PaperBLAST

PaperBLAST Hits for IAI46_07500 (85 a.a., MKNIKTFAAI...)

Show query sequence

>IAI46_07500
MKNIKTFAAIALSAASFTSFAADYVSAQDATQFEKAGVISASGATDLSSLKAQLSAKADA
AGAKAFTITSAGGNNLMHGTAVIYK

Running BLASTp...

Found 24 similar proteins in the literature:

YPTB2554 putative exported protein from Yersinia pseudotuberculosis IP 32953
YPO2521 putative exported protein from Yersinia pestis CO92
y1667 hypothetical protein from Yersinia pestis KIM
76% identity, 99% coverage

• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...(0.001) YPTB2540 or3654 conserved hypothetical protein 2.145 (0.008) YPTB2552 YPO2515 hypothetical 1.46 (0.023) 1.396 (0.042) YPTB2554 YPO2521 putative exported protein 0.648 (0.044) YPTB2562 YPO2530 conserved hypothetical protein 0.527 (0.026) YPTB2623 (flk) YPO2760 putative flagellar assembly regulatory protein. flk 0.549 (0.008) YPTB2699 YPO2976 conserved hypothetical protein 4.448...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...YPTB2540 or3654 conserved hypothetical protein 2.145 (0.008) YPTB2552 YPO2515 hypothetical 1.46 (0.023) 1.396 (0.042) YPTB2554 YPO2521 putative exported protein 0.648 (0.044) YPTB2562 YPO2530 conserved hypothetical protein 0.527 (0.026) YPTB2623 (flk) YPO2760 putative flagellar assembly regulatory protein. flk 0.549 (0.008) YPTB2699 YPO2976 conserved hypothetical protein 4.448 (<...”
• The Diverse Roles of the Global Transcriptional Regulator PhoP in the Lifecycle of Yersinia pestis
  Fukuto, Pathogens (Basel, Switzerland) 2020
  • “...[ 34 ]. Another example is that of the YhcN family genes ( y0666 and y1667 in KIM), which normally display induced expression and promote bacterial aggregation at low pH conditions in vitro [ 64 ]. These genes are highly expressed in fleas blocked from a...”
• Role of the PhoP-PhoQ gene regulatory system in adaptation of Yersinia pestis to environmental stress in the flea digestive tract
  Vadyvaloo, Microbiology (Reading, England) 2015
  • “...Technologies) as per the manufacturer's instructions. Samples were amplified using oligonucleotide primers for crr (y1485), y1667, y0666, y3909, y3519, y2882 ( psaA ), y1918 and the IQ SYBR Green Supermix (Bio-Rad) via a two-step protocol on a Bio-Rad CFX384 real-time system. Oligonucleotide sequences are tabulated in...”
  • “...family (DUF1471) multiple stress resistance y0666 yhcN Multiple stress resistance protein 9.3 (1.5) 1.3 1.1 y1667 Multiple stress resistance protein 12.4 (1.9) 1.0 1.2 * Gene not annotated in Y. pestis KIM (YPO number indicates Y. pestis CO92 homologue). Elevated transcription of four putative toxinantitoxin (TA)...”

CPT31_08740 multiple stress resistance protein BhsA from Enterobacter hormaechei
57% identity, 100% coverage

• The evolution of antibiotic resistance in an incurable and ultimately fatal infection: A retrospective case study
  Woods, Evolution, medicine, and public health 2023
  • “...of the divergently transcribed gene [ 40 ]. In this case, the divergently transcribed gene CPT31_08740 has homology to the multiple stress resistance protein BhsA. The meropenem-resistant isolates from the end of the infectious process also had higher levels of resistance against cefepime, yet they never...”

ComC / b1112 DUF1471 domain-containing multiple stress resistance outer membrane protein BhsA from Escherichia coli K-12 substr. MG1655 (see 10 papers)
BHSA_ECOLI / P0AB40 Multiple stress resistance protein BhsA; Copper-induced outer membrane component from Escherichia coli (strain K12) (see 2 papers)
bhsA multiple stress resistance protein bhsA from Escherichia coli K12 (see 4 papers)
NP_415630 DUF1471 domain-containing multiple stress resistance outer membrane protein BhsA from Escherichia coli str. K-12 substr. MG1655
ECs_1490, NP_309517 multiple stress resistance protein BhsA from Escherichia coli O157:H7 str. Sakai
b1112 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
ECs1490 hypothetical protein from Escherichia coli O157:H7 str. Sakai
B21_RS05900, DR76_RS20000, ETEC_1177 multiple stress resistance protein BhsA from Escherichia coli ATCC 25922
56% identity, 100% coverage

• function: Reduces the permeability of the outer membrane to copper. Seems to be involved in the regulation of biofilm formation. May decrease biofilm formation by repressing cell-cell interaction and cell surface interaction.
  disruption phenotype: Disruption of this gene increases copper sensitivity, induces stress response genes in biofilms, increases aggregation and cell surface hydrophobicity, and decreases indole synthesis.
• The copper-inducible ComR (YcfQ) repressor regulates expression of ComC (YcfR), which affects copper permeability of the outer membrane of Escherichia coli.
  Mermod, Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine 2012 (PubMed)
  • GeneRIF: ComC is an outer membrane protein which lowers the permeability of the outer membrane to copper, and its expression is controlled by ComR, a novel, TetR-like copper-responsive repressor.
• Antibacterial efficacy interference of the photocatalytic TiO₂ nanoparticle and the lytic bacteriophage vb_EcoS_bov25_1D on the Enterohaemorragic Escherichia coli strain Sakai
  Steinbach, Heliyon 2024
  • “...of phosphonate uptake and biodegradation protein_coding 914249 2,09165146 ECs_3407 hcaB 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase protein_coding 914919 2,09383064 ECs_1490 bhsA multiple stress resistance protein BhsA protein_coding 912348 2,13985583 ECs_3618 cysI sulfite reductase beta subunit protein_coding 914660 2,17216646 ECs_4581 escT T3SS structure protein EscT protein_coding 915450 2,18352571 ECs_5082 phnI ribophosphonate...”
  • “...resistance [ 64 ]. Our results show however a certain kind of keyrole of bhsA (ECs_1490, FC 1.93) under this stress situation. The high expression of the bhsA, and other protein membrane genes and the low expression of rcnR repressor, could indicate a response of the...”
• Functional analysis of ycfR and ycfQ in Escherichia coli O157:H7 linked to outbreaks of illness associated with fresh produce.
  Deng, Applied and environmental microbiology 2011
  • GeneRIF: These findings suggest that gene regulation via ycfQ and ycfR may be a mechanism by which Escherichia coli O157:H7 strain Sakai could survive in the postharvest processing environment.
• Serotype-dependent adhesion of Shiga toxin-producing Escherichia coli to bovine milk fat globule membrane proteins
  Bagel, Frontiers in microbiology 2022
  • “...13.00 (0.0002) 8.63 (0.0000) PMK5 Multiple stress resistance protein BhsA (Copper-induced outer membrane component) A0A070FQT8 (P0AB40) Cell outer membrane [GO:0009279]; response to copper ion [GO:0046688] 3.27 (0.0949) 3.01 (0.0451) 1.09 (0.7891) PMK5 Vitamin B12 transporter BtuB (Cobalamin receptor) (Outer membrane cobalamin translocator) A0A0E1LF30 (A8A774) Cell outer...”
• 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: 15 days, 4 C 1088.8935 +6 6527.32 -1.1 BhsA a P0AB40 35 -signal peptide 1094.2255 +8 8745.75 -0.6 YnaE P76073 62 1212.1269 +6 7266.72 -0.4 CspC P0A9Y6 37 Incubation: 24 h, 37 C Storage: 2 days, room temperature -Met 1356.6814 +3...”
• A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli
  Rodionova, Scientific reports 2022
  • “...b1889 motB Motility protein B 409.8 5.2 b4154 frdA Fumarate reductase flavoprotein subunit 2376.0 5.2 b1112 bhsA DUF1471 domain-containing multiple stress resistance outer membrane protein BhsA 3.5 5.2 b0621 dcuC Anaerobic C4-dicarboxylate transporter DcuC 120.9 5.1 b1878 flhE Flagellar protein 27.4 5.1 b2020 hisD Histidinal/histidinol dehydrogenase...”
• Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure
  LaVoie, BMC genomics 2018
  • “...Name Product Description Hg t10 Hg t30 Hg t60 PMA t10 PMA t30 PMA t60 b1112 bhsA Biofilm, cell surface and signaling defects, YhcN family 1949 563 94 46 21 n.s. b4458 oxyS OxyS sRNA activates genes that detoxify oxidative damage 1524 1292 150 10 6...”
  • “...n.s. b1531 marA Transcriptional activator for multiple antibiotic resistance; 15 9 n.s. 46 31 n.s. b1112 bhsA Biofilm, cell surface and signaling defects, YhcN family 1949 563 94 46 21 n.s. b1532 marB marRAB multiple antibiotic resistance operon 16 8 n.s. 45 27 n.s. b4663 azuC...”
• Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage
  Royce, PloS one 2014
  • “...0.002 0.003 3.5 Biofilm formation- rapid acid treatment b3516 gadX 0.001 0.014 3.5 AR2 TR b1112 bhsA 0.002 0.003 3.3 Influencing biofilm through hydrophobicity and SR b2012 yeeD 0.010 0.106 3.0 Uncharacterized b1164 ycgZ 0.006 0.107 2.9 Cold shock stimulon b4554 (c4419) yibT 0.001 0.056 2.8...”
• Global gene expression profiling of asymptomatic bacteriuria Escherichia coli during biofilm growth in human urine
  Hancock, Infection and immunity 2007
  • “...ycfR yhcN ibpB bfd b3782 b3556 b3687 b4414 b2153 b0802 b1112 b3238 b3686 b3337 6,476 6,387 6,120 6,025 5,942 5,817 5,804 5,790 5,787 5,582 1.8 15.9 8.7 1.0 1.2...”
• luxS-dependent gene regulation in Escherichia coli K-12 revealed by genomic expression profiling
  Wang, Journal of bacteriology 2005
  • “...b1022 b1437 b4186 b2406 b3939 b3945 b0648 b1680 b0823 b1112 b4288 b4310 b3103 b0621 b1407 b0076 b2723 b3683 b3028 b2968 b0579 b3220 b0260 b3046 b2919 b3906...”
• Gene expression in Escherichia coli biofilms
  Ren, Applied microbiology and biotechnology 2004 (PubMed)
  • “...of unknown function (ybaJ, ychM, yefM, ygfA, b1060, b1112, b2377, b3022, b1373, b1601, and b0836). The DNA microarray results were corroborated with RNA dot...”
  • “...3 trpE b1264 Unknown genes ybaJ b0461 b2377 b2377 b1112 b1112 b3022 b3022 2 4 Heat shock protein Regulation of superoxide response regulon, global regulator...”
• Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli
  Brown, Proceedings of the National Academy of Sciences of the United States of America 2004
  • “...(b1779) ydeA (b1528) hpt (b0125); ged (b0124) yefQ (b1111); ycfR (b1112) proP (b4111) ygiG (b3073); aer (b3072) -- -- 3.33 9.14 -- -- -- -- 5.87 -- 4.47 6.70...”
• Prominent roles of the NorR and Fur regulators in the Escherichia coli transcriptional response to reactive nitrogen species
  Mukhopadhyay, Proceedings of the National Academy of Sciences of the United States of America 2004
  • “...b1684 b0127 b4367 b2875 b3106 b4357 b2579 b0484 b3744 b4381 b3774 b0802 b2715 b1200 b1241 b1112 173 338 70 38 2 3 11 2 17 18 1 1 6 5 2 1 15 2 6 7 9 1 1 1 1 2 4...”
• More
• Pre-Harvest Survival and Post-Harvest Chlorine Tolerance of Enterohemorrhagic Escherichia coli on Lettuce
  Tyagi, Toxins 2019
  • “...3.7 3.9 ECs1417 csgD Transcriptional regulator CsgD 4.5 3.3 ECs1438 bssS biofilm regulator 3.4 4.2 ECs1490 bhsA multiple stress resistance protein (YcfR) 3.5 4.2 ECs1926 zntB Zinc transport protein ZntB 1.8 1.8 ECs2062 ybfL type IV secretion protein Rhs 3.9 3.0 ECs2155 nleG6-2 T3SS secreted effector...”
• Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice
  Bergholz, Applied and environmental microbiology 2009
  • “...ECs1318 ECs1342 ECs1350 ECs1397 ECs1438 ECs1441 ECs1488 ECs1490 ECs1576 ECs1588 ECs1593 ECs1612 ECs1654 ECs1655 ECs1691 ECs1760 ECs1763 ECs1771 ECs1775 ECs1823...”
• Cross-Kingdom Comparative Transcriptomics Reveals Conserved Genetic Modules in Response to Cadmium Stress
  Chen, mSystems 2021
  • “...B21_RS13600, and B21_RS07750), stress response (B21_RS19915), sugar import (B21_RS20540, B21_RS20565, and B21_RS21625), cell wall remodeling (B21_RS05900), and energy production and conversion (B21_RS21615) ( Fig.2A ). In S. cerevisiae AH109, 11 selected DEGs (YLR303W, YIR017C, YKL001C, YLL061W, YDR502C, YLR180W, YPL274W, YLL060C, YGR055W, YFR030W, and YPR167C) encoded proteins...”
• Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken
  Hussain, Scientific reports 2017
  • “...0.01 DR76_RS05090 HdeB Acid-resistance protein HdeB 5.17 0.01 DR76_RS05080 HdeD Acid-resistance protein HdeD 5.81 0.01 DR76_RS20000 BhsA Multiple stress resistance protein BhsA 1.30 0.01 DR76_RS04045 IbpB Heat shock chaperone IbpB 2.80 0.01 DR76_RS04040 IbpA Heat shock protein IbpA 1.91 0.01 DR76_RS14975 Hsp31 Heat shock protein Hsp31...”
• The molecular basis for control of ETEC enterotoxin expression in response to environment and host
  Haycocks, PLoS pathogens 2015
  • “...1263558 T T TGA CGGCTA TCAC G ETEC_1166 ptsG 1274886 TGTGA TCTGGA TCACA ETEC_1176 / ETEC_1177 ycfQ / bhsA 1301786 GA TGA TCCGCA TCACA ( ETEC_1206 )/ ETEC_1207 ETEC-specific/ETEC-specific 1348166 AT TGA ACAGGA TCACA (ETEC_1259)/ETEC_1260 (rluE)/icd 1376374 G GTGA GCTGGC TCACA ETEC_1292 / ETEC_1293 ycgB /...”

NP_460184 putative outer membrane protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
STM1214 putative outer membrane protein from Salmonella typhimurium LT2
SL1344_1151, STM14_1388 multiple stress resistance protein BhsA from Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
57% identity, 100% coverage

• Roles of YcfR in Biofilm Formation in Salmonella Typhimurium ATCC 14028.
  Kim, Molecular plant-microbe interactions : MPMI 2019 (PubMed)
  • GeneRIF: YcfR is an essential constituent of Salmonella outer membrane architecture and its absence may cause multifaceted structural changes, thereby compromising bacterial envelope integrity
• Stress response, amino acid biosynthesis and pathogenesis genes expressed in Salmonella enterica colonizing tomato shoot and root surfaces
  Han, Heliyon 2020
  • “...SIGNALING [M] Cell wall/membrane/envelope biogenesis yhdV STM3392 outer membrane lipoprotein 1.7 0.002 3.7 0.003 ycfR STM1214 Reduces the permeability of the outer membrane to copper. Seems to be involved in the regulation of biofilm formation. May decrease biofilm formation by repressing cell-cell interaction and cell surface...”
• Mapping and regulation of genes within Salmonella pathogenicity island 12 that contribute to in vivo fitness of Salmonella enterica Serovar Typhimurium
  Tomljenovic-Berube, Infection and immunity 2013
  • “...3.53 1.63E22 1.83E15 2.07E20 4.71E43 3.41E23 1.05E16 2.49E12 STM1214 STM3828 STM0701 STM0152 ycfR dgoA speF aceE 3.18 3.17 3.12 3.06 3.53E09 2.88E39 2.87E76...”
• Effects of indole on drug resistance and virulence of Salmonella enterica serovar Typhimurium revealed by genome-wide analyses
  Nikaido, Gut pathogens 2012
  • “...ybiJ Putative periplasmic protein 3.2 11 STM1156 yceA Putative enzyme related to sulfurtransferases 4.3 8.0 STM1214 ycfR Putative outer membrane protein 4.6 37 STM1251 Putative molecular chaperone (small heat shock protein) 11 9.2 STM1355 ydiP Putative transcription regulator, AraC family 11 7.5 STM1472 Putative periplasmic protein...”
• Transcriptomic responses of Salmonella enterica serovars Enteritidis and Typhimurium to chlorine-based oxidative stress
  Wang, Applied and environmental microbiology 2010
  • “...regulatory protein STM0823 ybiJ Putative periplasmic protein STM1214 ycfR Putative outer membrane protein STM2430 cysK O-Acetylserine sulfhydrolase A STM2338...”
• Integrative DNA methylome and transcriptome analysis reveals DNA adenine methylation is involved in Salmonella enterica Typhimurium response to oxidative stress
  Zhang, Microbiology spectrum 2023
  • “...symporter STM14_0180 aroP 0.84 0.017 Aromatic amino acid transporter STM14_1053 0.90 0.014 Hypothetical protein STM14_1053 STM14_1388 ycfR 0.68 0.05 Putative outer membrane protein STM14_2212 manX 0.82 0.024 Mannose-specific enzyme IIAB STM14_2213 manY 0.83 0.022 Mannose-specific enzyme IIC STM14_2492 0.93 0.0021 Hypothetical protein STM14_2492 STM14_2773 0.79 0.033...”
• Tigecycline challenge triggers sRNA production in Salmonella enterica serovar Typhimurium
  Yu, BMC microbiology 2012
  • “...in the cDNA library, e.g. dinF and a gene encoding a putative outer membrane protein (SL1344_1151). The dinF gene is a member of the SOS response family and encodes an efflux pump which belongs to the multidrug and toxic compound extrusion (MATE) family [ 31 ],...”

STY1254 putative secreted protein from Salmonella enterica subsp. enterica serovar Typhi str. CT18
56% identity, 100% coverage

• The footprint of gut microbiota in gallbladder cancer: a mechanistic review
  Liu, Frontiers in cellular and infection microbiology 2024
  • “...upregulate the expression of 35 genes related to the membrane matrix and antibiotic resistance ( STY1254, STY1255, yheA , etc.), downregulated 29 genes related to metabolic processes and biofilm regulation ( STY1856, yiiU, cspB , etc.), and enter a state of energy conservation in response to...”
  • “...biofilm phenotype of S. Typhi allows bacteria to upregulate the expression of 35 genes ( STY1254, STY1255, yheA , etc.) related to the membrane matrix and antibiotic resistance, downregulated 29 genes ( STY1856, yiiU, cspB , etc.) related to metabolic processes and biofilm regulation. Image made...”
• Better together-Salmonella biofilm-associated antibiotic resistance
  Aleksandrowicz, Gut microbes 2023
  • “...by H 2 0 2 and HOCl. 125 It is also referred to as the STY1254 gene, which is one of the most highly upregulated genes in S . Typhi biofilms. 63 Zhang et al. indicated that the bhsA gene in E. coli increases the stickiness...”
• Transcriptomic study of Salmonella enterica subspecies enterica serovar Typhi biofilm
  Chin, BMC genomics 2017
  • “...in the track represent the log 2 -fold change of each 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...”
  • “...bacteria membrane matrix The gene that was most highly up-regulated in the biofilm cells was STY1254 , a multiple stress resistance protein, bhsA . It plays a role in the membrane structure of S. Typhi [ 16 ]. According to a study by Zhang et al....”

KP1_2104 hypothetical protein from Klebsiella pneumoniae NTUH-K2044
53% identity, 100% coverage

• A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains
  Hennart, Molecular biology and evolution 2022
  • “...2014 ). Here, we updated the scgMLSTv1 scheme, with the following improvements. First, two loci (KP1_2104 and aceB =KP1_0253) were removed because they were absent or truncated in multiple strains, based on 751 high-quality assemblies available in the BIGSdb-Pasteur Klebsiella database on October 16, 2017 (project...”

AAF13_RS31850 DUF1471 family periplasmic protein McbA from Escherichia coli O104:H4 str. C227-11
46% identity, 98% coverage

• Broad time-dependent transcriptional activity of metabolic genes of E. coli O104:H4 strain C227/11Φcu in a soil microenvironment at low temperature
  Detert, Environmental microbiology reports 2023
  • “...domaincontaining protein n.d.e 5.36 AAF13_RS19105 DUF1328 domaincontaining protein 2.20 5.39 AAF13_RS19690 Nacetylmannosamine6phosphate 2epimerase 3.03 5.32 AAF13_RS31850 DUF1471 domaincontaining protein n.d.e 6.20 actP Cation/acetate symporter ActP 6.73 2.17 araD Lribulose5phosphate 4epimerase 8.45 2.78 dppF Dipeptide ABC transporter ATP binding subunit DppF 7.12 2.03 gabP GABA permease 7.39...”

YbiM / b0806 DUF1471 domain-containing protein McbA from Escherichia coli K-12 substr. MG1655 (see 2 papers)
MCBA_ECOLI / P0AAX6 Uncharacterized protein McbA; MqsR-controlled colanic acid and biofilm protein A from Escherichia coli (strain K12) (see paper)
mcbA / ECOCYC|G6415-MONOMER MqsR-controlled colanic acid and biofilm protein A from Escherichia coli K12 (see paper)
b0806 orf, hypothetical protein from Escherichia coli str. K-12 substr. MG1655
NP_415327 DUF1471 domain-containing protein McbA from Escherichia coli str. K-12 substr. MG1655
46% identity, 98% coverage

• function: Affects biofilm formation and mucoidy.
• 5-azacytidine induces transcriptome changes in Escherichia coli via DNA methylation-dependent and DNA methylation-independent mechanisms
  Militello, BMC microbiology 2016
  • “...A; homodimeric; selenate, azaserine, chromate resistance; alkali-inducible, sulfate starvation-inducible protein SSI5; cysteine desulfhydrase 1.58 2.86E-03 b0806 mcbA Stimulates colanic acid mucoidy, YhcN family, periplasmic; suppresses biofilm formation; repressed by McbR 1.71 5.11E-04 b2425 cysP Thiosulfate-binding protein, periplasmic 1.84 1.90E-04 b0506 allR Repressor for all (allantoin) and...”
• YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity
  Zhang, Journal of bacteriology 2007
  • “...function ybiM ybaA yceK yjbJ yjdN ygaM ymgE b0806 b0456 b1050 b4045 b4107 b2672 b1195 Hypothetical protein Hypothetical protein Hypothetical protein Highly...”
• Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
  Smulski, Journal of bacteriology 2001
  • “...b0607 b0643 b0662 b0707 b0753 b0786 b0789 b0790 b0800 b0806 b0836 b0865 b0897 b0964 b0966 b1003 b1045 b1050 b1060 b1103 b1104 b1105 b1107 b1108 b1111 b1112...”
• The C-terminal part of microcin B is crucial for DNA gyrase inhibition and antibiotic uptake by sensitive cells.
  Shkundina, Journal of bacteriology 2014
  • GeneRIF: The C-terminal part of McbA is crucial for DNA gyrase inhibition and antibiotic uptake.
• Proton motive force dissipation precludes interaction of microcin J25 with RNA polymerase, but enhances reactive oxygen species overproduction.
  Dupuy, Biochimica et biophysica acta 2009 (PubMed)
  • GeneRIF: Data show that the deleterious reactive oxygen species would be produced as a consequence of the minor fraction of MccJ25 that interacts with the bacterial plasma membrane from the periplasmic side.
• Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA).
  Zhang, The ISME journal 2008 (PubMed)
  • GeneRIF: YncC inhibits colanic acid overproduction and thereby inhibits mucoidy by repressing expression of periplasmic protein YbiM

Z1027 orf, hypothetical protein from Escherichia coli O157:H7 EDL933
ECs0884 hypothetical protein from Escherichia coli O157:H7 str. Sakai
46% identity, 63% coverage

• Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces
  Landstorfer, BMC genomics 2014
  • “...(2) 1.5 (45) 2.5 (25) 0.9 (3) 1.7 (35) 1.7 (31) 6.6 (945) 3.3 (28) Z1027 ybiM , biofilm formation [ 44 ] radish 1 (17) 0.3 (8) 5.6 (0) 3.1 (1) 0.3 (12) 0.0 (4) 5.6 (0) 5.6 (0) 2.3 (2) 7.5 (1751) 5.6 (0)...”
  • “...LB medium (B1), minimal medium (B2), and on radish sprouts (B3). C1-C3: regulated hypothetical gene Z1027 (see Table 2 ), in LB medium (C1), minimal medium (C2), and on radish sprouts (C3). D1-D3: regulated hypothetical gene Z4396 (Table 2 ), in LB medium (D1), minimal medium...”
• Transcriptional responses of Escherichia coli K-12 and O157:H7 associated with lettuce leaves
  Fink, Applied and environmental microbiology 2012
  • “...expression Symbol Description Day 1 Day 3 Biofilm Z1027 Z1697 ybiM yceP (bssS) Hypothetical protein Hypothetical protein 31.30 7.90 68.30 7.90 Cell envelope...”
• Influence of Glucose Availability and CRP Acetylation on the Genome-Wide Transcriptional Response of Escherichia coli: Assessment by an Optimized Factorial Microarray Analysis
  Guebel, Frontiers in microbiology 2018
  • “...significant classes a set of four genes that codify periplasmic proteins with dodecin-like structure (ECs5165, ECs0884, ECs5164, ECs5175; FDR = 2.1 10 2 ) and another set of five genes which codify enzymes involved in L-arginine degradation ( astA [arginine N-succinyltransferase], astB [N-succinylarginine dihydrolase], astC [bifunctional...”

S1196 hypothetical protein from Shigella flexneri 2a str. 2457T
54% identity, 82% coverage

• Addendum
  , Open forum infectious diseases 2019

Z1023 orf, hypothetical protein from Escherichia coli O157:H7 EDL933
ECs0880 hypothetical protein from Escherichia coli O157:H7 str. Sakai
56% identity, 99% coverage

• Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces
  Landstorfer, BMC genomics 2014
  • “...(0) 4.6 (3) 0.0 (0) 0.0 (0) 0.0 (0) 3.3 (1) 5.7 (4) 0.0 (0) Z1023 ybiJ , biofilm formation [ 42 , 43 ] radish 1 (17) 0.2 (8) 0.2 (3) 2.6 (2) 1.5 (45) 2.5 (25) 0.9 (3) 1.7 (35) 1.7 (31) 6.6 (945)...”
  • “...found on the forward strand of this region. B1-B3: example for a regulated hypothetical gene, Z1023 (see Table 2 ), in LB medium (B1), minimal medium (B2), and on radish sprouts (B3). C1-C3: regulated hypothetical gene Z1027 (see Table 2 ), in LB medium (C1), minimal...”
• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...ECs3081 b2190 ECs2359 ECs3396 ECs0128 ECs3328 ECs0503 ECs0880 ECs0927 ECs2042 b0802 b0847 b1438 b2530 b0124 b2466 b0449 ECs0512 ECs5566 ECs2316 ECs0252...”

YbiJ / b0802 DUF1471 domain-containing protein YbiJ from Escherichia coli K-12 substr. MG1655 (see 5 papers)
b0802 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
P0AAX3 Uncharacterized protein YbiJ from Escherichia coli (strain K12)
ETEC_0869 DUF1471 family protein YbiJ from Escherichia coli ETEC H10407
55% identity, 99% coverage

• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...ECs2359 ECs3396 ECs0128 ECs3328 ECs0503 ECs0880 ECs0927 ECs2042 b0802 b0847 b1438 b2530 b0124 b2466 b0449 ECs0512 ECs5566 ECs2316 ECs0252 b0459 b4458 b1610...”
• Global gene expression profiling of asymptomatic bacteriuria Escherichia coli during biofilm growth in human urine
  Hancock, Infection and immunity 2007
  • “...ybiJ ycfR yhcN ibpB bfd b3782 b3556 b3687 b4414 b2153 b0802 b1112 b3238 b3686 b3337 6,476 6,387 6,120 6,025 5,942 5,817 5,804 5,790 5,787 5,582 1.8 15.9 8.7 1.0...”
• Prominent roles of the NorR and Fur regulators in the Escherichia coli transcriptional response to reactive nitrogen species
  Mukhopadhyay, Proceedings of the National Academy of Sciences of the United States of America 2004
  • “...b2717 b0795 b1684 b0127 b4367 b2875 b3106 b4357 b2579 b0484 b3744 b4381 b3774 b0802 b2715 b1200 b1241 b1112 173 338 70 38 2 3 11 2 17 18 1 1 6 5 2 1 15 2 6 7...”
• Biodistribution of ⁸⁹Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
  Li, Poultry science 2023
  • “...8 P0AEQ3 GLNH Function unknown Periplasm 9 P09394 GLPQ Energy production and conversion Periplasm 10 P0AAX3 YBIJ Function unknown Periplasm 11 P0AES9 HDEA Function unknown Periplasm 12 P02925 RBSB Carbohydrate transport and metabolism Periplasm 13 P0A862 TPX Posttranslational modification, protein turnover, chaperones Periplasm 14 P64534 RCNB...”
• The molecular basis for control of ETEC enterotoxin expression in response to environment and host
  Haycocks, PLoS pathogens 2015
  • “...C GT T A CCCTTG TC G CA ETEC_0680 rihA 941002 TGTGA TGAGTA TCAC G ETEC_0869 ybiJ 958866 TGTGT ACGAAA TCACA ETEC_0886/ETEC_0887 ybiS/ybiT 1128472 n.d. ( ETEC_1030 ) ( yccS ) 1205350 A GTGA TGTAGA TCACA ETEC_1101 ycgZ TG A GA TCGAGCA CACA 1263558 T T...”

STM0823 putative periplasmic protein from Salmonella typhimurium LT2
STY0860 putative exported protein from Salmonella enterica subsp. enterica serovar Typhi str. CT18
59% identity, 99% coverage

• Effects of indole on drug resistance and virulence of Salmonella enterica serovar Typhimurium revealed by genome-wide analyses
  Nikaido, Gut pathogens 2012
  • “...Enterochelin synthetase, component D (phoshpantetheinyltransferase) 6.1 7.5 STM0707 kdpF Putative outer membrane protein 8.6 18 STM0823 ybiJ Putative periplasmic protein 3.2 11 STM1156 yceA Putative enzyme related to sulfurtransferases 4.3 8.0 STM1214 ycfR Putative outer membrane protein 4.6 37 STM1251 Putative molecular chaperone (small heat shock...”
• Transcriptomic responses of Salmonella enterica serovars Enteritidis and Typhimurium to chlorine-based oxidative stress
  Wang, Applied and environmental microbiology 2010
  • “...STM2544 yfhP Putative iron-sulfur cluster regulatory protein STM0823 ybiJ Putative periplasmic protein STM1214 ycfR Putative outer membrane protein STM2430 cysK...”
• Identification of in vivo-induced bacterial protein antigens during human infection with Salmonella enterica serovar Typhi
  Harris, Infection and immunity 2006
  • “...TcfB, and two antigens of unknown function encoded by STY0860 and STY3683. PagC is a virulence factor known to be upregulated in vivo in S. enterica serovar...”
  • “...of unknown function a pHCM1.176 pHMC1.257 pHCM2.0028 STY0860 STY1648 STY2156 STY2195 STY2761 STY3683 STY3684 TrhW--plasmid transfer protein, fimbrial regulation...”

LV106 hypothetical protein from Klebsiella pneumoniae
45% identity, 99% coverage

• Comparison of paenibacillus azotofixans strains isolated from rhizoplane, rhizosphere, and non-root-associated soil from maize planted in two different brazilian soils
  Seldin, Applied and environmental microbiology 1998
  • “...MRV100, MRV105, MRV106, MRV108, MRV111, MRV117 PV104, LV106, LV107, LV114, LV115, CRiP103, CRiP104, CRiP105, CRiP115, CRiP125, CRiP126, CRiP127, CRiP128,...”
  • “...MSV55, MSV63, MSV66, MSV68, LV53, LV56, MSV108, LV106, MRV153, MRV154, MRV156, CRiP21, CRiL56, CSM56, CRiP57, CSM116, CRiL151, CRiP165 LV107, LV115, PV104,...”

y0666 hypothetical protein from Yersinia pestis KIM
YPTB0458 putative exported protein from Yersinia pseudotuberculosis IP 32953
44% identity, 95% coverage

• Dissecting psa Locus Regulation in Yersinia pestis
  Li, Journal of bacteriology 2021 (secret)
• The Diverse Roles of the Global Transcriptional Regulator PhoP in the Lifecycle of Yersinia pestis
  Fukuto, Pathogens (Basel, Switzerland) 2020
  • “...flea blockage [ 34 ]. Another example is that of the YhcN family genes ( y0666 and y1667 in KIM), which normally display induced expression and promote bacterial aggregation at low pH conditions in vitro [ 64 ]. These genes are highly expressed in fleas blocked...”
  • “...PhoP. PhoP binding motifs have been identified by bioinformatic analysis in the promoter regions of y0666 and y3555/aspB [ 68 ], predicting that these genes are directly regulated by PhoP. Known PhoP-repressed genes psaABC and psaEF , which are involved in production of the pH 6...”
• Role of the PhoP-PhoQ gene regulatory system in adaptation of Yersinia pestis to environmental stress in the flea digestive tract
  Vadyvaloo, Microbiology (Reading, England) 2015
  • “...as per the manufacturer's instructions. Samples were amplified using oligonucleotide primers for crr (y1485), y1667, y0666, y3909, y3519, y2882 ( psaA ), y1918 and the IQ SYBR Green Supermix (Bio-Rad) via a two-step protocol on a Bio-Rad CFX384 real-time system. Oligonucleotide sequences are tabulated in Table...”
  • “...1.0 YPO1087 * HigB2 toxin 2.3 1.2 1.0 1.1 YhcN family (DUF1471) multiple stress resistance y0666 yhcN Multiple stress resistance protein 9.3 (1.5) 1.3 1.1 y1667 Multiple stress resistance protein 12.4 (1.9) 1.0 1.2 * Gene not annotated in Y. pestis KIM (YPO number indicates Y....”
• IscR is essential for yersinia pseudotuberculosis type III secretion and virulence
  Miller, PLoS pathogens 2014
  • “...biosynthetic protein pdxJ 2.2 Hypothetical Proteins(9) YPTB0391 putative exported protein 2.1 YPTB0449 hypothetical protein 3.3 YPTB0458 putative exported protein 2.2 YPTB1093 hypothetical protein 3.6 YPTB1571 hypothetical protein 2.1 YPTB2255 putative exported protein 2.3 YPTB2277 hypothetical protein 2.6 YPTB2496 hypothetical protein 2.8 YPTB3109 hypothetical protein 4.1 a...”

DSJ_21690 peroxide/acid stress response protein YhcN from Pantoea stewartii subsp. stewartii DC283
45% identity, 98% coverage

• The Transcription Factor Lrp of Pantoea stewartii subsp. stewartii Controls Capsule Production, Motility, and Virulence Important for in planta Growth
  Bartholomew, Frontiers in microbiology 2021
  • “...seven transcription factors (NsrR, IscR, Nac, Lrp, DSJ_00125, DSJ_03645, and DSJ_18135) and one hypothetical protein (DSJ_21690) were constructed to further evaluate the role of the encoded gene products during in vitro and in planta growth. Assays for capsule production and motility indicate that Lrp plays a...”
  • “...described ( Kernell Burke et al., 2015 ). The genes lrp , DSJ_00125 (00125), and DSJ_21690 (21690) underwent a deletion strategy from methods described by Stice et al. (2020) that was modified as described below. Overlap extension PCR products with attB sites for the upstream and...”
• Discovery of Pantoea stewartii ssp. stewartii genes important for survival in corn xylem through a Tn-Seq analysis
  Duong, Molecular plant pathology 2018 (secret)

P0E69_02545 peroxide/acid stress response protein YhcN from Chimaeribacter arupi
44% identity, 95% coverage

• Chimaeribacter arupi a new member of the Yersineacea family has the characteristics of a human pathogen
  Riediger, Frontiers in cellular and infection microbiology 2023
  • “...P0E69_02500 msrA 524986..525621 peptide-methionine (S)-S-oxide reductase MsrA P0E69_02540 yhcN 535610..535870 peroxide/acid stress response protein YhcN P0E69_02545 yhcN 536006..536269 peroxide/acid stress response protein YhcN P0E69_03070 trx-GI 660012..660452 heat resistance system thioredoxin Trx-GI P0E69_05270 bcp 1133791..1134261 thioredoxin-dependent thiol peroxidase P0E69_06695 1506872..1507075 thioredoxin reductase P0E69_09415 2087216..2087419 thioredoxin reductase P0E69_09865...”

ECs4111 hypothetical protein from Escherichia coli O157:H7 str. Sakai
40% identity, 82% coverage

• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...ECs4461 ECs4697 ECs4058 ECs0430 ECs0669 ECs2049 ECs2558 ECs3033 ECs4111 ECs4197 ECs4416 ECs5464 b3292 b3585 b3755 b3179 b0380 b0631 b1445 b1848 b2141 b3238...”

YhcN / b3238 DUF1471 domain-containing stress-induced protein YhcN from Escherichia coli K-12 substr. MG1655 (see 5 papers)
b3238 orf, hypothetical protein from Escherichia coli str. K-12 substr. MG1655
P64614 Uncharacterized protein YhcN from Escherichia coli (strain K12)
40% identity, 98% coverage

• Whole-Transcriptome Analysis of Verocytotoxigenic Escherichia coli O157:H7 (Sakai) Suggests Plant-Species-Specific Metabolic Responses on Exposure to Spinach and Lettuce Extracts
  Crozier, Frontiers in microbiology 2016
  • “...accounted for high levels of differential expression: e.g., in spinach leaf lysates two hypothetical genes (b3238, b1722) were ranked as #2 and 3 for level of induction, at 50-fold. Probes corresponding to Z5022 and ECs4474 were induced 270- to 300-fold in spinach root exudates, but repressed...”
• Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds
  Yung, Scientific reports 2016
  • “...1.70 1.99 1.43 UPF0304 family protein; K09161 hypothetical protein Oxidative stress b dms nmp t b3238 yhcN 1.92 1.11 1.39 1.39 1.6 2.25 1.26 1.69 Cadmium and peroxide resistance protein Oxidative stress b chp cp dma dms nmp nms t b3495 uspA* 1.79 1.63 1.49 1.29...”
• Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage
  Royce, PloS one 2014
  • “...b1493 gadB 0.000 0.015 25.3 AR2 decarboxylase b3509 hdeB 0.000 0.004 21.1 AR1 chaperone protein b3238 yhcN 0.002 0.064 15.2 Acid response b3510 hdeA 0.000 0.000 13.7 AR1 chaperone protein b4439 micF 0.003 0.078 11.9 Antisense RNA regulator of OmpF porin b3512 gadE 0.004 0.115 10.1...”
• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...b3585 b3755 b3179 b0380 b0631 b1445 b1848 b2141 b3238 b3346 b3536 b4537 Translation, ribosomal structure and biogenesis Poorly characterized or not present in...”
• The BaeSR two-component regulatory system mediates resistance to condensed tannins in Escherichia coli
  Zoetendal, Applied and environmental microbiology 2008
  • “...marB marR 2.6 2.6 21.5 27.4 b0005 b2390 b0618 b3687 b3686 b3238 b2675 yaaX ypeC citC ibpA ibpB yhcN nrdE 4.9 2.8 34.6 6.9 9.5 3.1 26.8 26.6 20.5 14.7 10.4 48.0...”
• Global gene expression profiling of asymptomatic bacteriuria Escherichia coli during biofilm growth in human urine
  Hancock, Infection and immunity 2007
  • “...mdtL yhcN yqgA rydB sgaB c2436 c2424 b2583 c3859 b3710 b3238 b2966 b4430 b4194 19.8 19.6 19.0 18.9 18.3 17.3 17.2 17.1 16.5 1,196 1,408 1,863 3,664 1,862 5,790...”
  • “...yhcN ibpB bfd b3782 b3556 b3687 b4414 b2153 b0802 b1112 b3238 b3686 b3337 6,476 6,387 6,120 6,025 5,942 5,817 5,804 5,790 5,787 5,582 1.8 15.9 8.7 1.0 1.2 8.2...”
• Global gene expression profiling of the asymptomatic bacteriuria Escherichia coli strain 83972 in the human urinary tract
  Roos, Infection and immunity 2006
  • “...c3973 c1382 b1445 b0620 c2901 b3241 b1335 Z1954 b1430 b3238 b0849 b0151 fepE ydhC evgA nlpI Z4919 c0674 b1660 b2369 b3163 Z4919 a Function or product...”
• Genome-wide localization of mobile elements: experimental, statistical and biological considerations
  Martinez-Vaz, BMC genomics 2005
  • “...yi52_8, ccmH 10. glcC, b2981, yi52_9, b2983, pitB 11. yhcD, yhcE, yi52_10, b3219, b3221, sspB, b3238 12. yhiS, yi52_11 , yhiF, tnaA We confirmed the presence of an IS5 element in the flhDC / yecG intergenic region by PCR. A 2720 bp PCR product was obtained...”
• More
• Optimized Signal Peptide for Secretory Expression of Human Recombinant Somatropin in E. coli
  Ahmadi, Advanced pharmaceutical bulletin 2023
  • “...Escherichia coli (strain K12) Q47702 MKKIICLVITLLMTLPVYA UPF0379 protein yhcN yhcN 22 Escherichia coli (strain K12) P64614 MKIKTTVAALSVLSVLSFGAFA Uncharacterized protein yncJ yncJ 22 Escherichia coli (strain K12) P64459 MFTKALSVVLLTCALFSGQLMA UPF0482 protein ynfB ynfB 28 Escherichia coli (strain K12) P76170 MKITLSKRIGLLAILLPCALALSTTVHA Zinc resistance-associated protein zraP 26 Escherichia coli...”
• Stress response of Escherichia coli to essential oil components - insights on low-molecular-weight proteins from MALDI-TOF
  Božik, Scientific reports 2018
  • “...protein spectrum were observed. Guaiacol induced the most distinct protein profile: UPF0434 protein (m/z 6960.26, P64614, YcaR) and 23S rRNA methylase leader peptide (Erythromycin resistance leader peptide, m/z 3802.46, P10739, ermC) were detected only in the guaiacol-treated sample at very high levels. The former protein is...”

t3276 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
STM3361 putative outer membrane protein from Salmonella typhimurium LT2
SENTW_3490 peroxide/acid stress response protein YhcN from Salmonella enterica subsp. enterica serovar Weltevreden str.
41% identity, 98% coverage

• A whole-genome screen identifies Salmonella enterica serovar Typhi genes involved in fluoroquinolone susceptibility
  Turner, The Journal of antimicrobial chemotherapy 2020
  • “...membrane protein 2.04 2.61 10 58 t2964 putative membrane protein; conserved 1.86 3.43 10 35 t3276 putative outer membrane protein; conserved 1.75 4.27 10 12 mrcA penicillin-binding protein 1A 1.60 5.3 10 49 plsC 1-acyl-glycerol-3-phosphate acyltransferase 1.57 1.03 10 8 t3147 putative exported protein 1.50 3.08...”
• Stress response, amino acid biosynthesis and pathogenesis genes expressed in Salmonella enterica colonizing tomato shoot and root surfaces
  Han, Heliyon 2020
  • “...protein 1.5 0.002 1.7 0.003 yhaK STM3236 pirin domain protein 2.1 0.002 1.4 0.003 yhcN STM3361 Putative outer membrane protein 0.004 STM3362 STM3362 Putative periplasmic protein 0.004 yjbE STM4222.S Exopolysaccharide production protein YjbE 3.0 0.003 5.9 0.003 yhhW STM3544 quercetin 2,3-dioxygenase 3.5 0.009 STM0910 STM0910 terminase,...”
• Mapping and regulation of genes within Salmonella pathogenicity island 12 that contribute to in vivo fitness of Salmonella enterica Serovar Typhimurium
  Tomljenovic-Berube, Infection and immunity 2013
  • “...STM1519.S marA 2.61 9.14E19 STM3882 STM0162 STM1518 STM3829 STM3512 STM3361 STM1520 rbsA marB dgoK gntT yhcN marR 2.59 2.53 2.46 2.42 2.40 2.36 2.35 7.30E47...”
• In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection
  Marchal, Genome biology 2004
  • “...slsA STM3761 ; putative inner membrane protein 0.765418 CTTTATGTTATTTAAAT nd / 1110 Other distributions yhcN STM3361 ; Ortholog of E. coli orf , hypothetical protein (AAC76270.1); Blast hit to putative outer membrane protein 0.764452 ATTAGTGTATACTTAAT m + 1111 All nine genomes? yceP STM1161 ; Ortholog of...”
• Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization
  Brankatschk, Microbial biotechnology 2014
  • “...7.03 Protein TdcF yiaL SENTW_3768 7.86 Protein YiaL ytfK SENTW_4510 8.24 Uncharacterized protein YtfK yhcN3 SENTW_3490 5.82 Protein YdgH ygaU SENTW_2883 5.51 Uncharacterized protein YgaU yggE SENTW_3181 6.70 Uncharacterized protein YggE yfeK SENTW_2617 5.38 Uncharacterized protein YfeK yjfN SENTW_4481 6.70 UPF0379 protein YjfN Genes more transcribed...”

YahO / b0329 DUF1471 domain-containing protein YahO from Escherichia coli K-12 substr. MG1655 (see 3 papers)
b0329 hypothetical protein from Escherichia coli str. K-12 substr. MG1655
P75694 Uncharacterized protein YahO from Escherichia coli (strain K12)
ETEC_0386 DUF1471 family periplasmic protein YahO from Escherichia coli ETEC H10407
36% identity, 93% coverage

• A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space
  Zea, PloS one 2016
  • “...16 genes, we have data for 15 (we did not find the expression of yahO (b0329) in the E . coli (DH10B) sequence that was downloaded from the UCSC genome browser), 12 of which were overexpressed (80%) in the spaceflight samples in between 2.10x and 24.76x....”
• Evolutionary dynamics of small RNAs in 27 Escherichia coli and Shigella genomes
  Skippington, Genome biology and evolution 2012
  • “...sdaC b2796 omrA 27 Core Incongruent No ompR b3405 omrA 27 Core Incongruent No yahO b0329 omrA 20 Variable Incongruent No dppB b3543 omrA 27 Core Incongruent No yjcH b4068 omrA 24 Variable Congruent No dppF b3540 omrA 27 Core Incongruent No fimA b4314 omrA 2...”
• Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
  Lee, Applied and environmental microbiology 2009
  • “...ompF expression Hypothetical yahK yahO ybaS b0325 b0329 b0485 5.7 7.0 7.5 2.6 2.8 2.3 Hypothetical zinc-type alcohol dehydrogenase-like protein Hypothetical...”
• Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022)
  González, Journal of bacteriology 2006
  • “...b3717 b1511 b2252 b3143 b4217 b1160 b1257 b3690 b0513 b1258 b0329 b4068 b1443 yncG spf yjcO ymgB ymgC yeaQ amyA gatC b1454 b3864 b4078 b1166 b1167 b1795 b1927...”
• Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states
  Fong, Genome research 2005
  • “...Hypothetical/putative None Annotated ppsA, yihK p=1- i=0 Glycerol b0329, b1266, b1678, b1934, b2302, b3021, b4109, proM, alaX, murA, prfC, psiF, rpsV, motA,...”
• SigmaS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sigmaS-dependent genes and identification of their promoter sequences
  Lacour, Journal of bacteriology 2004
  • “...(adherence) protein (b0232) Hypothetical protein (b0329) Hypothetical (inner membrane) protein (b0707) Putative enzyme (b0865) Hypothetical protein,...”
• Definition of the Escherichia coli MC4100 genome by use of a DNA array
  Peters, Journal of bacteriology 2003
  • “...b0309, b0317, b0319, b0320, b0321, b0322, b0326, b0327, b0329, b0332, b0334, b0335, b0347, b1137,a b1138, b1141, b1142, b1143, b1144, b1146, b1147, b1148,...”
• Global analysis of genes regulated by EvgA of the two-component regulatory system in Escherichia coli
  Nishino, Journal of bacteriology 2003
  • “...b3512 b0867 b1597 b2359 b1492 b2390 b0897 b0329 b2358 b3514 b0485 b4242 b2371 Adaptation (starvation) Regulation Metabolism Adaptation (stress) Extrachromosomal...”
• More
• Identification of specific protein amino acid substitutions of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli ST131: a proteomics approach using mass spectrometry
  Nakamura, Scientific reports 2019
  • “...this study. The m/z 7655 peak was identified as uncharacterized protein YahO (Uniprot accession no. P75694) belonging to the Bhs/McbA family. The chain domain of the YahO protein was DUF1471, and its function is unknown. The m/z 8351 peak was identified as UPF0337 protein YjbJ (Uniprot...”
• Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria
  Kocurek, Journal of the American Society for Mass Spectrometry 2017
  • “...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 10,457.58 +1.02 Da YbgS P0AAV6 45 -signal peptide;...”
• Identification of RpoS (sigma(S))-regulated genes in Salmonella enterica serovar typhimurium
  Ibanez-Ruiz, Journal of bacteriology 2000
  • “...P37663 (YhjY), P07003 (PoxB), P76114 (YncC), P27250 (YjgB), P75694 (YahO), P39169 (YgaU), P31677 (OtsA), P77391 (YeaG), P21179 (KatE), P21362 (YciF), and P29013...”
• The molecular basis for control of ETEC enterotoxin expression in response to environment and host
  Haycocks, PLoS pathogens 2015
  • “...G C G TTCCACG TCACA (ETEC_0150) (hemL) 408885 TGTGA TCTCTC TC G CA ETEC_0385 / ETEC_0386 yahN / yahO 461874 TGTG CGCAAGA TCACA ETEC_0434 ddlA 463095 TT TG CGCGAGG TCACA (ETEC_0436) (phoA) 468009 A G G GA TCTGCG TCACA ETEC_0443 aroM 492973 ATC GA TTGCGT TCAC...”

EDL933_0387 DUF1471 family periplasmic protein YahO from Escherichia coli O157:H7 str. EDL933
ECs0383 hypothetical protein from Escherichia coli O157:H7 str. Sakai
36% identity, 93% coverage

• Overexpressed Proteins in Hypervirulent Clade 8 and Clade 6 Strains of Escherichia coli O157:H7 Compared to E. coli O157:H7 EDL933 Clade 3 Strain
  Amigo, PloS one 2016
  • “...3.6808 0.0001 ECSP_5106 [TW14359] b 3.25 0.021 General secretion pathway protein G EDL933_p0034 3.2944 0.00078 EDL933_0387 3.14 0.00078 Type III secretion protein EscF 3.2944 0.021 YicS, putative secreted protein (EDL933_4982) 3.12 0.0001 Conserved phage protein EDL933_1401 3.1383 0.0001 Phage protein ECSP_2742 [TW14359] b 2.91 0.0001 Phage...”
  • “...ECSP_5106 present in clade 8 and present but not annotated in EDL933 and Sakai; and EDL933_0387 are also overexpressed; as well as two putative exported proteins, YebF and YicS. YebF was found in the cell extract of the three stains tested in this study ( S2...”
• Physiological Response of Escherichia coli O157:H7 Sakai to Dynamic Changes in Temperature and Water Activity as Experienced during Carcass Chilling
  King, Molecular & cellular proteomics : MCP 2016
  • “.../ ECs2098 ), cell filamentation ( fic / ECs4212 ), and encoding hypothetical proteins ( ECs0383 , ECs0886 , ycaC / ECs0982 , ECs1692 , ECs2695 , ECs2785 , ECs2888 , ECs3588 , ECs4112 , yhfG / ECs4213 , ECs4323 , ysgA / ECs4760 , ECs5089...”
• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...dinJ 2.46 2 ECs0991 aroA -4.24 1 ECs0269 proB -2.11 1 ECs1007 mukB -2.12 1 ECs0383 yahO 4.53 2 ECs1013 asnS -2.74 1 ECs0384 prpR 3.63 2 ECs1014 pncB -2.37 1 ECs0390 codA -2.78 1 ECs1022 ycbR -3.16 1 ECs0415 afuA 5.21 2 ECs1048 - 2.44...”

Q1RFK1 YdgH/BhsA/McbA-like domain-containing protein from Escherichia coli (strain UTI89 / UPEC)
UTI89_C0362 hypothetical protein from Escherichia coli UTI89
36% identity, 93% coverage

• Adhesive fiber stratification in uropathogenic Escherichia coli biofilms unveils oxygen-mediated control of type 1 pili
  Floyd, PLoS pathogens 2015
  • “...chaperone protein, HdeB (UniProt KB Q1R595, m/z 9,064), and the uncharacterized protein YahO (UniProt KB Q1RFK1, m/z 7,718) were also identified ( Table 1 ). HdeB localized to the air-liquid interface and was most abundant towards the liquid-exposed surface, while YahO localized throughout the biofilm (...”
  • “...Response Acid stress-response protein, HdeB Q1R595 12,522 aa133 / 3,475 Da 9,065 9,064 Uncharacterized YahO Q1RFK1 9,929 aa121 / 2,240 Da 7,707 7,718 *Predicted signal peptides obtained using the SignalP Server. # Observed average mass obtained from IMS analysis of one representative 48 hour UPEC biofilm....”
• Defining the phylogenomics of Shigella species: a pathway to diagnostics
  Sahl, Journal of clinical microbiology 2015
  • “...EcHS_A0402 HMPREF9530_02672 ECNG_01839 ECSTEC94C_0398 ECAA86_00424 ECSE_0359 UTI89_C0362 EIQ72748 EcSMS35_0562 0.98 0.98 0.97 0.86 0.9 0.96 0.99 0.98 0.97...”

c3599 Hypothetical protein from Escherichia coli CFT073
34% identity, 93% coverage

• Redox-Mediated Inactivation of the Transcriptional Repressor RcrR is Responsible for Uropathogenic Escherichia coli's Increased Resistance to Reactive Chlorine Species
  Sultana, mBio 2022
  • “...regulon confers resistance to HOCl stress. Including a gene cluster consisting of the three genes, c3599 , c3600 , and c3601 , 32.4% of the differentially expressed genes identified in our RNAseq analysis are uncharacterized and their biological function is still unknown ( Fig.2 ; TableS1...”
  • “...downstream (i.e., c3597 and c3602 , respectively) ( Fig.3A ). c3600 is located downstream of c3599 and upstream of c3601 and encodes a putative TetR-family transcriptional regulator; however, the functions of the c3599 and c3601 genes are unknown ( Fig.3A ). We renamed the c3599 ,...”

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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.