild type at both 23 and 37C ( Fig. 2A and B ). This effect could...”
• The stressosome is required to transduce low pH signals leading to increased transcription of the amino acid-based acid tolerance mechanisms in Listeria monocytogenes
  Guerreiro, Access microbiology 2022
  • “...at pH 5 for 15min increased the transcription of highly B -dependent genes lmo2230 and lmo0596 , and enhanced L. monocytogenes acid tolerance in a stressosome-dependent manner. The genes lmo2230 and lmo0596 encode a putative arsenate reductase and a transmembrane protein with unknown function, respectively [...”
• Mild Stress Conditions during Laboratory Culture Promote the Proliferation of Mutations That Negatively Affect Sigma B Activity in Listeria monocytogenes
  Guerreiro, Journal of bacteriology 2020 (secret)
• Transcriptomic and Phenotypic Analyses of the Sigma B-Dependent Characteristics and the Synergism between Sigma B and Sigma L in Listeria monocytogenes EGD-e
  Mattila, Microorganisms 2020
  • “...protein pai 1, putative 2.1 3 lmo2158 choloylglycine hydrolase lmo0170 conserved domain protein 3 3.6 lmo0596 conserved hypothetical protein 4.7 3.8 lmo0911 conserved hypothetical protein 1.7 1.5 lmo0995 conserved hypothetical protein 1.6 3.9 lmo1241 conserved hypothetical protein 2 1.6 lmo1776 conserved hypothetical protein 2.3 1.9 lmo2213...”
• Transcriptional and phenotypic responses of Listeria monocytogenes to chlorine dioxide
  Pleitner, Applied and environmental microbiology 2014
  • “...Hypothetical protein lmo0170 lmo0229 lmo0231 lmo0439 lmo0496 lmo0596 lmo0670 lmo0720 lmo0761 lmo0796 lmo0869 lmo0911 lmo0964 lmo1059 lmo1069 lmo1137 lmo1332...”
• Cycles of light and dark co-ordinate reversible colony differentiation in Listeria monocytogenes
  Tiensuu, Molecular microbiology 2013
  • “...dependent on B ( Fig. 1 E). Also, expression of the genuinely B -regulated genes, lmo0596 and lmo2230 was highly induced at light conditions as compared with dark conditions (Fig. S3). Absence of Lmo0799 at light conditions decreased lmo0596 and lmo2230 expression to a level observed...”
  • “...lysine permease Lmo0798) and in the promoter region of the gene encoding the membrane protein Lmo0596 respectively (Table S1). Interestingly, the level of the B protein was only slightly decreased (a maximum of threefold) in the above tested transposon mutants apart from one. Previously, expression of...”
• More
• Physiological and transcriptional characterization of persistent and nonpersistent Listeria monocytogenes isolates
  Fox, Applied and environmental microbiology 2011
  • “...Downregulated Downregulated LMOf6854_1483 LMOf6854_0650 LMOf6854_0329 LMOf6854_0637 Putative membrane protein LPXTG-motif cell wall anchor domain protein...”

lin0605 similar to unknown proteins from Listeria innocua Clip11262
3 alignments in 11:175 / 175 (94.3%), covering up to 100.0% of PF03729, 110.7 bits

• In vivo transcriptional profiling of Listeria monocytogenes and mutagenesis identify new virulence factors involved in infection
  Camejo, PLoS pathogens 2009
  • “...lin0460 2,76 lmo0539 lmo0539 similar to tagatose-1,6-diphosphate aldolase lin0543 18,71 24,03 lmo0596 lmo0596 unknown protein lin0605 23,31 68,15 lmo0781 lmo0781 similar to mannose-specific phosphotransferase system (PTS) component IID lin0774 2,57 lmo0782 lmo0782 similar to mannose-specific phosphotransferase system (PTS) component IIC lin0775 4,69 lmo0783 lmo0783 similar to...”

Q9AK72 Integral membrane protein from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
3 alignments in 57:223 / 226 (73.9%), covering up to 98.6% of PF03729, 97.7 bits

• Comparative genomics of transport proteins in developmental bacteria: Myxococcus xanthus and Streptomyces coelicolor
  Getsin, BMC microbiology 2013
  • “...ArAE Family 8.A.3.4.1 Q9KYG0 239 2 MPA1-C Family 9.A.31.1.2 Q9XA27 436 10 SdpAB Family 9.B.36.1.2 Q9AK72 226 6 Hde Family 9.B.74.4.1 Q9K3K9 357 6 PIP Family 9.B.140.1.1 Q9K4J8 280 6 DUF1206 Family Proteins were retrieved with GBLAST e-values between 0.1 and 0.001, individually verified and assigned...”
  • “...Streptomyces species. The second Class 9 protein identified in Sco was a 6 TMS homologue (Q9AK72; 6 TMSs; 226 aas), a member of the Acid Resistance Membrane Protein (HdeD) Family. It was assigned TC# 9.B.36.1.2, but no functional assignment was possible. The third Class 9 protein...”

MAP1317c hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
3 alignments in 28:196 / 197 (85.8%), covering up to 98.6% of PF03729, 89.6 bits

• Gene expression profiling of Mycobacterium avium subsp. paratuberculosis in simulated multi-stress conditions and within THP-1 cells reveals a new kind of interactive intramacrophage behaviour
  Cossu, BMC microbiology 2012
  • “...for the protein folding along with resistance factors such as acid resistance membrane protein ( MAP1317c ) for resistance to acids and three entries of acyltransferase 3 ( MAP3276c MAP3514 MAP1271c ) required for peptidoglycan O-acylation in order to increase its resistance [ 48 ]. There...”
  • “...) that are repressed. The stress metabolism shows an up-regulation of acid-resistance membrane protein ( MAP1317c ) specific for resistance to acidic environment, uspA ( MAP1754c ) and two entries for the repair of damaged DNA such as recR and end . On the other hand,...”

Rv1624c Probable conserved membrane protein from Mycobacterium tuberculosis H37Rv
3 alignments in 29:194 / 195 (85.1%), covering up to 98.6% of PF03729, 83.6 bits

• Inhibition of apoptosis by Rv2456c through Nuclear factor-κB extends the survival of Mycobacterium tuberculosis
  Jurcic, International journal of mycobacteriology 2016
  • “...that may interact or have homology with other genes identified in the literature. For example, Rv1624c (FID12) is a conserved hypothetical protein with some similarity to M. tuberculosis NuoK. This gene lies in an operon with NuoG, part of a nicotinamide adenine dinucleotide + hydrogen dehydrogenase...”
  • “...protein 10 Rv0110 Probable conserved integral membrane transport protein 11 Rv2019 Unknown, conserved protein 12 Rv1624c Probable conserved membrane protein, similarity to nuoK 13 Rv1781c malQ Probable 4-alpha-glucanotransferase 14 Rv2663 Hypothetical protein 15 Rv2141c Conserved protein 16 Rv3738c PPE66 Unknown 17 Rv1704c cycA Probable D-serine/alanine/glycine transporter...”
• Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (DevR) dormancy regulon
  Ranganathan, Nucleic acids research 2016
  • “...competitor DNA; Lane denoted NS was supplemented with a 40 bp DNA fragment upstream of Rv1624c, as non-specific competitor DNA. ( D ) DNase I footprinting assay with His-Cmr using 1C1 DNA as template. 1C1 DNA was digested in the absence of Cmr (lane indicated )...”
• Dysregulation of serine biosynthesis contributes to the growth defect of a Mycobacterium tuberculosis crp mutant
  Bai, Molecular microbiology 2011
  • “...Bai et al ., 2005 ); 4, a 40 bp DNA sequence upstream of the Rv1624c orf that does not contain a CRP Mt -binding site, which is used as a negative control; 5, native serC -Rv0885 motif probe; 6, modified G4-to-C; and 7, modified C17-to-G....”
• Characterization of Mycobacterium tuberculosis Rv3676 (CRPMt), a cyclic AMP receptor protein-like DNA binding protein
  Bai, Journal of bacteriology 2005
  • “...by EMSA. A 40-bp intergenic DNA fragment upstream of Rv1624c was used as a nonspecific control. The presence of CRPMt retarded, in a dose-dependent manner, the...”
  • “...DNA, but not by the 40-bp intergenic DNA upstream of Rv1624c (1624c) that was used as a negative control. This control Rv1624c DNA probe also failed to bind to...”
• Cloning and expression of multiple integral membrane proteins from Mycobacterium tuberculosis in Escherichia coli
  Korepanova, Protein science : a publication of the Protein Society 2005
  • “...Rv1440 Rv1446c Rv1459c Rv1487 Rv1567c Rv1607 Rv1616 Rv1624c Rv1634 Rv1635c Rv1819c Rv1824 Rv1857 Rv1861 Rv1892 Rv1902c Rv1924c Rv1974 Rv2076c Rv2144c Rv2146c...”
• Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis
  Kana, Journal of bacteriology 2001
  • “...open reading frame that is highly homologous to the Rv1624c gene from M. tuberculosis (7), preceded by a further 962 bp of upstream sequence. The PstI fragment...”
  • “...open reading frame that showed high homology to Rv1624c from M. tuberculosis was found upstream of cydA, confirming that the genetic organization at this...”

EF0025 membrane protein, putative from Enterococcus faecalis V583
3 alignments in 15:175 / 175 (92.0%), covering up to 100.0% of PF03729, 82.7 bits

• The cell wall-targeting antibiotic stimulon of Enterococcus faecalis
  Abranches, PloS one 2014
  • “...and a peptidyl-prolyl cis-trans isomerase (EF1534). (D) EF0026 is flanked by a putative membrane protein (EF0025) and a putative transcriptional regulator (EF0027) whereas EF0024 and EF0023 encode a hypothetical protein and a mannose-fructose-sorbose PTS porter, respectively. Under standard growth conditions, e.g. brain heart infusion (BHI) broth...”
• Growth rate-dependent control in Enterococcus faecalis: effects on the transcriptome and proteome, and strong regulation of lactate dehydrogenase
  Mehmeti, Applied and environmental microbiology 2012
  • “...These genes encode a putative membrane protein (EF0025), a major facilitator family transporter (EF0082), L-lactate dehydrogenase ldh-1 (EF0255), putative...”
• Genetic variation and evolution of the pathogenicity island of Enterococcus faecalis
  McBride, Journal of bacteriology 2009
  • “...by CHEF analysis and probed with portions of PAI gene EF0025, a gene highly related in sequence to that encoding open reading frame 8 of pAM373 (8). Using a...”
  • “...rRNA gene, to identify chromosomal fragments and for EF0025 to localize to the pAM373-like sequence to either a chromosomal fragment or the extrachromosomal...”

CPE2079 hypothetical protein from Clostridium perfringens str. 13
CPF_2336 hypothetical protein from Clostridium perfringens ATCC 13124
3 alignments in 11:164 / 164 (93.9%), covering up to 100.0% of PF03729, 81.9 bits

• Comparative transcription analysis and toxin production of two fluoroquinolone-resistant mutants of Clostridium perfringens
  Park, BMC microbiology 2013
  • “...1.9 CPE0495 CPF_0468 UDP-glucose/GDP-mannose dehydrogenase family 3.5 2.4 CPE2059 CPF_2316 putative membrane protein 7.1 3.2 CPE2079 CPF_2336 putative membrane protein 14.2 2.1 CPE0785 CPF_0787 putative membrane protein 2.3 2.1 Energy metabolism CPE2186 CPF_2451 ( atpE ) ATP synthase epsilon subunit 3.3 2.9 CPE2187 CPF_2452 ( atpB...”
• Comparative transcription analysis and toxin production of two fluoroquinolone-resistant mutants of Clostridium perfringens
  Park, BMC microbiology 2013
  • “...CPE0495 CPF_0468 UDP-glucose/GDP-mannose dehydrogenase family 3.5 2.4 CPE2059 CPF_2316 putative membrane protein 7.1 3.2 CPE2079 CPF_2336 putative membrane protein 14.2 2.1 CPE0785 CPF_0787 putative membrane protein 2.3 2.1 Energy metabolism CPE2186 CPF_2451 ( atpE ) ATP synthase epsilon subunit 3.3 2.9 CPE2187 CPF_2452 ( atpB )...”

YP_2910 putative membrane protein from Yersinia pestis biovar Medievalis str. 91001
YPO0590 putative membrane protein from Yersinia pestis CO92
YPTB3468 putative HdeD-like membrane protein. from Yersinia pseudotuberculosis IP 32953
2 alignments in 26:154 / 189 (68.3%), covering up to 98.6% of PF03729, 80.8 bits

• TyrR, the regulator of aromatic amino acid metabolism, is required for mice infection of Yersinia pestis
  Deng, Frontiers in microbiology 2015
  • “...3.7 Hypothetical protein YP_pCD82 sycE pCD1 plasmid 57327 57719 + 3.8 Putative YopE chaperone SycE YP_2910 hdeD Chromosome 3232385 3232954 3.9 6.1 Acid-resistance membrane protein YP_pCRY17 pCRY plasmid 13516 13914 + 3.9 Hypothetical protein YP_pCD41 yscP pCD1 plasmid 29542 30909 4.2 Putative type III secretion protein...”
• A multi-omic systems approach to elucidating Yersinia virulence mechanisms
  Ansong, Molecular bioSystems 2013
  • “...(psaABC; Suppl. Figure 1 ). The fourth chromosomally-encoded gene is an acid resistance membrane protein (YPO0590). The pH6 antigen (Psa) is conserved across pathogenic Yersinia species and is thought to contribute to both YP and YPT virulence in the mammalian host. In YPT, Psa was reported...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...conserved hypothetical protein 0.768 (0.028) 0.753 (0.019) YPTB3429 YPO0626 Conserved hypothetical 0.619 (0.034) YPTB3468 (hdeD) YPO0590 putative membrane protein 0.209 (< 0.001) YPTB3484 YPO0572 putative exported protein 0.533 (0.013) YPTB3485 (yqjD) YPO0570 putative membrane protein 0.674 (0.02) 0.576 (0.002) YPTB3486 YPO0569A 0.606 (0.026) YPTB3510 YPO3565 putative...”
• Temporal global changes in gene expression during temperature transition in Yersinia pestis
  Motin, Journal of bacteriology 2004
  • “...islands displaying differential expression included YPO0590, YPO0595-0597, YPO0623-0628, YPO0881, YPO1091, and YPO1242-1252. These genes are typically...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPTB3403 YPO0659 conserved hypothetical protein 0.768 (0.028) 0.753 (0.019) YPTB3429 YPO0626 Conserved hypothetical 0.619 (0.034) YPTB3468 (hdeD) YPO0590 putative membrane protein 0.209 (< 0.001) YPTB3484 YPO0572 putative exported protein 0.533 (0.013) YPTB3485 (yqjD) YPO0570 putative membrane protein 0.674 (0.02) 0.576 (0.002) YPTB3486 YPO0569A 0.606 (0.026) YPTB3510...”

blr7327 blr7327 from Bradyrhizobium japonicum USDA 110
2 alignments in 46:171 / 208 (60.6%), covering up to 100.0% of PF03729, 79.6 bits

• Identification of the Important Genes of Bradyrhizobium diazoefficiens 113-2 Involved in Soybean Nodule Development and Senescence
  Yuan, Frontiers in microbiology 2021
  • “...113-2GL001126 113-2GL004687 blr4637,blr7961 MCHK_RS12390 , SM2011_RS03045 Nitrogen fixation MCHK_RS18535 113-2GL001654 blr7491 MCHK_RS11600 Nodule senescence 113-2GL001841 blr7327 MAFF_RS27500 Nodule senescence 113-2GL001851 blr7321 MAFF_RS27480 SM2011_RS04580 Nodule senescence 113-2GL001863 bll7310 MAFF_RS27520 MCHK_RS18460 SM2011_RS04570 , Nodule senescence SM2011_RS01895 113-2GL002091 bsl7109 SM2011_RS33980 Nitrogen fixation 113-2GL002109 blr7089 MCHK_RS17580 SM2011_RS03405 Nodule senescence 113-2GL002468...”
• Metabolomic Profiling of Bradyrhizobium diazoefficiens-Induced Root Nodules Reveals Both Host Plant-Specific and Developmental Signatures
  Lardi, International journal of molecular sciences 2016
  • “...hypothetical protein 4.2 blr2505 hypothetical protein 4.3 blr6172 hypothetical protein 4.7 blr7321 hypothetical protein 4.3 blr7327 hypothetical protein 6.0 bsr1749 hypothetical protein 4.4 Intracellular trafficking, secretion, and vesicular transport blr1813 RhcJ protein rhcJ 5.7 blr1819 RhcR protein rhcR 4.5 bsr1820 RhcS protein rhcS 4.9 Other bll1634...”

blr2987 blr2987 from Bradyrhizobium japonicum USDA 110
2 alignments in 41:167 / 205 (62.0%), covering up to 98.6% of PF03729, 79.3 bits

• Comprehensive assessment of the regulons controlled by the FixLJ-FixK2-FixK1 cascade in Bradyrhizobium japonicum
  Mesa, Journal of bacteriology 2008
  • “...bll2471 blr2659 bll2662 bsr2670 blr2761 blr2763 blr2767 blr2987 bsr3073 bll3835 bll6987 bsr7036 bll7086 bsr7087 blr7345 bsl7372 bll7553 bsl7781 bll7787 blr7961...”

KQ76_RS13890 HdeD family acid-resistance protein from Staphylococcus aureus
3 alignments in 14:170 / 170 (92.4%), covering up to 100.0% of PF03729, 75.2 bits

• Efficacy of Antimicrobial Peptide DP7, Designed by Machine-Learning Method, Against Methicillin-Resistant Staphylococcus aureus
  Zhang, Frontiers in microbiology 2019
  • “...in upregulation of the carotenoid biosynthetic pathway (GO:0016117)-related genes and lysostaplin resistance protein A (lyra, KQ76_RS13890) and toxin (KQ76_RS11290). The Growth Inhibitory Rate of DP7 on S. aureus RN4220 Was Lower Than That in S. aureus ATCC 25923 In this section, we used RT-PCR to verify...”

NWMN_2597 hypothetical protein from Staphylococcus aureus subsp. aureus str. Newman
SAOUHSC_03035 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_2632 hypothetical protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
3 alignments in 14:170 / 170 (92.4%), covering up to 100.0% of PF03729, 74.3 bits

• Transcriptional Response of Staphylococcus aureus to Sunlight in Oxic and Anoxic Conditions
  McClary, Frontiers in microbiology 2018
  • “...protein 0.22 5.0 NWMN_2088 Conserved hypothetical protein 0.22 9.9 ebpS Elastin binding protein 0.22 0.5 NWMN_2597 Conserved hypothetical protein 0.22 8.8 citZ Citrate synthase II 0.21 9.9 NWMN_2548 Conserved hypothetical protein 0.21 3.2 qoxC Quinol oxidase polypeptide III 0.21 2.4 NWMN_2087 Conserved hypothetical protein 0.21 11.1...”
• Genomic and Long-Term Transcriptomic Imprints Related to the Daptomycin Mechanism of Action Occurring in Daptomycin- and Methicillin-Resistant Staphylococcus aureus Under Daptomycin Exposure
  Cafiso, Frontiers in microbiology 2020
  • “...the GO Cellular Component term (GO-CC): 0016021in the CM, whereas over-expression was recorded only in SAOUHSC_03035 integral membrane protein. Metabolism A complex network involving differential expression was shown in metabolic genes. As regards the generation of precursor metabolites and energy, L -lactate dehydrogenase-2 encoding gene ldh...”
• Cigarette Smoke Extract-Exposed Methicillin-Resistant Staphylococcus aureus Regulates Leukocyte Function for Pulmonary Persistence
  Kulkarni, American journal of respiratory cell and molecular biology 2016
  • “...arginine deiminase SAUSA300_0971 SAUSA300_2573 SAUSA300_2632 SAUSA300_1938 SAUSA300_2566 SAUSA300_0970 SAUSA300_0969 SAUSA300_0786 SAUSA300_2097 SAUSA300_0968...”
  • “...C xpt tyrS treP sbi SAUSA300_2632 SAUSA300_2511 SAUSA300_2510 SAUSA300_2489 SAUSA300_2454 SAUSA300_2453 SAUSA300_2415 SAUSA300_2379 SAUSA300_2343 SAUSA300_2321...”

SA2491 hypothetical protein from Staphylococcus aureus subsp. aureus N315
3 alignments in 14:170 / 170 (92.4%), covering up to 100.0% of PF03729, 73.7 bits

• The C-terminal region of the RNA helicase CshA is required for the interaction with the degradosome and turnover of bulk RNA in the opportunistic pathogen Staphylococcus aureus
  Giraud, RNA biology 2015
  • “...2.5 2.1 2.7 2.7 SA2487 Uncharacterized protein, similar to transporter SA2487 2.1 2.1 2.1 2.1 SA2491 Uncharacterized protein SA2491 2.4 2.1 1.3 9.4 SA2495 Uncharacterized protein, similar to Cro/Cl family transcriptional regulator SA2495 2.6 2.5 1.7 2.0 Destabilized mRNAs SA0156 SA0144-SA0159 Capsular polysaccharide synthesis enzyme Cap5M...”
• Mutation of RNA polymerase β-subunit gene promotes heterogeneous-to-homogeneous conversion of β-lactam resistance in methicillin-resistant Staphylococcus aureus
  Aiba, Antimicrobial agents and chemotherapy 2013
  • “...SA0830 SA1002 SA1049 SA1222 SA1268 SA1664 SA1755 SA2299 SA2491 a b ssl11 sdrC IP-H5/N315IP N315rpoB(N967I)/ N315 Similar to comF operon protein 3 Similar to...”
• Direct targets of CodY in Staphylococcus aureus
  Majerczyk, Journal of bacteriology 2010
  • “...postexponential growth and include positions near capK, SA2491 (a conserved hypothetical protein), and sspB1 (a cysteine protease precursor). The fact that...”
• Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
  Anderson, FEMS immunology and medical microbiology 2010
  • “...SA2197 putative surface protein sa_c5458s4723_a_at 3.4 2.5 15 SA2365 hypothetical protein sa_c5906s5139_a_at 4.1 2.5 2.5 SA2491 hypothetical protein sa_c10236s10653_at 4.7 ND 2.5 SA2547 hypothetical protein sa_c6206s5387_a_at * 21.1 ND 2.5 SA2571 hypothetical protein sa_c6248s5424_a_at 2.2 ND 2.5 SA2580 hypothetical protein sa_c6312s5485_a_at 3.2 2.5 2.5 SA2601 hypothetical...”
• Insights into the mode of action of chitosan as an antibacterial compound
  Raafat, Applied and environmental microbiology 2008
  • “...SA0772 SA0890 SA1942 SA0536 SA1162 SA1476 SA1665 SA2049 SA2491 SA2221 SA2268 Functiona Gene VOL. 74, 2008 ANTIBACTERIAL MODE OF ACTION OF CHITOSAN DISCUSSION...”
• Transcription profiling-based identification of Staphylococcus aureus genes regulated by the agr and/or sarA loci
  Dunman, Journal of bacteriology 2001
  • “...SA1319 SA1379 SA1436 SA1684 SA2128 SA2161 SA2321 SA2343 SA2491 SAS013 SAS016 SA0309 SA1007 SAS065 SA2209 SA2208 SA2463 SA2284 Unknown Unknown Unknown Unknown...”
  • “...SA1611 SA1684 SA1889 SA1928 SA1944 SA2161 SA2321 SA2343 SA2491 SAS016 SA2291 SA2291 SA1007 SAS065 SA2209 SA2208 SA2447 SA2006 Sar boxg Yes Yes Upstream Yes...”

VFMJ11_A0408 DUF308 domain-containing protein from Aliivibrio fischeri MJ11
VFMJ11_A0408 hypothetical protein from Vibrio fischeri MJ11
2 alignments in 20:146 / 186 (68.3%), covering up to 100.0% of PF03729, 73.7 bits

• Host-selected mutations converging on a global regulator drive an adaptive leap towards symbiosis in bacteria
  Pankey, eLife 2017
  • “...0.0000 0.6 5.10 0.2727 VFMJ11_A0398 1.4 7.07 0.0000 0.0 6.06 0.9926 HTH-type transcriptional regulator GalR VFMJ11_A0408 1.5 3.36 0.0010 0.6 3.62 0.5359 VFMJ11_A0487 1.4 7.99 0.0000 0.2 7.09 0.7403 Pts system N-acetylglucosamine-specific iibc component VFMJ11_A0619 0.7 8.61 0.0099 0.2 8.16 0.6350 ABC-type multidrug transport system ATPase...”

RSP_6139 hypothetical protein from Rhodobacter sphaeroides 2.4.1
2 alignments in 9:136 / 174 (73.6%), covering up to 100.0% of PF03729, 72.8 bits

• Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides
  Burger, mSystems 2017
  • “...sirohydrochlorin under aerobic conditions. Another hypothetical protein identified as essential for aerobic growth in SMM, RSP_6139, is likely to be involved in amino acid biosynthesis since it is potentially cotranscribed with genes encoding the two subunits of the isopropylmalate isomerase ( leuD and leuC ) in...”

SAR2780 putative membrane protein from Staphylococcus aureus subsp. aureus MRSA252
3 alignments in 14:170 / 170 (92.4%), covering up to 100.0% of PF03729, 72.7 bits

• A functional menadione biosynthesis pathway is required for capsule production by Staphylococcus aureus
  Altwiley, Microbiology (Reading, England) 2021
  • “...SAR0994 and tRNA-Ser 0.039515902 SAR2006 conserved hypothetical protein 0.039515902 SAR0636 putative membrane protein (pseudogene) 0.039515902 SAR2780 putative membrane protein 0.039515902 SAR1141 Similar to Staphylococcus aureus exotoxin 0.039515902 SAR1670 conserved hypothetical protein 0.039515902 SAR1685 putative biotin carboxylase subunit of acetyl-CoA carboxylase 0.039515902 lysS lysyl-tRNA synthetase 0.039515902 Intergenic...”
• The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications
  Kenny, PloS one 2009
  • “...protein 4.21 2.06E-03 SAR2740 conserved hypothetical protein 2.05 3.09E-02 SAR2777 putative DNA-binding protein 2.40 1.90E-03 SAR2780 putative membrane protein 7.38 4.80E-04 10.1371/journal.pone.0004344.t002 Table 2 MRSA252 genes down-regulated following the addition of linoleic acid (0.1 mM) to exponentially growing cells (linoleic acid challenge). Group Functions MRSA 252...”

ZMO1533 hypothetical protein from Zymomonas mobilis subsp. mobilis ZM4
2 alignments in 16:140 / 182 (68.7%), covering up to 98.6% of PF03729, 72.6 bits

• Investigation of the impact of a broad range of temperatures on the physiological and transcriptional profiles of Zymomonas mobilis ZM4 for high-temperature-tolerant recombinant strain development
  Li, Biotechnology for biofuels 2021
  • “...pyridine nucleotide-disulfide oxidoreductase 1.62 8.34 ZMO1237 Lactate dehydrogenase 2.82 9.39 ZMO1522 TonB-dependent receptor 1.01 3.88 ZMO1533 Hypothetical protein 3.01 12.07 ZMO1754 Succinate-semialdehyde dehydrogenase SSADH 3.95 11.33 ZMO1776 Aminopeptidase N 1.97 9.64 ZMO1940 Hypothetical protein 4.87 7.45 ZMO0003 Adenylyl-sulfate kinase 1.23 2.12 ZMO0246 ATP-dependent protease subunit HslV...”

EF0397 conserved hypothetical protein from Enterococcus faecalis V583
3 alignments in 18:171 / 171 (90.1%), covering up to 94.5% of PF03729, 70.7 bits

• Genes Contributing to the Unique Biology and Intrinsic Antibiotic Resistance of Enterococcus faecalis
  Gilmore, mBio 2020
  • “...in nutrient broth that warranted classification here as Critical or Important. These include genes EF0394, EF0397, EF0990, EF1043, EF1146, EF2923, and EF3061 (all Fitness Critical) and EF1195, EF1316, EF1724, EF1752, EF1753, EF2606, and EF3086 (Fitness Important) ( Data Set S1 ). Most encode unknown functions, whereas...”
  • “...( Data Set S8c ). Most of these genes lack known function (10/12). Half (EF0394, EF0397, EF1375, EF1190, EF1250, and EF1934) contribute to fitness in the absence of challenge and are discussed above. Genes EF1141, EF1610, EF1909, EF2149, and EF2789 contribute to fitness only in the...”

MAFF_RS27500 HdeD family acid-resistance protein from Mesorhizobium japonicum MAFF 303099
2 alignments in 20:145 / 182 (69.2%), covering up to 100.0% of PF03729, 70.5 bits

• Identification of the Important Genes of Bradyrhizobium diazoefficiens 113-2 Involved in Soybean Nodule Development and Senescence
  Yuan, Frontiers in microbiology 2021
  • “...113-2GL004687 blr4637,blr7961 MCHK_RS12390 , SM2011_RS03045 Nitrogen fixation MCHK_RS18535 113-2GL001654 blr7491 MCHK_RS11600 Nodule senescence 113-2GL001841 blr7327 MAFF_RS27500 Nodule senescence 113-2GL001851 blr7321 MAFF_RS27480 SM2011_RS04580 Nodule senescence 113-2GL001863 bll7310 MAFF_RS27520 MCHK_RS18460 SM2011_RS04570 , Nodule senescence SM2011_RS01895 113-2GL002091 bsl7109 SM2011_RS33980 Nitrogen fixation 113-2GL002109 blr7089 MCHK_RS17580 SM2011_RS03405 Nodule senescence 113-2GL002468 bll6756...”

DR76_RS05080, EcF11_5238 acid-resistance protein HdeD from Escherichia coli ATCC 25922
c4322 HdeD protein from Escherichia coli CFT073
2 alignments in 26:154 / 190 (67.9%), covering up to 98.6% of PF03729, 68.7 bits

• Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken
  Hussain, Scientific reports 2017
  • “...0.02 DR76_RS05085 HdeA Acid-resistance protein HdeA 5.30 0.01 DR76_RS05090 HdeB Acid-resistance protein HdeB 5.17 0.01 DR76_RS05080 HdeD Acid-resistance protein HdeD 5.81 0.01 DR76_RS20000 BhsA Multiple stress resistance protein BhsA 1.30 0.01 DR76_RS04045 IbpB Heat shock chaperone IbpB 2.80 0.01 DR76_RS04040 IbpA Heat shock protein IbpA 1.91...”
• Combining quantitative genetic footprinting and trait enrichment analysis to identify fitness determinants of a bacterial pathogen
  Wiles, PLoS genetics 2013
  • “.../ in vitro Stress adaptation and symbiosis [36] Sinorhizobium meliloti / in vivo plant model EcF11_5238 hdeD 0.0128 4.80 blood,PC Hypothetical Acid stress regulon [54] E. coli K12 lab strain/ in vitro EcF11_1255 lrhA 0.0001 3.35 blood,PC Hypothetical Regulation of virulence genes [31] EHEC/ in vitro...”
• Transcriptional responses of uropathogenic Escherichia coli to increased environmental osmolality caused by salt or urea
  Withman, Infection and immunity 2013
  • “...genes hdeB, hdeA, and hdeD (c3420, c4321, and c4322, 1.0, 0.3). Among the latter were transcriptional regulator cbl (c2447, 0.6, 0.3), sulfate adenyl...”

LSA0208 Hypothetical integral membrane protein from Lactobacillus sakei subsp. sakei 23K
3 alignments in 16:178 / 178 (91.6%), covering up to 97.3% of PF03729, 68.6 bits

• Global transcriptome response in Lactobacillus sakei during growth on ribose
  McLeod, BMC microbiology 2011
  • “...LSA0191 lsa0191 Hypothetical integral membrane protein -0.6 -0.6 LSA0199 lsa0199 Hypothetical protein 1.1 1.0 1.1 LSA0208 lsa0208 Hypothetical integral membrane protein 0.7 LSA0235 lsa0235 Hypothetical extracellular protein precursor 2.1 1.6 1.7 LSA0236 lsa0236 Hypothetical extracellular peptide precursor 2.0 1.3 1.5 LSA0244 lsa0244 Hypothetical integral membrane protein...”

YhiA / b3511 acid-resistance membrane protein from Escherichia coli K-12 substr. MG1655 (see 2 papers)
hdeD / RF|NP_417968 protein hdeD from Escherichia coli K12 (see 2 papers)
b3511 acid-resistance membrane protein from Escherichia coli str. K-12 substr. MG1655
NP_417968 acid-resistance membrane protein from Escherichia coli str. K-12 substr. MG1655
Z4923 orf, hypothetical protein from Escherichia coli O157:H7 EDL933
ECs4391 hypothetical protein from Escherichia coli O157:H7 str. Sakai
BHW77_01320 acid-resistance protein HdeD from Escherichia coli
2 alignments in 26:154 / 190 (67.9%), covering up to 98.6% of PF03729, 68.4 bits

• Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes
  Santos-Zavaleta, BMC genomics 2019
  • “...TorR(+) + MSI [ 10 ] response to pH change, cellular response to stress hdeD b3511 hdeD GadE(+), GadX(+), H-NS(), PhoP(+),RcsB(+) + MSI [ 10 ] response to pH change hdhA b1619 hdhA + GEA, IMP [ 11 ] lipid metabolic process, metabolic process, steroid metabolic...”
• Functional genomics analysis of free fatty acid production under continuous phosphate limiting conditions
  Youngquist, Journal of industrial microbiology & biotechnology 2017
  • “...1.6 10 2 DNA-binding transcriptional activator b3509 hdeB 4.9 8.1 10 3 acid resistance protein b3511 hdeD 6.8 3.6 10 2 acid-resistance membrane protein b0186 ldcC 3.1 2.7 10 2 lysine decarboxylase 2 b3506 slp 7.2 2.8 10 2 starvation lipoprotein b3508 yhiD 7.9 3.7 10...”
• Effect of Global Regulators RpoS and Cyclic-AMP/CRP on the Catabolome and Transcriptome of Escherichia coli K12 during Carbon- and Energy-Limited Growth
  Franchini, PloS one 2015
  • “...channel 6.0 feoA b3408 ferrous iron transport protein A -4.9 ** hdeD b , e b3511 putative transporter protein 11.5 dppA b3544 dipeptide transport protein 11.9 rbsD g , i b3748 D-ribose high-affinity transport system, membrane-associated protein 3.6 rbsB g b3751 D-ribose periplasmic binding protein 9.4...”
• Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage
  Royce, PloS one 2014
  • “...b3512 gadE 0.004 0.115 10.1 TA of AR2 b1492 gadC 0.000 0.013 9.3 AR2 antiporter b3511 hdeD 0.001 0.053 8.7 AR1 b1480 sra 0.001 0.009 5.1 SP component of the 30S ribosomal subunit b3508 yhiD 0.001 0.017 4.5 density-dependent acid resistance b0812 dps 0.004 0.101 4.4...”
• Global transcriptomic analysis of an engineered Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system during shikimic acid production in rich culture medium
  Cortés-Tolalpa, Microbial cell factories 2014
  • “...of acid-resistance protein Stress response 125.3695 hdeB b3509 Acid stress chaperone Stress response 104.9129 hdeD b3511 Acid-resistance membrane protein Stress response 140.6337 katE b1732 Heme d synthase/hydroperoxidase Stress response 15.6533 cysD b2752 Polypeptide: CysD Sulfur metabolism 34.5193 cysH b2762 3-Phospho-adenylylsulfate reductase Sulfur metabolism 15.6801 hisP b2306...”
• Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding
  Myers, PLoS genetics 2013
  • “...(Category 2) 3,656,030 gadE b3512 Transcriptional Activator 2 22.5 + + None [18] 3,654,924 hdeD b3511 Acid-Resistance Membrane Protein 1 43.5 + + None [18] 121,987 pdhR-aceEF-lpdA b0113 Pyruvate Dehydrogenase 1 50.5 + [29] [140] 770,404 cydAB b0733 Cytochrome bd -1 Terminal Oxidase 1 53.5 +...”
• Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli
  Santos, Proceedings of the National Academy of Sciences of the United States of America 2012
  • “...resistance rpoD3 Gene name b3517 b1493 b1492 b3512 b3510 b3509 b3511 b3506 rpoA27 Gene ID Function Log fold change Q value*, % Log fold change Q value, % gadA...”
• Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
  Lee, Applied and environmental microbiology 2009
  • “...hdeB hdeA hdeD b1166 b1167 b1492 b1493 b3516 b3517 b3509 b3510 b3511 4.9 4.0 14.9 32.0 5.7 21.1 19.7 14.9 11.3 3.7 3.7 3.0 3.5 2.5 3.5 3.2 3.2 2.6 AriR,...”
• More
• Contrasting silencing mechanisms of the same target mRNA by two regulatory RNAs in Escherichia coli.
  Lalaouna, Nucleic acids research 2018
  • GeneRIF: Both CyaR and RprA can block the translation initiation of hdeD but only CyaR induces mRNA decay.
• Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism
  Sharma, BMC microbiology 2017
  • “...Z4890 Inner membrane protein 14.43 0.01 yhiD Z4920 Mg 2+ transport ATPase 12.48 0.01 hdeD Z4923 Acid-resistance membrane protein 13.47 5.0E-03 gadA Z4930 Glutamate decarboxylase 13.99 0.01 Oxidative stress ybjW Z1107 Hydroxylamine reductase +1.98 0.01 marA Z2170 Transcriptional activator 1.52 0.04 marR Z2171 Transcriptional regulator 1.56...”
• Involvement of PatE, a prophage-encoded AraC-like regulator, in the transcriptional activation of acid resistance pathways of enterohemorrhagic Escherichia coli strain EDL933
  Bender, Applied and environmental microbiology 2012
  • “...Z0604 Z1649 Z2215 Z2216 Z4908 Z4921 Z4922 Z4923 Z4925 Z4926 ybaR P-type ATPase Hypothetical protein Glutamate decarboxylase isozyme Glutamate-GABAc antiporter...”
• RcsB contributes to the distinct stress fitness among Escherichia coli O157:H7 curli variants of the 1993 hamburger-associated outbreak strains
  Carter, Applied and environmental microbiology 2012
  • “...hdeA hdeD gadA Z2216 Z4890 Z4920 Z4921 Z4922 Z4923 Z4930 Acid sensitivity protein Hypothetical protein related to acid resistance Putative Mg2 transport ATPase...”
• Transcriptional responses of Escherichia coli K-12 and O157:H7 associated with lettuce leaves
  Fink, Applied and environmental microbiology 2012
  • “...Z1117 Z1406 Z2330 Z5182 Z3862 Z2216 Z4661 Z2950 Z4922 Z4921 Z4923 Z5479 Z2435 Z4895 Z4930 Z2216 Z4925 Z4928 cspE cspA cspD cspG hslJ ibpB yfiD xasA mscL otsB...”
• Differential expression of virulence and stress fitness genes between Escherichia coli O157:H7 strains with clinical or bovine-biased genotypes
  Vanaja, Applied and environmental microbiology 2010
  • “...and AFI genes ECs2097 ECs2098 ECs4377 ECs4389 ECs4390 ECs4391 ECs4392 ECs4394 ECs4395 ECs4397 64 KAILASAN VANAJA ET AL. APPL. ENVIRON. MICROBIOL. TABLE 3....”
• Characterization of the Escherichia coli O157:H7 Sakai GadE regulon
  Kailasan, Journal of bacteriology 2009
  • “...2017 by University of California, Berkeley ECs4389 ECs4390 ECs4391 ECs4397 ECs2097 ECs2098 Geneb GadE REGULON IN E. COLI O157:H7 VOL. 191, 2009 script levels...”
• Global regulation by horizontally transferred regulators establishes the pathogenicity of Escherichia coli
  Abe, DNA research : an international journal for rapid publication of reports on genes and genomes 2008
  • “...hdeB Hypothetical protein K12 P + L ECs4390 hdeA Hypothetical protein K12 P + L ECs4391 hdeD Hypothetical protein K12 P + L ECs4392 yhiE Hypothetical protein K12 P + L ECs4393 yhiU Putative membrane protein K12 P + L ECs4395 gadW Putative ARAC-type regulatory protein...”
• Genomewide transcriptional response of Escherichia coli O157:H7 to norepinephrine
  Sharma, BMC genomics 2022
  • “...gadW AraC family transcriptional regulator + 2.37 7.84E-04 BHW77_01315 gadE transcriptional regulator + 3.72 5.69E-07 BHW77_01320 hdeD protein + 4.76 9.22E-05 BHW77_01325 hdeA acid stress chaperone + 3.46 9.30E-05 BHW77_01330 hdeB acid stress chaperone + 3.94 8.70E-07 BHW77_14105 gadB glutamate decarboxylase + 4.36 1.09E-03 BHW77_14110 gadC...”

EC042_RS20255 acid-resistance protein HdeD from Escherichia coli 042
2 alignments in 26:154 / 190 (67.9%), covering up to 98.6% of PF03729, 68.0 bits

• Overexpression of the third H-NS paralogue H-NS2 compensates fitness loss in hns mutants of the enteroaggregative Escherichia coli strain 042
  Prieto, Scientific reports 2020
  • “...acid stress chaperone HdeA) 222.0 26.1 EC042_RS08380 (type VI secretion system PAAR protein) 221.3 5.6 EC042_RS20255 (putative acid resistance protein HdeD) 219.3 17.8 EC042_RS08045 (porin OmpN) 211.6 4.8 EC042_RS22645 (porin OmpL) 205.7 7.1 NCBI identifier (locus tag) Fold change hns 37C hns 25C (B) EC042_RS08585 (glutamate...”
  • “...fimbrial transcriptional regulator MatA) 22.7 30.6 EC042_RS05780 (tRNA-Ser) 19.3 EC042_RS15335 (DNA-binding protein StpA) 18.6 72.1 EC042_RS20255 (putative acid resistance protein HdeD) 17.8 219.3 EC042_RS20260 (transcriptional regulator GadE) 16.6 154.7 EC042_RS06765 (tRNA-Tyr) 16.3 EC042_RS13160 (hypothetical protein) 15.7 EC042_RS21295 (CesD/SycD/LcrH family type III secretion system chaperone) 15.6 22.9...”

PMI1702 hypothetical protein from Proteus mirabilis HI4320
2 alignments in 26:155 / 192 (67.7%), covering up to 100.0% of PF03729, 67.5 bits

• Transcriptional analysis of the MrpJ network: modulation of diverse virulence-associated genes and direct regulation of mrp fimbrial and flhDC flagellar operons in Proteus mirabilis
  Bode, Infection and immunity 2015
  • “...Pyruvate kinase lysA argB mrpA PMI2157 fruK PMI1079 PMI1702 PMI2292 ptsG PMI0287 PMI2528 hyfA PMI2755 lysC PMI2307 argA PMI0744 PMI0742 PMI2660 caiF PMI2825 def...”

lpp2789 hypothetical protein from Legionella pneumophila str. Paris
2 alignments in 24:150 / 187 (67.9%), covering up to 98.6% of PF03729, 63.8 bits

• Legionella spp. All Ears? The Broad Occurrence of Quorum Sensing Elements outside Legionella pneumophila
  Herran, Genome biology and evolution 2021
  • “...L.pneumophila . The protein sequences of L.pneumophila Paris were used: LqsA (Lpp2787), LqsR (Lpp2788), HdeD (Lpp2789), LqsS (Lpp2790), and LqsT (Lpp2574). All protein candidates obtained from the BLAST analysis are listed in the supplementary table T1 , Supplementary Material online, and corresponding phylogenetic trees are represented...”

lpg2733 Hypothetical protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
2 alignments in 24:150 / 187 (67.9%), covering up to 98.6% of PF03729, 63.8 bits

• Synergistic contribution of the Legionella pneumophila lqs genes to pathogen-host interactions
  Tiaden, Journal of bacteriology 2008
  • “...four ORFs, designated lqsA (lpg2731), lqsR (lpg2732), hdeD (lpg2733), and lqsS (lpg2734). The 5 flanking region contains two ORFs, lpg2730 (dsbB) and lpg2731...”

BAD_1583 hypothetical protein from Bifidobacterium adolescentis ATCC 15703
3 alignments in 115:284 / 285 (59.6%), covering up to 98.6% of PF03729, 60.5 bits

• Metagenomic identification, purification and characterisation of the Bifidobacterium adolescentis BgaC β-galactosidase
  Mulualem, Applied microbiology and biotechnology 2021
  • “...(Fig. 1 ). All the clones shared the -galactosidase BAD_1582 gene and the adjacent five BAD_1583 to BAD_1587 genes. The adjacent genes encoded a sugar transporting permease, required by many bacteria to access sugars for adaptable growth in the gut environment. BAD_1582 -specific PCR, using the...”
  • “...six shared genes. These include the -galactosidase gene (BAD_1582, bgaC ), HdeD family acid-resistance protein (BAD_1583), LacI family transcriptional regulator (BAD_1584), carbohydrate ABC transporter substrate-binding protein (BAD_1585), sugar ABC transporter permease (BAD_1586), and carbohydrate ABC transporter permease (BAD_1587). The numbers at the start and end of...”

BL1731 hypothetical protein from Bifidobacterium longum NCC2705
3 alignments in 161:326 / 326 (50.9%), covering up to 98.6% of PF03729, 58.9 bits

• Differential transcriptional response of Bifidobacterium longum to human milk, formula milk, and galactooligosaccharide
  González, Applied and environmental microbiology 2008
  • “...hypothetical protein and a putative methionine aminopeptidase (BL1731 and BL1732, respectively) could indicate removal of the N-terminal methionine from nascent...”

ACSP50_3940 DUF308 domain-containing protein from Actinoplanes sp. SE50/110
Aligns to 11:83 / 173 (42.2%), covers 98.6% of PF03729, 45.2 bits

• A maltose-regulated large genomic region is activated by the transcriptional regulator MalT in Actinoplanes sp. SE50/110
  Droste, Applied microbiology and biotechnology 2020
  • “..., ACSP50_3908 to ACSP50_3911 , ACSP50_3929 to ACSP50_3930 , ACSP50_3936 to ACSP50_3937 , ACSP50_3938 to ACSP50_3940 , and ACSP50_3949 to ACSP50_3950 . In ACSP50_ malT , a decreased transcription was observed, whereas an overexpression of malT leads to an increased transcription of these operons. The operon...”

LBA0860 hypothetical protein from Lactobacillus acidophilus NCFM
2 alignments in 366:535 / 537 (23.6%), covering up to 98.6% of PF03729, 38.5 bits

• Representational difference analysis and real-time PCR for strain-specific quantification of Lactobacillus sobrius sp. nov
  Konstantinov, Applied and environmental microbiology 2005
  • “...with highest similarity (70% at the AA level) to LBA0860, a hypothetical protein from L. acidophilus (1); C, a 950-bp fragment predicted to code for a...”
  • “...18, 2017 by University of California, Berkeley level) and LBA0860 (70% at the AA level) of L. acidophilus NCFM (1). The other two RDA fragments (Fig. 1,...”

Or search for genetic data about PF03729 in the Fitness Browser