PaperBLAST

PaperBLAST Hits for IAI47_12665 (55 a.a., MKRQKRDRLE...)

Show query sequence

>IAI47_12665
MKRQKRDRLERAHSRGYQAGITGRSKEMCPYQLIDAKSHWLGGWRQAMEDRSVAA

Running BLASTp...

Found 15 similar proteins in the literature:

CKS_4032 ribosome modulation factor from Pantoea stewartii subsp. stewartii DC283
96% identity, 100% coverage

• Analysis of the in planta transcriptome expressed by the corn pathogen Pantoea stewartii subsp. stewartii via RNA-Seq
  Packard, PeerJ 2017
  • “...A 52.64 34.17 1.09E85 CKS_3793 Cytochrome d ubiquinol oxidase subunit I A 36.48 23.81 2.78E59 CKS_4032 rmf Ribosome modulation factor A 28.23 17.29 3.37E21 CKS_1591 bfr Bacterioferritin iron storage and detoxification protein A 27.19 17.89 1.27E50 CKS_3570 AraC family transcriptional regulator A 19.33 12.66 2.19E33 CKS_4657...”
  • “...15.65 11.35 1.23E26 CKS_1591 bfr Bacterioferritin iron storage and detoxification protein A 14.97 10.99 1.79E24 CKS_4032 rmf Ribosome modulation factor A 3.70 b 2.84 5.81E07 CKS_2714 yeaG Serine-protein kinase A 3.16 b 2.42 2.80E08 CKS_2505 AsnC family transcriptional regulator A 2.13 b 1.61 2.34E02 CKS_0004 hupA...”

EAM_RS18215 ribosome modulation factor from Erwinia amylovora ATCC 49946
89% identity, 100% coverage

• A complete twelve-gene deletion null mutant reveals that cyclic di-GMP is a global regulator of phase-transition and host colonization in Erwinia amylovora
  Kharadi, PLoS pathogens 2022
  • “...protein CDS leucine-rich repeat domain-containing protein -3.014341576 2.76182E-19 EAM_RS06155 hutG CDS N-formylglutamate deformylase -3.010799292 3.27597E-16 EAM_RS18215 rmf CDS ribosome modulation factor -2.962193193 1.30948E-08 EAM_RS18330 hypothetical protein CDS hypothetical protein -2.89078444 5.49473E-28 EAM_RS01820 hchA CDS protein deglycase HchA -2.858429374 8.44902E-16 EAM_RS02925 hypothetical protein CDS hypothetical protein -2.796397476...”
  • “...pyridoxal phosphate-dependent enzyme -2.200310517 4.17E-09 EAM_RS14570 non-ribosomal peptide synthetase CDS non-ribosomal peptide synthetase -2.121916042 2.18E-07 EAM_RS18215 rmf CDS ribosome modulation factor -2.054007376 2.53E-05 EAM_RS03735 cas7e CDS type I-E CRISPR-associated protein Cas7/Cse4/CasC -2.035412707 1.38E-12 10.1371/journal.ppat.1010737.t006 Table 6 A list of the statistically significant differentially regulated genes (Log2...”

YPTB1448 putative ribosome modulation factor from Yersinia pseudotuberculosis IP 32953
YPO1423a putative ribosome modulation factor from Yersinia pestis CO92
84% identity, 100% coverage

• IscR is essential for yersinia pseudotuberculosis type III secretion and virulence
  Miller, PLoS pathogens 2014
  • “...2.0 YPTB1141 heat shock protein GrpE grpE 2.7 YPTB1417 30S ribosomal protein S1 rpsA 2.2 YPTB1448 putative ribosome modulation factor rmf 3.8 YPTB2820 putative protease 2.1 YPTB3000 ribosome recycling factor frr 2.1 YPTB3026 protease III precursor ptrA 2.4 YPTB3511 Protease degQ 3.4 YPTB3904 heat shock protein...”
• Global gene expression profiling of Yersinia pestis replicating inside macrophages reveals the roles of a putative stress-induced operon in regulating type III secretion and intracellular cell division
  Fukuto, Infection and immunity 2010
  • “...y0946 YPO1366 y1607 y0655 y2882 y1189 y1041 y0310 y1607 YPO1423a y3555 y0509 y0016 y0463 y0655 y1821 y2881 y2125 y3804 y2236 y0015 YPO3681 y3836 y2591 50S...”

STM1066 ribosome modulation factor (involved in dimerization of 70S ribosomes) from Salmonella typhimurium LT2
82% identity, 100% coverage

• Efflux pumps mediate changes to fundamental bacterial physiology via membrane potential
  Whittle, 2023

Res / b0953 ribosome modulation factor from Escherichia coli K-12 substr. MG1655 (see 30 papers)
RMF_ECOLI / P0AFW2 Ribosome modulation factor; RMF; Hibernation factor RMF; Protein E from Escherichia coli (strain K12) (see 13 papers)
6h4nv / P0AFW2 6h4nv (see paper)
b0953 ribosome modulation factor from Escherichia coli str. K-12 substr. MG1655
ECs_1037 ribosome modulation factor from Escherichia coli O157:H7 str. Sakai
NP_415473 ribosome modulation factor from Escherichia coli str. K-12 substr. MG1655
ECs1037 ribosome modulation factor from Escherichia coli O157:H7 str. Sakai
78% identity, 100% coverage

• function: During stationary phase, converts 70S ribosomes to an immature dimeric form (90S ribosomes) which are converted to inactive 100S ribosomes (a process called ribosomal hibernation) by the hibernation promoting factor HPF (PubMed:18174192, PubMed:7677746). Inactivates ribosomes by covering the peptidyl transferase (PTase) center of the 23S rRNA and the entrance of peptide exit tunnel (PubMed:12473202, PubMed:15066119). However crystallization with T.thermophilus 70S ribosomes shows it binds near the 3'-end of the 16S rRNA near the anti-Shine-Dalgarno sequence, where it would sterically hinder translation initiation (PubMed:22605777). In this crystal binding of RMF induces movement of the 30S head domain away from the rest of the ribosome, presumably so they would more easily form dimers (PubMed:22605777). Also involved in protection against heat stress, but this role is not dependent on the maintenance of ribosome dimers (PubMed:15278243).
  subunit: Associates exclusively with 100S ribosomes (PubMed:12473202, PubMed:15066119, PubMed:2181444). Contacts 16S rRNA, might contact ribosomal protein S18 (PubMed:22605777).
  disruption phenotype: Non-essential gene, 100S ribosome dimers are not formed, decreased cell viability during stationary phase (PubMed:8440252). A quadruple raiA-hpf-rmf-sra knockout strain is significantly outcompeted by wild-type after 4 days growth (PubMed:17277072). Very high sensitivity to aminoglycoside antiobiotic gentamicin in stationary phase cultures (PubMed:26324267).
• Ligand: rna (6h4nv)
• Comparative Analysis of Transcriptomic Response of Escherichia coli K-12 MG1655 to Nine Representative Classes of Antibiotics
  Bie, Microbiology spectrum 2023
  • “...3.39 6.49 4.05 4.13 4.11 4.29 2.89 3.26 2.33 Isoaspartyl dipeptidase proenzyme Amino acid biosynthesis b0953 rmf 35.74 5.48 3.41 4.10 35.20 44.40 5.92 17.44 6.48 Ribosome modulation factor Ribosome protection b1287 yciW 8.76 7.19 12.28 9.72 6.18 8.94 17.57 17.79 10.55 Putative peroxidase Cysteine tolerance...”
• Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding
  Bonocora, PLoS genetics 2015
  • “...b0854 potF 49 6.829 P OS09 1014824 4 G TGGC GTGAATT TTGC G 1014827 + b0953 rmf 92 10.773 OS10 1073263 6 C TGGC ATCCGCT TTGC A 1073271 - b1012 rutA 18 9.963 P OS11 1165190 4 T TGG TATGACCAA TGC A 1165182 + b1109 ndh...”
• The protein interaction network of bacteriophage lambda with its host, Escherichia coli
  Blasche, Journal of virology 2013
  • “...inhibitor Putative HTH-type transcriptional regulator YqhC b0953 ribosome modulation factor (rmf) Ribosomal protein L27 Hypothetical protein Ribosomal protein...”
• Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding
  Myers, PLoS genetics 2013
  • “...71.5 o None None 3,217,259 ygjG b3073 Putrescine Aminotransferase 1 96.5 None None 1,014,801 rmf b0953 Ribosome Modulation Factor 1 98.5 + o None None 4,231,491 lysC b4024 Aspartate Kinase III 2 115.5 + o None None 1,986,025 yecR b1904 Predicted Protein 1 +30 o None...”
• 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
  • “...ftsT hisL fis slp spf phnB mutL isrB isrC micF b0797 b0953 b0991 b1004 b1569 b2018 b3261 b3506 b3864 b4107 b4170 b4434 b4435 b4439 6.5 9.8 4.9 16.0 2.3 2.3 4.3...”
• Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid
  Ren, Applied and environmental microbiology 2005
  • “...0.0210 1.1 0.4985 rimL b1427 1.5 0.0220 1.0 0.7185 rmf b0953 1.5 0.0029 1.0 0.6617 rpmI b1717 1.6 0.0072 1.0 0.7076 slp ugpB b3506 b3453 1.5 0.0059 1.6 0.0020...”
• Role of SeqA and Dam in Escherichia coli gene expression: a global/microarray analysis
  Løbner-Olesen, Proceedings of the National Academy of Sciences of the United States of America 2003
  • “...sulA umuD intE* cysN* gltS* Probe set b0886 b1417 b0953 b3213 b1480 b3212 b0003 b2155 b1263 b1264 b1552 b0812 b1982 b3509 b2497 b2378 b2133 b3510 b1262 b1229...”
• 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
  • “...family transcriptional regulator protein_coding 917380 2,43714697 ECs_5777 ecnB entericidin B membrane lipoprotein protein_coding 62675859 2,43311298 ECs_1037 rmf ribosome modulation factor protein_coding 913590 2,41264487 ECs_5190 ytfH transcriptional regulator protein_coding 913947 2,41048321 ECs_3690 ygdR lipoprotein protein_coding 916497 2,38729769 ECs_2382 ydhZ hypothetical protein protein_coding 914156 2,35933833 ECs_5729 yneM inner...”
• Involvement of cyclic AMP receptor protein in regulation of the rmf gene encoding the ribosome modulation factor in Escherichia coli.
  Shimada, Journal of bacteriology 2013
  • GeneRIF: Data propose that CRP regulates transcription activation of the rmf gene for formation of 100S ribosome dimers.
• How hibernation factors RMF, HPF, and YfiA turn off protein synthesis.
  Polikanov, Science (New York, N.Y.) 2012
  • GeneRIF: crystal structure of Thermus thermophilus 70S ribosome in complex with stationary-phase factors RMF, HPF and YfiA; binding site of RMF overlaps with that of mRNA Shine-Dalgarno sequence, which prevents interaction between the mRNA and the 16S ribosomal RNA
• Activities of Escherichia coli ribosomes in IF3 and RMF change to prepare 100S ribosome formation on entering the stationary growth phase.
  Yoshida, Genes to cells : devoted to molecular & cellular mechanisms 2009 (PubMed)
  • GeneRIF: Ribosomes change into forms which are hard to bind with IF3 and easy to form 100S ribosomes by RMF and HPF concomitantly with transition from the log phase to the stationary phase.
• Depletion of the signal recognition particle receptor inactivates ribosomes in Escherichia coli.
  Bürk, Journal of bacteriology 2009
  • GeneRIF: Data showed that FtsY depletion inhibits the translation of both SRP-dependent and independent proteins. This synthesis defect is the result of a multifaceted response that includes the upregulation of the ribosome-inactivating protein RMF.
• Structure and probable genetic location of a "ribosome modulation factor" associated with 100S ribosomes in stationary-phase Escherichia coli cells.
  Wada, Proceedings of the National Academy of Sciences of the United States of America 1990
  • GeneRIF: N-terminus verified by Edman degradation on complete protein
• Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
  Bergholz, BMC microbiology 2007
  • “...ycbB 2.15 2 ECs2847 O157 -2.25 1 ECs1029 pyrD -2.88 1 ECs3038 yeiT 2.14 3 ECs1037 rmf 2.24 2 ECs3060 fruK -2.13 1 ECs1072 O157 -2.13 5 ECs3061 fruB -2.38 1 ECs1091 O157 3.24 2 ECs3136 yfaX -2.04 1 ECs1137 yccC -2.27 1 ECs3149 menC -2.06...”

S1019 ribosome modulation factor from Shigella flexneri 2a str. 2457T
78% identity, 100% coverage

• Addendum
  , Open forum infectious diseases 2019

SG1025 putative ribosome modulation factor from Sodalis glossinidius str. 'morsitans'
81% identity, 44% coverage

• Quorum sensing primes the oxidative stress response in the insect endosymbiont, Sodalis glossinidius
  Pontes, PloS one 2008
  • “...rRNA pseudouridylate synthase A (SG1570), a tRNA/rRNA methyltransferase (SG1908) and a putative ribosome modulation factor (SG1025) also displayed reduced expression in the presence of OHHL. This leads to an interesting hypothesis perhaps quorum sensing restricts the growth rate of S. glossinidius at high infection density by...”

PMI_RS03835 ribosome modulation factor from Proteus mirabilis HI4320
PMI0781 ribosome modulation factor from Proteus mirabilis HI4320
82% identity, 91% coverage

• Decreased biofilm formation in Proteus mirabilis after short-term exposure to a simulated microgravity environment
  Wang, Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] 2021
  • “...1.46649446000024 Down 7.08E-05 Probable phosphoglycerate mutase PMI_RS13405 279 1.90346273574243 Down 0.00028 Ethanolamine utilization protein EutM PMI_RS03835 rmf 171 1.77234261558484 Down 0.00025 Ribosome modulation factor PMI_RS06255 fumc 1398 1.53400675009522 Down 0.00031 Fumarate hydratase, class II PMI_RS04910 243 1.46880616244531 Down 0.00036 No PMI_RS12610 1071 1.35999327826646 Down 6.86E-06 Integrase/recombinase...”
• Perturbation of FliL interferes with Proteus mirabilis swarmer cell gene expression and differentiation
  Cusick, Journal of bacteriology 2012
  • “...442 jb.asm.org Locus tag Genea Product PMI1406 PMI0781 PMI1011 PMI1224 PMI0068 PMI2221 PMI0033 PMI1804 PMI2662 PMI3209 PMI0069 PMI1225 PMI1395 PMI1223 PMI1816...”

YP_856804 hypothetical protein from Aeromonas hydrophila subsp. hydrophila ATCC 7966
73% identity, 90% coverage

• Directed culturing of microorganisms using metatranscriptomics
  Bomar, mBio 2011
  • “...Aerobic respiration 301 Ribosomal protein S19 YP_854843 7.78 10 47 Translation 6,926 Ribosome modulation factor YP_856804 4.76 10 28 Stationary phase 40,628 RpoD YP_855378 0 Transcription 708 RpoS YP_855373 2.64 10 167 Transcription 2,018 a GenBank accession number for the top BLASTX hit at the NCBI....”

VV1_2630 Ribosome modulation factor from Vibrio vulnificus CMCP6
71% identity, 78% coverage

• Rifampicin-resistant RpoB S522L Vibrio vulnificus exhibits disturbed stress response and hypervirulence traits
  Cutugno, MicrobiologyOpen 2023
  • “...genes in Vibrio vulnificus . Gene Sequence (53) tuf (VV1_1203) Forward: AAGTTTACGGCGGTGCTGCT Reverse: CGTAGTGGCGAGCTGGAGTG rmf (VV1_2630) Forward: ACGAACGAGCGTCCATCTGT Reverse: TCCCAAGGCTACAAGGCAGG fusA (VV1_1338) Forward: TGGCATTCAAGAAGGGCGCA Reverse: GCGACGGTTCAAGTCACCCA relA (VV1_1575) Forward: GTGGGTGTTGGCAGTGGTGA Reverse: GCGGCTTTATTGCCCGCTTC putA (VV2_1118) Forward: CACTGGCCCCACATCGGTTT Reverse: GAGCAGGTGGTGCGTGATGT rpoS (VV1_1588) Forward: CCAGAGCGTGGTTTCCGCTT Reverse: GAGAAAGCTCACGCGCCGTA toxR (VV1_0190)...”

Q9KRZ9 Ribosome modulation factor from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
VC1484 ribosome modulation factor from Vibrio cholerae O1 biovar eltor str. N16961
65% identity, 89% coverage

• Comparative genome analysis of non-toxigenic non-O1 versus toxigenic O1 Vibrio cholerae.
  Mukherjee, Genomics discovery 2014
  • “...nanK Q9KR61 N-acetylneuraminate epimerase nanM Q9KR69 N5-carboxyaminoimidazole ribonucleotide mutase purE Q9KVT7 Ribosome modulation factor Rmf Q9KRZ9 Accessory colonization factor AcfA * VC_0844 H9L4S5 Accessory colonization factor AcfB * VC_0840 Q9KTQ7 TagE protein * VC_A1043 Q9KKQ9 TagE protein * VC_0843 H9L4P5 Uncharacterized protein VC_1460 * VC_1460 P38443...”
• Sleeping ribosomes: Bacterial signaling triggers RaiA mediated persistence to aminoglycosides
  Lang, iScience 2021
  • “...Notably, one translation related gene was markedly upregulated: raiA (VC0706, 20-fold up), together with rmf (VC1484, 3-fold up), which are both described as factors associated with inactive ribosomes in stationary phase ( Agafonov etal., 1999 ; Di Pietro etal., 2013 ). raiA expression is known to...”
• MerR and ChrR mediate blue light induced photo-oxidative stress response at the transcriptional level in Vibrio cholerae
  Tardu, Scientific reports 2017
  • “...total of 21 representative up- and down-regulated DEGs (VC0837, VC0943, VC1118, VC1248, VC1263, VC1359, VC1392, VC1484, VC1570, VC1643, VC1814, VC1922, VC2088, VC2301, VCA0055, VCA0615, VCA0782, VCA0798, VCA0809, VCA0957, VCA1087), designated as Set2 DEGs, were selected to validate the RNA-seq results. Among the selected DEGs, 12 were...”
  • “...RNA-seq results using qRT-PCR Twenty-one representative BL-responsive genes (VC0837, VC0943, VC1118, VC1248, VC1263, VC1359, VC1392, VC1484, VC1570, VC1643, VC1814, VC1922, VC2088, VC2301, VCA0055, VCA0615, VCA0782, VCA0798, VCA0809, VCA0957, VCA1087) were selected for validation by qRT-PCR. Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA)...”

PP_5502 ribosome modulation factor from Pseudomonas putida KT2440
54% identity, 70% coverage

• Bioprocess exploitation of microaerobic auto-induction using the example of rhamnolipid biosynthesis in Pseudomonas putida KT2440
  Grether, Journal of biological engineering 2025
  • “...of the adhP (PP_3839) gene was amplified. The 510bp upstream region of the gene rmf (PP_5502) was amplified for the construction of the biosensor plasmid pJG- rmf::gfp . For other purposes that are not associated with this manuscript, promoter regions for subsequent transcriptional fusion with the...”
• Pseudouridines of tRNA Anticodon Stem-Loop Have Unexpected Role in Mutagenesis in Pseudomonas sp
  Tagel, Microorganisms 2020
  • “...Uncharacterized protein 2.8 8.1 10 5 PP_1789 Haloacid dehalogenase-like family hydrolase 2.7 6.0 10 7 PP_5502 rmf Ribosome modulation factor 2.5 0.0014 PP_2264 Putative Sugar ABC transporter, periplasmic sugar-binding protein 2.4 1.3 10 5 PP_1788 Uncharacterized protein 2.1 0.0003 PP_0238 ssuD Alkanesulfonate monooxygenase 2.0 0.0024 PP_4496...”

PA3049 ribosome modulation factor from Pseudomonas aeruginosa PAO1
Q9HZF9 Ribosome modulation factor from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA14_24650 ribosome modulation factor from Pseudomonas aeruginosa UCBPP-PA14
D3C65_10015 ribosome modulation factor from Pseudomonas aeruginosa
52% identity, 71% coverage

• BatR: A novel regulator of antibiotic tolerance inPseudomonas aeruginosabiofilms
  Piazza, 2024
• Cold atmospheric pressure plasma-antibiotic synergy in Pseudomonas aeruginosa biofilms is mediated via oxidative stress response
  Maybin, Biofilm 2023
  • “...glyoxylate shunt [ 55 ]. The upregulation of expression of ribosome modulation factor at 4h (PA3049) (log 2 FC 1.73), induced by ppGpp, alters ribosomal RNA structures, impairs protein synthesis, and upregulates stress-related genes, leading to persister cell formation [ 56 ]. At 6h post-treatment, gene...”
• Functional Characterization of TetR-like Transcriptional Regulator PA3973 from Pseudomonas aeruginosa
  Kotecka, International journal of molecular sciences 2022
  • “...CHE 1,659,181 2.6 T D3C65_07870 PA3451 hypothetical protein 0.44 1.07 HUU 2,101,587 2.3 P D3C65_10015 PA3049 ribosome modulation factor 0.44 1.36 TPTMD 4,238,513 4.9 P+ D3C65_19955 PA1177 periplasmic nitrate reductase NapE protein 0.43 1.41 EM 5,605,641 2.1 P D3C65_26630 PA4889 ferredoxin reductase 0.43 0.72 PE 141,900...”
• Toward a Comprehensive Analysis of Posttranscriptional Regulatory Networks: a New Tool for the Identification of Small RNA Regulators of Specific mRNAs
  Han, mBio 2021
  • “...2 ReaL 15 sRNA PA3535 PA3536 55 3 sRmf 9 3 RNA of rmf mRNA PA3049 PA3050 4 sAdhC 7 3 RNA of adhC mRNA PA3628 PA3630 5 s3661 6 3 RNA of PA3661 mRNA PA3661 PA3665 C. rpoS Vc Rank Name Max coverage a Mapping...”
• Resuscitation of Pseudomonas aeruginosa from dormancy requires hibernation promoting factor (PA4463) for ribosome preservation
  Akiyama, Proceedings of the National Academy of Sciences of the United States of America 2017
  • “...(HPF)], but not the ribosome modulation factor (PA3049), is required for ribosomal RNA preservation during prolonged nutrient starvation conditions....”
  • “...homolog (19). P. aeruginosa PAO1 contains genes for rmf (PA3049) and hpf (PA4463), but does not encode the hpf paralog, yfiA (20). The involvement of HPF and...”
• Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions
  Yan, Journal of applied genetics 2017
  • “...), PA0230 and PA4515 were PAH degradation genes. In Fig. 8 , two quorum-sensing genes PA3049 and PA3922 are associated with two PAH degradation genes PA0865 and PA2418, respectively. Again, eight genes (PA0958, PA1432, PA1713, PA1723, PA1777, PA1947, PA4922, and PA5253) were focused in AES-2, however,...”
• Enzyme-Mediated Quenching of the Pseudomonas Quinolone Signal (PQS) Promotes Biofilm Formation of Pseudomonas aeruginosa by Increasing Iron Availability
  Tettmann, Frontiers in microbiology 2016
  • “...site a PA2426 PA14_33260 7.0 pvdS RNA polymerase ECF-subfamily sigma-70 factor PvdS Fur box a PA3049 PA14_24650 3.0 rmf Ribosome modulation factor PA3519 PA14_18810 3.2 Hypothetical protein CueR binding site b , PA3522 PA14_18780 3.7 mexQ Probable RND efflux transporter Operon 3523-3521: CueR binding site b...”
• Effect of Shear Stress on Pseudomonas aeruginosa Isolated from the Cystic Fibrosis Lung
  Dingemans, mBio 2016
  • “...validated c Fold change (RNA-Seq) sRNA10 d 202 IR PA3964PA3965 No 2.35 SPA0117 201 IR PA3049 ( rmf ) PA3050 ( pyrD ); overlapping both genes Yes 1.94 P8 78 IR PA1030PA1031 Yes 1.85 SPA0003 137 IR PA2729PA2730 Yes 1.58 a Downregulated 1.50-fold; P < 0.05,...”
• More
• Proteome-wide identification of druggable targets and inhibitors for multidrug-resistant <i>Pseudomonas aeruginosa</i> using an integrative subtractive proteomics and virtual screening approach
  Vemula, Heliyon 2025
• Pseudomonas aeruginosa and Staphylococcus aureus Display Differential Proteomic Responses to the Silver(I) Compound, SBC3
  Piatek, Antibiotics (Basel, Switzerland) 2023
  • “...11.7 nirQ Denitrification regulatory protein NirQ Q51481 Transcription; transcription regulation 13.8 rmf Ribosome modulation factor Q9HZF9 Translation regulation 36.7 PA2462 Haemagg_act domain-containing protein Q9I120 Macromolecule metabolic process; primary metabolic process; nitrogen compound metabolic process 39.4 antibiotics-12-00348-t002_Table 2 Table 2 The top 20 most differentially abundant proteins...”
• Enzyme-Mediated Quenching of the Pseudomonas Quinolone Signal (PQS) Promotes Biofilm Formation of Pseudomonas aeruginosa by Increasing Iron Availability
  Tettmann, Frontiers in microbiology 2016
  • “...a PA2426 PA14_33260 7.0 pvdS RNA polymerase ECF-subfamily sigma-70 factor PvdS Fur box a PA3049 PA14_24650 3.0 rmf Ribosome modulation factor PA3519 PA14_18810 3.2 Hypothetical protein CueR binding site b , PA3522 PA14_18780 3.7 mexQ Probable RND efflux transporter Operon 3523-3521: CueR binding site b PA3523...”
• Expression of antisense small RNAs in response to stress in Pseudomonas aeruginosa
  Gómez-Lozano, BMC genomics 2014
  • “...2982848 142 PA14_30020 < 2599053 rmf Ribosome modulation factor PA3049 > As135 3414435 3414491 57 PA14_24650 < 2154716 fadD2 Long-chain-fatty-acid--CoA ligase PA3300 < As150 3697506 3697616 111 PA14_21340 > 1849717 fpvB Second ferric pyoverdine receptor FpvB PA4168 > As174 4666087 4666202 116 PA14_09970 < 856527 pilY1...”
• Uracil influences quorum sensing and biofilm formation in Pseudomonas aeruginosa and fluorouracil is an antagonist
  Ueda, Microbial biotechnology 2009
  • “...PA2570 lecA 3 1.7 4.9 PAI galactophilic lectin PA14_26020 PA2939 22.6 1.1 22.6 Probable aminopeptidase PA14_24650 PA3049 rmf 22.6 1.6 39.4 Ribosome modulation factor PA14_20610 PA3361 lecB 2.1 1.2 3 Fucosebinding lectin PAIIL PA14_18120 PA3570 mmsA 16 1.4 11.3 Methylmalonatesemialdehyde dehydrogenase PA14_11140 PA4078 17.1 1.1 16...”
• Functional Characterization of TetR-like Transcriptional Regulator PA3973 from Pseudomonas aeruginosa
  Kotecka, International journal of molecular sciences 2022
  • “...AP; CHE 1,659,181 2.6 T D3C65_07870 PA3451 hypothetical protein 0.44 1.07 HUU 2,101,587 2.3 P D3C65_10015 PA3049 ribosome modulation factor 0.44 1.36 TPTMD 4,238,513 4.9 P+ D3C65_19955 PA1177 periplasmic nitrate reductase NapE protein 0.43 1.41 EM 5,605,641 2.1 P D3C65_26630 PA4889 ferredoxin reductase 0.43 0.72 PE...”

CJU75_22455 ribosome modulation factor from Pseudomonas fragi
48% identity, 70% coverage

• Transcriptional profiling of biofilms formed on chilled beef by psychrotrophic meat spoilage bacterium, Pseudomonas fragi 1793
  Wickramasinghe, Biofilm 2021
  • “...5.58 0.00098 8.00 NA unknown CJU75_22215 PAA32248.1 4.87 0.00503 4.07 K histidine kinase, response regulator CJU75_22455 PAA32141.1 4.86 0.00488 8.62 J ribosome modulation factor CJU75_18560 PAA33363.1 4.78 0.00233 4.92 S membrane protein CJU75_05405 PAA38134.1 4.77 0.00164 7.76 E Glutamate decarboxylase CJU75_05400 PAA38133.1 4.76 0.00128 6.82 E...”
  • “...biofilm initiation vs dispersal. Table3 Locus Query FC FDR Avg expression COG cat Description CJU75_22210 CJU75_22455 CJU75_18560 CJU75_16745 CJU75_19875 CJU75_01795 CJU75_08955 CJU75_08945 CJU75_22215 CJU75_06940 CJU75_05405 CJU75_10450 CJU75_10445 CJU75_08960 CJU75_09225 CJU75_05400 PAA32247.1 PAA32141.1 PAA33363.1 PAA34001.1 PAA32825.1 PAA40425.1 PAA37432.1 PAA37430.1 PAA32248.1 PAA37735.1 PAA38134.1 PAA36312.1 PAA36311.1 PAA37433.1 PAA36805.1 PAA38133.1...”

PSPTO2310 ribosome modulation factor-related protein from Pseudomonas syringae pv. tomato str. DC3000
PSPTO_2310 ribosome modulation factor from Pseudomonas syringae pv. tomato str. DC3000
50% identity, 70% coverage

• Protein domains and architectural innovation in plant-associated Proteobacteria
  Studholme, BMC genomics 2005
  • “...of IS elements, tRNAs, plasmid and phage genes in flanking regions. PSPTO3229, PSPTO4569, PSPTO2312, PSPTO2829, PSPTO2310, Glf, PSPTO2441, PSPTO4696 and PSPTO2326 are all located in close proximity to IS elements and phage-like sequences, or in defined regions of the genome flanked by IS elements and phage-like...”
• Molecular mechanisms of two-component system RhpRS regulating type III secretion system in Pseudomonas syringae
  Deng, Nucleic acids research 2014
  • “...implied a role of RhpR in regulating the stability of the bacterial genome. PSPTO_1205 and PSPTO_2310 encoded a putative ribosomal subunit interface protein and a ribosome modulation factor-related protein, respectively. Reduced expression of these two regulatory genes may contribute to the increased expression of other ribosomal...”
• Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000
  Butcher, Journal of bacteriology 2011
  • “...PSPTO_1490 Within PSPTO_1979 In divergent region between PSPTO_2310 (rmf) and PSPTO_2311 Upstream of PSPTO_2853 Within PSPTO_5056 (pseudogene) Within PSPTO_5375...”
  • “...a peak was found between two divergently transcribed genes (PSPTO_2310 and PSPTO_2311) in a region where a ncRNA (rmf) is predicted upstream of PSPTO_2310 (40)....”

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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.