PaperBLAST
PaperBLAST Hits for GFF6023 (75 a.a., VQVDRELDTR...)
Show query sequence
>GFF6023
VQVDRELDTRGLNCPLPILKAKKSLNEMASGQLLKVVSTDPGSIRDFQAFARQTGNELME
QETVGTDFIHVLKRR
Running BLASTp...
Found 42 similar proteins in the literature:
tusA / D3RPC0 TusA sulfur-carrier protein from Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D) (see 2 papers)
TUSA_ALLVD / D3RPC0 Sulfur carrier protein TusA from Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D) (Chromatium vinosum) (see 2 papers)
Alvin_2600 SirA family protein from Allochromatium vinosum DSM 180
63% identity, 93% coverage
- function: Sulfur carrier protein involved in sulfur trafficking for oxidative dissimilatory sulfur metabolism. Component of a sulfur relay system that starts with the sulfur-mobilizing rhodanese-like protein Rhd_2599 (Alvin_2599), which transfers the sulfur from a low-molecular- weight thiol, maybe glutathione, to the TusA protein (Alvin_2600); TusA serves as the sulfur donor for DsrEFH, which persulfurates DsrC; persulfurated DsrC very probably serves as a direct substrate for reverse-acting sulfite reductase, DsrAB. TusA seems to be not exclusively dedicated to sulfur oxidation and may have other important roles in the cell. Might also act as a sulfur mediator required for 2- thiouridine formation of tRNA.
subunit: Mostly a monomer, a small portion forms homodimer via intermolecular disulfide bonds. Tightly interacts with DsrEFH.
disruption phenotype: A mutant strain lacking rhd_2599, tusA and dsrE2, although not viable in liquid culture, is clearly sulfur oxidation negative upon growth on solid media containing sulfide, and shows massive accumulation of intercellular sulfur globules. - Evidence for autotrophic growth of purple sulfur bacteria using pyrite as electron and sulfur source
Alarcon, Applied and environmental microbiology 2024 - “...Biopolymer transport protein ExbD/TolR 135 Alvin_2551 2.64 5.0E-03 Photosynthetic reaction centre cytochrome c subunit 136 Alvin_2600 2.63 7.8E-23 SirA family protein 137 Alvin_0744 2.63 6.5E-11 Aigma54 specific transcriptional regulator, Fis family 138 Alvin_2432 2.62 8.7E-30 Triosephosphate isomerase 139 Alvin_0805 2.60 1.4E-23 2-Oxo-acid dehydrogenase E1 subunit, homodimeric...”
- The Complete Genome of a Novel Typical Species Thiocapsa bogorovii and Analysis of Its Central Metabolic Pathways
Petushkova, Microorganisms 2024 - “...the transfer of sulfur from a low-molecular-weight thiol (probably from glutathion) to the TusA protein (Alvin_2600); TusA serves as a sulfur donor for DsrEFH (genes Alvin_1253, Alvin_1254, and Alvin_1255), which in its turn perform the persulfation of DsrC (Alvin_1256); persulfated DsrC is likely to serve as...”
- A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex
Tanabe, Protein science : a publication of the Protein Society 2024 - “...Ts. sibirica (ThisiDRAFT_0966, according to JGI IMG); Tk, Thioalkalivibrio sp. K90mix (TK90_0631); Av, Ac. vinosum (Alvin_2600); Hd, Hm. denitrificans (Hden_0698); Aq, Aq. aeolicus (Aq_388a); Mc, Ms. cuprina (Mcup_0683). Triangles indicate the cysteines that were exchanged to serine in this work. Asterisk, fully conserved residues; colon, conservation...”
- A comparative quantitative proteomic study identifies new proteins relevant for sulfur oxidation in the purple sulfur bacterium Allochromatium vinosum
Weissgerber, Applied and environmental microbiology 2014 - “...from the low-molecular-weight thiol to the TusA protein (Alvin_2600). TusA serves as a sulfur donor for DsrEFH, which persulfurates DsrC. The latter very...”
- “...rhodanese-like protein Alvin_ 2599, A. vinosum TusA (Alvin_2600), and possibly also the membrane-bound DsrE2 protein (Alvin_2601) as components of a cytoplasmic...”
- Thiosulfate transfer mediated by DsrE/TusA homologs from acidothermophilic sulfur-oxidizing archaeon Metallosphaera cuprina
Liu, The Journal of biological chemistry 2014 - “...(88% coverage) and 34% (91% coverage) identity to TusA (AFE_2557) of A. ferrooxidans and TusA (Alvin_2600) of A. vinosum , respectively. Cloning, Site-directed Mutagenesis, and Expression of dsrE2B, dsrE3A, and tusA from M. cuprina in E. coli N-terminally His-tagged DsrE3A (Mcup_0681), DsrE2B (Mcup_0682), and TusA (Mcup_0683)...”
- New proteins involved in sulfur trafficking in the cytoplasm of Allochromatium vinosum
Stockdreher, The Journal of biological chemistry 2014 - “...Proteins--For the amplification of the Alvin_2599 (rhd_2599), Alvin_2600 (tusA), and Alvin_2601 (dsrE2) genes, genomic DNA of A. vinosum served as the...”
- “...no extra copies for tusA or tusBCD apart from Alvin_2600 and dsrEFH, respectively. The tusE homolog dsrC is present with five genomic copies. This implies that...”
- Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds
Weissgerber, Journal of bacteriology 2013 - “...and approximately 150-bp fragments of Alvin_0258, Alvin_2600, Alvin_2601, Alvin_3028, and the reference locus, Alvin_0486, encoding a uroporphyrinogen...”
- “...Alvin_2500 Alvin_2501 Alvin_2507 Alvin_2515 Alvin_2572 Alvin_2600 Alvin_2601 Alvin_2651 Alvin_2661 Alvin_2667 Alvin_2705 Alvin_2962 Alvin_2965 Alvin_2980...”
TK90_0631 SirA family protein from Thioalkalivibrio sp. K90mix
61% identity, 93% coverage
- A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex
Tanabe, Protein science : a publication of the Protein Society 2024 - “...YeeD, and b2012); Ts, Ts. sibirica (ThisiDRAFT_0966, according to JGI IMG); Tk, Thioalkalivibrio sp. K90mix (TK90_0631); Av, Ac. vinosum (Alvin_2600); Hd, Hm. denitrificans (Hden_0698); Aq, Aq. aeolicus (Aq_388a); Mc, Ms. cuprina (Mcup_0683). Triangles indicate the cysteines that were exchanged to serine in this work. Asterisk, fully...”
- Complete genome sequence of Thioalkalivibrio sp. K90mix
Muyzer, Standards in genomic sciences 2011 - “...]. However, we found a gene cluster encoding two sulfur transferases ( rhd, TK90_0630; sirA, TK90_0631) and a heterodisulfide reductase complex (TK90_0632 - TK90_0637) consisting of hdrA, hdrB, and hdrC ( Figure 6 ). dsrE was missing in this cascade, but was present at 3 other...”
AFE_2557 sulfurtransferase TusA family protein from Acidithiobacillus ferrooxidans ATCC 23270
58% identity, 97% coverage
- Proteomics Reveal Enhanced Oxidative Stress Responses and Metabolic Adaptation in Acidithiobacillus ferrooxidans Biofilm Cells on Pyrite
Bellenberg, Frontiers in microbiology 2019 - “...forming biofilms ( Mamani et al., 2016 ). Furthermore, in those cells a transcriptional regulator (AFE_2557), located in genomic context of sulfur metabolism related genes (AFE_2547AFE_2558) was found to be enhanced. This protein seems to be unique in Acidithiobacillus. A LysR family transcriptional regulator (AFE_0135), a...”
- Thiosulfate transfer mediated by DsrE/TusA homologs from acidothermophilic sulfur-oxidizing archaeon Metallosphaera cuprina
Liu, The Journal of biological chemistry 2014 - “...of M. cuprina Ar-4 has 39% (88% coverage) and 34% (91% coverage) identity to TusA (AFE_2557) of A. ferrooxidans and TusA (Alvin_2600) of A. vinosum , respectively. Cloning, Site-directed Mutagenesis, and Expression of dsrE2B, dsrE3A, and tusA from M. cuprina in E. coli N-terminally His-tagged DsrE3A...”
- New proteins involved in sulfur trafficking in the cytoplasm of Allochromatium vinosum
Stockdreher, The Journal of biological chemistry 2014 - “...conditions (8). In A. ferrooxidans the tusA gene (AFE_2557) is flanked in the same direction of transcription by two genes encoding a rhodanese-like protein...”
- Anaerobic sulfur metabolism coupled to dissimilatory iron reduction in the extremophile Acidithiobacillus ferrooxidans
Osorio, Applied and environmental microbiology 2013 - “...b (EC 3.6.3.14) ATP synthase C chain AFE_2556 1.3 AFE_2557 AFE_2177 AFE_2178 AFE_2179 AFE_2181 AFE_3207 AFE_3208 0.9 Fe3 O2 Fe3 O2 Fe3 O2 Fe3 O2 Unique Unique...”
- “...material). In contrast, both dsrE (AFE_2556) and tusA (AFE_2557) were upregulated during anaerobic growth on S0. Although it has not been experimentally...”
- Extending the models for iron and sulfur oxidation in the extreme acidophile Acidithiobacillus ferrooxidans
Quatrini, BMC genomics 2009 - “...hdrB heterodisulfide reductase subunit B, homolog -1,5 0,00* AFE_2558 rhd rhodanese-like domain protein 0,1 0,38 AFE_2557 tusA conserved hypothetical protein -2,4 0,00* AFE_2556 dsrE conserved hypothetical protein -2,1 0,00* AFE_2555 hdrC iron-sulfur cluster-binding protein -2,1 0,00* AFE_2554 hdrB heterodisulfide reductase subunit B, homolog -2,0 0,00* AFE_2553...”
- “...cytoplasmic rhodanase-related sulfurtransferase (AFE_2558, COG0607) [ 60 ], a cytoplasmic SirA-like disulfide bond formation regulator (AFE_2557, pfam01206, COG0425, IPR001455) and an inner membrane located peroxiredoxin of the DrsE superfamily (AFE_2556, COG2210 and 2044). The rhodanase AFE_2558 is 48% similar to the Sud protein from Wolinella succinogenes...”
Acaty_c2197 sulfurtransferase TusA family protein from Acidithiobacillus caldus ATCC 51756
55% identity, 97% coverage
Dsui_0002 sulfurtransferase TusA family protein from Azospira oryzae PS
63% identity, 96% coverage
WP_038092630 sulfurtransferase TusA family protein from Acidihalobacter prosperus
51% identity, 100% coverage
Pnuc_1718 SirA family protein from Polynucleobacter sp. QLW-P1DMWA-1
52% identity, 93% coverage
PSPTO_3957 conserved hypothetical protein from Pseudomonas syringae pv. tomato str. DC3000
WP_011104802 sulfurtransferase TusA family protein from Pseudomonas syringae pv. persicae
54% identity, 87% coverage
- The conserved hypothetical protein PSPTO_3957 is essential for virulence in the plant pathogen Pseudomonas syringae pv. tomato DC3000
D'Amico, FEMS microbiology letters 2017 (PubMed)- “...PSPTO_3957 is essential for virulence in the plant pathogen Pseudomonas syringae pv. tomato DC3000 Katherine D'Amico1,2 and Melanie J. Filiatrault1,2* 1 School of Integrative Plant Science, Section of...”
- “...been demonstrated to play important roles in disease. PSPTO_3957 encodes a conserved hypothetical protein of unknown function. To evaluate the role of...”
- Nitric Oxide Accumulation: The Evolutionary Trigger for Phytopathogenesis
Santana, Frontiers in microbiology 2017 - “...reduced virulence. Also, DAmico and Filiatrault (2017) demonstrated that a hypothetical protein of unknown function PSPTO_3957 was necessary for nitrate assimilation and full virulence in the plant pathogen Pseudomonas syringae . However, NO production via the denitrification pathway during pathogenic processes on plants has been poorly...”
- “.... 10.1128/mBio.02471-14 25784703 DAmico K. Filiatrault M. J. ( 2017 ). The conserved hypothetical protein PSPTO_3957 is essential for virulence in the plant pathogen Pseudomonas syringae pv. tomato DC3000. FEMS Microbiol. Lett. 364 : fnx004 . 10.1093/femsle/fnx004 28073812 Daval S. Lebreton L. Gazengel K. Boutin M....”
- Substrate and target sequence length influence RecTE(Psy) recombineering efficiency in Pseudomonas syringae
Bao, PloS one 2012 - “...flank substrate and included 1.0 g or 2.0 g of non-homologous double stranded PCR product (PSPTO_3957) or ssDNA oligonucleotides (oSWC1447) as carrier. The addition of carrier did not increase the recombination frequency (data not shown), suggesting that degradation is not responsible for the different recombination frequencies...”
- The conserved hypothetical protein PSPTO_3957 is essential for virulence in the plant pathogen Pseudomonas syringae pv. tomato DC3000.
D'Amico, FEMS microbiology letters 2017 (PubMed)- GeneRIF: findings show that PSPTO_3957 does not influence growth on rich media, motility or biofilm formation but is necessary for nitrate assimilation and full virulence
PA1006 hypothetical protein from Pseudomonas aeruginosa PAO1
52% identity, 88% coverage
- Unraveling bacterial stress responses: implications for next-generation antimicrobial solutions
Avci, World journal of microbiology & biotechnology 2024 - “...et al. 2007 ), and moeB1 (MacGurn and Cox 2007 ) in M. tuberculosis , PA1006 in P. aeruginosa (Filiatrault et al. 2013 ), and mobAB in E. coli (Zhang et al. 2019 ) have been shown to cause significantly reduced fitness or virulence. Although, there...”
- “...Res Microb Sci 3:100111. 10.1016/j.crmicr.2022.100111 35199072 10.1016/j.crmicr.2022.100111 Filiatrault MJ Tombline G Wagner VE Pseudomonas aeruginosa PA1006, which plays a role in Molybdenum Homeostasis, is required for nitrate utilization, Biofilm formation, and virulence PLoS ONE 2013 8 e55594 10.1371/journal.pone.0055594 23409004 Filiatrault MJ, Tombline G, Wagner VE et...”
- YeeD is an essential partner for YeeE-mediated thiosulfate uptake in bacteria and regulates thiosulfate ion decomposition
Ikei, PLoS biology 2024 - “...the purification process, the persulfide modification was also found by MS in purified Pseudomonas aeruginosa PA1006, an ortholog of E . coli TusA [ 20 ], which has one conserved cysteine residue corresponding to C17 of St YeeD. The third 77.0 m/z-increased peak (11,394.3 m/z) may...”
- “...is a membrane protein, unlike other TusA family proteins. Previously, the conserved cysteine residue of PA1006 was reported to be persulfide-modified [ 20 ]. Furthermore, St YeeD has several different sulfur-related modification statuses, including persulfide modification, perthiosulfonic acid, and thiosulfonate ( Fig 2D and 2F2H )....”
- A Selective Culture Medium for Screening Cefiderocol Resistance in Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii
Ibrahim, Journal of clinical microbiology 2023 (secret) - Pseudomonas aeruginosa Initiates a Rapid and Specific Transcriptional Response during Surface Attachment
Jones, Journal of bacteriology 2022 - “...levels under both aerobic and anaerobic conditions ( 49 ). Of note, a P. aeruginosa PA1006 mutant is deficient in biofilm formation ( 46 ). PA1006 is a TusA- or SirA-like protein required for nitrate utilization under anaerobic growth and for the homeostasis of molybdopterin biosynthesis...”
- “...K , Sokol P , Schwingel J , Iglewski BH . 2013 . Pseudomonas aeruginosa PA1006, which plays a role in molybdenum homeostasis, is required for nitrate utilization, biofilm formation, and virulence . PLoS One 8 : e55594 . 10.1371/journal.pone.0055594 . 23409004 47 Fritz C ,...”
- Resolving the Multidecade-Long Mystery in MoaA Radical SAM Enzyme Reveals New Opportunities to Tackle Human Health Problems
Yokoyama, ACS bio & med chem Au 2022 - “..., 34 Consistent with the significance of NarG, a mutation in a sulfide carrier protein (PA1006) involved in the MPT biosynthesis significantly diminished the virulence and biofilm formation. 35 , 36 While the amount of Moco production was not quantified, the involvement of PA1006 in Moco...”
- “...the other Moco biosynthesis enzymes and the significantly reduced level of nitrate assimilation in the PA1006 gene knockout strain. 35 Still, the mutation in PA1006 unlikely resulted in the complete loss of Moco production considering the presence of multiple sulfide carrier proteins in P. aeruginosa and...”
- Roles of Type VI Secretion System in Transport of Metal Ions
Yang, Frontiers in microbiology 2021 - “...bacterial competition under anaerobic conditions. Studies have shown that the molybdenum homeostasis of P. aeruginosa PA1006 is necessary for nitrate utilization, biofilm formation, and virulence ( Filiatrault et al., 2013 ; Tombline et al., 2013 ). In a mouse model of acute pneumonia, the P ....”
- “...Wagner V. E. Van Alst N. Rumbaugh K. Sokol P. ( 2013 ). Pseudomonas aeruginosa PA1006, which plays a role in molybdenum homeostasis, is required for nitrate utilization, biofilm formation, and virulence. PLoS One 8 : e55594 . 10.1371/journal.pone.0055594 23409004 Forbes J. R. Gros P. (...”
- Molybdenum Enzymes and How They Support Virulence in Pathogenic Bacteria
Zhong, Frontiers in microbiology 2020 - “...et al., 2014 moeB1 Mycobacterium tuberculosis Transposon mutant Macrophage infection ++ MacGurn and Cox, 2007 PA1006 ( tusA homolog) Pseudomonas aeruginosa Isogenic mutant Burned mouse model; rat lung infection ++ Filiatrault et al., 2013 Mo-bisPGD synthesis mobAB Escherichia coli Transposon mutant Mouse and duck systemic infection...”
- “...Cox, 2007 ; Filiatrault et al., 2013 ). A P. aeruginosa strain lacking the TusA-related PA1006 protein, which is part of the resulfurase complex (Kozmin et al., 2013 ), exhibited an ~10-fold reduction in cytoplasmic and membrane fraction molybdate concentrations, as well as impaired biofilm formation...”
- The conserved hypothetical protein PSPTO_3957 is essential for virulence in the plant pathogen Pseudomonas syringae pv. tomato DC3000
D'Amico, FEMS microbiology letters 2017 (PubMed)- “...Email: Melanie.filiatrault@ars.usda.gov Keywords: Pseudomonas syringae, PA1006, nitrate assimilation, molybdopterin, virulence, tomato 1 ABSTRACT The plant...”
- “...molybdenum as well as iron-sulfur clusters for their activity. PA1006 is a gene in P. aeruginosa that codes for a persulfide-modified protein and interacts with...”
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MHY1_00072 sulfurtransferase TusA family protein from Methylovirgula sp. HY1
59% identity, 79% coverage
- Sulfur and methane oxidation by a single microorganism
Gwak, Proceedings of the National Academy of Sciences of the United States of America 2022 - “...sulfur never occurs in free form, but is handled by further sulfurtransferases, such as TusA (MHY1_00072) and DsrEFH (MHY1_0008183), and treated by the concerted action of dsr -encoded enzymes ( Fig. 4 ) ( 49 , 50 , 67 ). Fully in line with this concept,...”
PP1233, PP_1233 conserved hypothetical protein from Pseudomonas putida KT2440
47% identity, 94% coverage
Hden_0698 sulfurtransferase TusA family protein from Hyphomicrobium denitrificans ATCC 51888
52% identity, 84% coverage
- A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex
Tanabe, Protein science : a publication of the Protein Society 2024 - “...to JGI IMG); Tk, Thioalkalivibrio sp. K90mix (TK90_0631); Av, Ac. vinosum (Alvin_2600); Hd, Hm. denitrificans (Hden_0698); Aq, Aq. aeolicus (Aq_388a); Mc, Ms. cuprina (Mcup_0683). Triangles indicate the cysteines that were exchanged to serine in this work. Asterisk, fully conserved residues; colon, conservation between groups of strongly...”
- In the Alphaproteobacterium Hyphomicrobium denitrificans SoxR Serves a Sulfane Sulfur-Responsive Repressor of Sulfur Oxidation
Li, Antioxidants (Basel, Switzerland) 2023 - “...between the lipX (Hden_0687) and dsrE3C (Hden_0688) genes, a 176-bp fragment located between the tusA (Hden_0698) and hyp (Hden_0697) genes, and a 151-bp fragment situated between the soxA (Hden_0703) and soxY (Hden_0704) genes. All primers used are listed in Table S1 . Native 6% polyacrylamide gels...”
WP_004375233 sulfurtransferase TusA family protein from Pseudomonas sp. LSJ-87
47% identity, 94% coverage
BSU26500 hypothetical protein from Bacillus subtilis subsp. subtilis str. 168
43% identity, 87% coverage
BSU26530 putative rhodanese-related sulfur transferase from Bacillus subtilis subsp. subtilis str. 168
40% identity, 37% coverage
BAS0738 rhodanese domain protein from Bacillus anthracis str. Sterne
35% identity, 40% coverage
BT_2434 pyridine nucleotide-disulphide oxidoreductase from Bacteroides thetaiotaomicron VPI-5482
43% identity, 8% coverage
PG0174 pyridine nucleotide-disulphide oxidoreductase family protein from Porphyromonas gingivalis W83
47% identity, 6% coverage
PGN_0285 pyridine nucleotide-disulphide oxidoreductase from Porphyromonas gingivalis ATCC 33277
47% identity, 7% coverage
- Metabolic plasticity enables lifestyle transitions of Porphyromonas gingivalis
Moradali, NPJ biofilms and microbiomes 2021 - “...of the Na + -translocating NADH:quinone oxidoreductase (Na + NQR; PGN_0116-0118), NADH oxidoreductases (possibly including PGN_0285, an uncharacterized NAD(FAD)-dependent dehydrogenase), and cytochrome bd ubiquinol oxidases (PGN_1041-42), which also mediate the engagement with the metabolism of pyruvate and lactate (Fig. 4c ; see Discussion for the proposed...”
- Regulon controlled by the GppX hybrid two component system in Porphyromonas gingivalis
Hirano, Molecular oral microbiology 2013 - “...0.81 0.01 PGN_1749 probable NADPH-quinone reductase 0.78 0.02 PGN_2013 cation efflux system protein 0.77 0.01 PGN_0285 pyridine nucleotide-disulphide oxidoreductase 0.77 0.02 PGN_0809 putative TonB protein 0.75 0.05 PGN_1750 putative 3-deoxy-D-manno-octulosonate cytidylyltransferase 0.75 0.04 PGN_2036 hypothetical protein 0.71 0.02 PGN_2085 putative Fe-S oxidoreductases 0.70 0.05 PGN_1061 hypothetical...”
LGS26_02870 sulfurtransferase TusA family protein from Dissulfurimicrobium hydrothermale
37% identity, 87% coverage
PA1564 hypothetical protein from Pseudomonas aeruginosa PAO1
36% identity, 94% coverage
- Pseudomonas aeruginosa PA1006 is a persulfide-modified protein that is critical for molybdenum homeostasis
Tombline, PloS one 2013 - “...yhhP/tusA , yedF , and yeeD genes. In Pae , in addition to PA1006 , PA1564 and PA3632 are also present. These proteins do not appear to be functionally redundant in either organism since mutation of either the yhhP/tusA gene in E. coli [10] , [11]...”
- “...elicits a phenotype that is not suppressed by the other orthologs. Moreover, unlike PA1006 , PA1564 appears to be essential in Pae strain PAO1 since several attempts to delete it failed, and PA3632 is not required for anaerobic growth with nitrate (data not shown). 10.1371/journal.pone.0055593.g001 Figure...”
- Pseudomonas aeruginosa PA1006, which plays a role in molybdenum homeostasis, is required for nitrate utilization, biofilm formation, and virulence
Filiatrault, PloS one 2013 - “...tRNAs [23] . PA1006 is also not the functional homolog of E. coli YhhP/TusA. Rather, PA1564 appears to be the equivalent (see alignment in Figure 1 of [24] ). E. coli YhhP/TusA mutants are barely viable, showing a severe growth arrest phenotype due to filamentation [24]...”
- Quorum-sensing antagonistic activities of azithromycin in Pseudomonas aeruginosa PAO1: a global approach
Nalca, Antimicrobial agents and chemotherapy 2006 - “...PA0650 PA0651 PA0805 PA0943 PA0996 PA1440 PA1493d PA1494 PA1564 PA1696b PA1706 b,d PA1707b PA1708b PA1709 b PA1710 b PA1711b PA1712b PA1714b PA1715b PA1754...”
M9U7N8 Putative redox protein, regulator of disulfidebond formation from Sulfolobus islandicus LAL14/1
34% identity, 92% coverage
Mcup_0683 sulfurtransferase TusA family protein from Metallosphaera cuprina Ar-4
35% identity, 75% coverage
- A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex
Tanabe, Protein science : a publication of the Protein Society 2024 - “...Av, Ac. vinosum (Alvin_2600); Hd, Hm. denitrificans (Hden_0698); Aq, Aq. aeolicus (Aq_388a); Mc, Ms. cuprina (Mcup_0683). Triangles indicate the cysteines that were exchanged to serine in this work. Asterisk, fully conserved residues; colon, conservation between groups of strongly similar properties; dot, conservation between groups of weakly...”
- Thiosulfate transfer mediated by DsrE/TusA homologs from acidothermophilic sulfur-oxidizing archaeon Metallosphaera cuprina
Liu, The Journal of biological chemistry 2014 - “...for a potential sulfide:quinone oxidoreductase (Mcup_1723) and TusA (Mcup_1722). Mcup_0682 and a further tusA homolog (Mcup_0683) immediately precede the hdrC1B1AhyphdrC2B2 cluster ( Fig. 2 B ). Mcup_0681 is transcribed in the opposite direction to Mcup_0682 and resides upstream of a genetic cluster that encodes a putative...”
- “...had 34% (100% coverage) and 35% (86% coverage) identity to AFE_2556 and Alvin_2601, respectively. TusA (Mcup_0683) of M. cuprina Ar-4 has 39% (88% coverage) and 34% (91% coverage) identity to TusA (AFE_2557) of A. ferrooxidans and TusA (Alvin_2600) of A. vinosum , respectively. Cloning, Site-directed Mutagenesis,...”
L21SP2_0797 FAD-dependent oxidoreductase from Salinispira pacifica
36% identity, 8% coverage
GF1_30700 sulfurtransferase TusA family protein from Desulfolithobacter dissulfuricans
41% identity, 76% coverage
BF638R_0572 FAD-dependent oxidoreductase from Bacteroides fragilis 638R
35% identity, 8% coverage
- Deletion of BmoR affects the expression of genes related to thiol/disulfide balance in Bacteroides fragilis
Teixeira, Scientific reports 2018 - “...phenotype of the isogenic bmoR mutant was also evaluated. Our results show that BmoR regulates BF638R_0572 and the trxP operon, a set of genes involved in the maintenance of intracellular redox state, particularly the thiol/disulfide balance of the cell. Results Deletion of bmoR severely impacts the...”
- “...). The most expressive change (11-fold upregulation in the mutant strain) was in the gene BF638R_0572, located directly upstream of bmoR . Besides BF638R_0572, most of the genes altered in this condition were related to LPS biosynthesis and carbohydrates metabolism. The most expressive changes (>5-fold upregulation...”
BC0795 Molybdopterin biosynthesis MoeB protein from Bacillus cereus ATCC 14579
32% identity, 84% coverage
BAS0740 conserved hypothetical protein from Bacillus anthracis str. Sterne
34% identity, 86% coverage
YP_3227 cell developmental protein SirA from Yersinia pestis biovar Medievalis str. 91001
32% identity, 85% coverage
NT01EI_0022 hypothetical protein from Edwardsiella ictaluri 93-146
32% identity, 87% coverage
- Transposon mutagenesis and identification of mutated genes in growth-delayed Edwardsiella ictaluri
Kalindamar, BMC microbiology 2019 - “...Ribonuclease, RNaseE/RNaseG family 2.00E-04 72 Eis157 NT01EI_0144 Twin-arginine translocation protein subunit TatB 8.00E-07 13 Eis158 NT01EI_0022 Sulfurtransferase, TusA 8.00E-46 10 Eis171 NT01EI_3723 Magnesium-translocating P-type ATPase 0 71 Eis172 NT01EI_3786 Hypothetical protein 1.00E-26 24 Eis173 NT01EI_3265 Acyltransferase/AMP-dependent synthetase and ligase family 0 2 54 Eis174 NT01EI_3721 Hypothetical...”
SA0044 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SERP2515 rhodanese-like domain protein from Staphylococcus epidermidis RP62A
42% identity, 16% coverage
- Cis-encoded non-coding antisense RNAs in streptococci and other low GC Gram (+) bacterial pathogens
Cho, Frontiers in genetics 2015 - “...2010 Teg6as SA0025 405 Teg7as SA0027 and SA0026 36 Teg8as SAS002 and SA0028 84 Teg10as SA0044 42 Teg14as SA0062 143 Teg15as SA0097 and SA0098 72 Teg16as SA0101 and SA0100 81 Teg17as capM 108 Teg18as SA0306 864 Teg19as SA0412 and SA0413 2475 Teg20as SA0620 1008 Teg21as SA1825...”
- Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis
Méric, Genome biology and evolution 2015 - “...181 142 0.521 2,519,564 SERP1460 blaR1-1 Beta-lactamase regulatory sensor-transducer BlaR1 132 115 0.513 1,526,822 SERP2515 SA0044 Disulfide bond regulator 124 111 0.468 2,571,330 SERP0265 Mobile element protein 173 142 0.462 272,732 SAR2595 SA2303, SE0213 Membrane spanning protein 181 61 0.443 2,680,724 SERP2520 mecR1 Methicillin resistance regulatory...”
- Comparative genomic analysis of European and Middle Eastern community-associated methicillin-resistant Staphylococcus aureus (CC80:ST80-IV) isolates by high-density microarray
Goering, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2009 - “...+ USA300+ USA400+ SA0043 Hypothetical protein pathogenicity island SaPIn1 + + + + USA300+ USA400+ SA0044 Conserved hypothetical protein + + + + USA300 USA400 SA0022 Hypothetical protein (N315) + + + USA300 USA400 ccrB SA0057 Cassette chromosome recombinase B (N315) + + + + USA300+...”
- Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis
Méric, Genome biology and evolution 2015 - “...lipoprotein 181 142 0.521 2,519,564 SERP1460 blaR1-1 Beta-lactamase regulatory sensor-transducer BlaR1 132 115 0.513 1,526,822 SERP2515 SA0044 Disulfide bond regulator 124 111 0.468 2,571,330 SERP0265 Mobile element protein 173 142 0.462 272,732 SAR2595 SA2303, SE0213 Membrane spanning protein 181 61 0.443 2,680,724 SERP2520 mecR1 Methicillin resistance...”
- Novel staphylococcal cassette chromosome mec type, tentatively designated type VIII, harboring class A mec and type 4 ccr gene complexes in a Canadian epidemic strain of methicillin-resistant Staphylococcus aureus
Zhang, Antimicrobial agents and chemotherapy 2009 - “...(RP62A) SERP2517 (RP62A) SERP2516 (RP62A) SERP2516 (RP62A) SERP2515 (RP62A) SERP2514 (RP62A) SERP2513 (RP62A) SERP2512 (RP62A) SERP2511 (RP62A) SERP2510 (RP62A)...”
tusA / P0A890 sulfur transfer protein TusA from Escherichia coli (strain K12) (see 12 papers)
TUSA_ECOLI / P0A890 Sulfur carrier protein TusA; Sulfur mediator TusA; Sulfur transfer protein TusA; tRNA 2-thiouridine synthesizing protein A from Escherichia coli (strain K12) (see 4 papers)
TUSA_ECO57 / P0A892 Sulfur carrier protein TusA; Sulfur mediator TusA; Sulfur transfer protein TusA; tRNA 2-thiouridine synthesizing protein A from Escherichia coli O157:H7 (see paper)
tusA sulfurtransferase TusA; EC 2.8.1; EC 2.8.1.- from Escherichia coli K12 (see 7 papers)
B21_RS17320 sulfurtransferase TusA from Escherichia coli BL21(DE3)
NP_417927 sulfur transfer protein TusA from Escherichia coli str. K-12 substr. MG1655
UTI89_C3986 possible RNA-binding protein required for wild-type FtsZ ring formation on rich media from Escherichia coli UTI89
b3470 cell developmental protein SirA from Escherichia coli str. K-12 substr. MG1655
31% identity, 88% coverage
- function: Sulfur carrier protein involved in sulfur trafficking in the cell. Part of a sulfur-relay system required for 2-thiolation during synthesis of 2-thiouridine of the modified wobble base 5- methylaminomethyl-2-thiouridine (mnm(5)s(2)U) in tRNA (PubMed:16387657). Interacts with IscS and stimulates its cysteine desulfurase activity (PubMed:16387657, PubMed:23281480). Accepts an activated sulfur from IscS, which is then transferred to TusD, and thus determines the direction of sulfur flow from IscS to 2-thiouridine formation (PubMed:16387657). Also appears to be involved in sulfur transfer for the biosynthesis of molybdopterin (PubMed:23281480). Seems to affect the stability of sigma-S, particularly during the logarithmic growth phase (PubMed:9555915).
subunit: Interacts with IscS.
disruption phenotype: Cells lacking this gene are not capable of growing in standard laboratory rich medium (i.e., Luria broth), and show filamentous shape (PubMed:9555915). FtsZ-ring formation appears to be severely impaired in tusA-deficient cells, resulting in the formation of a non-divided filamentous cell (PubMed:10830496). A tusA deletion mutant lacks the 2-thio modification of mnm5s2U in tRNA and has a severe growth defect (PubMed:16387657). Deletion of tusA has a pleiotropic effect on transcription, including increased expression of molybdenum cofactor biosynthesis genes (moaABCDE operon), but leads to reduced activity of molybdoenzymes, an overall low molybdopterin content and an accumulation of the molybdopterin precursor cyclic pyranopterin monophopshate (cPMP) (PubMed:23281480). - function: Sulfur carrier protein involved in sulfur trafficking in the cell. Part of a sulfur-relay system required for 2-thiolation during synthesis of 2-thiouridine of the modified wobble base 5- methylaminomethyl-2-thiouridine (mnm(5)s(2)U) in tRNA. Interacts with IscS and stimulates its cysteine desulfurase activity. Accepts an activated sulfur from IscS, which is then transferred to TusD, and thus determines the direction of sulfur flow from IscS to 2-thiouridine formation. Also appears to be involved in sulfur transfer for the biosynthesis of molybdopterin.
subunit: Forms a heterotetramer with IscS. Certain pairs of proteins can bind simultaneously to IscS but TusA does not seem to be one of them. IscU can displace TusA from IscS. - Cross-Kingdom Comparative Transcriptomics Reveals Conserved Genetic Modules in Response to Cadmium Stress
Chen, mSystems 2021 - “...involved in metal transport (B21_RS09935 and B21_RS17315), ferric iron import (B21_RS02785 and B21_RS22395), sulfur metabolism (B21_RS17320, B21_RS13610, B21_RS13605, B21_RS13600, and B21_RS07750), stress response (B21_RS19915), sugar import (B21_RS20540, B21_RS20565, and B21_RS21625), cell wall remodeling (B21_RS05900), and energy production and conversion (B21_RS21615) ( Fig.2A ). In S. cerevisiae...”
- The sulfur carrier protein TusA has a pleiotropic role in Escherichia coli that also affects molybdenum cofactor biosynthesis.
Dahl, The Journal of biological chemistry 2013 - GeneRIF: sulfur carrier protein TusA has a pleiotropic role in Escherichia coli that also affects molybdenum cofactor biosynthesis
- TusA (YhhP) and IscS are required for molybdenum cofactor-dependent base-analog detoxification.
Kozmin, MicrobiologyOpen 2013 - GeneRIF: TusA (YhhP) and IscS are required for molybdenum cofactor-dependent base-analog detoxification.
- Structural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions.
Shi, PLoS biology 2010 - GeneRIF: study determined the crystal structures of IscS-IscU and IscS-TusA complexes providing the first insight into their different modes of binding and the mechanism of sulfur transfer
- Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections
García, Microbial genomics 2021 - “...Outer membrane protein A Ion transport/host-virus interaction/conjugation (M) 2.20 UTI89_C3110 UTI89_C3110 Hypothetical protein (NI) 2.19 UTI89_C3986 sira (tusA) Possible RNA-binding protein required for wild-type FtsZ ring formation on rich media tRNA processing (J) 2.18 UTI89_C2311 rfbD dTDP-4-dehydrorhamnose reductase LPS biosynthesis (F) 2.12 UTI89_C2826 guaB Inosine-5'-monophosphate dehydrogenase...”
- A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex
Tanabe, Protein science : a publication of the Protein Society 2024 - “...TusA and related proteins from sulfur oxidizers and E. coli . Ec, E. coli (TusA, b3470, YedF, b1930, YeeD, and b2012); Ts, Ts. sibirica (ThisiDRAFT_0966, according to JGI IMG); Tk, Thioalkalivibrio sp. K90mix (TK90_0631); Av, Ac. vinosum (Alvin_2600); Hd, Hm. denitrificans (Hden_0698); Aq, Aq. aeolicus (Aq_388a);...”
- The sulfur carrier protein TusA has a pleiotropic role in Escherichia coli that also affects molybdenum cofactor biosynthesis
Dahl, The Journal of biological chemistry 2013 - “...protein 2-thiouridine formation b1133 b3343 b3470 mnmA tusB tusA tRNA-specific 2-thiouridylase 2-Thiouridine-synthesizing protein B 2-Thiouridine-synthesizing...”
ABUW_3504 sulfurtransferase TusA from Acinetobacter baumannii
36% identity, 69% coverage
Pcar_0429 uncharacterized NAD(FAD)-dependent dehydrogenase from Pelobacter carbinolicus str. DSM 2380
39% identity, 6% coverage
- The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features
Aklujkar, BMC genomics 2012 - “...involve two periplasmic thioredoxins (Pcar_0426, Pcar_0427), an outer membrane protein (Pcar_0428), and a cytoplasmic oxidoreductase (Pcar_0429) encoded by the most highly upregulated genes [ 9 ]. As the elemental form of S, circular S 8 , is insoluble, it is thought to react extracellularly with sulfide,...”
- “...yield no energy. A more economical S reductase must exist: either a cytoplasmic NADH-dependent enzyme (Pcar_0429) or a periplasmic c 7 -type cytochrome ( ppcA Pcar_1628), which reduces S in the related species Desulfuromonas acetoxidans [ 67 ]. Another role of CcdA is to reduce apocytochrome...”
- Turnover-dependent covalent inactivation of Staphylococcus aureus coenzyme A-disulfide reductase by coenzyme A-mimetics: mechanistic and structural insights
Wallace, Biochemistry 2012 - “...Shewanella loihica ( 10 ) and the Pelobacter carbinolicus NAD(FAD)-dependent dehydrogenase isoform encoded by the Pcar_0429 locus ( 11 ). In spite of clear similarities with regard to the reactions that they catalyze, the CoADR enzymes are mechanistically distinct from the D i s ulfide R...”
- Crystal structure and catalytic properties of Bacillus anthracis CoADR-RHD: implications for flavin-linked sulfur trafficking
Wallen, Biochemistry 2009 - “...in sulfur transfer for the DsrE domain as well, in this third CoADR isoform; the Pcar_0429 gene encoding P. carbinolicus CoADR-RHD-SirA-DsrE was upregulated over 20-fold during sulfur-dependent growth on Fe(III), compared with fermentative growth on acetoin ( 49 ). This is consistent with a possible function...”
- Genome-wide gene expression patterns and growth requirements suggest that Pelobacter carbinolicus reduces Fe(III) indirectly via sulfide production
Haveman, Applied and environmental microbiology 2008 - “...growth on Fe(III) were in the cluster Pcar_0426 to Pcar_0429 (Table 3). The same orientation and similar increase in expression of these adjacent genes suggest...”
- “...and longchain fatty acid transport (5, 56). Pcar_0429 is annotated as an uncharacterized NAD(FAD)-dependent dehydrogenase. The N-terminal domain of Pcar_0429...”
CS401_RS08470 CoA-disulfide reductase from Fusobacterium vincentii
39% identity, 7% coverage
- Porphyromonas gingivalis diffusible signaling molecules enhance Fusobacterium nucleatum biofilm formation via gene expression modulation
Yamaguchi-Kuroda, Journal of oral microbiology 2023 - “...4.496 CS401_RS07440 Queuosine precursor transporter 4.47 CS401_RS07445 Radical SAM protein 4.342 CS401_RS04345 Hypothetical protein 4.221 CS401_RS08470 CoA-disulfide reductase 4.058 CS401_RS08465 Helix-turn-helix transcriptional regulator 3.871 CS401_RS07475 Sodium-dependent transporter 3.767 purF Amidophosphoribosyltransferase 3.713 CS401_RS02225 Phosphoribosylaminoimidazole-succinocarboxamide synthase 3.712 CS401_RS04965 Hypothetical protein 3.641 bioA Adenosylmethionine8-amino-7-oxononanoate transaminase 3.633 purM Phosphoribosylfomylglycinamidine cyclo-ligase...”
Ta1414 conserved hypothetical protein from Thermoplasma acidophilum DSM 1728
36% identity, 76% coverage
AWC34_RS01880 persulfide response sulfurtransferase CstA from Staphylococcus equorum
36% identity, 16% coverage
LGS26_05795 sulfurtransferase TusA family protein from Dissulfurimicrobium hydrothermale
32% identity, 71% coverage
TRQ2_1812 SirA family protein from Thermotoga sp. RQ2
TM0983 conserved hypothetical protein from Thermotoga maritima MSB8
36% identity, 81% coverage
- A pipeline for completing bacterial genomes using in silico and wet lab approaches
Puranik, BMC genomics 2015 - “...hypothetical protein TM0981 TRQ2_1814 CTN_1597 Disrupted hypothetical protein TM0982 TRQ2_1813 CTN_1596 Present hypothetical protein TM0983 TRQ2_1812 CTN_1595 Disrupted hypothetical protein TM0984 TRQ2_1811 CTN_1594 Disrupted hypothetical protein TM0985 TRQ2_1810 CTN_1593 Present hypothetical protein TM0986 TRQ2_1809 CTN_1592 & CTN_1591 Present hypothetical protein TM0987 TRQ2_1808 CTN_1590 Disrupted hypothetical protein...”
- A pipeline for completing bacterial genomes using in silico and wet lab approaches
Puranik, BMC genomics 2015 - “...Present hypothetical protein TM0981 TRQ2_1814 CTN_1597 Disrupted hypothetical protein TM0982 TRQ2_1813 CTN_1596 Present hypothetical protein TM0983 TRQ2_1812 CTN_1595 Disrupted hypothetical protein TM0984 TRQ2_1811 CTN_1594 Disrupted hypothetical protein TM0985 TRQ2_1810 CTN_1593 Present hypothetical protein TM0986 TRQ2_1809 CTN_1592 & CTN_1591 Present hypothetical protein TM0987 TRQ2_1808 CTN_1590 Disrupted hypothetical...”
- Stationary phase and nutrient levels trigger transcription of a genomic locus containing a novel peptide (TM1316) in the hyperthermophilic bacterium Thermotoga maritima
Frock, Applied and environmental microbiology 2013 - “...medium included a putative sulfur relay operon (TM0979 to TM0983). TM0981, TM0980, and TM0979 are homologous to DsrEFH and TusBCD, which are involved in sulfur...”
- “...TM0977 66 N 98 N 1.2 1.7 1.2 1.8 TM1732 0.1 0.5 0.2 0.6 TM0983 79 N 59 N 0.8 1.1 0.3 0.2 TM1786 1.1 1.2 0.7 1.3 TM0994 37 Y 30 N 0.6 0.7 0.4 0.5 TM1829 -0.1 0.1...”
- Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex
Ravcheev, Journal of bacteriology 2012 - “...TM0012 TM0179 TM0201 TM0227 TM0379 TM0423 TM0686 TM0983 TM1400 TM1420 TM1586 TM1814 TRQ2_0578 hycABC-TM0009 TM0179 hycD hycE-hycC2 noxE gldA...”
- “...of gene regions containing Rex-binding sites: TM0012, TM0201, TM0983, TM1586 (A); TRQ2-0578 (1), TRQ2-0578 (2), TM0228 (B); TM1420, TM0423, TM0686, TM1400 (C);...”
- An NMR approach to structural proteomics
Yee, Proceedings of the National Academy of Sciences of the United States of America 2002 - “...1JSB; BMRB, 5106), Mth1880 (PDB, 1IQO; BMRB, 5129), TM0983 (PDB, 1JDQ; BMRB, 5060), YedF_ecoli (PDB, 1JE3; BMRB, 5059), Yjbj_ecoli (PDB, 1JYG; BMRB, 5106),...”
- “...place of the C-terminal strand in the PDZ domain. TM0983 and YedF_ecoli (which are members of the same COG) formed a two-layered fold that is structurally...”
CTN_1595 hypothetical protein from Thermotoga neapolitana DSM 4359
36% identity, 78% coverage
- A pipeline for completing bacterial genomes using in silico and wet lab approaches
Puranik, BMC genomics 2015 - “...protein TM0981 TRQ2_1814 CTN_1597 Disrupted hypothetical protein TM0982 TRQ2_1813 CTN_1596 Present hypothetical protein TM0983 TRQ2_1812 CTN_1595 Disrupted hypothetical protein TM0984 TRQ2_1811 CTN_1594 Disrupted hypothetical protein TM0985 TRQ2_1810 CTN_1593 Present hypothetical protein TM0986 TRQ2_1809 CTN_1592 & CTN_1591 Present hypothetical protein TM0987 TRQ2_1808 CTN_1590 Disrupted hypothetical protein TM0988...”
SAPIG0062 DsrE/DsrF/DrsH-like family protein from Staphylococcus aureus subsp. aureus ST398
31% identity, 21% coverage
- Sequence Analysis of Novel Staphylococcus aureus Lineages from Wild and Captive Macaques
Monecke, International journal of molecular sciences 2022 - “...cstA -SCC CsoR -like sulfur transferase-regulated gene A Reverse 77,640 78,707 1068 69,004 70,071 1068 SAPIG0062 cstR -SCC copper-sensing transcriptional repressor Forward 78,846 79,102 257 70,210 70,466 257 SAPIG0063 DUF81-SCC putative sulfite/sulfonate efflux Forward 79,130 79,861 732 70,494 71,225 732 SAPIG0064 copA2 -SCC copper-exporting ATPase Forward/truncated...”
D7DUT1 SirA family protein from Methanococcus voltae (strain ATCC BAA-1334 / A3)
32% identity, 76% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
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.
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.
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.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory