PaperBLAST

PaperBLAST Hits for reanno::DvH:206336 ATP-dependent reduction of co(II)balamin (Desulfovibrio vulgaris Hildenborough JW710) (543 a.a., MQPHPETTPV...)

Show query sequence

>reanno::DvH:206336 ATP-dependent reduction of co(II)balamin (Desulfovibrio vulgaris Hildenborough JW710)
MQPHPETTPVTSCTIIDATDRSIRQTLGETSTLARLIWVDAGLASPPLCSGLARCGRCRV
RITEAAPAPHEDDREFFSAEDISAGWRLACRHAPAHGMVVHVPLPVMPHRHASRPKHPGP
FRLAVDLGTTSLQWSLLAPDGTVAAQGSETNPQMGAGSDVMSRIAMARSDKGRGRLRELV
LQALRRIVADVEGTPATADAVPPAGSGDEPTTACGYESRVEELCVAGNTAMTAILADESV
EGLASAPYRLEMRGGTALALPGLPPAWIPPLPAPFVGGDLSAGYLAVLTDHAPAFPFVLA
DLGTNGEFVLALSPERTLVTSVALGPALEGIGLTFGTVAQRGAITSFTLTPGGLVPYVLD
GGEADGISGTGYISLVHALLRAGLLDVDGRFIQSPSSPLAARMARSIVSHRGEPCLPLAR
GLYLAARDIEEILKVKAAFSLAFERLLATAQMPSHALSGIHLAGALGQHALPADLEGLGF
IPPGSGGRTRAVGNTSLRGAELLLTSPPLRDTLNTWREGCTVVDLTAAPDFSAAFLRHMH
FHF

Running BLASTp...

Found 46 similar proteins in the literature:

DVU0908 ATP-dependent reduction of co(II)balamin from Desulfovibrio vulgaris Hildenborough JW710
100% identity, 100% coverage

• mutant phenotype: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM PF14574.

Dde_2711 2Fe-2S iron-sulfur cluster binding domains protein from Desulfovibrio desulfuricans G20
47% identity, 95% coverage

• Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics
  Price, PLoS genetics 2018
  • “...vitamin B12 reactivation, and we previously proposed that in Desulfovibrio alaskensis , a RamA-like protein (Dde_2711) would be involved in B12 reactivation because it is cofit with MetH (r = 0.90; [ 3 ]). We also found evidence that DUF4445 is involved in the reactivation of...”
• Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20
  Kuehl, mBio 2014
  • “...supplementation of minimal medium with methionine also rescued the fitness defects of the uncharacterized genes Dde_2711 and Dde_3007 ( Fig.4B ). The D.alaskensis G20 MetH is missing the N-terminal activation domain [for reducing Co(II) to Co(I)] that is present in E. coli MetH. To identify this...”
  • “...G20, we examined the new methionine auxotrophs identified by our fitness assay and found that Dde_2711 encodes a predicted ferredoxin and has homology to this missing activation domain of E. coli MetH. Dde_3007 encodes a conserved protein annotated as domain of unknown function DUF39. To determine...”

DvMF_1398 ATP-dependent reduction of co(II)balamin (RamA-like) from Desulfovibrio vulgaris Miyazaki F
DvMF_1398 iron-sulfur cluster-binding protein, putative from Desulfovibrio vulgaris str. Miyazaki F
54% identity, 63% coverage

• mutant phenotype: Cofit with the B12-dependent methionine synthase (DvMF_0476), which lacks a standard domain for the reactivation of vitamin B12.
• Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics
  Price, PLoS genetics 2018
  • “...the standard B12 activation domain. This methionine synthase has a very similar fitness pattern as DvMF_1398, which contains two DUF4445 domains (r = 0.92 across 170 experiments; also see Fig 3 ). We infer that DUF4445 proteins perform the reactivation of vitamin B12 in diverse bacteria....”

Dred_2206 ferredoxin from Desulfotomaculum reducens MI-1
27% identity, 91% coverage

• The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1
  Junier, Environmental microbiology 2010
  • “..., formate, CO as well as various reduced soluble electron transport proteins such as ferredoxin (dred_2206) and electron transfer flavoproteins (EtfAB) (dred_1778-9, dred_1538-9, dred_0572-3 and dred_0367-8) ( Fig. 2 ). Formate is oxidized via formate dehydrogenase (dred_1112-19) that includes a ten-TMH transmembrane subunit (dred_1116) annotated as...”

AF_0010 ASKHA domain-containing protein from Archaeoglobus fulgidus DSM 4304
26% identity, 70% coverage

• A novel methoxydotrophic metabolism discovered in the hyperthermophilic archaeon Archaeoglobus fulgidus
  Welte, Environmental microbiology 2021
  • “.... Genomic and transcriptomic analysis revealed cobalamin binding protein MtoC (AF_0006) and its activator MtoD (AF_0010), Odemethylase MtoB (AF_0007) and methyl transferase MtoA (AF_0009) to be essential for growth of A. fulgidus on methoxylated aromatic compounds. CoM: coenzyme M, H 4 folate: tetrahydrofolate, CO(III): cobalamin binding...”
  • “...VhtACDG (AF_137881), ATP synthase AtpAK (AF_115868), cobalamin binding protein MtoC (AF_0006) and its activator MtoD (AF_0010), Odemethylase MtoB (AF_0007) and methyl transferase MtoA (AF_0009), MFS transporters (AF_0008 & AF_0013). H 4 MPT: tetrahydromethanopterin, MQH 2 : reduced menaquinone (MQ), MFR: methanofuran, Fd: ferredoxin, F 420 H...”

BP07_RS03235, WP_042685513 ASKHA domain-containing protein from Methermicoccus shengliensis
26% identity, 68% coverage

• Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds
  Kurth, The ISME journal 2021
  • “...and MtoD The gene encoding the corrinoid protein MtoC (BP07_RS03260) and the corrinoid activating enzyme (BP07_RS03235) were amplified from genomic M. shengliensis DNA with primers 3235fw/3235Srev (CTCATATGAGCGTCAGAGTAACGTTCGAGC, CTGCGGCCGCTTATTTTTCGAACTGCGGGTGGCTCCAGCTAGCTGAAGAGAGTTTTTCTCC) and 3260fw/3260Srev (CTCATATGACGGACGTAAGAGAAGAGCTC/CTGCGGCCGCTTATTTTTCGAACTGCGGGTGGCTCCAGCTAGCCTCCACCCCCACCAGAGC) for cloning in expression vector pET-30a inserting an N-terminal Strep tag via the reverse primer....”
  • “...plasmid transformation. For production of the corrinoid protein MtoC (BP07_RS03260) and the corrinoid activating enzyme (BP07_RS03235) the plasmids pET-30a_BP07_RS03260 and pET-30a_BP07_RS03235 were used for transformation into E. coli Bl21 (DE3). For protein overexpression, one colony was inoculated in 600ml LB-medium containing 50g/ml kanamycin and incubated at...”
• Several ways one goal-methanogenesis from unconventional substrates
  Kurth, Applied microbiology and biotechnology 2020
  • “...MtvB O-demethylase BP07_RS03250 WP_042685515 Corrinoid protein BP07_RS03260 WP_042685521 MtrH-like methyltransferase BP07_RS03240 WP_042685937 Corrinoid activation protein BP07_RS03235 WP_042685513 Methanococcoides Tertiary amines ? ? ? Methanolobus vulcani Quaternary amines MtgB methyltransferase FKV42_RS08545 WP_154809802 Corrinoid protein FKV42_RS08550 WP_154809803 Corrinoid activator FKV42_RS10455 WP_154810143 CoM methyltransferase FKV42_RS10480 WP_154810148 For the organisms...”
  • “...O-demethylase BP07_RS03250 WP_042685515 Corrinoid protein BP07_RS03260 WP_042685521 MtrH-like methyltransferase BP07_RS03240 WP_042685937 Corrinoid activation protein BP07_RS03235 WP_042685513 Methanococcoides Tertiary amines ? ? ? Methanolobus vulcani Quaternary amines MtgB methyltransferase FKV42_RS08545 WP_154809802 Corrinoid protein FKV42_RS08550 WP_154809803 Corrinoid activator FKV42_RS10455 WP_154810143 CoM methyltransferase FKV42_RS10480 WP_154810148 For the organisms conducting...”

Awo_c10680 corrinoid activation/regeneration protein AcsV from Acetobacterium woodii DSM 1030
26% identity, 66% coverage

• A new metabolic trait in an acetogen: Mixed acid fermentation of fructose in a methylene-tetrahydrofolate reductase mutant of Acetobacterium woodii
  Moon, Environmental microbiology reports 2023
  • “...171,346 29,713 2.52 Awo_c10670 CODH Ni 2+ insertion accessory protein CooC1 ACS/CODH 1000 1997 0.99 Awo_c10680 Corrinoid activation/regeneration protein 4126 7952 0.94 Awo_c10690 Hypothetical protein 1356 2178 0.68 Awo_c10700 Hypothetical protein 933 1748 0.9 Awo_c10710 CFeS protein, SSU AcsD 16,808 36,479 1.11 Awo_c10720 CFeS protein, LSU...”

SSCH_450007 ASKHA domain-containing protein from Syntrophaceticus schinkii
29% identity, 68% coverage

• Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii
  Manzoor, PloS one 2016
  • “...Several ferredoxin-encoding genes were found dispersed in the genome of S . schinkii (SSCH _100042, SSCH_450007, SSCH_530010, SSCH_760007, SSCH_1120013) and one putative rubredoxin gene (SSCH_180038). 10.1371/journal.pone.0166520.g006 Fig 6 Comparison of the NADH-dependent [Fe-Fe] hydrogenase gene cluster (SSCH_21000810) predicted for S . schinkii strain Sp3 to the...”

Dhaf_2573 ferredoxin from Desulfitobacterium hafniense DCB-2
28% identity, 68% coverage

• Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2
  Studenik, Journal of bacteriology 2012
  • “...Expression cassettes for the genes Dhaf_1265, Dhaf_2573, Dhaf_2795, Dhaf_3310, Dhaf_3879, Dhaf_4322, Dhaf_4610, Dhaf_4611, and Dhaf_4612 (GenBank accession no....”
  • “...GAT CCT TAT TTT TCG AAC TGC GGG TGG C 1 Dhaf_2573 Dhaf_3310 Dhaf_3879 Dhaf_4322 Dhaf_4610 Dhaf_4611 Dhaf_4612 a 2 2 2 2 2 2 2 2 For details, see Materials and...”

Dhaf_1265 ferredoxin from Desulfitobacterium hafniense DCB-2
27% identity, 76% coverage

• Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2
  Studenik, Journal of bacteriology 2012
  • “...components. Expression cassettes for the genes Dhaf_1265, Dhaf_2573, Dhaf_2795, Dhaf_3310, Dhaf_3879, Dhaf_4322, Dhaf_4610, Dhaf_4611, and Dhaf_4612 (GenBank...”
  • “...Desulfitobacterium hafniense DCB-2 into pET11aa Gene Primer sequence PCR step Dhaf_1265 CGC GTT CAT ATG AAT CAT TAT CGG CC CTG CGG GTG GCT CCA AGC GCT GCA GAG...”

D9S251 Ferredoxin from Thermosediminibacter oceani (strain ATCC BAA-1034 / DSM 16646 / JW/IW-1228P)
29% identity, 68% coverage

• Analytical Validation of Loss of Heterozygosity and Mutation Detection in Pancreatic Fine-Needle Aspirates by Capillary Electrophoresis and Sanger Sequencing.
  Timmaraju, Diagnostics (Basel, Switzerland) 2024
  • “...150 chr5 119101810 119101960 GGTGTCAACAAAGTAATGTAAAG TGGATACATATTGTTTTCTGCTG 5q D5S615 330 chr5 125163290 125163620 GAGATAGGTAGGTAGGTAGG TCCACAGTGGTAAGAACCAG 9p D9S251 390 chr9 30819368 30819758 TGCATGTTTTATGTGCACTAAC CAATACTTTTTAAGGCTTTGTAGG 9p D9S254 120 chr9 126869098 126869218 TGGGTAATAACTGCCGGAGA GAGGATAAACCTGCTTCACTCAA 10q D10S520 180 chr10 96424526 96424706 CAGCCTATGCAACAGAACAAG GTCCTTGTGAGAAACTGGATGC 10q D10S523 150 chr10 87006333 87006483 GGTGGAGGTTGTGGTGA AACTGGGCATTTGTCTTTC...”
• Molecular Clues for Prediction of Hepatocellular Carcinoma Recurrence After Liver Transplantation.
  Badwei, Journal of clinical and experimental hepatology 2023
• Role of Allelic Imbalance in Predicting Hepatocellular Carcinoma (HCC) Recurrence Risk After Liver Transplant.
  Pagano, Annals of transplantation 2019
  • “...Results We report that AI was associated with HCC recurrence in 3 main loci (D3S2303, D9S251, and D9S254). Tumor recurrence was associated only with 2 specific panels with 9 microsatellites previously reported to be associated with high risk for HCC recurrence. Our data show that fractional...”
  • “...for D3S2303 (p=0.048) considering the presence of LOH ( Table 3A ), and D1S407 (p=0.006) D9S251 (p=0.02), D1S162 (p=0.005), D5S592 (p=0.005), D9S254 (p=0.002) and D10S520 (p=0.04) considering high-level LOH ( Table 3B ). Evaluation of specific panels and association with HCC recurrence Descriptive analysis of the...”
• The C9ORF72 expansion mutation is a common cause of ALS+/-FTD in Europe and has a single founder.
  Smith, European journal of human genetics : EJHG 2013
• Clinical, neuroimaging and neuropathological features of a new chromosome 9p-linked FTD-ALS family.
  Boxer, Journal of neurology, neurosurgery, and psychiatry 2011
  • “...Genome-wide linkage analysis conclusively linked family VSM-20 to a 28.3 cM region between D9S1808 and D9S251 on chromosome 9p, reducing the published minimal linked region to a 3.7 Mb interval. Genomic sequencing and expression analysis failed to identify mutations in the 10 known and predicted genes...”
  • “...GENESCAN and GENOTYPER software (Applied Biosystems) and normalised to the CEPH genotype database, except for D9S251 and D9S304 for which fragment sizes were not available. Mutation analyses In family VSM-20, a genomic DNA (gDNA) sequencing analysis was performed for all 10 candidate genes located within the...”
• Chromosome 9p21 in sporadic amyotrophic lateral sclerosis in the UK and seven other countries: a genome-wide association study.
  Shatunov, The Lancet. Neurology 2010
  • “...7 this 36 Mb locus is defined across studies by the flanking markers D9S169 and D9S251. The SNPs we have identified lie within this region, with the peak association at 1065 Kb. A GWAS that used pathological subtyping of patients with frontotemporal dementia to increase homogeneity...”
• Liver transplantation for hepatocellular carcinoma: extension of indications based on molecular markers.
  Schwartz, Journal of hepatology 2008
• Use of microsatellite marker loss of heterozygosity in accurate diagnosis of pancreaticobiliary malignancy from brush cytology samples.
  Khalid, Gut 2004

Dtox_1273 ferredoxin from Desulfotomaculum acetoxidans DSM 771
27% identity, 67% coverage

• Genome analysis of Desulfotomaculum kuznetsovii strain 17(T) reveals a physiological similarity with Pelotomaculum thermopropionicum strain SI(T)
  Visser, Standards in genomic sciences 2013
  • “...(Desku_1493) and acsE (Desku_1487), which in contrast is present in the genome of D. acetoxidans (Dtox_1273). Moreover, three genes similar to heterodisulfide reductase encoding genes (Desku_1486-1484) are located upstream of acsE in D. kuznetsovii , which is not the case in the genome of D. acetoxidans...”

Ccar_18775 corrinoid activation/regeneration protein AcsV from Clostridium carboxidivorans P7
26% identity, 65% coverage

• Combination of Trace Metal to Improve Solventogenesis of Clostridium carboxidivorans P7 in Syngas Fermentation
  Han, Frontiers in microbiology 2020
  • “...updated and remapped the WLP gene cluster ( Table 2 , and it ranged from Ccar_18775 to _18845 and contained 15 genes ( Pierce et al., 2008 ; Bruant et al., 2010 ). Formate dehydrogenase (FDH), the enzyme responsible for CO 2 reduction or formate oxidization,...”

Dtur_0730 ferredoxin from Dictyoglomus turgidum DSM 6724
25% identity, 79% coverage

• The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor
  Brumm, Frontiers in microbiology 2016
  • “...ubiquinone is scavenged from the environment, or an alternate electron acceptor is utilized, like ferridoxin (Dtur_0730) or ferredoxin-like proteins (Dtur_0076; Dtur_0457; Dtur_0556; Dtur_0730; Dtur_0774, and Dtur_1717). The proton gradient needed for ATP generation is produced by NADH oxidoreductase (Dtur_0558; Dtur_0559; Dtur_0916; Dtur_0919, and Dtur_1091), and succinate...”

TepiRe1_0615 corrinoid activation/regeneration protein AcsV from Tepidanaerobacter acetatoxydans Re1
28% identity, 67% coverage

• Genome-guided analysis of physiological capacities of Tepidanaerobacter acetatoxydans provides insights into environmental adaptations and syntrophic acetate oxidation
  Müller, PloS one 2015
  • “...genes encoding putative ferredoxins (TepiRe1_0333, 0615, 2026) were found in the genome. Ferredoxin encoding gene TepiRe1_0615 is part of the WL pathway operon; TepiRe1_0333 was found to be reverse-transcribed close to the second fhs cluster (described above). Six enzymatic activities were predicted to use ferredoxin as...”

3zyyX / Q3ACS2 Reductive activator for corrinoid,iron-sulfur protein (see paper)
27% identity, 67% coverage

• Ligands: fe2/s2 (inorganic) cluster; (r,r)-2,3-butanediol (3zyyX)

CAETHG_1606 corrinoid activation/regeneration protein AcsV from Clostridium autoethanogenum DSM 10061
28% identity, 65% coverage

• Deletion of genes linked to the C₁-fixing gene cluster affects growth, by-products, and proteome of Clostridium autoethanogenum
  Nwaokorie, Frontiers in bioengineering and biotechnology 2023
  • “...Clostridium autoethanogenum. The gene cluster contains 16 genes, including five genes with unconfirmed biochemical functions (CAETHG_1606; 1607; 1612; 1613; 1619). Gene names and annotations based on Valgepea et al., 2022 . Figure created using BioRender.com . Determination of gene functionalities in acetogens through genotype-phenotype studies has...”

ELI_0370 ASKHA domain-containing protein from Eubacterium callanderi
25% identity, 74% coverage

• Cloning, expression, and characterization of a four-component O-demethylase from human intestinal bacterium Eubacterium limosum ZL-II
  Chen, Applied microbiology and biotechnology 2016 (PubMed)
  • “...including ELI_2003 (MT-I), ELI_2004 (CP), ELI_2005 (MT-II), and ELI_0370 (AE), were confirmed to constitute the Odemethylase in E. limosum ZL-II. The complete...”
  • “...was oxidized to [CoII]-CP immediately in vitro, and ELI_0370 (AE) was responsible for catalyzing the reduction of [CoII]CP to its active form [CoI]-CP. The...”

CD0730 putative iron-sulfur protein from Clostridium difficile 630
25% identity, 67% coverage

• Diverse Energy-Conserving Pathways in Clostridium difficile: Growth in the Absence of Amino Acid Stickland Acceptors and the Role of the Wood-Ljungdahl Pathway
  Gencic, Journal of bacteriology 2020 (secret)
• Vegetative Cell and Spore Proteomes of Clostridioides difficile Show Finite Differences and Reveal Potential Protein Markers
  Abhyankar, Journal of proteome research 2019
  • “...C.difficile 630, which reinforces the acetogenic nature of C.difficile growth. Of these, CD3405, CD3407, and CD0730 have been detected only in single replicates and thus are not quantified. The other WoodLjungdahl pathway proteins have all been quantified, with only three proteinsMetF (CD0722), CD0728, and CD3258being highly...”

DET0670 iron-sulfur cluster binding protein from Dehalococcoides ethenogenes 195
DET0704 iron-sulfur cluster binding protein from Dehalococcoides ethenogenes 195
29% identity, 60% coverage

• Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains
  West, Applied and environmental microbiology 2008
  • “...DET0318 DET0343 DET0551 DET0666 DET0667 DET0668 DET0669 DET0670 DET0671 DET1158 DET1481 DET1483 DET1484 DET1488 DET1494 DET1559 DET1574 DET1630 Trichloroethene...”
• Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195
  Nonaka, Journal of bacteriology 2006
  • “...DET1175 DET1173 DET0516 DET0237 DET0109 DET0110 DET0701 DET0704 DET0699 DET0700 DET1371 DET0104 DET0685 DET0698 DET0926 DET1598 DET1387 DET0416 hydrogenase....”

TepiRe1_0333 ASKHA domain-containing protein from Tepidanaerobacter acetatoxydans Re1
23% identity, 76% coverage

• Genome-guided analysis of physiological capacities of Tepidanaerobacter acetatoxydans provides insights into environmental adaptations and syntrophic acetate oxidation
  Müller, PloS one 2015
  • “...proteins belonging to the family [ 57 ]. Energy conservation Three genes encoding putative ferredoxins (TepiRe1_0333, 0615, 2026) were found in the genome. Ferredoxin encoding gene TepiRe1_0615 is part of the WL pathway operon; TepiRe1_0333 was found to be reverse-transcribed close to the second fhs cluster...”

Dhaf_3879 ferredoxin from Desulfitobacterium hafniense DCB-2
26% identity, 68% coverage

• Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2
  Studenik, Journal of bacteriology 2012
  • “...for the genes Dhaf_1265, Dhaf_2573, Dhaf_2795, Dhaf_3310, Dhaf_3879, Dhaf_4322, Dhaf_4610, Dhaf_4611, and Dhaf_4612 (GenBank accession no. CP001336.1) as Strep...”
  • “...TAT TTT TCG AAC TGC GGG TGG C 1 Dhaf_2573 Dhaf_3310 Dhaf_3879 Dhaf_4322 Dhaf_4610 Dhaf_4611 Dhaf_4612 a 2 2 2 2 2 2 2 2 For details, see Materials and Methods....”

RAMQ_EUBLI / P0DX10 Corrinoid activation enzyme RamQ from Eubacterium limosum (see 2 papers)
WP_038351871 ASKHA domain-containing protein from Eubacterium limosum
26% identity, 72% coverage

• function: Involved in the degradation of the quaternary amines L- proline betaine and L-carnitine (PubMed:31341018, PubMed:32571881). Component of a corrinoid-dependent methyltransferase system that transfers a methyl group from L-proline betaine or L-carnitine to tetrahydrofolate (THF), forming methyl-THF, a key intermediate in the Wood-Ljungdahl acetogenesis pathway (PubMed:31341018, PubMed:32571881). RamQ is not required for the methyl transfer, but it stimulates reduction of reconstituted MtqC from the Co(II) state to the Co(I) state in vitro (PubMed:31341018). It also stimulates the rate of THF methylation (PubMed:32571881).
  cofactor: [2Fe-2S] cluster (Binds 1 2Fe-2S cluster.)
• MtpB, a member of the MttB superfamily from the human intestinal acetogen Eubacterium limosum, catalyzes proline betaine demethylation
  Picking, The Journal of biological chemistry 2019 (secret)

Dhaf_3310 ferredoxin from Desulfitobacterium hafniense DCB-2
27% identity, 69% coverage

• Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2
  Studenik, Journal of bacteriology 2012
  • “...for the genes Dhaf_1265, Dhaf_2573, Dhaf_2795, Dhaf_3310, Dhaf_3879, Dhaf_4322, Dhaf_4610, Dhaf_4611, and Dhaf_4612 (GenBank accession no. CP001336.1) as...”
  • “...CCT TAT TTT TCG AAC TGC GGG TGG C 1 Dhaf_2573 Dhaf_3310 Dhaf_3879 Dhaf_4322 Dhaf_4610 Dhaf_4611 Dhaf_4612 a 2 2 2 2 2 2 2 2 For details, see Materials and...”

Dhaf_2795 ferredoxin from Desulfitobacterium hafniense DCB-2
DSY1650 ferredoxin from Desulfitobacterium hafniense Y51
27% identity, 66% coverage

• Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2
  Studenik, Journal of bacteriology 2012
  • “...cassettes for the genes Dhaf_1265, Dhaf_2573, Dhaf_2795, Dhaf_3310, Dhaf_3879, Dhaf_4322, Dhaf_4610, Dhaf_4611, and Dhaf_4612 (GenBank accession no. CP001336.1)...”
  • “...on March 3, 2017 by University of California, Berkeley Dhaf_2795 2 Studenik et al. oriented in the reverse direction in comparison to the orientation in the...”
• Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195
  Nonaka, Journal of bacteriology 2006
  • “...DSY0391 DSY0393 DSY1228 DSY1247 DSY1596 DSY1598 DSY1648 DSY1650 DSY1651 DSY1652 DSY1671 DSY1890 DSY2085 DSY2558 DSY2585 DSY3715 DSY4099 DSY4876 Predicted...”

B8R2M5 [Co(II) methylated amine-specific corrinoid protein] reductase (EC 1.16.99.1) from Acetobacterium dehalogenans (see paper)
WP_026395886 ASKHA domain-containing protein from Acetobacterium dehalogenans DSM 11527
25% identity, 71% coverage

• Redox potential changes during ATP-dependent corrinoid reduction determined by redox titrations with europium(II)-DTPA
  Dürichen, Protein science : a publication of the Protein Society 2019
  • “...Germany). 4.2 Production and purification of the recombinant proteins The activating enzyme (AE; Accession number: WP_026395886) and corrinoid protein (CP; Accession number: WP_026394334) of the vanillate O demethylase of A. dehalogenans were heterologously produced as Cterminal Strep Tag fusions in Escherichia coli BL21 (DE3) as described...”

Dhaf_4322 ferredoxin from Desulfitobacterium hafniense DCB-2
28% identity, 69% coverage

• Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2
  Studenik, Journal of bacteriology 2012
  • “...the genes Dhaf_1265, Dhaf_2573, Dhaf_2795, Dhaf_3310, Dhaf_3879, Dhaf_4322, Dhaf_4610, Dhaf_4611, and Dhaf_4612 (GenBank accession no. CP001336.1) as Strep tag...”
  • “...BamHI according to the manufacturer's protocol. For Dhaf_4322, a compatible 3318 jb.asm.org Journal of Bacteriology Downloaded from http://jb.asm.org/ on March...”

SMc04347 CONSERVED HYPOTHETICAL PROTEIN from Sinorhizobium meliloti 1021
24% identity, 61% coverage

• An integrated approach to functional genomics: construction of a novel reporter gene fusion library for Sinorhizobium meliloti
  Cowie, Applied and environmental microbiology 2006
  • “...SMc04010 ................................Hypothetical protein SMc04347 ................................Conserved hypothetical protein SMb20057...”
• sinI- and expR-dependent quorum sensing in Sinorhizobium meliloti
  Gao, Journal of bacteriology 2005
  • “...CoA, coenzyme A. b SMc03864 SMc03930 SMc03969 SMc03972 SMc03983 SMc03983 SMc04040 SMc04330 SMc04347 33 44 29 47 17 19 58 10 15 31 42 43 a 111 56 70 55 112 96 77...”

PGA1_c15200 ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13) from Phaeobacter inhibens DSM 17395
PGA1_c15200 ASKHA domain-containing protein from Phaeobacter inhibens DSM 17395
27% identity, 60% coverage

• mutant phenotype: Apparently required for the reactivation of vitamin B12. Distantly related to RamA (see PMID: 19043046) (auxotroph)
• Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics
  Price, PLoS genetics 2018
  • “...are likely to be involved in B12 reactivation: a protein with ferredoxin and DUF4445 domains (PGA1_c15200) and a DUF1638 protein (PGA1_c13340). As shown in Fig 4B , mutants in these genes are rescued by added methionine. The DUF4445 protein is distantly related to RamA, which uses...”

CT740 Phenolhydrolase/NADH ubiquinone oxidoreductase from Chlamydia trachomatis D/UW-3/CX
37% identity, 17% coverage

• Genomic and phenotypic characterization of in vitro-generated Chlamydia trachomatis recombinants
  Jeffrey, BMC microbiology 2013
  • “...ORFs CT740-749, resulting in a progeny strain that contains only the C. suis homologs of CT740 through CT749. The results demonstrate that these C. suis sequences can complement any required function of the deleted C. trachomatis genes for growth in vitro. Figure 4 Schematic diagram of...”
  • “...crossover sites are shown in black. The deletion of the C. trachomatis homologous region of CT740 to CT749 in the RC-J(s)/122 sequence is indicated by the delta symbol. Nucleotide sequence analysis of the recombinant genomes showed that some of these isolates lacked the chlamydial plasmid (Table...”
• The alternative translational profile that underlies the immune-evasive state of persistence in Chlamydiaceae exploits differential tryptophan contents of the protein repertoire
  Lo, Microbiology and molecular biology reviews : MMBR 2012
  • “...Primary Na pump genes CT278 CT279 CT280 CT281 CT634b CT740 2.08 1.66 1.47 2.15 0.22 1.95 PC0301 PC0300 PC0299 PC0298 PC0095 PC1533 1.73 1.14 0.83 1.79 0.19...”
  • “...are homologous throughout. On the other hand, CT278 and CT740 encode proteins that are significantly larger than those encoded by their b1630 and b3844 E. coli...”
• Chlamydia trachomatis lacks an adaptive response to changes in carbon source availability
  Nicholson, Infection and immunity 2004
  • “...1.35 0.04 1.34 0.01 Aerobic CT278 CT279 CT280 CT281 CT634 CT714 CT740 nqr2 nqr3 nqr4 nqr5 nqrA gpdA nqr6 K I D B A E Continued on following page Downloaded from...”

CTLon_0109 Na(+)-translocating NADH-quinone reductase subunit F from Chlamydia trachomatis L2b/UCH-1/proctitis
37% identity, 17% coverage

• Horizontal transfer of tetracycline resistance among Chlamydia spp. in vitro
  Suchland, Antimicrobial agents and chemotherapy 2009
  • “...along with 10 neighboring C. suis genes (homologs of CTLon_0109 to CTLon_0118), flanked by the two rrn operons. The upstream (L2 parental) rrn operon was not...”

ramA / B8Y445 [Co(II) methylated amines-specific corrinoid protein] reductase (EC 1.16.99.1) from Methanosarcina barkeri (see 2 papers)
RAMA_METBA / B8Y445 [Co(II) methylated amine-specific corrinoid protein] reductase; Corrinoid activation enzyme RamA; EC 1.16.99.1 from Methanosarcina barkeri (see paper)
B8Y445 [Co(II) methylated amine-specific corrinoid protein] reductase (EC 1.16.99.1) from Methanosarcina barkeri (see paper)
24% identity, 73% coverage

• function: Reductase required for the activation of corrinoid-dependent methylamine methyltransferase reactions during methanogenesis (PubMed:19043046). Mediates the ATP-dependent reduction of corrinoid proteins from the inactive cobalt(II) state to the active cobalt(I) state (PubMed:19043046). Acts on the corrinoid proteins involved in methanogenesis from monomethylamine (MMA), dimethylamine (DMA) and trimethylamine (TMA), namely MtmC, MtbC and MttC, respectively (PubMed:19043046).
  catalytic activity: 2 Co(II)-[methylamine-specific corrinoid protein] + AH2 + ATP + H2O = 2 Co(I)-[methylamine-specific corrinoid protein] + A + ADP + phosphate + 3 H(+) (RHEA:65816)
  catalytic activity: 2 Co(II)-[dimethylamine-specific corrinoid protein] + AH2 + ATP + H2O = 2 Co(I)-[dimethylamine-specific corrinoid protein] + A + ADP + phosphate + 3 H(+) (RHEA:65832)
  catalytic activity: 2 Co(II)-[trimethylamine-specific corrinoid protein] + AH2 + ATP + H2O = 2 Co(I)-[trimethylamine-specific corrinoid protein] + A + ADP + phosphate + 3 H(+) (RHEA:65836)
  cofactor: [4Fe-4S] cluster (Binds 2 [4Fe-4S] clusters.)
  subunit: Monomer.

MA3972 conserved hypothetical protein from Methanosarcina acetivorans C2A
26% identity, 59% coverage

• Quantitative proteomic and microarray analysis of the archaeon Methanosarcina acetivorans grown with acetate versus methanol
  Li, Journal of proteome research 2007
  • “...pathway. NIH-PA Author Manuscript The protein product of MA3972 was in greater abundance, and expression of the gene up regulated in acetate-grown cells (Table...”
  • “...The results suggest that the product of MM0940 and MA3972 is a core flavoprotein with an unknown function in the acetate pathways of freshwater and marine...”

TC0116 NADH:ubiquinone oxidoreductase, beta subunit, putative from Chlamydia muridarum Nigg
34% identity, 17% coverage

• Identification of immunodominant antigens by probing a whole Chlamydia trachomatis open reading frame proteome microarray using sera from immunized mice
  Cruz-Fisher, Infection and immunity 2011
  • “...TC0066 TC0077 TC0078 TC0079 TC0084 TC0093 TC0104 TC0114 TC0116 TC0117 TC0133 TC0136 TC0137 TC0140 TC0144 TC0149 TC0151 TC0153 TC0160 TC0163 TC0166 TC0177 TC0178...”

MM1440 conserved protein from Methanosarcina mazei Goe1
27% identity, 55% coverage

• RamA, a protein required for reductive activation of corrinoid-dependent methylamine methyltransferase reactions in methanogenic archaea
  Ferguson, The Journal of biological chemistry 2009
  • “...(45) was examined, which led to identification of MM1440 (GenBankTM NP_633464), whose predicted product differed from the N terminus of the isolated protein by...”
  • “...1). Genes were identified in M. mazei (MM1440), M. barkeri Fusaro (Mbar_A0840), and Methanosarcina acetivorans (MA0150) genomes whose predicted gene products...”

MA0849 hypothetical protein (multi-domain) from Methanosarcina acetivorans C2A
24% identity, 71% coverage

• Genetic basis for metabolism of methylated sulfur compounds in Methanosarcina species
  Fu, Journal of bacteriology 2015
  • “...vs MeSH MA4164 MA4165 MA4166 MA4167 MA1617 MA1616 MA0849 MA3860 MA3861 MA3862 MA3863 MA3864 MA3865 MA3300 MA0859 MA4384 MA4558 MA3302 MA3130 MA0685 MA3736...”
  • “...scriptional regulation during growth on methylsulfides. The MA0849 locus, which encodes a protein with homology to the methylamine methyltransferase-activating...”
• RamA, a protein required for reductive activation of corrinoid-dependent methylamine methyltransferase reactions in methanogenic archaea
  Ferguson, The Journal of biological chemistry 2009
  • “...and methylcobamide:CoM methyltransferases (47, 48). A RamA homolog (MA0849) was also found in M. acetivorans adjacent to a gene encoding a methylcobamide:CoM...”

MM0940 putative Flavoprotein from Methanosarcina mazei Goe1
25% identity, 60% coverage

• Quantitative proteomic and microarray analysis of the archaeon Methanosarcina acetivorans grown with acetate versus methanol
  Li, Journal of proteome research 2007
  • “...of 59 kDa 52, the sequence is 90% identical to MM0940 of M. mazei encoding a 59-kDa putative flavoprotein of unknown function that is also up regulated in...”
  • “...cells 11. The results suggest that the product of MM0940 and MA3972 is a core flavoprotein with an unknown function in the acetate pathways of freshwater and...”

Mmah_1683 4Fe-4S ferredoxin iron-sulfur binding domain protein from Methanohalophilus mahii DSM 5219
25% identity, 71% coverage

• The genome sequence of Methanohalophilus mahii SLP(T) reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments
  Spring, Archaea (Vancouver, B.C.) 2010
  • “...activation of the corrinoid protein is catalyzed in methylotrophic methanogens by the iron-sulfur protein RamA (Mmah_1683) [ 49 ]. In Methanosarcina species it was demonstrated that the corrinoid protein and the substrate specific methyltransferase form a tight complex and that the corresponding genes are transcribed in...”

MA0150 methylamine methyltransferase corrinoid activation protein from Methanosarcina acetivorans C2A
27% identity, 55% coverage

• RamA, a protein required for reductive activation of corrinoid-dependent methylamine methyltransferase reactions in methanogenic archaea
  Ferguson, The Journal of biological chemistry 2009
  • “...M. barkeri Fusaro (Mbar_A0840), and Methanosarcina acetivorans (MA0150) genomes whose predicted gene products are 93-97% similar to that produced by the...”
• Cobalamin- and corrinoid-dependent enzymes
  Matthews, Metal ions in life sciences 2009
  • “.../hydrogenase [ 81 , 91 ] Methylamine:coenzyme M methyltransferases (5-OH-benzimidazolylcobamide) Methanosarcina barkeri Methanosarcina acetovorans RamA (MA0150) ATP/ [ 26 ] Energy-conserving methyltetrahydromethanopterin: coenzyme M methyltransferase (5-OH-benzimidazolylcobamide) Methanobacterium thermoautotrophicum not identified ATP/reduced ferredoxin [ 92 ] Veratrol:H 4 folate and vanillate:H 4 folate O-methyltransferases (cobalamin) Acetobacterium dehalogenans...”

MA4380 conserved hypothetical protein from Methanosarcina acetivorans C2A
26% identity, 60% coverage

• RamA, a protein required for reductive activation of corrinoid-dependent methylamine methyltransferase reactions in methanogenic archaea
  Ferguson, The Journal of biological chemistry 2009
  • “...RamM genes were found in M. acetivorans (MA4380), M. mazei (mm1071), and M. barkeri (Mbar_A1055). Additionally, other RamA homologs in Methanosarcina...”

Q8PXZ5 Conserved protein from Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)
MM1071 conserved protein from Methanosarcina mazei Goe1
28% identity, 45% coverage

• Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1
  Leon, Frontiers in microbiology 2015
  • “...Rpl1P 3 62 Q8PY39 MM1025 ThiC 3 58 Q8PXZ6 MM1070 MtaA1 methylcobalamin:CoM methyltransferase 7 374 Q8PXZ5 MM1071 4Fe:4S ferredoxin, hypothetical 2 121 Q8PXZ3 MM1073 MtaC2 methyl corrinoid protein 6 230 Q8PXZ2 MM1074 MtaB2 9 250 Q8PXZ1 MM1075 Putative regulatory protein 2 92 1 Y Q8PXX0 MM1096...”
• Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1
  Leon, Frontiers in microbiology 2015
  • “...3 62 Q8PY39 MM1025 ThiC 3 58 Q8PXZ6 MM1070 MtaA1 methylcobalamin:CoM methyltransferase 7 374 Q8PXZ5 MM1071 4Fe:4S ferredoxin, hypothetical 2 121 Q8PXZ3 MM1073 MtaC2 methyl corrinoid protein 6 230 Q8PXZ2 MM1074 MtaB2 9 250 Q8PXZ1 MM1075 Putative regulatory protein 2 92 1 Y Q8PXX0 MM1096 Thermosome,...”
• Transcriptional profiling of methyltransferase genes during growth of Methanosarcina mazei on trimethylamine
  Krätzer, Journal of bacteriology 2009
  • “...(C-terminal domain) MM0174 MM0175 MM0312 MM0408 MM0479 MM0924 MM1071 MM1073 MM1074 MM1075 MM1112 MM1271 MM1272 MM1273 MM1274 MM1275 MM1647 MM1648 MM1761 MM1762...”
• RamA, a protein required for reductive activation of corrinoid-dependent methylamine methyltransferase reactions in methanogenic archaea
  Ferguson, The Journal of biological chemistry 2009
  • “...were found in M. acetivorans (MA4380), M. mazei (mm1071), and M. barkeri (Mbar_A1055). Additionally, other RamA homologs in Methanosarcina spp. were found, but...”
• A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life
  Haas, BMC genomics 2009
  • “...( M. mazei COG0523) is induced to the same extent as its neighboring ramM homolog, MM1071 , during growth in high salt conditions (2.38 and 2.21 fold, respectively) [ 104 ]. Archaeal genomes sequenced to date lack any recognizable homolog of the Fur (Fe) or Zur...”
• Characterization of a novel bifunctional dihydropteroate synthase/dihydropteroate reductase enzyme from Helicobacter pylori
  Levin, Journal of bacteriology 2007
  • “...MM512 MM612 MM808 MM847 MM851 MM902 MM1059 MM1060 MM1061 MM1071 Genotype or description 4064 LEVIN ET AL. and E. coli Fre. The reaction mixture was incubated...”

pc1533 probable Na(+)-translocating NADH-quinone reductase, chain F from Parachlamydia sp. UWE25
35% identity, 17% coverage

• The alternative translational profile that underlies the immune-evasive state of persistence in Chlamydiaceae exploits differential tryptophan contents of the protein repertoire
  Lo, Microbiology and molecular biology reviews : MMBR 2012
  • “...1.66 1.47 2.15 0.22 1.95 PC0301 PC0300 PC0299 PC0298 PC0095 PC1533 1.73 1.14 0.83 1.79 0.19 1.33 Primary H pump genes CT013 CT014 3.54 2.08 PC1630 PC1629 2.66...”

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.