Family Search for PF02698 (DUF218)

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

PF02698 hits 76 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

SACOL2354 membrane protein, putative from Staphylococcus aureus subsp. aureus COL
SA2148 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAUSA300_2304 hypothetical protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
SAFDA_2221 YdcF family protein from Staphylococcus aureus
Aligns to 148:303 / 322 (48.4%), covers 98.5% of PF02698, 114.1 bits

• Further insights into the mode of action of the lipoglycopeptide telavancin through global gene expression studies
  Song, Antimicrobial agents and chemotherapy 2012
  • “...UDP-N-acetylglucosamine 1-carboxylvinyl transferase 2 PBP2 3.2 2.3 SACOL2354 SAV0470 SACOL1194 No data No data pbp1 Membrane protein, putative Conserved...”
• Transcriptional profiling reveals that daptomycin induces the Staphylococcus aureus cell wall stress stimulon and genes responsive to membrane depolarization
  Muthaiyan, Antimicrobial agents and chemotherapy 2008
  • “...SA2147 NA SA1003 NA SA1891 NA Signal transduction SA1457 SA2148 NA NA SA0759 NA SA1457 SA1942 NA vraR SA1943 vraS PTS system, IIA component PTS system,...”
• A New Natural Product Analog of Blasticidin S Reveals Cellular Uptake Facilitated by the NorA Multidrug Transporter
  Davison, Antimicrobial agents and chemotherapy 2017
  • “...substitutions in the untranscribed region (UTR) of tcaR and SAUSA300_2304 and in the coding DNA sequence (CDS) of sufB and SAUSA300_0730 (Table S7). June 2017...”
• Network analysis for identifying potential anti-virulence targets from whole transcriptome of Pseudomonas aeruginosa and Staphylococcus aureus exposed to certain anti-pathogenic polyherbal formulations
  Ruparel, Drug target insights 2023
  • “...transporter permease 2.64 0.01 65 SAFDA_0423 Orn Lys Arg decarboxylase family protein 2.63 1.62E-08 66 SAFDA_2221 Hypothetical protein 2.63 0.008 67 tagX glycosyltransferase 2.58 0.002 68 sraP Serine-rich adhesin for platelets 2.55 7.48E-10 69 SAFDA_2160 Transcription regulator 2.55 0.0003 70 SAFDA_0932 Hypothetical protein 2.53 1.10E-05 71...”

BP2323 conserved hypothetical membrane protein from Bordetella pertussis Tohama I
Aligns to 79:244 / 254 (65.4%), covers 100.0% of PF02698, 113.4 bits

• Posttranscriptional Regulation by Copper with a New Upstream Open Reading Frame
  Roy, mBio 2022
  • “...as proxies for their B. pertussis counterparts to seek Rho-dependent termination sites within the 5UTR- bp2323 -IGR region. Standard transcription termination experiments were performed with E. coli RNAP ( 69 ) with minor modifications. Briefly, DNA template (0.1 pmol), E. coli RNA polymerase (0.3 pmol; New...”
• A gel-free proteomic-based method for the characterization of Bordetella pertussis clinical isolates
  Williamson, Journal of microbiological methods 2012
  • “...BP2197 HP 23 U 25 (3) 47 (6) 32 (4) 35 (4) HP Hypothetical protein BP2323 NP_880961 BP2323 HP 28 U 24 (3) 18 (2) 18 (2) 18 (2) HP Hypothetical protein BP2534 NP_881161 BP2534 HP 58 U 25 (8) 18 (6) 18 (6) 17 (7)...”

SAR2444 putative membrane protein from Staphylococcus aureus subsp. aureus MRSA252
Aligns to 148:303 / 322 (48.4%), covers 98.5% of PF02698, 113.0 bits

• The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications
  Kenny, PloS one 2009
  • “...SAR2392 conserved hypothetical protein 3.03 5.20E-03 SAR2393 putative molydopterin dinucleotide binding domain protein 3.26 2.50E-03 SAR2444 putative membrane protein 4.38 2.77E-04 SAR2469 putative pyridoxamine 5-phosphate oxidase 4.72 1.11E-03 SAR2496 putative solute binding lipoprotein 2.60 3.66E-03 SAR2525 hypothetical protein 5.28 2.33E-05 SAR2532 CapD domain protein 2.48 4.16E-03...”

OG1RF_RS11085 YdcF family protein from Enterococcus faecalis OG1RF
Aligns to 39:184 / 193 (75.6%), covers 79.5% of PF02698, 113.0 bits

• CroR Regulates Expression of pbp4(5) to Promote Cephalosporin Resistance in Enterococcus faecalis
  Timmler, mBio 2022
  • “...which CroR itself as well as 5 CroR-upregulated genes from our transcriptomic data set (OG1RF_RS05385, OG1RF_RS11085, OG1RF_RS08985, OG1RF_RS11045 [ pbpA(2b) ] and OG1RF_RS09755 [ pbp4(5) ]) were found to contribute to cell wall-active antimicrobial resistance ( 28 ). Though a previous study dismissed a link between...”

Ccel_2459 protein of unknown function DUF218 from Clostridium cellulolyticum H10
Aligns to 102:247 / 256 (57.0%), covers 99.2% of PF02698, 112.6 bits

• A Novel Two-Component System, XygS/XygR, Positively Regulates Xyloglucan Degradation, Import, and Catabolism in Ruminiclostridium cellulolyticum
  Kampik, Applied and environmental microbiology 2020 (secret)

LT85_RS04640 YdcF family protein from Collimonas arenae
Aligns to 78:241 / 252 (65.1%), covers 100.0% of PF02698, 111.1 bits

• Identification of Collimonas gene loci involved in the biosynthesis of a diffusible secondary metabolite with broad-spectrum antifungal activity and plant-protective properties
  Akum, Microbial biotechnology 2021
  • “...transporter substratebinding protein WP_038485868.1 LT85_RS04630 3deoxyDmannooct2ulosonic acid (Kdo) hydroxylase WP_038485871.1 LT85_RS04635 3deoxyDmannooctulosonic acid transferase WP_038495045.1 LT85_RS04640 YdcF family protein WP_038485874.1 LT85_RS04645 Glycosyl transferase WP_052134654.1 LT85_RS04650 Oantigen ligase domaincontaining protein WP_038485877.1 LT85_RS04655 UDPglucose 4epimerase GalE subunit WP_038485880.1 a Highlighted in bold is the gene (LT85_RS04520) that carried...”

MXAN_5362 hypothetical protein from Myxococcus xanthus DK 1622
Aligns to 79:246 / 258 (65.1%), covers 100.0% of PF02698, 111.0 bits

• Identification of Functions Affecting Predator-Prey Interactions between Myxococcus xanthus and Bacillus subtilis
  Müller, Journal of bacteriology 2016
  • “...is encoded by an operon spanning MXAN_5365 to MXAN_5362 (see Fig. S4 in the supplemental material) and includes genes encoding HsfB, HsfA (NtrC-like response...”

EF1664 conserved hypothetical protein from Enterococcus faecalis V583
Aligns to 167:317 / 344 (43.9%), covers 100.0% of PF02698, 108.6 bits

• ace, Which encodes an adhesin in Enterococcus faecalis, is regulated by Ers and is involved in virulence
  Lebreton, Infection and immunity 2009
  • “...Berkeley ers ef0082 ef0049 ef0782 ace kat ef1656 ef1664 ef1816 ef2185 ef3146 aceRace1 aceRace2 aceRace3 Prom-ace Prom-ers aceDC-Ub Sequence (5-3)a REGULATION OF...”
  • “...by University of California, Berkeley ef0049 ef0782 ef1099 ef1656 ef1664 ef1816 ef2185 ef3146 Gene name 2835 2836 LEBRETON ET AL. ace is directly regulated by...”

BR1177 hypothetical protein from Brucella suis 1330
BAB1_1199 Protein of unknown function DUF218 from Brucella melitensis biovar Abortus 2308
Aligns to 84:251 / 268 (62.7%), covers 100.0% of PF02698, 108.6 bits

• Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens
  Liang, PLoS neglected tropical diseases 2010
  • “...0.849 VirB8 BMEI0228 BAB1_1830 BR1822 0.719 Hypothetical protein BMEI1890 BAB1_0051 BR0054 0.866 Transporter BMEI0810 BAB1_1199 BR1177 0.918 COG1434 Uncharacterized conserved protein BMEI1060 BAB1_0927 BR0909 0.763 DsbA Protein-disulfide isomerase BMEI0324 BAB1_1726 BR1714 0.822 COG1360 Flagellar Motor Protein BMEI0039 BAB1_2033 BR2032 0.700 Acetyl CoA carboxylase, carboxyltransferase, alpha subunit...”
• Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens
  Liang, PLoS neglected tropical diseases 2010
  • “...BRA0062 0.849 VirB8 BMEI0228 BAB1_1830 BR1822 0.719 Hypothetical protein BMEI1890 BAB1_0051 BR0054 0.866 Transporter BMEI0810 BAB1_1199 BR1177 0.918 COG1434 Uncharacterized conserved protein BMEI1060 BAB1_0927 BR0909 0.763 DsbA Protein-disulfide isomerase BMEI0324 BAB1_1726 BR1714 0.822 COG1360 Flagellar Motor Protein BMEI0039 BAB1_2033 BR2032 0.700 Acetyl CoA carboxylase, carboxyltransferase, alpha...”

BMEI0810 PUTATIVE MEMBRANE PROTEIN from Brucella melitensis 16M
Aligns to 80:247 / 264 (63.6%), covers 100.0% of PF02698, 108.6 bits

• Immuno-profiling of Brucella proteins for developing improved vaccines and DIVA capable serodiagnostic assays for brucellosis
  Nandini, Frontiers in microbiology 2023
  • “...Transporter BMEI1890 30S ribosomal protein S16 BMEI0227 Hypothetical protein BMEI1866 Immunogenic protein BMEI0536 Hypothetical protein BMEI0810 Protease Do BMEI0613 Type I restriction-modification enzyme S subunit BMEII0452 Preprotein translocase subunit SecA BMEI0121 HlyD family secretion protein BR_1060 Periplasmic oligopeptide-binding protein precursor BMEII0735 Nucleoside triphosphate pyrophosphohydrolase BMEI0920 Hypothetical...”
  • “...cattle sera. Protease Do BMEI1330 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase BMEII0684 Immunogenic protein BMEI0536 Hypothetical protein BMEI0810 Protease Do BMEI0613 tRNA pseudouridine synthase B BMEI1963 Membrane fusion protein MTRC BMEI0892 Hypothetical protein BMEI0179 Cell surface protein BMEI1872 Riboflavin synthase subunit beta BMEII0589 2-oxoisovalerate dehydrogenase subunit alpha BMEII0748...”
• Antigen-specific acquired immunity in human brucellosis: implications for diagnosis, prognosis, and vaccine development
  Cannella, Frontiers in cellular and infection microbiology 2012
  • “...containing protein 19,837 BMEII0589 6,7-dimethyl-8-ribityllumazine synthase 2 (riboflavin biosynthesis) 17,356 BMEII0691 Putative binding protein 69,388 BMEI0810 Putative membrane protein 29,529 BMEI0339 Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha 35,013 BMEI0368 Putative uncharacterized protein 12,741 BMEII0704 Bacterioferritin 18,659 BMEI0830 Outer membrane protein 85,919 BMEII1015 Sensor protein (kinase...”
• Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens
  Liang, PLoS neglected tropical diseases 2010
  • “...BAB2_0061 BRA0062 0.849 VirB8 BMEI0228 BAB1_1830 BR1822 0.719 Hypothetical protein BMEI1890 BAB1_0051 BR0054 0.866 Transporter BMEI0810 BAB1_1199 BR1177 0.918 COG1434 Uncharacterized conserved protein BMEI1060 BAB1_0927 BR0909 0.763 DsbA Protein-disulfide isomerase BMEI0324 BAB1_1726 BR1714 0.822 COG1360 Flagellar Motor Protein BMEI0039 BAB1_2033 BR2032 0.700 Acetyl CoA carboxylase, carboxyltransferase,...”

VC1718 conserved hypothetical protein from Vibrio cholerae O1 biovar eltor str. N16961
Aligns to 89:251 / 282 (57.8%), covers 100.0% of PF02698, 106.0 bits

• Impact of Gene Repression on Biofilm Formation of Vibrio cholerae
  Pombo, Frontiers in microbiology 2022
  • “...2 VC1707 Hypothetical protein 1 VC1714-1717 VC1714 Cell division protein MukB, chromosome partition protein 1 VC1718 Hypothetical protein 6 VC1766-1769 VC1766 Hypothetical protein 2 VC1768 Hypothetical protein 1 VC1769 DNA methylase HsdM; type I restriction enzyme M protein 1 VC1784 Neuraminidase, sialidase 1 VC1832 Hypothetical protein...”
• Suppressor Mutations in Type II Secretion Mutants of Vibrio cholerae: Inactivation of the VesC Protease
  Rule, mSphere 2020
  • “...Gluconate permease 100 VC0613 - N -acetylhexosaminidase 100 VC1133 HisD 100 VC1649 VesC 100 SV VC1718 Hypothetical 100 VC2252 BamA 100 VCA0254 Hypothetical 98 VC2701 DsbD SV VC2506 HepA SV VC1915 RpsA SV VC2323 Hypothetical SV a SNP, single-nucleotide polymorphism; SV, structural variant. TABLE2 Identity and...”
  • “...298A>T p. I100F 139 VC0613 - N -acetylhexosaminidase Nonsynonymous 100 c. 1012G>A p. G338S 116 VC1718 Hypothetical Nonsynonymous 100 c. 568G>A p. V190M 67 PU3 VC1133 HisD Synonymous 100 c. 927A>G p.(=) 212 a c. denotes nucleotide change at the indicated position; "p." denotes amino acid...”
• Isolation and characterization of the new mosaic filamentous phage VFJ Φ of Vibrio cholerae
  Wang, PloS one 2013
  • “...Tor, Ogawa 1977 Zhejiang + + ND VC126 O1, El Tor, Ogawa 2004 Liaoning ND VC1718 O1, El Tor, Ogawa 1999 Chongqing + + + 1.510 7 VC1707 O1, El Tor, Ogawa 2004 Liaoning + + + 1.310 5 VC4395 O139 1994 Zhejiang + + +...”

lmo2442 lmo2442 from Listeria monocytogenes EGD-e
Aligns to 39:180 / 189 (75.1%), covers 99.2% of PF02698, 104.6 bits

• Identification of a ferritin-like protein of Listeria monocytogenes as a mediator of β-lactam tolerance and innate resistance to cephalosporins
  Krawczyk-Balska, BMC microbiology 2012
  • “...[ 11 ] showed the same relationship between the induction of expression and significance of lmo2442 and lmo2568 genes in the susceptibility of L . monocytogenes to the -lactam antibiotic cefuroxime. These observations prompted us to attempt to identify L . monocytogenes genes induced in the...”
• The two-component system CesRK controls the transcriptional induction of cell envelope-related genes in Listeria monocytogenes in response to cell wall-acting antibiotics
  Gottschalk, Journal of bacteriology 2008
  • “...threefold by isoproponal (lmo0443. lmo1037, lmo1215, lmo1416, lmo2210, lmo2442, lmo2522, and lmo2812) were amplified by PCR (primers are listed in Table S1 in...”
  • “...3 3 9 9 36 3 12 ND 3 3 8 9 27 3 12 ND Noninducible genes lmo1037 lmo1215 lmo2442 4 5 4 4 5 6 3 4 5 ND ND ND 4 5 4 4 5 5 3 4 3 ND ND ND 3 5 4 4 4 5 4 4 3 ND ND...”

RSUY_31000, RSUY_RS15175 YdcF family protein from Ralstonia solanacearum
Aligns to 68:229 / 251 (64.5%), covers 99.2% of PF02698, 103.9 bits

• Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii
  Puigvert, Frontiers in plant science 2017
  • “...membrane protein RSUY_RS14980 RSUY_30600 RSc0211 2.4077 membrane protein RSUY_RS17045 RSUY_34880 RSp0420 2.58002 membrane protein RSUY_RS15175 RSUY_31000 RSc0146 2.83465 hypothetical protein PUTATIVE VIRULENCE GENES AND PLANT COLONIZATION METABOLIC ACTIVITIES Transporters RSUY_RS00490 RSUY_01050 RSc3386 3.50 metal ABC transporter substrate-binding protein RSUY_RS17605 RSUY_36050 RSp0429 3.24 MFS transporter RSUY_RS20020 RSUY_41100...”
  • “...2.22451 membrane protein RSUY_RS14980 RSUY_30600 RSc0211 2.4077 membrane protein RSUY_RS17045 RSUY_34880 RSp0420 2.58002 membrane protein RSUY_RS15175 RSUY_31000 RSc0146 2.83465 hypothetical protein PUTATIVE VIRULENCE GENES AND PLANT COLONIZATION METABOLIC ACTIVITIES Transporters RSUY_RS00490 RSUY_01050 RSc3386 3.50 metal ABC transporter substrate-binding protein RSUY_RS17605 RSUY_36050 RSp0429 3.24 MFS transporter RSUY_RS20020...”

SC0093 putative secreted protein from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
Aligns to 41:187 / 206 (71.4%), covers 98.5% of PF02698, 101.8 bits

• Prevalence and characterization of genotypic diversity of Haemophilus parasuis isolates from southern China
  Zhang, Canadian journal of veterinary research = Revue canadienne de recherche veterinaire 2012 (secret)

STM14_0118 YdcF family protein from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
STM0098 putative secreted protein from Salmonella typhimurium LT2
Aligns to 41:187 / 206 (71.4%), covers 98.5% of PF02698, 101.8 bits

• T3_MM: a Markov model effectively classifies bacterial type III secretion signals
  Wang, PloS one 2013
  • “...SL1076 STM14_1479 STM2703 SL2715 STM14_2428 STM0909 SL4268 STM14_5051 STM4539 SL0536 STM14_1417 STM4202 SL3702 STM14_0039 SL2941 STM14_0118 SL0277 STM14_0489 STM14_3042 STM14_5206 Discussion It is still an enigma how bacterial type III effectors are specifically recognized and secreted by type III secretion conduits. Previous experimental and bioinformatic analysis...”
• Identification of novel factors involved in modulating motility of Salmonella enterica serotype typhimurium
  Bogomolnaya, PloS one 2014
  • “...Swimming Mean SD Swarming Mean SD STM0026 bcfF 1.320.26 ** 2.550.64 STM0032 1.490.24 1.42 0.75 STM0098 1.650.37 1.460.29 STM0266 1.13 0.35 1.590.45 STM0387 yaiI 1.420.23 1.15 0.25 STM0549 fimZ 1.320.20 1.89 1.13 STM0557 gtrC 1.380.24 2.130.52 STM0573 1.14 0.17 1.640.32 STM0839 1.200.20 1.570.67 STM0847 ybiK 1.530.49...”

EF1366 conserved hypothetical protein from Enterococcus faecalis V583
Aligns to 177:328 / 359 (42.3%), covers 100.0% of PF02698, 101.7 bits

• Mutations associated with reduced surotomycin susceptibility in Clostridium difficile and Enterococcus species
  Adams, Antimicrobial agents and chemotherapy 2015
  • “...the text, EF1367 encodes a predicted cold shock protein. EF1366 and EF1365 encode two membrane proteins of unknown function. The red box indicates where the...”
  • “...result in increased expression of the downstream genes EF1366 and EF1365, which are likely cotranscribed (16-bp intergenic region between the two genes). The...”

K7B00_12805 YdcF family protein from Acidithiobacillus ferrooxidans
Aligns to 86:251 / 266 (62.4%), covers 100.0% of PF02698, 101.5 bits

• Phenomic and transcriptomic analyses reveal the sequential synthesis of Fe₃O₄ nanoparticles in Acidithiobacillus ferrooxidans BYM
  Yang, Microbiology spectrum 2023
  • “...K7B00_01245 MEmagenta 1,014 Ferrochelatase K7B00_04890 1,386 Voltage-gated ion channels K7B00_13060 1,263 NADH-quinone oxidoreductase subunit NuoF K7B00_12805 801 YdcF family protein K7B00_07875 837 Pantoate-beta-alanine ligase K7B00_01590 780 Iron export ABC transporter permease subunit K7B00_08905 MEblue 828 TonB family protein K7B00_11115 1,110 Hem-binding sites K7B00_09365 693 Glycosyltransferase K7B00_01680...”

FTN_0829 hypothetical protein from Francisella tularensis subsp. novicida U112
Aligns to 75:230 / 239 (65.3%), covers 99.2% of PF02698, 101.3 bits

• Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance
  Felix, Scientific reports 2021
  • “...FTN_0452 Hypothetical protein 1.274923951 4.08167E08 FTN_0006 Hypothetical protein 1.345660313 1.02878E06 FTN_0004 Aspartate/glutamate transporter 1.352713527 0.003023321 FTN_0829 Hypothetical protein 1.454738617 6.98601E07 FTN_1388 Oxidoreductase 1.515433578 0.000565317 FTN_1267 ABC transporter ATP-binding protein 1.74578111 3.84443E09 lptC FTN_0904 Lipopolysaccharide export ABC transporter periplasmic protein 1.999604273 1.63282E05 rnpA FTN_0075 Ribonuclease P protein...”

BPSL1927 putative exported protein from Burkholderia pseudomallei K96243
Aligns to 66:227 / 240 (67.5%), covers 99.2% of PF02698, 101.2 bits

• Global transcriptional analysis of Burkholderia pseudomallei high and low biofilm producers reveals insights into biofilm production and virulence
  Chin, BMC genomics 2015
  • “...3 and Additional file 4 ). Furthermore, 13 lipoprotein-encoding genes ( BPSL0092, BPSL0303, BPSL1233, BPSL1445, BPSL1927, BPSL1957, BPSL2026, BPSL2043, BPSL2359, BPSL2705, BPSS1847, BPSS1924 and BPSS1929 ) were also over-expressed in UM6. One of the putative lipoproteins ( BPSL2026 ) contained a spore coat protein U domain,...”

PM0506 unknown from Pasteurella multocida subsp. multocida str. Pm70
Aligns to 79:242 / 247 (66.4%), covers 100.0% of PF02698, 100.1 bits

• PmST2: a novel Pasteurella multocida glycolipid α2-3-sialyltransferase
  Thon, Glycobiology 2011
  • “...gene Pm0508 is in the midst of a locus (Pm0506 to Pm0512) of putative glycosyltransferases. It lines up very well with the so-called LOS synthesis genes (lsg)...”

RSc0146 PROBABLE LIPOPROTEIN TRANSMEMBRANE from Ralstonia solanacearum GMI1000
Aligns to 68:229 / 251 (64.5%), covers 99.2% of PF02698, 99.3 bits

• Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii
  Puigvert, Frontiers in plant science 2017
  • “...protein RSUY_RS14980 RSUY_30600 RSc0211 2.4077 membrane protein RSUY_RS17045 RSUY_34880 RSp0420 2.58002 membrane protein RSUY_RS15175 RSUY_31000 RSc0146 2.83465 hypothetical protein PUTATIVE VIRULENCE GENES AND PLANT COLONIZATION METABOLIC ACTIVITIES Transporters RSUY_RS00490 RSUY_01050 RSc3386 3.50 metal ABC transporter substrate-binding protein RSUY_RS17605 RSUY_36050 RSp0429 3.24 MFS transporter RSUY_RS20020 RSUY_41100 RSp0931...”

SCO2472 integral membrane protein from Streptomyces coelicolor A3(2)
Aligns to 57:211 / 228 (68.0%), covers 78.8% of PF02698, 99.1 bits

• Global Chromosome Topology and the Two-Component Systems in Concerted Manner Regulate Transcription in Streptomyces
  Gongerowska-Jac, mSystems 2021
  • “...Himar1 insertion site with the orientation of the inserted aadA(1) gene. (B) Transcriptional profile of sco2472 - 2475 genes in the wild-type strain (WT; blue), TopA-depleted transposon mutant (Tn TopA; green) and TopA-depleted parental PS04 strain (TopA; orange). Download FIGS3, JPG file, 2.2 MB . Copyright...”
• Streptomyces coelicolor strains lacking polyprenol phosphate mannose synthase and protein O-mannosyl transferase are hyper-susceptible to multiple antibiotics
  Howlett, Microbiology (Reading, England) 2018
  • “...of the vancomycin-induced putative cell wall glycan operon ( cwg ) [ 43 ], and sco2472, a homologue of an uncharacterized protein, SanA, that affects membrane permeability to vancomycin [ 44 ]. The gene sco3736 , encoding an ECF sigma factor and the two upstream genes...”

lmo1004 conserved hypothetical protein from Listeria monocytogenes EGD-e
Aligns to 164:313 / 344 (43.6%), covers 100.0% of PF02698, 98.6 bits

• Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes
  Orsi, BMC evolutionary biology 2008
  • “..., panB , lmo0028 , lmo2175 , lmo2348 , lmo2566 , lmo0487 , lmo0878 , lmo1004 , lmo1011 , and cbiH ) for evidence of recombination and to determine the recipient strains in the recombination events that were identified. Due to computational constraints, testing larger number...”
  • “...( lmo1902 ), lmo0028 , lmo2175 , lmo2348 , lmo2566 , lmo0487 , lmo0878 , lmo1004 , lmo1011 , cbiH ( lmo1199 ). "x" indicate substitutions inferred to have occurred in the respective branches. Red lines represent the probability for each nucleotide to have been imported...”

ElyC / b0920 envelope biogenesis factor from Escherichia coli K-12 substr. MG1655 (see 3 papers)
ELYC_ECOLI / P0AB01 Envelope biogenesis factor ElyC; Elevated frequency of lysis from Escherichia coli (strain K12) (see paper)
Z1267 orf, hypothetical protein from Escherichia coli O157:H7 EDL933
NP_415440 envelope biogenesis factor from Escherichia coli str. K-12 substr. MG1655
b0920 conserved inner membrane protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 80:245 / 259 (64.1%), covers 81.8% of PF02698, 97.7 bits

• function: Plays a critical role in the metabolism of the essential lipid carrier used for cell wall synthesis.
  disruption phenotype: Deletion causes a severe growth defect at low temperature and an elevated frequency of cell lysis resulting from impaired metabolism of the essential lipid precursor required for peptidoglycan synthesis.
• Role of the 5' end phosphorylation state for small RNA stability and target RNA regulation in bacteria
  Schilder, Nucleic acids research 2023
  • “...3.3 5P MicC 1.3 ompD 4.6 GlmZ- gfp ompD 5.7 Fig. S13 S. typhimurium rneR169K (Z1267) 5PPP MicC 6.21.6 ompD 3.41.1 GlmZ- gfp ompD 11.26.6 S. typhimurium rne WT (Z1266) 5PPP MicC 3.40.6 ompD 5.60.2 GlmZ- gfp ompD 6.31.1 Fig. S14 E. coli rne598 (Z1245) 5PPP...”
  • “...presence of MicC in Salmonella Typhimurium strains Z1266 ( wild-type rne , micC ) and Z1267 ( rneR169K , micC ), respectively. The strains carried either plasmid pYG215 ( glmZ-gfp , lanes 1, 2, 7, 8) or plasmid pYG314 ( micC , lanes 36 and 912)....”
• ElyC and Cyclic Enterobacterial Common Antigen Regulate Synthesis of Phosphoglyceride-Linked Enterobacterial Common Antigen.
  Rai, mBio 2021
  • GeneRIF: ElyC and Cyclic Enterobacterial Common Antigen Regulate Synthesis of Phosphoglyceride-Linked Enterobacterial Common Antigen.
• NfiS, a species-specific regulatory noncoding RNA of Pseudomonas stutzeri, enhances oxidative stress tolerance in Escherichia coli
  Hu, AMB Express 2019
  • “...Transcriptional activator of ttdABT 1.28E03 29.11 b1125 potB 1.05 Spermidine/putrescine ABC transporter permease 1.53E03 28.76 b0920 elyC 2.64 Envelope biogenesis factor DUF218 superfamily protein 1.56E03 28.73 b2135 yohC 4.70 Yip1 family inner membrane protein 2.18E03 28.06 b2475 ypfJ 1.26 Putative neutral zinc metallopeptidase 2.24E03 28.00 b0338...”
• The association of DNA damage response and nucleotide level modulation with the antibacterial mechanism of the anti-folate drug trimethoprim
  Sangurdekar, BMC genomics 2011
  • “...b1946 Flagellar switch protein JW5799 - mdoH b1049 Membrane glycosyltransferase tdk b1238 Deoxythymidine kinase ycbC b0920 Function unknown yciM b1280 Function unknown ydhA b1639 Function unknown yfgE (hda) b2496 Required for regulatory inactivation of DnaA; multicopy suppressor of dnaN(ts) alaS b2697 Alanine--tRNA ligase A total of...”

c1061 Hypothetical protein ycbC from Escherichia coli CFT073
Aligns to 80:245 / 259 (64.1%), covers 81.8% of PF02698, 97.7 bits

• Sunday: Poster Sessions, Pt.I
  , Molecular biology of the cell 1996

SM12261_0563 YdcF family protein from Streptococcus mitis NCTC 12261
Aligns to 163:310 / 339 (43.7%), covers 100.0% of PF02698, 97.7 bits

• High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes
  Salvadori, BMC genomics 2018
  • “...0- T c CGAATA 48- ATG SMSK321_0340 TTTT 0- T c CGAATA 48- ATG ccs50 SM12261_0563 TTT 18- a ACGAATA 74- ATG SMSK321_1204 TTT 18- a ACGAATA 74- ATG pilC SM12261_1288 TTT 0- TACGAATA 30- ATG SMSK321_0286 TTT 0- TACGAATA 30- ATG radC SM12261_1568 TTTTT 9-...”

SO1657 conserved hypothetical protein from Shewanella oneidensis MR-1
Aligns to 77:235 / 244 (65.2%), covers 99.2% of PF02698, 96.8 bits

• Involvement of Shewanella oneidensis MR-1 LuxS in biofilm development and sulfur metabolism
  Learman, Applied and environmental microbiology 2009
  • “...on April 16, 2019 by guest Hypothetical SO3482 SO1657 SO4067 SO3656 SO4137 Induction ratio (fold)a Gene name VOL. 75, 2009 SHEWANELLA ONEIDENSIS MR-1 LuxS...”

SMU_302 YdcF family protein from Streptococcus mutans UA159
Aligns to 163:311 / 337 (44.2%), covers 99.2% of PF02698, 96.2 bits

• Construction and verification of the transcriptional regulatory response network of Streptococcus mutans upon treatment with the biofilm inhibitor carolacton
  Sudhakar, BMC genomics 2014
  • “...S. mutans [ 50 ]. Ouyang et al. demonstrated that MbrC transcriptionally regulates the genes SMU_302, SMU_862, SMU_1006 and SMU_1856 by binding to their promoter elements via a conserved binding motif. The binding motif consensus consists of a conserved pair of inverted repeats separated by 2...”

Francci3_1277 protein of unknown function DUF218 from Frankia sp. CcI3
Aligns to 78:225 / 245 (60.4%), covers 100.0% of PF02698, 96.0 bits

• Identification by suppression subtractive hybridization of Frankia genes induced under nitrogen-fixing conditions
  Yamaura, Applied and environmental microbiology 2010
  • “...(1) (1) (2) (4) (1) Francci3_1000 (1) Francci3_1277 (1) Francci3_1531 (1) Francci3_1533 (1) Francci3_1601 (1) Francci3_1761 (1) Francci3_2461 (2) Francci3_2465...”

HI1701 conserved hypothetical protein from Haemophilus influenzae Rd KW20
Aligns to 78:239 / 247 (65.6%), covers 100.0% of PF02698, 95.9 bits

• Identification of the exported proteins of the oral opportunistic pathogen Actinobacillus actinomycetemcomitans by using alkaline phosphatase fusions
  Ward, Infection and immunity 2001
  • “...(269) 802 (204) (367) (371) 1301 (136) 748 (185) HI1085 HI1603 HI1701 HI1150 HI0693 HI0370 HI1236 HI1126.1 HI1628 HI0389 89 89 66 74 89 74 24 87 58 65 79 80 49...”
• Molecular characterization of a Brucella species large DNA fragment deleted in Brucella abortus strains: evidence for a locus involved in the synthesis of a polysaccharide
  Vizcaíno, Infection and immunity 1999
  • “...3.0 U58765 ORF C, Streptomyces coelicolor HI1701, Haemophilus influenzae GdmH, Staphylococcus gallinarum EpiH, Staphylococcus epidermidis 203 Inhibition of...”
  • “...found to the proteins encoded by orfC and HI1701 of Streptomyces coelicolor and Haemophilus influenzae, respectively (Table 2). The protein encoded by orfC is...”
• Transcription of genes encoding iron and heme acquisition proteins of Haemophilus influenzae during acute otitis media
  Whitby, Infection and immunity 1997
  • “...1. Bacterial strains Strain H. influenzae HI689 HI1699 HI1700 HI1701 HI1702 HI1703 Characteristic Source Type b NTa NT NT NT NT J. Musser This study This study...”
  • “...11, 2017 by University of California, Berkeley HI1699 HI1700 HI1701 HI1702 HI1703 NH212 NH213 NH214 NH215 NH216 NH217 Resulta with primer pair for: 4699 4700...”

CD1842 hypothetical protein from Clostridium difficile 630
Aligns to 91:239 / 248 (60.1%), covers 99.2% of PF02698, 94.9 bits

• Behavior and target site selection of conjugative transposon Tn916 in two different strains of toxigenic Clostridium difficile
  Mullany, Applied and environmental microbiology 2012
  • “...CDR20291_2642 CDR20291_2642 CDR20291_2855 CDR20291_2855 CDR20291_3079 CDR20291_3188 CD1842 CD1842 CD1842 CD1909 CD2094 CD2126 CD2126 CD2195 CD2475 CD2475 CD2544...”

BC3075 EpiH/GdmH-related protein from Bacillus cereus ATCC 14579
Aligns to 48:197 / 210 (71.4%), covers 81.1% of PF02698, 93.8 bits

• Irrigation and Nitrogen Fertilization Alter Soil Bacterial Communities, Soil Enzyme Activities, and Nutrient Availability in Maize Crop
  Muhammad, Frontiers in microbiology 2022
  • “...of Soil Enzyme Activities The activities of soil acid phosphatase (S_ACP; BC0145), acid invertase (S_AI; BC3075), -glucosides (S_-GC; BC0165), catalase (S_CAT; BC0105), cellulose (S_CL; BC0155), and urease (S_UR; BC0125) were determined using the soil enzyme kit from Solarbio Science & Technology Co., Ltd. (Beijing, China). The...”

lpp2681 hypothetical protein from Legionella pneumophila str. Paris
Aligns to 80:242 / 250 (65.2%), covers 99.2% of PF02698, 93.1 bits

• Comparative and functional genomics of legionella identified eukaryotic like proteins as key players in host-pathogen interactions
  Gomez-Valero, Frontiers in microbiology 2011
  • “...llb1219 + + + ceg33 Unknown lpg2603 lpp2656 lpl2526 lpc0539 lpa3807 lpw28521 lem28 Unknown lpg2628 lpp2681 lpl2553 lpc0513 lpa3846 lpw28781 Unknown lpg2637 lpp2690 lpl2562 lpc0503 lpa3859 lpw28871 Unknown lpg2638 lpp2691 lpl2563 lpc0502 lpa3861 lpw28891 llo2645 llb2690 + + + mavV Unknown lpg2692 lpp2746 lpl2619 lpc0444 lpa3929...”

CDR20291_1737 hypothetical protein from Clostridium difficile R20291
Aligns to 91:239 / 248 (60.1%), covers 99.2% of PF02698, 91.8 bits

• Behavior and target site selection of conjugative transposon Tn916 in two different strains of toxigenic Clostridium difficile
  Mullany, Applied and environmental microbiology 2012
  • “...42 20 74 14 35 CDR20291_1737 CDR20291_1737 CDR20291_1737 CDR20291_1830 CDR20291_2001 CDR20291_2033 CDR20291_2033 CDR20291_2101 CDR20291_2368 CDR20291_2368...”

lpl2553 hypothetical protein from Legionella pneumophila str. Lens
Aligns to 80:242 / 250 (65.2%), covers 99.2% of PF02698, 91.2 bits

• Comparative and functional genomics of legionella identified eukaryotic like proteins as key players in host-pathogen interactions
  Gomez-Valero, Frontiers in microbiology 2011
  • “...+ + + ceg33 Unknown lpg2603 lpp2656 lpl2526 lpc0539 lpa3807 lpw28521 lem28 Unknown lpg2628 lpp2681 lpl2553 lpc0513 lpa3846 lpw28781 Unknown lpg2637 lpp2690 lpl2562 lpc0503 lpa3859 lpw28871 Unknown lpg2638 lpp2691 lpl2563 lpc0502 lpa3861 lpw28891 llo2645 llb2690 + + + mavV Unknown lpg2692 lpp2746 lpl2619 lpc0444 lpa3929 lpw29461...”

lpg2628 membrane protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Aligns to 80:242 / 250 (65.2%), covers 99.2% of PF02698, 91.1 bits

• Genomic Insight into Symbiosis-Induced Insect Color Change by a Facultative Bacterial Endosymbiont, "Candidatus Rickettsiella viridis"
  Nikoh, mBio 2018
  • “...arp / ankH / sdcA , legK1/legK3 , lepB , L.pneumophila g2359 ( lpg2359 ), lpg2628 , mavN , ravC , ravJ , rsmE , and sidP , that are orthologous to the effector genes identified in L.pneumophila ( TableS6 ). In L.pneumophila , sidP contains...”
• Comparative and functional genomics of legionella identified eukaryotic like proteins as key players in host-pathogen interactions
  Gomez-Valero, Frontiers in microbiology 2011
  • “...llo0626 llb1219 + + + ceg33 Unknown lpg2603 lpp2656 lpl2526 lpc0539 lpa3807 lpw28521 lem28 Unknown lpg2628 lpp2681 lpl2553 lpc0513 lpa3846 lpw28781 Unknown lpg2637 lpp2690 lpl2562 lpc0503 lpa3859 lpw28871 Unknown lpg2638 lpp2691 lpl2563 lpc0502 lpa3861 lpw28891 llo2645 llb2690 + + + mavV Unknown lpg2692 lpp2746 lpl2619 lpc0444...”

llmg_1911 hypothetical protein from Lactococcus lactis subsp. cremoris MG1363
Aligns to 185:334 / 361 (41.6%), covers 97.7% of PF02698, 90.8 bits

• Genome sequences of Lactococcus lactis MG1363 (revised) and NZ9000 and comparative physiological studies
  Linares, Journal of bacteriology 2010
  • “...Synonymous Trp3Leu llmg_1860 llmg_1871 llmg_1872 llmg_1911 llmg_pseudo_59 llmg_1941 llmg_1941 llmg_1941 Change frameshift Change frameshift Change frameshift...”

HD0881 conserved hypothetical protein from Haemophilus ducreyi 35000HP
Aligns to 79:241 / 248 (65.7%), covers 100.0% of PF02698, 89.7 bits

• Putative vaccine candidates and drug targets identified by reverse vaccinology and subtractive genomics approaches to control Haemophilus ducreyi, the causative agent of chancroid
  de, Journal of the Royal Society, Interface 2018
  • “...0.574 0.615 HD_RS06605 HD_RS08300 HD_RS06065 HD_RS03600 HD1622 HD2025 HD1481 HD0881 HD0755 -- -- nlpc -- -- SEC SEC PSE PSE PSE PSE 22 and 23) yes (between...”

I35_1736 YdcF family protein from Burkholderia cenocepacia H111
Aligns to 64:225 / 238 (68.1%), covers 93.2% of PF02698, 88.9 bits

• NtrC-dependent control of exopolysaccharide synthesis and motility in Burkholderia cenocepacia H111
  Liu, PloS one 2017
  • “...BCAL1677 Type 1 fimbriae major subunit fimA 5.2 I35_1734 BCAL1818 Zn-dependent hydrolases, including glyoxylases -6.6 I35_1736 Oxidoreductase (flavoprotein) -5.2 I35_1739 BCAL1822 Putrescine transport system permease protein potH 3.9 I35_1872 BCAL1952 Hypothetical protein 4.4 I35_1881 BCAL1961 Ankyrin repeat protein -2.5 I35_1963 BCAL2039 Urate oxidase -3.4 I35_2376 BCAL2448...”
• σ54-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111
  Lardi, Applied and environmental microbiology 2015
  • “...I35_1214 I35_1215 I35_1420 I35_1421 I35_1734 I35_1735 I35_1736 I35_2149 I35_2150 I35_2151 I35_2727 I35_2935 I35_4051 I35_4450 I35_4452 I35_4669 I35_4672...”

VDA_000496 YdcF family protein from Photobacterium damselae subsp. damselae CIP 102761
Aligns to 154:303 / 326 (46.0%), covers 77.3% of PF02698, 86.4 bits

• Transcriptome changes in response to temperature in the fish pathogen Photobacterium damselae subsp. damselae: Clues to understand the emergence of disease outbreaks at increased seawater temperatures
  Matanza, PloS one 2018
  • “...-3.1 4.50201E-55 ChrI VDA_001660 Hypothetical protein -3.0 2.70017E-34 ChrI VDA_003210 Hypothetical protein -3.0 4.74045E-89 ChrI VDA_000496 Hypothetical protein -3.0 7.01092E-40 ChrII VDA_003208 Hypothetical protein -3.0 8.59014E-50 ChrI VDA_000405 Hypothetical protein -3.0 9.44929E-53 ChrII VDA_002379 Hypothetical protein -3.0 4.8787E-117 ChrI VDA_000439 Hypothetical protein -3.0 1.36579E-08 ChrII The...”

PPA2130 ElyC/SanA/YdcF family protein from Cutibacterium acnes KPA171202
Aligns to 36:203 / 206 (81.6%), covers 79.5% of PF02698, 83.1 bits

• Propionibacterium acnes and Acne Vulgaris: New Insights from the Integration of Population Genetic, Multi-Omic, Biochemical and Host-Microbe Studies
  McLaughlin, Microorganisms 2019
  • “...Dermatan sulphate adhesin (DsA2) (PTR) * PPA2210 Colonization/adhesion/inflammation PTRs * PPA1715, PPA1879, PPA180, PPA1881, PPA1906, PPA2130, PPA2270 Colonization/adhesion/inflammation GroEL PPA0453, PPA1772, PPA1773 Inflammation DnaK PPA1098, PPA2040 Inflammation DnaJ PPA0916, PPA2038 Inflammation * PTRs: Proline-Threonine Repeats likely involved in cell-cell and/or cell-matrix interactions....”

PPA2130 conserved membrane-associated protein (OmpA family) from Propionibacterium acnes KPA171202
Aligns to 58:225 / 228 (73.7%), covers 79.5% of PF02698, 82.7 bits

• Propionibacterium acnes and Acne Vulgaris: New Insights from the Integration of Population Genetic, Multi-Omic, Biochemical and Host-Microbe Studies
  McLaughlin, Microorganisms 2019
  • “...Dermatan sulphate adhesin (DsA2) (PTR) * PPA2210 Colonization/adhesion/inflammation PTRs * PPA1715, PPA1879, PPA180, PPA1881, PPA1906, PPA2130, PPA2270 Colonization/adhesion/inflammation GroEL PPA0453, PPA1772, PPA1773 Inflammation DnaK PPA1098, PPA2040 Inflammation DnaJ PPA0916, PPA2038 Inflammation * PTRs: Proline-Threonine Repeats likely involved in cell-cell and/or cell-matrix interactions....”

SEN3064 hypothetical protein from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
Aligns to 59:207 / 230 (64.8%), covers 85.6% of PF02698, 82.0 bits

• On the evolutionary history, population genetics and diversity among isolates of Salmonella Enteritidis PFGE pattern JEGX01.0004
  Allard, PloS one 2013
  • “...subsp. enterica serovar Enteritidis str. P125109] Length=230 50 826_input.aln 826_protein.fas 152 AG 51 DG ygjQ SEN3064 ref|YP_002245130.1| hypothetical protein SEN3064 [Salmonella enterica subsp. enterica serovar Enteritidis str. P125109] Length=230 51 864_input.aln 864_protein.fas 126 AC 42 ED ygiB SEN3030 ref|YP_002245097.1| hypothetical protein SEN3030 [Salmonella enterica subsp. enterica...”

STM3222 putative integral membrane protein from Salmonella typhimurium LT2
Aligns to 59:207 / 230 (64.8%), covers 85.6% of PF02698, 81.9 bits

• Novel DNA Binding and Regulatory Activities for σ⁵⁴ (RpoN) in Salmonella enterica Serovar Typhimurium 14028s
  Bono, Journal of bacteriology 2017
  • “...STM1390f STM1409 STM1594f STM1595 STM1990f STM2181f STM2430f STM2957f STM3222 STM3535f STM3832 STM3919f fdrA ybjX rimJ ydiM orf48 orf242 ssaJ srfB srfC yedA...”

VP1257 SanA protein from Vibrio parahaemolyticus RIMD 2210633
Aligns to 60:209 / 244 (61.5%), covers 98.5% of PF02698, 80.2 bits

• Comparative Genomic Analysis Reveals the Potential Risk of Vibrio parahaemolyticus Isolated From Ready-To-Eat Foods in China
  Pang, Frontiers in microbiology 2019
  • “...affected by filtered missense variants that correlate with RTE foods source. GeneName Annotation Missense_variant Synonymous_variant VP1257 SanA protein 1 0 VP1435 Sodium/glutamate symporter 1 0 VPA0027 Hypothetical protein 2 0 VPA0641 LysR family transcriptional regulator 1 0 VPA0642 Glutathione S-transferase 1 1 VPA0710 Sensor histidine kinase/response...”

BMEII0841 hypothetical protein from Brucella melitensis 16M
Aligns to 9:154 / 180 (81.1%), covers 98.5% of PF02698, 79.9 bits

• Molecular targets for rapid identification of Brucella spp
  Ratushna, BMC microbiology 2006
  • “...(410659 .. 411921) BMEII0842 877115 .. 878377 1263 hypothetical protein 2 BRA0426 (411918 .. 412535) BMEII0841 876576 .. 877118 618/543 hypothetical protein 2 BRA0427 (412532 .. 413413) BMEII0840 875548 .. 876504 882/957 glycosyltransferase involved in cell wall biogenesis 2 BRA0428 (413410 .. 414537) BMEII0839 874562 .....”

BRA0426 Bme2 protein from Brucella suis 1330
Aligns to 34:178 / 205 (70.7%), covers 98.5% of PF02698, 79.4 bits

• Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle
  Wattam, Journal of bacteriology 2009
  • “...BRA0419 BRA0421 BRA0422 BRA0423 BRA0424 BRA0426 BRA0427 BRA0428 VBI0007BS2_0414 VBI0007BS2_0415 VBI0007BS2_0417 VBI0007BS2_0418 VBI0007BS2_0419 VBI0007BS2_0420...”
• Molecular targets for rapid identification of Brucella spp
  Ratushna, BMC microbiology 2006
  • “...CysE/LacA/LpxA/NodL family 2 BRA0425 (410659 .. 411921) BMEII0842 877115 .. 878377 1263 hypothetical protein 2 BRA0426 (411918 .. 412535) BMEII0841 876576 .. 877118 618/543 hypothetical protein 2 BRA0427 (412532 .. 413413) BMEII0840 875548 .. 876504 882/957 glycosyltransferase involved in cell wall biogenesis 2 BRA0428 (413410 .....”

AOLE_07010 YdcF family protein from Acinetobacter oleivorans DR1
Aligns to 208:362 / 373 (41.6%), covers 98.5% of PF02698, 78.2 bits

• Endogenous hydrogen peroxide increases biofilm formation by inducing exopolysaccharide production in Acinetobacter oleivorans DR1
  Jang, Scientific reports 2016
  • “...linked to extracellular DNA generation for biofilm formation 32 . A hypothetical protein encoded by AOLE_07010 was 260-fold upregulated in our mature biofilm ( Table 1 ). Bioinformatics analysis suggested that this protein shares 35% protein identity with a lysophospholipase from Legionella pneumophila 33 . The...”
  • “...Spot no. MW pI gene Protein Locus tag Fold- change 7707 65.3 6.2 hypothetical protein AOLE_07010 H a 7409 51.8 5.9 hutI imidazolonepropionase AOLE_00370 21.0 7806 94.1 6.0 oprC outer membrane receptor protein, mostly Fe transport AOLE_18500 10.6 8212 35.5 6.9 dusA tRNA-dihydrouridine synthase A AOLE_16645...”

VC1186 sanA protein from Vibrio cholerae O1 biovar eltor str. N16961
Aligns to 71:218 / 254 (58.3%), covers 98.5% of PF02698, 77.6 bits

• A bistable switch and anatomical site control Vibrio cholerae virulence gene expression in the intestine
  Nielsen, PLoS pathogens 2010
  • “...expression levels in the different samples were calculated by using the comparative Ct method with VC1186 and VC2233 as internal controls. For quantitative real-time RT-PCR of samples isolated by fluorescence activated cell sorting, 15 cycles of pre-amplification were performed with the appropriate primers to ensure adequate...”
• RpoS controls the Vibrio cholerae mucosal escape response
  Nielsen, PLoS pathogens 2006
  • “...levels in the different samples were calculated by using the comparative cycle threshold method with VC1186 and VC2233 as internal control. Video tracing microscopy. The fraction of swimming bacteria after 11 h growth in M9 medium supplemented with 0.5% lactose was determined from video sequences captured...”

YgjQ / b3086 DUF218 domain-containing protein YgjQ from Escherichia coli K-12 substr. MG1655 (see 3 papers)
Aligns to 33:209 / 230 (77.0%), covers 83.3% of PF02698, 75.8 bits

YPO2511 putative exported protein from Yersinia pestis CO92
YPTB2547 putative exported protein from Yersinia pseudotuberculosis IP 32953
Aligns to 203:357 / 375 (41.3%), covers 78.0% of PF02698, 75.7 bits

• Cell membrane is impaired, accompanied by enhanced type III secretion system expression in Yersinia pestis deficient in RovA regulator
  Yang, PloS one 2010
  • “...exported protein 3.C.1 Cell envelop YPO2373 7.69 slyB, pcpY, pcp putative lipoprotein 3.C.1 Cell envelop YPO2511 2.11 ----- putative exported protein 3.C.1 Cell envelop YPO2782 2.93 ----- putative membrane protein 3.C.1 Cell envelop YPO3865 2.46 wzzE, wzz, b3785 putative lipopolysaccharide biosynthesis protein 3.C.2 Cell envelop YPO2477...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...lyase 1.666 (< 0.001) 1.229 (0.042) YPTB2437 (pepT) YPO1631 peptidase T 0.488 (0.007) YPTB2548 (glnH) YPO2511 putative glutamine-binding periplasmic protein 1.797 (0.014) YPTB2549 (glnP) YPO2512 putative glutamine transport system permease 1.704 (0.024) YPTB2550 (glnQ) YPO2513 putative glutamine transport ATP-binding protein 1.56 (0.027) YPTB2632 (aroC) YPO2751 chorismate...”
  • “...protein CheA 1.725 (0.015) YPTB2435 (phoQ) YPO1633 sensor protein kinase 0.527 (< 0.001) YPTB2548 (glnH) YPO2511 putative glutamine-binding periplasmic protein 1.797 (0.014) YPTB2635 (sixA) YPO2748 putative phosphohistidine phosphatase 1.508 (0.002) YPTB2763 (narP) YPO3041 nitrate/nitrite response regulator protein NarP 0.715 (0.043) YPTB2894 (rseC) YPO2714 sigma E factor...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...(0.001) YPTB2481 YPO1588 conserved hypothetical protein 0.759 (0.035) YPTB2526 YPO2489 conserved hypothetical protein 1.361 (0.02) YPTB2547 YPO2510 putative exported protein 0.31 (< 0.001) YPTB2594 YPO2563 conserved hypothetical protein 0.563 (< 0.001) YPTB2638 YPO2745 conserved hypothetical protein 0.483 (0.001) YPTB2651 (lemA) YPO2732 putative exported protein 0.381 (<...”

VP1152 conserved hypothetical protein from Vibrio parahaemolyticus RIMD 2210633
Aligns to 24:186 / 212 (76.9%), covers 68.2% of PF02698, 73.9 bits

• Prevalence of pandemic thermostable direct hemolysin-producing Vibrio parahaemolyticus O3:K6 in seafood and the coastal environment in Japan
  Hara-Kudo, Applied and environmental microbiology 2003
  • “...by University of California, Berkeley Japanese environmental VP1152 samples VP1153 VP1219 VP1280 VP1281 VP1282 1001A44 1001A46 VPF01-13 VP80 VPF01-5 19-13...”
  • “...BE98-2062; 5, VP1280; 6, KX-V225; 7, VP80; 8, VPF00-18; 9, VP1152; 10, APCC VP 9810; 11, 1001A44; 12, 1001A46; 13, APCC VP 00030; 14, APCC VP 00031; 15, 4917;...”

S3333 hypothetical protein from Shigella flexneri 2a str. 2457T
Aligns to 50:209 / 230 (69.6%), covers 83.3% of PF02698, 73.8 bits

• Analysis of the type 1 pilin gene cluster fim in Salmonella: its distinct evolutionary histories in the 5' and 3' regions
  Boyd, Journal of bacteriology 1999
  • “...IV VII IIIa S. bongori a fim1 fim2 fim3 fim4 fim5 fim6 S3333 S4194 S2985 S2993 S2995 S3057 S2978 S2979 S3015 S3027 S3013 S3014 S2980 S2983 1 1 1 1 1 1 1 1 1...”
  • “...for strain S4194, which matched the reference sequence. Strain S3333 also had a 3-bp deletion in the 39 coding sequence of fimA. Among the 17 Salmonella...”
• Comparative genetics of the inv-spa invasion gene complex of Salmonella enterica
  Boyd, Journal of bacteriology 1997
  • “...(Table 1) and 2 subspecies I isolates (S4194 and S3333) were digested with EcoRI, and the fragments were separated by agarose gel electrophoresis. The DNA...”
  • “...were identical, and that of a strain of Typhi (S3333) differed from them by only one amino acid substitution. The SpaN proteins in the host-adapted strains were...”

IC627_07795 ElyC/SanA/YdcF family protein from Photobacterium damselae subsp. piscicida
Aligns to 47:200 / 224 (68.8%), covers 83.3% of PF02698, 72.9 bits

• Complete, closed and curated genome sequences of Photobacterium damselae subsp. piscicida isolates from Australia indicate mobilome-driven localized evolution and novel pathogenicity determinants
  Baseggio, Microbial genomics 2021
  • “...in chromosome 1 of both Australian and USA strains is absent in the Japanese strain (IC627_07795 to IC627_07640) ( Fig. 2a , region ii). Here, genes encode a set of essential proteins, including a type VI secretion system protein VgrG (IC627_07640), tellurite-resistance protein TerB (IC627_07675), zinc...”

VF_A0085 transporter from Vibrio fischeri ES114
Aligns to 192:349 / 364 (43.4%), covers 78.0% of PF02698, 71.8 bits

• Ambient pH Alters the Protein Content of Outer Membrane Vesicles, Driving Host Development in a Beneficial Symbiosis
  Lynch, Journal of bacteriology 2019 (secret)

M892_03945 YdcF family protein from Vibrio campbellii ATCC BAA-1116
Aligns to 24:205 / 212 (85.8%), covers 68.2% of PF02698, 71.2 bits

• Vibrio campbellii hmgA-mediated pyomelanization impairs quorum sensing, virulence, and cellular fitness
  Wang, Frontiers in microbiology 2013
  • “...system, methyltransferase subunit 1.57E-06 2.19 1.34 1.63 V M892_20315 Beta-lactamase 1.56E-05 1.48 0.49 3.02 V M892_03945 Hypothetical protein 5.33E-05 0.36 0.00 UD M892_05165 Gonadoliberin III-related protein 9.73E-05 0.78 0.1 7.80 M892_05170 Hypothetical protein 2.71E-07 1.11 0.32 3.47 M892_05480 Hypothetical protein 1.76E-04 0.98 0.30 3.27 M892_07360 Phage...”

SPA0101 hypothetical protein from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
Aligns to 72:165 / 165 (57.0%), covers 61.4% of PF02698, 70.2 bits

• Comparative profiling of Pseudomonas aeruginosa strains reveals differential expression of novel unique and conserved small RNAs
  Ferrara, PloS one 2012
  • “...CrcZ SPA0096 I f 2751/2752 28520 + 50 SPA0097 I f 2771/2770 + 28250 20 SPA0101 II 1244 48150 + 80 SPA0102 II rpsA rpsA + MRE SPA0103 II 3229 + 22420 100 SPA0104 II rhlI rhlI + 70 SPA0106 II 4133 + ccoN 70 SPA0110...”
  • “...consistent with sRNA-Seq data (i.e. the read number of the corresponding nstSGRs). One exception was SPA0101 ( Figure 3B ) which showed a comparable read number in both strains, but gave a sharp signal corresponding to a 70 nt long transcript only in PA14. On the...”

SCO4629 hypothetical protein from Streptomyces coelicolor A3(2)
Aligns to 27:185 / 221 (71.9%), covers 70.5% of PF02698, 69.4 bits

• ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria
  Bi, Nucleic acids research 2012
  • “...sporulation-related proteins that are essential for intermycelial transfer and pock formation. In addition, SCO4628 and SCO4629 comprise the imp operon that regulates transfer functions and controls extra-chromosomal maintenance of SPL1 ( 30 ). Remarkably, we have recently found that the SLP1-encoded type IV restriction endonuclease ScoA3McrA...”

VPA1680 putative exported protein from Vibrio parahaemolyticus RIMD 2210633
Aligns to 193:352 / 365 (43.8%), covers 78.0% of PF02698, 68.3 bits

• Organic Hydroperoxide Resistance Gene ohr (VPA1681) Confers Protection against Organic Peroxides in the Presence of Alkyl Hydroperoxide Reductase Genes in Vibrio parahaemolyticus
  Chen, Applied and environmental microbiology 2021 (secret)

YeiF / b2144 DUF218 domain-containing protein SanA from Escherichia coli K-12 substr. MG1655 (see 6 papers)
TC 9.B.114.1.1 / P0AFY2 1 TMS SanA (YeiF) compliments the permeability defects of a vancomycin-susceptible mutant from Escherichia coli (strain K12) (see 4 papers)
sanA protein SanA from Escherichia coli K12 (see paper)
c2677 SanA protein from Escherichia coli CFT073
b2144 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 46:198 / 239 (64.0%), covers 82.6% of PF02698, 67.9 bits

• substrates: Vancomycin
• Transposon-Sequencing Analysis Unveils Novel Genes Involved in the Generation of Persister Cells in Uropathogenic Escherichia coli
  Molina-Quiroz, Antimicrobial agents and chemotherapy 2016
  • “...c2144 c2199 c2232 c2377 c2385 c2465 c2471 c2475 c2615 c2677 c2702 c2841 c3028 c3174 c3255 c3721 c3888 c4475 c4704 c4725 c4804 c4923 c5177 c5207 c5320 c5329...”
• Combinatorial strategies for improving multiple-stress resistance in industrially relevant Escherichia coli strains
  Lennen, Applied and environmental microbiology 2014
  • “...3.97 b0109 b3095 b1961 b0677 b3860 b0780 b3149 b0125 b3054 b2144 b1987 b0435 b2435 b4472 b4220 b4221 b3529 nadC yqjA dcm nagA dsbA ybhK diaA hpt ygiF sanA cbl...”

SC2201 vancomycin sensitivity from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
Aligns to 67:220 / 260 (59.2%), covers 84.8% of PF02698, 67.2 bits

• FlbT couples flagellum assembly to gene expression in Caulobacter crescentus
  Mangan, Journal of bacteriology 1999
  • “...SC1054 SC1055 SC1060 SC1066 SC1114 SC1132 SC2201 SC2204 SC3476 syn-1000 flgE806::Tn5-VB32 flbT650 flgE::IS511 fliQR153 flaF673 fla-674 syn-1000 fljK::lacZ...”
  • “...SC276 Phage SC1032 SC276 Phage SC1054 SC276 Phage SC2201 SC276 Phage SC2204 SC276 Phage SC1114 SC276 Phage SC1055 SC276 Phage SC3476 SC276 Transduction of...”
• Use of pulsed field gel electrophoresis and transposon mutagenesis to estimate the minimal number of genes required for motility in Caulobacter crescentus
  Ely, Genetics 1989
  • “...fragments" flbS Mutant strains 50 130 D 1100 A 600 S SC2201 (flbS636) 280 140 D SC1031 ( f l u - 1 9 3 , SC1047 (flaG617), SC1062 (fluE178), SC1065 (flbA604),...”

VK055_4938 outer membrane permeability protein SanA from Klebsiella pneumoniae subsp. pneumoniae
Aligns to 46:198 / 238 (64.3%), covers 96.2% of PF02698, 66.8 bits

• Klebsiella pneumoniae causes bacteremia using factors that mediate tissue-specific fitness and resistance to oxidative stress
  Holmes, PLoS pathogens 2023
  • “...0.002 NAD(P)H-flavin reductase VK055_4099 gshB -1.696 0.039 glutathione synthase VK055_3257 cpxR -1.641 0.006 response regulator VK055_4938 -1.632 0.017 hypothetical protein VK055_4619 purL -1.619 0.000 phosphoribosylformylglycinamidine synthase VK055_3184 wecE -1.434 0.004 TDP-4-keto-6-deoxy-D-glucose transaminase familyprotein VK055_3858 arcB -1.426 0.023 aerobic respiration control sensor protein ArcB VK055_5102 iroC -1.409...”

PMI_RS03160 outer membrane permeability protein SanA from Proteus mirabilis HI4320
PMI0641 transport protein from Proteus mirabilis HI4320
Aligns to 46:191 / 241 (60.6%), covers 96.2% of PF02698, 66.1 bits

• Organ agar serves as physiologically relevant alternative for in vivo bacterial colonization
  Pearson, Infection and immunity 2023
  • “...0.863 UKL Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex TCA cycle e Y PMI0641 sanA PMI_RS03160 215 C10 0.854 K Putative transport protein Y PMI0711 serC PMI_RS03500 219 C4 0.419 UK Phosphoserine aminotransferase Amino acid metabolism Y PMI0765 ompF/ nmpC PMI_RS03760 218 G6 0.716 UK Outer...”
• Organ agar serves as physiologically relevant alternative for in vivo bacterial colonization
  Pearson, Infection and immunity 2023
  • “...207 F6 0.863 UKL Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex TCA cycle e Y PMI0641 sanA PMI_RS03160 215 C10 0.854 K Putative transport protein Y PMI0711 serC PMI_RS03500 219 C4 0.419 UK Phosphoserine aminotransferase Amino acid metabolism Y PMI0765 ompF/ nmpC PMI_RS03760 218 G6 0.716...”
  • “...vivo c Function PMI0570 sucB UKL UKLBS UBK Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex PMI0641 sanA K KS US Putative transport protein PMI0711 serC UK KS UBKS Phosphoserine aminotransferase PMI1545 guaA UKL UKLBS UK GMP synthase (glutamine-hydrolyzing) PMI2870 UKL None d UBKS Hypothetical protein PMI3210...”

sfiX / CAA05289.1 Sfi protein from Salmonella enterica subsp. enterica serovar Typhimurium (see paper)
Aligns to 46:186 / 187 (75.4%), covers 80.3% of PF02698, 64.0 bits

BMEI2016 hypothetical protein from Brucella melitensis 16M
Aligns to 26:170 / 211 (68.7%), covers 100.0% of PF02698, 63.8 bits

• Identification of a Novel Small Non-Coding RNA Modulating the Intracellular Survival of Brucella melitensis
  Wang, Frontiers in microbiology 2015
  • “...suggested that BSR0602 negatively regulates BMEI0106, a transcriptional regulator of gntR family. Besides BMEI0106, BMEI0630, BMEI2016, BMEI0385, and BMEI1281 seem to be negatively regulated by BSR0602 as the abundance of their mRNA were decreased in the BSR0602 overexpression strains (Figure 3 A). Figure 3 BSR0602 directly...”

APL_0442 SanA protein from Actinobacillus pleuropneumoniae L20
Aligns to 67:206 / 229 (61.1%), covers 97.7% of PF02698, 60.9 bits

• Biofilm formation by virulent and non-virulent strains of Haemophilus parasuis
  Bello-Ortí, Veterinary research 2014
  • “...protein P5 precursor HS372_00060 APL_1206 putative ribonuclease FitB HS372_01900 APL_1173 Nicotinamide riboside transporter pnuC HS372_00666 APL_0442 vancomycin high temperature exclusion protein HS372_01587 APL_0484 Alpha-aminoadipate--lysW ligase lysX HS372_02062 APL_0038 hypothetical protein HS372_00364 APL_0222 Putative lipoprotein/NMB1162 precursor HS372_01892 APL_0133 Cys regulon transcriptional activator HS372_00988 APL_1295 Arginine repressor HS372_02252...”
• Effects of growth conditions on biofilm formation by Actinobacillus pleuropneumoniae
  Labrie, Veterinary research 2010
  • “...3.093 APL_0006 ompP2A Outer membrane protein P2 2.515 APL_0550 tadC Tight adherence protein C 1.985 APL_0442 sanA SanA protein 1.776 APL_0549 tadD Tight adherence protein D 1.749 APL_0332 hlpB Lipoprotein HlpB 1.627 APL_1364 gmhA Putative phosphoheptose isomerase 1.386 APL_0873 rlpB Putative rare lipoprotein B 1.391 APL_1028...”

EGX89_RS01790 YdcF family protein from Citrobacter freundii
Aligns to 38:216 / 265 (67.5%), covers 79.5% of PF02698, 57.2 bits

• Development and evaluation of a colorimetric LAMP-based biosensor for rapid detection of a nosocomial infection agent, Citrobacter freundii
  Mollasalehi, Scientific reports 2023
  • “...at NCBI. A distinct sequence of ydcF gene coding Ydc family protein with accession number EGX89_RS01790 was selected in C. freundii gene that varies in other related bacteria. Six primers, including two inner primers, two outer primers, and two loop primers, were designed by the LAMP...”

YdcF / b1414 DUF218 domain-containing protein YdcF from Escherichia coli K-12 substr. MG1655 (see 3 papers)
YDCF_ECOLI / P34209 Protein YdcF from Escherichia coli (strain K12) (see paper)
ydcF / ECOCYC|EG12110-MONOMER protein ydcF from Escherichia coli K12 (see 6 papers)
b1414 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
Aligns to 15:211 / 266 (74.1%), covers 78.8% of PF02698, 56.5 bits

• function: Binds S-adenosyl-L-methionine (AdoMet)
  subunit: Monomer.
• Metabolic shift of Escherichia coli under salt stress in the presence of glycine betaine
  Metris, Applied and environmental microbiology 2014
  • “...b0678 b1482 b4376 b1896 b1897 b0133 b3403 b1062 b3310 b1581 b2464 b2104 b2465 b0740 b1414 b2898 b3003 b3153 b3011 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Transcriptional profile of the Escherichia coli response to the antimicrobial insect peptide cecropin A
  Hong, Antimicrobial agents and chemotherapy 2003
  • “...pin (b1158) ychK (b1234) -- (b1364) ydbA 1(b1401) ydcF (b1414) fdnH (b1475) ynhA (b1679) -- (b1973) hisC (b2021) hisH (b2023) yiaT (b3584) yjbO (b4050) iadA...”
• Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
  Smulski, Journal of bacteriology 2001
  • “...b1205 b1256 b1257 b1273 b1285 b1321 b1333 b1376 b1378 b1414 b1446 b1454 b1586 b1598 b1667 b1678 b1725 b1778 b1783 b1816 b1869 b1870 b1871 b1953 b1955 b2007...”

Z2308 orf, hypothetical protein from Escherichia coli O157:H7 EDL933
ECs2020 hypothetical protein from Escherichia coli O157:H7 str. Sakai
Aligns to 15:211 / 266 (74.1%), covers 78.8% of PF02698, 56.4 bits

• 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
  • “...ycfJ Z1749 Unknown 24.98 1.5E-14 Z2283 Unknown 4.39 3.0#-06 ydeH Z2292 Unknown +2.69 2.0E-04 ydeF Z2308 Unknown +2.83 2.7E-06 Z2421 Unknown +1.79 0.03 yoaG Z2838 Unknown +2.54 0.02 Z2839 Unknown +2.36 0.04 Z2893 Unknown 1.61 0.01 rcnB Z3275 Putative nickel/cobalt efflux protein 1.61 0.02 ypeC Z3656...”
• Identification and characterization of molecular entities differentially expressed in bacteria genome upon treatment with glyphosate shock
  Fabunmi, Heliyon 2023
  • “...datasets, we discovered a protein with no unique features expressed when treated with glyphosate. The Ecs2020 model looks to be the most stable in structural modeling investigations, while the catalytic residues sought in drug development are anticipated. Furthermore, biological processes and cellular component enrichment analysis revealed...”
  • “...could be a good starting point for making new antibiotic medicines. Keywords Glyphosate Functional profile Ecs2020 Escherichia coli 1 Introduction Glyphosate is a non-selective herbicide that professionals and consumers extensively use. Its popularity has been growing since it was one of the first chemicals used to...”
• Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
  Bergholz, Applied and environmental microbiology 2009
  • “...ECs1824 ECs1829 ECs1830 ECs1831 ECs1845 ECs2000 ECs2019 ECs2020 ECs2085 ECs2144 Exponential phase/ stationary phasec Log2 expression ratio Category and ECs no.a...”

SMc00715 HYPOTHETICAL TRANSMEMBRANE PROTEIN from Sinorhizobium meliloti 1021
Aligns to 62:204 / 232 (61.6%), covers 87.9% of PF02698, 55.8 bits

• Transcriptome analysis of Sinorhizobium meliloti during symbiosis
  Ampe, Genome biology 2003
  • “...cluster contained genes, which were highly and constantly expressed in all conditions tested (for example, SMc00715 , SMc00979 ). Genes induced or repressed in planta , genes induced during infection, and genes induced by luteolin also formed individual clusters. A careful analysis of expression profiles and...”

SeKA_A1094 YdcF family protein from Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188
Aligns to 38:213 / 266 (66.2%), covers 79.5% of PF02698, 55.2 bits

• Genomic and Evolutionary Analysis of Two Salmonella enterica Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America
  Haley, PloS one 2016
  • “...Position a nt Poultry-associated nt Bovine-associated Substitution c aa Poultry aa Bovine aa Position Method SeKA_A1094 protein YdcF 1055798 T C NS Thr Ala 43 1, 2, 3 SeKA_A2591 hemolysin-3 2519134 A C NS Phe Val 32 3 SeKA_A2812 methyltransferase family protein 2713142 G A NS...”
  • “...coding genes, all resulting in non-synonymous mutations, that defined the bovine-poultry divergence for all strains (SeKA_A1094, SeKA_A2591, SeKA_A2812, SeKA_A4467) ( Table 2 ). No evidence of the role of these genes in host-specificity, colonization of the gut by S . enterica or persistence of S ....”

HI1262 SanA from Haemophilus influenzae Rd KW20
Aligns to 58:203 / 226 (64.6%), covers 86.4% of PF02698, 54.9 bits

• PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences
  Mrázek, Microbial informatics and experimentation 2011
  • “...796139 799618 - DNA polymerase III subunit alpha DnaE HI0740 799857 801509 + Phosphomannomutase YhxB HI1262 1339751 1340431 - SanA HI1263 1340589 1341665 + homoserine O-acetyltransferase MetX HI1264 1341719 1344361 - DNA gyrase subunit A GyrA HI1265 1344944 1346707 - hypothetical protein HI1266 1346844 1347230 -...”
• Position-based scanning for comparative genomics and identification of genetic islands in Haemophilus influenzae type b
  Bergman, Infection and immunity 2003
  • “...(Table 2). A small island between genes HI1261 and HI1262. The smallest genetic island identified in our PCR scanning, HiGI2, was found in the Eagan genome...”
  • “...genome Location (relative to Rd genome) 2 4 Between HI1261 and HI1262 Between HI1710 and HI1711 Within HI1266 5 Within HI1403 3 6 7 8 a Insert size (bp) % GC...”

PA2066 hypothetical protein from Pseudomonas aeruginosa PAO1
PA14_37780 hypothetical protein from Pseudomonas aeruginosa UCBPP-PA14
Aligns to 25:166 / 212 (67.0%), covers 73.5% of PF02698, 48.7 bits

• Effectiveness of Pseudomonas aeruginosa type VI secretion system relies on toxin potency and type IV pili-dependent interaction
  Rudzite, PLoS pathogens 2023
  • “...ncRNA pool causing growth arrest, contains RHS domain [ 61 , 84 , 85 ] PA2066 Unknown Putative Hcp2 associated effector [ 48 ] Azu (PA4922) - Common good effector, copper binding and uptake [ 86 , 87 ] ModA (PA1863) - Common good effector, molybdite...”
• The Breadth and Molecular Basis of Hcp-Driven Type VI Secretion System Effector Delivery
  Howard, mBio 2021
  • “...2 of which are significant Hcp2-specific interacting partners with molecular weights below that of Tse3 (PA2066 and PA2966) and 63 proteins enriched 3-fold by Hcp3, 9 of which are significant Hcp3-specific interacting partners with molecular weights below that of Tse3 (PA0256, PA3187, PA2372 [a 21-kDa protein...”
  • “...Hcp2-FLAG top interaction hits a Protein Fold change Significance b Description of protein Size (kDa) PA2066 10 2.71 Hypothetical, YdcF family protein 23.9 PA4226 PchE 4.4 1.52 Dihydroaeruginoic acid synthetase 156.4 PA2966 AcpP 3.1 1.35 Acyl carrier protein 8.7 a Hits are ordered by fold change,...”
• Traditional Chinese Medicine Tanreqing Inhibits Quorum Sensing Systems in Pseudomonas aeruginosa
  Yang, Frontiers in microbiology 2020
  • “...1.6 + Hypothetical protein PA2031 1.7 + Hypothetical protein PA2062 2.4 Probable pyridoxal-phosphate dependent enzyme PA2066 1.1 1.6 + Hypothetical protein PA2067 1.4 1.8 + Probable hydrolase PA2068 2.6 1.9 + Probable major facilitator superfamily (MFS) transporter PA2069 2.8 3.7 + Probable carbamoyl transferase PA2193 hcnA...”
• Effect of anaerobiosis and nitrate on gene expression in Pseudomonas aeruginosa
  Filiatrault, Infection and immunity 2005
  • “...PA1999 PA2003 PA2011 PA2012 PA2013 PA2014 PA2024 PA2052 PA2066 PA2067 PA2068 PA2069 PA2110 PA2112 PA2114 PA2194 PA2250 PA2266 PA2300 PA2306 PA2327 PA2329 PA2330...”
• A cystic fibrosis epidemic strain of Pseudomonas aeruginosa displays enhanced virulence and antimicrobial resistance
  Salunkhe, Journal of bacteriology 2005
  • “...PA1897 PA1901 PA1902 PA1903 PA1904 PA1905 PA1999 PA2000 PA2001 PA2030 PA2031 PA2066 aprI 2.6 11 3.3 osmC coxA 4.6 64 24 nuh 6.3 26 5.0 14 24 3.1 2.8 21 15 11...”
• Screening for quorum-sensing inhibitors (QSI) by use of a novel genetic system, the QSI selector
  Rasmussen, Journal of bacteriology 2005
  • “...PA2002 PA2013 PA2021 PA2030 PA2031 PA2035 PA2046 PA2050 PA2066 PA2067 PA2068 PA2069 PA2084 PA2086 PA2088 PA2090 PA2093 PA2110 Gene 1806 RASMUSSEN ET AL. J....”
• Identification, timing, and signal specificity of Pseudomonas aeruginosa quorum-controlled genes: a transcriptome analysis
  Schuster, Journal of bacteriology 2003
  • “...PA1896 PA1897 PA1914 PA1921 PA1930 PA1939 PA2030 PA2031 PA2066 PA2067 PA2068 PA2069 PA2076 PA2080 PA2081 PA2134 PA2142 PA2143 PA2144 PA2146 PA2147 PA2148 PA2151...”
• Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates
  Jeske, NPJ biofilms and microbiomes 2022
  • “...PA14_37745 PA14_51350 phnB PA14_19100 rhlA PA14_37760 PA14_51380 pqsE PA14_19110 rhlB PA14_37770 PA14_51390 pqsD PA14_19120 rhlR PA14_37780 PA14_51410 pqsC PA14_19130 rhlI PA14_38260 PA14_51420 pqsB PA14_19870 ldh PA14_39880 phzG2 PA14_51430 pqsA PA14_19900 PA14_39890 phzF2 PA14_53250 cpbD PA14_19910 pdhB PA14_39910 phzE2 PA14_55080 PA14_20610 lecB PA14_39925 phzD2 PA14_55940 PA14_20900 PA14_39945...”

ZMO0418 hypothetical protein from Zymomonas mobilis subsp. mobilis ZM4
Aligns to 42:183 / 203 (70.0%), covers 78.0% of PF02698, 44.2 bits

• Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates
  Skerker, Molecular systems biology 2013
  • “...mem Peptidase M48 Ste24p ZMO0200 auxo Anthranilate phosphoribosyltransferase ZMO0201 auxo Glutamine amidotransferase of anthranilate synthase ZMO0418 other Hypothetical protein ZMO0429 other Iron-sulfur cluster assembly accessory protein ZMO0468 auxo Anthranilate synthase component I ZMO0472 other rpsU-divergently transcribed protein ZMO0483 auxo Homoserine dehydrogenase ZMO0675 other Transcriptional regulator, LysR...”

ELI_11430 hypothetical protein from Erythrobacter litoralis HTCC2594
Aligns to 34:172 / 176 (79.0%), covers 81.8% of PF02698, 43.7 bits

• Gain and loss of phototrophic genes revealed by comparison of two Citromicrobium bacterial genomes
  Zheng, PloS one 2012
  • “...cell division ATP-binding protein FtsE; 3, cell division transport system permease protein; 4, hypothetical protein ELI_11430; 5, 1-acyl-sn-glycerol-3-phosphate acyltransferase; 6, histidinol-phosphate aminotransferase; 7, homoserine O-acetyltransferase; 8, succinate-semialdehyde dehydrogenase (NAD(P)+); 9, hypothetical protein ED21_17902; 10, glutathione S-transferase family protein; 11, protein-methionine-S-oxide reductase; 12, membrane carboxypeptidase; 13, trypsin-like...”

cg3330 putative secreted protein from Corynebacterium glutamicum ATCC 13032
Aligns to 45:177 / 191 (69.6%), covers 98.5% of PF02698, 33.1 bits

• Overexpression of the primary sigma factor gene sigA improved carotenoid production by Corynebacterium glutamicum: Application to production of β-carotene and the non-native linear C50 carotenoid bisanhydrobacterioruberin
  Taniguchi, Metabolic engineering communications 2017
  • “...et al., 2007 ): cg0096, cg0291, cg0753, cg0899, cg0998, cg1109, cg1147, cg1930, cg2704, cg3022 and cg3330. These genes represent a subset of the 95 SigB-dependent genes ( Larisch et al., 2007 ). In addition, two genes known to be differentially expressed in the stationary phase independent...”
• The alternative sigma factor SigB of Corynebacterium glutamicum modulates global gene expression during transition from exponential growth to stationary phase
  Larisch, BMC genomics 2007
  • “...of the six genes/operons cg0096/cg0097, cg1083 (cgtS10)/cg1084 (cgtR10), cg1417, cg2418 (ilvE), cg3141 (hmp) , and cg3330 . These genes were selected because their mRNA abundances showed high ratios during the transition phase only in the presence of SigB. The RACE-PCR was performed by using total RNA...”
  • “...glutamicum strain at transition phase Furthermore, transcription profiles of sigB, cg0096, cg1083, cg1417, cg2418, cg3141, cg3330, sigA, hom , and gap were determined by real-time RT-PCR during growth of C. glutamicum RES167. The house-keeping genes sigA , hom (encoding homoserine dehydrogenase) and gap (encoding glyceraldehyde-3-phosphate dehydrogenase)...”

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