PaperBLAST

PaperBLAST Hits for WP_002922276.1 DUF262 domain-containing protein (Campylobacter jejuni) (563 a.a., MAEMKTERKS...)

Show query sequence

>WP_002922276.1 DUF262 domain-containing protein (Campylobacter jejuni)
MAEMKTERKSVLDYLSKNKFLIPMYQRPYAWTLEECEQLWNDIVTFFNDEDRKPEDEYFL
GSIVMYKQNNHQNIIDGQQRTISLSLLLKALYVKAFKDRSEETKNLVAMLESCLWDIDDI
SGKADYNASHLESDVITKEDEDILKQILTNEYRLENNDIETKIKKVKSNYEKNYLFFLLK
SDEFAKENPTKWEKFCVVLLKSCILLPIECEGYDEDSRLENALRIFNTLNNRGIPLSDSD
IFKSIIFKSKKTLEGRKEFANKWKELEDKKDMDFIFRNYMHVIRARNKIKTSEIGLRVFF
TKEYKNILQDDNIISEIEQLSKFWNDEFSDLYNNRSYQFYEVLNELPNEYWKYLDSAYYM
YCQDQKINYYKNHENFLAKIIANFLVKLINKPTIAEVKPIVFNAYASLYSKGELNFQTDS
KQILENEILFKEQFFKANKLIPALLTLNLYIKYPNQKTDIKAEIEHIFPKTTQWRPSYTG
WDKEEAKSYIESIGNKMWLEKRLNIKAGNNYFDEKKEKYKKSNFLEAQELSKYTKNDWLK
EDIEKRNEEIYNRLVDFFKQNID

Running BLASTp...

Found 33 similar proteins in the literature:

DDV75_00040 DUF262 domain-containing protein from Campylobacter jejuni
100% identity, 100% coverage

• Identification of Novel Phage Resistance Mechanisms in Campylobacter jejuni by Comparative Genomics
  Sørensen, Frontiers in microbiology 2021
  • “...Position Product Gene Position Product Query cover Similarity E -value DDR89_00040 12.64214.393 DUF262 domain-containing protein DDV75_00040 12.65314.344 DUF262 domain-containing protein No significant similarity DDR89_00180 46.40450.144 Eco 57I restriction-modification methylase domain-containing protein DDV75_00180 46.52150.294 Eco 57I restriction-modification methylase domain-containing protein 88% 94.5% 0.0 DDR89_00185 50.147-52.291 AAA family...”
  • “...sensitive CAMSA2002 and phage resistant CAMSA2038 both encode a DUF262-containing protein ( DDR89_00040 in CAMSA2002, DDV75_00040 in CAMSA2038) in the same location of the genomes, but the protein sequences show no similarity ( Table 2 ). We therefore conducted a detailed in silico analysis to predict...”

NMA2230 hypothetical protein from Neisseria meningitidis Z2491
36% identity, 98% coverage

• Microarray genomotyping of key experimental strains of Neisseria gonorrhoeae reveals gene complement diversity and five new neisserial genes associated with Minimal Mobile Elements
  Snyder, BMC genomics 2004
  • “...probe for XNG1618 or to the alternate N. meningitidis strain Z2491 probes for NMA0001 and NMA2230 . Figure 2 The MME flanked by nuoL and nuoM . This MME contains a hypothetical gene in N. gonorrhoeae strain FA1090 [ 16 ], short intergenic sequences in N....”

HP1409 hypothetical protein from Helicobacter pylori 26695
HP0426 hypothetical protein from Helicobacter pylori 26695
24% identity, 96% coverage

• A Helicobacter pylori flagellar motor accessory is needed to maintain the barrier function of the outer membrane during flagellar rotation
  Rosinke, PLoS pathogens 2025
  • “...and the basal disk protein FlgP in a high-throughput yeast two-hybrid screen [ 30 ]. HP1409 and HP0426 are predicted cytoplasmic proteins and are unlikely to interact with FapH within the context of the flagellar basal body. To identify additional FapH interaction partners, we expressed a...”
• The Helicobacter pylori J99 jhp0106 Gene, under the Control of the CsrA/RpoN Regulatory System, Modulates Flagella Formation and Motility
  Kao, Frontiers in microbiology 2017
  • “...*** /3.24 jhp1049 b Putative 3.53 *** /2.94 jhp1242 HP1322 Putative 2.60 ** /2.48 jhp1302 HP1409 Putative 2.83 ns /2.70 jhp1332 HP1439 Putative 1.85 ns /1.23 jhp1333 HP1440 Putative 7.22 *** /11.63 jhp1430 HP1397 Putative 3.23 *** /2.97 jhp1431 HP1396 Putative 3.74 *** /4.12 jhp1436 HP1391...”
• Association between Helicobacter pylori cagA-related genes and clinical outcomes in Colombia and Japan
  Watada, BMC gastroenterology 2011
  • “...file 1 . Among the 37 genes, the status of 9 genes (hp0186, hp0713, hp0967, hp1409, hp1410, jhp0045, jhp0046, jhp0950 , and jhp0951 ) were significantly correlated with the cagA status in our microarray data [ 18 ] (P = 0.026, 0.026, 0.014, 0.048, 0.030, 0.033,...”
• New implications on genomic adaptation derived from the Helicobacter pylori genome comparison
  Lara-Ramírez, PloS one 2011
  • “...of beta bands. The interactions with three proteins HP0887 (vacuolating cytotoxin precursor), HP0588 (ferrodoxin-like protein), HP1409 (hypothetical protein) was demonstrated by two-hybrid test [60] . HP1580, an uncharacterized protein and its H. pylori homologs in other H. pylori strains have been annotated in two sizes in...”
• Differences in genome content among Helicobacter pylori isolates from patients with gastritis, duodenal ulcer, or gastric cancer reveal novel disease-associated genes
  Romo-González, Infection and immunity 2009
  • “...N/A, N/A, N/A, N/A, N/A, N/A, JHP0925 HP0992, N/A HP1409, JHP1301, JHP1302 HP1410, JHP1303 HP0425, N/A HP0674, N/A (absent in all cancer isolates) N/A, JHP0940...”
  • “...two-component system confers urease-independent acid adaptation. The HP1409 and HP1410 genes, of unknown function, were also less frequent in cancer isolates...”
• Identification of a genetic marker of Helicobacter pylori strains involved in gastric extranodal marginal zone B cell lymphoma of the MALT-type
  Lehours, Gut 2004
  • “...JHP961* JHP1297 JHP1409 JHP1462 HP322 HP476 HP1105 HP1116 HP1371 HP1409 HP1402 None None None None None None None None None None None Putative poly E-rich...”
• Identification of target genes regulated by the two-component system HP166-HP165 of Helicobacter pylori
  Dietz, Journal of bacteriology 2002
  • “...(PCR amplified with primer pair 1187-5-1187-3) and HP1409 (PCR amplified with primer pair 1409-5-1409-3), respectively. RNA isolation. RNA was prepared as...”
  • “...(9) and a 504-bp PstI-SacI fragment derived from ORF HP1409 which was obtained by PCR performed with primer pair HP1409-5-HP1409-3 on chromosomal DNA of H....”
• A Helicobacter pylori flagellar motor accessory is needed to maintain the barrier function of the outer membrane during flagellar rotation
  Rosinke, PLoS pathogens 2025
  • “...basal disk protein FlgP in a high-throughput yeast two-hybrid screen [ 30 ]. HP1409 and HP0426 are predicted cytoplasmic proteins and are unlikely to interact with FapH within the context of the flagellar basal body. To identify additional FapH interaction partners, we expressed a c-Myc-tagged FapH...”
• High-Salt Conditions Alter Transcription of Helicobacter pylori Genes Encoding Outer Membrane Proteins
  Loh, Infection and immunity 2018
  • “...HP0219 HP0213 HP0157 HP0135 HP0113 HP0112 HP0054 HP0427 HP0426 HP0426 HP0036 HP0025 HP0016 HP0015 HP1564 HP1541 HP1399 Gene name or function Membrane protein...”
• Screening Helicobacter pylori genes induced during infection of mouse stomachs
  Singh, World journal of gastroenterology 2012
  • “...Ycf5 F Ycf5 R HP0423 F HP0423 R HP0424 F HP0424 R HP0426 F HP0426 R HP0427 F HP0427 R Table 2 Primers used in this study Genes Primer sequences 5'-3' HP1 HP2A...”
  • “...Type IV secretion system Predicted coding region HP0426 Predicted coding region HP0427 Predicted coding region HP0423 Predicted coding region HP0424 Motility...”
• Using macro-arrays to study routes of infection of Helicobacter pylori in three families
  Raymond, PloS one 2008
  • “...HP0414 IS200 insertion sequence from SARA17 HP0423 hypothetical protein HP0424 hypothetical protein HP0425 hypothetical protein HP0426 hypothetical protein HP0428 phage/colicin/tellurite resistance cluster terY protein HP0431 protein phosphatase 2C homolog (ptc1) HP0432 protein kinase C-like protein HP0433 hypothetical protein HP0434 hypothetical protein HP0436 hypothetical protein HP0437 IS605...”
• Characterization of the ArsRS regulon of Helicobacter pylori, involved in acid adaptation
  Pflock, Journal of bacteriology 2006
  • “...HP0081 HP0118 HP0120 HP0242* HP0305 HP0307* HP0423 HP0425 HP0426 HP0641 HP0731 HP0733 HP0963 HP0964 HP1154 HP1187 HP1188 HP1223 HP1408 HP1412 JHP0110 JHP0227...”

SCO5329 hypothetical protein from Streptomyces coelicolor A3(2)
21% identity, 97% coverage

• Expression of genes of the Pho regulon is altered in Streptomyces coelicolor
  Millan-Oropeza, Scientific reports 2020
  • “...all time points on both carbon sources (Fig. S3 ). Interestingly the genes sco6638 , sco5329 and sco0324 encoding putative endonuclease or nucleosidase are present and expressed in SC but absent or truncated in the SL . The abundance of these proteins in SC suggests the...”
• Actinomycete integrative and conjugative elements
  te, Antonie van Leeuwenhoek 2008
  • “...proteins (ZP_01980106; ZP_01705385) of the -proteobacteria Vibrio cholerae MZO-2 and Shewanella putrefaciens 200. The gene SCO5329 (52% G + C) of AICE Sco 5349 (65% G + C) is 28% identical to a hypothetical protein (NP_463839) of the food-borne pathogen Listeria monocytogenes EGD-e. This indicates that...”

c5426 Conserved hypothetical protein from Escherichia coli CFT073
29% identity, 47% coverage

• The inner membrane protein YhiM links copper and CpxAR envelope stress responses in uropathogenic E. coli
  Saenkham-Huntsinger, mBio 2024
  • “...protein Cytosol ycjG c1797 Hypothetical protein Cytosol c5382 Hypothetical protein Cytosol c2508 Hypothetical protein Cytosol c5426 Conserved hypothetical protein Cytosol c5304 Putative conserved protein Cytosol c3171 Putative capsid protein of prophage Unknown ykfF c0279 Hypothetical protein Unknown c2748 Hypothetical protein Unknown c0293 Hypothetical protein Unknown c4303...”
• Pedigrees of some mutant strains of Escherichia coli K-12
  Bachmann, Bacteriological reviews 1972

HPYLSS1_01469 DUF262 domain-containing protein from Helicobacter pylori SS1
26% identity, 91% coverage

• Helicobacter pylori Biofilm Involves a Multigene Stress-Biased Response, Including a Structural Role for Flagella
  Hathroubi, mBio 2018
  • “...protein homD 3.26 HPYLSS1_01113 Putative outer membrane protein 2.91 HPYLSS1_01021 Outer membrane protein homC 2.69 HPYLSS1_01469 Putative outer membrane protein 2.52 Cellular processes cagE (HPYLSS1_00705) Type IV secretion system protein VirB4/DNA transfer 2.46 cagW (HPYLSS1_00718) cag pathogenicity island protein CagW ( cag10 ) 2.31 cagL (HPYLSS1_00710)...”

NP_463839 similar to unknown protein from Listeria monocytogenes EGD-e
25% identity, 99% coverage

• Actinomycete integrative and conjugative elements
  te, Antonie van Leeuwenhoek 2008
  • “...of AICE Sco 5349 (65% G + C) is 28% identical to a hypothetical protein (NP_463839) of the food-borne pathogen Listeria monocytogenes EGD-e. This indicates that AICEs may also mediate genetic exchange outside of the actinomycetes. However, database searches fail to identify clear AICE homologues in...”

HP1397 hypothetical protein from Helicobacter pylori 26695
31% identity, 44% coverage

• The Helicobacter pylori J99 jhp0106 Gene, under the Control of the CsrA/RpoN Regulatory System, Modulates Flagella Formation and Motility
  Kao, Frontiers in microbiology 2017
  • “...ns /2.70 jhp1332 HP1439 Putative 1.85 ns /1.23 jhp1333 HP1440 Putative 7.22 *** /11.63 jhp1430 HP1397 Putative 3.23 *** /2.97 jhp1431 HP1396 Putative 3.74 *** /4.12 jhp1436 HP1391 Putative 2.16 ** /2.13 jhp1437 b HcpA family protein 1.63 ** /1.69 jhp1474 HP1566 Membrane protein 1.77 ***...”
• Alteration of the Helicobacter pylori membrane proteome in response to changes in environmental salt concentration
  Voss, Proteomics. Clinical applications 2015
  • “...D7FFD6 NA 2.53 Outer membrane protein HopA HP0229 HPB8_1699 D7FGE9 NA 2.53 Putative uncharacterized protein HP1397 HPB8_957 * & D7FEA7 NA 2.48 Putative uncharacterized protein HP0750 HPB8_1043 D7FEJ3 NA 2.43 Putative uncharacterized protein HP0833 HPB8_385 * D7FCN5 NA 2.4 cysteine-rich protein X HcpX HP1117 HPB8_513 *...”
• Differences in genome content among Helicobacter pylori isolates from patients with gastritis, duodenal ulcer, or gastric cancer reveal novel disease-associated genes
  Romo-González, Infection and immunity 2009
  • “...JHP0899 N/A, HP0965, JHP0899 N/A, HP1396, JHP1431 N/A, HP1397, JHP1430 N/A, N/A, JHP0616 N/A, N/A, JHP0961 N/A, N/A, JHP0959 N/A, N/A, JHP0960 N/A, N/A,...”
• Using macro-arrays to study routes of infection of Helicobacter pylori in three families
  Raymond, PloS one 2008
  • “...HP1383 restriction modification system S subunit HP1388 hypothetical protein HP1390 hypothetical protein HP1396 hypothetical protein HP1397 hypothetical protein HP1400+ iron(III) dicitrate transport protein (fecA) HP1402 type I restriction enzyme R protein (hsdR) HP1410 hypothetical protein HP1411 hypothetical protein HP1412 hypothetical protein HP1415 tRNA delta(2)-isopentenylpyrophosphate transferase (miaA)...”
• Acid-adaptive genes of Helicobacter pylori
  Wen, Infection and immunity 2003
  • “...HP1207 HP1236 HP1288 HP1289 HP1326 HP1327 HP1391 HP1397 HP1412 HP1440 HP1457 HP1499 HP1520 HP0433 Downloaded from http://iai.asm.org/ on February 11, 2017...”
• Comparison of genetic divergence and fitness between two subclones of Helicobacter pylori
  Björkholm, Infection and immunity 2001
  • “...JHP0950, HP0999, HP1074, JHP0332, HP1250, HP1324, HP1396, HP1397, HP1405, HP1412, HP1439, JHP1408, HP1586 NA hsdS Ribosomal protein L28 Acyl carrier protein...”

jhp0462 putative from Helicobacter pylori J99
28% identity, 41% coverage

• Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori
  Saunders, BMC genomics 2005
  • “...159 176 49 121 hypothetical protein HP0058 JHP0051 394 16 53 122 hypothetical protein HP0513 JHP0462 104 28 15 125 type I restriction enzyme M protein (hsdM) HP1403 JHP1423 299 340 44 132 hypothetical protein HP0731 JHP0668 110 80 32 139 hypothetical protein HP0508 JHP0458 84...”
  • “...protein JHP0336 HP1089 27 54 53 hypothetical protein JHP0940 NAH 39 393 54 hypothetical protein JHP0462 HP0513 104 11 55 type II restriction enzyme (methyltransferase) JHP1409 NAH 37 15 58 hypothetical protein JHP1285 HP1371 55 25 59 hypothetical protein JHP0693 HP0756 19 1490 62 cag pathogenicity...”

jhp1430 putative from Helicobacter pylori J99
30% identity, 44% coverage

• The Helicobacter pylori J99 jhp0106 Gene, under the Control of the CsrA/RpoN Regulatory System, Modulates Flagella Formation and Motility
  Kao, Frontiers in microbiology 2017
  • “...2.83 ns /2.70 jhp1332 HP1439 Putative 1.85 ns /1.23 jhp1333 HP1440 Putative 7.22 *** /11.63 jhp1430 HP1397 Putative 3.23 *** /2.97 jhp1431 HP1396 Putative 3.74 *** /4.12 jhp1436 HP1391 Putative 2.16 ** /2.13 jhp1437 b HcpA family protein 1.63 ** /1.69 jhp1474 HP1566 Membrane protein 1.77...”
• Differences in genome content among Helicobacter pylori isolates from patients with gastritis, duodenal ulcer, or gastric cancer reveal novel disease-associated genes
  Romo-González, Infection and immunity 2009
  • “...JHP0899 N/A, HP0965, JHP0899 N/A, HP1396, JHP1431 N/A, HP1397, JHP1430 N/A, N/A, JHP0616 N/A, N/A, JHP0961 N/A, N/A, JHP0959 N/A, N/A, JHP0960 N/A, N/A, JHP0830...”

YPO3437 conserved hypothetical protein from Yersinia pestis CO92
29% identity, 42% coverage

• Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics
  Califf, Microbial genomics 2015
  • “...YOP2083 Y. pestis Hypothetical protein YPO0387 Y. pestis Hypothetical protein YPO0388 Y. pestis Hypothetical protein YPO3437 Y. pestis XRE family transcriptional regulator WP_002214362 Y. pestis Transcriptional regulator YPO4031 Y. pestis Transposase WP_002214360 Y. pestis Outer membrane receptor YPO3910 Y. pestis Hypothetical protein YPO3948 Y. pestis Hypothetical...”

B8F899 DUF262 domain-containing protein from Glaesserella parasuis serovar 5 (strain SH0165)
25% identity, 82% coverage

• Transcriptomics of Haemophilus (Glässerella) parasuis serovar 5 subjected to culture conditions partially mimetic to natural infection for the search of new vaccine antigens.
  Álvarez-Estrada, BMC veterinary research 2018
  • “...protein P CP HAPS_RS09000 hypothetical protein B8F7Q0 |HAPS_1850|Uncharacterized protein P IM HAPS_RS10195 DUF262 domain-containing protein B8F899 |HAPS_2100|Uncharacterized protein P CP HAPS_RS10530 TolC family protein tolC B8F8F2 |tolC|RND efflux system outer membrane lipoprotein/RND superfamily resistance-nodulation-cell division antiporter P OM HAPS_RS10585 ligand-gated channel B8F8G2 |hxuC|Heme/hemopexin utilization protein C/outer...”
  • “...domain HAPS_RS07950 CP Domain of the Thioredoxin-like superfamily HAPS_RS09000 B8F7Q0 IM Homology with permease HAPS_RS10195 B8F899 CP ParB-like and HNH nuclease domains The locus in the reference genome (SH0165 strain) is also indicated. a indicates that this was a single protein recognized as two different ones...”

jhp1301 putative from Helicobacter pylori J99
28% identity, 47% coverage

• Differences in genome content among Helicobacter pylori isolates from patients with gastritis, duodenal ulcer, or gastric cancer reveal novel disease-associated genes
  Romo-González, Infection and immunity 2009
  • “...N/A, N/A, N/A, N/A, JHP0925 HP0992, N/A HP1409, JHP1301, JHP1302 HP1410, JHP1303 HP0425, N/A HP0674, N/A (absent in all cancer isolates) N/A, JHP0940 (absent...”
• Identification of a genetic marker of Helicobacter pylori strains involved in gastric extranodal marginal zone B cell lymphoma of the MALT-type
  Lehours, Gut 2004
  • “...L M N JHP305 JHP428 JHP1031 JHP1044 JHP1285 JHP1301 JHP1424 JHP820 JHP921* JHP922* JHP946* JHP949* JHP950* JHP960* JHP961* JHP1297 JHP1409 JHP1462 HP322 HP476...”
• Identification of target genes regulated by the two-component system HP166-HP165 of Helicobacter pylori
  Dietz, Journal of bacteriology 2002
  • “...HP1411, and HP1412 are split into two separate ORFs (JHP1301 and JHP1302, JHP1304 and JHP1305, and JHP1306 and JHP1307, respectively). The ORFs adjacent to the...”

HPB8_729 DUF262 and DUF1524 domain-containing protein from Helicobacter pylori B8
D7FDN0 DUF262 domain-containing protein from Helicobacter pylori (strain B8)
28% identity, 42% coverage

• Alteration of the Helicobacter pylori membrane proteome in response to changes in environmental salt concentration
  Voss, Proteomics. Clinical applications 2015
  • “...Putative uncharacterized protein comL HP1378 HPB8_319 * D7FCG9 NA 1.78 Outer membrane protein HopQ HP1177 HPB8_729 D7FDN0 NA 1.78 Putative uncharacterized protein HP0513 HPB8_1047 * D7FEJ7 NA 1.78 Putative uncharacterized protein HP0836|HP0837 HPB8_972 * D7FEC2 NA 1.77 Putative uncharacterized protein HP0764 HPB8_24 D7FBM4 oxidation-reduction process 1.75...”
• Alteration of the Helicobacter pylori membrane proteome in response to changes in environmental salt concentration
  Voss, Proteomics. Clinical applications 2015
  • “...uncharacterized protein comL HP1378 HPB8_319 * D7FCG9 NA 1.78 Outer membrane protein HopQ HP1177 HPB8_729 D7FDN0 NA 1.78 Putative uncharacterized protein HP0513 HPB8_1047 * D7FEJ7 NA 1.78 Putative uncharacterized protein HP0836|HP0837 HPB8_972 * D7FEC2 NA 1.77 Putative uncharacterized protein HP0764 HPB8_24 D7FBM4 oxidation-reduction process 1.75 Riboflavin...”

BCAL1172 hypothetical protein from Burkholderia cenocepacia J2315
26% identity, 42% coverage

• Various Evolutionary Trajectories Lead to Loss of the Tobramycin-Potentiating Activity of the Quorum-Sensing Inhibitor Baicalin Hydrate in Burkholderia cenocepacia Biofilms
  Sass, Antimicrobial agents and chemotherapy 2019
  • “...CDS (10 bp 1012042 to 1012051) 100 repressor, GlpR BCAL1172 Conserved hypothetical protein, in BcenGI5 Deletion of first 148 bp of gene 100 92 BCAL1315...”
• The Mla Pathway Plays an Essential Role in the Intrinsic Resistance of Burkholderia cepacia Complex Species to Antimicrobials and Host Innate Components
  Bernier, Journal of bacteriology 2018
  • “...regulator 14C3 BCAL1048 Putative alpha/beta hydrolase 37B7 BCAL1172 Hypothetical protein 28H12 BCAL1246 Putative malonyl coenzyme A-acyl carrier protein 37H7...”
• Use of suppression-subtractive hybridization to identify genes in the Burkholderia cepacia complex that are unique to Burkholderia cenocepacia
  Bernier, Journal of bacteriology 2005
  • “...YP_109966g ZP_00213820 ZP_00222251 ZP_00222248 BCAL1291 BCAL1292 BCAL1172 BCAL1122 pBCA044 pBCA032 pBCA033 BCAM0327 BCAM0340 BCAM0514 BCAM0524 BCAS0034 BCAM2275...”

Z5949 orf; conserved hypothetical protein from Escherichia coli O157:H7 EDL933
42% identity, 16% coverage

• Cassette-like variation of restriction enzyme genes in Escherichia coli C and relatives
  Sibley, Nucleic acids research 2004
  • “...O157:H7 a frameshift breaks this ORF into two parts, Z5949 and Z5950 (29). Similarity to K-12 then resumes, with more framework genes of unknown function found...”
  • “...IB restriction genes (hsdRMS) and two ORFs of unknown function, Z5949 and Z5950; these are fused in C and CFT073 with a 10 amino acid linker relative to the...”

HPF57_0653 DUF262 domain-containing protein from Helicobacter pylori F57
21% identity, 82% coverage

• Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates
  Tuan, Microbial genomics 2021
  • “...HP1247 4.1 1111855 HPF57_1042 [1111772 1112203] (+) hemX haem interaction C 84 HP0375 4.1 686823 HPF57_0653 [686461688509] (+) mdr modification-specific restriction restriction C 363 no ortholog position in F57 reference genome. We also conducted a SNP-GWAS using another programme, pyseer, which can adjust for population structure,...”

cg0841 hypothetical protein from Corynebacterium glutamicum ATCC 13032
25% identity, 34% coverage

• Ciprofloxacin triggered glutamate production by Corynebacterium glutamicum
  Lubitz, BMC microbiology 2016
  • “...protein 1.88 0.000 cg1978 - Hypothetical protein 1.72 0.000 cg1917 - Hypothetical protein 1.50 0.002 cg0841 - Conserved hypothetical protein 1.39 0.016 cg1743 - Conserved hypothetical protein 1.38 0.006 cg1937 - Putative secreted protein 1.22 0.015 cg3018 - Hypothetical protein 1.22 0.002 cg0451 - Putative membrane...”
  • “..., radA , lexA (autoregulation) and divS and several genes of unknown function (cg2381, cg2026, cg0841, cg1977) of the 48 genes of the LexA regulon were upregulated. As known for C. glutamicum and other bacteria, autoproteolytic cleavage of the transcriptional regulator LexA is induced by RecA...”
• The Zur regulon of Corynebacterium glutamicum ATCC 13032
  Schröder, BMC genomics 2010
  • “...sequence representing a regulatory gene region with a LexA binding site located in front of cg0841 [ 40 ] served as additional negative control. Likewise, Zur did not interact in vitro with the 21-bp motif located upstream of the adhA promoter region (Fig. 8A ). Furthermore,...”
  • “...The negative control assay was performed with a 40-mer deduced from the upstream region of cg0841. (B) , DNA band shift assays with mutated versions of the 40-mers. Mutated versions were generated by introducing transitions into the candidate Zur-binding sites or into the genomic flanking regions....”

HP0629 hypothetical protein from Helicobacter pylori 26695
22% identity, 82% coverage

• Helicobacter pylori Modulates Heptose Metabolite Biosynthesis and Heptose-Dependent Innate Immune Host Cell Activation by Multiple Mechanisms
  Hauke, Microbiology spectrum 2023
  • “...2.2 0 HP0602 ( magIII ) 333.82 1.77 3.42 4.91E10 HP0603 80.49 1.86 3.64 2.29E03 HP0629 54.18 0.95 1.94 8.87E05 HP0715 556.56 1.71 3.27 0 HP0751 ( flaG ) 1,284.04 2.40 5.29 0 HP0752 ( fliD ) 688.1 1.59 3.01 0 HP0753 ( fliS ) 270.58...”
• The Helicobacter pylori J99 jhp0106 Gene, under the Control of the CsrA/RpoN Regulatory System, Modulates Flagella Formation and Motility
  Kao, Frontiers in microbiology 2017
  • “...UNKNOWN FUNCTION jhp0436 HP0484 Putative 3.38 *** /2.45 jhp0550 HP0603 Putative 2.17 *** /2.24 jhp0572 HP0629 Putative 1.54 * /3.54 jhp0753 HP0817 Putative 1.54 *** /1.69 jhp0936 b Putative 1.78 *** /3.24 jhp1049 b Putative 3.53 *** /2.94 jhp1242 HP1322 Putative 2.60 ** /2.48 jhp1302 HP1409...”
• Comparative genomic analysis of East Asian and non-Asian Helicobacter pylori strains identifies rapidly evolving genes
  Duncan, PloS one 2013
  • “...HP0635 hypothetical protein Hypothetical Conserved HP0897 hypothetical protein Hypothetical Conserved HP0398 hypothetical protein Hypothetical Conserved HP0629 hypothetical protein Hypothetical Conserved HP0973 hypothetical protein Hypothetical Conserved HP0167 hypothetical protein Hypothetical Conserved HP0120 hypothetical protein Hypothetical Conserved HP0583 hypothetical protein Hypothetical Conserved HP0119 hypothetical protein Hypothetical Conserved HP0681...”
• Differences in genome content among Helicobacter pylori isolates from patients with gastritis, duodenal ulcer, or gastric cancer reveal novel disease-associated genes
  Romo-González, Infection and immunity 2009
  • “...N/A pepA, HP0570, JHP0517 aspS, HP0617, JHP0560 N/A, HP0629, JHP0572 N/A, HP0698, N/A N/A, HP0704, N/A fecA, fecA_2, HP0807, JHP0743 omp19, babB, HP0896,...”

jhp0572 putative from Helicobacter pylori J99
21% identity, 81% coverage

• The Helicobacter pylori J99 jhp0106 Gene, under the Control of the CsrA/RpoN Regulatory System, Modulates Flagella Formation and Motility
  Kao, Frontiers in microbiology 2017
  • “...OR UNKNOWN FUNCTION jhp0436 HP0484 Putative 3.38 *** /2.45 jhp0550 HP0603 Putative 2.17 *** /2.24 jhp0572 HP0629 Putative 1.54 * /3.54 jhp0753 HP0817 Putative 1.54 *** /1.69 jhp0936 b Putative 1.78 *** /3.24 jhp1049 b Putative 3.53 *** /2.94 jhp1242 HP1322 Putative 2.60 ** /2.48 jhp1302...”
• Differences in genome content among Helicobacter pylori isolates from patients with gastritis, duodenal ulcer, or gastric cancer reveal novel disease-associated genes
  Romo-González, Infection and immunity 2009
  • “...pepA, HP0570, JHP0517 aspS, HP0617, JHP0560 N/A, HP0629, JHP0572 N/A, HP0698, N/A N/A, HP0704, N/A fecA, fecA_2, HP0807, JHP0743 omp19, babB, HP0896, JHP1164...”

UU527 conserved hypothetical from Ureaplasma parvum serovar 3 str. ATCC 700970
28% identity, 39% coverage

• Comparative genome analysis of Ureaplasma parvum clinical isolates
  Momynaliev, Research in microbiology 2007 (PubMed)
  • “...function prediction only (UU480), function unknown (UU033, UU527) and defense mechanisms (UU446, UU447) was low (2.36.6%). Hence, the genetic variability of...”

D7FGE9 GmrSD restriction endonucleases N-terminal domain-containing protein from Helicobacter pylori (strain B8)
39% identity, 16% coverage

• Alteration of the Helicobacter pylori membrane proteome in response to changes in environmental salt concentration
  Voss, Proteomics. Clinical applications 2015
  • “...uncharacterized protein HP1405 HPB8_1336 * & D7FFD6 NA 2.53 Outer membrane protein HopA HP0229 HPB8_1699 D7FGE9 NA 2.53 Putative uncharacterized protein HP1397 HPB8_957 * & D7FEA7 NA 2.48 Putative uncharacterized protein HP0750 HPB8_1043 D7FEJ3 NA 2.43 Putative uncharacterized protein HP0833 HPB8_385 * D7FCN5 NA 2.4 cysteine-rich...”

K747_06625 DUF262 and DUF1524 domain-containing protein from Helicobacter pylori UM298
38% identity, 11% coverage

• Immunometabolism in biofilm infection: lessons from cancer
  Mirzaei, Molecular medicine (Cambridge, Mass.) 2022
  • “...that seem to be correlated with biofilm production. Indeed, three hypothetical genes (K74_10375, K747_09130, and K747_06625) were remarkably associated with biofilm production (Wong et al. 2016 ). K747_06625 is prognosticated to hold a homing endonuclease and a ParB-like domain, the latter of which is correlated with...”
• Biophysical characterization of the homodimers of HomA and HomB, outer membrane proteins of Helicobacter pylori
  Tamrakar, Scientific reports 2021
  • “...globular domain likely contributes to dimer formation. Some of the hypothetical proteins (K74_10375, K747_09130, and K747_06625) and outer membrane protein is associated with biofilm formation, HomD, a member of Hom OMP family is associated with moderate biofilm former (58.3%) to hyper biofilm former (66.7%) H. pylori...”
• Helicobacter pylori Biofilm Formation and Its Potential Role in Pathogenesis
  Hathroubi, Microbiology and molecular biology reviews : MMBR 2018
  • “...Indeed, three hypothetical genes (K74_10375, K747_09130, and K747_06625) were significantly correlated with biofilm formation (34). K747_06625 is predicted to...”
  • “...formation by H. pylori Gene K74_10375 K747_09130 K747_06625 fucT homD cagA Gene product Hypothetical gene Hypothetical gene Hypothetical gene...”
• Comparative Genomics Revealed Multiple Helicobacter pylori Genes Associated with Biofilm Formation In Vitro
  Wong, PloS one 2016
  • “...95C, 5min; 35x (95C, 30s; 57C, 30s; 72C, 1min); 72C, 7min Reverse: AGCTCCAAAAGAGGGGTAGC hypothetical protein K747_06625 Forward: GGCTCACCACTATACCGCTT 1089 95C, 5min; 35x (95C, 30s; 57C, 30s; 72C, 1min); 72C, 7min Reverse: TGACCGGCTCTTTTGTGTCA outer membrane protein ( homD ) Forward: GACGCTCAAGGCAAGGTAGT 1409 95C, 5min; 35x (95C, 30s;...”
  • “...forming strains, with 3 hypothetical genes (Hypothetical protein K747_10375, Hypothetical protein K747_09130 and Hypothetical protein K747_06625) and 4 functional genes (flagellar protein, cag pathogenicity island protein, outer membrane protein ( homD ) and alpha-(1,3)- fucosyltransferase) were identified to be significantly correlating with capability of forming biofilm...”

CjjRM3420_1536 DUF262 domain-containing protein from Campylobacter jejuni subsp. jejuni str. RM3420
34% identity, 18% coverage

• Biomolecule sulphation and novel methylations related to Guillain-Barré syndrome-associated Campylobacter jejuni serotype HS:19
  Heikema, Microbial genomics 2021
  • “...97 33 CjjRM3420_1453 capsular polysaccharide biosynthesis protein 100 34 CjjRM3420_1454 Sam-dependent methyltransferase 97 6 ST-21/HS:8 CjjRM3420_1536, rloF cluster IIX restriction modification linked orf restriction modification 97 16 ST-257/HS:11, ST-574/HS:mix, ST:48/HS:4, ST-677/HS:4 CjjRM3420_1537, hsdS type I restriction-modification system, specificity subunit S 100 12 ST-257/HS:11, ST-574/HS:mix, ST:48/HS:4 CjjRM3420_1677...”

EF_B0059 hypothetical protein from Enterococcus faecalis V583
37% identity, 14% coverage

• An enterococcal phage protein inhibits type IV restriction enzymes involved in antiphage defense
  Bullen, Nature communications 2024
  • “...resistance to phi47 infection is solely conferred by the activity of one of these genes, EF_B0059, encoding a putative type IV restriction enzyme (TIV-RE). We subsequently isolated phages that are resistant to restriction by EF_B0059 and discovered that the orf65 gene of phi47 encodes a small...”
  • “...phi47 restriction were therefore likely encoded by one or more these 14 ORFs. Fig. 2 EF_B0059 encodes a putative type IV restriction enzyme that prevents infection by phi47. A Sequence alignments between the pheromone responsive plasmids pTEF2 and pCF10. Genes highlighted in yellow indicate a sequence...”

CDQ83_18880 DUF262 domain-containing protein from Clostridium thermosuccinogenes
25% identity, 43% coverage

• Breaking the Restriction Barriers and Applying CRISPRi as a Gene Silencing Tool in Pseudoclostridium thermosuccinogenes
  Ganguly, Microorganisms 2022
  • “...the gene cluster CDQ83_16045, CDQ83_16050, and CDQ83_16055. Scaffold 3 harbors the gene cluster CDQ83_18870, CDQ83_18875, CDQ83_18880, and CDQ83_18885. The ORFs from each Type I RM systems cloned in E. coli are highlighted in bold. Figure 3 Strategies to enhance transformation efficiency by breaking the restriction barriers....”

jhp0174 putative from Helicobacter pylori J99
25% identity, 73% coverage

• Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori
  Saunders, BMC genomics 2005
  • “...12 51 54 28 JHP1426 iron(III) dicitrate transport protein (fecA) HP1400 32 78 111 29 JHP0174 hypothetical protein HP0187 / 8 / 6 47&1127&596 88 90 30 JHP1297 type III restriction enzyme (res) NAH - 63 28 31 JHP0953 hypothetical protein NAH - 26 1463 32...”
  • “...46 histidine and glutamine-rich metal-binding protein HP1432 JHP1321 15 9 1432 47 hypothetical protein HP0186 JHP0174 29 130 276 48 fucosyltransferase HP0651 JHP0596 105 43 75 49 translation elongation factor EF-Tu (tufB) HP1205 JHP1128 81 64 166 50 virulence associated protein homolog (vacB) HP1248 JHP1169 79...”
• Genomic diversity in Campylobacter jejuni: identification of C. jejuni 81-176-specific genes
  Poly, Journal of clinical microbiology 2005
  • “...enterica serovar Typhi CT18 (NP_457434) Hypothetical protein jhp0174, H. pylori strain J99 (NP_222895) Hypothetical protein, Bacillus cereus ATCC 14579...”
• Identification of genes with fast-evolving regions in microbial genomes
  Zheng, Nucleic acids research 2004
  • “...jhp0786 jhp1070 jhp1293 jhp1392 jhp0320 jhp0372 jhp1365 jhp0174 jhp0596 jhp0346 jhp0649 jhp0613 jhp0989 jhp0530 jhp0684 jhp1281 jhp1410 jhp0189 jhp0967 jhp0655...”

VC0395_A1364 hypothetical protein from Vibrio cholerae O395
27% identity, 36% coverage

• Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems
  Vizzarro, Journal of bacteriology 2024
  • “...GmrSD fusion proteins ( 53 ). Notably, the TgvB homolog from classical biotype V. cholerae (VC0395_A1364) was also identified as a GmrSD homolog in this study ( 53 ). These double domain forms of GmrSD function as modification-dependent type IV restriction enzymes, and are known to...”
• Vibrio choleraepathogenicity island 2 encodes two distinct types of restriction systems
  Vizzarro, 2024

VC1766 conserved hypothetical protein from Vibrio cholerae O1 biovar eltor str. N16961
27% identity, 36% coverage

• A <i>Vibrio cholerae</i> Type IV restriction system targets glucosylated 5-hydroxymethylcytosine to protect against phage infection
  Gomez, Journal of bacteriology 2024 (secret)
• Vibrio choleraepathogenicity island 2 encodes two distinct types of restriction systems
  Vizzarro, 2024
• Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems
  Vizzarro, Journal of bacteriology 2024
  • “...ype I-embedded G mrSD-like system of V PI-2, tgvA ( VC1767 ) and tgvB ( VC1766 ). Interestingly, the strain carrying only the tgvAB genes showed significantly less protection (between 10- and 100-fold reduction) against several tested phages compared to the strain harboring the entire gene...”
  • “...Bioinformatic analysis of the TgvAB system revealed that TgvA ( VC1767 ) and TgvB ( VC1766 ) both possess an N-terminal DUF262 domain, while TgvB additionally contains a C-terminal DUF1524 domain ( Fig. 4a and b ). Interestingly, previous work by Machnicka et al. found that...”
• Impact of Gene Repression on Biofilm Formation of Vibrio cholerae
  Pombo, Frontiers in microbiology 2022
  • “...VC1714-1717 VC1714 Cell division protein MukB, chromosome partition protein 1 VC1718 Hypothetical protein 6 VC1766-1769 VC1766 Hypothetical protein 2 VC1768 Hypothetical protein 1 VC1769 DNA methylase HsdM; type I restriction enzyme M protein 1 VC1784 Neuraminidase, sialidase 1 VC1832 Hypothetical protein 2 VC1911 Orotidine 5-phosphate decarboxylase...”

CJJ81176_0034 hypothetical protein from Campylobacter jejuni subsp. jejuni 81-176
26% identity, 43% coverage

• The role of cydB gene in the biofilm formation by Campylobacter jejuni
  Korkus, Scientific reports 2024
  • “...CJJ81176_1185 Conserved hypothetical protein 15K CJJ81176_0128 Hypothetical protein C64 CJJ81176_1245 Sodium/hydrogen exchanger family protein E13 CJJ81176_0034 Hypothetical protein E17 CJJ81176_1363 Hypothetical protein E24 CJJ81176_1495 Bifunctional putA protein, putative E37 CJJ81176_0728 Conserved hypothetical protein TIGR00486 E40 CJJ81176_1309 Deoxycytidine triphosphate deaminase, putative E48 CJJ81176_1340 Motility accessory factor Effect...”

VC1767 conserved hypothetical protein from Vibrio cholerae O1 biovar eltor str. N16961
39% identity, 12% coverage

• Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems
  Vizzarro, Journal of bacteriology 2024
  • “...these two genes as t ype I-embedded G mrSD-like system of V PI-2, tgvA ( VC1767 ) and tgvB ( VC1766 ). Interestingly, the strain carrying only the tgvAB genes showed significantly less protection (between 10- and 100-fold reduction) against several tested phages compared to the...”
  • “...of type IV restriction enzymes Bioinformatic analysis of the TgvAB system revealed that TgvA ( VC1767 ) and TgvB ( VC1766 ) both possess an N-terminal DUF262 domain, while TgvB additionally contains a C-terminal DUF1524 domain ( Fig. 4a and b ). Interestingly, previous work by...”
• A <i>Vibrio cholerae</i> Type IV restriction system targets glucosylated 5-hydroxymethylcytosine to protect against phage infection
  Gomez, Journal of bacteriology 2024 (secret)
• Vibrio choleraepathogenicity island 2 encodes two distinct types of restriction systems
  Vizzarro, 2024

ACG06_19220 DUF262 domain-containing protein from Pseudomonas aeruginosa
27% identity, 15% coverage

• Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853
  Cao, BMC genomics 2017
  • “...unique C-terminal domain including a metal-binding cysteine cluster COG1223 ACG06_23485 Predicted ATPase (AAA+ superfamily) COG1479 ACG06_19220 Uncharacterized conserved protein COG1541 ACG06_14110 Coenzyme F390 synthetase COG1783 ACG06_12260 Phage terminase large subunit COG2189 ACG06_23500 Adenine specific DNA methylase Mod COG2253 ACG06_23380 Uncharacterized conserved protein COG2372 ACG06_12630 Uncharacterized protein,...”

alr5156 hypothetical protein from Nostoc sp. PCC 7120
29% identity, 18% coverage

• The insertion sequences of Anabaena sp. strain PCC 7120 and their effects on its open reading frames
  Wolk, Journal of bacteriology 2010
  • “...alr5158) is within a gene that fuses the start of alr5156 and the end of alr5159 and that has homologs in diverse cyanobacteria and other bacteria. BLASTn shows...”

New Search

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.