PaperBLAST

PaperBLAST Hits for sp|Q9HX17|3MGH_PSEAE Putative 3-methyladenine DNA glycosylase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA4010 PE=3 SV=1 (239 a.a., MSRDPILSLP...)

Show query sequence

>sp|Q9HX17|3MGH_PSEAE Putative 3-methyladenine DNA glycosylase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA4010 PE=3 SV=1
MSRDPILSLPWPDARPLPDTFFDRDALLVARELLGKVIRHRQGNLWLAARIIETEAYYLE
EKGSHASLGYTEKRKALFLDGGHIYMYYARGGDSLNFSAGGPGNAVLIKSGHPWLDRISD
HTALERMQSLNPDSQGRPREIGRLCAGQTLLCKAMGLKVPEWDAQRFDPQRLFVDDVGER
PSQVIQAARLGIPKGRDEHLPYRFVDAAFAAFCTRNPLRRGQVAGRDYHLLGHQDPHLQ

Running BLASTp...

Found 29 similar proteins in the literature:

PA4010 3-methyladenine DNA glycosylase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage

• Pseudomonas aeruginosa heteroresistance to levofloxacin caused by upregulated expression of essential genes for DNA replication and repair
  Li, Frontiers in microbiology 2022
  • “...RecJ ( recJ , PA3725), bifunctional glycosylase Fpg ( mutM , PA0357), monofunctional glycosylase MPG (PA4010), and AP-endonuclease Xth ( crc , PA5332) of the PAS71 strain were all upregulated following exposure to 0.125l/ml LVX. However, the expression level of the five genes encoding DpoIII (PA3232),...”
  • “...recJ encoding single-stranded-DNA-specific exonuclease RecJ, mutM encoding bifunctional glycosylase Fpg, crc encoding AP-endonuclease Xth, and PA4010 encoding monofunctional glycosylase MPG. After continuous exposure to LVX, the resistant subpopulation cells of P. aeruginosa selectively proliferated to become dominant populations. However, in the absence of antibiotic exposure, the...”
• Identification of Novel PhoP-PhoQ Regulated Genes That Contribute to Polymyxin B Tolerance in Pseudomonas aeruginosa
  Yang, Microorganisms 2021
  • “...by low concentrations of Mg 2+ [ 32 ] Peptidoglycan recycling [ 46 ] PA14_11970 PA4010 3-methyladenine DNA glycosylase mpl * PA14_46900 PA1343 palmitoyltransferase pagP Directly regulated by PhoP-PhoQ [ 32 ] Transfers palmitate to lipid A [ 31 ] PA14_50740 PA1053 outer membrane lipoprotein slyB...”
• Profiling the susceptibility of Pseudomonas aeruginosa strains from acute and chronic infections to cell-wall-targeting immune proteins
  Torrens, Scientific reports 2019
  • “...of the pair PAFQ11 20 revealed the mutational inactivation (premature stop codon) of the gene PA4010 ( mpl ) in PAFQ11-10, among other mutations. Since this gene is related with PGN recycling 21 , 22 , it was considered as potentially responsible for lysozyme susceptibility. Therefore,...”
• The Pseudomonas aeruginosa PAO1 Two-Component Regulator CarSR Regulates Calcium Homeostasis and Calcium-Induced Virulence Factor Production through Its Regulatory Targets CarO and CarP
  Guragain, Journal of bacteriology 2016
  • “...PA1179 PA1180 PA1343 PA3552 PA3553 PA3554 PA3556 PA3559 PA4010 PA4011 PA4359 PA4825 oprH phoP phoQ Hypothetical arnB arnC arnA arnT arnG Glycosylase...”
• Contribution of the PhoP-PhoQ and PmrA-PmrB two-component regulatory systems to Mg2+-induced gene regulation in Pseudomonas aeruginosa
  McPhee, Journal of bacteriology 2006
  • “...PA0921 PA1178 PA1179b PA1180b PA3522 PA3649 PA3885b PA4010 PA4011 PA4453 PA4454 PA4455 Negatively Mg2 and negatively PhoP regulated PA0836b PA1196b PA3309...”
• Construction of a mini-Tn5-luxCDABE mutant library in Pseudomonas aeruginosa PAO1: a tool for identifying differentially regulated genes
  Lewenza, Genome research 2005
  • “...aminoglycosides 6 PA5529 Antiporter transport protein 11 D7 6 PA4010 DNA glycosylase 19 C2 (Macfarlane et al. 1999, 2000; McPhee et 3 PA4496 Periplasmic binding...”

PA14_11970 methylpurine-DNA glycosylase family protein from Pseudomonas aeruginosa UCBPP-PA14
99% identity, 100% coverage

• Identification of Novel PhoP-PhoQ Regulated Genes That Contribute to Polymyxin B Tolerance in Pseudomonas aeruginosa
  Yang, Microorganisms 2021
  • “...the bacterial binding and susceptibility to polymyxin B. Meanwhile, mutation of PA14_11960 ( papP ), PA14_11970 ( mpl ), PA14_50740 ( slyB ), PA14_52350 ( ppgS ), and PA14_52370 ( ppgH ) reduced the bacterial survival rates and increased ethidium bromide influx under polymyxin B or...”
  • “...( Figure 1 C). However, deletion of the phoQ gene increased the expression levels of PA14_11970, PA14_46900, PA14_50740, PA14_52340 and PA14_52350 ( Figure 1 C). Meanwhile, deletion of phoP or both phoP and phoQ reduced the expression of these genes ( Figure 1 C). In wild-type...”

PputGB1_4865 3-methyladenine DNA glycosylase from Pseudomonas putida GB-1
76% identity, 90% coverage

• Pseudomonas putida AlkA and AlkB proteins comprise different defense systems for the repair of alkylation damage to DNA - in vivo, in vitro, and in silico studies
  Mielecki, PloS one 2013
  • “...tag2 PputGB1_1244, alkA2 PputGB1_2545, alkB PputGB1_2549, ogt PputGB1_2805, gcdH PputGB1_3505, atl PputGB1_4493, aidB PputGB1_4834, aag PputGB1_4865, ada p promoter region containing putative Ada box, hp hypothetical protein) and (B) E. coli species ( atl ECDH10B_0410, ogt ECDH10B_1455, alkA ECDH10B_2218, alkB ECDH10B_2369, ada ECDH10B_2370, tag ECDH10B_3728, aidB...”

PP_4812 DNA-3-methyladenine glycosylase, putative from Pseudomonas putida KT2440
76% identity, 90% coverage

• DNA Polymerases ImuC and DinB Are Involved in DNA Alkylation Damage Tolerance in Pseudomonas aeruginosa and Pseudomonas putida
  Jatsenko, PloS one 2017
  • “...DNA glycosylase I (Tag); an extra copy of the tag gene ( tag2 ) and pp_4812 gene, encoding for 3meA DNA glycosylase [ 66 ]. Therefore, it is possible that the absence of any phenotypical impact of the TLS polymerase deficiency upon MMS exposure in stationary...”

NP_034952 DNA-3-methyladenine glycosylase from Mus musculus
32% identity, 55% coverage

• Alkyladenine DNA glycosylase deficiency uncouples alkylation-induced strand break generation from PARP-1 activation and glycolysis inhibition.
  Alhumaydhi, Scientific reports 2020
  • GeneRIF: Alkyladenine DNA glycosylase deficiency uncouples alkylation-induced strand break generation from PARP-1 activation and glycolysis inhibition.
• ZEB1 promotes inflammation and progression towards inflammation-driven carcinoma through repression of the DNA repair glycosylase MPG in epithelial cells.
  de, Gut 2019 (PubMed)
  • GeneRIF: ZEB1 promotes colitis and inflammatory CRC through the inhibition of MPG in epithelial cells, thus offering new therapeutic strategies to modulate inflammation and inflammatory cancer
• Roles of Aag, Alkbh2, and Alkbh3 in the Repair of Carboxymethylated and Ethylated Thymidine Lesions.
  You, ACS chemical biology 2016
  • GeneRIF: The depletion of Aag did not significantly change the transcriptional inhibitory or mutagenic properties of all five examined lesions, suggesting a negligible role of Aag in the repair of these DNA adducts in mammalian cells.
• DNA repair by MGMT, but not AAG, causes a threshold in alkylation-induced colorectal carcinogenesis.
  Fahrer, Carcinogenesis 2015 (PubMed)
  • GeneRIF: This study demonstrates for the first time a non-linear dose-response for alkylation-induced colorectal carcinogenesis and reveals DNA repair by MGMT, but not AAG, as a key node in determining a carcinogenic threshold.
• Aag-initiated base excision repair promotes ischemia reperfusion injury in liver, brain, and kidney.
  Ebrahimkhani, Proceedings of the National Academy of Sciences of the United States of America 2014
  • GeneRIF: the detrimental effects of Aag-initiated BER during I/R and sterile inflammation, and present a novel target for controlling I/R-induced injury.
• Aag DNA glycosylase promotes alkylation-induced tissue damage mediated by Parp1.
  Calvo, PLoS genetics 2013
  • GeneRIF: These results provide in vivo evidence that Aag-initiated BER may play a critical role in determining the side-effects of alkylating agent chemotherapies and that Parp1 plays a crucial role in Aag-mediated tissue damage.
• The effect of Msh2 knockdown on toxicity induced by tert-butyl-hydroperoxide, potassium bromate, and hydrogen peroxide in base excision repair proficient and deficient cells.
  Cooley, BioMed research international 2013
  • GeneRIF: Toxicity, induced by tert-butyl-hydroperoxide and potassium bromate, differs in base excision repair proficient (Mpg (+/+), Nth1 (+/+)) and deficient (Mpg (-/-), Nth1 (-/-)) mouse embryonic fibroblasts following Msh2 knockdown, was examined.
• DNA repair is indispensable for survival after acute inflammation.
  Calvo, The Journal of clinical investigation 2012
  • GeneRIF: ALKBH2 and ALKBH3 provide cancer protection similar to that of the DNA glycosylase AAG and display apparent epistasis with Aag
• More

Krad_3154 DNA-3-methyladenine glycosylase from Kineococcus radiotolerans SRS30216 = ATCC BAA-149
41% identity, 38% coverage

• Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria
  Sghaier, BMC genomics 2008
  • “...Krad_2553 Rxyl_0448 Exonuclease SbcC 1.82 DR_1949 Dgeo_1623 Krad_1405 Rxyl_1394 Ribonuclease HII n.a. -1.642 DR_2074 Dgeo_1660 Krad_3154 Rxyl_1309 Putative 3-methyladenine DNA glycosylase 3.25 DR_2275 Dgeo_1890 Krad_2942 Rxyl_2021 Excinuclease ABC, subunit B* n.a. -1.767 DR_2285 Dgeo_0019 Krad_0599 Rxyl_2229 A/G-specific adenine glycosylase* 1.85 DR_2340 Dgeo_2138 Krad_1492 Rxyl_1423 RecA protein*...”
• Survival in nuclear waste, extreme resistance, and potential applications gleaned from the genome sequence of Kineococcus radiotolerans SRS30216
  Bagwell, PloS one 2008
  • “...helicase Mfd DR_1532 Rv1020 Krad_1067 MPG 3-Methylpurine DNA glycosylase MPG DR_2074 (also see AlkA) Rv1688 Krad_3154 Mrr Type IV restriction endonuclease Mrr DR_1877 DR_0508 DR_0587 Rv2528c No homologs Mug (ygjF) G/T mismatch-specific thymine DNA glycosylase, distantly related to DR_1751; Present as a domain of many multidomain...”

SCO1792 3-methyladenine DNA glycosylase from Streptomyces coelicolor A3(2)
33% identity, 61% coverage

• Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
  Hsiao, Antonie van Leeuwenhoek 2008
  • “...polymerase III 1.128049 0.423158 1.111964 0.326701 SCO1780 putative DNA repair protein 0.14578 0.09175 0.258713 0.32746 SCO1792 putative 3-methyladenine DNA glycosylase 0.20485 0.07755 0.083499 0.2824 SCO1827 putative DNA polymerase III 0.559715 0.711265 0.512873 0.343849 SCO1966 ABC excision nuclease subunit B 0.047382 0.06896 1.085903 0.05934 SCO1969 putative DNA-methyltransferase...”

AT3G12040 DNA-3-methyladenine glycosylase (MAG) from Arabidopsis thaliana
33% identity, 72% coverage

• How Do Plants Cope with DNA Damage? A Concise Review on the DDR Pathway in Plants
  Szurman-Zubrzycka, International journal of molecular sciences 2023
  • “...OF SILENCING 1 At2g36490 UNG (UDG) URACIL DNA GLYCOSYLASE At3g18630 Monofunctional glycosylases AAG ALKYLADENINE-DNA GLYCOSYLASE At3g12040 MBD4L METHYL-CPG-BINDING DOMAIN PROTEIN 4 LIKE At3g07930 ARP APURINIC ENDONUCLEASE-REDOX PROTEIN At2g41460 AP endonucleases APE1L APURINIC/APYRIMIDINIC ENDONUCLEASE1-LIKE PROTEIN At3g48425 APE2 APURINIC/APYRIMIDINIC ENDONUCLEASE2 At4g36050 ZDP ZINC 4 FINGER DNA 3-PHOSPHOESTERASE At3g14890...”
• Base Excision DNA Repair in Plants: Arabidopsis and Beyond
  Grin, International journal of molecular sciences 2023
  • “...At3g12710 At5g44680 At5g57970 Bacterial alkylpurineDNA glycosylase II AlkA At1g19480 At1g75230 At3g50880 Human alkylpurineDNA glycosylase MPG At3g12040 (AtMAG) Methyl-CpG-specific uracilDNA glycosylase MBD4 At3g07930 (AtMBD4) FormamidopyrimidineDNA glycosylase/endonuclease VIII Fpg At3g07930 (AtMMH) Nei NEIL1 NEIL2 NEIL3 Epigenetic 5-methylcytosineDNA glycosylases At5g04560 (AtDME) At2g36490 (AtROS1) At3g10010 (AtDML2) At4g34060 (AtDML3) At3g47830 AP...”
• Structural Aspects of DNA Repair and Recombination in Crop Improvement
  Verma, Frontiers in genetics 2020
  • “...human UDG (PDB: 3TKB) ( Cordoba-Canero et al., 2010 ) Alkylpurine DNA glycosylase (AAG) AtMAG (AT3G12040) AAG Superfamily - Removes alkylated purines. A role in DNA replication and cell growth. High expression of AtMAG in rapidly dividing tissues and growing leaves. No structure known. ( Santerre...”
• DNA Base Excision Repair in Plants: An Unfolding Story With Familiar and Novel Characters
  Roldán-Arjona, Frontiers in plant science 2019
  • “...UNG AtUNG AT3G18630 ( Cordoba-Caero et al., 2010 ) Mug TDG Smug1 AAG MPG AthAAG AT3G12040 ( Santerre and Britt, 1994 ) H2TH superfamily MutM AtFPG AT1G52500 ( Ohtsubo et al., 1998 ) Nei NEIL1 NEIL2 NEIL3 HhH-GPD superfamily Nth Ntg1p NTHL1 AtNTH1 AT2G31450 ( Roldan-Arjona...”
• Ancestor of land plants acquired the DNA-3-methyladenine glycosylase (MAG) gene from bacteria through horizontal gene transfer
  Fang, Scientific reports 2017
  • “...genes encoding MAG proteins in green plants, the protein sequence of the Arabidopsis gene AtMAG (AT3G12040) 20 , 60 was used as a query to search the NCBI nr and ref_seq protein, the spruce genome project 61 and Phytozome 62 databases. Then, the Pfam tool 63...”
• Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems
  Morita, Journal of nucleic acids 2010
  • “...(EndoIII) Ntg1p, Ntg2p AT1G05900 Nthl1 NTHL1 remove 3-meA, ethenoA, hypoxanthine AlkA (TTHA0329) AlkA, TagA Mag1p AT3G12040 (MAG) Mpg MPG, (MAG, AAG) Remove U UDGA (TTHA0718) Ung Ung1p AT3G18630 uracil DNA glycosylase family protein Ung Ung Hyper IgM syndromes, autosomal recessive type UDGB (TTHA1149) Remove U, hydroxymethyl...”
• The ASH1 HOMOLOG 2 (ASHH2) histone H3 methyltransferase is required for ovule and anther development in Arabidopsis
  Grini, PloS one 2009
  • “...1.18 2.26 At3g11980 MS2 Aarts et al., Plant J 12: 615623 (1997) stamens 1.86 3.64 At3g12040 DNA glycosylase - n.t. 0.82 1.77 At3g18960 B3 TF - seeds, shoot apex 0.73 1.66 At3g22880 ATDMC1 Couteau et al., Plant Cell 11: 16231634 (1999) shoot axep, carpels 0.73 1.66...”

LOC102847768 uncharacterized protein LOC102847768 from Elephantulus edwardii
29% identity, 27% coverage

• Is the number of DNA repair genes associated with evolution rate and size of genomes?
  Udroiu, Human genomics 2020
  • “...with a synonym) can be found on NCBI. However, a BLAST search indicates that gene LOC102847768 shares 77% identity with MPG of Loxodonta africana ; moreover, it is located between NPRL3 and RHBDF1 , exactly as MPG in Loxodonta Africana , and its product shows the...”

P23571 DNA-3-methyladenine glycosylase (Fragment) from Rattus norvegicus
33% identity, 46% coverage

• The Urine Proteome as a Biomarker of Radiation Injury: Submitted to Proteomics- Clinical Applications Special Issue: "Renal and Urinary Proteomics (Thongboonkerd)".
  Sharma, Proteomics. Clinical applications 2008

FTL_0940 Methylpurine-DNA glycosylase family protein from Francisella tularensis subsp. holarctica
27% identity, 73% coverage

• Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains
  Rohmer, Genome biology 2007
  • “...Hypothetical protein Hypothetical FTT1076 FTL_1125 424 31.1 hipA Transcription regulator Signal transduction and regulation FTT0666c FTL_0940 193 29.5 - Methylpurine-DNA glycosylase family protein DNA metabolism FTT1450c FTL_0606 348 33.6 wbtM dTDP-D-glucose 4,6-dehydratase Cell wall/LPS/capsule The genes are grouped in the table by genomic regions. a As...”

3MG_HUMAN / P29372 DNA-3-methyladenine glycosylase; 3-alkyladenine DNA glycosylase; 3-methyladenine DNA glycosidase; ADPG; N-methylpurine-DNA glycosylase; EC 3.2.2.21 from Homo sapiens (Human) (see paper)
32% identity, 46% coverage

• function: Hydrolysis of the deoxyribose N-glycosidic bond to excise 3- methyladenine, and 7-methylguanine from the damaged DNA polymer formed by alkylation lesions
  catalytic activity: Hydrolysis of alkylated DNA, releasing 3-methyladenine, 3- methylguanine, 7-methylguanine and 7-methyladenine.
  subunit: Binds MBD1. Binds SSBP1
• Network Pharmacology and Bioinformatics Analysis to Identify the Molecular Targets and its Biological Mechanisms of Sciadopitysin against Glioblastoma.
  Lian, Journal of Cancer 2024
  • “...II subunit alpha (CK II alpha) AKR1B10 O60218 Aldo-keto reductase family 1 member B10 MPG P29372 DNA-3-methyladenine glycosylase MELK Q14680 Maternal embryonic leucine zipper kinase (hMELK) CA2 P00918 Carbonic anhydrase 2 CA12 O43570 Carbonic anhydrase 12 KCNH2 Q12809 Potassium voltage-gated channel subfamily H member 2 CCR1...”
• Nuclear Phosphatidylinositol 3,4,5-Trisphosphate Interactome Uncovers an Enrichment in Nucleolar Proteins
  Mazloumi, Molecular & cellular proteomics : MCP 2021
  • “...repair UniProt ID Name description Gene name SILAC ratio K/R motif Study 1 2 3 P29372 DNA-3-methyladenine glycosylase MPG 18.81 - + - - P13010 X-ray repair cross-complementing protein 5 XRCC5 2.817 - - + - P09874 Poly [ADP-ribose] polymerase 1 PARP1 2.5 RWDDQQKVKK + +...”
• FUS-dependent liquid-liquid phase separation is important for DNA repair initiation.
  Levone, The Journal of cell biology 2021
  • “...ERCC-6 P11388 DNA topoisomerase 2- Q92547 DNA topoisomerase 2-binding protein 1 O60870 DNA/RNA-binding protein KIN17 P29372 DNA-3-methyladenine glycosylase P78527 DNA-dependent protein kinase catalytic subunit P24928 DNA-directed RNA polymerase II subunit RPB1 Q9Y5B9 FACT complex subunit SPT16 Q08945 FACT complex subunit SSRP1 Q9UBU8 Mortality factor 4-like protein...”
• Lasting DNA Damage and Aberrant DNA Repair Gene Expression Profile Are Associated with Post-Chronic Cadmium Exposure in Human Bronchial Epithelial Cells.
  Tan, Cells 2019
  • “...ERCC6 (Q03468); FEN1 (P39748); GADD45A (P24522); HUS1 (O60921); LIG1 (P18858); LIG3 (P49916); MBD4 (O95243); MPG (P29372); MUTYH (Q9UIF7); NEIL1 (Q96FI4); NEIL2 (Q969S2); NEIL3 (Q8TAT5); NTHL1 (P78549); OGG1 (O15527); PARP1 (P09874); PARP2 (Q9UGN5); PARP3 (Q9Y6F1); PCNA (P12004); POLB (P06746); POLD3 (Q15054); RAD23A (P54725); RAD23B (P54727); RAD52 (P43351);...”
• Identification of proteins interacting with the mitochondrial small heat shock protein Hsp22 of Drosophila melanogaster: Implication in mitochondrial homeostasis
  Dabbaghizadeh, PloS one 2018
  • “...Pyruvate dehydrogenase E1 component subunit beta, mitochondrial (P11177) 0.61 0.17 1 0.2 0.1 DNA-3-methyladenine glycosylase (P29372) 0.47 0.06 0 0 Phosphatidyl glycerophosphatase and protein-tyrosine phosphatase1 (Q8WUK0) 0.33 0.1 0 0 Methylcrotonyl-CoA carboxylase subunit alpha, mitochondrial (Q96RQ3) 0 0 0.34 0 Isoform 3 of Carbamoyl-phosphate synthase, mitochondrial...”
• DNA Repair Molecular Beacon assay: a platform for real-time functional analysis of cellular DNA repair capacity.
  Li, Oncotarget 2018
  • “...protein 4 8930 O95243 Nucleus [ 90 , 91 ] MPG N-methyl DNA glycosylase 4350 P29372 Cytoplasm [ 91 ] Nucleoplasm [ 92 ] MUTYH (MYH) mutY homolog (E. coli) 4595 Q9UIF7 Nucleoplasm [ 92 ] Nucleus [ 93 ] Mitochondrion [ 94 ] UNG Uracil...”
• Base Excision Repair in the Mitochondria.
  Prakash, Journal of cellular biochemistry 2015
  • “...is based on these deposited sequences (Uniprot IDs: UNG1: P13051-2, TDG: Q13569, SMUG1: Q53HV7, AAG: P29372, MBD4: O95243, MUTYH: Q9UIF7, NTH1: P78549, OGG1-1a: O15527, NEIL1: Q96FI4, NEIL2: Q969S2, NEIL3: Q8TAT5). The number of putative N-terminal amino acids in the leader sequence that get cleaved upon mitochondrial...”
• Proteomic study reveals a functional network of cancer markers in the G1-Stage of the breast cancer cell cycle
  Tenga, BMC cancer 2014
  • “...127376.1 5 Cancer P27695 APEX1_HUMAN DNA-(apurinic or apyrimidinic site) lyase 35532.2 78 Cancer Breast cancer P29372 3MG_HUMAN DNA-3-methyladenine glycosylase 32842.8 36 Cancer P35244 RFA3_HUMAN Replication protein A 14 kDa subunit 13559.9 29 Cancer P43246 MSH2_HUMAN DNA mismatch repair protein Msh2 104676.8 21 Cancer P46063 RECQ1_HUMAN ATP-dependent...”
• More

Dgeo_1660 DNA-3-methyladenine glycosylase from Deinococcus geothermalis DSM 11300
31% identity, 80% coverage

• Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria
  Sghaier, BMC genomics 2008
  • “...Dgeo_0823 Krad_2553 Rxyl_0448 Exonuclease SbcC 1.82 DR_1949 Dgeo_1623 Krad_1405 Rxyl_1394 Ribonuclease HII n.a. -1.642 DR_2074 Dgeo_1660 Krad_3154 Rxyl_1309 Putative 3-methyladenine DNA glycosylase 3.25 DR_2275 Dgeo_1890 Krad_2942 Rxyl_2021 Excinuclease ABC, subunit B* n.a. -1.767 DR_2285 Dgeo_0019 Krad_0599 Rxyl_2229 A/G-specific adenine glycosylase* 1.85 DR_2340 Dgeo_2138 Krad_1492 Rxyl_1423 RecA...”

NP_001015054 DNA-3-methyladenine glycosylase isoform c from Homo sapiens
30% identity, 56% coverage

• Transformed astrocytes confer temozolomide resistance on glioblastoma via delivering ALKBH7 to enhance APNG expression after educating by glioblastoma stem cells-derived exosomes.
  Liu, CNS neuroscience & therapeutics 2024
  • GeneRIF: Transformed astrocytes confer temozolomide resistance on glioblastoma via delivering ALKBH7 to enhance APNG expression after educating by glioblastoma stem cells-derived exosomes.
• Pilot Study to Detect Genes Involved in DNA Damage and Cancer in Humans: Potential Biomarkers of Exposure to E-Cigarette Aerosols.
  Hamad, Genes 2021
  • GeneRIF: Pilot Study to Detect Genes Involved in DNA Damage and Cancer in Humans: Potential Biomarkers of Exposure to E-Cigarette Aerosols.
• Recognition of 1,N2-ethenoguanine by alkyladenine DNA glycosylase is restricted by a conserved active-site residue.
  Thelen, The Journal of biological chemistry 2020
  • GeneRIF: Recognition of 1,N (2)-ethenoguanine by alkyladenine DNA glycosylase is restricted by a conserved active-site residue.
• Alkyladenine DNA glycosylase associates with transcription elongation to coordinate DNA repair with gene expression.
  Montaldo, Nature communications 2019
  • GeneRIF: AAG binds to chromatin and forms complex with RNA polymerase (pol) II. This occurs through direct interaction with Elongator and results in transcriptional co-regulation.
• Distinguishing Specific and Nonspecific Complexes of Alkyladenine DNA Glycosylase.
  Taylor, Biochemistry 2018
  • GeneRIF: Although AAG strongly prefers to excise lesions from duplex DNA, nonspecific binding is comparable for single- and double-stranded nonspecific sites. The electrostatically driven binding of AAG to small DNA sites ( approximately 5 nucleotides of single-stranded and approximately 6 base pairs of duplex) facilitates the search for DNA damage in chromosomal DNA, which is bound by nucleosomes and other proteins.
• PIG11 over-expression predicts good prognosis and induces HepG2 cell apoptosis via reactive oxygen species-dependent mitochondrial pathway.
  Wang, Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie 2018 (PubMed)
  • GeneRIF: PIG11 may act as a candidate liver tumor suppressor.
• Monitoring of the spatial and temporal dynamics of BER/SSBR pathway proteins, including MYH, UNG2, MPG, NTH1 and NEIL1-3, during DNA replication.
  Bj, Nucleic acids research 2017
  • GeneRIF: Data indicate that DNA glycosylases MYH, UNG2, MPG, NTH1, NEIL1, 2 and 3 on nascent DNA.
• APNG as a prognostic marker in patients with glioblastoma.
  Fosmark, PloS one 2017
  • GeneRIF: high levels of APNG were associated with better overall survival in patients with glioblastoma
• More

A2IDA3 DNA-3-methyladenine glycosylase II (Fragment) from Homo sapiens
30% identity, 63% coverage

• Quantitative proteomic analysis for high-throughput screening of differential glycoproteins in hepatocellular carcinoma serum
  Gao, Cancer biology & medicine 2015
  • “...(Fragment) OS=Homo sapiens GN=SFRS17A PE=2 SV=1 - [Q05DA9_HUMAN] 2.05 2 1 1 292 33.5 8.34 A2IDA3 N-methylpurine-DNA glycosylase (Fragment) OS=Homo sapiens GN=MPG PE=3 SV=1 - [A2IDA3_HUMAN] 3.19 3 1 1 251 27.3 9.03 B4DP13 cDNA FLJ56607 OS=Homo sapiens PE=2 SV=1 - [B4DP13_HUMAN] 1.62 2 1 1...”

1f6oA / P29372 Crystal structure of the human aag DNA repair glycosylase complexed with DNA (see paper)
32% identity, 58% coverage

• Ligand: dna (1f6oA)

LMOf2365_0949 DNA-3-methyladenine glycosylase, putative from Listeria monocytogenes str. 4b F2365
Q721N6 Putative 3-methyladenine DNA glycosylase from Listeria monocytogenes serotype 4b (strain F2365)
29% identity, 77% coverage

• Transcriptomic Analysis of Listeria monocytogenes in Response to Bile Under Aerobic and Anaerobic Conditions
  Chakravarty, Frontiers in microbiology 2021
  • “...family 3.1 LMOf2365_1533 ATPase, AAA family domain protein 3.3 LMOf2365_1998 Putative DNA-damage-inducible protein P 4.2 LMOf2365_0949 Putative DNA-3-methyladenine glycosylase 4.7 rnhA LMOf2365_1909 Ribonuclease HI 4.9 LMOf2365_2784 Replication and repair 5.9 dbpA LMOf2365_1260 ATP-dependent RNA helicase DbpA 8.4 recA LMOf2365_1417 Recombination protein RecA 9.2 LMOf2365_0863 Excinuclease ABC...”
• Proteomic Exploration of Listeria monocytogenes for the Purpose of Vaccine Designing Using a Reverse Vaccinology Approach
  Srivastava, International journal of peptide research and therapeutics 2021
  • “...0.577 Non-allergen 141 Q723G3 2.038 Non-allergen 142 Q71WV3 0.925 Non-allergen 143 Q71ZJ5 0.952 Non-allergen 144 Q721N6 0.586 Non-allergen 145 Q71ZK1 1.532 Non-allergen 146 Q71ZD0 1.746 Non-allergen 147 Q71WF4 0.935 Non-allergen 148 Q71YL9 2.126 Non-allergen 149 Q71WG9 1.537 Non-allergen 150 Q71YK0 2.221 Non-allergen 151 Q71WI2 2.143 Non-allergen...”
  • “...DRB1_0101 FRFVPINNF 1098 1.5957 Antigen DRB1_0701 FRFVPINNF 83.9 1.5957 Antigen DRB1_0701 IQPVGSKNL 287.2 0.534 Antigen Q721N6 DRB1_1301 QMVQNRHGK 18 1.5447 Antigen Q71ZK1 DRB1_1301 KKSEAARKR 46.5 1.9356 Antigen Q71ZD0 DRB1_1301 MLKFDIQHF 45 1.2032 Antigen Q71WF4 DRB1_0101 LFNLRFQLA 1029 2.5288 Antigen Q71YL9 DRB1_1301 MAVKIRLKR 4.3 1.4155 Antigen DRB1_1301...”

lmo0928 similar to 3-methyladenine DNA glycosylase from Listeria monocytogenes EGD-e
27% identity, 87% coverage

• Listeria monocytogenes {sigma}B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains
  Oliver, Applied and environmental microbiology 2010
  • “...lmo0649 lmo0650 lmo0759 lmo0760 lmo0811 lmo0818 lmo0819 lmo0928 lmo0929 lmo0995 lmo1037 lmo1064 lmo1072 lmo1121 lmo1226 lmo1242 lmo1243 lmo1360 lmo1388 lmo1421...”

CAB1_0249 DNA-3-methyladenine glycosylase from Chlamydia abortus LLG
29% identity, 79% coverage

• Data of de novo genome assembly of the Chlamydia psittaci strain isolated from the livestock in Volga Region, Russian Federation
  Feodorova, Data in brief 2020
  • “...protein 274,870..276,204 B598_0288 FI836_04045 91.09 21 C. abortus LLG CP018296.1 putative 3-methyladenine DNA glycosylase 253,058..253,630 CAB1_0249 FI836_03950 97.91 22 putative ribonuclease 253,630..255,678 CAB1_0250 FI836_03955 23 putative 3-methyladenine DNA glycosylase 253,058..253,630 CAB1_0249 FI836_03950 99.12 24 putative ribonuclease 253,630..255,678 CAB1_0250 FI836_03950 25 heat shock chaperone protein 255,832..257,811 CAB1_0251...”

B598_0269 DNA-3-methyladenine glycosylase from Chlamydia psittaci GR9
29% identity, 79% coverage

• Data of de novo genome assembly of the Chlamydia psittaci strain isolated from the livestock in Volga Region, Russian Federation
  Feodorova, Data in brief 2020
  • “...Locus tag Rostinovo-70 Identity,% 1 C. psittaci GR9 CP003791.1 DnaK DNA-3-methyladenine glycosylase family protein 253,092..253,664 B598_0269 FI836_03950 95.29 2 vacB and RNase II 3-5 exoribonucleases family protein 253,664..255,709 B598_0270 FI836_03955 93.40 3 chaperone protein 255,866..257,845 B598_0271 FI836_03960 95.30 4 grpE family protein 257,871..258,446 B598_0272 FI836_03965 93.40...”

BRE_425 3-methyladenine DNA glycosylase from Borrelia recurrentis A1
31% identity, 62% coverage

• The genome of Borrelia recurrentis, the agent of deadly louse-borne relapsing fever, is a degraded subset of tick-borne Borrelia duttonii
  Lescot, PLoS genetics 2008
  • “...BRE_423), adenylosuccinate lyase ( purB , BDU_420, BRE_424), and hypoxanthine phosphoribosyltransferase ( hpt , BDU_422, BRE_425). They were located between the 16S and 23S ribosomal DNA. Other genes unique to the relapsing fever group borreliae included a putative adenine-specific DNA methyltransferase (BDU_467, BRE_470), a copper homeostasis...”

SMb20709 putative 3-methyladenine DNA glycosylase protein from Sinorhizobium meliloti 1021
33% identity, 51% coverage

• The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti
  Finan, Proceedings of the National Academy of Sciences of the United States of America 2001
  • “...(SMb20708), a 3-methyladenine DNA glycosylase (SMb20709), and an exodeoxyribonuclease III (xthA4). Dehydrogenases, Oxidoreductases, and Sugar Kinases....”

NP_391741 3-alkylated purines and hypoxanthine DNA glycosidase from Bacillus subtilis subsp. subtilis str. 168
27% identity, 80% coverage

• Aag Hypoxanthine-DNA Glycosylase Is Synthesized in the Forespore Compartment and Involved in Counteracting the Genotoxic and Mutagenic Effects of Hypoxanthine and Alkylated Bases in DNA during Bacillus subtilis Sporulation.
  Ayala-García, Journal of bacteriology 2016
  • GeneRIF: Expression of aag is dependent on the forespore-specific sigma factor sigmaG.

CCA00239 DNA-3-methyladenine glycosylase from Chlamydophila caviae GPIC
27% identity, 79% coverage

• Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae
  Read, Nucleic acids research 2003
  • “...involved in pyrimidine biosynthesis, and DNA-3-methyladenine glycosylase (CCA00239; Table S1C) involved in DNA repair are identi(R)ed within this set, however...”

3MG_ENCCU / Q8SQI1 Probable DNA-3-methyladenine glycosylase; 3-methyladenine DNA glycosidase; EC 3.2.2.21 from Encephalitozoon cuniculi (strain GB-M1) (Microsporidian parasite) (see paper)
ECU05_1590 3-METHYLADENINE DNA GLYCOSYLASE from Encephalitozoon cuniculi GB-M1
28% identity, 79% coverage

• function: Hydrolysis of the deoxyribose N-glycosidic bond to excise 3- methyladenine, and 7-methylguanine from the damaged DNA polymer formed by alkylation lesions.
  catalytic activity: Hydrolysis of alkylated DNA, releasing 3-methyladenine, 3- methylguanine, 7-methylguanine and 7-methyladenine.
• Identification of transcriptional signals in Encephalitozoon cuniculi widespread among Microsporidia phylum: support for accurate structural genome annotation
  Peyretaillade, BMC genomics 2009
  • “...in green. The star character stands for a mispredicted start codon. For the following genes, ECU05_1590, ECU08_1610 and ECU11_0530, adenine-rich region was not present. Nevertheless, we can observe CCC- and/or GGG-like multiple motifs in these regions. Click here for file Additional file 5 Identification of upstream...”

WD_1110 DNA-3-methyladenine glycosylase from Wolbachia endosymbiont of Drosophila melanogaster
36% identity, 31% coverage

• Complete Genome Sequence of the Wolbachia wAlbB Endosymbiont of Aedes albopictus
  Sinha, Genome biology and evolution 2019
  • “...w Cle DgkA WD_1163 w Ri_011390 w Ha_09720 w No_07140 WP0909 - - - MPG WD_1110 w Ri_012850 w Ha_09290 w No_05480 WP0867 w Bm0254 w Oo_04680 w CLE_011920 CydA WD_0740 w Ri_007360 w Ha_06280 - - - - - CydB WD_0741 w Ri_007350 w Ha_06290...”

SACE_5255 DNA-3-methyladenine glycosylase II from Saccharopolyspora erythraea NRRL 2338
35% identity, 36% coverage

• Comparative genomics and transcriptional profiles of Saccharopolyspora erythraea NRRL 2338 and a classically improved erythromycin over-producing strain
  Peano, Microbial cell factories 2012
  • “...Frameshift (+G 353/354) G/U mismatch-specific DNA glycosidase SACE_5437 895 polA Frameshift (-C617) DNA polymerase I SACE_5255 207 alkA Missense (P68F) 3-methyladenine DNA glycosylase SACE_6108 693 uvrD2 IPM ATP-dependent DNA helicase UvrD-like Missense and in SACE_6681 873 uvrD frame deletion (G54-, G56R, S57I) ATP-dependent DNA helicase UvrD...”

EF_1978 DNA-3-methyladenine glycosylase from Enterococcus faecalis V583
26% identity, 79% coverage

• Identification and comparison of protein composition of biofilms in response to EGCG from <i>Enterococcus faecalis</i> and <i>Staphylococcus lugdunensis</i>, which showed opposite patterns in biofilm-forming abilities
  Cho, Biofilm 2024
  • “...EF_1239, EF_1264, EF_1411, xerC, EF_1679, EF_1690, EF_1711, purD, purH, purM, purS, purC, purE, EF_1955, EF_1958, EF_1978, EF_2207, EF_2473, EF_2479, atpE, EbgA, EF_2863, EF_2955, folk GO:0009152 GO Process Purine ribonucleotide biosynthetic process 7 purD, purH, purM, purS, purC, purE, atpE GO:1901135 GO Process Carbohydrate derivative metabolic process...”
  • “...EF_1154, EF_1238, EF_1239, EF_1264, EF_1411, xerC, EF_1679, EF_1690, purD, purH, purM, purS, purC, purE, EF_1958, EF_1978, EF_2207, EF_2473, EF_2479, atpE, EbgA, EF_2863, EF_2955, folK GO:0005975 GO Process Carbohydrate metabolic process 12 sdhA-1, EF_0123, EF_0362, mtlD, EF_0783, pgmB, EF_0972, EF_1238, EF_1239, EF_1411, EbgA, EF_2863 GO:0044238 GO Process...”

EF1978 DNA-3-methyladenine glycosylase from Enterococcus faecalis V583
Q833H5 Putative 3-methyladenine DNA glycosylase from Enterococcus faecalis (strain ATCC 700802 / V583)
26% identity, 79% coverage

• Use of recombinase-based in vivo expression technology to characterize Enterococcus faecalis gene expression during infection identifies in vivo-expressed antisense RNAs and implicates the protease Eep in pathogenesis
  Frank, Infection and immunity 2012
  • “...EF0798 EF1348 EF1591 EF1755 EF1809 EF1826 EF1918 EF1962 EF1978 EF2207 EF2380 EF2570 EF2668 EF2744 EF2889 EF3008 EF3056 EF3124 EF3177 EF3258 OG1RF0176 (EF2352)d...”
• Functional genomics of Enterococcus faecalis: multiple novel genetic determinants for biofilm formation in the core genome
  Ballering, Journal of bacteriology 2009
  • “...EF1727 EF1755 EF1809 EF1626 EF1918 EF1978 EF2207 EF2570 EF2744 Glutamate 5-kinase UDP-N-acetylglucosamine pyrophosphorylase Conserved hypothetical protein...”
• Gliotoxin-mediated bacterial growth inhibition is caused by specific metal ion depletion
  Downes, Scientific reports 2023
  • “...methyltransferase RlmN Absent N/A 9 34.5 Q833B6 Putative 3-methyladenine DNA glycosylase Absent N/A 4 19.2 Q833H5 YitT family protein Absent N/A 5 21.2 Q833I6 Uncharacterized protein Absent N/A 3 63.3 Q833K1 Glycerol uptake facilitator protein Absent N/A 2 9.8 Q833L8 Phosphate transport system permease protein PstA...”

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Statistics

How It Works

PaperBLAST builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot, BRENDA, CAZy (as made available by dbCAN), BioLiP, CharProtDB, MetaCyc, EcoCyc, TCDB, REBASE, the Fitness Browser, and a subset of the European Nucleotide Archive with the /experiment tag. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E < 0.001.

To build the database, we query EuropePMC with locus tags, with RefSeq protein identifiers, and with UniProt accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use queries of the form "locus_tag AND genus_name" to try to ensure that the paper is actually discussing that gene. Because EuropePMC indexes most recent biomedical papers, even if they are not open access, some of the links may be to papers that you cannot read or that our computers cannot read. We query each of these identifiers that appears in the open access part of EuropePMC, as well as every locus tag that appears in the 500 most-referenced genomes, so that a gene may appear in the PaperBLAST results even though none of the papers that mention it are open access. We also incorporate text-mined links from EuropePMC that link open access articles to UniProt or RefSeq identifiers. (This yields some additional links because EuropePMC uses different heuristics for their text mining than we do.)

For every article that mentions a locus tag, a RefSeq protein identifier, or a UniProt accession, we try to select one or two snippets of text that refer to the protein. If we cannot get access to the full text, we try to select a snippet from the abstract, but unfortunately, unique identifiers such as locus tags are rarely provided in abstracts.

PaperBLAST also incorporates manually-curated protein functions:

• Proteins from NCBI's RefSeq are included if a GeneRIF entry links the gene to an article in PubMed^®. GeneRIF also provides a short summary of the article's claim about the protein, which is shown instead of a snippet.
• Proteins from Swiss-Prot (the curated part of UniProt) are included if the curators identified experimental evidence for the protein's function (evidence code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that describe the protein's function are shown (with bold headings).
• Proteins from BRENDA, a curated database of enzymes, are included if they are linked to a paper in PubMed and their full sequence is known.
• Every protein from the non-redundant subset of BioLiP, a database of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself does not include descriptions of the proteins, those are taken from the Protein Data Bank. Descriptions from PDB rely on the original submitter of the structure and cannot be updated by others, so they may be less reliable. (For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every ligand is represented among a group of structures with similar sequences, but for PaperBLAST, we use the non-redundant set provided by BioLiP.)
• Every protein from EcoCyc, a curated database of the proteins in Escherichia coli K-12, is included, regardless of whether they are characterized or not.
• Proteins from the MetaCyc metabolic pathway database are included if they are linked to a paper in PubMed and their full sequence is known.
• Proteins from the Transport Classification Database (TCDB) are included if they have known substrate(s), have reference(s), and are not described as uncharacterized or putative. (Some of the references are not visible on the PaperBLAST web site.)
• Every protein from CharProtDB, a database of experimentally characterized protein annotations, is included.
• Proteins from the CAZy database of carbohydrate-active enzymes are included if they are associated with an Enzyme Classification number. Even though CAZy does not provide links from individual protein sequences to papers, these should all be experimentally-characterized proteins.
• Proteins from the REBASE database of restriction enzymes are included if they have known specificity.
• Every protein with an evidence-based reannotation (based on mutant phenotypes) in the Fitness Browser is included.
• Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators) with experimentally-determined DNA binding sites from the PRODORIC database of gene regulation in prokaryotes.
• Putative transcription factors from RegPrecise that have manually-curated predictions for their binding sites. These predictions are based on conserved putative regulatory sites across genomes that contain similar transcription factors, so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
• Coding sequence (CDS) features from the European Nucleotide Archive (ENA) are included if the /experiment tag is set (implying that there is experimental evidence for the annotation), the nucleotide entry links to paper(s) in PubMed, and the nucleotide entry is from the STD data class (implying that these are targeted annotated sequences, not from shotgun sequencing). Also, to filter out genes whose transcription or translation was detected, but whose function was not studied, nucleotide entries or papers with more than 25 such proteins are excluded. Descriptions from ENA rely on the original submitter of the sequence and cannot be updated by others, so they may be less reliable.

Except for GeneRIF and ENA, the curated entries include a short curated description of the protein's function. For entries from BioLiP, the protein's function may not be known beyond binding to the ligand. Many of these entries also link to articles in PubMed.

For more information see the PaperBLAST paper (mSystems 2017) or the code. You can download PaperBLAST's database here.

Changes to PaperBLAST since the paper was written:

• November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
• February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
• June 2022: incorporated some coding sequences from ENA with the /experiment tag.
• March 2022: incorporated BioLiP.
• April 2020: incorporated TCDB.
• April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
• February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
• January 2018: incorporated BRENDA.
• December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
• September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.

Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.

Secrets

PaperBLAST cannot provide snippets for many of the papers that are published in non-open-access journals. This limitation applies even if the paper is marked as "free" on the publisher's web site and is available in PubmedCentral or EuropePMC. If a journal that you publish in is marked as "secret," please consider publishing elsewhere.

Omissions from the PaperBLAST Database

Many important articles are missing from PaperBLAST, either because the article's full text is not in EuropePMC (as for many older articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an article that characterizes a protein's function but is missing from PaperBLAST, please notify the curators at UniProt or add an entry to GeneRIF. Entries in either of these databases will eventually be incorporated into PaperBLAST. Note that to add an entry to UniProt, you will need to find the UniProt identifier for the protein. If the protein is not already in UniProt, you can ask them to create an entry. To add an entry to GeneRIF, you will need an NCBI Gene identifier, but unfortunately many prokaryotic proteins in RefSeq do not have corresponding Gene identifers.

References

PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.

Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.

Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.

UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.

BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.

The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.

CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.

The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.

The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.

REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.

Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.