PaperBLAST
PaperBLAST Hits for yciG (59 a.a., MAEHRGGSGN...)
Show query sequence
>yciG
MAEHRGGSGNFAEDREKASDAGRKGGQHSGGNFKNDPQRASEAGKKGGQQSGGNKSGKS
Running BLASTp...
Found 19 similar proteins in the literature:
YciG / b1259 stress-induced bacterial acidophilic repeat motifs-containing protein YciG from Escherichia coli K-12 substr. MG1655 (see 9 papers)
yciG / EW|b1259 uncharacterized protein yciG from Escherichia coli K12 (see 3 papers)
ECs1831 hypothetical protein from Escherichia coli O157:H7 str. Sakai
P21361 Uncharacterized protein YciG from Escherichia coli (strain K12)
b1259 orf, hypothetical protein from Escherichia coli str. K-12 substr. MG1655
EC042_RS07290 general stress protein from Escherichia coli 042
100% identity, 100% coverage
- Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
Bergholz, Applied and environmental microbiology 2009 - “...ECs1763 ECs1771 ECs1775 ECs1823 ECs1824 ECs1829 ECs1830 ECs1831 ECs1845 ECs2000 ECs2019 ECs2020 ECs2085 ECs2144 Exponential phase/ stationary phasec Log2...”
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...oppA -2.75 1 ECs2397 - 2.44 2 ECs1747 oppF -2.11 1 ECs2423 rplT -3.11 1 ECs1831 yciG 2.91 2 ECs2430 ydiZ 2.09 2 ECs1848 - 2.73 2 ECs2450 ydjS 3.94 2 ECs1849 acnA 4.07 2 ECs2451 astB 4.11 2 ECs1858 yciR 3.14 2 ECs2452 astD 5.88...”
- Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria
Kocurek, Journal of the American Society for Mass Spectrometry 2017 - “...24 h, 37 C Storage: 4 days, room temperature -Met 978.9706 +6 5867.78 -2.0 YciG P21361 36 -Met 1101.2759 +7 7701.88 -1.5 YahO P75694 91 -signal peptide 1189.5904 +7 8320.08 -1.3 UPF0337 protein YjbJ a P68206 80 1254.2614 +7 8772.78 -2.2 YdfK P76154 31 1494.9477 +7...”
- Preprotein mature domains contain translocase targeting signals that are essential for secretion
Chatzi, The Journal of cell biology 2017 - “...by alanyl or threonyl substitutions causing reduced hydrophobicity at the specified regions. YciG (Uniprot entry P21361 ), a hydrophilic, polar, and nonfolded polypeptide (negative absorbance band at 200 nm in circular dichroism, characteristic of unstructured proteins), has no measurable affinity for the translocase in the in...”
- Ferric Citrate Uptake Is a Virulence Factor in Uropathogenic Escherichia coli
Frick-Cheng, mBio 2022 - “...b4511 ybgS Uncharacterized protein 4.3 b0753 ybiX PKHD-type hydroxylase 3.7 b0804 yciG Uncharacterized protein 4.5 b1259 yddM Putative DNA-binding transcriptional regulator 4.6 b1477 ydiE Uncharacterized protein 4.2 b1705 yjjZ Uncharacterized protein 7.3 b4567 yncE PQQ-like domain-containing protein 5.0 b1452 yohC Putative inner membrane protein 3.7 b2135...”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity
Weber, Journal of bacteriology 2005 - “...b0707 b0753 b0767 b0865 b1003 b1050 b1188 b1164 b1258 b1259 b1341 b1547 b1614 b1783 b1784 b1847 b1999 b2080 b2086 b2602 b2660 b2672 b2665 Putative acyl-CoA...”
- Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis
Tani, Proceedings of the National Academy of Sciences of the United States of America 2002 - “...Gene ORF Fold yciG ydcS yeaG ygaU yhiV yjgB yncC yohF b1259 b1440 b1783 b2665 b3514 b4269 b1450 b2137 4.6 2.3 7.0 6.4 3.2 3.0 2.7 3.1 Genes indicated in bold...”
- 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 - “...in the right column. NCBI identifier (locus tag) Fold change hns 25C hns 37C (A) EC042_RS07290 (general stress protein) 1137.5 9.3 EC042_RS07280 (ferritin-like domain-containing protein) 736.5 8.8 EC042_RS00760 (fimbrial protein) 718.8 4.3 EC042_RS12270 (colanic acid biosynthesis acetyltransfer WcaF) 581.7 9.8 EC042_RS12260 (GDP-L-fucose synthase WcaG) 505.7 5.4...”
STM1513 putative cytoplasmic protein from Salmonella typhimurium LT2
STY1548 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi str. CT18
t1434 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
STM14_1829 general stress protein from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
90% identity, 95% coverage
- RpoS-regulated SEN1538 gene promotes resistance to stress and influences Salmonella enterica serovar enteritidis virulence
Arunima, Virulence 2020 - “...10.1080/21505594.2020.1743540-F0001 Figure 1. SEN1538 belongs to KGG superfamily of proteins. (a) Pairwise sequence alignment of STM1513 protein (GenBank Accession ID: AAL20432.1) from Salmonella enterica subspecies I serovar Typhimurium str. LT2 and SEN1538 protein (GenBank Accession ID: CAR33117.1) from Salmonella enterica subspecies I serovar Enteritidis str. P125109....”
- Stress response, amino acid biosynthesis and pathogenesis genes expressed in Salmonella enterica colonizing tomato shoot and root surfaces
Han, Heliyon 2020 - “...terminase, large subunit - 2.0 0.003 STM1485 STM1485 Acid shock protein 5.7 0.012 8.0 0.008 STM1513 STM1513 Stress-induced bacterial acidophilic repeat motif 3.3 0.002 STM1808 STM1808 Putative cytoplasmic protein; NsrR regulon 0.008 STM1851 STM1851 hypothetical protein 1.3 0.003 1.6 0.003 STM05615 STM05615 hypothetical protein 2.2 0.002...”
- “...proteinIbpB - 5.3 hslJ Heat-inducible protein HslJ 1.0 1.1 STM1485 Acid shock protein 5.7 8.0 STM1513 Stress-induced bacterial acidophilic repeat motif 3.3 - yhhW quercetin 2,3-dioxygenase 3.5 - basS Member of the 2-component regulatory system BasS/BasR. Autophosphorylates and activates BasR by phosphorylation. Plays a role in...”
- The intestinal fatty acid propionate inhibits Salmonella invasion through the post-translational control of HilD
Hung, Molecular microbiology 2013 - “...STM2153 yehE 0.4 STM2315 yfbK 0.4 STM2897 invE 0.4 STM0271 - 0.4 STM4265 soxS 0.4 STM1513 - 0.4 STM2879 sicP 0.4 STM1774 sirC 0.4 STM2880 - 0.4 STM1239 - 0.4 STM2875 hilD 0.4 a Genes shown in bold are located within SPI1 or are controlled by...”
- An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs
Chao, The EMBO journal 2012 - “...encode major ABC transporters, and the yahO and STM1513 genes of unknown function X2-fold (Figure 5A). This rapid downregulation suggests that DapZ regulates...”
- “...-1 0 -3 yahO GcvB repressed genes dppB -2 ygaF oppF SL0645 STM1513 oppD oppC dppC dppF -2 glpF -1 0 1 Fold change (Log2) C 2 3 3500 1750 3000 1500 Miller units...”
- Rapid screening of epidemiologically important Salmonella enterica subsp. enterica serovars by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry
Dieckmann, Applied and environmental microbiology 2011 - “...Observed mass(es) (Da) Putative cytoplasmic protein (STM1513) 6,009, 6,036 Putative uncharacterized protein YciG (Q7CQG0_SALTY) Putative uncharacterized protein...”
- Computational prediction of type III and IV secreted effectors in gram-negative bacteria
McDermott, Infection and immunity 2011 - “...STM2139 PSLT037 STM0082 STM3762 STM1087 STM1599 STM1809 STM1513 STM1633 STM0211 STM1121 STM3392 STM4082 STM3595 STM1548 a SIEVE EffectiveT3 Lower and Schneider...”
- Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation
Ansong, PloS one 2009 - “...strongly up-regulated in the hfq mutant relative to wildtype in LB Log, while OsmY and STM1513 were strongly down-regulated in the hfq mutant relative to wildtype in AMM-1 and LB Stat respectively. Deletion of SmpB resulted in a significant decrease in protein expression levels of FliC...”
- “...in AMM-2. Western blot analysis of the relative protein levels of each of HtrA, OsmY, STM1513, FliC, and YciF ( Figure S2 ) served to further verify our global proteomics measurements. As transcript levels are often equated to protein expression levels, it was of particular interest...”
- In vivo expression of Salmonella enterica serotype Typhi genes in the blood of patients with typhoid fever in Bangladesh
Sheikh, PLoS neglected tropical diseases 2011 - “...hypothetical protein STY0321 t2569 Rhs-family protein STY1058-60,1063-64,1069 putative prophage proteins STY1323 t1640 conserved hypothetical protein STY1548 t1434 conserved hypothetical protein STY1732 t1256 ydhZ conserved hypothetical protein STY1916 t1087 hyaD hydrogenase-1 operon protein HyaD STY2244 t0835 pduB putative propanediol utilization protein PduB STY2608 t0487 conserved hypothetical protein...”
- In vivo expression of Salmonella enterica serotype Typhi genes in the blood of patients with typhoid fever in Bangladesh
Sheikh, PLoS neglected tropical diseases 2011 - “...protein STY0321 t2569 Rhs-family protein STY1058-60,1063-64,1069 putative prophage proteins STY1323 t1640 conserved hypothetical protein STY1548 t1434 conserved hypothetical protein STY1732 t1256 ydhZ conserved hypothetical protein STY1916 t1087 hyaD hydrogenase-1 operon protein HyaD STY2244 t0835 pduB putative propanediol utilization protein PduB STY2608 t0487 conserved hypothetical protein STY3448...”
- Adaptive evolution in asymptomatic host confers MDR Salmonella with enhanced environmental persistence and virulence
He, The Science of the total environment 2024 (PubMed)- “...herein we found that an adaptive evolution, driven by mutagenesis in a small protein-encoding gene (STM14_1829), conferred the multidrug resistant (MDR) Salmonella with increased fitness in asymptomatic host. Then the mechanistic study demonstrated that only one amino acid substitution in small protein STM14_1829 rendered MDR Salmonella...”
- L-Arabinose Transport and Metabolism in Salmonella Influences Biofilm Formation
Vasicek, Frontiers in cellular and infection microbiology 2021 - “...AdrA sitC -4.94 putative permease sitB -5.22 putative ATP-binding protein ycdC -5.25 putative transcriptional repressor STM14_1829 -5.37 putative cytoplasmic protein sitD -5.46 putative permease nrdI -5.47 Protein NrdI ymdF -16.91 putative cytoplasmic protein yjfY -21.02 putative outer membrane protein csgA -30.21 cryptic curlin major subunit csgB...”
- New genotypes of Helicobacter Pylori VacA d-region identified from global strains
Soyfoo, BMC molecular and cell biology 2021 - “...et al., where the authors found intrinsically disordered proteins in Salmonella enterica , namely YciG, STM14_1829, and YmdF [ 27 ]. Another feature of the IDR is that it consists of repeated motifs of amino acids [ 28 , 29 ]. Results from our study also...”
- RpoS-regulated SEN1538 gene promotes resistance to stress and influences Salmonella enterica serovar enteritidis virulence
Arunima, Virulence 2020 - “...in S . Typhimurium and E. coli [ 17 , 20 , 21 ]. Furthermore, STM14_1829 was reported to play a role in the swimming motility of S. Typhimurium ATCC14028 [ 19 ]. Nonetheless, the role of the KGG protein family in bacterial stress pathways and...”
- “...in 1538 corroborated with a previous report on phoP upregulation in the mutant of ortholog STM14_1829 [ 19 ]. We further investigated the expression of PhoP-regulated genes in 1538, as these have been previously reported in stress resistance by Salmonella [ 34 , 36 , 37...”
- A Family of Small Intrinsically Disordered Proteins Involved in Flagellum-Dependent Motility in Salmonella enterica
Oguri, Journal of bacteriology 2019 - “...we identified three paralogous small genes (ymdF, STM14_1829, and yciG) required for wild-type flagellum-dependent swimming and swarming motility. The ymdF,...”
- “...are unstructured in solution. A mutant deleted for STM14_1829 showed the most severe motility defect, indicating that among the three paralogs, STM14_1829 is a...”
- Proteome remodelling by the stress sigma factor RpoS/σS in Salmonella: identification of small proteins and evidence for post-transcriptional regulation
Lago, Scientific reports 2017 - “...1 , Supplementary Fig. S5 , Supplementary Dataset S1 ). The uncharacterized ORFs ymdF and STM14_1829 are paralogous to yciG (Table 1 , Supplementary Fig. S6 ). YciG 33 , 34 belongs to the group of hydrophilins, proteins defined by high glycine content and hydrophilicity index...”
- “...Paralogous genes e STM14_1275 KGG repeat IPR019626 55 Yes ymdF 13, 14 Bacteria and Eukaryota STM14_1829 KGG repeat IPR019626 60 Yes STM14_2091 KGG repeat IPR019626 60 Yes yciG 1214 a Information about protein families (DUF), motifs (Interpro IPR), 3D structures (PDB code), predicted -helical trans-membrane (TM)...”
SEN1538 hypothetical protein from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
IAF69_RS06740 general stress protein from Salmonella enterica subsp. enterica serovar Enteritidis
90% identity, 95% coverage
- Insights into the mechanism regulating the differential expression of the P28-OMP outer membrane proteins in obligatory intracellular pathogen Ehrlichia chaffeensis
Duan, Emerging microbes & infections 2021 - “...an important strategy employed by pathogenic bacteria [ 4 ]. In Salmonella enterica serovar Enteritidis, SEN1538 is regulated by RpoS in response to host and environmental stress, and is critical for bacterial invasion of and replication in macrophages, and systemic infection in mice [ 5 ]....”
- “.... 11018137 5 Arunima A , Swain SK , Ray S , et al. RpoS-regulated SEN1538 gene promotes resistance to stress and influences Salmonella enterica serovar enteritidis virulence . Virulence . 2020 ; 11 ( 1 ): 295 314 . 32193977 6 Schwan TG , Piesman...”
- RpoS-regulated SEN1538 gene promotes resistance to stress and influences Salmonella enterica serovar enteritidis virulence
Arunima, Virulence 2020 - “...KVIR kvir20 Virulence 2150-5594 2150-5608 Taylor & Francis 7161692 32193977 1743540 10.1080/21505594.2020.1743540 Research Paper RpoS-regulated SEN1538 gene promotes resistance to stress and influences Salmonella enterica serovar enteritidis virulence A. ARUNIMA ET AL. VIRULENCE Arunima Aryashree a Swain Sunil Kumar a Ray Shilpa a Prusty Birendra Kumar...”
- “...regulator, functional information regarding the genes of the regulon is currently limited. Here, we identified SEN1538 as a conserved RpoS-regulated gene belonging to the KGG protein superfamily. We further assessed its role in pathogenic stress responses and virulence. When SEN1538 was deleted (1538), the pathogen showed...”
- Draft Genome Sequence of Salmonella enterica subsp. enterica Serovar Enteritidis ODA 99-30581-13, a Heat-Resistant Strain Isolated from Shell Eggs
Xu, Microbiology resource announcements 2021 - “...( 13 ). Additionally, the general stress protein (NCBI Protein accession number WP_000807638.1 ; locus_tag IAF69_RS06740), which promotes heat resistance specific to Salmonella Enteritidis ( 14 ), was encoded in the ODA 99-30581-13 annotated genome sequence. The presence of these heat stress response-related genes might explain...”
KPN_01149 hypothetical protein from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
KPNIH1_10100 general stress protein from Enterobacter bugandensis
89% identity, 97% coverage
- RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection
Avican, Nature communications 2021 - “...d Proportion of reads mapped to the K. pneumoniae CsrB and to the region covering KPN_01149 CDS with 5-UTR and 3-UTR sequences under each stress condition. e Number and alignments of reads mapped to KPN_01149 and its UTRs in stationary phase. Green indicates forward reads, red...”
- “...blue indicates paired reads. The vertical dashed line indicates the position of the TSS of KPN_01149 53 . f Proportion of reads mapped to SRS42 in S. aureus MRSA and MSSA genomes under each stress condition. g Number and alignments of reads mapped to SRS42 in...”
- A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria
Kaleta, NPJ biofilms and microbiomes 2022 - “..., ymdF and csrA from E. coli , and the K. pneumoniae ymdF inparalogs (KPNIH1_09545, KPNIH1_10100, and KPNIH1_13915) were amplified using primers listed in Supplementary Table 5 from P. aeruginosa PAO1, E. coli BW25113, or K. pneumoniae MKP103 genomic DNA and placed under the control of...”
KPN_01841 hypothetical protein from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
A6T9K1 Stress-induced acidophilic repeat motif-containing protein from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
KPNIH1_13915 general stress protein from Klebsiella pneumoniae subsp. pneumoniae KPNIH1
KPHS_28070 general stress protein from Klebsiella pneumoniae subsp. pneumoniae HS11286
87% identity, 97% coverage
- Zinc limitation in Klebsiella pneumoniae profiled by quantitative proteomics influences transcriptional regulation and cation transporter-associated capsule production
Sukumaran, BMC microbiology 2021 - “...KPN_pKPN3p05911 Uncharacterized protein A6TC61 6.434 cysU Sulfate, thiosulfate transport system permease T protein A6T9K1 7.243 KPN_01841 Uncharacterized protein A6TF61 7.816 yhhA Uncharacterized protein A6TAE9 12.359 KPN_02142 Uncharacterized protein A6T769 13.369 acyP Acylphosphatase A6T6K9 13.487 hutC Histidine utilization repressor Secretome profiling of zinc availability highlights changes in...”
- Zinc limitation in Klebsiella pneumoniae profiled by quantitative proteomics influences transcriptional regulation and cation transporter-associated capsule production
Sukumaran, BMC microbiology 2021 - “...A6TI69 5.862 KPN_pKPN3p05911 Uncharacterized protein A6TC61 6.434 cysU Sulfate, thiosulfate transport system permease T protein A6T9K1 7.243 KPN_01841 Uncharacterized protein A6TF61 7.816 yhhA Uncharacterized protein A6TAE9 12.359 KPN_02142 Uncharacterized protein A6T769 13.369 acyP Acylphosphatase A6T6K9 13.487 hutC Histidine utilization repressor Secretome profiling of zinc availability highlights...”
- A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria
Kaleta, NPJ biofilms and microbiomes 2022 - “...and csrA from E. coli , and the K. pneumoniae ymdF inparalogs (KPNIH1_09545, KPNIH1_10100, and KPNIH1_13915) were amplified using primers listed in Supplementary Table 5 from P. aeruginosa PAO1, E. coli BW25113, or K. pneumoniae MKP103 genomic DNA and placed under the control of an arabinose-inducible...”
- Use of a combined antibacterial synergy approach and the ANNOgesic tool to identify novel targets within the gene networks of multidrug-resistant Klebsiella pneumoniae
Lee, mSystems 2024 - “...KPHS_46340 (putrescine aminotransferases) and KPHS_43350 (acetyl-CoA acetyltransferase) results in a connection with the target gene KPHS_28070, which is a novel noncoding sRNA. KPHS_02470 (glucose-6-phosphate isomerase) is a positively expressed lysine riboswitch-associated gene. KPHS_02470 reduced KPHS_09840 levels, and KPHS_46340 form a network indirectly through KPHS_13980 (carboxylate-amine ligase)....”
- “...downregulation of KPHS_31750 and the upregulation of KPHS_31180. In particular, KPHS_34140 is directly associated with KPHS_28070 (general stress protein), the target gene of a novel sRNA predicted by the ANNOgesic analysis. TABLE 1 Genomic RNA thermometer activity a #ID Genome Strand Associated_CDS Start_genome End_genome Rfam_ID Rfam_name...”
STM1728 putative cytoplasmic protein from Salmonella typhimurium LT2
STY1323 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi str. CT18
t1640 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
SL1344_1659, STM14_2091, STM14_RS09540 general stress protein from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
88% identity, 98% coverage
- Probing the ArcA regulon under aerobic/ROS conditions in Salmonella enterica serovar Typhimurium
Morales, BMC genomics 2013 - “...STM4165 STM14_5006 rsd 2.75 1.69 2.74 - 67 GTTAACAACATGCCA 1.20E-05 anti-RNA polymerase sigma 70 factor STM1728 STM14_2091 yciG 1.68 1.95 2.11 - 261 GTTAATGCATTGTTT 1.50E-05 putative cytoplasmic protein STM0292 STM14_0341 - 1.18 2.12 2.18 - 248 GTTCATCAAATGTAG 6.80E-05 putative RHS-like protein STM2220 STM14_2744 yejG 5.84 2.41...”
- Adrenaline modulates the global transcriptional profile of Salmonella revealing a role in the antimicrobial peptide and oxidative stress resistance responses
Karavolos, BMC genomics 2008 - “...fur regulated Salmonella Mn transporter 1.5 Oxidative Stress STM4055, sodA superoxide dismutase 1.9 Function unknown STM1728, yciG putative cytoplasmic protein 1.8 STM2263, yojI putative ABC-type multidrug/protein/lipid transport system 1.7 STM1586 putative periplasmic protein, similar to E. coli putative receptor 1.7 STM1729, yciF putative cytoplasmic protein 1.7...”
- Transcriptomic study of Salmonella enterica subspecies enterica serovar Typhi biofilm
Chin, BMC genomics 2017 - “...hupA Histone like DNA-binding protein HU-alpha 2.59176 5.00E-05 0.001837 STY1982 Hypothetical protein 2.61628 5.00E-05 0.001837 STY1323 Hypothetical protein 2.67081 5.00E-05 0.001837 ompC Outer membrane protein C 2.75117 5.00E-05 0.001837 lppA Major outer membrane lipoprotein 2.93078 5.00E-05 0.001837 STY1938 Hypothetical protein 3.30784 5.00E-05 0.001837 rpsV 30S ribosomal...”
- In vivo expression of Salmonella enterica serotype Typhi genes in the blood of patients with typhoid fever in Bangladesh
Sheikh, PLoS neglected tropical diseases 2011 - “...Unclassified and Unknown proteins t3166 hypothetical protein STY0321 t2569 Rhs-family protein STY1058-60,1063-64,1069 putative prophage proteins STY1323 t1640 conserved hypothetical protein STY1548 t1434 conserved hypothetical protein STY1732 t1256 ydhZ conserved hypothetical protein STY1916 t1087 hyaD hydrogenase-1 operon protein HyaD STY2244 t0835 pduB putative propanediol utilization protein PduB...”
- A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium
Barquist, Nucleic acids research 2013 - “...1646 20 118 SL1628 1355 t1612 1364 hypothetical protein 23 177 1 5 SL1659 183 t1640 183 yciG conserved hypothetical protein 78 617 16 104 SL1684 1014 t1664 1014 Hnr putative regulatory protein 37 277 4 25 SL1785 396 t1022 396 conserved hypothetical protein 166 2823...”
- In vivo expression of Salmonella enterica serotype Typhi genes in the blood of patients with typhoid fever in Bangladesh
Sheikh, PLoS neglected tropical diseases 2011 - “...and Unknown proteins t3166 hypothetical protein STY0321 t2569 Rhs-family protein STY1058-60,1063-64,1069 putative prophage proteins STY1323 t1640 conserved hypothetical protein STY1548 t1434 conserved hypothetical protein STY1732 t1256 ydhZ conserved hypothetical protein STY1916 t1087 hyaD hydrogenase-1 operon protein HyaD STY2244 t0835 pduB putative propanediol utilization protein PduB STY2608...”
- Phosphorus starvation response and PhoB-independent utilization of organic phosphate sources by <i>Salmonella enterica</i>
Bruna, Microbiology spectrum 2023 - “...depicting the genomic context of zitB ( STM14_RS04415 ), cydB ( STM14_RS02420 ), yciG ( STM14_RS09540 ), apeE ( STM14_RS03455 ), and phoN2 ( STM14_RS19030 ) loci in Salmonella . The bent arrows represent previously mapped transcriptional start sites ( 20 , 28 ). Protein-coding sequences...”
- Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon
Huesa, Nucleic acids research 2021 - “...2.68 1601764 SL1344_1494 yddX gene promoter-5UTR + 269 1601773 9 to 5 TGAGATTTATCCTA 2.96 1782070 SL1344_1659 yciG gene promoter + 340 1782355 55 to 41 TAAGAAAACTCCTA 3.01 1251955 SL1344_1149 ycfJ gene promoter + 123 1252055 100 to 86 TCGGAGTTGTCCGA 3.35 1.50 1756560 SL1344_1637 osmB gene promoter...”
- Proteome remodelling by the stress sigma factor RpoS/σS in Salmonella: identification of small proteins and evidence for post-transcriptional regulation
Lago, Scientific reports 2017 - “...IPR019626 55 Yes ymdF 13, 14 Bacteria and Eukaryota STM14_1829 KGG repeat IPR019626 60 Yes STM14_2091 KGG repeat IPR019626 60 Yes yciG 1214 a Information about protein families (DUF), motifs (Interpro IPR), 3D structures (PDB code), predicted -helical trans-membrane (TM) fragments, signal peptide (SP) and lipoprotein...”
- “...E . coli K12 orthologs in transcriptomic analyses. e STM14_1275 and STM14_1829 are paralogous to STM14_2091 (Supplementary Fig. S6 and Table S1 ). Global effects of S on protein abundance in Salmonella A comprehensive quantitative proteomic analysis was performed using the wild type and rpoS strains...”
- The Bacterial iprA Gene Is Conserved across Enterobacteriaceae, Is Involved in Oxidative Stress Resistance, and Influences Gene Expression in Salmonella enterica Serovar Typhimurium
Herman, Journal of bacteriology 2016 - “...iprA mutant, including operons SL1344_1488 to SL1344_1491, SL1344_1659 to SL1344_1661, and SL1344_0637 and SL1344_0638 (Table 2). Among the strongly altered...”
- “...SL1344_1443 SL1344_1491 SL1344_1516 SL1344_1519 SL1344_1659 SL1344_1660 SL1344_1661 SL1344_1830 SL1344_2116 SL1344_2185 SL1344_2343 SL1344_2345 SL1344_2887...”
- Probing the ArcA regulon under aerobic/ROS conditions in Salmonella enterica serovar Typhimurium
Morales, BMC genomics 2013 - “...STM14_5006 rsd 2.75 1.69 2.74 - 67 GTTAACAACATGCCA 1.20E-05 anti-RNA polymerase sigma 70 factor STM1728 STM14_2091 yciG 1.68 1.95 2.11 - 261 GTTAATGCATTGTTT 1.50E-05 putative cytoplasmic protein STM0292 STM14_0341 - 1.18 2.12 2.18 - 248 GTTCATCAAATGTAG 6.80E-05 putative RHS-like protein STM2220 STM14_2744 yejG 5.84 2.41 2.94...”
Z1924 unknown protein encoded by prophage CP-933X from Escherichia coli O157:H7 EDL933
ECs1655 hypothetical protein from Escherichia coli O157:H7 str. Sakai
88% identity, 93% coverage
KPN_01030 hypothetical protein from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
KPNIH1_09545 general stress protein from Klebsiella pneumoniae subsp. pneumoniae KPNIH1
85% identity, 93% coverage
- Capsule deletion via a λ-Red knockout system perturbs biofilm formation and fimbriae expression in Klebsiella pneumoniae MGH 78578
Huang, BMC research notes 2014 - “...change Up-regulated genes KPN_00042 Hypothetical 9.00 13.38 0.0021 20.82 KPN_00321 Hypothetical 6.63 9.20 0.0007 5.92 KPN_01030 Hypothetical 8.15 10.65 0.0170 5.66 KPN_01107 Hypothetical 9.41 13.32 0.0021 15.03 KPN_01226 Periplasmic protein 10.59 13.27 0.0052 6.38 KPN_01279 Lipoprotein, osmotically inducible 11.03 13.96 0.0012 7.62 KPN_01568 Hypothetical 7.46 10.07...”
- A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria
Kaleta, NPJ biofilms and microbiomes 2022 - “...aeruginosa , ymdF and csrA from E. coli , and the K. pneumoniae ymdF inparalogs (KPNIH1_09545, KPNIH1_10100, and KPNIH1_13915) were amplified using primers listed in Supplementary Table 5 from P. aeruginosa PAO1, E. coli BW25113, or K. pneumoniae MKP103 genomic DNA and placed under the control...”
STM14_1275 general stress protein from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
STM1121 putative cytoplasmic protein from Salmonella typhimurium LT2
87% identity, 92% coverage
- Proteome remodelling by the stress sigma factor RpoS/σS in Salmonella: identification of small proteins and evidence for post-transcriptional regulation
Lago, Scientific reports 2017 - “...to long 5 UnTranslated Regions (UTR) of the S -dependent genes STM14_0421, STM14_1558, STM14_5097, and STM14_1275, respectively (Supplementary Fig. S4 and Table S1 ). This hypothesis is consistent with the non-canonical start codons and lack of ribosome binding sites for the putative ORFs STM14_0419, STM14_1559 and...”
- “...YtjA, 2TM fragments, DUF1328 IPR009760 53 ytjA 13, 14 Bacteria and Archaea Paralogous genes e STM14_1275 KGG repeat IPR019626 55 Yes ymdF 13, 14 Bacteria and Eukaryota STM14_1829 KGG repeat IPR019626 60 Yes STM14_2091 KGG repeat IPR019626 60 Yes yciG 1214 a Information about protein families...”
- Repression of Salmonella enterica phoP expression by small molecules from physiological bile
Antunes, Journal of bacteriology 2012 - “...STM3511 STM3465 STM3505 STM1324 STM0629 STM3360 STM1200 STM1121 STM2856 STM3147 STM3302 STM0974 STM2532 STM0441 STM0439 STM3630 ORF01133 STM0544 STM0154 STM0158...”
- Computational prediction of type III and IV secreted effectors in gram-negative bacteria
McDermott, Infection and immunity 2011 - “...STM0082 STM3762 STM1087 STM1599 STM1809 STM1513 STM1633 STM0211 STM1121 STM3392 STM4082 STM3595 STM1548 a SIEVE EffectiveT3 Lower and Schneider 41 CyaA fusion...”
STY1156 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi str. CT18
84% identity, 93% coverage
- Transcriptomic study of Salmonella enterica subspecies enterica serovar Typhi biofilm
Chin, BMC genomics 2017 - “...gene, e.g. up-regulated genes STY1254 (1,207,090...1207347), and yheA (4,231,386...4231580), and down-regulated genes rmf (1,066,679...1066846) and STY1156 (1,116,294...1116461) Table 2 Selected differentially up-regulated genes and their functions in S. Typhi biofilm cells Gene Gene function log 2 -fold change p -value q-value STY1254 Hypothetical protein 7.92174 5.00E-05...”
YmdF / b4518 stress-induced bacterial acidophilic repeat motifs-containing protein YmdF from Escherichia coli K-12 substr. MG1655 (see 2 papers)
P56614 Uncharacterized protein YmdF from Escherichia coli (strain K12)
SSON53G_RS05440 general stress protein from Shigella sonnei 53G
87% identity, 90% coverage
- Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria
Kocurek, Journal of the American Society for Mass Spectrometry 2017 - “...UniProt accession no. Cov (%) Conditions Modifications Escherichia coli BL21 959.1288 +6 5748.73 -0.8 YmdF P56614 66 Incubation: 24 h, 37 C Storage: 4 days, room temperature -Met 978.9706 +6 5867.78 -2.0 YciG P21361 36 -Met 1101.2759 +7 7701.88 -1.5 YahO P75694 91 -signal peptide 1189.5904...”
- Shigella sonnei infection of zebrafish reveals that O-antigen mediates neutrophil tolerance and dysentery incidence
Torraca, PLoS pathogens 2019 - “...in D are: adhE_3, glyA, purF, purD, purL, SSON53G_RS25460 (treB-like), gcvP, gcvH, yjiY, gcvT, treC, SSON53G_RS05440 (ymdF-like), gadC, SSON53G_RS20945 (slp-like), otsA, SSON53G_RS02230 (bolA-like), suhB, katE, SSON53G_RS31575 (mcbA-like), hdeD, gadB_1, gadB_2, yohC, gadE, hdeB, SSON53G_RS09595 (narU-like), yegP, ycgB, hdeA, SSON53G_RS20815 (yhiM-like), fadB, yafH, fadA, dadA, artJ, argC,...”
RGVIR_PSEAE / Q9I1W9 Putative virulence-regulating protein PA2146 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 2 papers)
PA2146 hypothetical protein from Pseudomonas aeruginosa PAO1
PA14_36820 hypothetical protein from Pseudomonas aeruginosa UCBPP-PA14
80% identity, 92% coverage
- function: May be involved in the regulation of the production of pyocyanine, one of the major virulence factors secreted by P.aeruginosa, and other virulence factors.
disruption phenotype: Knockout of the gene increases production of pyocyanine and promotes P.aeruginosa pathogenicity in vivo (PubMed:33134189). Deletion of the gene has no effect on phagocytosis, but it significantly reduces the production of cytokines in murine macrophage-like RAW264.7 cells and human macrophage-like cell line THP- 1 (PubMed:33134189). In an acute pneumonia murine infection model, infection with the mutant inhibits cytokine secretion in the lungs but increases the infiltration of inflammatory cells compared to the wild- type strain (PubMed:33134189). In plant assays (poplar and barley), disruption of the gene increases motility and reduces virulence in barley (PubMed:21261818). - Direct prediction of antimicrobial resistance in Pseudomonas aeruginosa by metagenomic next-generation sequencing
Cao, Frontiers in microbiology 2024 - “...dysfunction can significantly reduce its virulence ( Corral et al., 2021 ). Moreover, ymdF as PA2146 homologs contributes to biofilm formation and drug tolerance in Escherichia coli , Klebsiella pneumoniae , and P. aeruginosa ( Kaleta et al., 2022 ; Kaleta and Sauer, 2023 ), indicating...”
- Virtual Screening and Meta-Analysis Approach Identifies Factors for Inversion Stimulation (Fis) and Other Genes Responsible for Biofilm Production in <i>Pseudomonas aeruginosa</i>: A Corneal Pathogen
Emeka, Current issues in molecular biology 2024 - “...M.F. Petrova O.E. Zampaloni C. Garcia-Alcalde F. Parker M. Sauer K. A Previously Uncharacterized Gene, PA2146, Contributes to Biofilm Formation and Drug Tolerance across the -Proteobacteria NPJ Biofilms Microbiomes 2022 8 54 10.1038/s41522-022-00314-y 35798749 24. Subramanian D. Natarajan J. Integrated Meta-Analysis and Machine Learning Approach Identifies...”
- “...III secretion outer membrane protein PscC precursor 1.81 0.0001 PA1296 - 2-hydroxyacid dehydrogenase 1.75 0.0006 PA2146 - conserved hypothetical protein 1.74 0.0007 PA0044 exoT exoenzyme T 1.74 0.0001 PA4571 - cytochrome c 1.73 1.81 10 5 PA2938 - transporter 1.73 4.82 10 6 PA5170 arcD arginine/ornithine...”
- Cross-Kingdom Pathogenesis of <i>Pantoea alfalfae</i> CQ10: Insights from Transcriptome and Proteome Analyses
Su, Microorganisms 2024 - “...in the CQ10 strain when intercropped with alfalfa and mouse hosts revealed four co-expression genes: PA2146 , LeuB , EadM , and Dps (atu2477) ( Figure 6 B). PA1246 was categorized as the category of increased pathogenicity, while the other three were categorized as the category...”
- MoaB1 Homologs Contribute to Biofilm Formation and Motility by Pseudomonas aeruginosa and Escherichia coli
Kaleta, Journal of bacteriology 2023 - “...wild-type levels. Moreover, MoaB1 was found to interact with other conserved biofilm-associated proteins, PA2184 and PA2146, as well as the sensor-kinase SagS. However, despite the interaction, MoaB1 failed to restore SagS-dependent expression of brlR encoding the transcriptional regulator BrlR, and inactivation of moaB1 or moaBEc had...”
- 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 - “...reductase NorD protein 4.14 0 15 PA5071 16S ribosomal RNA methyltransferase RsmE 3.57 0.001 16 PA2146 Hypothetical protein 3.53 0.001 17 nosY Cu-processing system permease protein 3.46 0.002 18 PA3377 Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase 3.45 0.0002 19 PA1211 Hypothetical protein 3.40 0.01 20 PA0818 Hypothetical...”
- “...208964.PA3395 9 9 PA3913 208964.PA3913 8 10 PA0515 208964.PA0515 6 11 PA0522 208964.PA0522 6 12 PA2146 208964.PA2146 6 13 narH 208964.PA3874 6 14 anvM 208964.PA3880 5 15 PA0177 208964.PA0177 3 16 PA1763 208964.PA1763 3 17 PA2180 208964.PA2180 3 18 PA3274 208964.PA3274 3 19 ku 208964.PA2150 3...”
- Recent advances in therapeutic targets identification and development of treatment strategies towards Pseudomonas aeruginosa infections
Sanya, BMC microbiology 2023 - “...research in this field highly relevant. Recently, the small hypothetical protein encoded by the gene PA2146 and conserved in -proteobacteria has been shown to regulate biofilm architecture and antimicrobial tolerance of P. aeruginosa PAO1. The deletion of this gene did not impact growth rate of planktonic...”
- “...MF Petrova OE Zampaloni C Garcia-Alcalde F Parker M Sauer K A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the -Proteobacteria NPJ Biofilms Microbiomes 2022 8 1 54 10.1038/s41522-022-00314-y 35798749 27. Bjarnsholt T Jensen P Fiandaca MJ Pedersen J Hansen CR...”
- Distinct Screening Approaches Uncover PA14_36820 and RecA as Negative Regulators of Biofilm Phenotypes in Pseudomonas aeruginosa PA14
Yahya, Microbiology spectrum 2023 - “...(Fig. S2A and B). Curiously, and in contrast to our findings, its ortholog in PAO1, PA2146 , has been characterized as a gene that is required for biofilm formation and resistance to tobramycin, as its inactivation suppresses biofilm formation and renders biofilms susceptible to tobramycin (...”
- “...Garcia-Alcalde F , Parker M , Sauer K . 2022 . A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the deltaproteobacteria . NPJ Biofilms Microbiomes 8 : 54 . doi: 10.1038/s41522-022-00314-y . 35798749 44 Ching C , Muller P , Brychcy...”
- A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria
Kaleta, NPJ biofilms and microbiomes 2022 - “...Microbiomes 2055-5008 Nature Publishing Group UK London 9262955 314 10.1038/s41522-022-00314-y Article A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the -Proteobacteria Kaleta Matthew F. 1 2 Petrova Olga E. 1 2 Zampaloni Claudia 3 Garcia-Alcalde Fernando 3 Parker Matthew 1 http://orcid.org/0000-0002-1177-6328...”
- “...with 8 genes affecting both biofilm phenotypes. Amongst the genes affecting both biofilm phenotypes was PA2146, encoding a small hypothetical protein that exhibited some of the most substantial increases in transcript abundance during biofilm growth by P. aeruginosa PAO1 and clinical isolates. PA2146 is highly conserved...”
- More
- Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria
Kocurek, Journal of the American Society for Mass Spectrometry 2017 - “...L29 Q9HWE3 29 Incubation: 48 h, 37 C Sampled fresh 1090.1381 +5 5445.65 0.4 PA2146 Q9I1W9 67 -Met 1223.5075 +7 8557.50 -0.7 PA4739 Q9HV60 61 -signal peptide (132) 1245.9733 +6 7469.80 -0.2 CspA P95459 31 -Met Staphylococcus aureus MSSA476 733.7894 +3 2198.35 0.6 Phenol-soluble modulin 4...”
- Distinct Screening Approaches Uncover PA14_36820 and RecA as Negative Regulators of Biofilm Phenotypes in Pseudomonas aeruginosa PA14
Yahya, Microbiology spectrum 2023 - “...Washington, DC 10100956 36971546 03774-22 10.1128/spectrum.03774-22 spectrum.03774-22 Research Article bacteriology Bacteriology Distinct Screening Approaches Uncover PA14_36820 and RecA as Negative Regulators of Biofilm Phenotypes in Pseudomonas aeruginosa PA14 Yahya Amal H. a Harston Sophie R. a Colton William L. a https://orcid.org/0000-0001-8252-1050 Cabeen Matthew T. a matthew.cabeen@okstate.edu...”
- “...of the 16550 deletion and found six differentially regulated genes. Among them, our results implicated PA14_36820 as a negative regulator of biofilm matrix production, while the remaining 5 had modest effects on swarming motility. We also screened a transposon library in a biofilm-impaired amrZ 16550 strain...”
- Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates
Jeske, NPJ biofilms and microbiomes 2022 - “...PA14_36330 hcnA PA14_48115 aprD PA14_13390 PA14_36530 PA14_48140 aprX PA14_15090 - PA14_36620 PA14_49260 napB PA14_16250 lasB PA14_36820 PA14_49310 PA14_18630 eprS 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...”
- Contribution of Veillonella parvula to Pseudomonas aeruginosa-mediated pathogenicity in a murine tumor model system
Pustelny, Infection and immunity 2015 - “...PA14_13650 PA14_06280 PA14_25140 PA14_36520 PA14_28880 PA14_07380 PA14_21470 PA14_36820 PA14_11060 PA14_36890 3.19 3.16 3.12 3.12 3.11 3.07 3.07 3.03 2.85 2.85...”
PA2190 hypothetical protein from Pseudomonas aeruginosa PAO1
70% identity, 45% coverage
- A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria
Kaleta, NPJ biofilms and microbiomes 2022 - “...be increased in burn wound infection, further noting that genes within the region of PA2134 PA2190 may possibly contribute to the accumulation and breakdown of storage materials such as glycogen and trehalose ( glgA, glgB, glgP ), in protection against oxidative stress like the catalase encoding...”
- “...QSGGNKSGKS, in Fig. 4a ). Likewise, P. aeruginosa PAO1 harbors an inparalog of PA2146, namely PA2190, which is approximately two times longer than the PA2146 genes, likely due to a duplication event (Fig. 4a , Supplementary Fig. 6c ). However, this inparalog was not further analyzed...”
- A Family of Small Intrinsically Disordered Proteins Involved in Flagellum-Dependent Motility in Salmonella enterica
Oguri, Journal of bacteriology 2019 - “...aa) in E. coli K-12, and PA2146 (55 aa) and PA2190 (114 aa) in P. aeruginosa PAO1 (Fig. 8A). All four homologs contain repeated motifs whose amino acid...”
- “...the last seven to ten C-terminal residues; additionally, PA2190 has a 34-aa-long extra N-terminal region and triple tandem repeats (Fig. 8A). Notably, although...”
- The Pseudomonas aeruginosa AlgZR two-component system coordinates multiple phenotypes
Okkotsu, Frontiers in cellular and infection microbiology 2014 - “...as several CF isolates have regions flanking exoY deleted (in the ORFs of PA2192 and PA2190) (Wolfgang et al., 2003a ), which remove the AlgR-dependent hcnA -ABS from the chromosome. As a consequence, cyanide production in strains with such deletions are responsive to Anr and the...”
- Analysis of the Pseudomonas aeruginosa regulon controlled by the sensor kinase KinB and sigma factor RpoN
Damron, Journal of bacteriology 2012 - “...PA2181 PA2182 PA2183 PA2184 PA2185 PA2186 PA2187 PA2188 PA2190 PA2192 Gene RpoN-Dependent KinB Regulon of P. aeruginosa TABLE 2 KinB regulon genes with...”
- “...to the transcriptome analyses, PA2169, PA2171, PA2184, and PA2190 were upregulated in the kinB mutant (Table 4) and repressed in the PAO1 kinB rpoN...”
- Food as a source for quorum sensing inhibitors: iberin from horseradish revealed as a quorum sensing inhibitor of Pseudomonas aeruginosa
Jakobsen, Applied and environmental microbiology 2012 - “...PA1905 PA1999 PA2000 PA2030 PA2031 PA2067 PA2069 PA2146 PA2190 PA2193 PA2194 PA2195 PA2300 PA2366 PA2384 PA2433 PA2566 PA2570 PA2588 PA2939 PA3326 PA3331 PA3361...”
- In-vivo expression profiling of Pseudomonas aeruginosa infections reveals niche-specific and strain-independent transcriptional programs
Bielecki, PloS one 2011 - “...successfully colonize this niche. It is also striking that the whole group of genes PA2134 PA2190 is expressed among the genes that are hypothesized to be specific for burn wound infections. This region contains genes with possible roles in the accumulation and breakdown of storage materials...”
- “...protection against oxidative stress like the catalase encoding gene katE, or in general stress response (PA2190). Plant infection We found that the up-regulation of sulfate reduction in P. aeruginosa ( cysAWT , cysND and cysI ,) was a prominent feature of the genetic program active upon...”
- Effects of antibiotics on quorum sensing in Pseudomonas aeruginosa
Skindersoe, Antimicrobial agents and chemotherapy 2008 - “...oxidase subunit. Many genes from the region from PA2134 to PA2190 of the genome were downregulated by AZM, CFT, and CPR. This region has been found to be...”
- “...PA2165 PA2166 PA2167 PA2170 PA2171 PA2176 PA2178 PA2184 PA2190 PA2193 PA2194 PA2195 PA2300 PA2302 PA2069 PA2137 PA2139 PA2141 PA2142 PA2143 PA2144 PA2146 PA2148...”
- Clustering of Pseudomonas aeruginosa transcriptomes from planktonic cultures, developing and mature biofilms reveals distinct expression profiles
Waite, BMC genomics 2006 - “...P. aeruginosa or are orthologues of stress induced genes in other bacteria; general stress (PA1753, PA2190, cspD , rpoS , and rmf ), nutrient stress ( glgA , glgB , glgP discussed in the next section), oxidative stress ( katE discussed in the next section), anaerobicity...”
- “...glucose starvation [ 22 ]. Other general stress genes in cluster 2 are rpoS , PA2190 (discussed in the next section) and rmf . rmf encodes a putative protein which is 66% similar to the characterised ribosome modulation factor of E. coli and was very highly...”
- More
AFK62_RS09870 general stress protein from Cronobacter condimenti 1330
81% identity, 73% coverage
PP_3269 conserved hypothetical protein from Pseudomonas putida KT2440
76% identity, 54% coverage
- Physiological responses of Pseudomonas putida to formaldehyde during detoxification
Roca, Microbial biotechnology 2008 - “...6 Y PP_3183 SCO1/SenC family protein/cytochrome c 3.13 5 PP_3254 Nucleosidase, putative uvrC 2.07 1 PP_3269 Conserved hypothetical protein 2.64 7 PP_3314 Heat shock protein, HSP20 family 1.91 2 PP_3321 Conserved hypothetical protein 1.89 7 PP_3349 Major facilitator family transporter 2.11 5 PP_3425 Multidrug efflux RND...”
K6R05_RS19660 general stress protein from Pantoea alfalfae
63% identity, 83% coverage
- Cross-Kingdom Pathogenesis of <i>Pantoea alfalfae</i> CQ10: Insights from Transcriptome and Proteome Analyses
Su, Microorganisms 2024 - “...In order to validate the accuracy of expression abundance from RNA-Seq, eight important DEGs ( K6R05_RS19660 , K6R05_RS18735 , K6R05_RS17085 , ssrA , K6R05_RS11135 , tssB , rplP , and rpsS ) were selected and tested via RTq-PCR, and rnpB was used as the reference gene....”
- “...rplP were significantly upregulated, and the expression of K6R05_RS18735 , K6R05_RS17085 , ssrA , and K6R05_RS19660 were significantly downregulated, but all of them were highly corrected by the RNA-seq results ( Figure S3 ). These results further proved that the transcriptome data were reliable. 3.11. The...”
PP3963, PP_3963 conserved domain protein from Pseudomonas putida KT2440
64% identity, 40% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory