PaperBLAST

PaperBLAST Hits for OHPLBJKB_03214 (72 a.a., MSEKPLTKTD...)

Show query sequence

>OHPLBJKB_03214
MSEKPLTKTDYLMRLRRCQTIDTLERVIEKNKYELSDNELAVFYSAADHRLAELTMNKLY
DKIPSSVWKFIR

Running BLASTp...

Found 16 similar proteins in the literature:

Hha / b0460 haemolysin expression-modulating protein Hha from Escherichia coli K-12 substr. MG1655 (see 37 papers)
HHA_ECOLI / P0ACE3 Hemolysin expression-modulating protein Hha from Escherichia coli (strain K12) (see 13 papers)
HHA_ECOL6 / P0ACE4 Hemolysin expression-modulating protein Hha from Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (see paper)
hha / CAA41043.1 Hha protein from Escherichia coli (see paper)
b0460 modulator of gene expression, with H-NS from Escherichia coli str. K-12 substr. MG1655
NP_414993 hemolysin expression-modulating protein Hha from Escherichia coli str. K-12 substr. MG1655
AP_001109 modulator of gene expression, with H-NS from Escherichia coli W3110
ECs0513 haemolysin expression modulating protein from Escherichia coli O157:H7 str. Sakai
CDCO157_0501, EC042_0498, K8B90_RS06040, NRG857_RS02210 HHA domain-containing protein from Escherichia coli O83:H1 str. NRG 857C
100% identity, 100% coverage

• function: Down-regulates hemolysin (hly) expression in complex with H- NS (PubMed:10778755, PubMed:11790731, PubMed:1956303, PubMed:21600204). Stimulates transposition events in vivo (PubMed:8145648). Modifies the set of genes regulated by H-NS; Hha and Cnu (YdgT) increase the number of genes DNA bound by H-NS/StpA and may also modulate the oligomerization of the H-NS/StpA-complex (PubMed:23543115). Binds DNA and influences DNA topology in response to environmental stimuli; does not however interact with DNA in the absence of H-NS (PubMed:23543115). Involved in persister cell formation, acting downstream of mRNA interferase (toxin) MqsR (PubMed:19909729). Decreases biofilm formation by repressing the transcription of fimbrial genes fimA and ihfA, and by repressing the transcription of tRNAs corresponding to rare codons, which are abundant in type 1 fimbrial genes (PubMed:18545668).
  subunit: Forms a heterotrimeric complex with the H-NS dimer in the absence of DNA.
  disruption phenotype: Deletion results in a large increase in the production of extracellular and intracellular hemolysin (PubMed:1956303). At low osmolarity minor changes in overall translation, at 0.4 M NaCl expression of about 25 proteins altered, including decreased OmpA, crr and AhpC (in strain 5K, not a K12 derivative) (PubMed:10322001). At 0.3 M NaCl in strain W3110 up- regulation of 113 genes and down-regulation of 8 genes was observed; a double cnu-hha deletion up-regulated 134 and down-regulated 5 genes, most of which are thought to have been acquired horizontally and are also up-regulated in double hns-stpA deletions (PubMed:23543115). However there are only 12 genes that were commonly up-regulated in the hha and cnu-hha deletions (PubMed:23543115). Represses the production of persister cells (PubMed:19909729). Deletion of hha and tomB (ybaJ), in the presence of a conjugative plasmid (R1drd19), decreases biofilm formation, cell aggregation and increases motility via flagella and motility gene expression (PubMed:16317765).
• function: Down-regulates hemolysin expression, in complex with H-NS, and can also stimulate transposition events in vivo. Modifies the set of genes regulated by H-NS; Hha and Cnu (YdgT) increase the number of genes DNA bound by H-NS/StpA and may also modulate the oligomerization of the H-NS/StpA-complex. Binds DNA and influences DNA topology in response to environmental stimuli. Decreases biofilm formation (By similarity).
  subunit: Forms a heterotrimeric complex with the H-NS dimer.
  disruption phenotype: Deletion of the tomB-hha operon causes reduced infection of the mouse bladder but not of the kidney.
• Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery
  Neusser, BMC genomics 2010
  • “...dual regulator b0607 uspG 1.58 universal stress protein UP12 b1376 uspF 1.57 stress-induced, ATP-binding protein b0460 hha 1.56 modulator of gene expression, with H-NS b4401 arcA 1.55 response regulator in two-component regulatory system with ArcB or CpxA b4045 yjbJ 1.53 predicted stress response protein b2869 ygeV...”
  • “...2.78 guanine deaminase b3755 yieP 2.94 predicted transcriptional regulator b3226 nanR 2.41 transcriptional regulator NanR b0460 hha 2.34 modulator of gene expression, with H-NS b1625 ydgT 1.82 H-NS and StpA-binding protein b0001 thrL 1.73 thr operon leader peptide b2865 ygeR 1.72 transcriptional regulator b2023 hisH 1.68...”
• Remaining flexible in old alliances: functional plasticity in constrained mutualisms
  Wernegreen, DNA and cell biology 2009
  • “...- RNA-binding protein that affects many cellular processes hha b0460 - - WGLp524 - - - Hemolysin expression modulating protein hns b1237 Bpen448 - WGLp367 BU272...”
• StpA and Hha stimulate pausing by RNA polymerase by promoting DNA-DNA bridging of H-NS filaments.
  Boudreau, Nucleic acids research 2018
  • GeneRIF: Hha and StpA greatly enhance H-NS-stimulated pausing by RNAP at 20 degrees C. StpA:H-NS or StpA-only filaments also stimulate pausing at 37 degrees C, a temperature at which Hha:H-NS or H-NS-only filaments have much less effect. In addition, both Hha and StpA greatly stimulate DNA-DNA bridging by H-NS filaments.
• An oxygen-sensitive toxin-antitoxin system.
  Marimon, Nature communications 2016
  • GeneRIF: TomB antitoxin activity is oxygen-dependent and its Yersinia orthologue, YmoB can replace TomB as the Hha antitoxin.
• The Hha protein facilitates incorporation of horizontally acquired DNA in enteric bacteria.
  Aznar, Microbiology (Reading, England) 2013 (PubMed)
  • GeneRIF: Authors provide evidence that, as has been shown for H-NS, Hha-like proteins play an essential role facilitating acquisition of horizontally transferred DNA in both Escherichia coli and Salmonella.
• Hha controls Escherichia coli O157:H7 biofilm formation by differential regulation of global transcriptional regulators FlhDC and CsgD.
  Sharma, Applied and environmental microbiology 2013
  • GeneRIF: In conclusion, Hha regulates biofilm formation in enterohemorrhagic Escherichia coli O157:H7 by differential regulation of FlhDC and CsgD, the global regulators of motility and curli production, respectively.
• Functions of the Hha and YdgT proteins in transcriptional silencing by the nucleoid proteins, H-NS and StpA, in Escherichia coli.
  Ueda, DNA research : an international journal for rapid publication of reports on genes and genomes 2013
  • GeneRIF: The results demonstrated that the chromosomal binding of Hha requires H-NS/StpA, and is necessary for the repression of a subset of genes in the H-NS/StpA regulon.
• Genomic characterization of enteroaggregative Escherichia coli from children in Mali
  Boisen, The Journal of infectious diseases 2012
  • “...and 75% amino acid similarity with Hha protein from E. coli K12 (GenBank accession number NP_414993). Table 4. Comparative Genomic Hybridization of Strains C701-09, C718-09, C801-09, and C46-10 Against a Microarray That Comprises the Full Genomes of 32 Escherichia coli and Shigella Strains and the Genes...”
• Essential residues in the H-NS binding site of Hha, a co-regulator of horizontally acquired genes in Enterobacteria.
  de, FEBS letters 2011 (PubMed)
  • GeneRIF: Hha has to undergo a conformational change to bind H-NS.
• Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms.
  Wang, The ISME journal 2009
  • GeneRIF: The authors show that Hha induces excision of prophages, CP4-57 and DLP12, by inducing excision genes and by reducing SsrA synthesis.
• More
• Functional Prediction of Biological Profile During Eutrophication in Marine Environment
  Sbaoui, Bioinformatics and biology insights 2022
  • “...dioxygenase subunit Hcp P75825 Hydroxylamine oxidoreductase-like protein HemH P23871 Ferrochelatase HemW P52062 Heme chaperone Hha P0ACE3 Hemolysin expression-modulating protein HlpA P0AEU7 Periplasmic molecular chaperone for outer membrane proteins HlyB P15492 Alpha-hemolysin translocation ATP-binding protein HlyE P77335 Hemolysin E, chromosomal Hns P0ACF8 DNA-binding protein HpcD Q05354 5-carboxymethyl-2-hydroxymuconate...”
• Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom.
  Amemiya, Transcription 2021 (no snippet)
• Thermally versus Chemically Denatured Protein States
  Narayan, Biochemistry 2019
  • “...A.N.N. iD ORCID Abhishek Narayan: 0000-0001-5390-2380 Athi N. Naganathan: 0000-0002-1655-7802 Accession Codes Cnu, P64467; Hha, P0ACE3; PurR, P0ACP7; and PDD, P11961. Notes The authors declare no competing financial interest. Abbreviations CD circular dichroism PPII polyproline II MRE mean residue ellipticity R S Stokes radius IDP intrinsically...”
• Distribution of genes encoding nucleoid-associated protein homologs in plasmids
  Takeda, International journal of evolutionary biology 2011
  • “...coverage). The complete amino acid sequences of Fis (DDBJ/EMBL/GenBank accession no. AP_003801), H-NS (AP_001863), Hha (AP_001109), HU (AP_003818), HU (AP_001090), IHF (AP_002332), IHF (AP_001542), Lrp (AP_001519), and NdpA (P33920) from E. coli K-12 W3110 and MvaT (AAP33788) from Pseudomonas aeruginosa PAO1 were used as query sequences....”
• Global regulation by horizontally transferred regulators establishes the pathogenicity of Escherichia coli
  Abe, DNA research : an international journal for rapid publication of reports on genes and genomes 2008
  • “...were regulated in close correlation with the LEE genes. These genes, ECs0512 ( ylaD ), ECs0513 ( hha ), and ECs0514 ( ybaJ ), are likely to comprise an operon. The hha gene encodes a transcription regulator for ler . 26 The expression profile of the...”
  • “...Hypothetical protein S-loop54 P + L ECs0512 ylaD Maltose O -acetyltransferase K12 P + L**** ECs0513 hha Hemolysin expression modulating protein K12 P + L**** ECs0514 ybaJ Hypothetical protein K12 P + L ECs0814 Putative outer membrane protein Sp3 P + L ECs1126/2715* espF-M/U Type-III secretion...”
• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...change in expression 56 h QT cluster ECs0342 ykgC 2.30 2 ECs0568 gcl 4.04 2 ECs0513 hha 2.55 2 ECs0569 gip 3.56 2 ECs0514 ybaJ 2.16 2 ECs0570 ybbQ 4.89 2 ECs0732 ybgA 2.27 2 ECs0571 ybbV 3.27 2 ECs0733 phrB 2.15 2 ECs2095 yddV 4.27...”
• Contribution of Toxin–Antitoxin Systems to Adherent-Invasive E. coli Pathogenesis
  Bustamante, Microorganisms 2024
  • “...(ccdA) ccdAB/CcdA (antitoxin) Type II TA214835 K8B90_RS05120 (yafO) K8B90_RS05115 (yafN) yafN-yafO (relBE)/YafO-YafN Type II TA214836 K8B90_RS06040 (Hha) K8B90_RS06045 (TomB) Hha-TomB/- Type II TA214837 K8B90_RS11255 (higB) K8B90_RS11250 (higA) higBA (relBE)/HigB-HigA Type II TA214838 K8B90_RS11415 (hipA) K8B90_RS11420 (hipB) hipBA/HipA-HipB Type II; related to MGE TA214847 K8B90_RS14005 (pemK) K8B90_RS14010...”
  • “...TA027332 NRG857_RS01300 (yafO) NRG857_RS01295 (yafN) yafN-yafO (relBE)/YafO-YafN Type II; TA18 at [ 9 ] TA027333 NRG857_RS02210 (Hha) NRG857_RS02215 (TomB) Hha-TomB/- Type II TA027334 NRG857_RS07485 (higB) NRG857_RS07480 (higA) higBA (relBE)/HigB-HigA Type II; TA20 at [ 9 ] TA027335 NRG857_RS07640 (hipA) NRG857_RS07645 (hipB) hipBA/HipA-HipB Type II; TA21 at...”
• Tracking bacterial virulence: global modulators as indicators
  Prieto, Scientific reports 2016
  • “...E. coli EAEC, Cm r Sm r Tc r Prof. I. Henderson 042Hha 042 hha (EC042_0498) This work 042Hha-2 042 4516 (EC042_4516) This work 042Hha-3 042 4796 (EC042_4796) This work 042Hhanull 042 0498 4516 4796 This work MG1655 E. coli , F , ilvG, rph1 48...”
• Global transcriptional and phenotypic analyses of Escherichia coli O157:H7 strain Xuzhou21 and its pO157_Sal cured mutant
  Zhao, PloS one 2013
  • “...have no significant similarity at DNA sequence level. The RPKM values of the chromosomal copy, CDCO157_0501, were 845.206 and 1022.92 in Xuzhou21 and Xuzhou21m respectively, indicating no transcriptional difference. In contrast, the RPKM values of the pO157 copy, CDCpO157_0071, were 117.155 and 0 in Xuzhou21 and...”

HHA_SALTS / A0A0H3N8G7 Hemolysin expression-modulating protein Hha from Salmonella typhimurium (strain SL1344) (see 2 papers)
HHA_SALTY / Q7CR17 Hemolysin expression-modulating protein Hha from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
NP_459468 hemolysin expression modulating protein (involved in environmental regulation of virulence factors) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
STM0473 hemolysin expression modulating protein (involved in environmental regulation of virulence factors) from Salmonella typhimurium LT2
99% identity, 100% coverage

• function: Binds to H-NS and modifies the range of genes it silences; H- NS alone silences 'core' genes while the H-NS-Hha complex (and presumably also H-NS-YdgT) silences genes acquired by horizontal gene transfer (PubMed:19521501). Plays a role silencing virulence factors in the absence of factors that induce pathogenicity (PubMed:17307861). Probably requires H-NS to bind DNA (By similarity).
  subunit: Interacts with H-NS (By similarity).
  disruption phenotype: Derepression of pathogenicity island 2 (SPI-2) which is usually repressed in culture; effect is slightly higher in double hha-ydgT deletions (PubMed:17307861). Double hha-ydgT deletion mutants lead to deregulation of many genes at least 2-fold, most of which are also deregulated in an hns deletion, suggesting there are a large number of hns-regulated genes whose expression is also modulated by Hha and/or YdgT (PubMed:19521501). Upon infection of C57BL/6 mice a single hha mutant has 10-100-fold reduced virulence compared to wild- type, while a double hha-ydgT deletion is 6 orders of magnitude less virulent (PubMed:17307861).
• function: Interacts with H-NS and in this complex might contact DNA, which could provide an additional surface for DNA binding to the H-NS- Hha complex; may not bind DNA in the absence of H-NS (PubMed:23515315). In vitro improves the ability of H-NS to bind DNA under a precise set of conditions (PubMed:23515315).
  subunit: Interacts with H-NS; crystal structures suggest each subunit of an H-NS dimer could bind 1 Hha monomer (PubMed:23515315).
  disruption phenotype: Derepression of genes that are usually coregulated by H-NS and Hha (PubMed:23515315).
• The Hha-TomB Toxin-Antitoxin System Shows Conditional Toxicity and Promotes Persister Cell Formation by Inhibiting Apoptosis-Like Death in S. Typhimurium.
  Jaiswal, Scientific reports 2016
  • GeneRIF: The Hha-TomB TA system was found to increase persistence and inhibit programmed cell death under antibiotic stress where a phenotypically diverse population expressing differential level of TA components was observed. Therefore we propose that Hha and TomB prevent cells from committing suicide thereby promoting persister cell formation.
• TTSS2-deficient hha mutant of Salmonella Typhimurium exhibits significant systemic attenuation in immunocompromised hosts.
  Vishwakarma, Virulence 2014
  • GeneRIF: Collectively, these findings implicate the involvement of hemolysin expression modulating protein (Hha) in establishment of bacterial infection.
• The non-motile phenotype of Salmonella hha ydgT mutants is mediated through PefI-SrgD.
  Wallar, BMC microbiology 2011
  • GeneRIF: Deletion of pefI-srgD in a hha ydgT deletion background resulted in transient restoration of class II/III and III transcription, expression of surface flagella, and motility in the quadruple mutant.
• Modulation of horizontally acquired genes by the Hha-YdgT proteins in Salmonella enterica serovar Typhimurium.
  Vivero, Journal of bacteriology 2008
  • GeneRIF: As Hha and YdgT interact with H-NS, our findings strongly suggest that Hha and/or YdgT must form complexes with H-NS when they silence these DNA regions.
• Repression of intracellular virulence factors in Salmonella by the Hha and YdgT nucleoid-associated proteins.
  Silphaduang, Journal of bacteriology 2007
  • GeneRIF: We demonstrate here that Hha is the major repressor responsible for silencing virulence genes carried in Salmonella pathogenicity island 2
• Genetic Determinants of Salmonella enterica Serovar Typhimurium Proliferation in the Cytosol of Epithelial Cells
  Wrande, Infection and immunity 2016
  • “...and macrophages. YdgT and its paralogue, Hha (STM0473), are widely present in the Enterobacteriaceae. Both proteins are nucleoid-associated proteins that act...”
• Regulatory principles governing Salmonella and Yersinia virulence
  Erhardt, Frontiers in microbiology 2015
  • “...87 Transcription Colonization, invasion, host defense HdfR/ YifA STM3897 YPK_4064 98 62 Transcription Colonization Hha STM0473 YmoA YPK_3214 93 82 Transcription Colonization, invasion, host defense HilA STM2876 NA NA NA Transcription Invasion HilC/ SirC STM2867 NA NA NA Transcription Invasion HilD STM2875 NA NA NA Transcription...”
• TTSS2-deficient hha mutant of Salmonella Typhimurium exhibits significant systemic attenuation in immunocompromised hosts
  Vishwakarma, Virulence 2014
  • “...homolog is present in the genome of S. Typhimurium (STM0473). The direct interaction of Hha and H-NS has been reported to alter the expression if invasion...”

KP1_1317 haemolysin expression modulating protein from Klebsiella pneumoniae NTUH-K2044
SP68_20685 HHA domain-containing protein from Klebsiella variicola
97% identity, 100% coverage

• The Capsule Regulatory Network of Klebsiella pneumoniae Defined by density-TraDISort
  Dorman, mBio 2018
  • “...E1 component 0.98 KP1_0941 glnD PII uridylyl-transferase 0.94 KP1_1019 hha Hemolysin expression modulating protein 0.99 KP1_1317 tolR Putative inner membrane protein involved in the tonB -independent uptake of group A colicins 1.00 KP1_1700 tolB Translocation protein TolB precursor 1.00 KP1_1702 mdoG Periplasmic glucans biosynthesis protein 1.00...”
• YjcC, a c-di-GMP phosphodiesterase protein, regulates the oxidative stress response and virulence of Klebsiella pneumoniae CG43
  Huang, PloS one 2013
  • “...nhaR 2.1 KP1_0838 LuxR family regulatory protein mrkI 2.6 KP1_4552 Hemolysin modulating protein hha 2.6 KP1_1317 Transcriptional antiterminator of glycerol uptake operon 2.1 KP1_1112 DNA binding transcriptional activator pspC 2.1 KP1_2344 Hypothetical proteins ParB family protein HP 3.3 KP1_2152 formylglycine generating sulfatase 2.6 KP1_3378 Membrane anchored...”
• Phenotypic and genomic changes in enteric <i>Klebsiella</i> populations during long-term ICU patient hospitalization: the role of RamR regulation
  Langlois, mSphere 2024
  • “...(log2FC: 0.83), which encode lipopolysaccharides, were slightly upregulated, as was the hemolysin hha transcriptional regulator (SP68_20685) (log2FC: 1.19), which is implicated in biofilm formation. The mrk operon (log2FC mrkD : 0.84, log2FC mrkF : 0.81, log2FC mrkC : 0.79) and another gene (SP68_01865) (log2FC: 0.99) associated...”

HBB05_RS08630 HHA domain-containing protein from Pantoea agglomerans
86% identity, 96% coverage

• Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen
  Guevarra, PloS one 2021
  • “...HBB05_RS06780 Toxin Hha , ShlB , FhaC , HecB , XhlA Hemolysin HBB05_RS23025, HBB05_RS03510, HBB05_RS04405, HBB05_RS08630, HBB05_RS11220, HBB05_RS14060, HBB05_RS15620 hlyIII Hemolysin III HBB05_RS00635 In the secretion system category, all the putative genes belonging to type VI secretion system (T6SS) were present. The genes encoding the complete...”

YMOA_YEREN / P0A3X1 Modulating protein YmoA; Histone-like protein from Yersinia enterocolitica (see 3 papers)
YpsIP31758_3073 haemolysin expression modulating protein from Yersinia pseudotuberculosis IP 31758
YPO3138 modulating protein YmoA (histone-like protein) from Yersinia pestis CO92
y1046 haemolysin expression modulating protein from Yersinia pestis KIM
YPK_3214 hemolysin expression modulating family protein from Yersinia pseudotuberculosis YPIII
YPTB0978 hemolysin expression modulating protein (involved in environmental from Yersinia pseudotuberculosis IP 32953
D5F51_RS13625 expression modulating protein YmoA from Yersinia hibernica
82% identity, 93% coverage

• function: Modulates the thermoregulation of VirF, and hence the yop regulon, as well as the expression of the enterotoxin gene yst (PubMed:1956283). Involved in chromosome structure and DNA topology probably by means of compaction of DNA in conjunction with H-NS; probably requires H-NS to bind DNA (By similarity).
  subunit: Interacts with H-NS, in the absence of DNA (PubMed:11790731, PubMed:26085102).
• The complete genome sequence of Yersinia pseudotuberculosis IP31758, the causative agent of Far East scarlet-like fever
  Eppinger, PLoS genetics 2007
  • “...protein H-NS. In Y. pseudotuberculosis IP31758, homologs of ymoA are present on both the chromosome (YpsIP31758_3073) and pYpsIP31758.1 (YpsIP31758_B0060), displaying 89% aa similarity. One could speculate on a concerted role for these regulators in modulating plasmid- and chromosome-encoded virulence determinants [ 93 ]. pYpsIP31758.1 appears to...”
• Comparative Global Gene Expression Profiles of Wild-Type Yersinia pestis CO92 and Its Braun Lipoprotein Mutant at Flea and Human Body Temperatures
  Galindo, Comparative and functional genomics 2010
  • “...in B. subtilis 3.2 YPPCP1.05c pesticin pst Bacteriocin that induces the formation of spheroplasts 1.7 YPO3138 modulating protein YmoA (histone-like protein) ymoA Protein modification and repair, invasion 2.2 Unknown functions various genes (y1333, 1850, 3268, YPO0102, 2307, 3137, 3518, 3707, and 4064) * Functions were obtained...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...curlin genes regulatory protein 2.098 (< 0.001) YPTB0957 YPO3159 hypothetical protein 1.521 (0.034) YPTB0978 (ymoA) YPO3138 modulating protein YmoA (histone-like protein) 0.509 (< 0.001) YPTB0979 YPO3137 conserved hypothetical protein 0.469 (< 0.001) YPTB0980 YPO3136 hypothetical protein 0.587 (0.01) YPTB1004 (wzx) or0734 putative O-unit flippase 0.642 (0.007)...”
• Identification and characterization of small RNAs in Yersinia pestis
  Beauregard, RNA biology 2013
  • “...> / > / y0914 (clpB) > Ysr156/Ffs 1179191 1179276 < y1045/ > / < y1046 (hha) Ysr145/157 1229994 1230059, 1230060 < y1090/ > / < y1091 Ysr158 1341830 1341894 y1196 (ubiF) > / > / < yt030 (tRNA-Gln) Ysr159/CyaR 1527324 1527218 < y1378/ < /...”
• Regulatory principles governing Salmonella and Yersinia virulence
  Erhardt, Frontiers in microbiology 2015
  • “...Colonization, invasion, host defense HdfR/ YifA STM3897 YPK_4064 98 62 Transcription Colonization Hha STM0473 YmoA YPK_3214 93 82 Transcription Colonization, invasion, host defense HilA STM2876 NA NA NA Transcription Invasion HilC/ SirC STM2867 NA NA NA Transcription Invasion HilD STM2875 NA NA NA Transcription Colonization, invasion,...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...(crl) YPO3223 curlin genes regulatory protein 2.098 (< 0.001) YPTB0957 YPO3159 hypothetical protein 1.521 (0.034) YPTB0978 (ymoA) YPO3138 modulating protein YmoA (histone-like protein) 0.509 (< 0.001) YPTB0979 YPO3137 conserved hypothetical protein 0.469 (< 0.001) YPTB0980 YPO3136 hypothetical protein 0.587 (0.01) YPTB1004 (wzx) or0734 putative O-unit flippase...”
• A Role for the SmpB-SsrA system in Yersinia pseudotuberculosis pathogenesis
  Okan, PLoS pathogens 2006
  • “...LcrH (pYV0056), LcrV (pYV0057), Rnr (YPTB0432), SmpB (YPTB1135), SsrA (YPTB_RNA_88), ThrA (YPTB0602), VirF (pYV0076), YmoA (YPTB0978); YopB (pYV0055), YopD (pYV0054), YopE (pYV0025), and YopM (pYV0047) . We thank Drs. Jorge L. Benach and Martha B. Furie for insightful comments on the manuscript, and members of the...”
• Comparative genomic insights into Yersinia hibernica - a commonly misidentified Yersinia enterocolitica-like organism
  Nguyen, Microbial genomics 2020
  • “...hibernica [ 48 ]. In contrast, Y. hibernica had homologues of classical virulence genes ymoA (D5F51_RS13625), heat-stable enterotoxin-encoding ystB (D5F51_RS06925) [ 49 ], fepA (D5F51_RS19110) and foxA (D5F51_RS01865) of which the latter two are involved in iron transport and uptake in Y. enterocolitica [ 50 ]....”

ETAE_1008 hemolysin expression modulating family protein from Edwardsiella tarda EIB202
CGL57_17110 HHA domain-containing protein from Edwardsiella anguillarum
79% identity, 93% coverage

• Genome sequence of the versatile fish pathogen Edwardsiella tarda provides insights into its adaptation to broad host ranges and intracellular niches
  Wang, PloS one 2009
  • “...adhesin/hemagglutinin/hemolysin ETAE_0821 ShlB/FhaC/HecB family haemolysin secretion/activation protein ETAE_0910 Hemolysin transporter protein ETAE_0911 Putative hemolysin precursor ETAE_1008 Hemolysin expression modulating family protein ETAE_1267 OmpA, outer membrane protein A ETAE_1528 OmpW, outer membrane protein W ETAE_2089 Pic serine protease precursor, FhaB filamentous heamagglutinin ETAE_2842 Putative adhesin ETAE_2937 Hemolysin...”
• Characterization of a Highly Virulent Edwardsiella anguillarum Strain Isolated From Greek Aquaculture, and a Spontaneously Induced Prophage Therein
  Katharios, Frontiers in microbiology 2019
  • “...and EthB (CGL57_17585), which are regulated by the two-component system EsrA-EsrB, -hemolysin regulator protein Hha (CGL57_17110) and ferric uptake regulator, Fur (CGL57_10755). Furthermore, quorum sensing (QS) plays an important role in the invasion and survival of Edwardsiella spp. intracellularly especially within the macrophages. QS controlled by...”

YpsIP31758_B0060 virulence modulating protein from Yersinia pseudotuberculosis IP 31758
69% identity, 93% coverage

• The complete genome sequence of Yersinia pseudotuberculosis IP31758, the causative agent of Far East scarlet-like fever
  Eppinger, PLoS genetics 2007
  • “...Y. pseudotuberculosis IP31758, homologs of ymoA are present on both the chromosome (YpsIP31758_3073) and pYpsIP31758.1 (YpsIP31758_B0060), displaying 89% aa similarity. One could speculate on a concerted role for these regulators in modulating plasmid- and chromosome-encoded virulence determinants [ 93 ]. pYpsIP31758.1 appears to lack a complete...”

O3K_26012 hemolysin expression modulator Hha from Escherichia coli O104:H4 str. 2011C-3493
56% identity, 92% coverage

• High-resolution genetic analysis of the requirements for horizontal transmission of the ESBL plasmid from Escherichia coli O104:H4
  Yamaichi, Nucleic acids research 2015
  • “...Hp27 0.57 0.42 0.01 81133 81276 O3K_26007 Hypothetical protein Hp28 0.22 0.76 0.02 81319 81528 O3K_26012 Putative regulator protein Hha/YmoA 0.40 0.59 0.02 81626 82240 O3K_26017 Surface exclusion protein ExcA 0.47 0.29 0.24 82316 84553 O3K_26022 TraY integral membrane protein TraY 0.01 0.16 0.84 84581 85165...”

EC042_4516 hemolysin expression modulator Hha from Escherichia coli 042
EC55989_3351 haemolysin expression-modulating protein from Escherichia coli 55989
58% identity, 90% coverage

• Differential Expression of Two Copies of the irmA Gene in the Enteroaggregative E. coli Strain 042
  Bernabeu, Microbiology spectrum 2022
  • “...the presence of additional copies of the hha gene (i.e., the hha2 gene, locus tag ec042_4516, located upstream of the irmA_4509 gene) and the yeeR irmA cluster in several pathogenic E. coli strains, including strain 042 (10). This result suggests that the irmA genes of strain...”
• Tracking bacterial virulence: global modulators as indicators
  Prieto, Scientific reports 2016
  • “...a new approach to identify and characterize pathogenic bacterial isolates. Results Identification of hha paralogues EC042_4516 and 4796 in the genome of the EAEC strain 042 hha paralogues EC042_4516 and EC042_4796 (from here on termed hha2 and hha3 respectively) were identified in the annotated genome of...”
  • “...and aminoacid ( B ) sequences of Hha, Hha2 and Hha3. PCR amplification of the EC042_4516 ( hha2 ) and EC042_4796 ( hha3 ) genes ( C ), and hha, hha2, hha3 and ydgT genes ( D ) in strain 042 and different commensals E. coli...”
• Genomic characterization of enteroaggregative Escherichia coli from children in Mali
  Boisen, The Journal of infectious diseases 2012
  • “...+ Type III secretion protein EprJ b ECO26_3933 + + + Other Hemolysin expression-modulating protein EC55989_3351 + + + Putative hemolysin expression-modulating protein RmoA ECUMN_0072 + + + Putative hemolysin co-regulated protein b SSON_0255 + + + ShiA-like protein ECB_03517 + a EAEC genes are listed...”

YpsIP31758_B0044 haemolysin expression modulating protein from Yersinia pseudotuberculosis IP 31758
56% identity, 92% coverage

• The complete genome sequence of Yersinia pseudotuberculosis IP31758, the causative agent of Far East scarlet-like fever
  Eppinger, PLoS genetics 2007
  • “...(YpsIP31758_B0123) found upstream of the type IVB secretion machinery and the hemolysin expressionmodulating protein Hha (YpsIP31758_B0044) [ 91 , 92 ]. YmoA is a virulence-modulating regulator that controls multiple virulence-associated genes and is known to interact with the DNA-binding protein H-NS. In Y. pseudotuberculosis IP31758, homologs...”

rmoA / CAA74168.1 RmoA from Escherichia coli (see paper)
53% identity, 92% coverage

DR76_RS12265 Hha/YmoA family nucleoid-associated regulatory protein from Escherichia coli ATCC 25922
58% identity, 67% coverage

• Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken
  Hussain, Scientific reports 2017
  • “...DR76_RS08005 Capsule polysaccharide transporter 12.24 0.01 DR76_RS09375 ImpG Type VI secretion protein ImpG 16.84 0.01 DR76_RS12265 HlyC Hemolysin activation protein hlyC 7.05 0.01 DR76_RS12560 FimE Type 1 fimbriae regulatory protein FimE 4.27 0.01 DR76_RS15150 ompC Outer membrane porin protein C 15.25 0.01 DR76_RS25010 YoeB Toxin YoeB...”

c0308 Haemolysin expression modulating protein from Escherichia coli CFT073
58% identity, 62% coverage

• The inner membrane protein YhiM links copper and CpxAR envelope stress responses in uropathogenic E. coli
  Saenkham-Huntsinger, mBio 2024
  • “...(c0631), FdrA protein (c0632) c1208 and c1209 Hypothetical protein (c1208), hypothetical protein (c1209) c0307 and c0308 Hypothetical protein (c0307), hemolysin expression modulating protein (c0308) Fig 1 YhiM contributes to Cu sensitivity in uropathogenic E. coli . ( A ) Wild-type UPEC (CFT073), Tn 5 insertion mutant...”

YDGT_SALTS / A0A0H3NGF1 Transcription modulator YdgT; H-NS/StpA-binding protein 2; OriC-binding nucleoid-associated protein from Salmonella typhimurium (strain SL1344) (see 2 papers)
STM1461.S putative cytoplasmic protein from Salmonella typhimurium LT2
34% identity, 95% coverage

• function: Binds to H-NS and modifies the range of genes it silences; H- NS alone silences 'core' genes while the H-NS-Hha complex (and presumably also H-NS-YdgT) silences genes acquired by horizontal gene transfer (PubMed:19521501). Plays a role silencing virulence factors in the absence of factors that induce pathogenicity (PubMed:17307861).
  disruption phenotype: No effect on expression of pathogenicity island 2 (SPI-2) which is usually repressed in culture; derepression of SPI-2 in double hha-ydgT deletions (PubMed:17307861). Double hha-ydgT deletion mutants lead to deregulation of many genes at least 2-fold, most of which are also deregulated in an hns deletion, suggesting there are a large number of hns-regulated genes whose expression is also modulated by Hha and/or YdgT (PubMed:19521501). Upon infection of C57BL/6 mice a single hha mutant has 10-100-fold reduced virulence compared to wild- type, while a double hha-ydgT deletion is 6 orders of magnitude less virulent (PubMed:17307861).
• The target spectrum of SdsR small RNA in Salmonella
  Fröhlich, Nucleic acids research 2016
  • “...membrane channel protein (250 to +60 in tolC)::gfp WB yes yes ( 17 ) ydgT STM1461.S 2,53 oriC-binding nucleoid-associated protein (130 to +60 in ydgT)::gfp FC yes no ( 14 , 16 ) ibpA 2) STM3809.S 2,53 heat shock protein IbpA (99 to +45 in ibpA)::gfp...”

YdgT / b1625 H-NS- and StpA-binding protein from Escherichia coli K-12 substr. MG1655 (see 15 papers)
CNU_ECOLI / P64467 OriC-binding nucleoid-associated protein; H-NS/StpA-binding protein 2; Transcription modulator YdgT from Escherichia coli (strain K12) (see 4 papers)
NP_416142 H-NS- and StpA-binding protein from Escherichia coli str. K-12 substr. MG1655
b1625 predicted regulator from Escherichia coli str. K-12 substr. MG1655
S1782 hypothetical protein from Shigella flexneri 2a str. 2457T
38% identity, 93% coverage

• function: Modifies the set of genes regulated by H-NS; Hha and Cnu (YdgT) increase the number of genes bound by H-NS/StpA and may also modulate the oligomerization of the H-NS/StpA-complex on DNA (PubMed:23543115). The complex formed with H-NS binds to the specific 26-bp cnb site in the origin of replication oriC (PubMed:16199570). Can complement, at least partially, the absence of the Hha protein in hha mutants.
  subunit: Forms complexes with both H-NS and StpA.
  disruption phenotype: At 0.3 M NaCl up-regulation of 1 gene and down- regulation of 6 genes was observed; a double cnu-hha deletion up- regulated 134 and down-regulated 5 genes, most of which are thought to have been acquired horizontally and are also up-regulated in double hns-stpA deletions (PubMed:23543115).
• A mutational study of Cnu reveals attractive forces between Cnu and H-NS.
  Yun, Molecules and cells 2012
  • GeneRIF: the attractive force that governs the Cnu-H-NS interaction is an ionic bond, unlike the hydrophobic interaction that is the major attractive force in most proteins.
• The CnuK9E H-NS complex antagonizes DNA binding of DicA and leads to temperature-dependent filamentous growth in E. coli.
  Yun, PloS one 2012
  • GeneRIF: The CnuK9E H-NS complex antagonizes DNA binding of DicA and leads to temperature-dependent filamentous growth in Escherichia coli.
• YdgT, the Hha paralogue in Escherichia coli, forms heteromeric complexes with H-NS and StpA.
  Paytubi, Molecular microbiology 2004 (PubMed)
  • GeneRIF: interacts both with H-NS and with StpA in vivo
• Thermally versus Chemically Denatured Protein States
  Narayan, Biochemistry 2019
  • “...IA/I/15/1/501837 to A.N.N. iD ORCID Abhishek Narayan: 0000-0001-5390-2380 Athi N. Naganathan: 0000-0002-1655-7802 Accession Codes Cnu, P64467; Hha, P0ACE3; PurR, P0ACP7; and PDD, P11961. Notes The authors declare no competing financial interest. Abbreviations CD circular dichroism PPII polyproline II MRE mean residue ellipticity R S Stokes radius...”
• Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure
  LaVoie, BMC genomics 2018
  • “...24 24 n.s. b4354 yjiY Predicted transporter, function unknown n.s. n.s. n.s. 20 77 n.s. b1625 cnu OriC-binding complex H-NS/Cnu n.s. 10 n.s. 20 24 n.s. Table is sorted by PMA at 10min column. n.s. = not significantly different from unexposed culture and boldface highlights actual...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery
  Neusser, BMC genomics 2010
  • “...b3226 nanR 2.41 transcriptional regulator NanR b0460 hha 2.34 modulator of gene expression, with H-NS b1625 ydgT 1.82 H-NS and StpA-binding protein b0001 thrL 1.73 thr operon leader peptide b2865 ygeR 1.72 transcriptional regulator b2023 hisH 1.68 imidazole glycerol phosphate synthase subunit HisH b0529 fold 1.67...”
• Cnu, a novel oriC-binding protein of Escherichia coli
  Kim, Journal of bacteriology 2005
  • “...corresponding plasmid, pHL355-36, revealed two open reading frames (b1625 and b1626) of unknown functions. Serial deletion of the insert and measurement of the...”
  • “...cells carrying each of the deleted plasmids indicated that b1625 is responsible for the high SF of the candidate (Fig. 3). DNA sequence analysis showed that the...”
• A functional update of the Escherichia coli K-12 genome
  Serres, Genome biology 2001
  • “...amino acids. One such CDS identified by MAGPIE (Magnum ec_2510) is located between b1624 and b1625 and encodes a protein of 66 amino acids. The carboxy-terminal 41 amino acids of this CDS are identical to the amino-acid sequence of the recently characterized beta-lactam resistance protein Blr...”
• Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli
  Reitzer, Microbiology and molecular biology reviews : MMBR 2001
  • “...yciK-btuR, brnQ, acs, yceC-yceF, purM, ybcLM, b1017, kbl-tdh, b1625, yjhQP, aroG, zipA, yiiP, cybC, yjjJ, dinG, prsA, ydcD, emrD, secE, mog, ybiH, b0836, ymdD,...”
• Yersinia pestis Interacts With SIGNR1 (CD209b) for Promoting Host Dissemination and Infection
  Yang, Frontiers in immunology 2019
  • “...the SIGNR1-mediated interaction, but the -D-Gal-(1 3)-D-GalNAc (A0167), -D-Gal-(1 6)-D-GlcNAc (A7916) and -NeuNAc-(2 3)--D-Gal-(1 4)(-L-Fuc-)-D-GlcNAc (S1782) oligosaccharides inhibit the core-LPS-hDC-SIGN interaction of Y. pestis KIM10- ail very well ( 25 ). The recovery rates of Y1 and KIM10- ail bacteria in both cell lines are dramatically...”
• Host Langerin (CD207) is a receptor for Yersinia pestis phagocytosis and promotes dissemination
  Yang, Immunology and cell biology 2015
  • “...Purified FLAGLangerin, mannan, several oligosaccharides (GalGalNAc, GlcNAcGalGlc (A8297), GalGlcNAc (A7916) and especially the 3'SialylLewisX tetrasaccharide, (S1782)), HisMermaid and one singlesugar residue (GlcNAc) inhibited the interaction between KIM10 and CHOhLangerin cells ( Figure 5e ; Table 1 ). In addition, the antihLangerin antibody appeared to inhibit the...”

YDGT_SALTY / Q7CQK5 Transcription modulator YdgT; H-NS/StpA-binding protein 2; OriC-binding nucleoid-associated protein from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
NP_460424, STM1461 putative cytoplasmic protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
35% identity, 93% coverage

• function: Binds to H-NS and modified the range of genes it silences; H- NS alonge silences core gene while the H-NS-Hha complex (and presumably also H-NS-YdgT) silences genes acquired by horizontal gene transfer. Plays a role silencing virulence factors in the absence of factors that induce pathogenicity (By similarity). The complex formed with H-NS binds to the specific 26-bp cnb site in the origin of replication oriC (By similarity).
  subunit: Forms complexes with both H-NS (PubMed:23515315) and StpA (By similarity).
• N-dodecanoyl-homoserine lactone influences the levels of thiol and proteins related to oxidation-reduction process in Salmonella
  de, PloS one 2018
  • “...ybaB Transcription 0.454 0.416 0.312 0.255 -0.286 0.349 -9.610 1.037 -0.817 1.249 Transcription modulator YdgT Q7CQK5 ydgT Transcription -9.106 2.324 ND ND ND ND ND ND ND ND Inorganic pyrophosphatase P65748 ppa Transcription -10.551 1.376 -2.442 0.737 0.540 0.598 0.730 0.480 -0.911 2.335 Modulator of Rho-dependent...”
• Genetic Determinants of Salmonella enterica Serovar Typhimurium Proliferation in the Cytosol of Epithelial Cells
  Wrande, Infection and immunity 2016
  • “...strain. Mutants of three S. Typhimurium genes, STM1461 (ydgT), STM2829 (recA), and STM3952 (corA), had reduced cytosolic proliferation compared to wild-type...”
  • “...Three genes, corA (STM3952), recA (STM2829), and ydgT (STM1461), are required for optimal bacterial proliferation in the host cell cytosol, and one gene, asmA...”
• The non-motile phenotype of Salmonella hha ydgT mutants is mediated through PefI-SrgD.
  Wallar, BMC microbiology 2011
  • GeneRIF: Deletion of pefI-srgD in a hha ydgT deletion background resulted in transient restoration of class II/III and III transcription, expression of surface flagella, and motility in the quadruple mutant.
• Modulation of horizontally acquired genes by the Hha-YdgT proteins in Salmonella enterica serovar Typhimurium.
  Vivero, Journal of bacteriology 2008
  • GeneRIF: As Hha and YdgT interact with H-NS, our findings strongly suggest that Hha and/or YdgT must form complexes with H-NS when they silence these DNA regions.
• Negative regulation of Salmonella pathogenicity island 2 is required for contextual control of virulence during typhoid
  Coombes, Proceedings of the National Academy of Sciences of the United States of America 2005
  • “...proteins. We identified a Salmonella gene designated ydgT (STM1461), located 38 ORFs downstream of the SPI-2-encoded gene ssaU. ydgT is annotated as a putative...”

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Statistics

How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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.